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[This corrects the article DOI: 10.1371/journal.pgen.1008348.].
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Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species' homing behaviour may promote the establishment of local adaptation. We genotyped 7829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. The results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidate single nucleotide polymorphisms associated with long-distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.
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Oncorhynchus kisutch , Humanos , Animais , Oncorhynchus kisutch/genética , Genética Populacional , Adaptação Fisiológica/genética , Deriva Genética , Genoma , Polimorfismo de Nucleotídeo Único/genéticaRESUMO
A thorough reconstruction of historical processes is essential for a comprehensive understanding of the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded recently, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.
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Distribuição Animal , Acúmulo de Mutações , Oncorhynchus kisutch/genética , Animais , Evolução Molecular , Modelos GenéticosRESUMO
Alternative migratory tactics in salmonids reflect the large observed interindividual variation in spatial behaviour which may range from strict freshwater residency to uninterrupted anadromy. In Salvelinus, sea migrations are performed during the ice-free period as freshwater overwintering is thought to be obligatory due to physiological constraints. As a result, individuals can either migrate the next spring or remain in freshwater, as anadromy is generally considered facultative. In Arctic charr (Salvelinus alpinus), skipped migrations are known to occur, but limited data are available regarding their frequencies within and among populations. Here, the authors used an otolith microchemistry approach relying on strontium (88 Sr) to infer movements between freshwater and marine habitats, and annual oscillations in zinc (64 Zn) to help with age identification. They determined the age-at-first-migration and the occurrence of subsequent annual migrations in two Nunavik Arctic charr populations sampled in Deception Bay (Salluit) and river systems linked to Hopes Advance Bay (Aupaluk), northern Québec, Canada. The mode for age-at-first-migration was 4+ for both populations, although it exhibited large variation (range: 0+ to 8+). Skipped migrations constituted a rare event, as 97.7% and 95.6% of the examined Arctic charr at Salluit (n = 43, mean age = 10.3 ± 2.0 years) and Aupaluk (n = 45, mean age = 6.0 ± 1.9 years), respectively, were found to have performed uninterrupted annual migrations after initiation of the behaviour. The consistency of the annual migrations suggests that the tactic is sufficiently fitness rewarding to be maintained under current environmental conditions. From a fisheries management perspective, these repeated migrations combined with low site fidelity in this species may lead to large interannual variations in abundance at the local scale, which may represent a challenge for monitoring Arctic charr demographics on a river-by-river basis.
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Água Doce , Membrana dos Otólitos , Humanos , Animais , Canadá , Quebeque , Truta/fisiologiaRESUMO
Migratory fishes commonly encounter large and rapid thermal variation, which has the potential to disrupt essential physiological functions. Thus, we acclimated wild, migratory Arctic char to 13°C (â¼7°C above a summer average) for an ecologically relevant period (3â days) and measured maximum heart rate (ƒH,max) during acute warming to determine their ability to rapidly improve cardiac function at high temperatures. Arctic char exhibited rapid compensatory cardiac plasticity similar to past observations following prolonged warm acclimation: they reduced ƒH,max over intermediate temperatures (-8%), improved their ability to increase ƒH,max during warming (+10%), and increased (+1.3°C) the temperature at the onset of an arrhythmic heartbeat, a sign of cardiac failure. This rapid cardiac plasticity may help migrating fishes such as Arctic char mitigate short-term thermal challenges. Furthermore, by using mobile Arctic research infrastructure in a remote field location, the present study illustrates the potential for field-based, experimental physiology in such locations.
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Aclimatação , Truta , Aclimatação/fisiologia , Animais , Regiões Árticas , Coração/fisiologia , Temperatura , Truta/fisiologiaRESUMO
Anadromy was documented in 16 lake trout, Salvelinus namaycush, from Canada's central Arctic using capture data and otolith microchemistry. For the first time, estuarine/marine habitat use was described for five individuals using acoustic telemetry. Age-at-first-migration to sea was variable (10-39 years) among individuals and most S. namaycush undertook multiple anadromous migrations within their lifetime. Telemetry data suggested that S. namaycush do not travel far into marine habitats and prefer surface waters (<2 m). These results further our collective understanding of the marine ecology of Arctic S. namaycush.
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Ecossistema , Truta/fisiologia , Animais , Regiões Árticas , Canadá , Membrana dos Otólitos/químicaRESUMO
Dispersal is a central process in ecology and evolution. At the individual level, the three stages of the dispersal process (i.e., emigration, transience and immigration) are affected by complex interactions between phenotypes and environmental factors. Condition- and context-dependent dispersal have far-reaching consequences, both for the demography and the genetic structuring of natural populations and for adaptive processes. From an applied point of view, dispersal also deeply affects the spatial dynamics of populations and their ability to respond to land-use changes, habitat degradation and climate change. For these reasons, dispersal has received considerable attention from ecologists and evolutionary biologists. Demographic and genetic methods allow quantifying non-effective (i.e., followed or not by a successful reproduction) and effective (i.e., with a successful reproduction) dispersal and to investigate how individual and environmental factors affect the different stages of the dispersal process. Over the past decade, demographic and genetic methods designed to quantify dispersal have rapidly evolved but interactions between researchers from the two fields are limited. We here review recent developments in both demographic and genetic methods to study dispersal in wild animal populations. We present their strengths and limits, as well as their applicability depending on study objectives and population characteristics. We propose a unified framework allowing researchers to combine methods and select the more suitable tools to address a broad range of important topics about the ecology and evolution of dispersal and its consequences on animal population dynamics and genetics.
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Migração Animal/fisiologia , Ecologia/métodos , Animais , Animais Selvagens , Evolução Biológica , Dinâmica PopulacionalRESUMO
Migration is a ubiquitous life history trait with profound evolutionary and ecological consequences. Recent developments in telemetry and genomics, when combined, can bring significant insights on the migratory ecology of nonmodel organisms in the wild. Here, we used this integrative approach to document dispersal, gene flow and potential for local adaptation in anadromous Arctic Char from six rivers in the Canadian Arctic. Acoustic telemetry data from 124 tracked individuals indicated asymmetric dispersal, with a large proportion of fish (72%) tagged in three different rivers migrating up the same short river in the fall. Population genomics data from 6,136 SNP markers revealed weak, albeit significant, population differentiation (average pairwise FST = 0.011) and asymmetric dispersal was also revealed by population assignments. Approximate Bayesian computation simulations suggested the presence of asymmetric gene flow, although in the opposite direction to that observed from the telemetry data, suggesting that dispersal does not necessarily lead to gene flow. These observations suggested that Arctic Char home to their natal river to spawn, but may overwinter in rivers with the shortest migratory route to minimize the costs of migration in nonbreeding years. Genome scans and genetic-environment associations identified 90 outlier markers putatively under selection, 23 of which were in or near a gene. Of these, at least four were involved in muscle and cardiac function, consistent with the hypothesis that migratory harshness could drive local adaptation. Our study illustrates the power of integrating genomics and telemetry to study migrations in nonmodel organisms in logistically challenging environments such as the Arctic.
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Migração Animal , Ecossistema , Fluxo Gênico , Truta/genética , Animais , Regiões Árticas , Teorema de Bayes , Genética Populacional , Genômica , Modelos Genéticos , Nunavut , Polimorfismo de Nucleotídeo Único , Rios , TelemetriaRESUMO
Using massively parallel sequencing data from two species with different life history traits, American lobster (Homarus americanus) and Arctic Char (Salvelinus alpinus), we highlight how an unbalanced sex ratio in the samples and a few sex-linked markers may lead to false interpretations of population structure and thus to potentially erroneous management recommendations. Here, multivariate analyses revealed two genetic clusters separating samples by sex instead of by expected spatial variation: inshore and offshore locations in lobster, or east and west locations in Arctic Char. To further investigate this, we created several subsamples artificially varying the sex ratio in the inshore/offshore and east/west groups and then demonstrated that significant genetic differentiation could be observed despite panmixia in lobster, and that FST values were overestimated in Arctic Char. This pattern was due to 12 and 94 sex-linked markers driving differentiation for lobster and Arctic Char, respectively. Removing sex-linked markers led to nonsignificant genetic structure in lobster and a more accurate estimation of FST in Arctic Char. The locations of these markers and putative identities of genes containing or nearby the markers were determined using available transcriptomic and genomic data, and this provided new information related to sex determination in both species. Given that only 9.6% of all marine/diadromous population genomic studies to date have reported sex information, we urge researchers to collect and consider individual sex information. Sex information is therefore relevant for avoiding unexpected biases due to sex-linked markers as well as for improving our knowledge of sex determination systems in nonmodel species.
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Genética Populacional , Sequenciamento de Nucleotídeos em Larga Escala , Nephropidae/genética , Razão de Masculinidade , Truta/genética , Animais , Feminino , Marcadores Genéticos , Masculino , Análise Multivariada , Polimorfismo de Nucleotídeo Único , Viés de SeleçãoRESUMO
Anadromous Atlantic salmon (Salmo salar) is a species of major conservation and management concern in North America, where population abundance has been declining over the past 30 years. Effective conservation actions require the delineation of conservation units to appropriately reflect the spatial scale of intraspecific variation and local adaptation. Towards this goal, we used the most comprehensive genetic and genomic database for Atlantic salmon to date, covering the entire North American range of the species. The database included microsatellite data from 9142 individuals from 149 sampling locations and data from a medium-density SNP array providing genotypes for >3000 SNPs for 50 sampling locations. We used neutral and putatively selected loci to integrate adaptive information in the definition of conservation units. Bayesian clustering with the microsatellite data set and with neutral SNPs identified regional groupings largely consistent with previously published regional assessments. The use of outlier SNPs did not result in major differences in the regional groupings, suggesting that neutral markers can reflect the geographic scale of local adaptation despite not being under selection. We also performed assignment tests to compare power obtained from microsatellites, neutral SNPs and outlier SNPs. Using SNP data substantially improved power compared to microsatellites, and an assignment success of 97% to the population of origin and of 100% to the region of origin was achieved when all SNP loci were used. Using outlier SNPs only resulted in minor improvements to assignment success to the population of origin but improved regional assignment. We discuss the implications of these new genetic resources for the conservation and management of Atlantic salmon in North America.
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Conservação dos Recursos Naturais , Genética Populacional , Salmo salar/genética , Animais , Teorema de Bayes , Análise por Conglomerados , Bases de Dados Genéticas , Genômica , Genótipo , Repetições de Microssatélites , América do Norte , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNARESUMO
The data underlying scientific papers should be accessible to researchers both now and in the future, but how best can we ensure that these data are available? Here we examine the effectiveness of four approaches to data archiving: no stated archiving policy, recommending (but not requiring) archiving, and two versions of mandating data deposition at acceptance. We control for differences between data types by trying to obtain data from papers that use a single, widespread population genetic analysis, structure. At one extreme, we found that mandated data archiving policies that require the inclusion of a data availability statement in the manuscript improve the odds of finding the data online almost 1000-fold compared to having no policy. However, archiving rates at journals with less stringent policies were only very slightly higher than those with no policy at all. We also assessed the effectiveness of asking for data directly from authors and obtained over half of the requested datasets, albeit with â¼8 d delay and some disagreement with authors. Given the long-term benefits of data accessibility to the academic community, we believe that journal-based mandatory data archiving policies and mandatory data availability statements should be more widely adopted.
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Arquivos , Pesquisa Biomédica , Revisão da Pesquisa por Pares , Coleta de Dados/métodos , Bases de Dados Factuais , Humanos , PolíticasRESUMO
We identify two processes by which humans increase genetic exchange among groups of individuals: by affecting the distribution of groups and dispersal patterns across a landscape, and by affecting interbreeding among sympatric or parapatric groups. Each of these processes might then have two different effects on biodiversity: changes in the number of taxa through merging or splitting of groups, and the extinction/extirpation of taxa through effects on fitness. We review the various ways in which humans are affecting genetic exchange, and highlight the difficulties in predicting the impacts on biodiversity. Gene flow and hybridization are crucially important evolutionary forces influencing biodiversity. Humans alter natural patterns of genetic exchange in myriad ways, and these anthropogenic effects are likely to influence the genetic integrity of populations and species. We argue that taking a gene-centric view towards conservation will help resolve issues pertaining to conservation and management. Editor's suggested further reading in BioEssays A systemic view of biodiversity and its conservation: Processes, interrelationships, and human culture Abstract.
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Biodiversidade , Fluxo Gênico/genética , Animais , Evolução Biológica , Mudança Climática , HumanosRESUMO
Most population genomic tools rely on accurate single nucleotide polymorphism (SNP) calling and filtering to meet their underlying assumptions. However, genomic complexity, resulting from structural variants, paralogous sequences, and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading to SNPs that deviate from Mendelian expected patterns of heterozygosity and allelic ratio. In this study, we employed the ngsParalog software to identify such deviant SNPs in whole-genome sequencing (WGS) data with low (1.5×) to intermediate (4.8×) coverage for four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), and the American Eel (Anguilla rostrata). The analyses revealed that deviant SNPs accounted for 22% to 62% of all SNPs in salmonid datasets and approximately 11% in the American Eel dataset. These deviant SNPs were particularly concentrated within repetitive elements and genomic regions that had recently undergone rediploidization in salmonids. Additionally, narrow peaks of elevated coverage were ubiquitous along all four reference genomes, encompassed most deviant SNPs, and could be partially associated with transposons and tandem repeats. Including these deviant SNPs in genomic analyses led to highly distorted site frequency spectra, underestimated pairwise FST values, and overestimated nucleotide diversity. Considering the widespread occurrence of deviant SNPs arising from a variety of sources, their important impact in estimating population parameters, and the availability of effective tools to identify them, we propose that excluding deviant SNPs from WGS datasets is required to improve genomic inferences for a wide range of taxa and sequencing depths.
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Genoma , Salmonidae , Animais , Genômica , Salmonidae/genética , Análise de Sequência de DNA , Truta/genética , Polimorfismo de Nucleotídeo ÚnicoRESUMO
Reproducibility is the benchmark for results and conclusions drawn from scientific studies, but systematic studies on the reproducibility of scientific results are surprisingly rare. Moreover, many modern statistical methods make use of 'random walk' model fitting procedures, and these are inherently stochastic in their output. Does the combination of these statistical procedures and current standards of data archiving and method reporting permit the reproduction of the authors' results? To test this, we reanalysed data sets gathered from papers using the software package STRUCTURE to identify genetically similar clusters of individuals. We find that reproducing structure results can be difficult despite the straightforward requirements of the program. Our results indicate that 30% of analyses were unable to reproduce the same number of population clusters. To improve this, we make recommendations for future use of the software and for reporting STRUCTURE analyses and results in published works.
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Biologia Computacional/métodos , Genética Populacional/métodos , Software , Teorema de Bayes , Análise por Conglomerados , Interpretação Estatística de Dados , Bases de Dados Genéticas , Reprodutibilidade dos TestesRESUMO
Conservation units (CUs) are important tools for supporting the implementation of standardized management practices for exploited species. Following the adoption of the Wild Salmon Policy in Canada, CUs were defined for Pacific salmon based on characteristics related to ecotype, life history and genetic variation using microsatellite markers as indirect measures of local adaptation. Genomic data sets have the potential to improve the definition of CUs by reducing variance around estimates of population genetic parameters, thereby increasing the power to detect more subtle patterns of population genetic structure and by providing an opportunity to incorporate adaptive information more directly with the identification of variants putatively under selection. We used one of the largest genomic data sets recently published for a nonmodel species, comprising 5662 individual Coho salmon (Oncorhynchus kisutch) from 149 sampling locations and a total of 24,542 high-quality SNPs obtained using genotyping-by-sequencing and mapped to the Coho salmon reference genome to (1) evaluate the current delineation of CUs for Coho in Canada and (2) compare patterns of population structure observed using neutral and outlier loci from genotype-environment association analyses to determine whether separate CUs that capture adaptive diversity are needed. Our results reflected CU boundaries on the whole, with the majority of sampling locations managed in the same CU clustering together within genetic groups. However, additional groups that are not currently represented by CUs were also uncovered. We observed considerable overlap in the genetic clusters identified using neutral or candidate loci, indicating a general congruence in patterns of genetic variation driven by local adaptation and gene flow in this species. Consequently, we suggest that the current CU boundaries for Coho salmon are largely well-suited for meeting the Canadian Wild Salmon Policy's objective of defining biologically distinct groups, but we highlight specific areas where CU boundaries may be refined.
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Acoustic telemetry (AT) is a rapidly evolving technique used to track the movements of aquatic animals. As the capacity of AT research expands it is important to optimize its relevance to management while still pursuing key ecological questions. A global review of AT literature revealed region-specific research priorities underscoring the breadth of how AT is applied, but collectively demonstrated a lack of management-driven objectives, particularly relating to fisheries, climate change, and protection of species. In addition to the need for more research with direct pertinence to management, AT research should prioritize ongoing efforts to create collaborative opportunities, establish long-term and ecosystem-based monitoring, and utilize technological advancements to bolster aquatic policy and ecological understanding worldwide.
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Ecossistema , Pesqueiros , Acústica , Animais , Conservação dos Recursos Naturais/métodos , Telemetria/métodosRESUMO
Distinguishing neutral and adaptive genetic variation is one of the main challenges in investigating processes shaping population structure in the wild, and landscape genomics can help identify signatures of adaptation to contrasting environments. Arctic Char (Salvelinus alpinus) is an anadromous salmonid and the most harvested fish species by Inuit people, including in Nunavik (Québec, Canada), one of the most recently deglaciated regions in the world. Unlike many other anadromous salmonids, Arctic Char occupy coastal habitats near their natal rivers during their short marine phase restricted to the summer ice-free period. Our main objective was to document putatively neutral and adaptive genomic variation in anadromous Arctic Char populations from Nunavik and bordering regions to inform local fisheries management. We used genotyping by sequencing (GBS) to genotype 18,112 filtered single nucleotide polymorphisms (SNP) in 650 individuals from 23 sampling locations along >2000 km of coastline. Our results reveal a hierarchical genetic structure, whereby neighboring hydrographic systems harbor distinct populations grouped by major oceanographic basins: Hudson Bay, Hudson Strait, Ungava Bay, and Labrador Sea. We found genetic diversity and differentiation to be consistent both with the expected postglacial recolonization history and with patterns of isolation-by-distance reflecting contemporary gene flow. Results from three gene-environment association methods supported the hypothesis of local adaptation to both freshwater and marine environments (strongest associations with sea surface and air temperatures during summer and salinity). Our results support a fisheries management strategy at a regional scale, and other implications for hatchery projects and adaptation to climate change are discussed.
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Despite immense concern over amplified warming in the Arctic, physiological research to address related conservation issues for valuable cold-adapted fish, such as the Arctic char (Salvelinus alpinus), is lacking. This crucial knowledge gap is largely attributable to the practical and logistical challenges of conducting sensitive physiological investigations in remote field settings. Here, we used an innovative, mobile aquatic-research laboratory to assess the effects of temperature on aerobic metabolism and maximum heart rate (f Hmax) of upriver migrating Arctic char in the Kitikmeot region of Nunavut in the central Canadian Arctic. Absolute aerobic scope was unchanged at temperatures from 4 to 16°C, while f Hmax increased with temperature (Q 10 = 2.1), as expected. However, f Hmax fell precipitously below 4°C and it began to plateau above ~ 16°C, reaching a maximum at ~ 19°C before declining and becoming arrhythmic at ~ 21°C. Furthermore, recovery from exhaustive exercise appeared to be critically impaired above 16°C. The broad thermal range (~4-16°C) for increasing f Hmax and maintaining absolute aerobic scope matches river temperatures commonly encountered by migrating Arctic char in this region. Nevertheless, river temperatures can exceed 20°C during warm events and our results confirm that such temperatures would limit exercise performance and thus impair migration in this species. Thus, unless Arctic char can rapidly acclimatize or alter its migration timing or location, which are both open questions, these impairments would likely impact population persistence and reduce lifetime fitness. As such, future conservation efforts should work towards quantifying and accounting for the impacts of warming, variable river temperatures on migration and reproductive success.
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Wild Pacific salmon, including Coho salmon Onchorynchus kisutch, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed. Implementation of parentage-based tagging (PBT) may overcome problems associated with coded-wire tag-based (CWT) assessment and management of coho salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. PBT and genetic stock identification (GSI) were used to identify coho salmon sampled in fisheries (8,006 individuals) and escapements (1,692 individuals) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Very high accuracy of assignment to population (100%) via PBT for 543 jack (age 2) assigned to correct age and collection location and 265 coded-wire tag (CWT, age 3) coho salmon assigned to correct age and release location was observed, with a 40,774-individual, 267-population baseline available for assignment. Coho salmon from un-CWTed enhanced populations contributed 65% of the catch in southern recreational fisheries in 2017. Application of a PBT-GSI system of identification to individuals in 2017 fisheries and escapements provided high-resolution estimates of stock composition, catch, and exploitation rate by CU or population, providing an alternate and more effective method in the assessment and management of Canadian-origin coho salmon relative to CWTs, and an opportunity for a genetic-based system to replace the current CWT system for coho salmon assessment.
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Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population-specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.