Publications by category
Journal articles
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.
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.
Gan HM, Grandjean F, Jenkins TL, Austin CM (2019). Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication.
BMC Genomics,
20(1).
Abstract:
Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication.
BACKGROUND: the recently published complete mitogenome of the European lobster (Homarus gammarus) that was generated using long-range PCR exhibits unusual gene composition (missing nad2) and gene rearrangements among decapod crustaceans with strong implications in crustacean phylogenetics. Such atypical mitochondrial features will benefit greatly from validation with emerging long read sequencing technologies such as Oxford Nanopore that can more accurately identify structural variation. RESULTS: We re-sequenced the H. gammarus mitogenome on an Oxford Nanopore Minion flowcell and performed a long-read only assembly, generating a complete mitogenome assembly for H. gammarus. In contrast to previous reporting, we found an intact mitochondrial nad2 gene in the H. gammarus mitogenome and showed that its gene organization is broadly similar to that of the American lobster (H. americanus) except for the presence of a large tandemly duplicated region with evidence of pseudogenization in one of each duplicated protein-coding genes. CONCLUSIONS: Using the European lobster as an example, we demonstrate the value of Oxford Nanopore long read technology in resolving problematic mitogenome assemblies. The increasing accessibility of Oxford Nanopore technology will make it an attractive and useful tool for evolutionary biologists to verify new and existing unusual mitochondrial gene rearrangements recovered using first and second generation sequencing technologies, particularly those used to make phylogenetic inferences of evolutionary scenarios.
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.
Evol Appl,
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.
Author URL.
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.
Head CEI, Bonsall MB, Jenkins TL, Koldewey H, Pratchett MS, Taylor ML, Rogers AD (2018). Exceptional biodiversity of the cryptofaunal decapods in the Chagos Archipelago, central Indian Ocean.
MARINE POLLUTION BULLETIN,
135, 636-647.
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.
Stevens JR, Holland LP, Jenkins TL (2017). Contrasting patterns of population structure and gene flow facilitate exploration of connectivity in two widely distributed temperate octocorals. Heredity
Publications by year
2020
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.
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.
2019
Gan HM, Grandjean F, Jenkins TL, Austin CM (2019). Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication.
BMC Genomics,
20(1).
Abstract:
Absence of evidence is not evidence of absence: Nanopore sequencing and complete assembly of the European lobster (Homarus gammarus) mitogenome uncovers the missing nad2 and a new major gene cluster duplication.
BACKGROUND: the recently published complete mitogenome of the European lobster (Homarus gammarus) that was generated using long-range PCR exhibits unusual gene composition (missing nad2) and gene rearrangements among decapod crustaceans with strong implications in crustacean phylogenetics. Such atypical mitochondrial features will benefit greatly from validation with emerging long read sequencing technologies such as Oxford Nanopore that can more accurately identify structural variation. RESULTS: We re-sequenced the H. gammarus mitogenome on an Oxford Nanopore Minion flowcell and performed a long-read only assembly, generating a complete mitogenome assembly for H. gammarus. In contrast to previous reporting, we found an intact mitochondrial nad2 gene in the H. gammarus mitogenome and showed that its gene organization is broadly similar to that of the American lobster (H. americanus) except for the presence of a large tandemly duplicated region with evidence of pseudogenization in one of each duplicated protein-coding genes. CONCLUSIONS: Using the European lobster as an example, we demonstrate the value of Oxford Nanopore long read technology in resolving problematic mitogenome assemblies. The increasing accessibility of Oxford Nanopore technology will make it an attractive and useful tool for evolutionary biologists to verify new and existing unusual mitochondrial gene rearrangements recovered using first and second generation sequencing technologies, particularly those used to make phylogenetic inferences of evolutionary scenarios.
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.
Evol Appl,
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.
Author URL.
2018
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.
Head CEI, Bonsall MB, Jenkins TL, Koldewey H, Pratchett MS, Taylor ML, Rogers AD (2018). Exceptional biodiversity of the cryptofaunal decapods in the Chagos Archipelago, central Indian Ocean.
MARINE POLLUTION BULLETIN,
135, 636-647.
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.
2017
Stevens JR, Holland LP, Jenkins TL (2017). Contrasting patterns of population structure and gene flow facilitate exploration of connectivity in two widely distributed temperate octocorals. Heredity