1
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Gross IP, Wilson AE, Wolak ME. The fitness consequences of wildlife conservation translocations: a meta-analysis. Biol Rev Camb Philos Soc 2024; 99:348-371. [PMID: 37844577 DOI: 10.1111/brv.13025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 10/01/2023] [Accepted: 10/04/2023] [Indexed: 10/18/2023]
Abstract
Conservation translocation is a common strategy to offset mounting rates of population declines through the transfer of captive- or wild-origin organisms into areas where conspecific populations are imperilled or completely extirpated. Translocations that supplement existing populations are referred to as reinforcements and can be conducted using captive-origin animals [ex situ reinforcement (ESR)] or wild-origin animals without any captive ancestry [in situ reinforcement (ISR)]. These programs have been criticized for low success rates and husbandry practices that produce individuals with genetic and performance deficits, but the post-release performance of captive-origin or wild-origin translocated groups has not been systematically reviewed to quantify success relative to wild-resident control groups. To assess the disparity in post-release performance of translocated organisms relative to wild-resident conspecifics and examine the association of performance disparity with organismal and methodological factors across studies, we conducted a systematic review and meta-analysis of 821 performance comparisons from 171 studies representing nine animal classes (101 species). We found that translocated organisms have 64% decreased odds of out-performing their wild-resident counterparts, supporting claims of systemic issues hampering conservation translocations. To help identify translocation practices that could maximize program success in the future, we further quantified the impact of broad organismal and methodological factors on the disparity between translocated and wild-resident conspecific performance. Pre-release animal enrichment significantly reduced performance disparities, whereas our results suggest no overall effects of taxonomic group, sex, captive generation time, or the type of fitness surrogate measured. This work is the most comprehensive systematic review to date of animal conservation translocations in which wild conspecifics were used as comparators, thereby facilitating an evaluation of the overall impact of this conservation strategy and identifying specific actions to increase success. Our review highlights the need for conservation managers to include both sympatric and allopatric wild-reference groups to ensure the post-release performance of translocated animals can be evaluated. Further, our analyses identify pre-release animal enrichment as a particular strategy for improving the outcomes of animal conservation translocations, and demonstrate how meta-analysis can be used to identify implementation choices that maximize translocated animal contributions to recipient population growth and viability.
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Affiliation(s)
- Iwo P Gross
- Department of Biological Sciences, Auburn University, 120 W. Samford Avenue, Auburn, AL, 36849, USA
| | - Alan E Wilson
- School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, 382 Mell Street, Auburn, AL, 36849, USA
| | - Matthew E Wolak
- Department of Biological Sciences, Auburn University, 120 W. Samford Avenue, Auburn, AL, 36849, USA
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2
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Osborne MJ, Archdeacon TP, Yackulic CB, Dudley RK, Caeiro-Dias G, Turner TF. Genetic erosion in an endangered desert fish during a megadrought despite long-term supportive breeding. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14154. [PMID: 37489292 DOI: 10.1111/cobi.14154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 06/08/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023]
Abstract
Human water use combined with a recent megadrought have reduced river and stream flow through the southwest United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande silvery minnow (Hybognathus amarus). This species is subject to boom-and-bust population dynamics, under which large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Rates of diversity loss are also affected by additions of hatchery-origin fish used to supplement the wild population. We used demographic and genetic data from wild and hatchery individuals to examine the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen's d = 1.34) and remained low despite hatchery stocking and brief wild population recovery. Across the time series, single-sample estimates of effective population size based on linkage disequilibrium (LD Ne ) were positively associated (r = 0.53) with wild abundance and total abundance, but as the proportion of hatchery-origin spawners increased, LD Ne declined (r = -0.55). Megadrought limited wild spawner abundance and precluded refreshment of hatchery brood stocks with wild fish; hence, we predict a riverine population increasingly dominated by hatchery-origin individuals and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought.
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Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
| | - Thomas P Archdeacon
- U.S. Fish and Wildlife Service, New Mexico Fish and Wildlife Conservation Office, Albuquerque, New Mexico, USA
| | - Charles B Yackulic
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, Arizona, USA
| | - Robert K Dudley
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
- American Southwest Ichthyological Researchers, Albuquerque, New Mexico, USA
| | - Guilherme Caeiro-Dias
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, MSC 03-2020, University of New Mexico, Albuquerque, New Mexico, USA
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3
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Rougemont Q, Leroy T, Rondeau EB, Koop B, Bernatchez L. Allele surfing causes maladaptation in a Pacific salmon of conservation concern. PLoS Genet 2023; 19:e1010918. [PMID: 37683018 PMCID: PMC10545117 DOI: 10.1371/journal.pgen.1010918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 10/02/2023] [Accepted: 08/11/2023] [Indexed: 09/10/2023] Open
Abstract
How various factors, including demography, recombination or genome duplication, may impact the efficacy of natural selection and the burden of deleterious mutations, is a central question in evolutionary biology and genetics. In this study, we show that key evolutionary processes, including variations in i) effective population size (Ne) ii) recombination rates and iii) chromosome inheritance, have influenced the genetic load and efficacy of selection in Coho salmon (Oncorhynchus kisutch), a widely distributed salmonid species on the west coast of North America. Using whole genome resequencing data from 14 populations at different migratory distances from their southern glacial refugium, we found evidence supporting gene surfing, wherein reduced Ne at the postglacial recolonization front, leads to a decrease in the efficacy of selection and a surf of deleterious alleles in the northernmost populations. Furthermore, our results indicate that recombination rates play a prime role in shaping the load along the genome. Additionally, we identified variation in polyploidy as a contributing factor to within-genome variation of the load. Overall, our results align remarkably well with expectations under the nearly neutral theory of molecular evolution. We discuss the fundamental and applied implications of these findings for evolutionary and conservation genomics.
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Affiliation(s)
- Quentin Rougemont
- Centre d’Ecologie Fonctionnelle et Evolutive, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Thibault Leroy
- GenPhySE, INRAE, INP, ENVT, Université de Toulouse, Auzeville- Tolosane, France
| | - Eric B. Rondeau
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, Canada
| | - Ben Koop
- Department of Biology, University of Victoria, Victoria, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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4
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Ropp AJ, Reece KS, Snyder RA, Song J, Biesack EE, McDowell JR. Fine-scale population structure of the northern hard clam ( Mercenaria mercenaria) revealed by genome-wide SNP markers. Evol Appl 2023; 16:1422-1437. [PMID: 37622097 PMCID: PMC10445094 DOI: 10.1111/eva.13577] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 08/26/2023] Open
Abstract
Aquaculture is growing rapidly worldwide, and sustainability is dependent on an understanding of current genetic variation and levels of connectivity among populations. Genetic data are essential to mitigate the genetic and ecological impacts of aquaculture on wild populations and guard against unintended human-induced loss of intraspecific diversity in aquacultured lines. Impacts of disregarding genetics can include loss of diversity within and between populations and disruption of local adaptation patterns, which can lead to a decrease in fitness. The northern hard clam, Mercenaria mercenaria (Linnaeus, 1758), is an economically valuable aquaculture species along the North American Atlantic and Gulf coasts. Hard clams have a pelagic larval phase that allows for dispersal, but the level of genetic connectivity among geographic areas is not well understood. To better inform the establishment of site-appropriate aquaculture brood stocks, this study used DArTseq™ genotyping by sequencing to characterize the genetic stock structure of wild clams sampled along the east coast of North America and document genetic diversity within populations. Samples were collected from 15 locations from Prince Edward Island, Canada, to South Carolina, USA. Stringent data filtering resulted in 4960 single nucleotide polymorphisms from 448 individuals. Five genetic breaks separating six genetically distinct populations were identified: Canada, Maine, Massachusetts, Mid-Atlantic, Chesapeake Bay, and the Carolinas (F ST 0.003-0.046; p < 0.0001). This is the first study to assess population genetic structure of this economically important hard clam along a large portion of its native range with high-resolution genomic markers, enabling identification of previously unrecognized population structure. Results of this study not only broaden insight into the factors shaping the current distribution of M. mercenaria but also reveal the genetic population dynamics of a species with a long pelagic larval dispersal period along the North American Atlantic and Gulf coasts.
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Affiliation(s)
- Ann J. Ropp
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Kimberly S. Reece
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Richard A. Snyder
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Jingwei Song
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Ellen E. Biesack
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Jan R. McDowell
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
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5
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Zheng S, Zhang T, Tu K, Li L, Liu Z, Wu B, Zhou L, Sun X. Population Genetics of Manila Clam ( Ruditapes philippinarum) in China Inferred from Microsatellite Markers. BIOLOGY 2023; 12:biology12040557. [PMID: 37106757 PMCID: PMC10135866 DOI: 10.3390/biology12040557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023]
Abstract
The Manila clam (Ruditapes philippinarum) is one of the most commercially important bivalves along the coast of China. With the continuous expansion of clam farming scale, it may lead to some serious problems, including loss of genetic variation, inbreeding depression, and reduced effective population size (Ne). In the present study, eleven microsatellite markers were used to investigate the genetic diversity and differentiation among 13 clam populations along the coast of China. As a result, 150 alleles were detected according to the genotyping results of eleven microsatellite loci. The observed heterozygosity (Ho) was estimated to be ranging from 0.437 to 0.678, while the expected heterozygosity (He) was calculated to be varying from 0.587 to 0.700. Fst values between populations ranged from 0.0046-0.1983. In particular, the Laizhou population had the highest genetic variability, which was significantly different from the others (all Fst values > 0.1). For all the clam populations, there was no significant linear regression between genetic and geographic distance, indicating that these populations do not follow a pattern of isolation by distance (IBD). Genetic structure was estimated according to NJ, principal coordinates (PCoA), and structure-based clustering. Estimates of effective population size range from dozens to thousands among different populations, based on linkage-disequilibrium and molecular coancestry methods. The results reveal the genetic diversity of clams and verify the hypothesis that clam population differentiation may be influenced by the mode of southern breeding and northern culture, providing guiding information for natural resource conservation and genetic breeding of clams.
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Affiliation(s)
- Sichen Zheng
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Tianshi Zhang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Kang Tu
- Putian Institute of Aquaculture Science of Fujian Province, Putian 351100, China
| | - Li Li
- National Oceanographic Center, Marine Science Research Institute of Shandong Province, Qingdao 266104, China
| | - Zhihong Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Biao Wu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Liqing Zhou
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiujun Sun
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
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6
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Appraising the Genetic Makeup of an Allochthonous Southern Pike Population: An Opportunity to Predict the Evolution of Introgressive Hybridization in Isolated Populations? Animals (Basel) 2023; 13:ani13030380. [PMID: 36766269 PMCID: PMC9913590 DOI: 10.3390/ani13030380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Biological invasions are a major threat to the conservation of biodiversity, as invasive species affect native biota through competition, predation, pathogen introduction, habitat alteration, and hybridisation. The present study focuses on a southern pike population, Esox cisalpinus (Teleostei: Esocidae), that has been introduced outside the species' native range. Using microsatellite markers, this study's objective was to gather baseline genetic information and assess the presence of hybrids between this species and E. lucius in the introduced population. The resulting estimates of genetic diversity and effective population size are comparable to those observed in the species' native range. Although different methods yield contrasting and uncertain evidence regarding introgressive hybridization, the presence of late-generation hybrids cannot be completely ruled out. Large numbers of breeders as well as multiple introductions of genetically divergent cohorts and introgressive hybridisation may explain the high genetic diversity of this recently introduced southern pike population. The present study issues a warning that the conservation of southern pike' introgressive hybridisation between northern and southern pike might be underestimated. The genetic information gathered herein may unravel the origin, number of introduction events, and evolutionary trajectory of the introduced population. This information may help us understand the evolution of introgressive hybridisation in the southern pike's native areas.
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7
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Xuereb A, Rougemont Q, Dallaire X, Moore J, Normandeau E, Bougas B, Perreault‐Payette A, Koop BF, Withler R, Beacham T, Bernatchez L. Re‐evaluating Coho salmon (
Oncorhynchus kisutch
) conservation units in Canada using genomic data. Evol Appl 2022; 15:1925-1944. [DOI: 10.1111/eva.13489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Amanda Xuereb
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Quentin Rougemont
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
- CEFE, Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS, Univ Montpellier, CNRS, EPHE, IRD Univ Paul Valéry Montpellier Montpellier France
| | - Xavier Dallaire
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Jean‐Sébastien Moore
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Eric Normandeau
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Bérénice Bougas
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Alysse Perreault‐Payette
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Ben F. Koop
- Department of Biology University of Victoria Victoria British Columbia Canada
| | - Ruth Withler
- Department of Fisheries and Ocean Pacific Biological Station Nanaimo British Columbia Canada
| | - Terry Beacham
- Department of Fisheries and Ocean Pacific Biological Station Nanaimo British Columbia Canada
| | - Louis Bernatchez
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
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8
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Dimond JL, Bouma JV, Carson HS, Gavery MR, O’Brien C, Simchick C, Sowul K. Efficacy of Endangered Pinto Abalone (Haliotis kamtschatkana) Stock Restoration in the Southern Salish Sea From a Genomic Perspective. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.911218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Declines in abalone populations throughout the world have led to conservation measures including fishery closures and captive breeding programs aimed at stock restoration. Restoration of endangered pinto abalone (Haliotis kamtschatkana) in the southern Salish Sea (Washington State, USA) began in the mid-2000s, and since 2009, nearly 40,000 hatchery-produced juvenile abalone have been outplanted at 21 restoration sites. We used genotyping by sequencing to evaluate the efficacy of this restoration program from a genomic standpoint. Over 49,000 SNPs and 8,000 haplotypes were evaluated across both wild and hatchery-produced abalone. Compared to wild abalone, hatchery-bred abalone had similar heterozygosity, lower allelic richness and effective population size, and higher relatedness. However, more recently bred hatchery progeny sampled prior to outplanting showed intermediate allelic richness, lower relatedness and genomic divergence, and higher effective population size compared to older hatchery outplants sampled after outplanting. We attribute these differences to genetic drift among older hatchery outplants due to mortality and emigration as well as larger numbers of broodstock families in more recent hatchery operations. This suggests that current hatchery practices that combine higher output with larger numbers of broodstock families may more effectively overcome the effects of genetic drift. Effective population size estimates among wild Salish Sea abalone had no upper limit, indicating that these abalone have sufficient genetic diversity to support the restoration program, but also highlighting the need for large broodstock sizes to overcome potential Ryman-Laikre effects. The greatest challenge for the future of the restoration program will be finding sufficient numbers of wild broodstock in the Salish Sea, where pinto abalone remain extremely rare.
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9
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Dimond JL, Crim RN, Unsell E, Barry V, Toft JE. Population genomics of the basket cockle
Clinocardium nuttallii
in the southern Salish Sea: Assessing genetic risks of stock enhancement for a culturally important marine bivalve. Evol Appl 2022; 15:459-470. [PMID: 35386400 PMCID: PMC8965374 DOI: 10.1111/eva.13359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/18/2022] [Accepted: 02/08/2022] [Indexed: 11/29/2022] Open
Abstract
Coastal Indigenous communities that rely on subsistence harvests are uniquely vulnerable to declines in nearshore species. The basket cockle Clinocardium nuttallii is among the favored foods of Indigenous people along the northwest Pacific coast of North America, yet localized declines in their abundance have led to interest in stock enhancement efforts. We used a population genomics approach to examine potential risks associated with stock enhancement of C. nuttallii in the southern Salish Sea, a large inland estuary that includes Puget Sound. More than 8000 single nucleotide polymorphisms across 349 individuals at 12 locations were assembled de novo using restriction site‐associated DNA sequencing. Results indicated that C. nuttallii within the southern Salish Sea were distinct from those along the outer Pacific coast (FST = 0.021–0.025). Within the southern Salish Sea, C. nuttallii populations appear to be well‐connected despite numerous potential impediments to gene flow; Hood Canal, which experiences the lowest flushing rates of all Puget Sound sub‐basins, was a minor exception to this strong connectivity. We found evidence of isolation by distance within the southern Salish Sea, but the slope of this relationship was shallow, and FST values were low (FST = 0.001–0.004). Meanwhile, outlier analyses did not support the hypothesis that southern Salish Sea sub‐populations are locally adapted. Estimates of effective population size had no upper bound, suggesting potentially very high adaptive capacity in C. nuttallii, but also making it difficult to assess potential reductions in effective population size resulting from stock enhancement. We present several strategies to augment cockle populations for subsistence harvest that would limit risk to the genetic diversity of wild cockle populations.
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Affiliation(s)
- James L. Dimond
- Puget Sound Restoration Fund 8001 Day Road West, Ste. B Bainbridge Island WA 98110 USA
- Western Washington University Shannon Point Marine Center 1900 Shannon Point Rd Anacortes WA 98221 USA
| | - Ryan N. Crim
- Puget Sound Restoration Fund 8001 Day Road West, Ste. B Bainbridge Island WA 98110 USA
| | - Elizabeth Unsell
- Suquamish Tribe Fisheries Department 18490 Suquamish Way Suquamish WA 98392 USA
| | - Viviane Barry
- Suquamish Tribe Fisheries Department 18490 Suquamish Way Suquamish WA 98392 USA
| | - Jodie E. Toft
- Puget Sound Restoration Fund 8001 Day Road West, Ste. B Bainbridge Island WA 98110 USA
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10
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Zhang YW, Pan XF, Wang XA, Fan W, Yang JX. Restocking of Anabarilius grahami in Lake Fuxian, Southwest China: morphological and genetic effects. Zool Res 2021; 41:741-747. [PMID: 33058573 PMCID: PMC7671908 DOI: 10.24272/j.issn.2095-8137.2020.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The restocking of the endangered Kanglang white minnow (Anabarilius grahami) in Lake Fuxian, China, has been conducted for 13 years. However, few studies have reported on the effectiveness of the captive breeding and release of this species. Here, we investigated variations in morphology, including body shape and skeletal deformities, and genetic features among hatchery-born and recaptured A. grahami from Lake Fuxian. Results showed that current hatchery-reared fish displayed a stubbier body shape than their wild conspecifics from the 1980s. Furthermore, high skeletal deformity ratios were found in two aquafarms (Luchong, 50%; Haikou, 45.2%), and the release of malformed fish elevated the skeletal deformity rate of wild stocks found near the Lake Fuxian release sites (west coast, 19.0%; east coast, 12.5%). Based on variations in the cytochrome b (cyt b) gene, existing A. grahami populations showed relatively high haplotype diversity and low nucleotide diversity. Hatchery populations exhibited reduced genetic variations based on microsatellite markers and reintroduction led to markedly lower genetic diversity around the west coast release sites of Lake Fuxian. Analysis of molecular variance (AMOVA) of cyt b and microsatellite analysis showed that the greatest genetic variations were found within populations, and genetic distance and Bayesian clustering analysis showed that the 14 populations clustered into one group. Based on morphological and genetic tests, we discuss corresponding recommendations, including release size, feed formulations, breeding strategies, and release tags, to minimize potential risks and improve hatchery practices for better restocking of this species.
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Affiliation(s)
- Yuan-Wei Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xiao-Fu Pan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xiao-Ai Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wei Fan
- Fisheries Technology Extension Station of Yunnan, Kunming, Yunnan 660034, China
| | - Jun-Xing Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Plateau Fish Breeding, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Engineering Research Center for Plateau-Lake Health and Restoration, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
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11
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Cossu P, Mura L, Scarpa F, Lai T, Sanna D, Azzena I, Fois N, Casu M. Genetic patterns in Mugil cephalus and implications for fisheries and aquaculture management. Sci Rep 2021; 11:2887. [PMID: 33536511 PMCID: PMC7859195 DOI: 10.1038/s41598-021-82515-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 01/18/2021] [Indexed: 01/30/2023] Open
Abstract
Exploitation of fisheries and aquaculture practices are exposing marine fish populations to increasing genetic risks. Therefore, the integration of genetic information into fisheries and aquaculture management is becoming crucial to ensure species' long-term persistence. The raising commercial value of grey mullet (Mugil cephalus) and its roe represents a growing challenge to the sustainable management of this economically important fishery resource. Here, microsatellites were used to investigate patterns of genetic variation in a Mediterranean area that harbor flourishing fisheries and practice semi-intensive farming of grey mullet. Genetic diversity within populations is smaller than values reported in previous studies as a result of the lower polymorphism displayed by the new microsatellite loci. Lack of genetic structuring points to the existence of a unique genetic stock, which is consistent with the species' high dispersal capabilities. Nonetheless, differences in local population effective size as well as the excess of related individuals do not completely fit the picture of a large panmictic population. Baseline genetic information here gathered will allow to set up the genetic monitoring of regional fish stocks, which is needed to assess the impact of both harvesting and aquaculture on the genetic integrity of Mugil cephalus wild populations.
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Affiliation(s)
- Piero Cossu
- grid.11450.310000 0001 2097 9138Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy ,grid.11450.310000 0001 2097 9138Department of Veterinary Medicine, University of Sassari, Sassari, SS Italy
| | - Laura Mura
- Dipartimento per la Ricerca Nelle Produzioni Animali, Agris Sardegna, Olmedo, SS Italy
| | - Fabio Scarpa
- grid.11450.310000 0001 2097 9138Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy ,grid.11450.310000 0001 2097 9138Department of Veterinary Medicine, University of Sassari, Sassari, SS Italy
| | - Tiziana Lai
- grid.11450.310000 0001 2097 9138Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy
| | - Daria Sanna
- grid.11450.310000 0001 2097 9138Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy ,grid.11450.310000 0001 2097 9138Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Ilenia Azzena
- grid.11450.310000 0001 2097 9138Department of Veterinary Medicine, University of Sassari, Sassari, SS Italy ,grid.11450.310000 0001 2097 9138Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Nicola Fois
- Dipartimento per la Ricerca Nelle Produzioni Animali, Agris Sardegna, Olmedo, SS Italy
| | - Marco Casu
- grid.11450.310000 0001 2097 9138Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy ,grid.11450.310000 0001 2097 9138Department of Veterinary Medicine, University of Sassari, Sassari, SS Italy
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12
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Jansson E, Besnier F, Malde K, André C, Dahle G, Glover KA. Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations. BMC Genet 2020; 21:118. [PMID: 33036553 PMCID: PMC7547435 DOI: 10.1186/s12863-020-00921-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022] Open
Abstract
Background Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (FST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean FST_173_loci = 0.065, FST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.
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Affiliation(s)
- Eeva Jansson
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway.
| | - Francois Besnier
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Ketil Malde
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Carl André
- Department of Marine Sciences-Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Geir Dahle
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway.,Institute of Biology, University of Bergen, P. O. Box 7803, 5020, Bergen, Norway
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13
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Barros J, Winkler FM, Velasco LA. Assessing the genetic diversity in Argopecten nucleus (Bivalvia: Pectinidae), a functional hermaphrodite species with extremely low population density and self-fertilization: Effect of null alleles. Ecol Evol 2020; 10:3919-3931. [PMID: 32489620 PMCID: PMC7244797 DOI: 10.1002/ece3.6080] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 11/15/2022] Open
Abstract
Argopecten nucleus is a functional hermaphroditic pectinid species that exhibits self-fertilization, whose natural populations have usually very low densities. In the present study, the genetic diversity of a wild population from Neguanje Bay, Santa Marta (Colombia), was estimated using microsatellite markers, and the effect of the presence of null alleles on this estimation was assessed. A total of 8 microsatellite markers were developed, the first described for this species, and their amplification conditions were standardized. They were used to determine the genotype of 48 wild individuals from Naguanje Bay, and 1,010 individuals derived from the offspring of 38 directed crosses. For each locus, the frequencies of the identified alleles, including null alleles, were estimated using the statistical package Micro-Checker, and the parental genotypes were confirmed using segregation analysis. Three to 8 alleles per locus with frequencies from 0.001 to 0.632 were detected. The frequencies of null alleles ranged from 0.10 to 0.45, with Ho from 0.0 to 0.79, and He from 0.53 to 0.80. All loci were in H-W disequilibrium. The null allele frequencies values were high, with lower estimations using segregation analysis than estimated using Micro-Checker. The present results show high levels of population genetic diversity and indicate that null alleles were not the only cause of deviation from H-W equilibrium in all loci, suggesting that the wild population under study presents signs of inbreeding and Wahlund effect.
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Affiliation(s)
- Judith Barros
- Laboratorio de Moluscos y MicroalgasUniversidad del MagdalenaSanta MartaColombia
| | - Federico M. Winkler
- Departamento de Biología MarinaFacultad de Ciencias del MarUniversidad Católica del NorteCoquimboChile
- Centro de Innovación Acuícola AquaPacíficoCoquimboChile
- Centro de Estudios Avanzados en Zona Áridas (CEAZA)CoquimboChile
| | - Luz Adriana Velasco
- Laboratorio de Moluscos y MicroalgasUniversidad del MagdalenaSanta MartaColombia
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14
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Molnár T, Benedek I, Kovács B, Zsolnai A, Lehoczky I. Genetic consequences of pond production of a pikeperch ( Sander lucioperca L.) stock with natural origin: the effects of changed selection pressure and reduced population size. PeerJ 2020; 8:e8745. [PMID: 32211234 PMCID: PMC7083162 DOI: 10.7717/peerj.8745] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 02/13/2020] [Indexed: 11/20/2022] Open
Abstract
The pikeperch (Sander lucioperca L.) possesses great potential for diversifying European aquaculture. However, studies on the genetic risk of stocking natural waters with farmed individuals of this species have been limited. Even the effect of pond culture on the genetic composition of stocks with natural-origin has not yet been determined. Our study aimed to compare the genetic variability of a wild living pikeperch population, a pond cultured broodstock (originating from the wild population) and its offspring generation. We also aimed to detect the potential signs of selection using three different methods. By analyzing the molecular data with 14 microsatellite markers, we illustrated that the impact of pond culture on the genetic diversity of fish stocks is similar to hatchery rearing due to its diversity reducing effect caused by using lower effective population sizes. Although the heterozygosity was similar in all populations (Ho = 0.68–0.71), the average number of alleles and allelic richness were significantly lower in the pond cultured stocks (NA = 7.5 and 6; AR = 7.5 and 5.9) compared to the wild population (NA = 11.00, AR = 10.47). Despite the semi-natural conditions of the present study, we detected changing selection pressure in one of the 14 microsatellite markers.
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Affiliation(s)
- Tamás Molnár
- Institute of Environmental Sciences and Nature Conservation, Kaposvár University, Kaposvár, Hungary.,Department of Aquaculture, Szent István University, Gödöllő, Hungary.,Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, Gödöllő, Hungary
| | - Ildikó Benedek
- Institute of Environmental Sciences and Nature Conservation, Kaposvár University, Kaposvár, Hungary
| | - Balázs Kovács
- Department of Aquaculture, Szent István University, Gödöllő, Hungary
| | - Attila Zsolnai
- Research Institute for Animal Breeding, Nutrition and Meat Science (ATHK), National Agricultural Research and Innovation Centre, Herceghalom, Hungary
| | - István Lehoczky
- Institute for Farm Animal Gene Conservation, National Centre for Biodiversity and Gene Conservation, Gödöllő, Hungary
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15
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Hornick KM, Plough LV. Tracking genetic diversity in a large-scale oyster restoration program: effects of hatchery propagation and initial characterization of diversity on restored vs. wild reefs. Heredity (Edinb) 2019; 123:92-105. [PMID: 30833745 PMCID: PMC6781163 DOI: 10.1038/s41437-019-0202-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/18/2019] [Accepted: 02/11/2019] [Indexed: 01/25/2023] Open
Abstract
The release of hatchery-propagated fish and shellfish is occurring on a global scale, but the genetic impacts of these practices are often not fully understood and rarely monitored. Slow recovery of depleted eastern oyster populations in the Chesapeake Bay, USA has prompted a hatchery-based restoration program focused in the Choptank River, Maryland consisting of the mass release of hatchery-produced juveniles from local, wild broodstock. To evaluate potential genetic effects of this program, we (1) examined changes in genetic diversity (allelic richness, heterozygosity) and the effective number of breeders (Nb) over the hatchery production cycle with microsatellite-based parentage of natural, mass- and controlled-spawned cohorts, and (2) compared genetic diversity and effective population size (Ne) of a restored reef to wild source populations. Mass-spawned cohorts showed high variance in reproductive contribution, particularly among males, leading to a 45% average reduction in Nb from spawning adult numbers and higher relatedness-lower magnitude reductions in heterozygosity and significant reductions in allelic richness were also observed. While controlled-spawns (single-male fertilizations of pooled eggs) reduced male variance, overall reproductive variance (Vk) remained high. Finally, oysters sampled from a restored reef displayed comparable Ne, genetic diversity, and relatedness to samples from wild populations, with no significant genetic differentiation among them. Overall, the hatchery-based results and initial field-based population genetic analyses suggest that despite reductions in diversity from parents to offspring owing to high Vk, enhancement with rotated, wild broodstock appears to have maintained genetic diversity in a restored reef population compared to proximal wild populations.
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Affiliation(s)
- Katherine M Hornick
- University of Maryland Center for Environmental Science, Horn Point Laboratory, 2020 Horns Pt. Rd., Cambridge, MD, 21613, USA.
| | - Louis V Plough
- University of Maryland Center for Environmental Science, Horn Point Laboratory, 2020 Horns Pt. Rd., Cambridge, MD, 21613, USA
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16
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Crozier LG, McClure MM, Beechie T, Bograd SJ, Boughton DA, Carr M, Cooney TD, Dunham JB, Greene CM, Haltuch MA, Hazen EL, Holzer DM, Huff DD, Johnson RC, Jordan CE, Kaplan IC, Lindley ST, Mantua NJ, Moyle PB, Myers JM, Nelson MW, Spence BC, Weitkamp LA, Williams TH, Willis-Norton E. Climate vulnerability assessment for Pacific salmon and steelhead in the California Current Large Marine Ecosystem. PLoS One 2019; 14:e0217711. [PMID: 31339895 PMCID: PMC6655584 DOI: 10.1371/journal.pone.0217711] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/16/2019] [Indexed: 12/25/2022] Open
Abstract
Major ecological realignments are already occurring in response to climate change. To be successful, conservation strategies now need to account for geographical patterns in traits sensitive to climate change, as well as climate threats to species-level diversity. As part of an effort to provide such information, we conducted a climate vulnerability assessment that included all anadromous Pacific salmon and steelhead (Oncorhynchus spp.) population units listed under the U.S. Endangered Species Act. Using an expert-based scoring system, we ranked 20 attributes for the 28 listed units and 5 additional units. Attributes captured biological sensitivity, or the strength of linkages between each listing unit and the present climate; climate exposure, or the magnitude of projected change in local environmental conditions; and adaptive capacity, or the ability to modify phenotypes to cope with new climatic conditions. Each listing unit was then assigned one of four vulnerability categories. Units ranked most vulnerable overall were Chinook (O. tshawytscha) in the California Central Valley, coho (O. kisutch) in California and southern Oregon, sockeye (O. nerka) in the Snake River Basin, and spring-run Chinook in the interior Columbia and Willamette River Basins. We identified units with similar vulnerability profiles using a hierarchical cluster analysis. Life history characteristics, especially freshwater and estuary residence times, interplayed with gradations in exposure from south to north and from coastal to interior regions to generate landscape-level patterns within each species. Nearly all listing units faced high exposures to projected increases in stream temperature, sea surface temperature, and ocean acidification, but other aspects of exposure peaked in particular regions. Anthropogenic factors, especially migration barriers, habitat degradation, and hatchery influence, have reduced the adaptive capacity of most steelhead and salmon populations. Enhancing adaptive capacity is essential to mitigate for the increasing threat of climate change. Collectively, these results provide a framework to support recovery planning that considers climate impacts on the majority of West Coast anadromous salmonids.
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Affiliation(s)
- Lisa G. Crozier
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
- * E-mail:
| | - Michelle M. McClure
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Tim Beechie
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Steven J. Bograd
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Monterey, California, United States of America
| | - David A. Boughton
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, United States of America
| | - Mark Carr
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, United States of America
| | - Thomas D. Cooney
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Jason B. Dunham
- Forest & Rangeland Ecosystem Science Center, U.S. Geological Survey, Corvallis, Oregon, United States of America
| | - Correigh M. Greene
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Melissa A. Haltuch
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Elliott L. Hazen
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Monterey, California, United States of America
| | - Damon M. Holzer
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - David D. Huff
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Rachel C. Johnson
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, United States of America
- Center for Watershed Sciences, University of California, Davis, California, United States of America
| | - Chris E. Jordan
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Isaac C. Kaplan
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Steven T. Lindley
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, United States of America
| | - Nathan J. Mantua
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, United States of America
| | - Peter B. Moyle
- Department of Wildlife, Fish and Conservation Biology, University of California, Davis, California, United States of America
| | - James M. Myers
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Mark W. Nelson
- ECS Federal, Inc. Under Contract to Office of Sustainable Fisheries, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Silver Spring, Maryland, United States of America
| | - Brian C. Spence
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, United States of America
| | - Laurie A. Weitkamp
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, United States of America
| | - Thomas H. Williams
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, United States of America
| | - Ellen Willis-Norton
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, California, United States of America
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17
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Cossu P, Scarpa F, Sanna D, Lai T, Dedola GL, Curini-Galletti M, Mura L, Fois N, Casu M. Influence of genetic drift on patterns of genetic variation: The footprint of aquaculture practices in Sparus aurata (Teleostei: Sparidae). Mol Ecol 2019; 28:3012-3024. [PMID: 31125994 DOI: 10.1111/mec.15134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 11/30/2022]
Abstract
Aquaculture finfish production based on floating cage technology has raised increasing concerns regarding the genetic integrity of natural populations. Accidental mass escapes can induce the loss of genetic diversity in wild populations by increasing genetic drift and inbreeding. Farm escapes probably represent an important issue in the gilthead sea bream (Sparus aurata), which accounted for 76.4% of total escapees recorded in Europe during a 3-year survey. Here, we investigated patterns of genetic variation in farmed and wild populations of gilthead sea bream from the Western Mediterranean, a region of long gilthead sea bream farming. We focused on the role that genetic drift may play in shaping these patterns. Results based on microsatellite markers matched those observed in previous studies. Farmed populations showed lower levels of genetic diversity than wild populations and were genetically divergent from their wild counterparts. Overall, farmed populations showed the smallest effective population size and increased levels of relatedness compared to wild populations. The small broodstock size coupled with breeding practices that may favour the variance in individual reproductive success probably boosted genetic drift. This factor appeared to be a major driver of the genetic patterns observed in the gilthead sea bream populations analysed in the present study. These results further stress the importance of recommendations aimed at maintaining broodstock sizes as large as possible and equal sex-ratios among breeders, as well as avoiding unequal contributions among parents.
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Affiliation(s)
- Piero Cossu
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Fabio Scarpa
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Daria Sanna
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Tiziana Lai
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Gian Luca Dedola
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy
| | - Marco Curini-Galletti
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Laura Mura
- AGRIS Sardegna, Servizio Ricerca Prodotti Ittici, Olmedo, Italy
| | - Nicola Fois
- AGRIS Sardegna, Servizio Ricerca Prodotti Ittici, Olmedo, Italy
| | - Marco Casu
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
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18
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Rougemont Q, Carrier A, Le Luyer J, Ferchaud A, Farrell JM, Hatin D, Brodeur P, Bernatchez L. Combining population genomics and forward simulations to investigate stocking impacts: A case study of Muskellunge ( Esox masquinongy) from the St. Lawrence River basin. Evol Appl 2019; 12:902-922. [PMID: 31080504 PMCID: PMC6503833 DOI: 10.1111/eva.12765] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 12/17/2018] [Indexed: 01/03/2023] Open
Abstract
Understanding the genetic and evolutionary impacts of stocking on wild fish populations has long been of interest as negative consequences such as reduced fitness and loss of genetic diversity are commonly reported outcomes. In an attempt to sustain a fishery, managers implemented nearly five decades of extensive stocking of over a million Muskellunge (Esox masquinongy), a native species in the Lower St. Lawrence River (Québec, Canada). We investigated the effect of this stocking on population genetic structure and allelic diversity in the St. Lawrence River in addition to tributaries and several stocked inland lakes. Using genotype by sequencing, we genotyped 643 individuals representing 22 locations and combined this information with forward simulations to investigate the genetic consequences of long-term stocking. Individuals native to the St. Lawrence watershed were genetically differentiated from stocking sources and tributaries, and inland lakes were naturally differentiated from the main river. Empirical data and simulations within the St. Lawrence River revealed weak stocking effects on admixture patterns. Our data suggest that the genetic structure associated with stocked fish was diluted into its relatively large effective population size. This interpretation is also consistent with a hypothesis that selection against introgression was in operation and relatively efficient within the large St. Lawrence River system. In contrast, smaller populations from adjacent tributaries and lakes displayed greater stocking-related admixture that resulted in comparatively higher heterozygosity than the St. Lawrence. Finally, individuals from inland lakes that were established by stocking maintained a close affinity with their source populations. This study illustrated a benefit of combining extensive genomic data with forward simulations for improved inference regarding population-level genetic effects of long-term stocking, and its relevance for fishery management decision making.
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Affiliation(s)
- Quentin Rougemont
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Anne Carrier
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Jeremy Le Luyer
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
- IFREMER, Unité Ressources Marines en Polynésie, Centre Océanologique du PacifiqueTaravao, TahitiFrench Polynesia
| | - Anne‐Laure Ferchaud
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - John M. Farrell
- Department of Environmental and Forest Biology, College of Environmental Science and ForestryState University of New YorkSyracuseNew York
| | - Daniel Hatin
- Ministère des Forêts, de la Faune et des Parcs, Direction de la Gestion de la FauneEstrie‐Montréal‐Montérégie‐LavalLongueuilQuébecCanada
| | - Philippe Brodeur
- Ministère des Forêts, de la Faune et des ParcsDirection de la gestion de la faune de la Mauricie et du Centre‐du‐QuébecTrois‐RivièresQuebecCanada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
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19
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Kitada S, Nakajima K, Hamasaki K, Shishidou H, Waples RS, Kishino H. Rigorous monitoring of a large-scale marine stock enhancement program demonstrates the need for comprehensive management of fisheries and nursery habitat. Sci Rep 2019; 9:5290. [PMID: 30918306 PMCID: PMC6437203 DOI: 10.1038/s41598-019-39050-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 01/16/2019] [Indexed: 12/16/2022] Open
Abstract
Release of captively-bred individuals into the wild is one of the most popular tools in fisheries, forestry, and wildlife management, and introgression of hatchery-reared animals into wild populations is of global concern. However, research and monitoring of impacts on wild populations are generally lacking, and the benefit of hatcheries for long-term fisheries and conservation goals is unclear. Using spatio-temporal genetic monitoring and a four-dacade time series of catch data, we quantified the effects on the size and genetic diversity of wild populations of one of the world’s largest marine stock enhancement programs–the red sea bream (Pagrus major) in Kagoshima Bay, Japan. Our analyses found that the stock enhancement program reduced genetic diversity of the population, but the genetic effect diminished with increased size of the wild population. Increases to the seaweed communities and reduced fishing efforts were the primary factors associated with the wild population recovery; effects of aquaculture were much smaller. Our results represent crucial evidence that hatcheries for enhancement and conservation of populations cannot be successful over the long term unless sufficient efforts are also made to reduce harvest rates and rehabilitate natural habitats.
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Affiliation(s)
- Shuichi Kitada
- Tokyo University of Marine Science and Technology, Tokyo, 108-8477, Japan.
| | - Kaori Nakajima
- Tokyo University of Marine Science and Technology, Tokyo, 108-8477, Japan
| | - Katsuyuki Hamasaki
- Tokyo University of Marine Science and Technology, Tokyo, 108-8477, Japan
| | - Hirotoshi Shishidou
- Kagoshima Prefectural Fisheries Technology and Development Center, Kagoshima, 891-0315, Japan
| | - Robin S Waples
- Northwest Fisheries Science Center, NOAA, Seattle, WA, 98112, USA
| | - Hirohisa Kishino
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
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20
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Hard JJ. Robin S. Waples—Recipient of the 2018 Molecular Ecology Prize. Mol Ecol 2019; 28:29-32. [DOI: 10.1111/mec.14959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 11/09/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Jeffrey J. Hard
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service National Oceanic and Atmospheric Administration Seattle Washington
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21
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Eldon B, Riquet F, Yearsley J, Jollivet D, Broquet T. Current hypotheses to explain genetic chaos under the sea. Curr Zool 2016; 62:551-566. [PMID: 29491945 PMCID: PMC5829445 DOI: 10.1093/cz/zow094] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 08/27/2016] [Indexed: 01/07/2023] Open
Abstract
Chaotic genetic patchiness (CGP) refers to surprising patterns of spatial and temporal genetic structure observed in some marine species at a scale where genetic variation should be efficiently homogenized by gene flow via larval dispersal. Here we review and discuss 4 mechanisms that could generate such unexpected patterns: selection, sweepstakes reproductive success, collective dispersal, and temporal shifts in local population dynamics. First, we review examples where genetic differentiation at specific loci was driven by diversifying selection, which was historically the first process invoked to explain CGP. Second, we turn to neutral demographic processes that may drive genome-wide effects, and whose effects on CGP may be enhanced when they act together. We discuss how sweepstakes reproductive success accelerates genetic drift and can thus generate genetic structure, provided that gene flow is not too strong. Collective dispersal is another mechanism whereby genetic structure can be maintained regardless of dispersal intensity, because it may prevent larval cohorts from becoming entirely mixed. Theoretical analyses of both the sweepstakes and the collective dispersal ideas are presented. Finally, we discuss an idea that has received less attention than the other ones just mentioned, namely temporal shifts in local population dynamics.
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Affiliation(s)
- Bjarki Eldon
- Museum für Naturkunde Berlin, Leibniz Institut für Evolutions- und
Biodiversitätsforschung, Berlin 10115, Germany
| | - Florentine Riquet
- Université Montpellier 2, Place Eugène Bataillon, 34095 Montpellier Cedex 5,
France
- ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, Sète 34200, France
| | - Jon Yearsley
- School of Biology and Environmental Science and UCD Earth Institute,
University College Dublin, Belfield, Dublin 4, Ireland
| | - Didier Jollivet
- Centre National de la Recherche Scientifique, Team Adaptation and Biology of
Invertebrates in Extreme Environments, Station Biologique de Roscoff, Roscoff 29680,
France
- Sorbonne Universités, Université Pierre et Marie Curie, Unité Mixte de
Recherche 7144, Station Biologique de Roscoff, Roscoff 29680, France
| | - Thomas Broquet
- Sorbonne Universités, Université Pierre et Marie Curie, Unité Mixte de
Recherche 7144, Station Biologique de Roscoff, Roscoff 29680, France
- Centre National de la Recherche Scientifique, Team Diversity and
Connectivity of Coastal Marine Landscapes, Station Biologique de Roscoff, Roscoff 29680,
France
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22
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Bierne N, Bonhomme F, Arnaud-Haond S. Dedicated population genomics for the silent world: the specific questions of marine population genetics. Curr Zool 2016; 62:545-550. [PMID: 29491944 PMCID: PMC5804263 DOI: 10.1093/cz/zow107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Nicolas Bierne
- Université de Montpellier, Montpellier, France
- CNRS – Institut des Sciences de l’Evolution Montpellier, UMR 5554 UM – CNRS
– IRD – EPHE, Station Marine OREME, Sète, France
| | - François Bonhomme
- Université de Montpellier, Montpellier, France
- CNRS – Institut des Sciences de l’Evolution Montpellier, UMR 5554 UM – CNRS
– IRD – EPHE, Station Marine OREME, Sète, France
| | - Sophie Arnaud-Haond
- Université de Montpellier, Montpellier, France
- Ifremer – MARine Biodiversity, Exploitation and Conservation, UMR 9190 IRD –
IFREMER – UM – CNRS, Sète, France
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