Publications by year
In Press
Finnegan AK, Griffiths AM, King RA, Machado-Schiaffino G, Porcher J-P, Garcia-Vasquez E, Bright D, Stevens JR (In Press). Use of multiple markers demonstrates a cryptic western refugium and postglacial colonisation routes of Atlantic salmon (Salmo salar L.) in northwest Europe.
Heredity,
111(1), 34-43.
Abstract:
Use of multiple markers demonstrates a cryptic western refugium and postglacial colonisation routes of Atlantic salmon (Salmo salar L.) in northwest Europe
Glacial and post-glacial processes are known to be important determinants of contemporary population structuring for many species. In Europe, refugia in the Italian, Balkan and Iberian peninsulas are believed to be the main sources of species colonising northern Europe after the glacial retreat, however, there is increasing evidence of small, cryptic refugia existing north of these for many cold-tolerant species. This study examined the glacial history of Atlantic salmon in Western Europe using two independent classes of molecular markers, microsatellites (nuclear) and mitochondrial DNA variation. Alongside the well-documented refuge in the Iberian Peninsula, evidence for a cryptic refuge in northwest France is also presented. Critically, methods utilised to estimate divergence times between the refugia indicated that salmon in these two regions had diverged a long time before the last glacial maximum; coalescence analysis (as implemented in the program IMa2) estimated divergence times at around 60,000 years before present. Through the examination of haplotype frequencies, previously glaciated areas of northwest Europe, i.e. Britain and Ireland, appear to have been colonised from salmon expanding out of both refugia, with the southwest of England being the primary contact zone and exhibiting the highest genetic diversity.
Abstract.
2023
Osmond DR, King RA, Stockley B, Launey S, Stevens JR (2023). A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales.
J Fish Biol,
102(1), 258-270.
Abstract:
A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales.
The rivers of southern England and northern France which drain into the English Channel contain several genetically unique groups of trout (Salmo trutta L.) that have suffered dramatic declines in numbers over the past 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 95 single nucleotide polymorphism (SNP) loci for trout from this region and investigate their applicability and variability in both target (i.e. southern English) and non-target trout populations from northern Britain and Ireland. In addition, we present three case studies which demonstrate the utility and resolution of these genetic markers at three levels of spatial separation:(a) between closely related populations in nearby rivers, (b) within a catchment and (c) when determining parentage and familial relationships between fish sampled from a single site, using both empirical and simulated data. The SNP loci will be useful for population genetic and assignment studies on brown trout within the UK and beyond.
Abstract.
Author URL.
Ellis CD, MacLeod KL, Jenkins TL, Rato LD, Jézéquel Y, Pavičić M, Díaz D, Stevens JR (2023). Shared and distinct patterns of genetic structure in two sympatric large decapods. Journal of Biogeography
2022
King RA, Toms S, Stevens JR (2022). Evaluating the importance of accurate sex ratios on egg deposition targets and conservation limit compliance for Atlantic salmon (. <i>Salmo salar</i>. L.) in the River Tamar, south‐west England. Fisheries Management and Ecology, 30(2), 161-170.
Tinlin-Mackenzie A, Ellis CD, Lodola A, Martin-Ruiz C, Stevens JR, Fitzsimmons C (2022). New kid on the block: first record of juvenile American lobster, Homarus americanus H. Milne Edwards, 1837, in European waters.
BioInvasions Records,
11(4), 991-1000.
Abstract:
New kid on the block: first record of juvenile American lobster, Homarus americanus H. Milne Edwards, 1837, in European waters
A juvenile American lobster, Homarus americanus, H. Milne Edwards, 1837, was recorded for the first time in European waters in August 2019, with the capture of a single early benthic phase specimen during surveys along the North East England coast. Identification was determined by a combination of morphological and molecular approaches. The record raises serious questions of whether the species is now breeding in the region, with associated implications for its invasiveness. The mechanisms of introduction, invasion status, risks to native shellfisheries, and directions of future study are discussed.
Abstract.
Jenkins TL, Stevens JR (2022). Predicting habitat suitability and range shifts under projected climate change for two octocorals in the north-east Atlantic.
PeerJ,
10Abstract:
Predicting habitat suitability and range shifts under projected climate change for two octocorals in the north-east Atlantic.
Species distribution models have become a valuable tool to predict the distribution of species across geographic space and time. In this study, maximum entropy models were constructed for two temperate shallow-water octocoral species, the pink sea fan (Eunicella verrucosa) and dead man's fingers (Alcyonium digitatum), to investigate and compare habitat suitability. The study area covered the north-east Atlantic from the Bay of Biscay to the British Isles and southern Norway; this area includes both the northern range of E. verrucosa and the middle-northern range of A. digitatum. The optimal models for each species showed that, overall, slope, temperature at the seafloor and wave orbital velocity were important predictors of distribution in both species. Predictions of habitat suitability showed areas of present-day (1951-2000) suitable habitat where colonies have not yet been observed, particularly for E. verrucosa, where areas beyond its known northern range limit were identified. Moreover, analysis with future layers (2081-2100) of temperature and oxygen concentration predicted a sizable increase in habitat suitability for E. verrucosa beyond these current range limits under the Representative Concentration Pathway 8.5 scenario. This suggests that projected climate change may induce a potential range expansion northward for E. verrucosa, although successful colonisation would also be conditional on other factors such as dispersal and interspecific competition. For A. digitatum, this scenario of projected climate change may result in more suitable habitat in higher latitudes, but, as with E. verrucosa, there is a degree of uncertainty in the model predictions. Importantly, the results from this study highlight present-day areas of high habitat suitability which, if combined with knowledge on population density, could be used to identify priority areas to enhance protection and ensure the long-term survival of these octocoral species in the region.
Abstract.
Author URL.
2021
King RA, Stevens JR (2021). Development of SNP markers derived from RAD sequencing for Atlantic salmon (Salmo salar L.) inhabiting the rivers of southern England.
CONSERVATION GENETICS RESOURCES,
13(4), 369-373.
Author URL.
Bekkevold D, Piper A, Campbell R, Rippon P, Wright RM, Crundwell C, Wysujack K, Stevens JR, King RA, Aarestrup K, et al (2021). Genetic stock identification of sea trout (<i>Salmo trutta</i> L.) along the British North Sea Coast shows prevalent long-distance migration.
ICES Journal of Marine Science,
78(3), 952-966.
Abstract:
Genetic stock identification of sea trout (Salmo trutta L.) along the British North Sea Coast shows prevalent long-distance migration
Abstract
. Knowledge of migration behaviour and spatio-temporal habitat use is important for management and conservation, not least for diadromous species where population dynamics are affected by processes occurring in both freshwater and marine habitats. Sampling from a commercial capture fishery for the ecologically and economically important salmonid Salmo trutta L. we genotyped 189 single nucleotide polymorphisms and carried out genetic assignment of origin for 916 migratory sea trout sampled along ∼500 km of Britain’s North Sea coast. Population contributions to stocks showed strong geographical differences. Trout from rivers in the northern part of this coast (Tweed, Aln, Coquet, and Tyne) contributed the majority of migrants, irrespective of location, but fish from local rivers contributed to catches in most locations. Almost all (99%) trout assigned to native British populations and a large proportion (34%) of the sampled catches originated in rivers more than 100 km from capture sites, suggesting long-distance migration to be a common trait, confirming and enlarging historical trends from tagging data. Repeated sampling across years indicated short-term stability in migration patterns. Findings illustrate the scope for genetic stock identification to identify marine habitat use and monitor population-specific migration behaviours in species where stock assessment has not traditionally incorporated marine phase dynamics.
Abstract.
Andrew King R, Miller AL, Stevens JR (2021). Has stocking contributed to an increase in the rod catch of anadromous trout (Salmo trutta L.) in the Shetland Islands, UK?.
J Fish Biol,
99(3), 980-989.
Abstract:
Has stocking contributed to an increase in the rod catch of anadromous trout (Salmo trutta L.) in the Shetland Islands, UK?
The stocking of hatchery-origin fish into rivers and lakes has long been used in fisheries management to try to enhance catches, especially for trout and salmon species. Frequently, however, the long-term impacts of stocking programmes have not been evaluated. In this study, the authors investigate the contribution of a stocking programme undertaken to support the rod catch of sea trout in the Shetland Islands, UK. Once a highly productive recreational fishery, Shetland sea trout catches crashed in the mid-1990s. Around the time that stocking began, increases in rod catches were also reported, with advocates of the stocking highlighting the apparent success of the programme. Using a suite of genetic markers (microsatellites), this study explores the contribution of the stocking programme to the Shetland sea trout population. The authors found that the domesticated broodstock and wild spawned brown trout from seven streams were genetically distinct. Despite extensive stocking, wild spawned brown trout dominated, even in those streams with a long history of supplementation. The majority of sea trout caught and analysed were of wild origin - only a single individual was of pure stocked origin, with a small number of fish being of wild × stocked origins. This study suggests that stocking with a domesticated strain of brown trout has made only a very limited contribution to the Shetland Islands rod catch, and that the revival of sea trout numbers appears to be driven almost exclusively by recovery of trout spawned in the wild.
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Westbury MV, Thompson KF, Louis M, Cabrera AA, Skovrind M, Castruita JAS, Constantine R, Stevens JR, Lorenzen ED (2021). Ocean-wide genomic variation in Gray's beaked whales. <i>Mesoplodon grayi</i>.
Royal Society Open Science,
8(3).
Abstract:
Ocean-wide genomic variation in Gray's beaked whales. Mesoplodon grayi
. The deep oceans of the Southern Hemisphere are home to several elusive and poorly studied marine megafauna. In the absence of robust observational data for these species, genetic data can aid inferences on population connectivity, demography and ecology. A previous investigation of genetic diversity and population structure in Gray's beaked whale (
. Mesoplodon grayi
. ) from Western Australia and New Zealand found high levels of mtDNA diversity, no geographic structure and stable demographic history. To further investigate phylogeographic and demographic patterns across their range, we generated complete mitochondrial and partial nuclear genomes of 16 of the individuals previously analysed and included additional samples from South Africa (
. n
. = 2) and South Australia (
. n
. = 4), greatly expanding the spatial range of genomic data for the species. Gray's beaked whales are highly elusive and rarely observed, and our data represents a unique and geographically broad dataset. We find relatively high levels of diversity in the mitochondrial genome, despite an absence of population structure at the mitochondrial and nuclear level. Demographic analyses suggest these whales existed at stable levels over at least the past 1.1 million years, with an approximately twofold increase in female effective population size approximately 250 thousand years ago, coinciding with a period of increased Southern Ocean productivity, sea surface temperature and a potential expansion of suitable habitat. Our results suggest that Gray's beaked whales are likely to be resilient to near-future ecosystem changes, facilitating their conservation. Our study demonstrates the utility of low-effort shotgun sequencing in providing ecological information on highly elusive species.
.
Abstract.
Bache-Jeffreys M, de Moraes BLC, Ball RE, Menezes G, Pálsson J, Pampoulie C, Stevens JR, Griffiths AM (2021). Resolving the spatial distributions of Dipturus intermedius and Dipturus batis—the two taxa formerly known as the ‘common skate’.
Environmental Biology of Fishes,
104(8), 923-936.
Abstract:
Resolving the spatial distributions of Dipturus intermedius and Dipturus batis—the two taxa formerly known as the ‘common skate’
AbstractBatoid fishes are among the most endangered marine vertebrates, yet conservation efforts have been confounded by incomplete taxonomy. Evidence suggest that the critically endangered ‘common skate’ actually represents two species: the flapper skate (Dipturus intermedius) and the blue skate (Dipturus batis). However, knowledge of the geographic range of these two nominal species is limited. Here, DNA sequencing is used to distinguish these species, allowing their spatial distributions to be clarified. These records were also used as the basis for species distribution modelling, providing the first broad scale models for each species across the Northeast Atlantic. Samples were obtained from Iceland, the UK (specifically Shetland), the North Sea and the Azores. Results suggest that D. batis was commonly distributed in the Western Approaches and Celtic Sea, extending out to Rockall and Iceland. D. intermedius generally appears to be less abundant, but was most frequent around northern Scotland and Ireland, including the northern North Sea, and was also present in Portugal. Two individuals were also identified from seamounts in remote areas of the Atlantic around the Azores, the furthest south and west the species has been found. This supports reports that the flapper skate historically had a much wider distribution (which was also highlighted in the distribution model), emphasising the large scale over which fisheries may have led to extirpations. Furthermore, these Azorean samples shared a unique control region haplotype, highlighting the importance of seamounts in preserving genetic diversity.
Abstract.
Hooper L, Jenkins TL, Griffiths AM, Moore KA, Stevens JR (2021). The complete mitochondrial genome of the pink sea fan, <i>Eunicella verrucosa</i> (Pallas, 1766). Mitochondrial DNA Part B, 6(11), 3309-3311.
Gilbey J, Utne KR, Wennevik V, Beck AC, Kausrud K, Hindar K, Garcia de Leaniz C, Cherbonnel C, Coughlan J, Cross TF, et al (2021). The early marine distribution of Atlantic salmon in the North-east Atlantic: a genetically informed stock-specific synthesis.
FISH AND FISHERIES,
22(6), 1274-1306.
Author URL.
Jenkins TL, Guillemin M, Simon‐Nutbrown C, Burdett HL, Stevens JR, Peña V (2021). Whole genome genotyping reveals discrete genetic diversity in north‐east Atlantic maerl beds. Evolutionary Applications, 14(6), 1558-1571.
2020
Bache-Jeffreys M (2020). A Phylogenetic Study of Vulnerable Batoid Species from the North Atlantic.
Abstract:
A Phylogenetic Study of Vulnerable Batoid Species from the North Atlantic
Successful resolution of the nomenclature and taxonomy of batoid fish complicated by the high degree of morphological and ecological conservatism in this group. However, both mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) phylogenies have been utilised to resolve batoid phylogenies and even to identify cryptic species. As a result, the number of ray species described in recent decades has dramatically increased- although questions still remain regarding the taxonomic status of many batoid species. In chapter one of this thesis, the importance of taxonomy in skate conservation and management is reviewed. In chapter two, control region (CR) and cytochrome oxidase I (COI) sequencing of the blue skate (Dipturus batis) and the flapper skate (Dipturus intermedius) from across the Northeast Atlantic was performed, in order to clarify their geographical distribution. Although now formally recognised as distinct species, before 2010 these two taxa were classified together as the critically endangered ‘common skate’, D. batis. Although this has important conservation implications, their protection is currently being hindered by a lack of spatiotemporal data. In the present study, the blue skate generally appears to be more common than the flapper skate, with a distribution extending from Rockall and Iceland to the Western Approaches and the Celtic Sea. Whilst the flapper skate appears most frequent around northern Scotland, the North Sea and Ireland, novel data also suggests that it may have once had a much wider distribution. For the first time, this species was identified in the Azores, where unique haplotypes were also isolated, potentially highlighting the genetic distinctiveness of the population in this region. In chapter three, nextRAD and mtDNA (concatenated CR and COI) sequencing were utilised to explore the phylogenetics of several vulnerable species of European skate. Whilst the current designation of the Madeiran skate (Raja maderensis) and the thornback ray (Raja clavata) as distinct species wasn’t fully supported, genetically distinct populations were identified in the Azores and surrounding seamounts. The presence of a cryptic Dipturus species in the Azores wasn’t supported, as suggested by previous work on the longnosed skate (Dipturus oxyrinchus). However, Azorean longnosed skate and flapper skate were distinct from their geographically proximate counterparts, and may represent distinct populations. The uniqueness of the Azores highlights the importance of seamounts as ‘hotspots’ of biodiversity, which has important implications for marine protected areas that include these batoid species as a protected feature. In addition to resolving these phylogenies, this thesis also offered an opportunity to comment on the utility of mtDNA and nextRAD sequencing for batoid phylogenetics, the latter of which has never been applied to skates and rays before.
Abstract.
King RA, Stevens JR (2020). An improved genetic sex test for Atlantic salmon (Salmo salar L.).
Conservation Genetics Resources,
12(2), 191-193.
Abstract:
An improved genetic sex test for Atlantic salmon (Salmo salar L.)
Accurate determination of sex ratios is an important metric for the conservation and management of wild Atlantic salmon populations. Previously published primers for a male-specific gene were shown to be unreliable at determining sex due to the presence of deletions in the forward primer-binding site. A new forward primer, used in conjunction with the existing reverse primer, greatly improved reliability of the genetic test, correctly assigning gender in samples of known sex. Using DNA extracted from both contemporary and archive tissues, comparison between the two primer sets screened on collections of unknown sex ratio showed significant discrepancies in the number of males identified. The new primer will help improve the management and conservation of Atlantic salmon by providing accurate sex ratios for the setting of Conservation Limits.
Abstract.
Ellis CD, Jenkins TL, Svanberg L, Eriksson SP, Stevens JR (2020). Crossing the pond: genetic assignment detects lobster hybridisation.
Sci Rep,
10(1).
Abstract:
Crossing the pond: genetic assignment detects lobster hybridisation.
American lobsters (Homarus americanus) imported live into Europe as a seafood commodity have occasionally been released or escaped into the wild, within the range of an allopatric congener, the European lobster (H. gammarus). In addition to disease and competition, introduced lobsters threaten native populations through hybridisation, but morphological discriminants used for species identification are unable to discern hybrids, so molecular methods are required. We tested an array of 79 single nucleotide polymorphisms (SNPs) for their utility to distinguish 1,308 H. gammarus from 38 H. americanus and 30 hybrid offspring from an American female captured in Sweden. These loci provide powerful species assignment in Homarus, enabling the robust identification of hybrid and American individuals among a survey of European stock. Moreover, a subset panel of the 12 most powerful SNPs is sufficient to separate the two pure species, even when tissues have been cooked, and can detect the introduced component of hybrids. We conclude that these SNP loci can unambiguously identify hybrid lobsters that may be undetectable via basic morphology, and offer a valuable tool to investigate the prevalence of cryptic hybridisation in the wild. Such investigations are required to properly evaluate the potential for introgression of alien genes into European lobster populations.
Abstract.
Author URL.
Hand AMS (2020). Does the restoration of shallow marginal peatlands impact on the distribution and abundance of Bog Asphodel?.
Abstract:
Does the restoration of shallow marginal peatlands impact on the distribution and abundance of Bog Asphodel?
Healthy functional peatlands sequester carbon and are therefore important in the mitigation of climate change. In the United Kingdom 80% of peatland has been damaged by anthropogenic activities such as drainage and peat cutting. Most of the degraded peat is globally rare blanket bog found in upland regions, where the principal land use is livestock grazing.
Bog asphodel is a common British wildflower found on blanket bog and other very wet peatland habitats, which can also be fatally poisonous to grazing herbivores especially youngstock. Any increase could compromise the grazing in an already difficult environment.
This thesis investigated the growth and distribution of bog asphodel on shallow marginal restored peatlands on Exmoor in south-western United Kingdom, both in the field and from a vegetation survey database spanning 11 years from pre-restoration to present at 40 restored sites. The aims were to describe bog asphodel’s phenology, and to assess its life history strategy and its contribution to sward quality in post-restoration habitats.
Bog asphodel’s life history strategy is one of tolerating stress, rather than growing quickly or producing large numbers of seeds. This predicts that it will not respond rapidly to peatland restoration. On Exmoor, this prediction is confirmed by the historic data which show bog asphodel growing only slowly after restoration, and not spreading to other restored sites. Bog asphodel can contribute up to 20% of forage value in the transitional bog habitats that develop after rewetting, both in spring and autumn.
The implication for the restoration of shallow marginal peatlands is that bog asphodel persists post restoration but does not spread beyond pre-restoration patches or to other sites. Although it can contribute substantially to forage value in rewetted areas no significant injurious effects have been reported, either because more palatable and accessible grazing is available or because bog asphodel itself is less toxic on account of specific environmental conditions.
Abstract.
Van Der zee M (2020). Genomics of adaptation in experimental populations of Trinidadian guppies (Poecilia reticulata).
Abstract:
Genomics of adaptation in experimental populations of Trinidadian guppies (Poecilia reticulata)
Natural populations are increasingly affected by human-mediated changes in the environment. Despite substantial evidence for rapid phenotypic evolution in response to changing environments, the role of genetics underlying rapid adaptation remains relatively unexplored. Natural populations of guppies (Poecilia reticulata) in Trinidad show clear repeatable phenotypic adaptation to low- (LP) and high (HP) -predation environments. Experiments where guppies were transplanted from HP to LP environments showed the LP phenotypes can evolve in as little as four years. Using whole genome sequencing of two well-established introductions (sampled at 64 and 114 generations post introduction), and four newly introduced populations (sampled 8-10 generations post introduction), I investigate the genetic response to novel environments. I uncover varying demographic histories between the two established populations, with evidence of bottlenecks in one and extensive population growth in the other. Both experimental populations showed signatures of convergent evolution with a natural LP population, but I found little evidence of convergence between them, indicating they explored different molecular pathways to achieve similar phenotypes. In the second half of the thesis, I show four recently introduced populations evolved minor genetic changes with respect to their HP source, and find no evidence of bottlenecks in three of the four populations. I find signals of selection in all four populations, and a 2Mb region on chromosome 15 showed a consistent signal of selection in three of the four populations. Finally, using a multivariate analysis of allele frequency changes I uncovered subtle parallel changes at multiple loci across all four populations, indicating the approach has potential to detect convergent evolution in rapidly evolving populations, as well as identifying signatures of polygenic selection. Taken together, the findings in this thesis contribute to a better understanding of the process of rapid genetic adaptation after a sudden environment shift in natural populations.
Abstract.
Houston RD, Bean TP, Macqueen DJ, Gundappa MK, Jin YH, Jenkins TL, Selly SLC, Martin SAM, Stevens JR, Santos EM, et al (2020). Harnessing genomics to fast-track genetic improvement in aquaculture. Nature Reviews Genetics, 21(7), 389-409.
Jenkins TL, Ellis CD, Durieux EDH, Filippi J, Bracconi J, Stevens JR (2020). Historical translocations and stocking alter the genetic structure of a Mediterranean lobster fishery. Ecology and Evolution, 10(12), 5631-5636.
Hamilton PB, Lockyer AE, Uren Webster TM, Studholme DJ, Paris JR, Baynes A, Nicol E, Dawson DA, Moore K, Farbos A, et al (2020). Investigation into Adaptation in Genes Associated with Response to Estrogenic Pollution in Populations of Roach (Rutilus rutilus) Living in English Rivers.
Environ Sci Technol,
54(24), 15935-15945.
Abstract:
Investigation into Adaptation in Genes Associated with Response to Estrogenic Pollution in Populations of Roach (Rutilus rutilus) Living in English Rivers.
Exposure of male fish to estrogenic substances from wastewater treatment works (WwTWs) results in feminization and reduced reproductive fitness. Nevertheless, self-sustaining populations of roach (Rutilus rutilus) inhabit river stretches polluted with estrogenic WwTW effluents. In this study, we examine whether such roach populations have evolved adaptations to tolerate estrogenic pollution by comparing frequency differences in single-nucleotide polymorphisms (SNPs) between populations sampled from rivers receiving either high- or low-level WwTW discharges. SNPs within 36 "candidate" genes, selected for their involvement in estrogenic responses, and 120 SNPs in reference genes were genotyped in 465 roaches. There was no evidence for selection in highly estrogen-dependent candidate genes, including those for the estrogen receptors, aromatases, and vitellogenins. The androgen receptor (ar) and cytochrome P450 1A genes were associated with large shifts in allele frequencies between catchments and in individual populations, but there is no clear link to estrogen pollution. Selection at ar in the effluent-dominated River Lee may have resulted from historical contamination with endocrine-disrupting pesticides. Critically, although our results suggest population-specific selection including at genes related to endocrine disruption, there was no strong evidence that the selection resulted from exposure to estrogen pollution.
Abstract.
Author URL.
Hooper L (2020). Phylogenetic and phylogeographic assessment of the temperate octocoral Eunicella verrucosa.
Abstract:
Phylogenetic and phylogeographic assessment of the temperate octocoral Eunicella verrucosa
The three-dimensional structure of gorgonian octocoral, like Eunicella, can provide vital habitat for other marine organisms and are thus considered ecosystem engineers. As they are ecosystem engineers, the conservation of Eunicella can deliver benefit to other marine organisms and thus their conservation can have a significant impact. Phylogenetic assessment of a species is pivotal in order to inform management efforts and conservation strategies accurately. Unfortunately, phylogenetic assessment of octocoral has been massively hindered by a lack of variation in their mitochondrial genomes. This is highly evident in the Eunicella genus, as previous studies have shown no variation in the mitochondrial protein-coding gene cox1. In Chapter 2, novel primers were successfully developed and exploited to explore the phylogenetic relationships between three predominant Atlantic-Mediterranean members of Eunicella (E. verrucosa, E. singularis and E. cavolini). This is one of the first studies to identify variation in the mitochondrial genomes of Eunicella. In Chapter 3, complete mitochondrial genomes of 19 E. verrucosa individuals were sequenced. Only two E. verrucosa genotypes were observed. 17 E. verrucosa individuals showed a widespread genotype and two E. verrucosa individuals, from Lion Rock, Isle of Scilly, southwest England, showed a unique genotype. Even compared to the known low levels of variation in the mitogenomes of octocoral, extremely low levels of variation were observed between the mitogenomes of E. verrucosa and E. cavolini, suggesting a recent divergence of the species. Holaxonia-phylogenies were produced by exploiting partial contigs of mtMutS and complete mitochondrial protein-coding sequences. These phylogenies support the inclusion of Eunicella in the family Gorgonidae, in line with previous research. The confirmation of Eunicella spp. position within the octocoral phylogeny will allow for properly informed conservation efforts. The conservation of Eunicella spp. is especially important, as they are ecosystem engineers it is highly probable the conservation of Eunicella spp. will have secondary impact on other marine organisms that rely on Eunicella spp. for habitat or resources.
Abstract.
Sherman KD, Paris J, King RA, Moore KA, Dahlgren CP, Knowles LC, Stump K, Tyler CR, Stevens JR (2020). RAD-Seq Analysis and in situ Monitoring of Nassau Grouper Reveal Fine-Scale Population Structure and Origins of Aggregating Fish.
FRONTIERS IN MARINE SCIENCE,
7 Author URL.
King RA, Stockley B, Stevens JR (2020). Small coastal streams—Critical reservoirs of genetic diversity for trout (<i>Salmo trutta</i>L.) in the face of increasing anthropogenic stressors. Ecology and Evolution, 10(12), 5651-5669.
2019
Jenkins T (2019). Connectivity between MPAs: selecting appropriate taxa and assessing genetic connectivity in two benthic marine invertebrates.
Abstract:
Connectivity between MPAs: selecting appropriate taxa and assessing genetic connectivity in two benthic marine invertebrates
Connectivity is fundamental for the persistence of many populations of marine species and is formally identified as one of five key principles for designing an ecologically coherent network of Marine Protected Areas (MPAs) in European waters. However, the process of assessing connectivity between MPAs, and which taxa to include in assessments of connectivity, is challenging. Managers of MPAs have typically concentrated their efforts on species that are endangered or rare, or on so-called 'umbrella', 'keystone' or 'flagship' species; however, these species may not always be the best candidates for assessing connectivity of a MPA network. In this thesis, a meta-analysis was firstly conducted to study genetic patterns across a broad range of coastal marine taxa in the northeast Atlantic. This meta-analysis provided insights into the biological and methodological information needed to ascertain which taxa may be considered as good candidates for assessing genetic connectivity between MPAs across Britain and the wider northeast Atlantic. The knowledge gained from this literature survey facilitated the design of a set of criteria that identified ideal traits of a candidate species for assessments of genetic connectivity between MPAs; subsequently, based on these criteria, two species were selected to assess connectivity between MPAs in the British network: the pink sea fan (Eunicella verrucosa) and the European lobster (Homarus gammarus). Using 13 microsatellites and 3,743 SNPs, the results for the pink sea fan indicated the presence of three distinct genetic groups, partitioned between sites from western Ireland, southern Portugal and Britain-France. For the European lobster, 86 SNPs indicated strong genetic differentiation between the northeast Atlantic, the middle Mediterranean and the eastern Mediterranean (Aegean Sea). In addition, there was a pronounced genetic cline across the northeast Atlantic, suggesting that connectivity in the European lobster follows a stepping-stone model of dispersal, which was supported by simulations of larval dispersal. Taken together, the results from these two studies suggests that the MPA network in Britain is sufficient to maintain connectivity in the pink sea fan and the European lobster, and possibly other species living in comparable habitats with similar life histories and dispersal traits. Moreover, the criteria applied in this thesis to select species appears to facilitate the identification of ideal surrogate taxa to assess connectivity between MPAs, which could easily be applied to assessments of MPA network connectivity in other seas and oceans around the world.
Abstract.
Mitson C (2019). Construction of a robust phylogeny facilitates development of an environmental DNA-based survey tool for the bog hoverfly, Eristalis cryptarum.
Abstract:
Construction of a robust phylogeny facilitates development of an environmental DNA-based survey tool for the bog hoverfly, Eristalis cryptarum
Surveying an endangered species is vital for its successful conservation. The use of environmental DNA (eDNA) as surveying tool for rare and elusive species has gained popularity over recent years. Eristalis cryptarum, commonly known as the bog hoverfly is listed as a priority species on the UK Biodiversity Action Plan, is Critically Endangered and restricted to few sites on Dartmoor National Park. It is widely assumed E. cryptarum have an aquatic, rat-tailed larval stage, as is the case for other closely related species. The larvae however, have never been discovered in the UK in order to determine this. In Chapter 1, using the mitochondrial gene cytochrome c oxidase subunit 1 (cox1), the phylogeny of E. cryptarum is explored. Using molecular data and morphological characteristics, E. cryptarum is placed within the Eristalini tribe, a tribe distinguished by an aquatic, rat-tailed larval stage. This offers further support for the assumption that E. cryptarum possesses an aquatic, rat-tailed larval stage. The use of eDNA as a tool to survey endangered species has been widely used in previous studies and offers a sensitive, non-invasive approach to survey elusive and rare species. Here, larval E. cryptarum eDNA will be screened for in water samples collected from known habitat sites on Dartmoor National Park. Chapter 2 is focused on the development on taxa-specific primer sets and are tested for specificity and sensitivity in preparation for eDNA screening in Chapter 3. Primer sets were designed and developed successfully with high specificity to target taxa and shown to be sensitive through a number of dilution series. The use of an environmental DNA technique to determine the presence or absence of E. cryptarum eDNA in water samples is an exciting alternative to traditional surveying techniques. Chapter 3 explores this, and there was no amplification of E. cryptarum eDNA but a successful amplification of a closely related species, E. arbustorum from water samples where E. arbustorum was known to be present (using E. arbustorum specific primer sets). This suggests the need for further research and optimisation of this method for successful surveying of E. cryptarum using an eDNA methodology.
Abstract.
Smith M (2019). Damsels and distress: Factors affecting Haemulidae distribution on Bahamian reefs.
Abstract:
Damsels and distress: Factors affecting Haemulidae distribution on Bahamian reefs
The interconnected habitats of coral reefs, mangroves and seagrass are home to a quarter of all known species in the marine environment. The interconnectivity of these areas improves species richness and density, even for species that do not use the habitats as a nursery. The communities that live as part of these ecosystems, just like many other marine species, are vulnerable to the effects of anthropogenic noise. Haemulidae spp. use the patch reef system protected by the Cape of Eleuthera as an intermediate nursery and exhibit a complex relationship with Stegastes spp. The importance of coral reef flats, such as those of Eleuthera, remains a crucial knowledge gap in our understanding of the coral reef nursery ecosystem. Also lacking is an understanding of the effect of chronic boat traffic on entire coral reef fish communities. This thesis aims to address these knowledge gaps across three chapters. Chapter 1 provides a literature review exploring Haemulidae spp. in the tropical marine environment and the importance of nursery habitats; Stegastes species in the tropical marine environment; and, the effects of anthropogenic noise in the marine environment. This highlights the current knowledge gaps and guides the data chapters. Chapter 2 presents a study in the patch reef system identifying the settlement habits of three Stegastes spp. (S. leucostictus, S. diencaeus, S. partitus) and the relationship with local Haemulidae spp. populations. This study identifies that this interaction may be an indication of reef health, as well as shedding light on a competitive hierarchy that exists amongst Stegastes spp. Chapter 3 presents a community level study (53 species, 14,970 individuals, 6 patch reefs) comparing the reactions of the patch reefs either communities protected from or exposed to chronic boat traffic. The chronic effect of boat traffic had a detrimental effect on density, species richness and recruitment compared to similar reefs. This was particularly noticeable with the Haemulidae spp. using the patch reef system as an intermediate nursery. This could mean that chronic boat traffic is influencing recruitment as well as having wider implications for reef health.
Abstract.
Arias-Robledo G, Wall R, Szpila K, Shpeley D, Whitworth T, Stark T, King RA, Stevens JR (2019). Ecological and geographical speciation in Lucilia bufonivora: the evolution of amphibian obligate parasitism.
International Journal for Parasitology: Parasites and Wildlife,
10, 218-230.
Abstract:
Ecological and geographical speciation in Lucilia bufonivora: the evolution of amphibian obligate parasitism
Lucilia (Diptera: Calliphoridae) is a genus of blowflies comprised largely of saprophagous and facultative parasites of livestock. Lucilia bufonivora, however, exhibits a unique form of obligate parasitism of amphibians, typically affecting wild hosts. The evolutionary route by which amphibian myiasis arose, however, is not well understood due to the low phylogenetic resolution in existing nuclear DNA phylogenies. Furthermore, the timing of when specificity for amphibian hosts arose in L. bufonivora is also unknown. In addition, this species was recently reported for the first time in North America (Canada) and, to date, no molecular studies have analysed the evolutionary relationships between individuals from Eastern and Western hemispheres. To provide broader insights into the evolution of the amphibian parasitic life history trait and to estimate when the trait first arose, a time-scaled phylogeny was inferred from a concatenated data set comprising mtDNA, nDNA and non-coding rDNA (COX1, per and ITS2 respectively). Specimens from Canada, the UK, Poland, Switzerland, the Netherlands and Germany were analysed, as well as individuals from its sister taxa, the saprophage Lucilia silvarum and a Nearctic species also implicated in amphibian myiasis, Lucilia elongata. Obligate amphibian parasitism appears to have arisen ~4 mya, likely as a result of niche displacement of a saprophagous/facultative parasite ancestor. Consistent paraphyly of L. bufonivora with respect to L. elongata across single-gene phylogenies and high mtDNA genetic distances between Nearctic and Palearctic individuals suggest on-going cryptic speciation facilitated by geographical isolation. These findings suggest that recent reports of L. bufonivora in the Nearctic do not constitute a recent introduction, but instead suggest that it remained unrecorded due to taxonomic confusion and low abundance. This is the first study to confirm the involvement of L. bufonivora in amphibian myiasis in Canada using DNA-based identification methods.
Abstract.
Horreo JL, Griffiths AM, Machado-Schiaffino G, Stevens JR, Garcia-Vazquez E (2019). Northern areas as refugia for temperate species under current climate warming: Atlantic salmon (Salmo salar L.) as a model in northern Europe.
J Fish Biol,
95(1), 304-310.
Abstract:
Northern areas as refugia for temperate species under current climate warming: Atlantic salmon (Salmo salar L.) as a model in northern Europe.
In this work, patterns of geographical genetic diversity in Atlantic salmon Salmo salar were studied across the whole Atlantic Arc; whether these patterns (and thus genetic population structure) were affected by water temperatures was also evaluated. Salmo salar populations were characterized using microsatellite loci and then analysed with reference to ocean surface temperature data from across the region. Analysis showed the presence of a latitudinal cline of genetic variability (higher in northern areas) and water temperatures (sea surface temperatures) determining genetic population structure (the latter in combination with genetic drift in southern populations). Under the current global change scenario, northern areas of Europe would constitute refugia for diversity in the future. This is effectively the inverse of what appears to have happened in glacial refugia during the last glacial maximum. From this perspective, the still abundant and large northern populations S. salar should be considered as precious as the small almost relict southern ones and given appropriate protection. Careful management of the species, coordinated across countries and latitudes, is needed in order to avoid its extinction in Europe.
Abstract.
Author URL.
Jenkins TL, Ellis CD, Triantafyllidis A, Stevens JR (2019). Single nucleotide polymorphisms reveal a genetic cline across the north-east Atlantic and enable powerful population assignment in the European lobster.
Evolutionary Applications,
12(10), 1881-1899.
Abstract:
Single nucleotide polymorphisms reveal a genetic cline across the north-east Atlantic and enable powerful population assignment in the European lobster
Resolving stock structure is crucial for fisheries conservation to ensure that the spatial implementation of management is commensurate with that of biological population units. To address this in the economically important European lobster (Homarus gammarus), genetic structure was explored across the species' range using a small panel of single nucleotide polymorphisms (SNPs) previously isolated from restriction-site-associated DNA sequencing; these SNPs were selected to maximize differentiation at a range of both broad and fine scales. After quality control and filtering, 1,278 lobsters from 38 sampling sites were genotyped at 79 SNPs. The results revealed a pronounced phylogeographic break between the Atlantic and Mediterranean basins, while structure within the Mediterranean was also apparent, partitioned between lobsters from the central Mediterranean and the Aegean Sea. In addition, a genetic cline across the north-east Atlantic was revealed using both putatively neutral and outlier SNPs, but the precise driver(s) of this clinal pattern—isolation by distance, secondary contact, selection across an environmental gradient, or a combination of these factors—remains undetermined. Putatively neutral markers differentiated lobsters from Oosterschelde, an estuary on the Dutch coast, a finding likely explained by past bottlenecks and limited gene flow with adjacent North Sea populations. Building on the findings of our spatial genetic analysis, we were able to test the accuracy of assigning lobsters at various spatial scales, including to basin of origin (Atlantic or Mediterranean), region of origin and sampling location. The predictive model assembled using 79 SNPs correctly assigned 99.7% of lobsters not used to build the model to their basin of origin, but accuracy decreased to region of origin and again to sampling location. These results are of direct relevance to managers of lobster fisheries and hatcheries, and provide the basis for a genetic tool for tracing the origin of European lobsters in the food supply chain.
Abstract.
Arias-Robledo G, Stevens JR, Wall R (2019). Spatial and temporal habitat partitioning by calliphorid blowflies.
Med Vet Entomol,
33(2), 228-237.
Abstract:
Spatial and temporal habitat partitioning by calliphorid blowflies.
Calliphorid blowflies perform an essential ecosystem service in the consumption, recycling and dispersion of carrion nutrients and are considered amongst the most important functional groups in an ecosystem. Some species are of economic importance as facultative agents of livestock myiasis. The interspecific ecological differences that facilitate coexistence within the blowfly community are not fully understood. The aim of this work was to quantify differences in habitat use by calliphorid species. Thirty traps were distributed among three habitats at two sites in southwest England for collections made during March-August 2016. A total of 17 246 specimens were caught, of which 2427 were Lucilia sericata, 51 Lucilia richardsi, 6580 Lucilia caesar, 307 Lucilia ampullacea, 4881 Calliphora vicina and 2959 Calliphora vomitoria (all: Diptera: Calliphoridae). Lucilia sericata was the dominant species in open habitats, whereas L. caesar was the most abundant species in shaded habitats. Calliphora specimens were more abundant in the cooler months. These findings suggest that Calliphora and Lucilia species show strong temporal segregation mediated by temperature, and that species of the genus Lucilia show differences in the use of habitats that are likely to be driven by differences in humidity tolerance and light intensity. These factors in combination result in effective niche partitioning.
Abstract.
Author URL.
Kennedy EV, Tonk L, Foster NL, Mumby PJ, Stevens JR (2019). Temporal stability of Orbicella annularis symbioses: a case study in the Bahamas.
Bulletin of Marine Science,
95Abstract:
Temporal stability of Orbicella annularis symbioses: a case study in the Bahamas
Orbicella annularis (Ellis and Solander,
1786), a key reef building species, is unusual among
Caribbean corals in the flexibility it displays in its symbioses
with dinoflagellates in the family Symbiodiniaceae. This
variability has been documented at a range of spatial scales;
from within and between colonies to scales spanning the
entire species range. However, temporal variability in
Symbiodiniaceae communities found within O. annularis
colonies is not well understood. Evidence suggests that
symbiont communities in this coral species fluctuate
temporally in response to environmental stressors (sporadic
changes in abundance and in community composition). In
this study, we investigated temporal stability of symbiont
communities in O. annularis at four sites in the Bahamas
over a period spanning 6 yrs. While the dominant symbiont
species, Breviolum minutum (LaJeunesse et al.) J.E.Parkinson
& LaJeunesse (formerly ITS2-type B1), remained stable
across four patch-reef study sites, finer resolution molecular
techniques revealed inter-annual variability in the presence/
absence of cryptic species Durusdinium trenchii (LaJeunesse)
LaJeunesse (formerly ITS2-type D1a). Durusdinium trenchii
is known to play a role in resistance to environmental stress
and may have a protective effect under warm conditions.
These results suggest that, while it might take an extreme
environmental perturbation to trigger a long-term shift in
the dominant symbiont, at background levels, less prevalent
symbiont taxa are likely to be continually shuffling their
relative abundances as they change in response to seasonal
or environmental changes.
Abstract.
Arias-Robledo G, Stark T, Wall RL, Stevens JR (2019). The toad fly Lucilia bufonivora: its evolutionary status and molecular identification.
Med Vet Entomol,
33(1), 131-139.
Abstract:
The toad fly Lucilia bufonivora: its evolutionary status and molecular identification.
The blow fly genus Lucilia is composed largely of saprophages and facultative myasis agents, including the economically important species Lucilia cuprina (Wiedemann) (Diptera: Calliphoridae) and Lucilia sericata (Meigen). Only one species is generally recognized as an obligate agent of myiasis, Lucilia bufonivora Moniez, and this is an obligate parasite of toads. Lucilia silvarum (Meigen), a sister species, behaves mainly as a carrion breeder; however, it has also been reported as a facultative parasite of amphibians. Morphologically, these species are almost identical, and historically this has led to misidentification, taxonomic ambiguity and a paucity of studies of L. bufonivora. In this study, dipterous larvae were analysed from toad myiasis cases from the U.K. the Netherlands and Switzerland, together with adult specimens of fly species implicated in amphibian parasitism: L. bufonivora, L. silvarum and Lucilia elongata Shannon (from North America). Partial sequences of two genes, cox1 and ef1α, were amplified. Seven additional blow fly species were analysed as outgroups. Bayesian inference trees of cox1, ef1α and a combined-gene dataset were constructed. All larvae isolated from toads were identified as L. bufonivora and no specimens of L. silvarum were implicated in amphibian myiasis. This study confirms L. silvarum and L. bufonivora as distinct sister species and provides unambiguous molecular identification of L. bufonivora.
Abstract.
Author URL.
2018
Hamston TJ, de Vere N, King RA, Pellicer J, Fay MF, Cresswell JE, Stevens JR (2018). Apomixis and hybridization drives reticulate evolution and phyletic differentiation in sorbus l.: Implications for conservation.
Frontiers in Plant Science,
9Abstract:
Apomixis and hybridization drives reticulate evolution and phyletic differentiation in sorbus l.: Implications for conservation
© 2018 Hamston, de Vere, King, Pellicer, Fay, Cresswell and Stevens. Hybridization and polyploidy are major forces in the evolution of plant diversity and the study of these processes is of particular interest to understand how novel taxa are formed and how they maintain genetic integrity. Sorbus is an example of a genus where active diversification and speciation are ongoing and, as such, represents an ideal model to investigate the roles of hybridization, polyploidy and apomixis in a reticulate evolutionary process. To elucidate breeding systems and evolutionary origins of a complex of closely related Sorbus taxa, we assessed genotypic diversity and population structure within and among taxa, combining data from nuclear DNA microsatellite markers and flow cytometry. Clonal analysis and low genotypic diversity within the polyploid taxa suggest apomixis is obligate. However, genetic variation has led to groups of ‘clone-mates’ within apomictic taxa that strongly suggest mutation is responsible for the genotypic diversity of these apomictic lineages. In addition, microsatellite profiles and site demographics suggest hybridization events among apomictic polyploid Sorbus may have contributed to the extant diversity of recognized taxa in this region. This research demonstrates that both macro- and micro-evolutionary processes are active within this reticulate Sorbus complex. Conservation measures should be aimed at maintaining this process and should therefore be prioritized for those areas of Sorbus species richness where the potential for interspecific gene flow is greatest.
Abstract.
Jenkins TL, Stevens JR (2018). Assessing connectivity between MPAs: Selecting taxa and translating genetic data to inform policy.
Marine Policy,
94, 165-173.
Abstract:
Assessing connectivity between MPAs: Selecting taxa and translating genetic data to inform policy
Connectivity is frequently cited as a vital component of Marine Protected Area (MPA) networks and was formally identified as one of five key principles for marine network design in European waters. Yet, without the ability to demonstrate connectivity, it is impossible to be certain that sites designated within a MPA network do in fact constitute a network, when they may –irrespective of the diversity and rarity of the taxa within them– be in reality a set of unlinked habitats and associated species assemblages. However, the process of assessing connectivity between MPAs, and which taxa to include in assessments of connectivity, is often difficult and can be dependent on a variety of factors that can be outside the control of managers, stakeholders and policymakers. Among the many methods that have been used to assess connectivity, genetic markers are often used to infer connectivity indirectly by estimating the degree of genetic differentiation between populations of a species or by inferring the origin(s) of migrants using assignment methods. While modern molecular methods can be extremely robust and are now routinely used to address conservation issues, genetic data are, to the authors’ knowledge, rarely used to inform designation of MPA networks. In this paper, several biological and methodological factors are highlighted, consideration of which may help to inform the selection of species for assessments of connectivity between MPAs in a network, and this paper suggests ways in which genetic data may be interpreted to inform MPA design and policy.
Abstract.
Ikediashi C, Paris JR, King RA, Beaumont WRC, Ibbotson A, Stevens JR (2018). Atlantic salmon Salmo salar in the chalk streams of England are genetically unique.
J Fish Biol,
92(3), 621-641.
Abstract:
Atlantic salmon Salmo salar in the chalk streams of England are genetically unique.
Recent research has identified genetic groups of Atlantic salmon Salmo salar that show association with geological and environmental boundaries. This study focuses on one particular subgroup of the species inhabiting the chalk streams of southern England, U.K. These fish are genetically distinct from other British and European S. salar populations and have previously demonstrated markedly low admixture with populations in neighbouring regions. The genetic population structure of S. salar occupying five chalk streams was explored using 16 microsatellite loci. The analysis provides evidence of the genetic distinctiveness of chalk-stream S. salar in southern England, in comparison with populations from non-chalk regions elsewhere in western Europe. Little genetic differentiation exists between the chalk-stream populations and a pattern of isolation by distance was evident. Furthermore, evidence of temporal stability of S. salar populations across the five chalk streams was found. This work provides new insights into the temporal stability and lack of genetic population sub-structuring within a unique component of the species' range of S. salar.
Abstract.
Author URL.
Hutchinson R, Stevens JR (2018). Barcoding in trypanosomes.
Parasitology,
145(5), 563-573.
Abstract:
Barcoding in trypanosomes.
Trypanosomes (genus Trypanosoma) are parasites of humans, and wild and domestic mammals, in which they cause several economically and socially important diseases, including sleeping sickness in Africa and Chagas disease in the Americas. Despite the development of numerous molecular diagnostics and increasing awareness of the importance of these neglected parasites, there is currently no universal genetic barcoding marker available for trypanosomes. In this review we provide an overview of the methods used for trypanosome detection and identification, discuss the potential application of different barcoding techniques and examine the requirements of the 'ideal' trypanosome genetic barcode. In addition, we explore potential alternative genetic markers for barcoding Trypanosoma species, including an analysis of phylogenetically informative nucleotide changes along the length of the 18S rRNA gene.
Abstract.
Author URL.
Jenkins TL, Castilho R, Stevens JR (2018). Meta-analysis of northeast Atlantic marine taxa shows contrasting phylogeographic patterns following post-LGM expansions.
PeerJ,
6Abstract:
Meta-analysis of northeast Atlantic marine taxa shows contrasting phylogeographic patterns following post-LGM expansions.
BACKGROUND: Comparative phylogeography enables the study of historical and evolutionary processes that have contributed to shaping patterns of contemporary genetic diversity across co-distributed species. In this study, we explored genetic structure and historical demography in a range of coastal marine species across the northeast Atlantic to assess whether there are commonalities in phylogeographic patterns across taxa and to evaluate whether the timings of population expansions were linked to the Last Glacial Maximum (LGM). METHODS: a literature search was conducted using Web of Science. Search terms were chosen to maximise the inclusion of articles reporting on population structure and phylogeography from the northeast Atlantic; titles and abstracts were screened to identify suitable articles within the scope of this study. Given the proven utility of mtDNA in comparative phylogeography and the availability of these data in the public domain, a meta-analysis was conducted using published mtDNA gene sequences. A standardised methodology was implemented to ensure that the genealogy and demographic history of all mtDNA datasets were reanalysed in a consistent and directly comparable manner. RESULTS: Mitochondrial DNA datasets were built for 21 species. The meta-analysis revealed significant population differentiation in 16 species and four main types of haplotype network were found, with haplotypes in some species unique to specific geographical locations. A signal of rapid expansion was detected in 16 species, whereas five species showed evidence of a stable population size. Corrected mutation rates indicated that the majority of expansions were estimated to have occurred after the earliest estimate for the LGM (∼26.5 Kyr), while few expansions were estimated to have pre-dated the LGM. CONCLUSION: This study suggests that post-LGM expansion appeared to be common in a range of marine taxa, supporting the concept of rapid expansions after the LGM as the ice sheets started to retreat. However, despite the commonality of expansion patterns in many of these taxa, phylogeographic patterns appear to differ in the species included in this study. This suggests that species-specific evolutionary processes, as well as historical events, have likely influenced the distribution of genetic diversity of marine taxa in the northeast Atlantic.
Abstract.
Author URL.
Jenkins TL, Ellis CD, Stevens JR (2018). SNP discovery in European lobster (Homarus gammarus) using RAD sequencing. Conservation Genetics Resources, 11(3), 253-257.
Espinosa-Álvarez O, Ortiz PA, Lima L, Costa-Martins AG, Serrano MG, Herder S, Buck GA, Camargo EP, Hamilton PB, Stevens JR, et al (2018). Trypanosoma rangeli is phylogenetically closer to Old World trypanosomes than to Trypanosoma cruzi.
Int J Parasitol,
48(7), 569-584.
Abstract:
Trypanosoma rangeli is phylogenetically closer to Old World trypanosomes than to Trypanosoma cruzi.
Trypanosoma rangeli and Trypanosoma cruzi are generalist trypanosomes sharing a wide range of mammalian hosts; they are transmitted by triatomine bugs, and are the only trypanosomes infecting humans in the Neotropics. Their origins, phylogenetic relationships, and emergence as human parasites have long been subjects of interest. In the present study, taxon-rich analyses (20 trypanosome species from bats and terrestrial mammals) using ssrRNA, glycosomal glyceraldehyde-3-phosphate dehydrogenase (gGAPDH), heat shock protein-70 (HSP70) and Spliced Leader RNA sequences, and multilocus phylogenetic analyses using 11 single copy genes from 15 selected trypanosomes, provide increased resolution of relationships between species and clades, strongly supporting two main sister lineages: lineage Schizotrypanum, comprising T. cruzi and bat-restricted trypanosomes, and Tra[Tve-Tco] formed by T. rangeli, Trypanosoma vespertilionis and Trypanosoma conorhini clades. Tve comprises European T. vespertilionis and African T. vespertilionis-like of bats and bat cimicids characterised in the present study and Trypanosoma sp. Hoch reported in monkeys and herein detected in bats. Tco included the triatomine-transmitted tropicopolitan T. conorhini from rats and the African NanDoum1 trypanosome of civet (carnivore). Consistent with their very close relationships, Tra[Tve-Tco] species shared highly similar Spliced Leader RNA structures that were highly divergent from those of Schizotrypanum. In a plausible evolutionary scenario, a bat trypanosome transmitted by cimicids gave origin to the deeply rooted Tra[Tve-Tco] and Schizotrypanum lineages, and bat trypanosomes of diverse genetic backgrounds jumped to new hosts. A long and independent evolutionary history of T. rangeli more related to Old World trypanosomes from bats, rats, monkeys and civets than to Schizotrypanum spp. and the adaptation of these distantly related trypanosomes to different niches of shared mammals and vectors, is consistent with the marked differences in transmission routes, life-cycles and host-parasite interactions, resulting in T. cruzi (but not T. rangeli) being pathogenic to humans.
Abstract.
Author URL.
Paris JR, Sherman KD, Bell E, Boulenger C, Delord C, El-Mahdi MBM, Fairfield EA, Griffiths AM, Gutmann Roberts C, Hedger RD, et al (2018). Understanding and managing fish populations: keeping the toolbox fit for purpose.
J Fish Biol,
92(3), 727-751.
Abstract:
Understanding and managing fish populations: keeping the toolbox fit for purpose.
Wild fish populations are currently experiencing unprecedented pressures, which are projected to intensify in the coming decades. Developing a thorough understanding of the influences of both biotic and abiotic factors on fish populations is a salient issue in contemporary fish conservation and management. During the 50th Anniversary Symposium of the Fisheries Society of the British Isles at the University of Exeter, UK, in July 2017, scientists from diverse research backgrounds gathered to discuss key topics under the broad umbrella of 'Understanding Fish Populations'. Below, the output of one such discussion group is detailed, focusing on tools used to investigate natural fish populations. Five main groups of approaches were identified: tagging and telemetry; molecular tools; survey tools; statistical and modelling tools; tissue analyses. The appraisal covered current challenges and potential solutions for each of these topics. In addition, three key themes were identified as applicable across all tool-based applications. These included data management, public engagement, and fisheries policy and governance. The continued innovation of tools and capacity to integrate interdisciplinary approaches into the future assessment and management of fish populations is highlighted as an important focus for the next 50 years of fisheries research.
Abstract.
Author URL.
Hume BCC, D'Angelo C, Smith EG, Stevens JR, Burt JA, Wiedenmann J (2018). Validation of the binary designation Symbiodinium thermophilum (Dinophyceae).
J Phycol,
54(5), 762-764.
Abstract:
Validation of the binary designation Symbiodinium thermophilum (Dinophyceae).
The binary designation Symbiodinium thermophilum was invalid due to the absence of an illustration as required by Article 44.2 of the ICN. Herein, it is validated. This species is the most common symbiont in reef corals in the southern Persian/Arabian Gulf, the world's hottest body of water sustaining reef coral growth.
Abstract.
Author URL.
2017
Hamilton PB, Stevens JR (2017). 15 Classification and phylogeny of Trypanosoma cruzi. In (Ed) American Trypanosomiasis Chagas Disease, 321-344.
Gilbey J, Coughlan J, Wennevik V, Prodöhl P, Stevens JR, Garcia de Leaniz C, Ensing D, Cauwelier E, Cherbonnel C, Consuegra S, et al (2017). A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.).
ICES Journal of Marine Science,
75(2), 662-674.
Abstract:
A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.)
AbstractAtlantic salmon (Salmo salar L.) populations from different river origins mix in the North Atlantic during the marine life stage. To facilitate marine stock identification, we developed a genetic baseline covering the European component of the species’ range excluding the Baltic Sea, from the Russian River Megra in the north-east, the Icelandic Ellidaar in the west, and the Spanish Ulla in the south, spanning 3737 km North to South and 2717 km East to West. The baseline encompasses data for 14 microsatellites for 26 822 individual fish from 13 countries, 282 rivers, and 467 sampling sites. A hierarchy of regional genetic assignment units was defined using a combination of distance-based and Bayesian clustering. At the top level, three assignment units were identified comprising northern, southern, and Icelandic regions. A second assignment level was also defined, comprising eighteen and twenty-nine regional units for accurate individual assignment and mixed stock estimates respectively. The baseline provides the most comprehensive geographical coverage for an Atlantic salmon genetic data-set, and a unique resource for the conservation and management of the species in Europe. It is freely available to researchers to facilitate identification of the natal origin of European salmon.
Abstract.
Hamston TJ, Wilson RJ, de Vere N, Rich TCG, Stevens JR, Cresswell JE (2017). Breeding system and spatial isolation from congeners strongly constrain seed set in an insect-pollinated apomictic tree: Sorbus subcuneata (Rosaceae).
Sci Rep,
7Abstract:
Breeding system and spatial isolation from congeners strongly constrain seed set in an insect-pollinated apomictic tree: Sorbus subcuneata (Rosaceae).
In plants, apomixis results in the production of clonal offspring via seed and can provide reproductive assurance for isolated individuals. However, many apomicts require pollination to develop functional endosperm for successful seed set (pseudogamy) and therefore risk pollination-limitation, particularly in self-incompatible species that require heterospecific pollen. We used microsatellite paternity analysis and hand pollinations to investigate pollen-limitation in Sorbus subcuneata, a threatened endemic tree that co-occurs with its congener, S. admonitor. We confirmed that S. subcuneata is an obligate pseudogamous apomict, but open-pollinated flowers rarely produced seed (flower-to-seed conversion
Abstract.
Author URL.
Hamilton PB, Stevens JR (2017). Classification and phylogeny of Trypanosoma cruzi. In (Ed)
American Trypanosomiasis Chagas Disease: One Hundred Years of Research: Second Edition, 321-344.
Abstract:
Classification and phylogeny of Trypanosoma cruzi
Abstract.
Holland LP, Jenkins TL, Stevens JR (2017). Contrasting patterns of population structure and gene flow facilitate exploration of connectivity in two widely distributed temperate octocorals.
Heredity (Edinb),
119(1), 35-48.
Abstract:
Contrasting patterns of population structure and gene flow facilitate exploration of connectivity in two widely distributed temperate octocorals.
Connectivity is an important component of metapopulation dynamics in marine systems and can influence population persistence, migration rates and conservation decisions associated with Marine Protected Areas (MPAs). In this study, we compared the genetic diversity, gene flow and population structure of two octocoral species, Eunicella verrucosa and Alcyonium digitatum, in the northeast Atlantic (ranging from the northwest of Ireland and the southern North Sea, to southern Portugal), using two panels of 13 and 8 microsatellite loci, respectively. Our results identified regional genetic structure in E. verrucosa partitioned between populations from southern Portugal, northwest Ireland and Britain/France; subsequent hierarchical analysis of population structure also indicated reduced gene flow between southwest Britain and northwest France. However, over a similar geographical area, A. digitatum showed little evidence of population structure, suggesting high gene flow and/or a large effective population size; indeed, the only significant genetic differentiation detected in A. digitatum occurred between North Sea samples and those from the English Channel/northeast Atlantic. In both species the vast majority of gene flow originated from sample sites within regions, with populations in southwest Britain being the predominant source of contemporary exogenous genetic variants for the populations studied. Overall, historical patterns of gene flow appeared more complex, though again southwest Britain appeared to be an important source of genetic variation for both species. Our findings have major conservation implications, particularly for E. verrucosa, a protected species in UK waters and listed by the IUCN as 'Vulnerable', and for the designation and management of European MPAs.
Abstract.
Author URL.
Sherman KD, King RA, Dahlgren CP, Simpson SD, Stevens JR, Tyler CR (2017). Historical processes and contemporary anthropogenic activities influence genetic population dynamics of Nassau grouper (Epinephelus striatus) within the Bahamas.
Frontiers in Marine Science,
4(DEC).
Abstract:
Historical processes and contemporary anthropogenic activities influence genetic population dynamics of Nassau grouper (Epinephelus striatus) within the Bahamas
Severe declines of endangered Nassau grouper (Epinephelus striatus) across the Bahamas and Caribbean have spurred efforts to improve their fisheries management and population conservation. The Bahamas is reported to hold the majority of fish spawning aggregations for Nassau grouper, however, the status and genetic population structure of fish within the country is largely unknown, presenting a major knowledge gap for their sustainable management. Between August 2014-February 2017, 464 individual Nassau grouper sampled from the Bahamas were genotyped using 15 polymorphic microsatellite loci to establish measures of population structure, genetic diversity and effective population size (Ne). Nassau grouper were characterized by mostly high levels of genetic diversity, but we found no evidence for geographic population structure. Microsatellite analyses revealed weak, but significant genetic differentiation of Nassau grouper throughout the Bahamian archipelago (Global FST 0.00236, p = 0.0001). Temporal analyses of changes in Ne over the last 1,000 generations provide evidence in support of a pronounced historic decline in Bahamian Nassau grouper that appears to pre-date anthropogenic fishing activities. M-ratio results corroborate significant reductions in Ne throughout the Bahamas, with evidence for population bottlenecks in three islands and an active fish spawning aggregation along with apparent signs of inbreeding at two islands. Current estimates of Ne for Nassau grouper are considerably lower compared with historic levels. These findings represent important new contributions to our understanding of the evolutionary history, demographics and genetic connectivity of this endangered species, which are of critical importance for advancing their sustainable management.
Abstract.
Paris JR, Stevens JR, Catchen JM (2017). Lost in parameter space: a road map for STACKS.
Methods in Ecology and Evolution,
8(10), 1360-1373.
Abstract:
Lost in parameter space: a road map for STACKS
© 2017 the Authors. Methods in Ecology and Evolution © 2017 British Ecological Society Restriction site-Associated DNA sequencing (RAD-seq) has become a widely adopted method for genotyping populations of model and non-model organisms. Generating a reliable set of loci for downstream analysis requires appropriate use of bioinformatics software, such as the program stacks. Using three empirical RAD-seq datasets, we demonstrate a method for optimising a de novo assembly of loci using stacks. By iterating values of the program's main parameters and plotting resultant core metrics for visualisation, researchers can gain a much better understanding of their dataset and select an optimal set of parameters; we present the 80% rule as a generally effective method to select the core parameters for stacks. Visualisation of the metrics plotted for the three RAD-seq datasets shows that they differ in the optimal parameters that should be used to maximise the amount of available biological information. We also demonstrate that building loci de novo and then integrating alignment positions is more effective than aligning raw reads directly to a reference genome. Our methods will help the communi ty in honing the analytical skills necessary to accurately assemble a RAD-seq dataset.
Abstract.
Nicol E, Stevens JR, Jobling S (2017). Riverine fish diversity varies according to geographical isolation and land use modification. Ecology and Evolution, 7(19), 7872-7883.
2016
Goodwin JCA, Andrew King R, Iwan Jones J, Ibbotson A, Stevens JR (2016). A small number of anadromous females drive reproduction in a brown trout (Salmo trutta) population in an English chalk stream.
Freshwater Biology,
61(7), 1075-1089.
Abstract:
A small number of anadromous females drive reproduction in a brown trout (Salmo trutta) population in an English chalk stream
Brown trout, Salmo trutta, exhibit one of the most highly variable and polytypic life-history strategies of all salmonids. Populations may be wholly freshwater-resident or almost exclusively migratory (anadromous), or fish of a single population may exhibit varying proportions of the two life-history strategies. Both anadromous and freshwater-resident trout freely interbreed to produce fertile offspring. We quantify maternal reproductive provisioning by anadromous and freshwater-resident brown trout to their offspring and assess relative parental fitness (in terms of number, size and time of emergence of offspring). Newly emerged juvenile trout (fry) were sampled (n = 119) over the emergence period in March–April 2007 in a lowland English chalk stream; samples of adult trout [anadromous (6F : 12M) and freshwater-resident (22F : 56M)], river-resident trout parr and macroinvertebrate prey were also collected. Using a novel combination of stable isotope analysis and microsatellite genotyping we demonstrate the overwhelming contribution of anadromous parents (both female and male) to fry production, despite the obvious presence and numerical dominance of resident adults. We unambiguously identify the maternal origins of 78% of juveniles sampled and show that maternal reproductive contribution to juvenile production in the river was higher for anadromous females (76%) than freshwater-resident fish (2.5%). Offspring of anadromous females emerged earlier and at a larger body size than offspring of resident females. Similarly, while the relative contribution of resident males (37%) was higher than that of resident females, anadromous males sired considerably more offspring (63%) than resident males. This is the first study of its kind to accurately assess the reproductive contribution of anadromous male trout. Overall, this study suggests that anadromous maternal traits provide offspring with an adaptive advantage and greater fitness in early ontogeny, and that a small number of anadromous females (six of 96 adults sampled) are the main drivers of reproduction in this system.
Abstract.
Sherman KD, Dahlgren CP, Stevens JR, Tyler CR (2016). Integrating population biology into conservation management for endangered Nassau grouper Epinephelus striatus.
Marine Ecology Progress Series,
554, 263-280.
Abstract:
Integrating population biology into conservation management for endangered Nassau grouper Epinephelus striatus
Groupers are a phylogenetically diverse group and include many ecologically and economically valuable predatory marine fishes that have experienced drastic population declines. Reproduction via spawning aggregations increases the vulnerability of grouper species such as Nassau grouper Epinephelus striatus to overfishing, and this is likely to be a major contributing factor to population declines. However, the lack of information pertaining to population structure and dynamics of Nassau grouper spawning aggregations has impeded effective ecosystem-based fisheries management for remaining stocks. Worldwide, the Bahamas has the largest number of known Nassau grouper spawning aggregations, yet very little is known about the overall status of groupers in the region. Landings of Nassau grouper in the Bahamas have declined by 86% in the last 20 years from a peak of 514 t in 1997. Available data suggest that existing management measures are failing in their attempts to prevent further declines. Effective management strategies are urgently needed that balance ecological and socioeconomic considerations to enable a sustainable Nassau grouper fishery. This review provides an analysis of the reproductive and population biology of Nassau grouper and a suggested framework to direct future research efforts for enhancing conservation management of this endangered marine fish species.
Abstract.
King RA, Hillman R, Elsmere P, Stockley B, Stevens JR (2016). Investigating patterns of straying and mixed stock exploitation of sea trout, Salmo trutta, in rivers sharing an estuary in south-west England.
Fisheries Management and Ecology,
23(5), 376-389.
Abstract:
Investigating patterns of straying and mixed stock exploitation of sea trout, Salmo trutta, in rivers sharing an estuary in south-west England
For effective management, information on the stock composition of a fishery is essential. Here, the utility of a resident trout, Salmon trutta L, microsatellite baseline to determine the origins of sea trout entering the rivers Tamar, Tavy and Lynher in south-west England is highlighted – all share a common estuary and have major runs of sea trout. There is a high degree of geographical structuring of the genetic variation in the baseline rivers. Testing with simulated and real data sets showed fish can be assigned to reporting group with a high degree of accuracy. Mixed stock analysis of >1000 sea trout showed that fish entering the Tamar and Tavy constituted mixed stocks. Significantly, in the Tamar, non-natal origin sea trout are restricted to the lower catchment. As well as providing insight into sea trout behaviour, this study also has important implications for the management of recreational rod and line fisheries.
Abstract.
Hamilton PB, Cowx IG, Oleksiak MF, Griffiths AM, Grahn M, Stevens JR, Carvalho GR, Nicol E, Tyler CR (2016). Population-level consequences for wild fish exposed to sublethal concentrations of chemicals – a critical review.
Fish and Fisheries,
17(3), 545-566.
Abstract:
Population-level consequences for wild fish exposed to sublethal concentrations of chemicals – a critical review
Concentrated chemical spills have been shown to impact adversely on fish populations and even cause localized population extinctions. Evaluating population-level impacts of sublethal exposure concentrations is, however, complex and confounded by other environmental pressures. Applying effect measures derived from laboratory-based chemical exposures to impacts in wild fish populations is constrained by uncertainty on how biochemical response measures (biomarkers) translate into health outcomes, lack of available data for chronic exposures and the many uncertainties in available fish population models. Furthermore, wild fish show phenotypic plasticity and local adaptations can occur that adds geographic and temporal variance on responses. Such population-level factors are rarely considered in the chemical risk assessment process and can probably be derived only from studies on wild fish. Molecular technologies, including microsatellite and SNP genotyping, and RNASeq for gene expression studies, are advancing our understanding of mechanisms of eco-toxicological response, tolerance, adaptation and selection in wild populations. We examine critically the application of such approaches with examples including using microsatellites that has identified roach (Rutilus rutilus) populations living in rivers contaminated with sewage effluents that are self-sustaining, and studies of stickleback (Gasterosteus aculeatus) and killifish (Fundulus heteroclitus) that have identified genomic regions under selection putatively related to pollution tolerance. Integrating data on biological effects between laboratory-based studies and wild populations, and building understanding on adaptive responses to sublethal exposure are some of the priority research areas for more effective evaluation of population risks and resilience to contaminant exposure.
Abstract.
Kennedy EV, Tonk L, Foster NL, Chollett I, Ortiz J-C, Dove S, Hoegh-Guldberg O, Mumby PJ, Stevens JR (2016). Symbiodinium biogeography tracks environmental patterns rather than host genetics in a key Caribbean reef-builder, Orbicella annularis.
Proc Biol Sci,
283(1842).
Abstract:
Symbiodinium biogeography tracks environmental patterns rather than host genetics in a key Caribbean reef-builder, Orbicella annularis.
The physiological performance of a reef-building coral is a combined outcome of both the coral host and its algal endosymbionts, Symbiodinium While Orbicella annularis-a dominant reef-building coral in the Wider Caribbean-is known to be a flexible host in terms of the diversity of Symbiodinium types it can associate with, it is uncertain how this diversity varies across the Caribbean, and whether spatial variability in the symbiont community is related to either O. annularis genotype or environment. Here, we target the Symbiodinium-ITS2 gene to characterize and map dominant Symbiodinium hosted by O. annularis at an unprecedented spatial scale. We reveal northwest-southeast partitioning across the Caribbean, both in terms of the dominant symbiont taxa hosted and in assemblage diversity. Multivariate regression analyses incorporating a suite of environmental and genetic factors reveal that observed spatial patterns are predominantly explained by chronic thermal stress (summer temperatures) and are unrelated to host genotype. Furthermore, we were able to associate the presence of specific Symbiodinium types with local environmental drivers (for example, Symbiodinium C7 with areas experiencing cooler summers, B1j with nutrient loading and B17 with turbidity), associations that have not previously been described.
Abstract.
Author URL.
Dillon MJ, Bowkett AE, Bungard MJ, Beckman K, O'Brien M, Bates K, Fisher MC, Stevens JR, Thornton CR (2016). Tracking the amphibian pathogens Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans by using a highly specific monoclonal antibody and lateral-flow technology.
Microbial BiotechnologyAbstract:
Tracking the amphibian pathogens Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans by using a highly specific monoclonal antibody and lateral-flow technology
The fungus Batrachochytrium dendrobatidis (Bd) causes chytridiomycosis, a lethal epizootic disease of amphibians. Rapid identification of the pathogen and biosecurity are essential to prevent its spread, but current laboratory-based tests are time-consuming and require specialist equipment. Here, we describe the generation of an IgM monoclonal antibody (mAb), 5C4, specific to Bd as well as the related salamander and newt pathogen Batrachochytrium salamandrivorans (Bsal). The mAb, which binds to a glycoprotein antigen present on the surface of zoospores, sporangia and zoosporangia, was used to develop a lateral-flow assay (LFA) for rapid (15 min) detection of the pathogens. The LFA detects known lineages of Bd and also Bsal, as well as the closely related fungus Homolaphlyctis polyrhiza, but does not detect a wide range of related and unrelated fungi and oomycetes likely to be present in amphibian habitats. When combined with a simple swabbing procedure, the LFA was 100% accurate in detecting the water-soluble 5C4 antigen present in skin, foot and pelvic samples from frogs, newts and salamanders naturally-infected with Bd or Bsal. Our results demonstrate the potential of the portable LFA as a rapid qualitative assay for tracking these amphibian pathogens, and as an adjunct test to nucleic acid-based detection methods
Abstract.
Hall MJR, Wall RL, Stevens JR (2016). Traumatic Myiasis: a Neglected Disease in a Changing World.
Annu Rev Entomol,
61, 159-176.
Abstract:
Traumatic Myiasis: a Neglected Disease in a Changing World.
Traumatic myiasis, the parasitic infestation by fly larvae in traumatic lesions of the tissues of living vertebrates, is a serious medical condition in humans and a welfare and economic issue in domestic animals. New molecular studies are providing insights into its evolution and epidemiology. Nevertheless, its incidence in humans is generally underreported, particularly in tropical and subtropical regions. Myiasis in domestic animals has been studied more extensively, but continuous management is difficult and expensive. A key concern is the inadvertent introduction and global spread of agents of myiasis into nonendemic areas, facilitated by climate change and global transport. The incursion of the New World screwworm fly (Cochliomyia hominivorax) into Libya is the most notable of many such range shifts and demonstrates the potential risks of these parasites and the costs of removing them once established in a geographic area. Nevertheless, the insect agents of myiasis can be of societal benefit to forensic science and in medicine as an aid to wound treatment (larval therapy).
Abstract.
Author URL.
McDonagh LM, West H, Harrison JW, Stevens JR (2016). Which mitochondrial gene (if any) is best for insect phylogenetics?.
INSECT SYSTEMATICS & EVOLUTION,
47(3), 245-266.
Author URL.
2015
Kennedy EV, Foster NL, Mumby PJ, Stevens JR (2015). Erratum to: Widespread prevalence of cryptic Symbiodinium D in the key Caribbean reef builder, Orbicella annularis. Coral Reefs
Pountney A, Filby AL, Thomas GO, Simpson VR, Chadwick EA, Stevens JR, Tyler CR (2015). High liver content of polybrominated diphenyl ether (PBDE) in otters (Lutra lutra) from England and Wales.
Chemosphere,
118, 81-86.
Abstract:
High liver content of polybrominated diphenyl ether (PBDE) in otters (Lutra lutra) from England and Wales.
Polybrominated diphenyl ethers (PBDEs), used as flame retardants since the 1970s, are being phased out of use, but are persistent and widespread in the environment. Historical declines in Eurasian otter (Lutra lutra) populations have been associated with exposure to dieldrin and polychlorinated biphenyls (PCBs), but links with other persistent organic pollutants have not been explored. In this study, liver samples from 129 otters, collected across England and Wales from 1995-2006, were analysed for PBDEs, together with PCBs, DDT breakdown products, and hexachlorobenzene. Associations with geographical location and life history parameters were explored. Concentrations of PBDEs in otters (∑BDE 12-70000ngg(-1) lipid) paralleled those measured in marine mammals, with PBDE-47 the dominant congener and high levels of PBDE-99 and -100. Otter livers contained high concentrations of PBDE-153 and -209, typical of terrestrial top predators. Inter-individual variation in PBDE concentrations was high and correlated with geographical location. ∑PBDE was 25% of ∑PCB, and comparable with ∑DDT, identifying PBDEs as a major contaminant in otter populations in England and Wales.
Abstract.
Author URL.
Paris JR, King RA, Stevens JR (2015). Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations.
Evolutionary ApplicationsAbstract:
Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations
Humans have exploited the earth's metal resources for thousands of years leaving behind a legacy of toxic metal contamination and poor water quality. The southwest of England provides a well-defined example, with a rich history of metal mining dating to the Bronze Age. Mine water washout continues to negatively impact water quality across the region where brown trout (Salmo trutta L.) populations exist in both metal-impacted and relatively clean rivers. We used microsatellites to assess the genetic impact of mining practices on trout populations in this region. Our analyses demonstrated that metal-impacted trout populations have low genetic diversity and have experienced severe population declines. Metal-river trout populations are genetically distinct from clean-river populations, and also from one another, despite being geographically proximate. Using approximate Bayesian computation (ABC), we dated the origins of these genetic patterns to periods of intensive mining activity. The historical split of contemporary metal-impacted populations from clean-river fish dated to the Medieval period. Moreover, we observed two distinct genetic populations of trout within a single catchment and dated their divergence to the Industrial Revolution. Our investigation thus provides an evaluation of contemporary population genetics in showing how human-altered landscapes can change the genetic makeup of a species.
Abstract.
Hume BCC, D'Angelo C, Smith EG, Stevens JR, Burt J, Wiedenmann J (2015). SYMBIODINIUM THERMOPHILUM SP NOV. a THERMOTOLERANT SYMBIOTIC ALGA PREVALENT IN CORALS OF THE WORLD'S HOTTEST SEA, THE PERSIAN/ARABIAN GULF.
EUROPEAN JOURNAL OF PHYCOLOGY,
50, 58-58.
Author URL.
Hume BCC, D'Angelo C, Smith EG, Stevens JR, Burt J, Wiedenmann J (2015). Symbiodinium thermophilum sp. nov. a thermotolerant symbiotic alga prevalent in corals of the world's hottest sea, the Persian/Arabian Gulf.
Sci Rep,
5Abstract:
Symbiodinium thermophilum sp. nov. a thermotolerant symbiotic alga prevalent in corals of the world's hottest sea, the Persian/Arabian Gulf.
Coral reefs are in rapid decline on a global scale due to human activities and a changing climate. Shallow water reefs depend on the obligatory symbiosis between the habitat forming coral host and its algal symbiont from the genus Symbiodinium (zooxanthellae). This association is highly sensitive to thermal perturbations and temperatures as little as 1°C above the average summer maxima can cause the breakdown of this symbiosis, termed coral bleaching. Predicting the capacity of corals to survive the expected increase in seawater temperatures depends strongly on our understanding of the thermal tolerance of the symbiotic algae. Here we use molecular phylogenetic analysis of four genetic markers to describe Symbiodinium thermophilum, sp. nov. from the Persian/Arabian Gulf, a thermally tolerant coral symbiont. Phylogenetic inference using the non-coding region of the chloroplast psbA gene resolves S. thermophilum as a monophyletic lineage with large genetic distances from any other ITS2 C3 type found outside the Gulf. Through the characterisation of Symbiodinium associations of 6 species (5 genera) of Gulf corals, we demonstrate that S. thermophilum is the prevalent symbiont all year round in the world's hottest sea, the southern Persian/Arabian Gulf.
Abstract.
Author URL.
Kennedy EV, Foster NL, Mumby PJ, Stevens JR (2015). Widespread prevalence of cryptic Symbiodinium D in the key Caribbean reef builder, Orbicella annularis.
Coral ReefsAbstract:
Widespread prevalence of cryptic Symbiodinium D in the key Caribbean reef builder, Orbicella annularis
Symbiodinium D, a relatively rare clade of algal endosymbiont with a global distribution, has attracted interest as some of its sub-cladal types induce increased thermal tolerance and associated trade-offs, including reduced growth rate in its coral hosts. Members of Symbiodinium D are increasingly reported to comprise low-abundance ‘cryptic’ (30 % of corals per site found to harbour the symbiont. When the same samples were analysed using the conventional screening technique, denaturing gradient gel electrophoresis, Symbiodinium D1 was only detected in 12 populations and appeared to be hosted by
Abstract.
2014
Selly SLC, Hickey J, Stevens JR (2014). A tale of two hatcheries: Assessing bias in the hatchery process for Atlantic salmon (Salmo salar L.).
Aquaculture,
434, 254-263.
Abstract:
A tale of two hatcheries: Assessing bias in the hatchery process for Atlantic salmon (Salmo salar L.)
Stock enhancement of Atlantic salmon (Salmo salar L.), a fish of considerable economic and social importance, is commonplace. Supportive-breeding is a well-recognised method of enhancement which, when compared with traditional hatchery practices, is thought to reduce the severity of selection pressures on broodstock fish. Critically, in supportive-breeding programmes, the eggs and sperm used in the breeding process are taken from wild adult fish originating from the same catchment that resulting juvenile fish are subsequently stocked into, thereby avoiding problems associated with a lack of local adaptation in the stocked fish. Previous studies have indicated that sex bias during the hatchery process may result in reduced genetic diversity of the offspring. Utilising 16 microsatellite loci and two expressed sequence tag (EST) loci, we examined progeny from two hatcheries located on the rivers Exe and Tamar in southwest England, assessing the genetic diversity and parental contribution at each. Two strains were assessed within each hatchery. Genetic diversity was found to be reduced in offspring compared with that of the parent fish. This is likely the result of utilising a small number of broodstock in combination with parental bias. In the four hatchery strains studied (Bar, LEx, Lyd and TXL), parental contribution ranged between 2.1 and 29.2%, 12.2-51.0%, 2.0-70.0% and 4.0-40.0%, respectively. If this practice is to be continued, efforts should be made to improve adherence to national rearing guidelines by increasing the number of broodstock fish utilised and ensuring a more balanced contribution of all adults during the crossing process. Ultimately, we suggest a need to review the suitability of current national Atlantic salmon hatchery guidelines, particularly with regard to their use and relevance in small European rearing systems. © 2014 Elsevier B.V.
Abstract.
Bowkett AE, Jones T, Rovero F, Nielsen MR, Davenport TRB, Hawkins DM, Plowman AB, Stevens JR (2014). Distribution and genetic diversity of the Endangered Abbott's duiker Cephalophus spadix in the Udzungwa Mountains, Tanzania.
ENDANGERED SPECIES RESEARCH,
24(2), 105-114.
Author URL.
Stevens JR (2014). Free-living bodonids and derived parasitic trypanosomatids: but what lies in between?.
Trends Parasitol,
30(3), 113-114.
Abstract:
Free-living bodonids and derived parasitic trypanosomatids: but what lies in between?
Inclusion of suitable out-group taxa has been of particular importance in accurate reconstruction of evolutionary relationships among trypanosomatids. However, the persistence of researchers focusing on insect trypansomatids appears to have paid off, and a novel, apparently-monoxenous parasite isolated from mosquitoes has recently been characterised. Critically, phylogenetic and phylogenomic analyses robustly position this new species, Paratrypanosoma confusum, between free-living bodonid out-group taxa and other trypanosomatids, thereby overcoming some of the issues associated with previously utilised out-groups.
Abstract.
Author URL.
Horreo JL, Machado-Schiaffino G, Griffiths AM, Bright D, Stevens JR, Garcia-Vazquez E (2014). Long-term effects of stock transfers: Synergistic introgression of allochthonous genomes in salmonids. Journal of Fish Biology
Hamilton PB, Nicol E, De-Bastos ESR, Williams RJ, Sumpter JP, Jobling S, Stevens JR, Tyler CR (2014). Populations of a cyprinid fish are self-sustaining despite widespread feminization of males.
BMC Biol,
12Abstract:
Populations of a cyprinid fish are self-sustaining despite widespread feminization of males.
BACKGROUND: Treated effluents from wastewater treatment works can comprise a large proportion of the flow of rivers in the developed world. Exposure to these effluents, or the steroidal estrogens they contain, feminizes wild male fish and can reduce their reproductive fitness. Long-term experimental exposures have resulted in skewed sex ratios, reproductive failures in breeding colonies, and population collapse. This suggests that environmental estrogens could threaten the sustainability of wild fish populations. RESULTS: Here we tested this hypothesis by examining population genetic structures and effective population sizes (N(e)) of wild roach (Rutilus rutilus L.) living in English rivers contaminated with estrogenic effluents. N(e) was estimated from DNA microsatellite genotypes using approximate Bayesian computation and sibling assignment methods. We found no significant negative correlation between N(e) and the predicted estrogen exposure at 28 sample sites. Furthermore, examination of the population genetic structure of roach in the region showed that some populations have been confined to stretches of river with a high proportion of estrogenic effluent for multiple generations and have survived, apparently without reliance on immigration of fish from less polluted sites. CONCLUSIONS: These results demonstrate that roach populations living in some effluent-contaminated river stretches, where feminization is widespread, are self-sustaining. Although we found no evidence to suggest that exposure to estrogenic effluents is a significant driving factor in determining the size of roach breeding populations, a reduction in N(e) of up to 65% is still possible for the most contaminated sites because of the wide confidence intervals associated with the statistical model.
Abstract.
Author URL.
2013
Bowkett AE, Jones T, Laizzer RL, Plowman AB, Stevens JR (2013). Can molecular data validate morphometric identification of faecal pellets in Tanzanian forest antelope species?.
CONSERVATION GENETICS RESOURCES,
5(4), 1095-1100.
Author URL.
Berry CM, Wall R, Morgan E, Stevens J (2013). Identifying ticks. Veterinary Record, 172(8).
Holland LP, Dawson DA, Horsburgh GJ, Stevens JR (2013). Isolation and characterization of 11 microsatellite loci from the ubiquitous temperate octocoral Alcyonium digitatum (Linnaeus, 1758).
Conservation Genetics Resources,
5(3), 767-770.
Abstract:
Isolation and characterization of 11 microsatellite loci from the ubiquitous temperate octocoral Alcyonium digitatum (Linnaeus, 1758)
We isolated 116 unique microsatellite sequences from an enriched genomic library generated from a single colony of the temperate octocoral Alcyonium digitatum sampled off the Lizard, Cornwall, southwest England. Primer pairs were designed for 54 loci and tested in four individuals from a neighbouring site. Subsequently, 11 polymorphic loci were selected and characterized in 42 individuals sampled from the Isles of Scilly, southwest England. All loci were polymorphic in the Scilly population, with 3-27 alleles per locus and expected heterozygosities of 0.07-0.96. Two loci deviated from Hardy-Weinberg equilibrium possibly due to the presence of null alleles. No loci showed significant evidence of linkage disequilibrium following correction for multiple tests. Cross-amplification was assessed in Alcyonium coralloides, Alcyonium acaule and Alcyonium palmatum collected from the French Mediterranean; six loci amplified successfully in at least one other species. These markers should prove useful for future conservation studies of this ubiquitous animal. © 2013 Springer Science+Business Media Dordrecht.
Abstract.
Holland LP, Dawson DA, Horsburgh GJ, Krupa AP, Stevens JR (2013). Isolation and characterization of fourteen microsatellite loci from the endangered octocoral Eunicella verrucosa (Pallas 1766).
Conservation Genetics Resources,
5(3), 825-829.
Abstract:
Isolation and characterization of fourteen microsatellite loci from the endangered octocoral Eunicella verrucosa (Pallas 1766)
We isolated 165 unique microsatellite sequences from the threatened and IUCN red-listed octocoral Eunicella verrucosa (common name: pink sea fan). Two enriched genomic libraries were created from a single individual collected in Lyme Bay, Dorset, England. Following testing of 76 markers, 14 loci were then selected, multiplexed and characterised in 44 individuals sampled at the Mewstone Ledges, Plymouth Sound, Devon, England. The number of alleles per locus ranged from 2 to 10 and expected heterozygosities from 0.05 to 0.82. The presence of null alleles was suggested for four loci, with three showing significant deviations from Hardy-Weinberg equilibrium. No linkage disequilibrium was detected. Cross-species utility was assessed in Eunicella singularis (n = 20), E. cavolinii (n = 12) and Leptogorgia sarmentosa (n = 3) collected from the Mediterranean and southern Portugal. At least ten loci were polymorphic in each Eunicella species and five in L. sarmentosa. These markers should prove useful in exploring population structure in these as yet poorly studied animals. © 2013 Springer Science+Business Media Dordrecht.
Abstract.
2012
Söffker M, Stevens JR, Tyler CR (2012). Comparative breeding and behavioral responses to ethinylestradiol exposure in wild and laboratory maintained zebrafish (Danio rerio) populations.
Environ Sci Technol,
46(20), 11377-11383.
Abstract:
Comparative breeding and behavioral responses to ethinylestradiol exposure in wild and laboratory maintained zebrafish (Danio rerio) populations.
Genetic variation has a significant effect on behavior, fitness, and response to toxicants; however, this is rarely considered in ecotoxicological studies. We compared fitness-related behavioral traits, breeding activity, and the effects of exposure to the environmental estrogen ethinylestradiol (EE(2)) on reproduction in a laboratory (Wild Indian Karyotype, WIK) strain and a wild-caught population (Bangladesh, BLD01) of Danio rerio (zebrafish). In WIK fish, males with higher observed heterozygocity were more active reproductively and more successful in securing parentage, but these relationships were not apparent in the BLD01 fish. The frequency of reproductive behaviors increased in WIK zebrafish for exposure to 0.4 ng/L EE(2), which was not apparent in the BLD01 zebrafish. The different strains showed the same threshold for hepatic vitellogenin gene (vtg) induction (2.2 ng EE(2)/L), but results suggested an elevated response level in the BLD01. There were no effects on total egg production up to 2.2 ng EE(2)/L in either population; however, there was reduced egg fertilization rate at 2.2 ng EE(2)/L in the BLD01 fish. These results show consistency in the general responses to EE(2) between these two genetically divergent strains of zebrafish, but also illustrate differences in their breeding biology and response sensitivities. These findings highlight the need for due consideration of the source (and genetics) of populations used in ecological risk assessment for accurate comparisons among studies.
Abstract.
Author URL.
Foster NL, Paris CB, Kool JT, Baums IB, Stevens JR, Sanchez JA, Bastidas C, Agudelo C, Bush P, Day O, et al (2012). Connectivity of Caribbean coral populations: complementary insights from empirical and modelled gene flow.
Mol Ecol,
21(5), 1143-1157.
Abstract:
Connectivity of Caribbean coral populations: complementary insights from empirical and modelled gene flow.
Understanding patterns of connectivity among populations of marine organisms is essential for the development of realistic, spatially explicit models of population dynamics. Two approaches, empirical genetic patterns and oceanographic dispersal modelling, have been used to estimate levels of evolutionary connectivity among marine populations but rarely have their potentially complementary insights been combined. Here, a spatially realistic Lagrangian model of larval dispersal and a theoretical genetic model are integrated with the most extensive study of gene flow in a Caribbean marine organism. The 871 genets collected from 26 sites spread over the wider Caribbean subsampled 45.8% of the 1900 potential unique genets in the model. At a coarse scale, significant consensus between modelled estimates of genetic structure and empirical genetic data for populations of the reef-building coral Montastraea annularis is observed. However, modelled and empirical data differ in their estimates of connectivity among northern Mesoamerican reefs indicating that processes other than dispersal may dominate here. Further, the geographic location and porosity of the previously described east-west barrier to gene flow in the Caribbean is refined. A multi-prong approach, integrating genetic data and spatially realistic models of larval dispersal and genetic projection, provides complementary insights into the processes underpinning population connectivity in marine invertebrates on evolutionary timescales.
Abstract.
Author URL.
Morgan ER, Clare EL, Jefferies R, Stevens JR (2012). Parasite epidemiology in a changing world: can molecular phylogeography help us tell the wood from the trees?.
Parasitology,
139(14), 1924-1938.
Abstract:
Parasite epidemiology in a changing world: can molecular phylogeography help us tell the wood from the trees?
SUMMARY Molecular phylogeography has revolutionised our ability to infer past biogeographic events from cross-sectional data on current parasite populations. In ecological parasitology, this approach has been used to address fundamental questions concerning host-parasite co-evolution and geographic patterns of spread, and has raised many technical issues and problems of interpretation. For applied parasitologists, the added complexity inherent in adding population genetic structure to perceived parasite distributions can sometimes seem to cloud rather than clarify approaches to control. In this paper, we use case studies firstly to illustrate the potential extent of cryptic diversity in parasite and parasitoid populations, secondly to consider how anthropogenic influences including movement of domestic animals affect the geographic distribution and host associations of parasite genotypes, and thirdly to explore the applied relevance of these processes to parasites of socio-economic importance. The contribution of phylogeographic approaches to deeper understanding of parasite biology in these cases is assessed. Thus, molecular data on the emerging parasites Angiostrongylus vasorum in dogs and wild canids, and the myiasis-causing flies Lucilia spp. in sheep and Cochliomyia hominovorax in humans, lead to clear implications for control efforts to limit global spread. Broader applications of molecular phylogeography to understanding parasite distributions in an era of rapid global change are also discussed.
Abstract.
Author URL.
Hamilton PB, Cruickshank C, Stevens JR, Teixeira MMG, Mathews F (2012). Parasites reveal movement of bats between the New and Old Worlds.
Mol Phylogenet Evol,
63(2), 521-526.
Abstract:
Parasites reveal movement of bats between the New and Old Worlds.
The global distribution of bat taxa indicates that the Atlantic and Pacific Oceans are effective barriers to movement between the Old and New Worlds. For instance, one of the major suborders, Yinpterochiroptera, has an exclusively Old World distribution, and within the other, Yangochiroptera, no species and only five genera are common to both. However, as bats are sometimes blown out to sea, and have colonised isolated islands, occasional natural movement between the New and Old Worlds does appear to be possible. Here we identify new genotypes of a blood parasite, Trypanosoma dionisii, in Old World bats that are closely related to South American strains. Using highly conservative calibration points, divergence of Old and New World strains is estimated to have occurred 3.2-5.0 million years ago (MYA), depending on the method used (upper 95% CL for maximum time 11.4MYA). The true date of divergence is likely to be considerably more recent. These results demonstrate that taxon-specific parasites can indicate historical movements of their hosts, even where their hosts may have left no lasting phylogenetic footprint.
Abstract.
Author URL.
Hamilton PB, Teixeira MMG, Stevens JR (2012). The evolution of Trypanosoma cruzi: the 'bat seeding' hypothesis.
Trends Parasitol,
28(4), 136-141.
Abstract:
The evolution of Trypanosoma cruzi: the 'bat seeding' hypothesis.
Recent discussions on the evolution of Trypanosoma cruzi have been dominated by the southern super-continent hypothesis, whereby T. cruzi and related parasites evolved in isolation in the mammals of South America, Antarctica and Australia. Here, we consider recent molecular evidence suggesting that T. cruzi evolved from within a broader clade of bat trypanosomes, and that bat trypanosomes have successfully made the switch into other mammalian hosts in both the New and Old Worlds. Accordingly, we propose an alternative hypothesis--the bat seeding hypothesis--whereby lineages of bat trypanosomes have switched into terrestrial mammals, thereby seeding the terrestrial lineages within the clade. One key implication of this finding is that T. cruzi may have evolved considerably more recently than previously envisaged.
Abstract.
Author URL.
Ikediashi C, Billington S, Stevens JR (2012). The origins of Atlantic salmon (Salmo salar L.) recolonizing the River Mersey in northwest England.
Ecol Evol,
2(10), 2537-2548.
Abstract:
The origins of Atlantic salmon (Salmo salar L.) recolonizing the River Mersey in northwest England.
By the 1950s, pollution had extirpated Atlantic salmon in the river Mersey in northwest England. During the 1970s, an extensive restoration program began and in 2001, an adult salmon was caught ascending the river. Subsequently, a fish trap was installed and additional adults are now routinely sampled. In this study, we have genotyped 138 adults and one juvenile salmon at 14 microsatellite loci from across this time period (2001-2011). We have used assignment analysis with a recently compiled pan-European microsatellite baseline to identify their most probable region of origin. Fish entering the Mersey appear to originate from multiple sources, with the greatest proportion (45-60%, dependent on methodology) assigning to rivers in the geographical region just north of the Mersey, which includes Northwest England and the Solway Firth. Substantial numbers also appear to originate from rivers in western Scotland, and from rivers in Wales and Southwest England; nonetheless, the number of fish originating from proximal rivers to the west of the Mersey was lower than expected. Our results suggest that the majority of salmon sampled in the Mersey are straying in a southerly direction, in accordance with the predominantly clockwise gyre present in the eastern Irish Sea. Our findings highlight the complementary roles of improving water quality and in-river navigability in restoring salmon to a river and underlines further the potential benefits of restoration over stocking as a long-term solution to declining fish stocks.
Abstract.
Author URL.
2011
Horreo JL, Machado-Schiaffino G, Griffiths AM, Bright D, Stevens JR, Garcia-Vazquez E (2011). Atlantic Salmon at Risk: Apparent Rapid Declines in Effective Population Size in Southern European Populations.
TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY,
140(3), 605-610.
Author URL.
Hamilton PB, Lewis MD, Cruickshank C, Gaunt MW, Yeo M, Llewellyn MS, Valente SA, Maia da Silva F, Stevens JR, Miles MA, et al (2011). Identification and lineage genotyping of South American trypanosomes using fluorescent fragment length barcoding.
Infect Genet Evol,
11(1), 44-51.
Abstract:
Identification and lineage genotyping of South American trypanosomes using fluorescent fragment length barcoding.
Trypanosoma cruzi and Trypanosoma rangeli are human-infective blood parasites, largely restricted to Central and South America. They also infect a wide range of wild and domestic mammals and are transmitted by a numerous species of triatomine bugs. There are significant overlaps in the host and geographical ranges of both species. The two species consist of a number of distinct phylogenetic lineages. A range of PCR-based techniques have been developed to differentiate between these species and to assign their isolates into lineages. However, the existence of at least six and five lineages within T. cruzi and T. rangeli, respectively, makes identification of the full range of isolates difficult and time consuming. Here we have applied fluorescent fragment length barcoding (FFLB) to the problem of identifying and genotyping T. cruzi, T. rangeli and other South American trypanosomes. This technique discriminates species on the basis of length polymorphism of regions of the rDNA locus. FFLB was able to differentiate many trypanosome species known from South American mammals: T. cruzi cruzi, T. cruzi marinkellei, T. dionisii-like, T. evansi, T. lewisi, T. rangeli, T. theileri and T. vivax. Furthermore, all five T. rangeli lineages and many T. cruzi lineages could be identified, except the hybrid lineages TcV and TcVI that could not be distinguished from lineages III and II respectively. This method also allowed identification of mixed infections of T. cruzi and T. rangeli lineages in naturally infected triatomine bugs. The ability of FFLB to genotype multiple lineages of T. cruzi and T. rangeli together with other trypanosome species, using the same primer sets is an advantage over other currently available techniques. Overall, these results demonstrate that FFLB is a useful method for species diagnosis, genotyping and understanding the epidemiology of American trypanosomes.
Abstract.
Author URL.
Horreo JL, Machado-Schiaffino G, Ayllon F, Griffiths AM, Bright D, Stevens JR, Garcia-Vasquez E (2011). Impact of climate change and human-mediated
introgression on southern European Atlantic
salmon populations.
Global Change Biology,
17(5), 1778-1787.
Abstract:
Impact of climate change and human-mediated
introgression on southern European Atlantic
salmon populations
This study focuses on temporal changes in Atlantic salmon (Salmo salar) populations from the vulnerable periphery of the species range (northern Spain). Using microsatellite markers to assess population structuring and introgression of exogenous genes in four different temporal samples collected across 20 years, we have determined the relative weights of climate and stocking practices in shaping contemporary regional population genetic patterns. Climate, represented by the North Atlantic Oscillation Index, was identified as the main factor for determining the level of population genetic differentiation. Populations within the region have become homogenized through gene flow enhanced by straying of adult salmon from natal rivers and subsequent interchange of genes among rivers due to warmer temperatures. At the same time, and in line with documented changes in stock transfer strategies, evidence of genetic introgression from past stock transfers has decreased throughout the study period, becoming a secondary factor in erasing population structuring. The ability to disentangle the effects of climatic changes and anthropogenic factors (fisheries management practices)is essential for effective long-term conservation of this iconic species. We emphasize the importance of evaluating all factors which may be linked to stocking practices in vulnerable species, particularly those sensitive to climate change.
Abstract.
Ellis JS, Gilbey J, Armstrong A, Balstad T, Cauwelier E, Cherbonnel C, Consuegra S, Coughlan J, Cross TF, Crozier W, et al (2011). Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.).
Genetica,
139(3), 353-367.
Abstract:
Microsatellite standardization and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.).
Microsatellite genotyping is a common DNA characterization technique in population, ecological and evolutionary genetics research. Since different alleles are sized relative to internal size-standards, different laboratories must calibrate and standardize allelic designations when exchanging data. This interchange of microsatellite data can often prove problematic. Here, 16 microsatellite loci were calibrated and standardized for the Atlantic salmon, Salmo salar, across 12 laboratories. Although inconsistencies were observed, particularly due to differences between migration of DNA fragments and actual allelic size ('size shifts'), inter-laboratory calibration was successful. Standardization also allowed an assessment of the degree and partitioning of genotyping error. Notably, the global allelic error rate was reduced from 0.05 ± 0.01 prior to calibration to 0.01 ± 0.002 post-calibration. Most errors were found to occur during analysis (i.e. when size-calling alleles; the mean proportion of all errors that were analytical errors across loci was 0.58 after calibration). No evidence was found of an association between the degree of error and allelic size range of a locus, number of alleles, nor repeat type, nor was there evidence that genotyping errors were more prevalent when a laboratory analyzed samples outside of the usual geographic area they encounter. The microsatellite calibration between laboratories presented here will be especially important for genetic assignment of marine-caught Atlantic salmon, enabling analysis of marine mortality, a major factor in the observed declines of this highly valued species.
Abstract.
Author URL.
Ellis JS, Sumner KJ, Griffiths AM, Bright DI, Stevens JR (2011). Population genetic structure of Atlantic salmon, Salmo salar L. in the River Tamar, southwest England.
Fisheries Management and Ecology,
18(3), 233-245.
Abstract:
Population genetic structure of Atlantic salmon, Salmo salar L. in the River Tamar, southwest England
Population genetic studies can be useful for informing conservation and management. In Atlantic salmon, Salmo salar L. population structuring frequently occurs between river systems, but contrasting patterns occur within rivers, highlighting the need for catchment-specific studies to inform management. Here, population structure of Atlantic salmon was examined in the River Tamar, United Kingdom, using 12 microsatellite loci. Gene diversity and allelic richness ranged from 0.80 to 0.84 and from 8.96 to 10.24, respectively. Some evidence of genetic structure was found, including significant genetic differentiation between samples in different subcatchments (pairwise θ and tests of genic differentiation), results from assignment tests and a pattern of isolation by distance. Conversely, structure revealed only one population cluster, and an analysis of molecular variance showed no significant variation between subcatchments. Evidence of population bottlenecks depended on the mutation model assumed and is discussed with reference to catchment-specific studies of stock abundance. Implications for implementing management actions are considered. © 2010 Blackwell Publishing Ltd.
Abstract.
Mumby PJ, Elliott IA, Eakin CM, Skirving W, Paris CB, Edwards HJ, Enríquez S, Iglesias-Prieto R, Cherubin LM, Stevens JR, et al (2011). Reserve design for uncertain responses of coral reefs to climate change.
Ecol Lett,
14(2), 132-140.
Abstract:
Reserve design for uncertain responses of coral reefs to climate change.
Rising sea temperatures cause mass coral bleaching and threaten reefs worldwide. We show how maps of variations in thermal stress can be used to help manage reefs for climate change. We map proxies of chronic and acute thermal stress and develop evidence-based hypotheses for the future response of corals to each stress regime. We then incorporate spatially realistic predictions of larval connectivity among reefs of the Bahamas and apply novel reserve design algorithms to create reserve networks for a changing climate. We show that scales of larval dispersal are large enough to connect reefs from desirable thermal stress regimes into a reserve network. Critically, we find that reserve designs differ according to the anticipated scope for phenotypic and genetic adaptation in corals, which remains uncertain. Attempts to provide a complete reserve design that hedged against different evolutionary outcomes achieved limited success, which emphasises the importance of considering the scope for adaptation explicitly. Nonetheless, 15% of reserve locations were selected under all evolutionary scenarios, making them a high priority for early designation. Our approach allows new insights into coral holobiont adaptation to be integrated directly into an adaptive approach to management.
Abstract.
Author URL.
Hamilton PB, Stevens JR (2011). Resolving relationships between Australian trypanosomes using DNA barcoding data.
Trends Parasitol,
27(3).
Author URL.
Leonard G, Soanes DM, Stevens JR (2011). Resolving the question of trypanosome monophyly: a comparative genomics approach using whole genome data sets with low taxon sampling.
Infect Genet Evol,
11(5), 955-959.
Abstract:
Resolving the question of trypanosome monophyly: a comparative genomics approach using whole genome data sets with low taxon sampling.
Since the first attempts to classify the evolutionary history of trypanosomes, there have been conflicting reports regarding their true phylogenetic relationships and, in particular, their relationships with other vertebrate trypanosomatids, e.g. Leishmania sp. as well as with the many insect parasitising trypanosomatids. Perhaps the issue that has provided most debate is that concerning the monophyly (or otherwise) of genus Trypanosoma and, even with the advent of molecular methods, the findings of numerous studies have varied significantly depending on the gene sequences analysed, number of taxa included, choice of outgroup and phylogenetic methodology. While of arguably limited applied importance, resolution of the question as to whether or not trypanosomes are monophyletic is critical to accurate evaluation of competing, mutually exclusive evolutionary scenarios for these parasites, namely the 'vertebrate-first' or 'insect-first' hypotheses. Therefore, a new approach, which could overcome previous limitations was needed. At its most simple, the problem can be defined within the framework of a trifurcated tree with three hypothetical positions at which the root can be placed. Using BLASTp and whole-genome gene-by-gene phylogenetic analyses of Trypanosoma brucei, Trypanosoma cruzi, Leishmania major and Naegleria gruberi, we have identified 599 gene markers--putative homologues--that were shared between the genomes of these four taxa. of these, 75 homologous gene families that demonstrate monophyly of the kinetoplastids were identified. We then used these data sets in combination with an additional outgroup, Euglena gracilis, coupled with large-scale gene concatenation and diverse phylogenetic techniques to investigate the relative branching order of T. brucei, T. cruzi and L. major. Our findings confirm the monophyly of genus Trypanosoma and demonstrate that
Abstract.
Author URL.
Griffiths AM, Ellis JS, Clifton-Dey D, Machado-Schiaffino G, Bright D, Garcia-Vazquez E, Stevens JR (2011). Restoration versus recolonisation: the origin of Atlantic salmon (Salmo salar L.) currently in the River Thames. Biological Conservation, 144(11), 2733-2738.
Durrant CJ, Stevens JR, Hogstrand C, Bury NR (2011). The effect of metal pollution on the population genetic structure of brown trout (Salmo trutta L.) residing in the River Hayle, Cornwall, UK. Environmental Pollution
Durrant CJ, Stevens JR, Hogstrand C, Bury NR (2011). The effect of metal pollution on the population genetic structure of brown trout (Salmo trutta L.) residing in the River Hayle, Cornwall, UK.
Environmental Pollution,
159(12), 3595-3603.
Abstract:
The effect of metal pollution on the population genetic structure of brown trout (Salmo trutta L.) residing in the River Hayle, Cornwall, UK
The River Hayle in south-west England is impacted with metals and can be divided into three regions depending on the copper and zinc concentrations: a low-metal upper section; a highly-contaminated middle section and a moderately contaminated lower section. Hayle river water is toxic to metal-naive brown trout, but brown trout are found in the upper and lower regions. The study aimed to evaluate the population genetic structure of River Hayle brown trout and to determine if the highly-contaminated section acts as a chemical barrier to migration. Population genetic analysis indicated that metals were not a barrier to gene flow within the river, but there was a high level of differentiation observed between fish sampled at two sites in the upper region, despite being separated by only 1 km. The metal tolerance trait exhibited by this brown trout population may represent an important component of the species genetic diversity in this region. © 2011 Elsevier Ltd. All rights reserved.
Abstract.
McDonagh LM, Stevens JR (2011). The molecular systematics of blowflies and screwworm flies (Diptera: Calliphoridae) using 28S rRNA, COX1 and EF-1α: insights into the evolution of dipteran parasitism.
Parasitology,
138(13), 1760-1777.
Abstract:
The molecular systematics of blowflies and screwworm flies (Diptera: Calliphoridae) using 28S rRNA, COX1 and EF-1α: insights into the evolution of dipteran parasitism.
The Calliphoridae include some of the most economically significant myiasis-causing flies in the world - blowflies and screwworm flies - with many being notorious for their parasitism of livestock. However, despite more than 50 years of research, key taxonomic relationships within the family remain unresolved. This study utilizes nucleotide sequence data from the protein-coding genes COX1 (mitochondrial) and EF1α (nuclear), and the 28S rRNA (nuclear) gene, from 57 blowfly taxa to improve resolution of key evolutionary relationships within the family Calliphoridae. Bayesian phylogenetic inference was carried out for each single-gene data set, demonstrating significant topological difference between the three gene trees. Nevertheless, all gene trees supported a Calliphorinae-Luciliinae subfamily sister-lineage, with respect to Chrysomyinae. In addition, this study also elucidates the taxonomic and evolutionary status of several less well-studied groups, including the genus Bengalia (either within Calliphoridae or as a separate sister-family), genus Onesia (as a sister-genera to, or sub-genera within, Calliphora), genus Dyscritomyia and Lucilia bufonivora, a specialised parasite of frogs and toads. The occurrence of cross-species hybridisation within Calliphoridae is also further explored, focusing on the two economically significant species Lucilia cuprina and Lucilia sericata. In summary, this study represents the most comprehensive molecular phylogenetic analysis of family Calliphoridae undertaken to date.
Abstract.
Author URL.
2010
Hamilton PB, Stevens JR (2010). 13 Classification and Phylogeny of Trypanosoma cruzi. In (Ed) American Trypanosomiasis, 321-338.
Hamilton PB, Stevens, J.R. (2010). Classification and Phylogeny of Trypanosoma cruzi. In Tibayrenc M, Tellería J (Eds.) American Trypanosomiasis, an Elsevier Title.
Hamilton PB, Stevens JR (2010). Classification and phylogeny of Trypanosoma cruzi. In (Ed)
American Trypanosomiasis: Chagas Disease One Hundred Years of Research, 321-338.
Abstract:
Classification and phylogeny of Trypanosoma cruzi
Abstract.
Griffiths AM, Machado-Schiaffino G, Dillane E, Coughlan J, Horreo JL, Bowkett AE, Minting P, Toms S, Roche W, Gargan P, et al (2010). Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range.
BMC Genet,
11Abstract:
Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range.
BACKGROUND: Anadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range. RESULTS: to facilitate mixed stock analysis (MSA) of Atlantic salmon, we have produced a baseline of genetic data for salmon populations originating from the largest rivers from Spain to northern Scotland, a region in which declines have been particularly marked. Using 12 microsatellites, 3,730 individual fish from 57 river catchments have been genotyped. Detailed patterns of population genetic diversity of Atlantic salmon at a sub-continent-wide level have been evaluated, demonstrating the existence of regional genetic signatures. Critically, these appear to be independent of more commonly recognised terrestrial biogeographical and political boundaries, allowing reporting regions to be defined. The implications of these results on the accuracy of MSA are evaluated and indicate that the success of MSA is not uniform across the range studied; our findings indicate large differences in the relative accuracy of stock composition estimates and MSA apportioning across the geographical range of the study, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the area studied. This result probably reflects the more genetically distinct nature of populations in the database from Spain, northwest France and southern England. Genetic stock identification has been undertaken and validation of the baseline microsatellite dataset with rod-and-line and estuary net fisheries of known origin has produced realistic estimates of stock composition at a regional scale. CONCLUSIONS: This southern European database and supporting phylogeographic and mixed-stock analyses of net samples provide a unique tool for Atlantic salmon research and management, in both their natal rivers and the marine environment. However, the success of MSA is not uniform across the area studied, with large differences in the relative accuracy of stock composition estimates and MSA apportioning, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the region. More broadly, this study provides a basis for long-term salmon management across the region and confirms the value of this genetic approach for fisheries management of anadromous species.
Abstract.
Author URL.
2009
Griffiths AM, Koizumi I, Bright D, Stevens JR (2009). A case of isolation by distance and short-term temporal stability of population structure in brown trout (Salmo trutta) within the River Dart, southwest England.
Evolutionary Applications,
2(4), 537-554.
Abstract:
A case of isolation by distance and short-term temporal stability of population structure in brown trout (Salmo trutta) within the River Dart, southwest England
Salmonid fishes exhibit high levels of population differentiation. In particular, the brown trout (Salmo trutta L.) demonstrates complex within river drainage genetic structure. Increasingly, these patterns can be related to the underlying evolutionary models, of which three scenarios (member-vagrant hypothesis, metapopulation model and panmixia) facilitate testable predictions for investigations into population structure. We analysed 1225 trout collected from the River Dart, a 75 km long river located in southwest England. Specimens were collected from 22 sample sites across three consecutive summers (2001-2003) and genetic variation was examined at nine microsatellite loci. A hierarchical analysis of molecular variance revealed that negligible genetic variation was attributed among temporal samples. The highest levels of differentiation occurred among samples isolated above barriers to fish movement, and once these samples were removed, a significant effect of isolation-by-distance was observed. These results suggest that, at least in the short-term, ecological events are more important in shaping the population structure of Dart trout than stochastic extinction events, and certainly do not contradict the expectations of a member-vagrant hypothesis. Furthermore, individual-level spatial autocorrelation analyses support previous recommendations for the preservation of a number of spawning sites spaced throughout the tributary system to conserve the high levels of genetic variation identified in salmonid species. © 2009 the Authors. Journal compilation © 2009 Blackwell Publishing Ltd.
Abstract.
Griffiths AM, Evans LM, Stevens JR (2009). Characterization and utilization of microsatellite loci in the New World screwworm fly, Cochliomyia hominivorax.
Med Vet Entomol,
23 Suppl 1, 8-13.
Abstract:
Characterization and utilization of microsatellite loci in the New World screwworm fly, Cochliomyia hominivorax.
New World screwworm populations in North and Central America have been the targets of virtually continuous eradication attempts by sterile insect technique (SIT) since the 1950s. Nevertheless, in some areas, such as Jamaica, SIT control programmes have failed. Reasons for the failure of SIT-based control programmes in some locations are unknown, but it has been hypothesized that failure may be related to mating incompatibility between sterile and wild fly populations or to the existence of sexually incompatible cryptic species. This paper outlines the development of a suite of four new microsatellite loci which can be used to study intra-specific relationships between populations of Cochliomyia hominivorax from the Caribbean and South America, which represent those populations involved in, or earmarked for, forthcoming SIT control. Cross-amplification with the secondary screwworm, Cochliomyia macellaria, was also successful with three of the new loci. We present results which suggest that populations from Trinidad and Jamaica form distinct groupings of flies and that C. hominivorax from Trinidad appears particularly distinct.
Abstract.
Author URL.
Griffiths AM, Bright D, Stevens JR (2009). Comparison of patterns of genetic variability in wild and supportively bred stocks of brown trout, Salmo trutta. Fisheries Management and Ecology, 16(6), 514-519.
Griffiths AM, Bright D, Stevens JR (2009). Complete mitochondrial control region sequences indicate a distinct variety of brown trout Salmo trutta in the Aral Sea.
J Fish Biol,
74(5), 1136-1142.
Abstract:
Complete mitochondrial control region sequences indicate a distinct variety of brown trout Salmo trutta in the Aral Sea.
Complete sequencing of the mtDNA control region (CR) from five specimens of brown trout Salmo trutta from the Amu Darya River identified two novel haplotypes belonging to the Danubian lineage. This finding supports the long-standing hypothesis that brown trout in the Aral Sea represent a distinct genetic stock and also illustrates the benefits that complete sequencing of the CR can provide for elucidating phylogeographic relationships.
Abstract.
Author URL.
McDonagh L, Thornton C, Wallman JF, Stevens JR (2009). Development of an antigen-based rapid diagnostic test for the identification of blowfly (Calliphoridae) species of forensic significance.
Abstract:
Development of an antigen-based rapid diagnostic test for the identification of blowfly (Calliphoridae) species of forensic significance.
Abstract.
Author URL.
Long RM, Lappin-Scott HM, Stevens JR (2009). Enrichment and identification of polycyclic aromatic compound-degrading bacteria enriched from sediment samples.
Biodegradation,
20(4), 521-531.
Abstract:
Enrichment and identification of polycyclic aromatic compound-degrading bacteria enriched from sediment samples.
The degradation of polycyclic aromatic compounds (PACs) has been widely studied. Knowledge of the degradation of PACs by microbial populations can be utilized in the remediation of contaminated sites. To isolate and identify PAC-degrading bacteria for potential use in future bioremediation programmes, we established a series of PAC enrichments under the same experimental conditions from a single sediment sample taken from a highly polluted estuarine site. Enrichment cultures were established using the pollutants: anthracene, phenanthrene and dibenzothiophene as a sole carbon source. The shift in microbial community structure on each of these carbon sources was monitored by analysis of a time series of samples from each culture using 16S rRNA polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Significantly, our findings demonstrate that shifts in the constituent species within each degradative community are directly attributable to enrichment with different PACs. Subsequently, we characterized the microorganisms comprising the degradative communities within each enrichment using 16S rRNA sequence data. Our findings demonstrate that the ability to degrade PACs is present in five divisions of the Proteobacteria and Actinobacteria. By determining the precise identity of the PAC-degrading bacterial species isolated from a single sediment sample, and by comparing our findings with previously published research, we demonstrate how bacteria with similar PAC degrading capabilities and 16S rRNA signatures are found in similarly polluted environments in geographically very distant locations, e.g. China, Italy, Japan and Hawaii. Such a finding suggests that geographical barriers do not limit the distribution of key PAC-degrading bacteria; this finding is in accordance with the Baas-Becking hypothesis "everything is everywhere; the environment selects" and may have significant consequences for the global distribution of PAC-degrading bacteria and their use in bioremediation.
Abstract.
Author URL.
Bowkett AE, Plowman AB, Stevens JR, Davenport TRB, van Vuuren BJ (2009). Genetic testing of dung identification for antelope surveys in the Udzungwa Mountains, Tanzania.
Conservation Genetics,
10, 251-255.
Abstract:
Genetic testing of dung identification for antelope surveys in the Udzungwa Mountains, Tanzania
Dung counts are frequently employed to infer
abundance of antelope species in African forests, but the accuracy of dung identification has rarely been tested. We used non-invasive genetic methods to test the accuracy of both field identification and morphometrics for identifying dung samples collected in the Udzungwa Mountains, Tanzania. Species identity was established by sequencing part of the mitochondrial control region from faecal DNA. Field identification was found to be correct in only 58–76% of cases depending on the observer. Discriminant analysis of dung pellet length correctly classified 80% of samples but a larger reference sample size is needed before using this method to classify dung of unknown origin. The results of this study illustrate the potential inaccuracy of dung counts as a monitoring tool for sympatric forest antelope species when the probability of correct identification is unknown. We recommend molecular testing of species identity during forest antelope surveys before conclusions are drawn on the basis of other identification methods.
Abstract.
Wells JD, Stevens JR (2009). Molecular Methods for Forensic Entomology. In Byrd JH, Castner JL (Eds.)
Forensic Entomology, CRC, 437-452.
Abstract:
Molecular Methods for Forensic Entomology
Abstract.
Colwell DD, Otranto D, Stevens JR (2009). Oestrid flies: eradication and extinction versus biodiversity.
Trends in Parasitology,
25(11), 500-504.
Abstract:
Oestrid flies: eradication and extinction versus biodiversity
Larvae of oestrid flies are obligate parasites of mammals. This article focuses on two potential drivers that could be forcing these flies into extinction: (i) the highly effective and widespread use of anti-parasitic drugs for domestic livestock; and (ii) the co-extinction of oestrids associated with non-domestic hosts that are endangered. Other oestrid species could be the victims of benign neglect in that they are so poorly studied that their disappearance might go unnoticed. In addition, we explore current knowledge in each of these categories of vulnerability for oestrids, and address the potential impacts of their disappearance. Finally, we examine the potential consequences of eradicating a group of livestock parasites, and ask what possibilities for improvement of the health of humans and animals might also be lost. © 2009.
Abstract.
McDonagh L, García R, Stevens JR (2009). Phylogenetic analysis of New World screwworm fly, Cochliomyia hominivorax, suggests genetic isolation of some Caribbean island populations following colonization from South America.
Med Vet Entomol,
23 Suppl 1, 14-22.
Abstract:
Phylogenetic analysis of New World screwworm fly, Cochliomyia hominivorax, suggests genetic isolation of some Caribbean island populations following colonization from South America.
Larval infestations of the New World screwworm (NWS) fly, Cochliomyia hominivorax, cause considerable economic losses through the direct mortality and reduced production of livestock. Since the 1950s, NWS populations in North and Central America have been the target of virtually continuous eradication attempts by sterile insect technique (SIT). Nevertheless, in some areas, such as Jamaica, SIT-based control programmes have failed. Reasons for the failure of SIT-based programmes in some locations are unknown, but it is hypothesized that failure may be related to the mating incompatibility between sterile and wild flies or to the existence of sexually incompatible cryptic species. Accordingly, the current research investigates intraspecific phylogenetic relationships and associated biogeographic patterns between NWS populations from the Caribbean and South America, which represent those populations involved in, or earmarked for, forthcoming SIT programmes. Uniquely, this study also includes analyses of two North American samples, collected in Texas in 1933 and 1953 prior to initiation of the SIT-based eradication programme. The study utilizes three nucleotide datasets: elongation factor-1alpha (nuclear); cytochrome oxidase subunit 1 (mitochondrial), and 12S rRNA (mitochondrial). Phylogenetic analysis of these data, representing populations from across the Caribbean, South America and Texas, indicates sub-structuring of fly populations on several of the larger Caribbean islands, suggesting a period of isolation and/or founder effects following colonization from South America; significantly, our findings do not support a North American origin for Cuban flies. The importance of these findings in the light of proposed SIT programmes in the region is discussed.
Abstract.
Author URL.
Leonard G, Stevens JR, Richards TA (2009). REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era.
Evolutionary Bioinformatics,
5Abstract:
REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era
The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment file, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree files (with a user-defined combination of species name and/or database accession number). Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file) and generation of species and accession number lists for use in supplementary materials or figure legends.
Abstract.
Leonard G, Stevens JR, Richards TA (2009). REFGEN and TREENAMER: automated sequence data handling for phylogenetic analysis in the genomic era.
Evol Bioinform Online,
5, 1-4.
Abstract:
REFGEN and TREENAMER: automated sequence data handling for phylogenetic analysis in the genomic era.
The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment file, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree files (with a user-defined combination of species name and/or database accession number). Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file) and generation of species and accession number lists for use in supplementary materials or figure legends.
Abstract.
Author URL.
2008
Coe TS, Hamilton PB, Hodgson D, Paull GC, Stevens JR, Sumner K, Tyler CR (2008). An environmental estrogen alters reproductive hierarchies, disrupting sexual selection in group-spawning fish.
Environ Sci Technol,
42(13), 5020-5025.
Abstract:
An environmental estrogen alters reproductive hierarchies, disrupting sexual selection in group-spawning fish.
There is global concern regarding the potential impacts of endocrine-disrupting chemicals (EDCs) on the health of wildlife and humans. Exposure to some estrogens, at concentrations found in the environment impairs reproductive function and behavior. However, nearly all work on endocrine disruption has investigated the effects of exposure on individuals and there is an urgent need to understand impacts on populations. Many fish have mating systems with complex social structures and it is not known whether EDCs will exaggerate or buffer the reproductive skews caused by the dominance hierarchies that normally occur for these species. This study investigated the impact of exposure to the pharmaceutical estrogen ethinylestradiol (EE2) on reproductive hierarchies and sexual selection in group-spawning fish. Breeding zebrafish were exposed to environmentally relevant concentrations of EE2, and effects were determined on reproductive output, plasma androgen concentrations (in males), and reproductive success through microsatellite analyses of the offspring. Reproductive hierarchies in breeding colonies of zebrafish were disrupted by exposure to EE2 at a concentration that did not affect the number of eggs produced. The effect was a reduction in the skew in male paternity and increased skew in female maternity. This disruption in the reproductive hierarchy in group spawning fish, if it occurs in the wild, has potentially major implications for population genetic diversity. Reproductive success in male zebrafish was associated with elevated plasma concentrations of the male sex hormone 11-ketotestosterone and this hormone was suppressed in EE2-exposed males.
Abstract.
Author URL.
Wells JD, Stevens JR (2008). Application of DNA-Based Methods in Forensic Entomology. Annual Review of Entomology, 53, 103-120.
Finnegan AK, Stevens JR (2008). Assessing the long-term genetic impact of historical stocking events on contemporary populations of Atlantic salmon, Salmo salar.
Fisheries Management and Ecology,
15(4), 315-326.
Abstract:
Assessing the long-term genetic impact of historical stocking events on contemporary populations of Atlantic salmon, Salmo salar
Supplementation of wild fish with non-native or domesticated fish is common practice. However, these stocked and native fish differ both ecologically and genetically and, in the wild, they interact in a multitude of ways, often with negative repercussions for the native population. This study assessed the long-term genetic impact of historical stocking activities on a contemporary population of Atlantic salmon, Salmo salar L. During the 1960s salmon from hatcheries in Scotland and Iceland were transplanted to the River Dart, England. Microsatellite loci were used to assess the current level of population admixture between samples taken from the source location of the stocked fish during the 1960s and contemporary Dart populations. After allowances were made for natural genetic relationships between donor and recipient populations, the long-term impact of the historical stocking events on a catchment scale appears minimal. However, one tributary consistently reflected closer genetic relationships with the donor populations, indicating a possible long-term impact on a localised scale. © 2008 the Authors. Journal compilation © 2008 Blackwell Publishing Ltd.
Abstract.
Horreo JL, Machado-Schiaffino G, Griffiths A, Bright D, Stevens J, Garcia-Vazquez E (2008). Identification of differential broodstock contribution affecting genetic variability in hatchery stocks of Atlantic salmon (Salmo salar).
Aquaculture,
280(1-4), 89-93.
Abstract:
Identification of differential broodstock contribution affecting genetic variability in hatchery stocks of Atlantic salmon (Salmo salar)
Supportive breeding of Atlantic salmon (Salmo salar) is commonly employed to maintain numbers of fish where the species has become locally endangered. Increasingly, one of the main aims of population management is the preservation of natural genetic diversity. If the stocks employed in supportive breeding exhibit reduced variation they can alter the natural pattern of genetic variation observed in wild populations. In northern Spain, wild adult salmon are caught every year from local rivers and artificially crossed in order to create supportive stocks. The offspring are hatchery reared until the juvenile stage, then released into the same river where their parents were caught. In the current study, our findings demonstrate that although adult broodstock exhibit a pattern of variation similar to the wild populations, variability at microsatellite loci was drastically reduced in the juveniles released into one of three rivers analyzed. The contribution of broodstock to this juvenile stock was examined by pedigree analysis. A restricted number of females contributing to the hatchery stock was identified as the main cause of loss in genetic variation, possibly due to overmaturity of some multi-sea-winter females. We suggest that better monitoring and control of parental contribution will help in solving the problem of loss of genetic diversity in hatchery populations. © 2008 Elsevier B.V. All rights reserved.
Abstract.
Stevens JR (2008). Kinetoplastid phylogenetics, with special reference to the evolution of parasitic trypanosomes.
Parasite,
15(3), 226-232.
Abstract:
Kinetoplastid phylogenetics, with special reference to the evolution of parasitic trypanosomes.
To fully understand the evolutionary history of parasitic kinetoplastids and to understand the context within which the evolution of each parasite group has developed, an understanding not just of the parasites, but of all kinetoplastids is required. Accordingly, this paper provides an overview of kinetoplastid evolution and systematics, including coverage of the proposal by Moreira et al. (2004) to divide kinetoplasts into Prokinetoplastina (Ichthyobodo and Perkinsiella) and Metakinetoplastina (other bodonids and trypanosomatids). The implications of such a revision, with regard to correctly identifying outgroup taxa for studies of evolution within taxa of medical importance, are addressed, together with a more detailed review of the evolution and origins of the trypanosomes in the light of new phylogenies, new approaches and revisions in kinetoplastid systematics.
Abstract.
Author URL.
Stevens JR, West H, Wall R (2008). Mitochondrial genomes of the sheep blowfly, Lucilia sericata, and the secondary blowfly, Chrysomya megacephala. Medical and Veterinary Entomology, 22
Otranto D, Stevens JR, Testini G, Cantacessi C, MácA J (2008). Molecular characterization and phylogenesis of Steganinae (Diptera, Drosophilidae) inferred by the mitochondrial cytochrome c oxidase subunit 1.
Medical and Veterinary Entomology,
22(1), 37-47.
Abstract:
Molecular characterization and phylogenesis of Steganinae (Diptera, Drosophilidae) inferred by the mitochondrial cytochrome c oxidase subunit 1
The subfamily Steganinae (Diptera, Drosophilidae) includes flies which display zoophilic feeding behaviour in the larval and/or adult stages, some of which act as vectors of Spirurida eyeworms, which infect both carnivores and humans. To date, the taxonomy and phylogeny of the subfamily Steganinae has been studied only superficially and many aspects of their systematics remain unresolved. Thus, the present study aimed to provide a molecular dataset to facilitate the identification and phylogenetic analysis of Steganinae species based on partial (∼ 700 basepairs) mitochondrial cytochrome c oxidase subunit 1 (cox1) sequences. A total of 134 flies belonging to 13 species and eight genera of Steganinae were subjected to molecular and phylogenetic analyses. The mean nucleotide variation within the Steganinae subfamily was 8.1%, with a variation within genera for which more than one species was examined ranging from 1.6% (in Phortica spp.) to 21.8% (in Amiota spp.). Interspecific pairwise divergence ranged from 1.6% (Phortica variegata vs. Phortica semivirgo) to 24.8% (Cacoxenus indagator vs. Amiota alboguttata) and intraspecific variation ranged from 0% to 1%. Seventy of the 233 amino acids were variable, including 26 parsimony informative sites and 44 singleton sites, with some highly conserved residues identified within the genera Stegana and Amiota. Parsimony and maximum likelihood-based phylogenetic analyses provided strong support for the genus Phortica, phylogenetically distinct from the genus Amiota. Gitona distigma was placed in an unresolved position adjacent to the outgroup taxa, Drosophila yakuba and Drosophila melanogaster. The molecular data reported here represent the first molecular dataset based on cox1 of Steganinae flies and provide a base for further investigations into the evolutionary relationships among this little-studied subfamily. © 2008 the Authors.
Abstract.
Otranto, D. Stevens, J. R. Cantacessi, C.Gasser, R. B. (2008). Parasite transmission by insects: a female affair?. Trends in Parasitology, 24
2007
Hamilton PB, Gibson, W.C. Stevens, J.R. (2007). Patterns of co-evolution between trypanosomes and their hosts deduced from ribosomal RNA and protein-coding gene phylogenies. Molecular Phylogenetics and Evolution, 44(1), 15-25.
Wells JD, Wall, R. Stevens, J.R. (2007). Phylogenetic analysis of forensically important Lucilia flies based on cytochrome oxidase I sequence: a cautionary tale for forensic species determination. International Journal of Legal Medicine, 121, 229-233.
Stevens, J.R. (2007). Phylogenetic methods for the analysis of parasites and pathogens. In Tibayrenc M (Ed) Encyclopedia of Infectious Diseases: modern approaches, 265-297.
2006
Hartley CJ, Newcomb RD, Russell RJ, Yong CG, Stevens JR, Yeates DK, La Salle J, Oakeshott JG (2006). Amplification of DNA from preserved specimens shows blowflies were preadapted for the rapid evolution of insecticide resistance. Proceedings of the National Academy of Sciences, 103(23), 8757-8762.
Otranto D, Stevens, J.R. Brianti, E. Dorchies, P. (2006). Human and livestock migrations: a history of bot fly biodiversity in the mediterranean region. Trends in Parasitology, 22(5), 209-213.
Otranto D, Stevens, J.R. (2006). Molecular Phylogeny and Identification. In Colwell DD, Hall MJR, Scholl PJ (Eds.) The Oestrid Flies: Biology, Host-Parasite Relationships, Impact and Management, 51-66.
Rodrigues AC, Paiva F, Campaner M, Stevens JR, Noyes HA, Teixeira MMG (2006). Phylogeny of Trypanosoma (Megatrypanum) theileri and related trypanosomes reveals lineages of isolates associated with artiodactyl hosts diverging on SSU and ITS ribosomal sequences.
Parasitology,
132(2), 215-224.
Abstract:
Phylogeny of Trypanosoma (Megatrypanum) theileri and related trypanosomes reveals lineages of isolates associated with artiodactyl hosts diverging on SSU and ITS ribosomal sequences
SSU ribosomal sequences of trypanosomes from Brazilian cattle and water buffalo were used to infer phylogenetic relationships between non-pathogenic T. theileri and allied species parasitic in artiodactyls. T. theileri trypanosomes from distinct geographical regions in Brazil and from other countries were tightly clustered into the 'clade T. theileri' distant from the 'T. brucei clade' of pathogenic parasites of artiodactyls, and also distinct from trypanosomes of other mammals. The existence of this monophyletic assemblage (T. theileri clade) composed only by isolates from artiodactyl species justifies the continued recognition of the subgenus T. (Megatrypanum) with T. theileri as its type species. Phylogenies based on SSU and ITS1 ribosomal sequences produced the same branching pattern with isolates from different mammalian hosts clustered in 5 lineages: A, related to water buffalo; B, C and D, to cattle; E, to fallow deer. The pattern of host specificity allied to some congruence between host and parasite phylogenies suggested association of these trypanosomes with their respective hosts. Segregation of cattle isolates into three lineages revealed an overall geographical structure. Moreover, positioning of trypanosomes infecting tabanids in the T. theileri clade is consistent with the role of these flies as important vectors of these trypanosomes. © 2005 Cambridge University Press.
Abstract.
Stevens JR, Griffiths AM, Garcia-Vasquez E, Machado G, Bright D (2006). The Atlantic Salmon Arc Project (ASAP): construction of a spatial database of genetic population profiles for Atlantic salmon (Salmo salar) to facilitate the sustainable management and conservation of this trans-national migratory species.
Author URL.
Simpson AGB, Stevens, J.R. Lukes, J. (2006). The evolution and diversity of kinetoplastid flagellates. Trends in Parasitology, 22(4), 168-174.
Stevens JR, Wallman, J.F. (2006). The evolution of myiasis in humans and other animals in the Old and New Worlds (part I): phylogenetic analyses. Trends in Parasitology, 22(3), 129-136.
Stevens JR, Wallman, J.F. Otranto, D. Wall, R. Pape T (2006). The evolution of myiasis in humans and other animals in the Old and New Worlds (part II): biological and life-history studies. Trends in Parasitology, 22(4), 181-188.
Griffiths A, Stevens J, Bright D (2006). The, population structure of brown trout (Salmo trutta) on Dartmoor National Park (England) and short-term temporal stability of microsatellite markers.
Author URL.
2005
Hamilton PB, Stevens, J.R. Gidley, P. Holz, P. Gibson WC (2005). A new lineage of trypanosomes from Australian vertebrates and terrestrial bloodsucking leeches (Haemadipsidae). International Journal for Parasitology, 35, 431-443.
Kerridge A, Lappin-Scott, H. Stevens, J.R. (2005). Antibacterial properties of larval secretions of the blowfly, Lucilia sericata. Medical and Veterinary Entomology, 19, 333-337.
Pegler KR, Evans, L. Stevens, J.R. Wall, R. (2005). Morphological and molecular comparison of host-derived populations of parasitic Psoroptes mites. Medical and Veterinary Entomology, 19, 392-403.
Hamilton PB, Stevens JR, Holz P, Boag B, Cooke B, Gibson WC (2005). The inadvertent introduction into Australia of Trypanosoma nabiasi, the trypanosome of the European rabbit (Oryctolagus cuniculus), and its potential for biocontrol.
Mol Ecol,
14(10), 3167-3175.
Abstract:
The inadvertent introduction into Australia of Trypanosoma nabiasi, the trypanosome of the European rabbit (Oryctolagus cuniculus), and its potential for biocontrol.
Wild rabbits (Oryctolagus cuniculus) in Australia are the descendents of 24 animals from England released in 1859. We surveyed rabbits and rabbit fleas (Spilopsyllus cuniculi) in Australia for the presence of trypanosomes using parasitological and PCR-based methods. Trypanosomes were detected in blood from the European rabbits by microscopy, and PCR using trypanosome-specific small subunit ribosomal RNA (SSU rRNA) gene primers and those in rabbit fleas by PCR. This is the first record of trypanosomes from rabbits in Australia. We identified these Australian rabbit trypanosomes as Trypanosoma nabiasi, the trypanosome of the European rabbit, by comparison of morphology and SSU rRNA gene sequences of Australian and European rabbit trypanosomes. Phylogenetic analysis places T. nabiasi in a clade with rodent trypanosomes in the subgenus Herpetosoma and their common link appears to be transmission by fleas. Despite the strict host specificity of trypanosomes in this clade, phylogenies presented here suggest that they have not strictly cospeciated with their vertebrate hosts. We suggest that T. nabiasi was inadvertently introduced into Australia in the 1960s in its flea vector Spilopsyllus cuniculi, which was deliberately introduced as a potential vector of the myxoma virus. In view of the environmental and economic damage caused by rabbits in Australia and other islands, the development of a virulent or genetically modified T. nabiasi should be considered to control rabbits.
Abstract.
Author URL.
Otranto D, Traversa, D. Milillo, P. De Luca F, Stevens J (2005). Utility of mitochondrial and ribosomal genes for differentiation and phylogenesis of species of gastrointestinal bot flies. Journal of Economic Entomology, 98(6), 2235-2245.
2004
Stevens, J. (2004). Computational aspects of host–parasite phylogenies. Briefings in Bioinformatics, 5(4), 339-349.
Maia Da Silva F, Noyes H, Campaner M, Junqueira ACV, Coura JR, Añez N, Shaw JJ, Stevens JR, Teixeira MMG (2004). Phylogeny, taxonomy and grouping of Trypanosoma rangeli isolates from man, triatomines and sylvatic mammals from widespread geographical origin based on SSU and ITS ribosomal sequences.
Parasitology,
129(5), 549-561.
Abstract:
Phylogeny, taxonomy and grouping of Trypanosoma rangeli isolates from man, triatomines and sylvatic mammals from widespread geographical origin based on SSU and ITS ribosomal sequences
Phylogenetic relationships among Trypanosoma rangeli isolates from man, wild mammals and triatomine bugs from widespread geographical origin were inferred by comparison of the small subunit of ribosomal gene sequences. The phylogenetic trees indicated that the subgenus Herpetosoma is polyphyletic and strongly supported division of this group into two monophyletic lineages, one made up of T. rangeli, T. rangeli-like and allied species and other consisting of T. lewisi and related taxa. Based on phylogenetic analysis, morphology, behaviour in vertebrate and invertebrate hosts and epidemiology we propose: a) the validation of Herpetosoma as a taxon comprised only for species of group lewisi and the maintenance of T. lewisi as the type-species of this subgenus; b) the classification of T. rangeli, T. rangeli-like and allied species into a 'T. rangeli-clade' more closely related to Schizotrypanum than to T. lewisi or T. brucei. The phylogenetic tree disclosed at least 4 groups within the clade T. rangeli, all confirmed by polymorphism of the internal transcribed spacer, thus conferring for the first time phylogenetic support to groups of T. rangeli and corroborating the high complexity of this taxon. Grouping was independent of their mammalian host-species and geographical origin, indicating that other factors are determining this segregation.
Abstract.
Stevens JR, Brisse, S. (2004). The Systematics of Trypanosomes of Medical and Veterinary Importance. In Maudlin I, Holmes P, Miles M (Eds.) Trypanosomiasis, 1-23.
Hamilton PB, Stevens, J.R. Gaunt, M.W. Gidley, J. Gibson WC (2004). Trypanosomes are monophyletic: evidence from genes for glyceraldehyde phosphate dehydrogenase and small subunit ribosomal RNA. International Journal for Parasitology, 34, 1393-1404.
2003
Evans LM, Dawson, D.A. Wall, R. Burke, T. Stevens J (2003). Isolation of Psoroptes scab mite microsatellite markers (Acari: Psoroptidae). Molecular Ecology Notes, 3, 420-424.
Otranto D, Traversa, D. Guida, B. Tarsitano, E. Fiorente P, Stevens JR (2003). Molecular characterization of the mitochondrial cytochrome oxidase I gene of Oestridae species causing obligate myiasis. Medical and Veterinary Entomology, 17, 307-315.
Otranto D, Traversa, D. Tarsitano, E. Stevens, J. (2003). Molecular differentiation of Hypoderma bovis and Hypoderma lineatum (Diptera, Oestridae) by polymerase chain reaction-restriction fragment length polymorphism. Veterinary Parasitology, 112, 197-201.
Stevens JR, Schofield, C.J. (2003). Phylogenetics and sequence analysis – some problems for the unwary. Trends in Parasitology, 19(12), 582-588.
Otranto D, Coldwell, D.D. Traversa, D. Stevens, J.R. (2003). Species identification of Hypoderma affecting domestic and wild ruminants by morphological and molecular characterization. Medical and Veterinary Entomology, 17, 316-325.
Stevens JR (2003). The evolution of myiasis in blowflies (Calliphoridae). International Journal for Parasitology, 33(10), 1105-1113.
2002
Michon P, Stevens JR, Kaneko O, Adams JH (2002). Evolutionary relationships of conserved cysteine-rich motifs in the adhesion molecules of malaria parasites. Molecular Biology and Evolution, 19(7), 1128-1142.
Griffiths AM, Stevens JRF (2002). Internet sites relevant to the common methodologies and themes of data exploration used in the study of infection genetics and evolution. Infection, Genetics and Evolution, 1(4), 321-325.
Otranto D, Stevens, J.R. (2002). Molecular approaches to the study of myiasis-causing larvae. International Journal for Parasitology, 32, 1345-1360.
Stevens JR, Wall R, Wells J (2002). Paraphyly in Hawaiian hybrid blowfly populations and the evolutionary history of anthropophilic species. Insect Molecular Biology, 11(2), 141-148.
Stevens, J. (2002). Sleeping sickness. In Pimentel D (Ed) Encyclopedia of Pest Management.
2001
Stevens J, Rambaut A (2001). Evolutionary rate differences in trypanosomes.
Infect Genet Evol,
1(2), 143-150.
Abstract:
Evolutionary rate differences in trypanosomes.
Ribosomal RNA-based studies of trypanosome phylogenies have highlighted considerable differences in genetic diversity within clades in the genus Trypanosoma and several-fold substitution rate differences between clades have been identified. While early 18S rRNA-based studies were hampered by highly variable substitution rates and long-branch attraction, it is apparent that genuine differences in evolution rates within localized clades do exist and questions remain regarding what rate or rates such clades are evolving at and why is the application of a single clock to trypanosome evolution so inappropriate? in this study, we explore rate heterogeneity in the commonly used 18S rRNA gene across genus Trypanosoma, using a maximum likelihood (ML) approach to explore local rate variations in clades of biological interest.
Abstract.
Author URL.
Stevens J, Wall R (2001). Genetic relationships between blowflies (Calliphoridae) of forensic importance.
Forensic Sci Int,
120(1-2), 116-123.
Abstract:
Genetic relationships between blowflies (Calliphoridae) of forensic importance.
Phylogenetic relationships among blowfly (Calliphoridae) species of forensic importance are explored using DNA sequence data from the large sub-unit (lsu, 28S) ribosomal RNA (rRNA) gene, the study includes representatives of a range of calliphorid species commonly encountered in forensic analysis in Britain and Europe. The data presented provide a basis to define molecular markers, including the identification of highly informative intra-sequence regions, which may be of use in the identification of larvae for forensic entomology. Phylogenetic analysis of the sequences also provides new insights into the different evolutionary patterns apparent within the family Calliphoridae which, additionally, can provide a measure of the degree of genetic variation likely to be encountered within taxonomic groups of differing forensic utility.
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Author URL.
Fitch W, Brisse S, Stevens J, Tibayrenc M (2001). Infectious diseases and the golden age of phylogenetics:: an E-debate. Infection, Genetics and Evolution, 1(1), 69-74.
Stevens JR, Noyes, H.A. Schofield, C.J. Gibson, W. (2001). The Molecular Evolution of Trypanosomatidae. Advances in Parasitology, 48, 1-56.
Gibson WC, Stevens, J.R. Mwendia, C.M.T. Makumi, J.N. Ngotho JM, Ndung'u JM (2001). Unravelling the phylogenetic relationships of African trypanosomes of suids. Parasitology, 122, 625-631.
2000
Noyes HA, Stevens JR, Teixeira M, Phelan J, Holz P (2000). A nested PCR for the ssrRNA gene detects Trypanosoma binneyi in the platypus and Trypanosoma sp. in wombats and kangaroos in Australia (vol 29, pg 331, 1999).
INTERNATIONAL JOURNAL FOR PARASITOLOGY,
30(2), 228-228.
Author URL.
Barker GLA, Handley BA, Vacharapiyasophon P, Stevens JR, Hayes PK (2000). Allele-specific PCR shows that genetic exchange occurs among genetically diverse Nodularia (cyanobacteria) filaments in the Baltic Sea.
Microbiology (Reading),
146 ( Pt 11), 2865-2875.
Abstract:
Allele-specific PCR shows that genetic exchange occurs among genetically diverse Nodularia (cyanobacteria) filaments in the Baltic Sea.
Some cyanobacteria have been shown to exchange genetic information under laboratory conditions, but it has not been clear whether such genetic exchange occurs in the natural environment. To address this, a population genetic study was carried out on the filamentous diazotrophic cyanobacterium Nodularia in the Baltic Sea. Nodularia filaments were collected from 20 widely distributed sampling stations in the Baltic Sea during June and July 1998. Allele-specific PCR (AS-PCR) was used to characterize over 2000 filaments at three loci: a non-coding spacer between adjacent copies of the main structural gas vesicle gene gvpA (gvpA-IGS), the phycocyanin intergenic spacer (PC-IGS) and the rDNA internal transcribed spacer (rDNA-ITS). The three loci were all found to be polymorphic in the 1998 population: two alternative alleles were distinguished at the gvpA-IGS and PC-IGS loci, and three at the rDNA-ITS locus. All 12 possible combinations of alleles were found in the filaments studied, but some were much more common than others. The index of association (I:(A)) for all possible pairwise combinations of isolates was found to differ significantly from zero, which implies that there is some linkage disequilibrium between loci. The I:(A) values for 16 out of 20 individual sampling stations also differed significantly from zero: this shows that the observed linkage disequilibrium is not due to pooling data from genetically distinct subpopulations. Monte-Carlo simulations with random subsets of the data confirmed that some combinations showed significantly more linkage disequilibrium than expected by chance alone. It is concluded that genetic exchange occurs in the natural Nodularia population, but the frequency is not high enough for the loci to be in linkage equilibrium. The distribution of the 12 genotypes across the Baltic Sea was found to be non-random, but did not correlate with temperature, salinity or major nutrient concentrations. A significant relationship was found between the gene diversity among filaments at each station and the distance of the station from the centre of the sampling area: possible reasons for this trend are discussed.
Abstract.
Author URL.
Gibson W, Bingle L, Blendeman W, Brown J, Wood J, Stevens J (2000). Structure and sequence variation of the trypanosome spliced leader transcript.
Mol Biochem Parasitol,
107(2), 269-277.
Abstract:
Structure and sequence variation of the trypanosome spliced leader transcript.
We have assessed the potential of using the spliced leader (SL) or mini-exon gene as a marker for molecular phylogenetic analysis of genus Trypanosoma. A total of 27 trypanosome sequences were compared, 18 of these being newly reported. In contrast to genus Leishmania, we found the non-transcribed spacer region of the SL locus in trypanosomes to be far too variable for informative comparison of all but the most closely related species. At the other extreme, the short (39 nt) SL exon was usually completely conserved and hence uninformative. The SL RNA showed variation in both length (97-152 nt) and sequence among different trypanosome species, with most variation occurring in stem-loop II. Consequently, this region could not be aligned with confidence in multiple sequence alignment, severely reducing the number of phylogenetically informative nucleotide positions. In computer simulation, most of the SL RNAs readily folded into the 3 stem-loop secondary structure predicted previously, but again stem-loop II was highly variable. No obvious correlation could be seen between the length of this stem-loop and trypanosome biology. We conclude that the SL repeat is not an informative phylogenetic marker for long range evolutionary studies of genus Trypanosoma.
Abstract.
Author URL.
Stevens J (2000). The trypanosomatid evolution workshop London School of Hygiene and Tropical Medicine. 17-18 February 2000.
Mem Inst Oswaldo Cruz,
95(4), 507-508.
Abstract:
The trypanosomatid evolution workshop London School of Hygiene and Tropical Medicine. 17-18 February 2000.
The trypanosome evolution workshop, a joint meeting of the University of Exeter and the London School of Hygiene and Tropical Medicine, focused on topics relating to trypanosomatid and vector evolution. The meeting, sponsored by the Wellcome Trust, the Special Programme for Research and Training in Tropical Disease of World Health Organization and the British Section of the Society of Protozoologists, brought together an international group of experts who presented papers on a wide range of topics including parasite and vector phylogenies, molecular methodology and relevant biogeographical data.
Abstract.
Author URL.
Stevens J, Gibson W, Noyes H (2000). Trypanosome evolution under the microscope.
PARASITOLOGY TODAY,
16(7), 270-271.
Author URL.
Stothard JR, Stevens J, Gibson W (2000). Trypanosome trees and homologies (multiple letters) [1]. Parasitology Today, 16(4).
Stevens J, Gibson W (2000). Trypanosome trees and homologies - Reply.
PARASITOLOGY TODAY,
16(4), 173-173.
Author URL.
1999
Noyes HA, Stevens JR, Teixeira M, Phelan J, Holz P (1999). A nested PCR for the ssrRNA gene detects Trypanosoma binneyi in the platypus and Trypanosoma sp. in wombats and kangaroos in Australia.
International Journal for Parasitology,
29(2), 331-339.
Abstract:
A nested PCR for the ssrRNA gene detects Trypanosoma binneyi in the platypus and Trypanosoma sp. in wombats and kangaroos in Australia
Trypanosome infections in their natural hosts are frequently difficult to detect by microscopy, and culture methods are unreliable and not suitable for all species of Trypanosoma. A nested PCR strategy for detecting and identifying Trypanosoma species, suitable for detecting both known and unknown trypanosomes, is presented. Thirty-two blood samples from 23 species of Australian birds and mammals were screened by a nested PCR for the presence of Trypanosoma sp. ssrRNA. Three infections were detected, one in an eastern grey kangaroo (Macropus giganteus), one in a common wombat (Vombatus ursinus) and one in a platypus (Ornithorhynchus anatinus). The kangaroo and wombat are new host records for Trypanosoma sp.; the platypus parasite was Trypanosoma binneyi. The three parasites could be distinguished by restriction fragment length polymorphisms of the amplified fragment of the ssrRNA gene. The kangaroo and wombat parasites were also isolated in a semi-solid blood agar medium. The culture forms of the kangaroo trypanosome had an expanded flagellar sheath in which structures similar to hemidesmosomes were detected by EM. The nested PCR was at least as sensitive as culture, and analysis of the PCR products gave parasite-specific fingerprints. Therefore this method could be suitable for rapidly screening host animals for the presence of trypanosomes and identifying the infecting strain. Copyright (C) 1999 Elsevier Science B.V.
Abstract.
Gibson W, Stevens J (1999). Genetic exchange in the trypanosomatidae.
Adv Parasitol,
43, 1-46.
Abstract:
Genetic exchange in the trypanosomatidae.
The only trypanosomatid so far proved to undergo genetic exchange is Trypanosoma brucei, for which hybrid production after co-transmission of different parental strains through the tsetse fly vector has been demonstrated experimentally. Analogous mating experiments have been attempted with other Trypanosoma and Leishmania species, so far without success. However, natural Leishmania hybrids, with a combination of the molecular characters of two sympatric species, have been described amongst both New and Old World isolates. Typical homozygotic and heterozygotic banding patterns for isoenzyme and deoxyribonucleic acid markers have also been demonstrated amongst naturally-occurring T. cruzi isolates. The mechanism of genetic exchange in T. brucei remains unclear, although it appears to be a true sexual process involving meiosis. However, no haploid stage has been observed, and intermediates in the process are still a matter for conjecture. The frequency of sex in trypanosomes in nature is also a matter for speculation and controversy, with conflicting results arising from population genetics analysis. Experimental findings for T. brucei are discussed in the first section of this review, together with laboratory evidence of genetic exchange in other species. The second section covers population genetics analysis of the large body of data from field isolates of Leishmania and Trypanosoma species. The final discussion attempts to put the evidence from experimental and population genetics into its biological context.
Abstract.
Author URL.
Gibson W, Stevens J, Truc P (1999). Identification of trypanosomes: from morphology to molecular biology. In Dumas M, Bouteille B, Buguet A (Eds.)
Progress in human African trypanosomiasis, sleeping sickness, Springer Verlag, 7-29.
Abstract:
Identification of trypanosomes: from morphology to molecular biology
Abstract.
Stevens JR, Noyes HA, Dover GA, Gibson WC (1999). The ancient and divergent origins of the human pathogenic trypanosomes, Trypanosoma brucei and T. cruzi.
Parasitology,
118 ( Pt 1), 107-116.
Abstract:
The ancient and divergent origins of the human pathogenic trypanosomes, Trypanosoma brucei and T. cruzi.
This study presents new findings concerning the evolution of the human pathogens, Trypanosoma brucei and T. cruzi, which suggest that these parasites have divergent origins and fundamentally different patterns of evolution. Phylogenetic analysis of 18S rRNA sequences places T. brucei in a clade comprising exclusively mammalian trypanosomes of African origin, suggesting an evolutionary history confined to Africa. T. cruzi (from humans and sylvatic mammals) clusters with trypanosomes specific to Old and New World bats, T. rangeli and a trypanosome species isolated from an Australian kangaroo. The origins of parasites within this clade, other than some of those from bats, lie in South America and Australia suggesting an ancient southern super-continent origin for T. cruzi, possibly in marsupials; the only trypanosomes from this clade to have spread to the Old World are those infecting bats, doubtless by virtue of the mobility of their hosts. Viewed in the context of palaeogeographical evidence, the results date the divergence of T. brucei and T. cruzi to the mid-Cretaceous, around 100 million years before present, following the separation of Africa, South America and Euramerica. The inclusion in this study of a broad range of trypanosome species from various different hosts has allowed long phylogenetic branches to be resolved, overcoming the limitations of many previous studies. Moreover, T. brucei and the other mammalian tsetse-transmitted trypanosomes appear, from these data, to be evolving several times faster than T. cruzi and its relatives.
Abstract.
Author URL.
Stevens JR, Gibson WC (1999). The evolution of pathogenic trypanosomes.
Cad Saude Publica,
15(4), 673-684.
Abstract:
The evolution of pathogenic trypanosomes.
In the absence of a fossil record, the evolution of protozoa has until recently largely remained a matter for speculation. However, advances in molecular methods and phylogenetic analysis are now allowing interpretation of the "history written in the genes". This review focuses on recent progress in reconstruction of trypanosome phylogeny based on molecular data from ribosomal RNA, the miniexon and protein-coding genes. Sufficient data have now been gathered to demonstrate unequivocally that trypanosomes are monophyletic; the phylogenetic trees derived can serve as a framework to reinterpret the biology, taxonomy and present day distribution of trypanosome species, providing insights into the coevolution of trypanosomes with their vertebrate hosts and vectors. Different methods of dating the divergence of trypanosome lineages give rise to radically different evolutionary scenarios and these are reviewed. In particular, the use of one such biogeographically based approach provides new insights into the coevolution of the pathogens, Trypanosoma brucei and Trypanosoma cruzi, with their human hosts and the history of the diseases with which they are associated.
Abstract.
Author URL.
Stevens J, Gibson W (1999). The evolution of salivarian trypanosomes.
Stevens J, Gibson W (1999). The evolution of salivarian trypanosomes.
Mem Inst Oswaldo Cruz,
94(2), 225-228.
Author URL.
Stevens JR, Gibson W (1999). The molecular evolution of trypanosomes.
Parasitol Today,
15(11), 432-437.
Abstract:
The molecular evolution of trypanosomes.
The absence of a fossil record has meant that the evolution of protozoa has remained largely a matter for speculation. Recent advances in molecular biology and phylogenetic analysis, however, are allowing the 'history written in the genes' to be interpreted. Here, Jamie Stevens and Wendy Gibson review progress in reconstruction of trypanosome phylogeny based on molecular data from rRNA and protein-coding genes.
Abstract.
Author URL.
Stevens JR, Teixeira MM, Bingle LE, Gibson WC (1999). The taxonomic position and evolutionary relationships of Trypanosoma rangeli.
Int J Parasitol,
29(5), 749-757.
Abstract:
The taxonomic position and evolutionary relationships of Trypanosoma rangeli.
This paper presents a re-evaluation of the taxonomic position and evolutionary relationships of Trypanosoma (Herpetosoma) rangeli based on the phylogenetic analysis of ssrRNA sequences of 64 Trypanosoma species and comparison of mini-exon sequences. All five isolates of T. rangeli grouped together in a clade containing Trypanosoma (Schizotrypanum) cruzi and a range of closely related trypanosome species from bats [Trypanosoma (Schizotrypanum) dionisii, Trypanosoma (Schizotrypanum) vespertilionis] and other South American mammals [Trypanosoma (Herpetosoma) leeuwenhoeki, Trypanosoma (Megatrypanum) minasense, Trypanosoma (Megatrypanum) conorhini] and an as yet unidentified species of trypanosome from an Australian kangaroo. Significantly T. rangeli failed to group with (a) species of subgenus Herpetosoma, other than those which are probably synonyms of T. rangeli, or (b) species transmitted via the salivarian route, although either of these outcomes would have been more consistent with the current taxonomic and biological status of T. rangeli. We propose that use of the names Herpetosoma and Megatrypanum should be discontinued, since these subgenera are clearly polyphyletic and lack evolutionary and taxonomic relevance. We hypothesise that T. rangeli and T. cruzi represent a group of mammalian trypanosomes which completed their early evolution and diversification in South America.
Abstract.
Author URL.
1998
Stevens J, Gibson W, Noyes HA, Rambaut A (1998). A key to understanding Trypanosoma trees [3] (multiple letters). Parasitology Today, 14(8), 334-335.
Stevens J, Gibson W (1998). A key to understanding Trypanosoma trees.
Parasitol Today,
14(8), 334-335.
Author URL.
Stevens J, Noyes H, Gibson W (1998). The evolution of trypanosomes infecting humans and primates.
Abstract:
The evolution of trypanosomes infecting humans and primates.
Abstract.
Author URL.
1997
Komba EK, Kibona SN, Ambwene AK, Stevens JR, Gibson WC (1997). Genetic diversity among Trypanosoma brucei rhodesiense isolates from Tanzania.
Parasitology,
115(6), 571-579.
Abstract:
Genetic diversity among Trypanosoma brucei rhodesiense isolates from Tanzania
We compared 19 stocks of Trypanosoma brucei rhodesiense collected in 1991 and 1994 from Tanzania with representative stocks from other foci of Rhodesian sleeping sickness in Zambia, Kenya and Uganda. Stocks were characterized by isoenzyme electrophoresis, restriction fragment length polymorphisms in variant surface glycoprotein genes and random amplification of polymorphic DNA; the banding patterns obtained were coded for numerical analysis. In addition, the Tanzanian stocks were compared by pulsed field gel electrophoresis. Overall the Tanzanian stocks formed a homogeneous group and the predominant genotype isolated in 1991 was still present in the 1994 sample, although at a reduced level. The Tanzanian stocks were distinct from representative stocks from other East African foci. This observation does not support the proposal that there are northern and southern strains of T. b. rhodesiense, but is consistent with the view that T. b. rhodesiense stocks form a mosaic of different genotypes varying from focus to focus in East Africa.
Abstract.
Enyaru JCK, Matovu E, Odiit M, Okedi LA, Rwendeire AJJ, Stevens JR (1997). Genetic diversity in Trypanosoma (Trypanozoon) brucei isolates from mainland and Lake Victoria island populations in south-eastern Uganda: Epidemiological and control implications. Annals of Tropical Medicine and Parasitology, 91(1), 107-113.
Stevens J, Wall R (1997). Genetic variation in populations of the blowflies Lucilia cuprina and lucilia sericata (Diptera: Calliphoridae). Random amplified polymorphic DNA analysis and mitochondrial DNA sequences.
Abstract:
Genetic variation in populations of the blowflies Lucilia cuprina and lucilia sericata (Diptera: Calliphoridae). Random amplified polymorphic DNA analysis and mitochondrial DNA sequences
Abstract.
Stevens J, Wall R (1997). The evolution of ectoparasitism in the genus Lucilia (Diptera: Calliphoridae).
International Journal for Parasitology,
27, 51-59.
Abstract:
The evolution of ectoparasitism in the genus Lucilia (Diptera: Calliphoridae)
To consider the evolutionary origin of the ectoparasitic habit in the blowfly genus Lucilia (Diptera: Calliphoridae), phylogenetic analyses of mitochondrial DNA sequence data were performed for ten species, including all the common Lucilia agents of myiasis, collected from Africa, Australasia, North America and Europe. Complementary genetic distance and parsimony analyses are used to consider inter and intraspecific relationships within the genus with reference to previous morphological work. The results support the hypothesis of independent multiple evolution of the ectoparasitic habit in Lucilia sericata, Lucilia cuprina and the Lucilia caesar/Lucilia illustris group and suggest that it has coevolved in relatively recent history along with the domestication and husbandry of sheep. The geographic differences in pathogenic importance of various species of Lucilia also suggest that there is a strong climatic influence determining which species has dominated. Lucilia cuprina has become the predominant pathogenic species in sub-tropical and warm temperate habitats (e.g. Australia and South Africa), L. sericata in cool temperate habitats (e.g. Europe and New Zealand) and L. caesar and L. illustris become more common in sheep myiasis in more northerly Palaearctic regions.
Abstract.
1996
Kanmogne GD, Stevens JR, Asonganyi T, Gibson WC (1996). Characterization of Trypanosoma brucei gambiense isolates using restriction fragment length polymorphisms in 5 variant surface glycoprotein genes.
Acta Trop,
61(3), 239-254.
Abstract:
Characterization of Trypanosoma brucei gambiense isolates using restriction fragment length polymorphisms in 5 variant surface glycoprotein genes.
Fifty-eight Type I Trypanosoma brucei gambiense (G) stocks, including 16 from 3 sleeping sickness foci in Cameroon, were compared by Restriction Fragment Length Polymorphism (RFLP) analysis with 14 T.b. brucei and T.b. rhodesiense stocks from various endemic areas of Africa. Loci examined were for 5 variant surface glycoprotein (VSG) genes: the LiTat 1.3, AnTat 11.17 and 2K genes were present as single copy genes, while the VSG 117 and U2 gene probes hybridised with a family of related genes. The RFLP data were subjected to cluster analysis to produce a dendrogram constructed from similarity coefficients. The LiTat 1.3 and AnTat 11.17 genes are considered to be characteristic of G stocks, and neither gene was found in the non-G stocks; however, the LiTat 1.3 gene was absent from 6 of the 58 G stocks, while the AnTat 11.17 gene was absent from 8. Supplementation of the LiTat 1.3 antigen in the Card Agglutination Test for Trypanosomiasis with the AnTat 11.17 antigen might thus improve performance of the test, particularly in Cameroon. The U2 VSG gene probe gave a characteristic RFLP pattern for G stocks, as did the VSG 117 gene; the latter is an isogene of AnTat 1.8 previously used extensively to characterise G stocks by other workers. The 2K gene was absent in some G stocks, while present in some non-G stocks, and was not therefore useful for characterisation of G stocks. In cluster analysis, the T.b. gambiense stocks formed a large homogeneous group, subdivided into 5 subgroups, with the non-gambiense stocks as a heterogeneous outgroup.
Abstract.
Author URL.
Stevens J, Wall R (1996). Classification of the genus lucilia (Diptera: Calliphoridae): a preliminary parsimony analysis.
Journal of Natural History,
30(7), 1087-1094.
Abstract:
Classification of the genus lucilia (Diptera: Calliphoridae): a preliminary parsimony analysis
A parsimony analysis was performed for 25 species of the genus Lucilia (Diptera: Calliphoridae) using the phylogenetic analysis package PAUP, based on 14 of the morphological characters most commonly used for Lucilia species identification. Species descriptions were derived primarily from those given by Aubertin (1933). Parsimony analysis, using equally weighted characters, produced 45 trees and the strict consensus tree derived from these identified three groupings to be present in all 45 trees. The first group was composed of two uniquely North American species Lucilia caeruleiviridis and Lucilia cluvia. The second group contained Lucilia ampullacea, Lucilia caesar and Lucilia illustris. The third group, contained the six species previously described by some authors as the sub-genus Phaenicia: Lucilia cuprina, Lucilia pilosiventris, Lucilia regalis, Lucilia richardsi, Lucilia sericata and Lucilia thatuna, but also contained Lucilia bufonivora and Lucilia silvarum. Using a majority rule consensus tree the 12 unresolved species grouped together in 98% of the trees. The results are discussed in terms of the classification of the genus and the evolution of the myiasis habit. However, the lack of resolution observed in this study indicates the limitations of the current data set and suggests that more detailed studies using a greater number of characters are needed to uncover the evolutionary pathways which have given rise to the diversity of this genus. © 1996 Taylor & Francis Group, LLC.
Abstract.
Kanmogne GD, Stevens JR, Asonganyi T, Gibson WC (1996). Genetic heterogeneity in the Trypanosoma brucei gambiense genome analysed by random amplification of polymorphic DNA.
Parasitol Res,
82(6), 535-541.
Abstract:
Genetic heterogeneity in the Trypanosoma brucei gambiense genome analysed by random amplification of polymorphic DNA.
The random amplification of polymorphic DNA (RAPD) technique has the potential to produce large amounts of characterisation data very quickly and simply, using far less DNA than conventional restriction-fragment-length polymorphism (RFLP) analysis. In the present study we assessed genetic heterogeneity among 34 Trypanosoma brucei gambiense isolates from various endemic areas in Africa by the RAPD technique using 8 arbitrary primers and compared the results with those obtained previously from RFLP analysis of polymorphisms in 5 variant surface glycoprotein (VSG) genes. The isolates were compared both among themselves and with 3 T. b. non-gambiense isolates. Most of the primers produced RAPD profiles specific for T. b. gambiense, with 4 primers showing marked polymorphisms between T. b. gambiense and non-gambiense stocks. These primers also showed minor variations between the T. b. gambiense stocks, and 2 revealed differences between Cameroonian stocks. These results were comparable with those produced by RFLP analysis, where certain polymorphisms are characteristic of T. b. gambiense. Numerical analysis showed a high correlation between the RAPD and RFLP data, with genetic variation being detected at a finer level by RAPD analysis. We conclude that RAPD analysis provides a simple and accurate method for the characterisation of T. b. gambiense.
Abstract.
Author URL.
Stevens J, Wall R (1996). Species, sub-species and hybrid populations of the blowflies Lucilia cuprina and Lucilia sericata (Diptera: Calliphoridae).
Proceedings of the Royal Society of London: B,
263, 1335-1341.
Abstract:
Species, sub-species and hybrid populations of the blowflies Lucilia cuprina and Lucilia sericata (Diptera: Calliphoridae)
The blowflies Lucilia cuprina Wiedmann and Lucilia sericata Meigen (Diptera: Calliphoridae) are facultative ectoparasites of warm blooded vertebrates, particularly domestic sheep. Despite being similar in morphology and ecology, the two species and different populations of each species, are known to vary in their importance as pests in different regions of the world. To elucidate the genetic basis of these species and population level differences, flies were collected from sites in Africa, Europe, Australasia, North America and the islands of Hawaii, and examined using a combination of morphology, the random amplified polymorphic DNA (RAPD) technique and a complementary mitochondrial DNA (mtDNA) analysis. The results confirm the species integrity of L. sericata and L. cuprina and support the existence of intra-specific genetic variation in L. cuprina, but not L. sericata.
Abstract.
Stevens JR, Tibayrenc M (1996). Trypanosoma brucei s.l: evolution, linkage and the clonality debate.
Parasitology,
112 ( Pt 5), 481-488.
Abstract:
Trypanosoma brucei s.l: evolution, linkage and the clonality debate.
The Index of Association (IA) has been proposed by Maynard Smith et al. (1993) as a general method for characterizing the population structures of microorganisms as either: clonal, epidemic, cryptic species or panmictic. With reference to the current debate surrounding the mode of reproduction in parasitic protozoa, this study explores (i) the suitability and limitations of the IA for characterizing populations of Trypanosoma brucei s.l. and (ii) the idea that the significance of genetic differences between populations may be better understood if the evolution, spread and temporal stability of certain parasite genotypes are also considered. Four populations of T. brucei from Côte d'Ivoire, Uganda and Zambia are analysed using the IA and a complementary test for linkage disequilibrium, test f of Tibayrenc, Kjellberg & Ayala (1990). The two populations from Uganda are characterized as epidemic, while the others appear more or less clonal; the merits of the two methods are compared. The implications of the various population classifications are discussed with reference to genotype longevity in each region; the evolution and biomedical consequences of the genetic non-homogeneity of T. brucei are reviewed.
Abstract.
Author URL.
1995
Stevens JR, Tibayrenc M (1995). Detection of linkage disequilibrium in Trypanosoma brucei isolated from tsetse flies and characterized by RAPD analysis and isoenzymes.
Parasitology,
110 ( Pt 2), 181-186.
Abstract:
Detection of linkage disequilibrium in Trypanosoma brucei isolated from tsetse flies and characterized by RAPD analysis and isoenzymes.
This study analyses the different populations of Trypanosoma brucei spp. which may coexist within the midgut of wild tsetse flies (Stevens et al. 1994). Cloned trypanosome populations characterized by multilocus enzyme electrophoresis (MLEE) were further analysed by the random amplified polymorphic DNA (RAPD) technique, allowing detection of genetic variation at a finer level than that possible by MLEE. Genetic distance matrices derived from the results of each of the two biochemical methods were calculated and compared using a computer program based on the method of Mantel (1967). The observed correlation was used to investigate the degree of linkage disequilibrium (LD) in the data, association between unrelated polymorphic markers providing a measure of the departure from panmixia. The potential of each biochemical method to detect linkage was evaluated by an extended Mantel test. The MLEE/RAPD correlation test evidenced significant LD within the population, suggesting a predominantly clonal method of reproduction for these West African trypanosomes. Analysis of RAPD data by the extended Mantel test also showed significant LD, while the results with MLEE data were less conclusive, providing an indication of the relative potential of the two techniques to detect fine genetic variation.
Abstract.
Author URL.
Mathieu-Daudé F, Stevens J, Welsh J, Tibayrenc M, McClelland M (1995). Genetic diversity and population structure of Trypanosoma brucei: clonality versus sexuality.
Molecular and Biochemical Parasitology,
72, 89-101.
Abstract:
Genetic diversity and population structure of Trypanosoma brucei: clonality versus sexuality
Genomic fingerprinting by arbitrarily primed PCR was used to analyze the genetic variability among 59 Trypanosoma brucei stocks representing the three T. brucei subspecies isolated from various hosts and different countries in Africa. 14 oligonucleotide primers revealed 355 polymorphic binary characters which were used for phenetic and phylogenetic analysis and to perform recombination tests exploring the linkage disequilibrium in the sample. These was good concordance between arbitrarily primed PCR polymorphisms and isoenzyme data previously collected for many of the same strains [1]. However, the arbitrarily primed PCR typing was more discerning than multilocus enzyme electrophoresis typing. Phenetic and phylogenetic analysis using arbitrarily primed PCR markers did not confirm T. brucei brucei and T. brucei rhodesiense as separate subspecies, but T. brucei gambiense group I was monophyletic, confirming this group as suitable for the subspecies status. With this exception, there were no clear lineages among the sample, other than clustering of East African stocks and clustering of West African stocks. Some features of the phylogenetic analysis suggested that the population structure was not strictly clonal though recombination tests showed linkage disequilibrium, even in the absence of repeated genotypes. While genotypes appear stable enough for tracking in applied studies, sexuality will impact at the evolutionary time scale, and may be more frequent under some ecological conditions. The arbitrarily primed PCR approach should be an effective and simple approach to follow epidemics and to quantify the role of sexuality in T. brucei populations.
Abstract.
Stevens J, Wall R (1995). Use of random amplified polymorphic DNA (RAPD) analysis for studies of genetic variation in populations of the blowfly Lucilia sericata (Diptera: Calliphoridae) in southern England.
BULLETIN OF ENTOMOLOGICAL RESEARCH,
85(4), 549-555.
Author URL.
1994
Stevens JR, Mathieu-Daudé F, McNamara JJ, Mizen VH, Nzila A (1994). Mixed populations of Trypanosoma brucei in wild Glossina palpalis palpalis.
Trop Med Parasitol,
45(4), 313-318.
Abstract:
Mixed populations of Trypanosoma brucei in wild Glossina palpalis palpalis.
In many previous characterization studies of Trypanozoon, isolates have been subpassaged numerous times in laboratory rodents until a quantity of trypanosomes sufficient for analysis has been obtained. In addition to the numerous biochemical effects of such a process on the parasite, it appears probable that adaptation to an unnatural host may also serve to filter out less virulent populations from mixed infections, leading to an underestimate of the true level of genetic diversity. By the early cloning of trypanosomes from susceptible captive flies infected from the primary isolate--the midgut of a wild tsetse--the present study provides evidence of the range of genetically different Trypanosoma brucei populations which may coexist within the midgut of individual tsetse flies in nature. The three primary isolates from tsetse yielded one, five and nine genetically distinct populations. Cloned populations were confirmed as T. brucei using the polymerase chain reaction, and were characterized by karyotype analysis and multilocus isoenzyme electrophoresis. These data allowed a limited assessment of the level of genetic variability in natural populations of T. brucei.
Abstract.
Author URL.
Muller E, Gargani D, Schaeffer V, Stevens J, Fernandez-Becerra C, Sanchez-Moreno M, Dollet M (1994). Variability in the phloem restricted plant trypanosomes (Phytomonas spp) associated with wilts of cultivated crops - Isoenzyme comparison with the lower trypanosomatids.
European Journal of Plant Pathology,
100(6), 425-434.
Abstract:
Variability in the phloem restricted plant trypanosomes (Phytomonas spp) associated with wilts of cultivated crops - Isoenzyme comparison with the lower trypanosomatids
Plant trypanosomatids (Phytomonas spp) have been isolated from the crude sap of coconut tress and oil palm trees affected with Hartrot or Marchitex diseases in South America and Alpinia purpurata affected with wilt in the Caribbean. They are also commonly isolated from the fruits and latex of Euphorbiaceae or Asclepiadaceae. Thirty-four Phytomonas stocks were studied by isoenzyme electrophoresis (11 loci) in order to investigate genetic variability in the intraphloemic group. Our results showed that variability in phloem restricted Phytomonas is very high, and that Marchitez or Hartrot associated trypanosomatids are not readily separated into two distinct groups. Moreover, the two isolates from Alpinia are very close to the other intraphloemic isolates. The results confirm the existence of several distinct groups, comprising of at least 2 groups of phloem restricted trypanosomatids, not related to the host species, 3 groups of latex trypanosomatids, and one group of fruit trypanosomatids. © 1994 Kluwer Academic Publishers.
Abstract.
1993
Stevens JR, Welburn SC (1993). Genetic processes within an epidemic of sleeping sickness in Uganda.
Parasitol Res,
79(5), 421-427.
Abstract:
Genetic processes within an epidemic of sleeping sickness in Uganda.
Reproductive processes within the current Ugandan epidemic of sleeping sickness are investigated. Genotype frequencies derived from isoenzyme patterns in 44 stocks of Trypanosoma brucei s.l. collected in 1988 from Tororo, south-east Uganda are analysed by single and multiple loci methods. In the single locus method, the hypothesis of random mating is tested by agreement with Hardy-Weinberg equilibrium. The multiple loci method uses a contingency table approach to detect non-random associations between pairs of loci; this equates to the detection of disequilibrium. The results do not support the concept of a randomly mating population of T. brucei within the current epidemic. Results from the epidemic data set are discussed in relation to the broader problem of genetic exchange in Trypanozoon.
Abstract.
Author URL.
Enyaru JCK, Stevens JR, Odiit M, Okuna NM, Carasco JF (1993). Isoenzyme comparison of Trypanozoon isolates from two sleeping sickness areas of south-eastern Uganda.
Acta Tropica,
55(3), 97-115.
Abstract:
Isoenzyme comparison of Trypanozoon isolates from two sleeping sickness areas of south-eastern Uganda
The study characterized 151 Trypanozoon isolates from south-east Uganda by isoenzyme electrophoresis. Stocks were from a range of hosts, including man, cattle, pigs, dogs and Glossina fuscipes fuscipes; 104 isolates were from the Busoga area, 47 were from the Tororo district. Stocks were characterized on thin layer starch gel using eight enzyme systems: ALAT, ASAT, ICD, MDH, ME, NHD, NHI, PGM. Enzyme profiles were generally typical of East Africa; new patterns for ICD and ME were detected. Trypanosomes were classified on the basis of their profile by similarity coefficient analysis and the unweighted pair-group method using arithmetic averages (UPGMA). The majority of trypanosomes were classified in one or other of two genetically distinct groups which corresponded to the strain groups busoga and zambezi, both of which are associated with Rhodesian sleeping sickness in East Africa. Contingency table analyses indicated associations between certain isoenzymes of ICD and PGM, according to host and geographical origin. Significant relationships between trypanosome strain group and geographic origin were also demonstrated for some host groups. © 1993.
Abstract.
1992
Stevens JR, Lanham SM, Allingham R, Gashumba JK (1992). A simplified method for identifying subspecies and strain groups in Trypanozoon by isoenzymes.
Ann Trop Med Parasitol,
86(1), 9-28.
Abstract:
A simplified method for identifying subspecies and strain groups in Trypanozoon by isoenzymes.
To characterize trypanosomes from the subgenus Trypanozoon, 272 stocks in 111 zymodemes were analysed by the polymorphisms seen in a rationalized range of nine enzymes, resolved by electrophoresis, mostly on cellulose acetate. Several highly polymorphic or invariant enzymes used previously were omitted, while two new enzymes, NHD and SOD were included; the isoenzymes seen for SOD were interpreted as two separate enzymes, SODA and SODB. Isoenzyme band patterns were analysed by two complementary numerical methods to elucide taxonomic relationships within the subgenus; groups of zymodemes corresponding to subspecies and strain groups were defined, which agreed closely with previous studies. Except for one zymodeme, Trypanosoma evansi could not be clearly distinguished from the bouaflé strain group. This strain group had enzymic features that overlapped to some extent those of the busoga group. Trypanosoma brucei gambiense and the zambezi, kakumbi, kiboko and sindo groups were clearly defined. Eight zymodemes could not be classified. A rapid identification system using a limited number of enzymes is presented.
Abstract.
Author URL.
Stevens JR, Godfrey DG (1992). Numerical taxonomy of Trypanozoon based on polymorphisms in a reduced range of enzymes.
Parasitology,
104 Pt 1, 75-86.
Abstract:
Numerical taxonomy of Trypanozoon based on polymorphisms in a reduced range of enzymes.
Numerical analyses of Trypanozoon taxonomy are presented, based on the isoenzyme data of Stevens et al. (1992). The previous study used a reduced range of enzymes compared with earlier work; the analyses indicate the value of this rationalized system. Both recently isolated trypanosome stocks and previously studied populations were included, allowing detailed comparison with earlier studies. Relationships between zymodemes were calculated with an improved similarity coefficient program, using Jaccard's coefficient (1908), and by Nei's method (1972). Dendrograms were constructed from the matrices produced with the group-average method. The groupings produced by both numerical methods were in close agreement, and the clusters of related principal zymodemes largely matched the species, subspecies and strain groups proposed by previous workers. Trypanozoon biochemical taxonomy is reviewed and the groupings reinforced by this study are: the mainly East African strain groups, busoga, zambezi, kakumbi, kiboko and sindo; T.b. gambiense and the bouaflé strain group from West Africa, and T. evansi; an intermediate bouaflé/busoga group was also recognized.
Abstract.
Author URL.
1990
Wall R, Langley PA, Stevens J, Clarke GA (1990). Age determination in the old-world screw-worm fly Chrysomya bezziana by pteridine fluorescence.
Journal of Insect Physiology,
36, 213-218.
Abstract:
Age determination in the old-world screw-worm fly Chrysomya bezziana by pteridine fluorescence
Highly significant positive relationships were observed between pteridine fluorescence in the head and chronological age for both sexes of the old-world screw-worm fly Chrysomya bezziana Villeneuve in the laboratory and in field mark-release-recapture trials in Papua New Guinea. The relationships were multiplicative in form and, in most cases, age accounted for in excess of 80–90% of the variance in fluorescence. The rate of accumulation of pteridines with age was greater for males than females, was not affected by the absence or presence of protein in the diet, but was highly dependent on temperature. Pteridine levels appear to be a good indicator of age in this species and will enable the chronological age of wild flies to be determined with a relatively high degree of accuracy.
Abstract.
Stevens JR, Cibulskis RE (1990). Analysing isoenzyme band patterns using similarity coefficients: a personal computer program.
Comput Methods Programs Biomed,
33(4), 205-212.
Abstract:
Analysing isoenzyme band patterns using similarity coefficients: a personal computer program.
A computer program in Fortran 77 was developed to analyse the isoenzyme patterns of trypanosomes isolated from African sleeping sickness patients, to allow biochemical relationships between populations of trypanosomes from different hosts and geographic areas to be elucidated. However, the generality of the design allows it to be used with presence/absence data from a variety of sources, including DNA fingerprints. The program reads in isoenzyme band patterns from an ASCII file and calculates a matrix of similarity coefficients. Four different similarity measures are offered, suitable for presence/absence data from a range of organisms and experimental procedures. The matrix of similarity values produced is suitable for analysis by ordination methods including principal coordinates analysis, and the production of dendrograms and icicle plots using SPSS/PC+.
Abstract.
Author URL.
WALL R, STEVENS J (1990). THE TURN OF THE SCREW WORM.
NEW SCIENTIST,
126(1720), 54-57.
Author URL.
1989
Stevens JR, Nunes VLB, Lanham SM, Oshiro ET (1989). Isoenzyme characterization of Trypanosoma evansi isolated from capybaras and dogs in Brazil.
Acta Tropica,
46, 213-222.
Abstract:
Isoenzyme characterization of Trypanosoma evansi isolated from capybaras and dogs in Brazil
Trypanosoma evansi was seen in blood samples taken randomly from both wild and semi-captive capybaras caught in Mato Grosso do Sul State, Brazil and in sick dogs brought into local veterinary clinics. Trypanosome stocks from capybaras and dogs were significantly different in their patterns of growth in mice, while trypanosomes from dogs were mostly dyskinetoplastic. By isoenzyme electrophoresis all the trypanosomes were of the most common type of T. evansi found elsewhere.
Abstract.
