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Berrebi P, Jesenšek D, Laporte M, Crivelli AJ. Restoring marble trout genes in the Soča River (Slovenia). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01430-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Ackiss AS, Magee MR, Sass GG, Turnquist K, McIntyre PB, Larson WA. Genomic and environmental influences on resilience in a cold-water fish near the edge of its range. Evol Appl 2021; 14:2794-2814. [PMID: 34950230 PMCID: PMC8674893 DOI: 10.1111/eva.13313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 10/05/2021] [Accepted: 10/07/2021] [Indexed: 02/06/2023] Open
Abstract
Small, isolated populations present a challenge for conservation. The dueling effects of selection and drift in a limited pool of genetic diversity make the responses of small populations to environmental perturbations erratic and difficult to predict. This is particularly true at the edge of a species range, where populations often persist at the limits of their environmental tolerances. Populations of cisco, Coregonus artedi, in inland lakes have experienced numerous extirpations along the southern edge of their range in recent decades, which are thought to result from environmental degradation and loss of cold, well-oxygenated habitat as lakes warm. Yet, cisco extirpations do not show a clear latitudinal pattern, suggesting that local environmental factors and potentially local adaptation may influence resilience. Here, we used genomic tools to investigate the nature of this pattern of resilience. We used restriction site-associated DNA capture (Rapture) sequencing to survey genomic diversity and differentiation in southern inland lake cisco populations and compared the frequency of deleterious mutations that potentially influence fitness across lakes. We also examined haplotype diversity in a region of the major histocompatibility complex involved in stress and immune system response. We correlated these metrics to spatial and environmental factors including latitude, lake size, and measures of oxythermal habitat and found significant relationships between genetic metrics and broad and local factors. High levels of genetic differentiation among populations were punctuated by a phylogeographic break and residual patterns of isolation-by-distance. Although the prevalence of deleterious mutations and inbreeding coefficients was significantly correlated with latitude, neutral and non-neutral genetic diversity were most strongly correlated with lake surface area. Notably, differences among lakes in the availability of estimated oxythermal habitat left no clear population genomic signature. Our results shed light on the complex dynamics influencing these isolated populations and provide valuable information for their conservation.
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Affiliation(s)
- Amanda S. Ackiss
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
- U.S. Geological SurveyGreat Lakes Science CenterAnn ArborMichiganUSA
| | | | - Greg G. Sass
- Escanaba Lake Research StationWisconsin Department of Natural ResourcesBoulder JunctionWisconsinUSA
| | - Keith Turnquist
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
| | - Peter B. McIntyre
- Department of Natural Resources and the EnvironmentCornell UniversityIthacaNew YorkUSA
| | - Wesley A. Larson
- U.S. Geological SurveyWisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
- National Oceanographic and Atmospheric AdministrationNational Marine Fisheries ServiceAlaska Fisheries Science CenterAuke Bay LaboratoriesJuneauAlaskaUSA
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4
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Hierarchical genetic structure and implications for conservation of the world's largest salmonid, Hucho taimen. Sci Rep 2021; 11:20508. [PMID: 34654859 PMCID: PMC8520000 DOI: 10.1038/s41598-021-99530-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/20/2021] [Indexed: 11/09/2022] Open
Abstract
Population genetic analyses can evaluate how evolutionary processes shape diversity and inform conservation and management of imperiled species. Taimen (Hucho taimen), the world’s largest freshwater salmonid, is threatened, endangered, or extirpated across much of its range due to anthropogenic activity including overfishing and habitat degradation. We generated genetic data using high throughput sequencing of reduced representation libraries for taimen from multiple drainages in Mongolia and Russia. Nucleotide diversity estimates were within the range documented in other salmonids, suggesting moderate diversity despite widespread population declines. Similar to other recent studies, our analyses revealed pronounced differentiation among the Arctic (Selenge) and Pacific (Amur and Tugur) drainages, suggesting historical isolation among these systems. However, we found evidence for finer-scale structure within the Pacific drainages, including unexpected differentiation between tributaries and the mainstem of the Tugur River. Differentiation across the Amur and Tugur basins together with coalescent-based demographic modeling suggests the ancestors of Tugur tributary taimen likely diverged in the eastern Amur basin, prior to eventual colonization of the Tugur basin. Our results suggest the potential for differentiation of taimen at different geographic scales, and suggest more thorough geographic and genomic sampling may be needed to inform conservation and management of this iconic salmonid.
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Lutz ML, Tonkin Z, Yen JD, Johnson G, Ingram BA, Sharley J, Lyon J, Chapple DG, Sunnucks P, Pavlova A. Using multiple sources during reintroduction of a locally extinct population benefits survival and reproduction of an endangered freshwater fish. Evol Appl 2021; 14:950-964. [PMID: 33897813 PMCID: PMC8061264 DOI: 10.1111/eva.13173] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 11/26/2022] Open
Abstract
Through using different sources, population reintroductions can create genetically diverse populations at low risk of harmful inbreeding and well equipped for adaptation to future environments. Genetic variation from one source can mask locally nonoptimal alleles from another, thereby enhancing adaptive potential and population persistence. We assessed the outcomes in survival, growth and reproduction of using two differentiated sources (genetically diverse Yarra and moderately diverse Dartmouth) for translocations and stocking to reintroduce the endangered Australian freshwater Macquarie perch Macquaria australasica into the Ovens River. For stocking, same- and different-population parents ("cross-types") were used during hatchery production. Genetic samples and data on individual fish were collected over three years of monitoring the Ovens. We genetically assigned Ovens fish to their broodstock parents and tested whether cross-type and genetic dissimilarity between parents are associated with offspring survival, and whether cross-type and parental dissimilarity or individual genetic diversity are associated with somatic growth rates of stocked fish. We genetically identified translocated fish and assessed local recruit ancestry. Of 296 Ovens fish, 31.1% were inferred to be stocked, 1.3% translocated and 67.6% locally born. Cross-type strongly predicted survival of stocked offspring: those with two Yarra parents had the highest survival, followed by offspring with two-population, then Dartmouth, ancestry. Of the Ovens recruits, 59.5% had Yarra, 33.5% two-population and 7.0% Dartmouth ancestry, despite 67% of stocked and 98% of translocated fish originating from Dartmouth. Offspring with two Yarra parents grew faster than offspring of Dartmouth or two-population ancestry. Although Dartmouth fish appear to be less fit in the Ovens compared to Yarra fish, possibly due to deleterious variation or genetic or plastic maladaptation, they contribute to the reintroduced population through local interbreeding with Yarra fish and relatively high survival of stocked offspring of two-population ancestry. Thus, combining compatible stocks is likely to benefit restoration of other wildlife populations.
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Affiliation(s)
- Maiko L. Lutz
- School of Biological SciencesMonash UniversityClaytonVic.Australia
| | - Zeb Tonkin
- Arthur Rylah Institute for Environmental Research (ARI)HeidelbergVic.Australia
| | - Jian D.L. Yen
- Arthur Rylah Institute for Environmental Research (ARI)HeidelbergVic.Australia
- School of BioSciencesThe University of MelbourneParkvilleVic.Australia
| | - Glen Johnson
- Department of Environment, Land, Water and PlanningWodongaVic.Australia
| | | | - Joanne Sharley
- Arthur Rylah Institute for Environmental Research (ARI)HeidelbergVic.Australia
| | - Jarod Lyon
- Arthur Rylah Institute for Environmental Research (ARI)HeidelbergVic.Australia
| | - David G. Chapple
- School of Biological SciencesMonash UniversityClaytonVic.Australia
| | - Paul Sunnucks
- School of Biological SciencesMonash UniversityClaytonVic.Australia
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6
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Bootsma ML, Miller L, Sass GG, Euclide PT, Larson WA. The ghosts of propagation past: haplotype information clarifies the relative influence of stocking history and phylogeographic processes on contemporary population structure of walleye ( Sander vitreus). Evol Appl 2021; 14:1124-1144. [PMID: 33897825 PMCID: PMC8061267 DOI: 10.1111/eva.13186] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Stocking of fish is an important tool for maintaining fisheries but can also significantly alter population genetic structure and erode the portfolio of within-species diversity that is important for promoting resilience and adaptability. Walleye (Sander vitreus) are a highly valued sportfish in the midwestern United States, a region characterized by postglacial recolonization from multiple lineages and an extensive history of stocking. We leveraged genomic data and recently developed analytical approaches to explore the population structure of walleye from two midwestern states, Minnesota and Wisconsin. We genotyped 954 walleye from 23 populations at ~20,000 loci using genotyping by sequencing and tested for patterns of population structure with single-SNP and microhaplotype data. Populations from Minnesota and Wisconsin were highly differentiated from each other, with additional substructure found in each state. Population structure did not consistently adhere to drainage boundaries, as cases of high intra-drainage and low inter-drainage differentiation were observed. Low genetic structure was observed between populations from the upper Wisconsin and upper Chippewa river watersheds, which are found as few as 50 km apart and were likely homogenized through historical stocking. Nevertheless, we were able to differentiate these populations using microhaplotype-based co-ancestry analysis, providing increased resolution over previous microsatellite studies and our other single SNP-based analyses. Although our results illustrate that walleye population structure has been influenced by past stocking practices, native ancestry still exists in most populations and walleye populations may be able to purge non-native alleles and haplotypes in the absence of stocking. Our study is one of the first to use genomic tools to investigate the influence of stocking on population structure in a nonsalmonid fish and outlines a workflow leveraging recently developed analytical methods to improve resolution of complex population structure that will be highly applicable in many species and systems.
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Affiliation(s)
- Matthew L. Bootsma
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Loren Miller
- Minnesota Department of Natural ResourcesUniversity of MinnesotaSt. PaulMNUSA
| | - Greg G. Sass
- Office of Applied ScienceWisconsin Department of Natural ResourcesEscanaba Lake Research StationBoulder JunctionWIUSA
| | - Peter T. Euclide
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Wesley A. Larson
- U.S. Geological SurveyWisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
- Present address:
Ted Stevens Marine Research InstituteAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationJuneauAKUSA
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O'Sullivan RJ, Aykanat T, Johnston SE, Rogan G, Poole R, Prodöhl PA, de Eyto E, Primmer CR, McGinnity P, Reed TE. Captive-bred Atlantic salmon released into the wild have fewer offspring than wild-bred fish and decrease population productivity. Proc Biol Sci 2020; 287:20201671. [PMID: 33081620 PMCID: PMC7661298 DOI: 10.1098/rspb.2020.1671] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The release of captive-bred animals into the wild is commonly practised to restore or supplement wild populations but comes with a suite of ecological and genetic consequences. Vast numbers of hatchery-reared fish are released annually, ostensibly to restore/enhance wild populations or provide greater angling returns. While previous studies have shown that captive-bred fish perform poorly in the wild relative to wild-bred conspecifics, few have measured individual lifetime reproductive success (LRS) and how this affects population productivity. Here, we analyse data on Atlantic salmon from an intensely studied catchment into which varying numbers of captive-bred fish have escaped/been released and potentially bred over several decades. Using a molecular pedigree, we demonstrate that, on average, the LRS of captive-bred individuals was only 36% that of wild-bred individuals. A significant LRS difference remained after excluding individuals that left no surviving offspring, some of which might have simply failed to spawn, consistent with transgenerational effects on offspring survival. The annual productivity of the mixed population (wild-bred plus captive-bred) was lower in years where captive-bred fish comprised a greater fraction of potential spawners. These results bolster previous empirical and theoretical findings that intentional stocking, or non-intentional escapees, threaten, rather than enhance, recipient natural populations.
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Affiliation(s)
- Ronan James O'Sullivan
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Tutku Aykanat
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | | | - Ger Rogan
- Marine Institute, Furnace, Newport, Mayo, Ireland
| | | | - Paulo A Prodöhl
- Institute for Global Food Security, School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, UK
| | | | - Craig R Primmer
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Philip McGinnity
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland.,Marine Institute, Furnace, Newport, Mayo, Ireland
| | - Thomas Eric Reed
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
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8
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Genetic Structure and Population Demography of White-Spotted Charr in the Upstream Watershed of a Large Dam. WATER 2020. [DOI: 10.3390/w12092406] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
White-spotted charr (Salvelinus leucomaenis leucomaenis) is an anadromous fish that has been severely harmed by human land-use development, particularly through habitat fragmentation. However, the anthropogenic impacts on populations of this species have not been evaluated, except those on small dammed-off populations. Using multiplexed ISSR genotyping by sequencing, we investigated the genetic structure of white-spotted charr in four tributaries in the upper section of the Kanayama Dam in the Sorachi River, Hokkaido Island, Japan. There were no distinct genetic structures (FST = 0.014), probably because some active individuals migrate frequently among tributaries. By model-flexible demographic simulation, historical changes in the effective population size were inferred. The result indicates that the population size has decreased since the end of the last glacial period, with three major population decline events, including recent declines that were probably associated with recent human activities. Nevertheless, populations in the watershed upstream of the Kanayama Dam are still expected to be at low risk of immediate extinction, owing to the large watershed size and the limited number of small check dams. An effective conservation measure for sustaining the white-spotted charr population is to maintain high connectivity between tributaries, such as by providing fishways in check dams during construction.
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Ferchaud AL, Leitwein M, Laporte M, Boivin-Delisle D, Bougas B, Hernandez C, Normandeau É, Thibault I, Bernatchez L. Adaptive and maladaptive genetic diversity in small populations: Insights from the Brook Charr (Salvelinus fontinalis) case study. Mol Ecol 2020; 29:3429-3445. [PMID: 33463857 DOI: 10.1111/mec.15566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 12/12/2022]
Abstract
Investigating the relative importance of neutral versus selective processes governing the accumulation of genetic variants is a key goal in both evolutionary and conservation biology. This is particularly true in the context of small populations, where genetic drift can counteract the effect of selection. Using Brook Charr (Salvelinus fontinalis) from Québec, Canada, as a case study, we investigated the importance of demographic versus selective processes governing the accumulation of both adaptive and maladaptive mutations in closed versus open and connected populations to assess gene flow effect. This was achieved by using 14,779 high-quality filtered SNPs genotyped among 1,416 fish representing 50 populations from three life history types: lacustrine (closed populations), riverine and anadromous (connected populations). Using the PROVEAN algorithm, we observed a considerable accumulation of putative deleterious mutations across populations. The absence of correlation between the occurrence of putatively beneficial or deleterious mutations and local recombination rate supports the hypothesis that genetic drift might be the main driver of the accumulation of such variants. However, despite a lower genetic diversity observed in lacustrine than in riverine or anadromous populations, lacustrine populations do not exhibit more deleterious mutations than the two other history types, suggesting that the negative effect of genetic drift in lacustrine populations may be mitigated by that of relaxed purifying selection. Moreover, we also identified genomic regions associated with anadromy, as well as an overrepresentation of transposable elements associated with variation in environmental variables, thus supporting the importance of transposable elements in adaptation.
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Affiliation(s)
- Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Maeva Leitwein
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Damien Boivin-Delisle
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Bérénice Bougas
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Cécilia Hernandez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Éric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Isabel Thibault
- Direction de l'expertise Sur la Faune Aquatique, Ministère des Forêts, de la Faune et des Parcs du Québec, Québec, QC, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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Ferchaud AL, Laporte M, Wellenreuther M. From the woods to the halls of science: Louis Bernatchez's contributions to science, wildlife conservation and people. Evol Appl 2020; 13:1105-1116. [PMID: 32684949 PMCID: PMC7359837 DOI: 10.1111/eva.13043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Maren Wellenreuther
- School of Biological Sciences The University of Auckland Auckland New Zealand
- The New Zealand Institute for Plant and Food Research Ltd Nelson New Zealand
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11
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Bourret V, Albert V, April J, Côté G, Morissette O. Past, present and future contributions of evolutionary biology to wildlife forensics, management and conservation. Evol Appl 2020; 13:1420-1434. [PMID: 32684967 PMCID: PMC7359848 DOI: 10.1111/eva.12977] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022] Open
Abstract
Successfully implementing fundamental concepts into concrete applications is challenging in any given field. It requires communication, collaboration and shared will between researchers and practitioners. We argue that evolutionary biology, through research work linked to conservation, management and forensics, had a significant impact on wildlife agencies and department practices, where new frameworks and applications have been implemented over the last decades. The Quebec government's Wildlife Department (MFFP: Ministère des Forêts, de la Faune et des Parcs) has been proactive in reducing the “research–implementation” gap, thanks to prolific collaborations with many academic researchers. Among these associations, our department's outstanding partnership with Dr. Louis Bernatchez yielded significant contributions to harvest management, stocking programmes, definition of conservation units, recovery of threatened species, management of invasive species and forensic applications. We discuss key evolutionary biology concepts and resulting concrete examples of their successful implementation that derives directly or indirectly from this successful partnership. While old and new threats to wildlife are bringing new challenges, we expect recent developments in eDNA and genomics to provide innovative solutions as long as the research–implementation bridge remains open.
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Affiliation(s)
- Vincent Bourret
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Vicky Albert
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Julien April
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Guillaume Côté
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Olivier Morissette
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
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12
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Lehnert SJ, Baillie SM, MacMillan J, Paterson IG, Buhariwalla CF, Bradbury IR, Bentzen P. Multiple decades of stocking has resulted in limited hatchery introgression in wild brook trout ( Salvelinus fontinalis) populations of Nova Scotia. Evol Appl 2020; 13:1069-1089. [PMID: 32431753 PMCID: PMC7232767 DOI: 10.1111/eva.12923] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 12/06/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022] Open
Abstract
Many populations of freshwater fishes are threatened with losses, and increasingly, the release of hatchery individuals is one strategy being implemented to support wild populations. However, stocking of hatchery individuals may pose long-term threats to wild populations, particularly if genetic interactions occur between wild and hatchery individuals. One highly prized sport fish that has been heavily stocked throughout its range is the brook trout (Salvelinus fontinalis). In Nova Scotia, Canada, hatchery brook trout have been stocked since the early 1900s, and despite continued stocking efforts, populations have suffered declines in recent decades. Before this study, the genetic structure of brook trout populations in the province was unknown; however, given the potential negative consequences associated with hatchery stocking, it is possible that hatchery programs have adversely affected the genetic integrity of wild populations. To assess the influence of hatchery supplementation on wild populations, we genotyped wild brook trout from 12 river systems and hatchery brook trout from two major hatcheries using 100 microsatellite loci. Genetic analyses of wild trout revealed extensive population genetic structure among and within river systems and significant isolation-by-distance. Hatchery stocks were genetically distinct from wild populations, and most populations showed limited to no evidence of hatchery introgression (<5% hatchery ancestry). Only a single location had a substantial number of hatchery-derived trout and was located in the only river where a local strain is used for supplementation. The amount of hatchery stocking within a watershed did not influence the level of hatchery introgression. Neutral genetic structure of wild populations was influenced by geography with some influence of climate and stocking indices. Overall, our study suggests that long-term stocking has not significantly affected the genetic integrity of wild trout populations, highlighting the variable outcomes of stocking and the need to evaluate the consequences on a case-by-case basis.
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Affiliation(s)
- Sarah J. Lehnert
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
| | - Shauna M. Baillie
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
| | - John MacMillan
- Inland Fisheries DivisionNova Scotia Department of Fisheries and AquaculturePictouNSCanada
| | - Ian G. Paterson
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
| | - Colin F. Buhariwalla
- Inland Fisheries DivisionNova Scotia Department of Fisheries and AquaculturePictouNSCanada
| | - Ian R. Bradbury
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt. John'sNLCanada
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
| | - Paul Bentzen
- Marine Gene Probe LabBiology DepartmentDalhousie UniversityHalifaxNSCanada
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13
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Yoshida K, Ravinet M, Makino T, Toyoda A, Kokita T, Mori S, Kitano J. Accumulation of Deleterious Mutations in Landlocked Threespine Stickleback Populations. Genome Biol Evol 2020; 12:479-492. [PMID: 32232440 PMCID: PMC7197494 DOI: 10.1093/gbe/evaa065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2020] [Indexed: 02/06/2023] Open
Abstract
Colonization of new habitats often reduces population sizes and may result in the accumulation of deleterious mutations by genetic drift. Compared with the genomic basis for adaptation to new environments, genome-wide analysis of deleterious mutations in isolated populations remains limited. In the present study, we investigated the accumulation of deleterious mutations in five endangered freshwater populations of threespine stickleback (Gasterosteus aculeatus) in the central part of the mainland of Japan. Using whole-genome resequencing data, we first conducted phylogenomic analysis and confirmed at least two independent freshwater colonization events in the central mainland from ancestral marine ecotypes. Next, analyses of single nucleotide polymorphisms showed a substantial reduction of heterozygosity in freshwater populations compared with marine populations. Reduction in heterozygosity was more apparent at the center of each chromosome than the peripheries and on X chromosomes compared with autosomes. Third, bioinformatic analysis of deleterious mutations showed increased accumulation of putatively deleterious mutations in the landlocked freshwater populations compared with marine populations. For the majority of populations examined, the frequencies of putatively deleterious mutations were higher on X chromosomes than on autosomes. The interpopulation comparison indicated that the majority of putatively deleterious mutations may have accumulated independently. Thus, whole-genome resequencing of endangered populations can help to estimate the accumulation of deleterious mutations and inform us of which populations are the most severely endangered. Furthermore, analysis of variation among chromosomes can give insights into whether any particular chromosomes are likely to accumulate deleterious mutations.
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Affiliation(s)
- Kohta Yoshida
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Mark Ravinet
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.,Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway.,School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tomoyuki Kokita
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui, Japan
| | - Seiichi Mori
- Biological Laboratories, Gifu-kyoritsu University, Ogaki, Gifu, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
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14
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Leitwein M, Cayuela H, Ferchaud AL, Normandeau É, Gagnaire PA, Bernatchez L. The role of recombination on genome-wide patterns of local ancestry exemplified by supplemented brook charr populations. Mol Ecol 2019; 28:4755-4769. [PMID: 31579957 DOI: 10.1111/mec.15256] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022]
Abstract
Assessing the immediate and long-term evolutionary consequences of human-mediated hybridization is of major concern for conservation biology. Several studies have documented how selection in interaction with recombination modulates introgression at a genome-wide scale, but few have considered the dynamics of this process within and among chromosomes. Here, we used an exploited freshwater fish, the brook charr (Salvelinus fontinalis), for which decades of stocking practices have resulted in admixture between wild populations and an introduced domestic strain, to assess both the temporal dynamics and local chromosomal variation in domestic ancestry. We provide a detailed picture of the domestic ancestry patterns across the genome using about 33,000 mapped single nucleotide polymorphisms genotyped in 611 individuals from 24 supplemented populations. For each lake, we distinguished early- and late-generation hybrids using information regarding admixture tracts. To assess the selective outcomes following admixture we then evaluated the relationship between recombination and admixture proportions at three different scales: the whole genome, chromosomes and within 2-Mb windows. This allowed us to detect a wide range of evolutionary mechanisms varying along the genome, as reflected by the finding of favoured or disfavoured introgression of domestic haplotypes. Among these, the main factor modulating local ancestry was probably the presence of deleterious recessive mutations in the wild populations, which can be efficiently hidden to selection in the presence of long admixture tracts. Overall, our results emphasize the relevance of taking into consideration local ancestry information to assess both the temporal and the chromosomal variation in local admixture ancestry toward better understanding post-hybridization evolutionary outcomes.
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Affiliation(s)
- Maeva Leitwein
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Anne-Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Éric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | | | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
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15
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Dorant Y, Benestan L, Rougemont Q, Normandeau E, Boyle B, Rochette R, Bernatchez L. Comparing Pool-seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster ( Homarus americanus) as a case study. Ecol Evol 2019; 9:6606-6623. [PMID: 31236247 PMCID: PMC6580275 DOI: 10.1002/ece3.5240] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/10/2019] [Accepted: 04/13/2019] [Indexed: 01/02/2023] Open
Abstract
Unraveling genetic population structure is challenging in species potentially characterized by large population size and high dispersal rates, often resulting in weak genetic differentiation. Genotyping a large number of samples can improve the detection of subtle genetic structure, but this may substantially increase sequencing cost and downstream bioinformatics computational time. To overcome this challenge, alternative, cost-effective sequencing approaches, namely Pool-seq and Rapture, have been developed. We empirically measured the power of resolution and congruence of these two methods in documenting weak population structure in nonmodel species with high gene flow comparatively to a conventional genotyping-by-sequencing (GBS) approach. For this, we used the American lobster (Homarus americanus) as a case study. First, we found that GBS, Rapture, and Pool-seq approaches gave similar allele frequency estimates (i.e., correlation coefficient over 0.90) and all three revealed the same weak pattern of population structure. Yet, Pool-seq data showed F ST estimates three to five times higher than GBS and Rapture, while the latter two methods returned similar F ST estimates, indicating that individual-based approaches provided more congruent results than Pool-seq. We conclude that despite higher costs, GBS and Rapture are more convenient approaches to use in the case of species exhibiting very weak differentiation. While both GBS and Rapture approaches provided similar results with regard to estimates of population genetic parameters, GBS remains more cost-effective in project involving a relatively small numbers of genotyped individuals (e.g., <1,000). Overall, this study illustrates the complexity of estimating genetic differentiation and other summary statistics in complex biological systems characterized by large population size and migration rates.
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Affiliation(s)
- Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Laura Benestan
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Pêches et Océans CanadaInstitut Maurice‐LamontagneMont‐JoliCanada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Brian Boyle
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
- Plateforme d'analyses génomiques, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
| | - Rémy Rochette
- Department of BiologyUniversity of New BrunswickSaint JohnCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecCanada
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16
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Hohenlohe PA, McCallum HI, Jones ME, Lawrance MF, Hamede RK, Storfer A. Conserving adaptive potential: lessons from Tasmanian devils and their transmissible cancer. CONSERV GENET 2019; 20:81-87. [PMID: 31551664 PMCID: PMC6759055 DOI: 10.1007/s10592-019-01157-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/09/2019] [Indexed: 11/26/2022]
Abstract
Maintenance of adaptive genetic variation has long been a goal of management of natural populations, but only recently have genomic tools allowed identification of specific loci associated with fitness-related traits in species of conservation concern. This raises the possibility of managing for genetic variation directly relevant to specific threats, such as those due to climate change or emerging infectious disease. Tasmanian devils (Sarcophilus harrisii) face the threat of a transmissible cancer, devil facial tumor disease (DFTD), that has decimated wild populations and led to intensive management efforts. Recent discoveries from genomic and modeling studies reveal how natural devil populations are responding to DFTD, and can inform management of both captive and wild devil populations. Notably, recent studies have documented genetic variation for disease-related traits and rapid evolution in response to DFTD, as well as potential mechanisms for disease resistance such as immune response and tumor regression in wild devils. Recent models predict dynamic persistence of devils with or without DFTD under a variety of modeling scenarios, although at much lower population densities than before DFTD emerged, contrary to previous predictions of extinction. As a result, current management that focuses on captive breeding and release for maintaining genome-wide genetic diversity or demographic supplementation of populations could have negative consequences. Translocations of captive devils into wild populations evolving with DFTD can cause outbreeding depression and/or increases in the force of infection and thereby the severity of the epidemic, and we argue that these risks outweigh any benefits of demographic supplementation in wild populations. We also argue that genetic variation at loci associated with DFTD should be monitored in both captive and wild populations, and that as our understanding of DFTD-related genetic variation improves, considering genetic management approaches to target this variation is warranted in developing conservation strategies for Tasmanian devils.
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Affiliation(s)
- Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID 83843, USA
| | - Hamish I. McCallum
- Environmental Futures Research Institute, Griffith University, Brisbane, QLD 4111, Australia
| | - Menna E. Jones
- School of Biological Sciences, University of Tasmania, Hobart, TAS 7001, Australia
| | - Matthew F. Lawrance
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
| | - Rodrigo K. Hamede
- School of Biological Sciences, University of Tasmania, Hobart, TAS 7001, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA 99164, USA
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17
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Hunter ME, Hoban SM, Bruford MW, Segelbacher G, Bernatchez L. Next-generation conservation genetics and biodiversity monitoring. Evol Appl 2018; 11:1029-1034. [PMID: 30026795 PMCID: PMC6050179 DOI: 10.1111/eva.12661] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/01/2018] [Accepted: 06/04/2018] [Indexed: 12/13/2022] Open
Abstract
This special issue of Evolutionary Applications consists of 10 publications investigating the use of next-generation tools and techniques in population genetic analyses and biodiversity assessment. The special issue stems from a 2016 Next Generation Genetic Monitoring Workshop, hosted by the National Institute for Mathematical and Biological Synthesis (NIMBioS) in Tennessee, USA. The improved accessibility of next-generation sequencing platforms has allowed molecular ecologists to rapidly produce large amounts of data. However, with the increased availability of new genomic markers and mathematical techniques, care is needed in selecting appropriate study designs, interpreting results in light of conservation concerns, and determining appropriate management actions. This special issue identifies key attributes of successful genetic data analyses in biodiversity evaluation and suggests ways to improve analyses and their application in current population and conservation genetics research.
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Affiliation(s)
- Margaret E. Hunter
- U.S. Geological SurveyWetland and Aquatic Research CenterGainesvilleFlorida
| | | | - Michael W. Bruford
- Cardiff School of Biosciences and Sustainable Places InstituteCardiff UniversityCardiffUK
| | | | - Louis Bernatchez
- GIROQDépartement de BiologieUniversité LavalSte‐Foy, QuébecQCCanada
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