1
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Mobley KB, Barton HJ, Ellmén M, Ruokolainen A, Guttorm O, Pieski H, Orell P, Erkinaro J, Primmer CR. Sex-specific overdominance at the maturation vgll3 gene for reproductive fitness in wild Atlantic salmon. Mol Ecol 2024; 33:e17435. [PMID: 38877757 DOI: 10.1111/mec.17435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 04/11/2024] [Accepted: 05/15/2024] [Indexed: 06/16/2024]
Abstract
Linking reproductive fitness with adaptive traits at the genomic level can shed light on the mechanisms that produce and maintain sex-specific selection. Here, we construct a multigenerational pedigree to investigate sex-specific selection on a maturation gene, vgll3, in a wild Atlantic salmon population. The vgll3 locus is responsible for ~40% of the variation in maturation (sea age at first reproduction). Genetic parentage analysis was conducted on 18,265 juveniles (parr) and 685 adults collected at the same spawning ground over eight consecutive years. A high proportion of females (26%) were iteroparous and reproduced two to four times in their lifetime. A smaller proportion of males (9%) spawned at least twice in their lifetime. Sex-specific patterns of reproductive fitness were related to vgll3 genotype. Females showed a pattern of overdominance where vgll3*EL genotypes had three-fold more total offspring than homozygous females. In contrast, males demonstrated that late-maturing vgll3*LL individuals had two-fold more offspring than either vgll3*EE or vgll3*EL males. Taken together, these data suggest that balancing selection in females contributes to the maintenance of variation at this locus via increased fitness of iteroparous vgll3*EL females. This study demonstrates the utility of multigenerational pedigrees for uncovering complex patterns of reproduction, sex-specific selection and the maintenance of genetic variation.
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Affiliation(s)
- Kenyon B Mobley
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Genetics, Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Henry J Barton
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Mikko Ellmén
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Annukka Ruokolainen
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Olavi Guttorm
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Hans Pieski
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Panu Orell
- Natural Resources Institute Finland (Luke), Oulu, Finland
| | | | - Craig R Primmer
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Institute for Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
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2
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Andersson A, Karlsson S, Ryman N, Laikre L. Monitoring genetic diversity with new indicators applied to an alpine freshwater top predator. Mol Ecol 2022; 31:6422-6439. [PMID: 36170147 PMCID: PMC10091952 DOI: 10.1111/mec.16710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
Genetic diversity is the basis for population adaptation and long-term survival, yet rarely considered in biodiversity monitoring. One key issue is the need for useful and straightforward indicators of genetic diversity. We monitored genetic diversity over 40 years (1970-2010) in metapopulations of brown trout (Salmo trutta) inhabiting 27 small mountain lakes representing 10 lake systems in central Sweden using >1200 fish per time point. We tested six newly proposed indicators; three were designed for broad, international use in the UN Convention on Biological Diversity (CBD) and are currently applied in several countries. The other three were recently elaborated for national use by a Swedish science-management effort and applied for the first time here. The Swedish indicators use molecular genetic data to monitor genetic diversity within and between populations (indicators ΔH and ΔFST , respectively) and assess the effective population size (Ne -indicator). We identified 29 genetically distinct populations, all retained over time. Twelve of the 27 lakes harboured more than one population indicating that brown trout biodiversity hidden as cryptic, sympatric populations are more common than recognized. The Ne indicator showed values below the threshold (Ne ≤ 500) in 20 populations with five showing Ne < 100. Statistically significant genetic diversity reductions occurred in several populations. Metapopulation structure appears to buffer against diversity loss; applying the indicators to metapopulations suggest mostly acceptable rates of change in all but one system. The CBD indicators agreed with the Swedish ones but provided less detail. All these indicators are appropriate for managers to initiate monitoring of genetic biodiversity.
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Affiliation(s)
- Anastasia Andersson
- Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden
| | - Sten Karlsson
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Nils Ryman
- Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden
| | - Linda Laikre
- Department of Zoology, Division of Population Genetics, Stockholm University, Stockholm, Sweden
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3
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Saha A, Andersson A, Kurland S, Keehnen NLP, Kutschera VE, Hössjer O, Ekman D, Karlsson S, Kardos M, Ståhl G, Allendorf FW, Ryman N, Laikre L. Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes. Mol Ecol 2021; 31:498-511. [PMID: 34699656 DOI: 10.1111/mec.16252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 10/16/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022]
Abstract
The sympatric existence of genetically distinguishable populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves certain parts of the genome. We returned to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (coding for lactate dehydrogenase A) in brown trout in the small Lakes Bunnersjöarna, Sweden. First, we verified the existence of the two coexisting demes using a 96-SNP fluidigm array. We then applied whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; nucleotide diversity was higher in deme I than in deme II. Strong genetic divergence is observed with genome-wide FST ≈ 0.2. Compared with data from populations of similar small lakes, this divergence is of similar magnitude as that between reproductively isolated populations. Individual whole-genome resequencing of two individuals per deme suggests higher inbreeding in deme II versus deme I, indicating different degree of isolation. We located two gene-copies for LDH-A and found divergence between demes in a regulatory section of one of these genes. However, we did not find a perfect fit between the sequence data and previous allozyme results, and this will require further research. Our data demonstrates genome-wide divergence governed mostly by genetic drift but also by diversifying selection in coexisting populations. This type of hidden biodiversity needs consideration in conservation management.
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Affiliation(s)
- Atal Saha
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Anastasia Andersson
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Sara Kurland
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Naomi L P Keehnen
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Ola Hössjer
- Department of Mathematics, Stockholm University, Stockholm, Sweden
| | - Diana Ekman
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Sten Karlsson
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
| | - Marty Kardos
- Flathead Lake Biological Station, University of Montana, Montana, USA.,National Marine Fisheries Service, Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Seattle, Washington, USA
| | | | - Fred W Allendorf
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Nils Ryman
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Linda Laikre
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
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4
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Sebastian W, Sukumaran S, Abdul Azeez S, Muraleedharan KR, Dinesh Kumar PK, Zacharia PU, Gopalakrishnan A. Genomic investigations provide insights into the mechanisms of resilience to heterogeneous habitats of the Indian Ocean in a pelagic fish. Sci Rep 2021; 11:20690. [PMID: 34667208 PMCID: PMC8526693 DOI: 10.1038/s41598-021-00129-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 10/05/2021] [Indexed: 11/08/2022] Open
Abstract
The adaptive genetic variation in response to heterogeneous habitats of the Indian Ocean was investigated in the Indian oil sardine using ddRAD sequencing to understand the subpopulation structure, stock complexity, mechanisms of resilience, and vulnerability in the face of climate change. Samples were collected from different ecoregions of the Indian ocean and ddRAD sequencing was carried out. Population genetic analyses revealed that samples from the Gulf of Oman significantly diverged from other Indian Ocean samples. SNP allele-environment correlation revealed the presence of candidate loci correlated with the environmental variables like annual sea surface temperature, chlorophyll-a, and dissolved oxygen concentration which might represent genomic regions allegedly diverging as a result of local adaptation. Larval dispersal modelling along the southwest coast of India indicated a high dispersal rate. The two major subpopulations (Gulf of Oman and Indian) need to be managed regionally to ensure the preservation of genetic diversity, which is crucial for climatic resilience.
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Affiliation(s)
- Wilson Sebastian
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India.
| | - Sandhya Sukumaran
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - S Abdul Azeez
- CSIR-National Institute of Oceanography, Regional Centre Kochi, Dr Salim Ali Road, Post Box No. 1913, Kochi, Kerala, India
| | - K R Muraleedharan
- CSIR-National Institute of Oceanography, Regional Centre Kochi, Dr Salim Ali Road, Post Box No. 1913, Kochi, Kerala, India
| | - P K Dinesh Kumar
- CSIR-National Institute of Oceanography, Regional Centre Kochi, Dr Salim Ali Road, Post Box No. 1913, Kochi, Kerala, India
| | - P U Zacharia
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
| | - A Gopalakrishnan
- Marine Biotechnology Division, ICAR-Central Marine Fisheries Research Institute, Ernakulam North P.O., Kochi, Kerala, 682018, India
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5
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Abstract
Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.
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Affiliation(s)
- M. Lisette Delgado
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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6
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Zueva KJ, Lumme J, Veselov AE, Primmer CR, Pritchard VL. Population genomics reveals repeated signals of adaptive divergence in the Atlantic salmon of north‐eastern Europe. J Evol Biol 2020; 34:866-878. [DOI: 10.1111/jeb.13732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Affiliation(s)
| | - Jaakko Lumme
- Department of Biology University of Oulu Oulu Finland
| | | | - Craig R. Primmer
- Organismal and Evolutionary Biology Research Programme University of Helsinki Helsinki Finland
- Institute of Biotechnology University of Helsinki Helsinki Finland
| | - Victoria L. Pritchard
- Organismal and Evolutionary Biology Research Programme University of Helsinki Helsinki Finland
- Rivers and Lochs Institute Inverness College University of Highlands and Islands Inverness UK
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7
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Thorstensen MJ, Jeffrey JD, Treberg JR, Watkinson DA, Enders EC, Jeffries KM. Genomic signals found using RNA sequencing show signatures of selection and subtle population differentiation in walleye ( Sander vitreus) in a large freshwater ecosystem. Ecol Evol 2020; 10:7173-7188. [PMID: 32760520 PMCID: PMC7391302 DOI: 10.1002/ece3.6418] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/04/2020] [Accepted: 05/07/2020] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing is an effective approach for studying aquatic species yielding both physiological and genomic data. However, its population genetic applications are not well-characterized. We investigate this possible role for RNA sequencing for population genomics in Lake Winnipeg, Manitoba, Canada, walleye (Sander vitreus). Lake Winnipeg walleye represent the largest component of the second-largest freshwater fishery in Canada. In the present study, large female walleye were sampled via nonlethal gill biopsy over two years at three spawning sites representing a latitudinal gradient in the lake. Genetic variation from sequenced mRNA was analyzed for neutral and adaptive markers to investigate population structure and possible adaptive variation. We find low population divergence (F ST = 0.0095), possible northward gene flow, and outlier loci that vary latitudinally in transcripts associated with cell membrane proteins and cytoskeletal function. These results indicate that Lake Winnipeg walleye may be effectively managed as a single demographically connected metapopulation with contributing subpopulations and suggest genomic differences possibly underlying observed phenotypic differences. Despite its high cost relative to other genotyping methods, RNA sequencing data can yield physiological in addition to genetic information discussed here. We therefore argue that it is useful for addressing diverse molecular questions in the conservation of freshwater species.
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Affiliation(s)
| | | | - Jason R. Treberg
- Department of Biological SciencesUniversity of ManitobaWinnipegMBCanada
| | | | - Eva C. Enders
- Freshwater Institute, Fisheries and Oceans CanadaWinnipegMBCanada
| | - Ken M. Jeffries
- Department of Biological SciencesUniversity of ManitobaWinnipegMBCanada
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8
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Mobley KB, Granroth‐Wilding H, Ellmén M, Orell P, Erkinaro J, Primmer CR. Time spent in distinct life history stages has sex‐specific effects on reproductive fitness in wild Atlantic salmon. Mol Ecol 2020; 29:1173-1184. [DOI: 10.1111/mec.15390] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Kenyon B. Mobley
- Organismal and Evolutionary Biology Research Program Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
| | - Hanna Granroth‐Wilding
- Organismal and Evolutionary Biology Research Program Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
| | - Mikko Ellmén
- Department of Biology University of Turku Turku Finland
| | - Panu Orell
- Natural Resources Institute Finland (Luke) Oulu Finland
| | | | - Craig R. Primmer
- Organismal and Evolutionary Biology Research Program Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
- Institute for Biotechnology University of Helsinki Helsinki Finland
- Helsinki Institute of Sustainability Science University of Helsinki Helsinki Finland
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9
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Zhou Q, Su Z, Li Y, Liu Y, Wang L, Lu S, Wang S, Gan T, Liu F, Zhou X, Wei M, Liu G, Chen S. Genome-Wide Association Mapping and Gene Expression Analyses Reveal Genetic Mechanisms of Disease Resistance Variations in Cynoglossus semilaevis. Front Genet 2019; 10:1167. [PMID: 31824570 PMCID: PMC6880758 DOI: 10.3389/fgene.2019.01167] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 10/23/2019] [Indexed: 12/15/2022] Open
Abstract
The sustainable development of aquaculture has been impeded by infectious diseases worldwide. However, the genomic architecture and the genetic basis underlying the disease resistance remain poorly understood, which severely hampers both the understanding of the evolution of fish disease resistance traits and the prevention of these diseases in the aquaculture community. Cynoglossus semilaevis is a representative and commercially-important flatfish species. Here we combined genome-wide association study and Fst and nucleotide diversity filtration to identify loci important for the disease resistance. Based on 1,016,774 single-nucleotide polymorphisms (SNPs) identified from 650 Gb genome resequencing data of 505 individuals, we detected 33 SNPs significantly associated with disease resistance and 79 candidate regions after filtration steps. Both the allele frequencies and genotype frequencies of the associated loci were significantly different between the resistant and susceptible fish, suggesting a role in the genetic basis of disease resistance. The SNP with strongest association with disease resistance was located in Chr 17, at 145 bp upstream of fblx19 gene, and overlapped with the major quantitative trait locus previously identified. Several genes, such as plekha7, nucb2, and fgfr2, were also identified to potentially play roles in the disease resistance. Furthermore, the expression of some associating genes were likely under epigenetic regulations between the bacterial resistant and susceptible families. These results provide insights into the mechanism that enable variation of disease resistance to bacterial pathogen infection. The identified polymorphisms and genes are valuable targets and molecular resources for disease resistance and other traits, and for advanced breeding practice for superior germplasm in fish aquaculture.
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Affiliation(s)
- Qian Zhou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory for Marine Fishery Biotechnology and Genetic Breeding, Qingdao, China
| | - Zhencheng Su
- Novogene Bioinformatics Technology Co., Ltd, Beijing, China
| | - Yangzhen Li
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Yang Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Lei Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Sheng Lu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Shuanyan Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Tian Gan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Feng Liu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Xun Zhou
- Novogene Bioinformatics Technology Co., Ltd, Beijing, China
| | - Min Wei
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China
| | - Guangjian Liu
- Novogene Bioinformatics Technology Co., Ltd, Beijing, China
| | - Songlin Chen
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences/Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory for Marine Fishery Biotechnology and Genetic Breeding, Qingdao, China
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10
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Abstract
Salmon were among the first nonmodel species for which systematic population genetic studies of natural populations were conducted, often to support management and conservation. The genomics revolution has improved our understanding of the evolutionary ecology of salmon in two major ways: (a) Large increases in the numbers of genetic markers (from dozens to 104-106) provide greater power for traditional analyses, such as the delineation of population structure, hybridization, and population assignment, and (b) qualitatively new insights that were not possible with traditional genetic methods can be achieved by leveraging detailed information about the structure and function of the genome. Studies of the first type have been more common to date, largely because it has taken time for the necessary tools to be developed to fully understand the complex salmon genome. We expect that the next decade will witness many new studies that take full advantage of salmonid genomic resources.
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Affiliation(s)
- Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington 98112, USA;
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington 98195-5020, USA;
| | - Craig R Primmer
- Organismal & Evolutionary Biology Research Program and Biotechnology Institute, University of Helsinki, 00014 Helsinki, Finland;
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11
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Schmidt DJ, Huey JA, Hughes JM. Genome-Wide SNPs Identify Limits to Connectivity in the Extreme Freshwater Disperser, Spangled Perch Leiopotherapon unicolor (Terapontidae). J Hered 2019; 109:320-325. [PMID: 29228349 DOI: 10.1093/jhered/esx101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 11/10/2017] [Indexed: 12/31/2022] Open
Abstract
The utility of restriction-site associated DNA sequencing (RADseq) to resolve fine-scale population structure was tested on an abundant and vagile fish species in a tropical river. Australia's most widespread freshwater fish, the "extreme disperser" Leiopotherapon unicolor was sampled from 6 locations in an unregulated system, the Daly River in Australia's Northern Territory. Despite an expectation of high connectivity based on life history knowledge of this species derived from arid zone habitats, L. unicolor was not a panmictic population in the tropical lower Daly. Using ~14000 polymorphic RADseq loci, we found a pattern of upstream versus downstream population subdivision and evidence for differentiation among tributary populations. The magnitude of population structure was low with narrow confidence intervals (global FST = 0.014; 95% CI = 0.012-0.016). Confidence intervals around pairwise FST estimates were all nonzero and consistent with the results of clustering analyses. This population structure was not explained by spatially heterogeneous selection acting on a subset of loci, or by sampling groups of closely related individuals (average within-site relatedness ≈ 0). One implication of the low but significant structure observed in the tropics is the possibility that L. unicolor may exhibit contrasting patterns of migratory biology in tropical versus arid zone habitats. We conclude that the RADseq revolution holds promise for delineating subtle patterns of population subdivision in species characterized by high within-population variation and low among-population differentiation.
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Affiliation(s)
- Daniel J Schmidt
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia
| | - Joel A Huey
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia.,Terrestrial Zoology & Molecular Systematics Unit, Western Australian Museum, Welshpool, Western Australia, Australia
| | - Jane M Hughes
- Australian Rivers Institute, Griffith University, Nathan, Queensland, Australia
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12
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Mastrochirico-Filho VA, Del Pazo F, Hata ME, Villanova GV, Foresti F, Vera M, Martínez P, Porto-Foresti F, Hashimoto DT. Assessing Genetic Diversity for a Pre-Breeding Program in Piaractus mesopotamicus by SNPs and SSRs. Genes (Basel) 2019; 10:genes10090668. [PMID: 31480436 PMCID: PMC6771149 DOI: 10.3390/genes10090668] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/28/2019] [Accepted: 08/28/2019] [Indexed: 11/16/2022] Open
Abstract
The pacu (Piaractus mesopotamicus) is a Neotropical fish with remarkable productive performance for aquaculture. Knowledge of genetic resources in Neotropical fish is essential for their applications in breeding programs. The aim of this study was to characterize the genetic diversity of seven farmed populations of pacu which will constitute the basis for a broodstock foundation for coming breeding programs in Brazil. Analysis of one wild population (Paraná River) was used as a reference to compare genetic parameters in the farmed populations. The analyses were performed using 32 single-nucleotide polymorphisms (SNP) and 8 simple sequence repeat (SSR) markers. No significant differences in genetic diversity between populations estimated through the number of alleles and allelic richness, observed heterozygosity, expected heterozygosity, and minimum allele frequency were detected (p > 0.05). Low genetic diversity was observed in all farmed stocks and the wild population. Moreover, we detected low genetic structure when comparing farmed and wild populations for SNPs (FST = 0.07; K = 3) and SSRs (FST = 0.08; K = 2). Analysis of molecular variance (AMOVA) demonstrated that genetic variation was mostly within populations. Kinship analysis showed that most fish farms included related individuals at a proportion of at least 25%. Our results suggest that the basal broodstock for pacu breeding programs should be founded with individuals from different fish farms for higher genetic diversity and to avoid inbreeding risks.
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Affiliation(s)
| | - Felipe Del Pazo
- Laboratorio Mixto de Biotecnología Acuática - Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas - Ministerio de Ciencia, Tecnología e Innovación productiva de Santa Fe. Centro Científico y Tecnológico Acuario del Río Paraná, Rosario, Santa Fe 2000, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario, Santa Fe 2000, Argentina
| | - Milene Elissa Hata
- Aquaculture Center of Unesp, São Paulo State University (Unesp), Jaboticabal, SP 14884-900, Brazil
| | - Gabriela Vanina Villanova
- Laboratorio Mixto de Biotecnología Acuática - Universidad Nacional de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas - Ministerio de Ciencia, Tecnología e Innovación productiva de Santa Fe. Centro Científico y Tecnológico Acuario del Río Paraná, Rosario, Santa Fe 2000, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario, Santa Fe 2000, Argentina
| | - Fausto Foresti
- Institute of Biosciences, São Paulo State University (Unesp), Botucatu, SP 18618-970, Brazil
| | - Manuel Vera
- Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), ES27002 Lugo, Spain
- Instituto de Acuicultura, Universidad de Santiago de Compostela (USC), 15705 Santiago de Compostela, Spain
| | - Paulino Martínez
- Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), ES27002 Lugo, Spain
- Instituto de Acuicultura, Universidad de Santiago de Compostela (USC), 15705 Santiago de Compostela, Spain
| | - Fábio Porto-Foresti
- São Paulo State University (Unesp), School of Sciences, Bauru, SP 17033-360, Brazil
| | - Diogo Teruo Hashimoto
- Aquaculture Center of Unesp, São Paulo State University (Unesp), Jaboticabal, SP 14884-900, Brazil.
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13
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Aykanat T, Ozerov M, Vähä JP, Orell P, Niemelä E, Erkinaro J, Primmer CR. Co-inheritance of sea age at maturity and iteroparity in the Atlantic salmon vgll3 genomic region. J Evol Biol 2019; 32:343-355. [PMID: 30697850 DOI: 10.1101/412288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 12/03/2018] [Accepted: 01/24/2019] [Indexed: 05/25/2023]
Abstract
Co-inheritance in life-history traits may result in unpredictable evolutionary trajectories if not accounted for in life-history models. Iteroparity (the reproductive strategy of reproducing more than once) in Atlantic salmon (Salmo salar) is a fitness trait with substantial variation within and among populations. In the Teno River in northern Europe, iteroparous individuals constitute an important component of many populations and have experienced a sharp increase in abundance in the last 20 years, partly overlapping with a general decrease in age structure. The physiological basis of iteroparity bears similarities to that of age at first maturity, another life-history trait with substantial fitness effects in salmon. Sea age at maturity in Atlantic salmon is controlled by a major locus around the vgll3 gene, and we used this opportunity demonstrate that these two traits are co-inherited around this genome region. The odds ratio of survival until second reproduction was up to 2.4 (1.8-3.5 90% CI) times higher for fish with the early-maturing vgll3 genotype (EE) compared to fish with the late-maturing genotype (LL). The L allele was dominant in individuals remaining only one year at sea before maturation, but the dominance was reversed, with the E allele being dominant in individuals maturing after two or more years at sea. Post hoc analysis indicated that iteroparous fish with the EE genotype had accelerated growth prior to first reproduction compared to first-time spawners, across all age groups, whereas this effect was not detected in fish with the LL genotype. These results broaden the functional link around the vgll3 genome region and help us understand constraints in the evolution of life-history variation in salmon. Our results further highlight the need to account for genetic correlations between fitness traits when predicting demographic changes in changing environments.
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Affiliation(s)
- Tutku Aykanat
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Department of Biology, University of Turku, Turku, Finland
| | - Mikhail Ozerov
- Department of Biology, University of Turku, Turku, Finland
- Kevo Subarctic Research Institute, University of Turku, Turku, Finland
| | - Juha-Pekka Vähä
- Kevo Subarctic Research Institute, University of Turku, Turku, Finland
- Association for Water and Environment of Western Uusimaa, Lohja, Finland
| | - Panu Orell
- Natural Resources Institute Finland (Luke), Oulu, Finland
| | - Eero Niemelä
- Natural Resources Institute Finland (Luke), Oulu, Finland
| | | | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Helsinki Institute of Sustainability Science, University of Helsinki, Helsinki, Finland
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14
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Aykanat T, Ozerov M, Vähä J, Orell P, Niemelä E, Erkinaro J, Primmer CR. Co‐inheritance of sea age at maturity and iteroparity in the Atlantic salmonvgll3genomic region. J Evol Biol 2019; 32:343-355. [DOI: 10.1111/jeb.13418] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 12/03/2018] [Accepted: 01/24/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Tutku Aykanat
- Organismal and Evolutionary Biology Research ProgrammeUniversity of Helsinki Helsinki Finland
- Department of BiologyUniversity of Turku Turku Finland
| | - Mikhail Ozerov
- Department of BiologyUniversity of Turku Turku Finland
- Kevo Subarctic Research InstituteUniversity of Turku Turku Finland
| | - Juha‐Pekka Vähä
- Kevo Subarctic Research InstituteUniversity of Turku Turku Finland
- Association for Water and Environment of Western Uusimaa Lohja Finland
| | - Panu Orell
- Natural Resources Institute Finland (Luke) Oulu Finland
| | - Eero Niemelä
- Natural Resources Institute Finland (Luke) Oulu Finland
| | | | - Craig R. Primmer
- Organismal and Evolutionary Biology Research ProgrammeUniversity of Helsinki Helsinki Finland
- Institute of BiotechnologyUniversity of Helsinki Helsinki Finland
- Helsinki Institute of Sustainability ScienceUniversity of Helsinki Helsinki Finland
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15
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Mobley KB, Granroth-Wilding H, Ellmen M, Vähä JP, Aykanat T, Johnston SE, Orell P, Erkinaro J, Primmer CR. Home ground advantage: Local Atlantic salmon have higher reproductive fitness than dispersers in the wild. SCIENCE ADVANCES 2019; 5:eaav1112. [PMID: 30820455 PMCID: PMC6392789 DOI: 10.1126/sciadv.aav1112] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/14/2019] [Indexed: 05/04/2023]
Abstract
A long-held, but poorly tested, assumption in natural populations is that individuals that disperse into new areas for reproduction are at a disadvantage compared to individuals that reproduce in their natal habitat, underpinning the eco-evolutionary processes of local adaptation and ecological speciation. Here, we capitalize on fine-scale population structure and natural dispersal events to compare the reproductive success of local and dispersing individuals captured on the same spawning ground in four consecutive parent-offspring cohorts of wild Atlantic salmon (Salmo salar). Parentage analysis conducted on adults and juvenile fish showed that local females and males had 9.6 and 2.9 times higher reproductive success than dispersers, respectively. Our results reveal how higher reproductive success in local spawners compared to dispersers may act in natural populations to drive population divergence and promote local adaptation over microgeographic spatial scales without clear morphological differences between populations.
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Affiliation(s)
- Kenyon B. Mobley
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
- Corresponding author.
| | - Hanna Granroth-Wilding
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
- Department of Biology, University of Turku, Finland, Itäinen 10 Pitkäkatu 4, Turku FI-20520, Finland
| | - Mikko Ellmen
- Department of Biology, University of Turku, Finland, Itäinen 10 Pitkäkatu 4, Turku FI-20520, Finland
| | - Juha-Pekka Vähä
- Association for Water and Environment of Western Uusimaa, P.O. Box 51, FI-08101, Lohja, Finland
| | - Tutku Aykanat
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Susan E. Johnston
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Panu Orell
- Natural Resources Institute Finland (Luke), P.O. Box 413, FI-90014 Oulu, Finland
| | - Jaakko Erkinaro
- Natural Resources Institute Finland (Luke), P.O. Box 413, FI-90014 Oulu, Finland
| | - Craig R. Primmer
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
- Institute for Biotechnology, University of Helsinki, 00014 Helsinki, Finland
- Helsinki Institute of Sustainability Science, University of Helsinki, 00014 Helsinki, Finland
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16
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Wellband K, Mérot C, Linnansaari T, Elliott JAK, Curry RA, Bernatchez L. Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon. Mol Ecol 2018; 28:1439-1459. [PMID: 30506831 DOI: 10.1111/mec.14965] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/30/2022]
Abstract
Chromosomal inversions have been implicated in facilitating adaptation in the face of high levels of gene flow, but whether chromosomal fusions also have similar potential remains poorly understood. Atlantic salmon are usually characterized by population structure at multiple spatial scales; however, this is not the case for tributaries of the Miramichi River in North America. To resolve genetic relationships between populations in this system and the potential for known chromosomal fusions to contribute to adaptation, we genotyped 728 juvenile salmon using a 50 K SNP array. Consistent with previous work, we report extremely weak overall population structuring (Global FST = 0.004) and failed to support hierarchical structure between the river's two main branches. We provide the first genomic characterization of a previously described polymorphic fusion between chromosomes 8 and 29. Fusion genomic characteristics included high LD, reduced heterozygosity in the fused homokaryotes, and strong divergence between the fused and the unfused rearrangement. Population structure based on fusion karyotype was five times stronger than neutral variation (FST = 0.019), and the frequency of the fusion was associated with summer precipitation supporting a hypothesis that this rearrangement may contribute local adaptation despite weak neutral differentiation. Additionally, both outlier variation among populations and a polygenic framework for characterizing adaptive variation in relation to climate identified a 250-Kb region of chromosome 9, including the gene six6 that has previously been linked to age-at-maturity and run-timing for this species. Overall, our results indicate that adaptive processes, independent of major river branching, are more important than neutral processes for structuring these populations.
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Affiliation(s)
- Kyle Wellband
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Tommi Linnansaari
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - J A K Elliott
- Cooke Aquaculture Inc, Oak Bay, New Brunswick, Canada
| | - R Allen Curry
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
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Ősz Á, Horváth Á, Hoitsy G, Kánainé Sipos D, Keszte S, Sáfrány AJ, Marić S, Palkó C, Tóth B, Urbányi B, Kovács B. The genetic status of the Hungarian brown trout populations: exploration of a blind spot on the European map of Salmo trutta studies. PeerJ 2018; 6:e5152. [PMID: 30258703 PMCID: PMC6152457 DOI: 10.7717/peerj.5152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/11/2018] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Analyses of the control region sequences of European brown trout populations' mitrochondrial DNA have revealed five main evolutionary lineages (Atlantic, Danubian, Mediterranean, Adriatic, Marble) mostly relating to the main water basins; however, the hybridization between lineages were increasingly reported. Due to the hydrogeography of Hungary, wild populations should theoretically belong to the Danubian lineage, however, this has not been verified by genetic studies. METHODS In our study multiple molecular marker sets (mitochondrial sequence, microsatellites, PCR-RFLP of nuclear markers and sex marker) were used to investigate the genetic composition and population genetics of the brown trout populations in two broodstocks, six wild streams in Hungary and one Serbian population. RESULTS The admixture of Atlantic and Danubian lineages in these populations, except the Serbian population with pure Danubian origin, was observed by control region sequences of mitochondrial DNA and PCR-RFLP markers in the nuclear genome, and one unpublished Danubian haplotype was found in Hungarian populations. A sex-specific marker revealed equal gender ratio in broodstocks and Kemence stream, whereas in other wild streams the proportion of female individuals were less than 50%. Structure and principal component analyses based on the alleles of microsatellite loci also revealed overlapping populations, however the populations were still significantly different from each other and were mostly in Hardy-Weinberg equilibrium. DISCUSSION Stocking and migration can have a significant genetic impact on trout populations of wild streams, however there are no guidelines or common practices for stocking of small streams in Hungary, thus the genetic background of these populations should be considered when developing conservation actions.
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Affiliation(s)
- Ágnes Ősz
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Ákos Horváth
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | | | - Dóra Kánainé Sipos
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Szilvia Keszte
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Anna Júlia Sáfrány
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Saša Marić
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Csaba Palkó
- Department of Animal Nutrition, Institute of Animal Science, Faculty of Agricultural and Food Sciences, Széchenyi István University, Mosonmagyaróvár, Hungary
| | - Balázs Tóth
- Danube-Ipoly National Park Directorate, Budapest, Hungary
| | - Béla Urbányi
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Balázs Kovács
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
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18
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Almojil D, Cliff G, Spaet JLY. Weak population structure of the Spot-tail shark Carcharhinus sorrah and the Blacktip shark C. limbatus along the coasts of the Arabian Peninsula, Pakistan, and South Africa. Ecol Evol 2018; 8:9536-9549. [PMID: 30377521 PMCID: PMC6194305 DOI: 10.1002/ece3.4468] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 07/22/2018] [Accepted: 07/23/2018] [Indexed: 11/24/2022] Open
Abstract
The increase in demand for shark meat and fins has placed shark populations worldwide under high fishing pressure. In the Arabian region, the spot-tail shark Carcharhinus sorrah and the Blacktip shark Carcharhinus limbatus are among the most exploited species. In this study, we investigated the population genetic structure of C. sorrah (n = 327) along the coasts of the Arabian Peninsula and of C. limbatus (n = 525) along the Arabian coasts, Pakistan, and KwaZulu-Natal, South Africa, using microsatellite markers (15 and 11 loci, respectively). Our findings support weak population structure in both species. Carcharhinus sorrah exhibited a fine structure, subdividing the area into three groups. The first group comprises all samples from Bahrain, the second from the UAE and Yemen, and the third from Oman. Similarly, C. limbatus exhibited population subdivision into three groups. The first group, comprising samples from Bahrain and Kuwait, was highly differentiated from the second and third groups, comprising samples from Oman, Pakistan, the UAE, and Yemen; and South Africa and the Saudi Arabian Red Sea, respectively. Population divisions were supported by pairwise F ST values and discriminant analysis of principal components (DAPC), but not by STRUCTURE. We suggest that the mostly low but significant pairwise F ST values in our study are suggestive of fine population structure, which is possibly attributable to behavioral traits such as residency in C. sorrah and site fidelity and philopatry in C. limbatus. However, for all samples obtained from the northern parts of the Gulf (Bahrain and/or Kuwait) in both species, the higher but significant pairwise F ST values could possibly be a result of founder effects during the Tethys Sea closure. Based on DAPC and F ST results, we suggest each population to be treated as independent management unit, as conservation concerns emerge.
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Affiliation(s)
| | - Geremy Cliff
- KwaZulu‐Natal Shark BoardUmhlanga, South Africa and School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Julia L. Y. Spaet
- Department of ZoologyUniversity of CambridgeCambridgeUK
- Red Sea Research CenterDivision of Biological and Environmental Science and EngineeringKing Abdullah University of Science and TechnologyThuwalSaudi Arabia
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19
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Jorde PE, Andersson A, Ryman N, Laikre L. Are we underestimating the occurrence of sympatric populations? Mol Ecol 2018; 27:4011-4025. [PMID: 30137668 DOI: 10.1111/mec.14846] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 08/07/2018] [Indexed: 12/25/2022]
Abstract
Sympatric populations are conspecific populations that coexist spatially. They are of interest in evolutionary biology by representing the potential first steps of sympatric speciation and are important to identify and monitor in conservation management. Reviewing the literature pertaining to sympatric populations, we find that most cases of sympatry appear coupled to phenotypic divergence, implying ease of detection. In comparison, phenotypically cryptic, sympatric populations seem rarely documented. We explore the statistical power for detecting population mixtures from genetic marker data, using commonly applied tests for heterozygote deficiency (i.e., Wahlund effect) and the structure software, through computer simulations. We find that both tests are efficient at detecting population mixture only when genetic differentiation is high, sample size and number of genetic markers are reasonable and the sympatric populations happen to occur in similar proportions in the sample. We present an approximate expression based on these experimental factors for the lower limit of FST , beyond which power for structure collapses and only the heterozygote-deficiency tests retain some, although low, power. The findings suggest that cases of cryptic sympatry may have passed unnoticed in population genetic screenings using number of loci typical of the pre-genomics era. Hence, cryptic sympatric populations may be more common than hitherto thought, and we urge more attention being diverted to their detection and characterization.
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Affiliation(s)
| | - Anastasia Andersson
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Nils Ryman
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Linda Laikre
- Division of Population Genetics, Department of Zoology, Stockholm University, Stockholm, Sweden
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20
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Genomic signatures of parasite-driven natural selection in north European Atlantic salmon (Salmo salar). Mar Genomics 2018; 39:26-38. [DOI: 10.1016/j.margen.2018.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 12/16/2017] [Accepted: 01/08/2018] [Indexed: 02/06/2023]
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21
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Pritchard VL, Mäkinen H, Vähä JP, Erkinaro J, Orell P, Primmer CR. Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes. Mol Ecol 2018; 27:2560-2575. [DOI: 10.1111/mec.14705] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Hannu Mäkinen
- Department of Biology; University of Turku; Turku Finland
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | - Juha-Pekka Vähä
- Kevo Subarctic Research Institute; University of Turku; Turku Finland
| | | | - Panu Orell
- Natural Resources Institute Finland (LUKE); Oulu Finland
| | - Craig R. Primmer
- Department of Biology; University of Turku; Turku Finland
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Institute of Biotechnology; University of Helsinki; Helsinki Finland
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22
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Stojanova B, Šurinová M, Klápště J, Koláříková V, Hadincová V, Münzbergová Z. Adaptive differentiation of Festuca rubra along a climate gradient revealed by molecular markers and quantitative traits. PLoS One 2018; 13:e0194670. [PMID: 29617461 PMCID: PMC5884518 DOI: 10.1371/journal.pone.0194670] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 03/07/2018] [Indexed: 12/02/2022] Open
Abstract
Species response to climate change is influenced by predictable (selective) and unpredictable (random) evolutionary processes. To understand how climate change will affect present-day species, it is necessary to assess their adaptive potential and distinguish it from the effects of random processes. This will allow predicting how different genotypes will respond to forecasted environmental change. Space for time substitution experiments are an elegant way to test the response of present day populations to climate variation in real time. Here we assess neutral and putatively adaptive variation in 11 populations of Festuca rubra situated along crossed gradients of temperature and moisture using molecular markers and phenotypic measurements, respectively. By comparing population differentiation in putatively neutral molecular markers and phenotypic traits (QST-FST comparisons), we show the existence of adaptive differentiation in phenotypic traits and their plasticity across the climatic gradient. The observed patterns of differentiation are due to the high genotypic and phenotypic differentiation of the populations from the coldest (and wettest) environment. Finally, we observe statistically significant covariation between markers and phenotypic traits, which is likely caused by isolation by adaptation. These results contribute to a better understanding of the current adaptation and evolutionary potential to face climate change of a widespread species. They can also be extrapolated to understand how the studied populations will adjust to upcoming climate change without going through the lengthy process of phenotyping.
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Affiliation(s)
- Bojana Stojanova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Mária Šurinová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| | - Jaroslav Klápště
- Scion (New Zealand Forest Research Institute Ltd.), Whakarewarewa, Rotorua, New Zealand
| | - Veronika Koláříková
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Věroslava Hadincová
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
| | - Zuzana Münzbergová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic
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23
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Wollebaek J, Heggenes J, Roed KH. Life histories and ecotype conservation in an adaptive vertebrate: Genetic constitution of piscivorous brown trout covaries with habitat stability. Ecol Evol 2018; 8:2729-2745. [PMID: 29531690 PMCID: PMC5838037 DOI: 10.1002/ece3.3828] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 11/30/2017] [Accepted: 12/06/2017] [Indexed: 12/23/2022] Open
Abstract
Ecotype variation in species exhibiting different life history strategies may reflect heritable adaptations to optimize reproductive success, and potential for speciation. Traditionally, ecotypes have, however, been defined by morphometrics and life history characteristics, which may be confounded with individual plasticity. Here, we use the widely distributed and polytypic freshwater fish species brown trout (Salmo trutta) as a model to study piscivorous life history and its genetic characteristics in environmentally contrasting habitats; a large lake ecosystem with one major large and stable tributary, and several small tributaries. Data from 550 fish and 13 polymorphic microsatellites (He = 0.67) indicated ecotype-specific genetic differentiation (θ = 0.0170, p < .0001) among Bayesian assigned small riverine resident and large, lake migrating brown trout (>35 cm), but only in the large tributary. In contrast, large trout did not constitute a distinct genetic group in small tributaries, or across riverine sites. Whereas life history data suggest a small, river resident and a large migratory piscivorous ecotype in all studied tributaries, genetic data indicated that a genetically distinct piscivorous ecotype is more likely to evolve in the large and relatively more stable river habitat. In the smaller tributaries, ecotypes apparently resulted from individual plasticity. Whether different life histories and ecotypes result from individual plasticity or define different genetic types, have important consequence for conservation strategies.
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Affiliation(s)
- Jens Wollebaek
- Department of Natural Sciences and Environmental HealthThe University College of Southeast NorwayBø i TelemarkNorway
| | - Jan Heggenes
- Department of Natural Sciences and Environmental HealthThe University College of Southeast NorwayBø i TelemarkNorway
| | - Knut H. Roed
- Department of Basic Science & Aquatic MedicineThe Norwegian University of Life ScienceOsloNorway
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24
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Canales-Aguirre CB, Seeb LW, Seeb JE, Cádiz MI, Musleh SS, Arismendi I, Gajardo G, Galleguillos R, Gomez-Uchida D. Contrasting genetic metrics and patterns among naturalized rainbow trout ( Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture. Ecol Evol 2017; 8:273-285. [PMID: 29321870 PMCID: PMC5756871 DOI: 10.1002/ece3.3574] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 10/01/2017] [Accepted: 10/04/2017] [Indexed: 11/29/2022] Open
Abstract
Different pathways of propagation and dispersal of non‐native species into new environments may have contrasting demographic and genetic impacts on established populations. Repeated introductions of rainbow trout (Oncorhynchus mykiss) to Chile in South America, initially through stocking and later through aquaculture escapes, provide a unique setting to contrast these two pathways. Using a panel of single nucleotide polymorphisms, we found contrasting genetic metrics and patterns among naturalized trout in Lake Llanquihue, Chile's largest producer of salmonid smolts for nearly 50 years, and Lake Todos Los Santos (TLS), a reference lake where aquaculture has been prohibited by law. Trout from Lake Llanquihue showed higher genetic diversity, weaker genetic structure, and larger estimates for the effective number of breeders (Nb) than trout from Lake TLS. Trout from Lake TLS were divergent from Lake Llanquihue and showed marked genetic structure and a significant isolation‐by‐distance pattern consistent with secondary contact between documented and undocumented stocking events in opposite shores of the lake. Multiple factors, including differences in propagule pressure, origin of donor populations, lake geomorphology, habitat quality or quantity, and life history, may help explain contrasting genetic metrics and patterns for trout between lakes. We contend that high propagule pressure from aquaculture may not only increase genetic diversity and Nb via demographic effects and admixture, but also may impact the evolution of genetic structure and increase gene flow, consistent with findings from artificially propagated salmonid populations in their native and naturalized ranges.
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Affiliation(s)
- Cristian B Canales-Aguirre
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile.,Laboratorio de Genética y Acuicultura Departamento de Oceanografía Facultad de Ciencias Naturales y Oceanográficas Universidad de Concepción Concepción Chile.,Nucleo Milenio INVASAL Concepción Chile.,Centro i-mar Universidad de Los Lagos Camino Chinquihue 6 km Puerto Montt Chile
| | - Lisa W Seeb
- Nucleo Milenio INVASAL Concepción Chile.,School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - James E Seeb
- Nucleo Milenio INVASAL Concepción Chile.,School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - María I Cádiz
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile
| | - Selim S Musleh
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile.,Nucleo Milenio INVASAL Concepción Chile
| | - Ivan Arismendi
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad Universidad de Los Lagos Osorno Chile
| | - Ricardo Galleguillos
- Laboratorio de Genética y Acuicultura Departamento de Oceanografía Facultad de Ciencias Naturales y Oceanográficas Universidad de Concepción Concepción Chile
| | - Daniel Gomez-Uchida
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile.,Nucleo Milenio INVASAL Concepción Chile.,Centro i-mar Universidad de Los Lagos Camino Chinquihue 6 km Puerto Montt Chile
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25
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Population genomics of an endemic Mediterranean fish: differentiation by fine scale dispersal and adaptation. Sci Rep 2017; 7:43417. [PMID: 28262802 PMCID: PMC5338269 DOI: 10.1038/srep43417] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/24/2017] [Indexed: 12/04/2022] Open
Abstract
The assessment of the genetic structuring of biodiversity is crucial for management and conservation. For species with large effective population sizes a low number of markers may fail to identify population structure. A solution of this shortcoming can be high-throughput sequencing that allows genotyping thousands of markers on a genome-wide approach while facilitating the detection of genetic structuring shaped by selection. We used Genotyping-by-Sequencing (GBS) on 176 individuals of the endemic East Atlantic peacock wrasse (Symphodus tinca), from 6 locations in the Adriatic and Ionian seas. We obtained a total of 4,155 polymorphic SNPs and we observed two strong barriers to gene flow. The first one differentiated Tremiti Islands, in the northwest, from all the other locations while the second one separated east and south-west localities. Outlier SNPs potentially under positive selection and neutral SNPs both showed similar patterns of structuring, although finer scale differentiation was unveiled with outlier loci. Our results reflect the complexity of population genetic structure and demonstrate that both habitat fragmentation and positive selection are on play. This complexity should be considered in biodiversity assessments of different taxa, including non-model yet ecologically relevant organisms.
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26
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Piccolo JJ. Conservation genomics: coming to a salmonid near you. JOURNAL OF FISH BIOLOGY 2016; 89:2735-2740. [PMID: 27730637 DOI: 10.1111/jfb.13172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 09/08/2016] [Indexed: 06/06/2023]
Abstract
Using the examples on hereditary and environmental factors affecting salmonid populations, this paper demonstrates that ecologists have long appreciated the importance of local adaptation and intraspecific diversity for salmonid conservation. Conservationists, however, need to embrace the genomics revolution and use new insights to improve salmonid management. At the same time, researchers must be forthcoming with the uses and limitations of genomics, and conservation must move forward in the face of scientific uncertainty.
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Affiliation(s)
- J J Piccolo
- River Ecology and Management Group, Institute for Environmental and Life Sciences, Karlstad University, 651 88, Karlstad, Sweden
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27
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Aykanat T, Lindqvist M, Pritchard VL, Primmer CR. From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmon Salmo salar. JOURNAL OF FISH BIOLOGY 2016; 89:2658-2679. [PMID: 27709620 DOI: 10.1111/jfb.13149] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
A genotyping assay for the Ion Torrent Ion PGM platform was developed for fast and cost-effective targeted genotyping of key single nucleotide polymorphisms (SNPs) earlier identified using a genome-wide SNP array in Atlantic salmon Salmo salar. The method comprised a simple primer design step for multiplex-polymerase chain reaction (PCR), followed by two rounds of Ion Torrent Ion PGM sequencing to empirically evaluate marker efficiency in large multiplexes and to optimise or exclude them when necessary. Of 282 primer pairs initially tested, 217 were successfully amplified, indicating good amplification success (>75%). These markers included the sdy partial gene product to determine genetic sex, as well as three additional modules comprising SNPs for assessing neutral genetic variation (NSNP = 150), examining functional genetic variation associated with sea age at maturity (NSNP = 5), and for performing genetic subpopulation assignment (NSNP = 61). The assay was primarily developed to monitor long-term genetic changes in S. salar from the Teno River, but modules are likely suitable for application in a wide range of S. salar populations. Furthermore, the fast and versatile assay development pipeline offers a strategy for developing targeted sequencing assays in any species.
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Affiliation(s)
- T Aykanat
- Department of Biology, University of Turku, Turku, 20014, Finland
| | - M Lindqvist
- Department of Biology, University of Turku, Turku, 20014, Finland
| | - V L Pritchard
- Department of Biology, University of Turku, Turku, 20014, Finland
| | - C R Primmer
- Department of Biology, University of Turku, Turku, 20014, Finland
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28
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Pritchard VL, Erkinaro J, Kent MP, Niemelä E, Orell P, Lien S, Primmer CR. Single nucleotide polymorphisms to discriminate different classes of hybrid between wild Atlantic salmon and aquaculture escapees. Evol Appl 2016; 9:1017-31. [PMID: 27606009 PMCID: PMC4999531 DOI: 10.1111/eva.12407] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 06/07/2016] [Indexed: 12/14/2022] Open
Abstract
Many wild Atlantic salmon (Salmo salar) populations are threatened by introgressive hybridization from domesticated fish that have escaped from aquaculture facilities. A detailed understanding of the hybridization dynamics between wild salmon and aquaculture escapees requires discrimination of different hybrid classes; however, markers currently available to discriminate the two types of parental genome have limited power to do this. Using a high‐density Atlantic salmon single nucleotide polymorphism (SNP) array, in combination with pooled‐sample allelotyping and an Fst outlier approach, we identified 200 SNPs that differentiated an important Atlantic salmon stock from the escapees potentially hybridizing with it. By simulating multiple generations of wild–escapee hybridization, involving wild populations in two major phylogeographic lineages and a genetically diverse set of escapees, we showed that both the complete set of SNPs and smaller subsets could reliably assign individuals to different hybrid classes up to the third hybrid (F3) generation. This set of markers will be a useful tool for investigating the genetic interactions between native wild fish and aquaculture escapees in many Atlantic salmon populations.
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Affiliation(s)
| | | | - Matthew P Kent
- Centre for Integrative Genetics (CIGENE) Department of Animal and Aquacultural Sciences Norwegian University of Life Sciences Aas Norway
| | - Eero Niemelä
- Natural Resources Institute Finland (Luke) Utsjoki Finland
| | - Panu Orell
- Natural Resources Institute Finland (Luke) Utsjoki Finland
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE) Department of Animal and Aquacultural Sciences Norwegian University of Life Sciences Aas Norway
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29
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Richardson JL, Brady SP, Wang IJ, Spear SF. Navigating the pitfalls and promise of landscape genetics. Mol Ecol 2016; 25:849-63. [PMID: 26756865 DOI: 10.1111/mec.13527] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 12/12/2015] [Accepted: 01/07/2016] [Indexed: 12/17/2022]
Abstract
The field of landscape genetics has been evolving rapidly since its emergence in the early 2000s. New applications, techniques and criticisms of techniques appear like clockwork with each new journal issue. The developments are an encouraging, and at times bewildering, sign of progress in an exciting new field of study. However, we suggest that the rapid expansion of landscape genetics has belied important flaws in the development of the field, and we add an air of caution to this breakneck pace of expansion. Specifically, landscape genetic studies often lose sight of the fundamental principles and complex consequences of gene flow, instead favouring simplistic interpretations and broad inferences not necessarily warranted by the data. Here, we describe common pitfalls that characterize such studies, and provide practical guidance to improve landscape genetic investigation, with careful consideration of inferential limits, scale, replication, and the ecological and evolutionary context of spatial genetic patterns. Ultimately, the utility of landscape genetics will depend on translating the relationship between gene flow and landscape features into an understanding of long-term population outcomes. We hope the perspective presented here will steer landscape genetics down a more scientifically sound and productive path, garnering a field that is as informative in the future as it is popular now.
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Affiliation(s)
- Jonathan L Richardson
- Department of Biology, Providence College, 1 Cunningham Square, Providence, RI, 02918, USA
| | - Steven P Brady
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Ian J Wang
- Department of Environmental Science, Policy & Management, University of California, Berkeley, CA, 94720, USA
| | - Stephen F Spear
- The Orianne Society, 100 Phoenix Rd., Athens, GA, 30605, USA
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30
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Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon. Nature 2015; 528:405-8. [DOI: 10.1038/nature16062] [Citation(s) in RCA: 401] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/07/2015] [Indexed: 01/14/2023]
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