Publications by year
In Press
Paris JR, Whiting JR, Daniel MJ, Obiol JF, Parsons PJ, van der Zee MJ, Wheat CW, Hughes KA, Fraser BA (In Press). A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy.
Abstract:
A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy
ABSTRACTColour polymorphism provides a tractable trait that can be harnessed to explore the evolution of sexual selection and sexual conflict. Male colour patterns of the Trinidadian guppy (Poecilia reticulata) are governed by both natural and sexual selection, and are typified by extreme pattern colour variation as a result of negative frequency dependent selection. Since guppy colour patterns are often inherited faithfully from fathers to sons, it has been historically presumed that colour genes are physically linked to sex determining loci as a ‘supergene’ on the sex chromosome. Yet the actual identity and genomic location of the colour pattern genes has remained elusive. We phenotyped and genotyped four guppy ‘Iso-Y lines’, where colour was inherited along the patriline, but backcrossed into the stock population every 2 to 3 generations for 40 generations, thereby homogenising the genome at regions unrelated to colour. Using an unbiased phenotyping method to proportion colour pattern differences between and among the Iso-Y lines, we confirmed that the breeding design was successful in producing four distinct colour patterns. Our analysis of genome resequencing data of the four Iso-Y lines uncovered a surprising genetic architecture for colour pattern polymorphism. Genetic differentiation among Iso-Y lines was repeatedly associated with a large and diverse haplotype (∼5Mb) on an autosome (LG1), not the sex chromosome (LG12). Moreover, the LG1 haplotype showed elevated linkage disequilibrium and exhibited evidence of sex-specific diversity when we examined whole-genome sequencing data of the natural source population. We hypothesise that colour pattern polymorphism is driven by Y-autosome epistasis, and conclude that predictions of sexual conflict should focus on incorporating the effects of epistasis in understanding complex adaptive architectures.
Abstract.
Whiting JR, Paris JR, van der Zee MJ, Fraser BA (In Press). AF-vapeR: a multivariate genome scan for detecting parallel evolution using allele frequency change vectors.
Abstract:
AF-vapeR: a multivariate genome scan for detecting parallel evolution using allele frequency change vectors
ABSTRACTThe repeatability of evolution at the genetic level has been demonstrated to vary along a continuum from complete parallelism to divergence. In order to better understand why this continuum exists within and among systems, hypotheses must be tested using high confidence sets of candidate loci for repeatability. Despite this, few methods have been developed to scan SNP data for signatures specifically associated with repeatability, as opposed to local adaptation.Here we present AF-vapeR (Allele Frequency Vector Analysis of Parallel Evolutionary Responses), an approach designed to identify genome regions exhibiting highly correlated allele frequency changes within haplotypes and among replicated allele frequency change vectors. The method divides the genome into windows of an equivalent number of SNPs, and within each window performs eigen decomposition over normalised allele frequency change vectors (AFV), each derived from a replicated pair of populations/species. Properties of the resulting eigenvalue distribution can be used to compare regions of the genome for those exhibiting strong parallelism, and can also be compared against a null distribution derived from randomly permuted AFV. Further, the shape of the eigenvalue distribution can reveal multiple axes of parallelism within datasets.We demonstrate the utility of this approach to detect different modes of parallel evolution using simulations, and also demonstrate a reduction in error rate compared with intersecting FST outliers. Lastly, we apply AF-vapeR to three previously published datasets (stickleback, guppies, and Galapagos finches) which comprise a range of sampling and sequencing strategies, and lineage ages. We detect known parallel regions whilst also identifying novel candidates.The main benefits of this approach include a reduced false-negative rate under many conditions, an emphasis on signals associated specifically with repeatable evolution as opposed to local adaptation, and an opportunity to identify different modes of parallel evolution at the first instance.
Abstract.
Whiting JR, Paris JR, van der Zee MJ, Parsons PJ, Weigel D, Fraser BA (In Press). Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies.
Abstract:
Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies
ABSTRACTStudies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here, we explore these processes in naturally adapted high- (HP) and low-predation (LP) populations of the Trinidadian guppy, Poecilia reticulata. As a model for phenotypic change this system provided some of the earliest evidence of rapid and repeatable evolution in vertebrates; the genetic basis of which has yet to be studied at the whole-genome level. We collected whole-genome sequencing data from ten populations (176 individuals) representing five independent HP-LP river pairs across the three main drainages in Northern Trinidad. We evaluate population structure, uncovering several LP bottlenecks and variable between-river introgression that can lead to constraints on the sharing of adaptive variation between populations. Consequently, we found limited selection on common genes or loci across all drainages. Using a pathway type analysis, however, we find evidence of repeated selection on different genes involved in cadherin signalling. Finally, we found a large repeatedly selected haplotype on chromosome 20 in three rivers from the same drainage. Taken together, despite limited sharing of adaptive variation among rivers, we found evidence of convergent evolution associated with HP-LP environments in pathways across divergent drainages and at a previously unreported candidate haplotype within a drainage.
Abstract.
Whiting JR, Paris JR, Parsons PJ, Matthews S, Reynoso Y, Hughes KA, Reznick D, Fraser BA (In Press). On the genetic architecture of rapidly adapting and convergent life history traits in guppies.
Abstract:
On the genetic architecture of rapidly adapting and convergent life history traits in guppies
ABSTRACTThe genetic basis of traits can shape and constrain how adaptation proceeds in nature; rapid adaptation can be facilitated by polygenic traits, whereas polygenic traits may restrict re-use of the same genes in adaptation (genetic convergence). The rapidly evolving life histories of guppies in response to predation risk provide an opportunity to test this proposition. Guppies adapted to high- (HP) and low-predation (LP) environments in northern Trinidad evolve rapidly and convergently among natural populations. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use an F2 QTL design to examine the genetic basis of seven (five female, two male) guppy life history phenotypes. We use RAD-sequencing data (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform linkage mapping, estimates of genome-wide and per-chromosome heritability (multi-locus associations), and QTL mapping (single-locus associations). Our results are consistent with architectures of many-loci of small effect for male age and size at maturity and female interbrood period. Male trait associations are clustered on specific chromosomes, but female interbrood period exhibits a weak genome-wide signal suggesting a potentially highly polygenic component. Offspring weight and female size at maturity are also associated with a single significant QTL each. These results suggest rapid phenotypic evolution of guppies may be facilitated by polygenic trait architectures, but these may restrict gene-reuse across populations, in agreement with an absence of strong signatures of genetic convergence from recent population genomic analyses of wild HP-LP guppies.
Abstract.
2022
Paris JR, Whiting JR, Daniel MJ, Ferrer Obiol J, Parsons PJ, van der Zee MJ, Wheat CW, Hughes KA, Fraser BA (2022). A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy.
Nature Communications,
13(1).
Abstract:
A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy
AbstractMale colour patterns of the Trinidadian guppy (Poecilia reticulata) are typified by extreme variation governed by both natural and sexual selection. Since guppy colour patterns are often inherited faithfully from fathers to sons, it has been hypothesised that many of the colour trait genes must be physically linked to sex determining loci as a ‘supergene’ on the sex chromosome. Here, we phenotype and genotype four guppy ‘Iso-Y lines’, where colour was inherited along the patriline for 40 generations. Using an unbiased phenotyping method, we confirm the breeding design was successful in creating four distinct colour patterns. We find that genetic differentiation among the Iso-Y lines is repeatedly associated with a diverse haplotype on an autosome (LG1), not the sex chromosome (LG12). Moreover, the LG1 haplotype exhibits elevated linkage disequilibrium and evidence of sex-specific diversity in the natural source population. We hypothesise that colour pattern polymorphism is driven by Y-autosome epistasis.
Abstract.
Whiting JR, Paris JR, Parsons PJ, Matthews S, Reynoso Y, Hughes KA, Reznick D, Fraser BA (2022). On the genetic architecture of rapidly adapting and convergent life history traits in guppies.
Heredity,
128(4), 250-260.
Abstract:
On the genetic architecture of rapidly adapting and convergent life history traits in guppies
The genetic basis of traits shapes and constrains how adaptation proceeds in nature; rapid adaptation can proceed using stores of polygenic standing genetic variation or hard selective sweeps, and increasing polygenicity fuels genetic redundancy, reducing gene re-use (genetic convergence). Guppy life history traits evolve rapidly and convergently among natural high- and low-predation environments in northern Trinidad. This system has been studied extensively at the phenotypic level, but little is known about the underlying genetic architecture. Here, we use four independent F2 QTL crosses to examine the genetic basis of seven (five female, two male) guppy life history phenotypes and discuss how these genetic architectures may facilitate or constrain rapid adaptation and convergence. We use RAD-sequencing data (16,539 SNPs) from 370 male and 267 female F2 individuals. We perform linkage mapping, estimates of genome-wide and per-chromosome heritability (multi-locus associations), and QTL mapping (single-locus associations). Our results are consistent with architectures of many loci of small-effect for male age and size at maturity and female interbrood period. Male trait associations are clustered on specific chromosomes, but female interbrood period exhibits a weak genome-wide signal suggesting a potentially highly polygenic component. Offspring weight and female size at maturity are also associated with a single significant QTL each. These results suggest rapid, repeatable phenotypic evolution of guppies may be facilitated by polygenic trait architectures, but subsequent genetic redundancy may limit gene re-use across populations, in agreement with an absence of strong signatures of genetic convergence from recent analyses of wild guppies.
Abstract.
van der Zee MJ, Whiting JR, Paris JR, Bassar RD, Travis J, Weigel D, Reznick DN, Fraser BA (2022). Rapid genomic convergent evolution in experimental populations of Trinidadian guppies (Poecilia reticulata).
Evolution Letters,
6(2), 149-161.
Abstract:
Rapid genomic convergent evolution in experimental populations of Trinidadian guppies (Poecilia reticulata)
Although rapid phenotypic evolution has been documented often, the genomic basis of rapid adaptation to natural environments is largely unknown in multicellular organisms. Population genomic studies of experimental populations of Trinidadian guppies (Poecilia reticulata) provide a unique opportunity to study this phenomenon. Guppy populations that were transplanted from high-predation (HP) to low-predation (LP) environments have been shown to evolve toward the phenotypes of naturally colonized LP populations in as few as eight generations. These changes persist in common garden experiments, indicating that they have a genetic basis. Here, we report results of whole genome variation in four experimental populations colonizing LP sites along with the corresponding HP source population. We examined genome-wide patterns of genetic variation to estimate past demography and used a combination of genome scans, forward simulations, and a novel analysis of allele frequency change vectors to uncover the signature of selection. We detected clear signals of population growth and bottlenecks at the genome-wide level that matched the known history of population numbers. We found a region on chromosome 15 under strong selection in three of the four populations and with our multivariate approach revealing subtle parallel changes in allele frequency in all four populations across this region. Investigating patterns of genome-wide selection in this uniquely replicated experiment offers remarkable insight into the mechanisms underlying rapid adaptation, providing a basis for comparison with other species and populations experiencing rapidly changing environments.
Abstract.
2021
Whiting JR, Paris JR, van der Zee MJ, Parsons PJ, Weigel D, Fraser BA (2021). Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies.
PLOS Genetics,
17(5), e1009566-e1009566.
Abstract:
Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies
Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here, we explore these processes in naturally adapted high- (HP) and low-predation (LP) populations of the Trinidadian guppy, Poecilia reticulata. As a model for phenotypic change this system provided some of the earliest evidence of rapid and repeatable evolution in vertebrates; the genetic basis of which has yet to be studied at the whole-genome level. We collected whole-genome sequencing data from ten populations (176 individuals) representing five independent HP-LP river pairs across the three main drainages in Northern Trinidad. We evaluate population structure, uncovering several LP bottlenecks and variable between-river introgression that can lead to constraints on the sharing of adaptive variation between populations. Consequently, we found limited selection on common genes or loci across all drainages. Using a pathway type analysis, however, we find evidence of repeated selection on different genes involved in cadherin signaling. Finally, we found a large repeatedly selected haplotype on chromosome 20 in three rivers from the same drainage. Taken together, despite limited sharing of adaptive variation among rivers, we found evidence of convergent evolution associated with HP-LP environments in pathways across divergent drainages and at a previously unreported candidate haplotype within a drainage.
Abstract.
2020
Wannell GJ, Griffiths AM, Spinou A, Batista R, Mendonca MB, Wosiacki WB, Fraser B, Wintner S, Papadopoulos AI, Krey G, et al (2020). A new minibarcode assay to gacilitate species identification from processed, degraded or historic ray (batoidea) samples.
CONSERVATION GENETICS RESOURCES,
12(4), 659-668.
Author URL.
Whiting JR, Fraser BA (2020). Contingent Convergence: the Ability to Detect Convergent Genomic Evolution is Dependent on Population Size and Migration.
G3 Genes|Genomes|Genetics,
10(2), 677-693.
Abstract:
Contingent Convergence: the Ability to Detect Convergent Genomic Evolution is Dependent on Population Size and Migration
Abstract
. Outlier scans, in which the genome is scanned for signatures of selection, have become a prominent tool in studies of local adaptation, and more recently studies of genetic convergence in natural populations. However, such methods have the potential to be confounded by features of demographic history, such as population size and migration, which are considerably varied across natural populations. In this study, we use forward-simulations to investigate and illustrate how several measures of genetic differentiation commonly used in outlier scans (FST, DXY and Δπ) are influenced by demographic variation across multiple sampling generations. In a factorial design with 16 treatments, we manipulate the presence/absence of founding bottlenecks (N of founding individuals), prolonged bottlenecks (proportional size of diverging population) and migration rate between two populations with ancestral and diverged phenotypic optima. Our results illustrate known constraints of individual measures associated with reduced population size and a lack of migration; but notably we demonstrate how relationships between measures are similarly dependent on these features of demography. We find that false-positive signals of convergent evolution (the same simulated outliers detected in independent treatments) are attainable as a product of similar population size and migration treatments (particularly for DXY), and that outliers across different measures (for e.g. FST and DXY) can occur with little influence of selection. Taken together, we show how underappreciated, yet quantifiable measures of demographic history can influence commonly employed methods for detecting selection.
Abstract.
Fraser BA, Whiting JR, Paris JR, Weadick CJ, Parsons PJ, Charlesworth D, Bergero R, Bemm F, Hoffmann M, Kottler VA, et al (2020). Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata).
Genome Biology and Evolution,
12(10), 1789-1805.
Abstract:
Improved Reference Genome Uncovers Novel Sex-Linked Regions in the Guppy (Poecilia reticulata)
Abstract
. Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favor the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict. Early genetics studies revealed that male color patterning genes are mostly but not entirely Y-linked, and that X-linkage may be most common in low-predation populations. More recent population genomic studies of guppies have reached varying conclusions about the size and placement of the Y-linked region. However, this previous work used a reference genome assembled from short-read sequences from a female guppy. Here, we present a new guppy reference genome assembly from a male, using long-read PacBio single-molecule real-time sequencing and chromosome contact information. Our new assembly sequences across repeat- and GC-rich regions and thus closes gaps and corrects mis-assemblies found in the short-read female-derived guppy genome. Using this improved reference genome, we then employed broad population sampling to detect sex differences across the genome. We identified two small regions that showed consistent male-specific signals. Moreover, our results help reconcile the contradictory conclusions put forth by past population genomic studies of the guppy sex chromosome. Our results are consistent with a small Y-specific region and rare recombination in male guppies.
Abstract.
2019
Fraser B, Whiting JR (2019). What can be learned by scanning the genome for molecular convergence in wild populations?. Annals of the New York Academy of Sciences
2017
Zhan L, Paterson IG, Fraser BA, Watson B, Bradbury IR, Nadukkalam Ravindran P, Reznick D, Beiko RG, Bentzen P (2017). megasat: automated inference of microsatellite genotypes from sequence data.
Molecular Ecology Resources,
17(2), 247-256.
Abstract:
megasat: automated inference of microsatellite genotypes from sequence data
megasat is software that enables genotyping of microsatellite loci using next-generation sequencing data. Microsatellites are amplified in large multiplexes, and then sequenced in pooled amplicons. megasat reads sequence files and automatically scores microsatellite genotypes. It uses fuzzy matches to allow for sequencing errors and applies decision rules to account for amplification artefacts, including nontarget amplification products, replication slippage during PCR (amplification stutter) and differential amplification of alleles. An important feature of megasat is the generation of histograms of the length–frequency distributions of amplification products for each locus and each individual. These histograms, analogous to electropherograms traditionally used to score microsatellite genotypes, enable rapid evaluation and editing of automatically scored genotypes. megasat is written in Perl, runs on Windows, Mac OS X and Linux systems, and includes a simple graphical user interface. We demonstrate megasat using data from guppy, Poecilia reticulata. We genotype 1024 guppies at 43 microsatellites per run on an Illumina MiSeq sequencer. We evaluated the accuracy of automatically called genotypes using two methods, based on pedigree and repeat genotyping data, and obtained estimates of mean genotyping error rates of 0.021 and 0.012. In both estimates, three loci accounted for a disproportionate fraction of genotyping errors; conversely, 26 loci were scored with 0–1 detected error (error rate ≤0.007). Our results show that with appropriate selection of loci, automated genotyping of microsatellite loci can be achieved with very high throughput, low genotyping error and very low genotyping costs.
Abstract.
2016
K�nstner A, Hoffmann M, Fraser BA, Kottler VA, Sharma E, Weigel D, Dreyer C (2016). The genome of the trinidadian guppy, Poecilia reticulata, and variation in the Guanapo population.
PLoS ONE,
11(12).
Abstract:
The genome of the trinidadian guppy, Poecilia reticulata, and variation in the Guanapo population
For over a century, the live bearing guppy, Poecilia reticulata, has been used to study sexual selection as well as local adaptation. Natural guppy populations differ in many traits that are of intuitively adaptive significance such as ornamentation, age at maturity, brood size and body shape. Water depth, light supply, food resources and predation regime shape these traits, and barrier waterfalls often separate contrasting environments in the same river. We have assembled and annotated the genome of an inbred single female from a high-predation site in the Guanapo drainage. The final assembly comprises 731.6 Mb with a scaffold N50 of 5.3 MB. Scaffolds were mapped to linkage groups, placing 95% of the genome assembly on the 22 autosomes and the X-chromosome. To investigate genetic variation in the population used for the genome assembly, we sequenced 10 wild caught male individuals. The identified 5 million SNPs correspond to an average nucleotide diversity (77) of 0.0025. The genome assembly and SNP map provide a rich resource for investigating adaptation to different predation regimes. In addition, comparisons with the genomes of other Poeciliid species, which differ greatly in mechanisms of sex determination and maternal resource allocation, as well as comparisons to other teleost genera can begin to reveal how live bearing evolved in teleost fish.
Abstract.
2015
Fraser BA, Künstner A, Reznick DN, Dreyer C, Weigel D (2015). Population genomics of natural and experimental populations of guppies (<i>Poecilia reticulata</i>). Molecular Ecology, 24(2), 389-408.
2014
Fraser BA, Janowitz I, Thairu M, Travis J, Hughes KA (2014). Phenotypic and genomic plasticity of alternative male reproductive tactics in sailfin mollies.
Proceedings of the Royal Society B: Biological Sciences,
281(1781).
Abstract:
Phenotypic and genomic plasticity of alternative male reproductive tactics in sailfin mollies
A major goal of modern evolutionary biology is to understand the causes and consequences of phenotypic plasticity, the ability of a single genotype to produce multiple phenotypes in response to variable environments. While ecological and quantitative genetic studies have evaluated models of the evolution of adaptive plasticity, some long-standing questions about plasticity require more mechanistic approaches. Here, we address two of those questions: does plasticity facilitate adaptive evolution? and do physiological costs place limits on plasticity? We examine these questions by comparing genetically and plastically regulated behavioural variation in sailfin mollies (Poecilia latipinna), which exhibit striking variation in plasticity for male mating behaviour. In this species, some genotypes respond plastically to a change in the social environment by switching between primarily courting and primarily sneaking behaviour. In contrast, other genotypes have fixed mating strategies (either courting or sneaking) and do not display plasticity.We found that genetic and plastic variation in behaviour were accompanied by partially, but not completely overlapping changes in brain gene expression, in partial support of models that predict that plasticity can facilitate adaptive evolution. We also found that behavioural plasticity was accompanied by broader and more robust changes in brain gene expression, suggesting a substantial physiological cost to plasticity. We also observed that sneaking behaviour, but not courting, was associated with upregulation of genes involved in learning and memory, suggesting that sneaking is more cognitively demanding than courtship. © 2014 the Author(s) Published by the Royal Society. All rights reserved.
Abstract.
Sharma E, Künstner A, Fraser BA, Zipprich G, Kottler VA, Henz SR, Weigel D, Dreyer C (2014). Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata.
BMC Genomics,
15(1).
Abstract:
Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata
Background: Sexually dimorphic phenotypes are generally associated with differential gene expression between the sexes. The study of molecular evolution and genomic location of these differentially expressed, or sex-biased, genes is important for understanding inter-sexual divergence under sex-specific selection pressures. Teleost fish provide a unique opportunity to examine this divergence in the presence of variable sex-determination mechanisms of recent origin. The guppy, Poecilia reticulata, displays sexual dimorphism in size, ornaments, and behavior, traits shaped by natural and sexual selection in the wild.Results: to gain insight into molecular mechanisms underlying the guppy's sexual dimorphism, we assembled a reference transcriptome combining genome-independent as well as genome-guided assemblies and analyzed sex-biased gene expression between different tissues of adult male and female guppies. We found tissue-associated sex-biased expression of genes related to pigmentation, signal transduction, and spermatogenesis in males; and growth, cell-division, extra-cellular matrix organization, nutrient transport, and folliculogenesis in females. While most sex-biased genes were randomly distributed across linkage groups, we observed accumulation of ovary-biased genes on the sex linkage group, LG12. Both testis-biased and ovary-biased genes showed a significantly higher rate of non-synonymous to synonymous substitutions (dN/dS) compared to unbiased genes. However, in somatic tissues only female-biased genes, including those co-expressed in multiple tissues, showed elevated ratios of non-synonymous substitutions.Conclusions: Our work identifies a set of annotated gene products that are candidate factors affecting sexual dimorphism in guppies. The differential genomic distribution of gonad-biased genes provides evidence for sex-specific selection pressures acting on the nascent sex chromosomes of the guppy. The elevated rates of evolution of testis-biased and female-biased genes indicate differing evolution under distinct selection pressures on the reproductive versus non-reproductive tissues. © 2014 Sharma et al.; licensee BioMed Central Ltd.
Abstract.
2013
Fraser BA, Hughes KA, Tosh DN, Rodd FH (2013). The role of learning by a predator, Rivulus hartii, in the rare-morph survival advantage in guppies.
Journal of Evolutionary Biology,
26(12), 2597-2605.
Abstract:
The role of learning by a predator, Rivulus hartii, in the rare-morph survival advantage in guppies
Negative frequency-dependent selection (NFDS), where rare types are favoured by selection, can maintain diversity. However, the ecological processes that mediate NFDS are often not known. Male guppies (Poecilia reticulata) exhibit extreme diversity of colour patterning and, in a previous field experiment, rare morphs had a survival advantage. Here, we test the hypothesis that predators impose NFDS because they are efficient at capturing familiar prey morphs, but are less efficient at capturing unfamiliar morphs. Over a series of trials, we presented Rivulus hartii, a natural predator of guppies, with male guppies with the same colour patterning (A trials); then, for a second series of trials, we presented the rivulus with guppies with a new colour pattern (B trials). The success of rivulus at capturing guppies on the first attack increased over successive a trials. First attack success decreased significantly for the early B trials, and then increased during successive B trials, eventually reaching the same level as in the best a trials. This experiment demonstrates that learning, perhaps through long-term search image formation, plays a role in predation success on familiar vs. unfamiliar prey morphs. These results support the hypothesis that predator learning contributes to the maintenance of the extreme male guppy polymorphism seen in nature. © 2013 European Society for Evolutionary Biology.
Abstract.
2011
Fraser BA, Weadick CJ, Janowitz I, Rodd FH, Hughes KA (2011). Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome. BMC Genomics, 12(1).
2010
NEFF BD, FRASER BA (2010). A program to compare genetic differentiation statistics across loci using resampling of individuals and loci.
Molecular Ecology Resources,
10(3), 546-550.
Abstract:
A program to compare genetic differentiation statistics across loci using resampling of individuals and loci
AbstractComparisons of genetic differentiation across populations based on different loci can provide insight into the evolutionary patterns acting on various regions of genomes. Here, we develop a program to statistically compare population genetic differentiation statistics (FST or G′ST) calculated from different loci. The program employs a routine that resamples either or both of individuals and loci and calculates a bootstrap confidence interval in the statistics. Resampling individuals is important when fewer than 25 individuals are sampled per population and when confidence intervals are required for individual loci. Resampling loci provides confidence intervals for sets of loci, such as a set presumed to be neutral, but can be anticonservative if fewer than 20 loci are analysed. We demonstrate the program using previously published data on the genetic differentiation at a major histocompatibility complex locus and at microsatellite loci across 10 populations of the guppy (Poecilia reticulata).
Abstract.
Fraser BA, Ramnarine IW, Neff BD (2010). Selection at the MHC class IIB locus across guppy (Poecilia reticulata) populations.
Heredity,
104(2), 155-167.
Abstract:
Selection at the MHC class IIB locus across guppy (Poecilia reticulata) populations
The highly diverse genes of the major histocompatibility complex (MHC) are important in the adaptive immune system and are expected to be under selection from pathogens. Thus, the MHC genes provide an exceptional opportunity to investigate patterns of selection within and across populations. In this study, we analyzed genetic variation at the MHC class IIB gene and six microsatellite loci across 10 populations of guppies (Poecilia reticulata) in the northern range of Trinidad. We found a high level of diversity at the MHC, with a total of 43 alleles in 142 individuals. At the population level, we found that neutral evolution could not fully account for the variability found at the MHC. Instead, we found that MHC FST statistics were lower than F STderived from the microsatellite loci; 33 of 45 population pairwise estimates for the MHC were significantly lower than those for the microsatellite loci, and MHC FST estimates were consistently lower than those predicted by a coalescent model of neutral evolution. These results suggest a similar selection acting across populations, and we discuss the potential roles of directional and balancing selection. At the sequence level, we found evidence for both positive and purifying selection. Furthermore, positive selection was detected within and adjacent to the putative peptide-binding region (PBR) of the MHC. Surprisingly, we also found a purifying selection at two sites within the putative PBR. Overall, our data provide evidence for selection for functional diversity at the MHC class IIB gene at both the population and nucleotide levels of guppy populations. © 2010 Macmillan Publishers Limited. All rights reserved.
Abstract.
Fraser BA, Ramnarine IW, Neff BD (2010). TEMPORAL VARIATION AT THE MHC CLASS IIB IN WILD POPULATIONS OF THE GUPPY (<i>POECILIA RETICULATA</i>). Evolution
2009
Fraser BA, Neff BD (2009). MHC class IIB additive and non-additive effects on fitness measures in the guppy Poecilia reticulata.
Journal of Fish Biology,
75(9), 2299-2312.
Abstract:
MHC class IIB additive and non-additive effects on fitness measures in the guppy Poecilia reticulata
The genetic architecture of fitness at the class IIB gene of the major histocompatibility complex (MHC) in the guppy Poecilia reticulata was analysed. Diversity at the MHC is thought to be maintained by some form of balancing selection; heterozygote advantage, frequency-dependent selection or spatially and temporally fluctuating selection. Here these hypotheses are evaluated by using an algorithm that partitions the effect of specific MHC allele and genotypes on fitness measures. The effect of MHC genotype on surrogate measures of fitness was tested, including growth rate (at high and low bulk food diets), parasite load following a parasite challenge and survival. The number of copies of the Pore-a132 MHC allele was inversely related to infection by Gyrodactylus flukes and it appeared to be positively related to faster growth. Also, genotypes combining the Pore-a132 or other relatively common alleles paired with rare MHC alleles produced both advantageous and detrimental non-additive effects. Thus, the genetic architecture underlying fitness at the MHC is complex in the P. reticulata. © 2009 the Fisheries Society of the British Isles.
Abstract.
Fraser BA, Neff BD (2009). Parasite mediated homogenizing selection at the MHC in guppies. Genetica, 138(2), 273-278.
2005
Fraser BA, Mandrak NE, McLaughlin RL (2005). Lack of morphological differentiation in eastern (<i>Rhinichthys atratulus</i>) and western (<i>Rhinichthys obtusus</i>) blacknose dace in Canada.
Canadian Journal of Zoology,
83(11), 1502-1509.
Abstract:
Lack of morphological differentiation in eastern (Rhinichthys atratulus) and western (Rhinichthys obtusus) blacknose dace in Canada
We tested whether eastern (Rhinichthys atratulus (Herman, 1804)) and western (Rhinichthys obtusus Agassiz, 1854) blacknose dace could be differentiated in Canada. Eastern, western, and southern forms of blacknose dace had been considered subspecies until recently, when separation of eastern and western species was accepted (J.S. Nelson et al. 2004. Am. Fish. Soc. Spec. Publ. No. 29). However, no study has examined morphological differences in purported diagnostic characters between the two species in Canada. Mensural, meristic, and colouration pattern characters purported to distinguish the two species were measured for blacknose dace across their Canadian range, including likely zones of sympatry. Univariate and multivariate analyses of morphological characters could not distinguish between individuals in allopatric populations from eastern and western regions. Variation among individuals within sympatric populations did not differ significantly from the variation among individuals within allopatric populations, providing no evidence of divergence of the species in sympatry. The delineation of eastern and western species using morphology is not supported by this study, given the lack of differentiation in key distinguishing characters within the Canadian range of the species.
Abstract.
