1
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Bertram A, Bell J, Brauer C, Fairclough D, Hamer P, Sandoval‐Castillo J, Wellenreuther M, Beheregaray LB. Estimation of effective number of breeders and effective population size in an abundant and heavily exploited marine teleost. Evol Appl 2024; 17:e13758. [PMID: 39040813 PMCID: PMC11261160 DOI: 10.1111/eva.13758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/16/2024] [Accepted: 07/03/2024] [Indexed: 07/24/2024] Open
Abstract
Obtaining reliable estimates of the effective number of breeders (N b) and generational effective population size (N e) for fishery-important species is challenging because they are often iteroparous and highly abundant, which can lead to bias and imprecision. However, recent advances in understanding of these parameters, as well as the development of bias correction methods, have improved the capacity to generate reliable estimates. We utilized samples of both single-cohort young of the year and mixed-age adults from two geographically and genetically isolated stocks of the Australasian snapper (Chrysophrys auratus) to investigate the feasibility of generating reliable N b and N e estimates for a fishery species. Snapper is an abundant, iteroparous broadcast spawning teleost that is heavily exploited by recreational and commercial fisheries. Employing neutral genome-wide SNPs and the linkage-disequilibrium method, we determined that the most reliable N b and N e estimates could be derived by genotyping at least 200 individuals from a single cohort. Although our estimates made from the mixed-age adult samples were generally lower and less precise than those based on a single cohort, they still proved useful for understanding relative differences in genetic effective size between stocks. The correction formulas applied to adjust for biases due to physical linkage of loci and age structure resulted in substantial upward modifications of our estimates, demonstrating the importance of applying these bias corrections. Our findings provide important guidelines for estimating N b and N e for iteroparous species with large populations. This work also highlights the utility of samples originally collected for stock structure and stock assessment work for investigating genetic effective size in fishery-important species.
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Affiliation(s)
- Andrea Bertram
- Molecular Ecology Laboratory, College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Justin Bell
- Victorian Fisheries AuthorityQueenscliffVictoriaAustralia
| | - Chris Brauer
- Molecular Ecology Laboratory, College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - David Fairclough
- Department of Primary Industries and Regional DevelopmentAquatic Sciences and AssessmentHillarysWestern AustraliaAustralia
| | | | - Jonathan Sandoval‐Castillo
- Molecular Ecology Laboratory, College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research LimitedNelsonNew Zealand
- The School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory, College of Science and EngineeringFlinders UniversityBedford ParkSouth AustraliaAustralia
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2
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Wooldridge B, Orland C, Enbody E, Escalona M, Mirchandani C, Corbett-Detig R, Kapp JD, Fletcher N, Cox-Ammann K, Raimondi P, Shapiro B. Limited genomic signatures of population collapse in the critically endangered black abalone (Haliotis cracherodii). Mol Ecol 2024:e17362. [PMID: 38682494 DOI: 10.1111/mec.17362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/05/2024] [Accepted: 04/09/2024] [Indexed: 05/01/2024]
Abstract
The black abalone, Haliotis cracherodii, is a large, long-lived marine mollusc that inhabits rocky intertidal habitats along the coast of California and Mexico. In 1985, populations were impacted by a bacterial disease known as withering syndrome (WS) that wiped out >90% of individuals, leading to the closure of all U.S. black abalone fisheries since 1993. Current conservation strategies include restoring diminished populations by translocating healthy individuals. However, population collapse on this scale may have dramatically lowered genetic diversity and strengthened geographic differentiation, making translocation-based recovery contentious. Additionally, the current prevalence of WS remains unknown. To address these uncertainties, we sequenced and analysed the genomes of 133 black abalone individuals from across their present range. We observed no spatial genetic structure among black abalone, with the exception of a single chromosomal inversion that increases in frequency with latitude. Outside the inversion, genetic differentiation between sites is minimal and does not scale with either geographic distance or environmental dissimilarity. Genetic diversity appears uniformly high across the range. Demographic inference does indicate a severe population bottleneck beginning just 15 generations in the past, but this decline is short lived, with present-day size far exceeding the pre-bottleneck status quo. Finally, we find the bacterial agent of WS is equally present across the sampled range, but only in 10% of individuals. The lack of population genetic structure, uniform diversity and prevalence of WS bacteria indicates that translocation could be a valid and low-risk means of population restoration for black abalone species' recovery.
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Affiliation(s)
- Brock Wooldridge
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA
| | - Chloé Orland
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Cade Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
| | - Joshua D Kapp
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Nathaniel Fletcher
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Karah Cox-Ammann
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Peter Raimondi
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Beth Shapiro
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, California, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
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3
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Orland C, Escalona M, Sahasrabudhe R, Marimuthu MPA, Nguyen O, Beraut E, Marshman B, Moore J, Raimondi P, Shapiro B. A Draft Reference Genome Assembly of the Critically Endangered Black Abalone, Haliotis cracherodii. J Hered 2022; 113:665-672. [PMID: 35567593 PMCID: PMC9709981 DOI: 10.1093/jhered/esac024] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/11/2022] [Indexed: 12/16/2022] Open
Abstract
The once abundant black abalone, Haliotis cracherodii, is a large, long-lived grazing marine mollusk that inhabits the rocky intertidal along the coast of California. The species has experienced dramatic declines since the mid-1980s largely due to the fatal bacterial disease called withering syndrome, leading to the collapse of an economically important fishery and to its inclusion into the IUCN listing as a critically endangered species. In some places impacted by the disease, populations of black abalone have declined by more than 90%, prompting population crashes associated with very little recruitment of new individuals and changes to intertidal communities. Habitats that were dominated by crustose coralline algae and bare rock have become dominated instead by fleshy algae and sessile invertebrates. Here, we present the first high-quality black abalone reference genome, assembled with PacBio HiFi long-reads and assembled with Dovetail Omni-C data to generate a scaffold-level assembly. The black abalone reference genome will be an essential resource in understanding the evolutionary history of this species as well as for exploring its current levels of genetic diversity and establishing future management and restoration plans.
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Affiliation(s)
- Chloé Orland
- Address correspondence to C. Orland at the address above, or e-mail:
| | | | - Ruta Sahasrabudhe
- UC Davis Genome Center, DNA Technologies and Expression Analysis Cores, University of California, Davis, Davis, CA, USA
| | - Mohan P A Marimuthu
- UC Davis Genome Center, DNA Technologies and Expression Analysis Cores, University of California, Davis, Davis, CA, USA
| | - Oanh Nguyen
- UC Davis Genome Center, DNA Technologies and Expression Analysis Cores, University of California, Davis, Davis, CA, USA
| | - Eric Beraut
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Blythe Marshman
- Marine Laboratory, University of California Davis, Davis, CA, USA
| | - James Moore
- Marine Laboratory, University of California Davis, Davis, CA, USA
| | - Peter Raimondi
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Beth Shapiro
- Ecology and Evolutionary Biology Department, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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4
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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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Fuller AM, VanBlaricom GR, Neuman MJ, Witting DA, Friedman CS. A field sentinel study investigating withering syndrome transmission dynamics in California abalones. MARINE ENVIRONMENTAL RESEARCH 2022; 173:105540. [PMID: 34864337 DOI: 10.1016/j.marenvres.2021.105540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 06/13/2023]
Abstract
We examined the risk of withering syndrome (WS) rickettsia-like organism (WS-RLO) infection in sentinel red abalone (Haliotis rufescens) deployed in modules at two Southern California field sites, one adjacent to an abalone farm and one adjacent to wild abalones. WS-RLO DNA was detected in seawater near modules at the wild abalone site but not near the farm (WS-RLO DNA was detected in the farm effluent). More WS-RLO DNA was detected in tissue from abalone near the farm relative to those near wild abalones (p < 0.05). However, infection prevalence and intensity based on histology were low and similar between sites (p > 0.05) and were independent of WS-RLO DNA loads in abalone tissue and seawater. More stippled (ST)-RLO than WS-RLO were observed with more ST-RLO infections near wild abalone than near the abalone farm (p < 0.05). We demonstrate the utility of caged sentinel abalone to better understand pathogen transmission patterns in the field.
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Affiliation(s)
- Ava M Fuller
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA, 98195, USA.
| | - Glenn R VanBlaricom
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA, 98195, USA; US Geological Survey, Washington Cooperative Fish and Wildlife Research Unit, University of Washington, Box 355020, Seattle, WA, 98195, USA
| | - Melissa J Neuman
- NOAA National Marine Fisheries Service Protected Resources Division, 501 West Ocean Blvd, Suite 4200 Long Beach, CA, 90802, USA
| | - David A Witting
- NOAA National Marine Fisheries Service Protected Resources Division, 501 West Ocean Blvd, Suite 4200 Long Beach, CA, 90802, USA
| | - Carolyn S Friedman
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA, 98195, USA
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6
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Nam BH, Kim H, Seol D, Kim H, Noh ES, Kim EM, Noh JK, Kim YO, Park JY, Kwak W. Genotyping-by-Sequencing of the regional Pacific abalone (Haliotis discus) genomes reveals population structures and patterns of gene flow. PLoS One 2021; 16:e0247815. [PMID: 33826655 PMCID: PMC8026068 DOI: 10.1371/journal.pone.0247815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 02/12/2021] [Indexed: 01/05/2023] Open
Abstract
Continuous monitoring of the present genetic status is essential to preserve the genetic resource of wild populations. In this study, we sequenced regional Pacific abalone Haliotis discus samples from three different locations around the Korean peninsula to assess population structure, utilizing Genotyping-by-Sequencing (GBS) method. Using PstI enzyme for genome reduction, we demonstrated the resultant library represented the whole genome region with even spacing, and as a result 16,603 single nucleotide variants (SNVs) were produced. Genetic diversity and population structure were investigated using several methods, and a strong genetic heterogeneity was observed in the Korean abalone populations. Additionally, by comparison of the variant sets among population groups, we were able to discover 26 Korean abalone population-specific SNVs, potentially associated with phenotype differences. This is the first study demonstrating the feasibility of GBS for population genetic study on H. discus. Our results will provide valuable data for the genetic conservation and management of wild abalone populations in Korea and help future GBS studies on the marine mollusks.
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Affiliation(s)
- Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Hyaekang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Genome, Inc, Seoul, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Genome, Inc, Seoul, Republic of Korea
| | - Eun Soo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Eun Mi Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jae Koo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Woori Kwak
- Genome, Inc, Seoul, Republic of Korea
- * E-mail:
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7
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Mejía-Ruíz P, Perez-Enriquez R, Mares-Mayagoitia JA, Valenzuela-Quiñonez F. Population genomics reveals a mismatch between management and biological units in green abalone ( Haliotis fulgens). PeerJ 2020; 8:e9722. [PMID: 32879800 PMCID: PMC7443094 DOI: 10.7717/peerj.9722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 07/23/2020] [Indexed: 11/20/2022] Open
Abstract
Effective fishery management strategies should be based on stock delimitation and knowledge of the spatial scale at which species are distributed. However, a mismatch often occurs between biological and management units of fishery resources. The green abalone (Haliotis fulgens) supports an important artisanal fishery in the west coast of the Baja California Peninsula (BCP), Mexico, which has shown a declining tendency despite the several management measures. Thus, the aim of this study was to characterize the spatial patterns of neutral genomic variation of green abalone along the BCP to test whether the genomic structure patterns support the current green abalone management areas. To test this hypothesis, a set of 2,170 putative neutral single nucleotide polymorphisms discovered by a double digest restriction-site associated DNA approach was used on 10 locations along the BCP. The results revealed a population structure with three putative groups: Guadalupe Island and northern and southern BCP locations. The contemporary gene flow might be explained by local oceanographic features, where it is bidirectional within the southern region but with a predominant southward flow from the northern region. These findings indicated that the administrative areas did not match the biological units of H. fulgens fishery; hence, the stock assessment and management areas should be revised.
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Affiliation(s)
- Paulina Mejía-Ruíz
- Centro de Investigaciones Biológicas del Noroeste S.C., La Paz, Baja California Sur, México
| | - Ricardo Perez-Enriquez
- Centro de Investigaciones Biológicas del Noroeste S.C., La Paz, Baja California Sur, México
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Dittberner H, Becker C, Jiao WB, Schneeberger K, Hölzel N, Tellier A, de Meaux J. Strengths and potential pitfalls of hay transfer for ecological restoration revealed by RAD-seq analysis in floodplain Arabis species. Mol Ecol 2019; 28:3887-3901. [PMID: 31338892 DOI: 10.1111/mec.15194] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 06/21/2019] [Accepted: 07/03/2019] [Indexed: 12/24/2022]
Abstract
Achieving high intraspecific genetic diversity is a critical goal in ecological restoration as it increases the adaptive potential and long-term resilience of populations. Thus, we investigated genetic diversity within and between pristine sites in a fossil floodplain and compared it to sites restored by hay transfer between 1997 and 2014. RAD-seq genotyping revealed that the stenoecious floodplain species Arabis nemorensis is co-occurring with individuals that, based on ploidy, ITS-sequencing and morphology, probably belong to the close relative Arabis sagittata, which has a documented preference for dry calcareous grasslands but has not been reported in floodplain meadows. We show that hay transfer maintains genetic diversity for both species. Additionally, in A. sagittata, transfer from multiple genetically isolated pristine sites resulted in restored sites with increased diversity and admixed local genotypes. In A. nemorensis, transfer did not create novel admixture dynamics because genetic diversity between pristine sites was less differentiated. Thus, the effects of hay transfer on genetic diversity also depend on the genetic make-up of the donor communities of each species, especially when local material is mixed. Our results demonstrate the efficiency of hay transfer for habitat restoration and emphasize the importance of prerestoration characterization of microgeographic patterns of intraspecific diversity of the community to guarantee that restoration practices reach their goal, that is maximize the adaptive potential of the entire restored plant community. Overlooking these patterns may alter the balance between species in the community. Additionally, our comparison of summary statistics obtained from de novo- and reference-based RAD-seq pipelines shows that the genomic impact of restoration can be reliably monitored in species lacking prior genomic knowledge.
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Affiliation(s)
| | - Christian Becker
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Wen-Biao Jiao
- Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
| | | | - Norbert Hölzel
- Institute of Landscape Ecology, University of Münster, Münster, Germany
| | - Aurélien Tellier
- Center of Life and Food Sciences Weihenstephan, Technical University of Munich, Freising, Germany
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Afiq-Rosli L, Huang D, Toh TC, Taira D, Ng CSL, Song T, Chou LM. Maximising genetic diversity during coral transplantation from a highly impacted source reef. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01164-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Jaris H, Brown DS, Proestou DA. Assessing the contribution of aquaculture and restoration to wild oyster populations in a Rhode Island coastal lagoon. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01153-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Ackiss AS, Bird CE, Akita Y, Santos MD, Tachihara K, Carpenter KE. Genetic patterns in peripheral marine populations of the fusilier fish Caesio cuning within the Kuroshio Current. Ecol Evol 2018; 8:11875-11886. [PMID: 30598783 PMCID: PMC6303744 DOI: 10.1002/ece3.4644] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/25/2018] [Accepted: 09/05/2018] [Indexed: 01/16/2023] Open
Abstract
AIM Mayr's central-peripheral population model (CCPM) describes the marked differences between central and peripheral populations in genetic diversity, gene flow, and census size. When isolation leads to genetic divergence, these peripheral populations have high evolutionary value and can influence biogeographic patterns. In tropical marine species with pelagic larvae, powerful western-boundary currents have great potential to shape the genetic characteristics of peripheral populations at latitudinal extremes. We tested for the genetic patterns expected by the CCPM in peripheral populations that are located within the Kuroshio Current for the Indo-Pacific reef fish, Caesio cuning. METHODS We used a panel of 2,677 SNPs generated from restriction site-associated DNA (RAD) sequencing to investigate genetic diversity, relatedness, effective population size, and spatial patterns of population connectivity from central to peripheral populations of C. cuning along the Kuroshio Current. RESULTS Principal component and cluster analyses indicated a genetically distinct lineage at the periphery of the C. cuning species range and examination of SNPs putatively under divergent selection suggested potential for local adaptation in this region. We found signatures of isolation-by-distance and significant genetic differences between nearly all sites. Sites closest to the periphery exhibited increased within-population relatedness and decreased effective population size. MAIN CONCLUSIONS Despite the potential for homogenizing gene flow along the Kuroshio Current, peripheral populations in C. cuning conform to the predictions of the CCPM. While oceanography, habitat availability, and dispersal ability are all likely to shape the patterns found in C. cuning across this central-peripheral junction, the impacts of genetic drift and natural selection in increasing smaller peripheral populations appear to be probable influences on the lineage divergence found in the Ryukyu Islands.
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Affiliation(s)
- Amanda S. Ackiss
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginia
| | - Christopher E. Bird
- Department of Life SciencesTexas A&M University – Corpus ChristiCorpus ChristiTexas
| | - Yuichi Akita
- Okinawa Prefectural Fisheries Research and Extension CenterItomanOkinawaJapan
| | - Mudjekeewis D. Santos
- Genetic Fingerprinting LaboratoryNational Fisheries Research and Development InstituteQuezon CityPhilippines
| | - Katsunori Tachihara
- Laboratory of Fisheries Biology & Coral Reef Studies, Faculty of ScienceUniversity of the RyukyusRyukyusOkinawaJapan
| | - Kent E. Carpenter
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginia
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12
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Lopez JV, Kamel B, Medina M, Collins T, Baums IB. Multiple Facets of Marine Invertebrate Conservation Genomics. Annu Rev Anim Biosci 2018; 7:473-497. [PMID: 30485758 DOI: 10.1146/annurev-animal-020518-115034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Conservation genomics aims to preserve the viability of populations and the biodiversity of living organisms. Invertebrate organisms represent 95% of animal biodiversity; however, few genomic resources currently exist for the group. The subset of marine invertebrates includes the most ancient metazoan lineages and possesses codes for unique gene products and possible keys to adaptation. The benefits of supporting invertebrate conservation genomics research (e.g., likely discovery of novel genes, protein regulatory mechanisms, genomic innovations, and transposable elements) outweigh the various hurdles (rare, small, or polymorphic starting materials). Here we review best conservation genomics practices in the laboratory and in silico when applied to marine invertebrates and also showcase unique features in several case studies of acroporid corals, crown-of-thorns starfish, apple snails, and abalone. Marine conservation genomics should also address how diversity can lead to unique marine innovations, the impact of deleterious variation, and how genomic monitoring and profiling could positively affect broader conservation goals (e.g., value of baseline data for in situ/ex situ genomic stocks).
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Affiliation(s)
- Jose V Lopez
- Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, Florida 33004, USA;
| | - Bishoy Kamel
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, New Mexico 87131, USA;
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
| | - Timothy Collins
- Department of Biological Sciences, Florida International University, Miami, Florida 33199, USA;
| | - Iliana B Baums
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA; ,
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13
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Drinan DP, Gruenthal KM, Canino MF, Lowry D, Fisher MC, Hauser L. Population assignment and local adaptation along an isolation-by-distance gradient in Pacific cod ( Gadus macrocephalus). Evol Appl 2018; 11:1448-1464. [PMID: 30151052 PMCID: PMC6100185 DOI: 10.1111/eva.12639] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/12/2018] [Indexed: 01/03/2023] Open
Abstract
The discernment of populations as management units is a fundamental prerequisite for sustainable exploitation of species. A lack of clear stock boundaries complicates not only the identification of spatial management units, but also the assessment of mixed fisheries by population assignment and mixed stock analysis. Many marine species, such as Pacific cod, are characterized by isolation by distance, showing significant differentiation but no clear stock boundaries. Here, we used restriction-site-associated DNA (RAD) sequencing to investigate population structure and assess power to genetically assign Pacific cod to putative populations of origin. Samples were collected across the species range in the eastern Pacific Ocean, from the Salish Sea to the Aleutian Islands. A total of 6,425 putative biallelic single nucleotide polymorphisms were identified from 276 individuals. We found a strong isolation-by-distance signal along coastlines that mirrored previous microsatellite results and pronounced genetic differentiation between coastal samples and those from the inland waters of the Salish Sea, with no evidence for hybridization between these two populations. Individual assignment success based on two methods was high overall (≥84%) but decreased from south to north. Assignment to geographic location of origin also was successful, with average distance between capture and assignment location of 220 km. Outlier analyses identified more loci potentially under selection along the coast than between Salish Sea and coastal samples, suggesting more diverse adaptation to latitudinal environmental factors than inshore vs. offshore environments. Our results confirm previous observations of sharp genetic differentiation of the Salish Sea population and isolation by distance along the coast, but also highlight the feasibility of using modern genomic techniques to inform stock boundaries and fisheries management in a low FST marine species.
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Affiliation(s)
- Daniel P. Drinan
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashington
| | | | | | - Dayv Lowry
- Washington Department of Fish and WildlifeOlympiaWashington
| | - Mary C. Fisher
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashington
| | - Lorenz Hauser
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashington
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14
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Taylor ML, Roterman CN. Invertebrate population genetics across Earth's largest habitat: The deep-sea floor. Mol Ecol 2017; 26:4872-4896. [PMID: 28833857 DOI: 10.1111/mec.14237] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/16/2017] [Accepted: 06/19/2017] [Indexed: 01/04/2023]
Abstract
Despite the deep sea being the largest habitat on Earth, there are just 77 population genetic studies of invertebrates (115 species) inhabiting non-chemosynthetic ecosystems on the deep-sea floor (below 200 m depth). We review and synthesize the results of these papers. Studies reveal levels of genetic diversity comparable to shallow-water species. Generally, populations at similar depths were well connected over 100s-1,000s km, but studies that sampled across depth ranges reveal population structure at much smaller scales (100s-1,000s m) consistent with isolation by adaptation across environmental gradients, or the existence of physical barriers to connectivity with depth. Few studies were ocean-wide (under 4%), and 48% were Atlantic-focused. There is strong emphasis on megafauna and commercial species with research into meiofauna, "ecosystem engineers" and other ecologically important species lacking. Only nine papers account for ~50% of the planet's surface (depths below 3,500 m). Just two species were studied below 5,000 m, a quarter of Earth's seafloor. Most studies used single-locus mitochondrial genes revealing a common pattern of non-neutrality, consistent with demographic instability or selective sweeps; similar to deep-sea hydrothermal vent fauna. The absence of a clear difference between vent and non-vent could signify that demographic instability is common in the deep sea, or that selective sweeps render single-locus mitochondrial studies demographically uninformative. The number of population genetics studies to date is miniscule in relation to the size of the deep sea. The paucity of studies constrains meta-analyses where broad inferences about deep-sea ecology could be made.
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Affiliation(s)
- M L Taylor
- Department of Zoology, University of Oxford, Oxford, UK
| | - C N Roterman
- Department of Zoology, University of Oxford, Oxford, UK
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15
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Narum SR, Gallardo P, Correa C, Matala A, Hasselman D, Sutherland BJG, Bernatchez L. Genomic patterns of diversity and divergence of two introduced salmonid species in Patagonia, South America. Evol Appl 2017; 10:402-416. [PMID: 28352299 PMCID: PMC5367078 DOI: 10.1111/eva.12464] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 01/26/2017] [Indexed: 12/25/2022] Open
Abstract
Invasive species have become widespread in aquatic environments throughout the world, yet there are few studies that have examined genomic variation of multiple introduced species in newly colonized environments. In this study, we contrast genomic variation in two salmonid species (anadromous Chinook Salmon, Oncorhynchus tshawytscha, 11,579 SNPs and resident Brook Charr Salvelinus fontinalis, 13,522 SNPs) with differing invasion success after introduction to new environments in South America relative to populations from their native range in North America. Estimates of genetic diversity were not significantly different between introduced and source populations for either species, indicative of propagule pressure that has been shown to maintain diversity in founding populations relative to their native range. Introduced populations also demonstrated higher connectivity and gene flow than those in their native range. Evidence for candidate loci under divergent selection was observed, but was limited to specific introduced populations and was not widely evident. Patterns of genomic variation were consistent with general dispersal potential of each species and therefore also the notion that life history variation may contribute to both invasion success and subsequent genetic structure of these two salmonids in Patagonia.
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Affiliation(s)
- Shawn R. Narum
- Hagerman Fish Culture Experiment StationColumbia River Inter‐Tribal Fish CommissionHagermanIDUSA
| | - Pablo Gallardo
- Centro de Cultivos Marinos Bahía LaredoUniversity of MagallanesPunta ArenasChile
| | - Cristian Correa
- Facultad de Ciencias Forestales y Recursos NaturalesInstituto de Conservación Biodiversidad y TerritorioUniversidad Austral de ChileValdiviaChile
- Facultad de CienciasInstituto de Ciencias Marinas y LimnológicasUniversidad Austral de ChileValdiviaChile
| | - Amanda Matala
- Hagerman Fish Culture Experiment StationColumbia River Inter‐Tribal Fish CommissionHagermanIDUSA
| | - Daniel Hasselman
- Hagerman Fish Culture Experiment StationColumbia River Inter‐Tribal Fish CommissionHagermanIDUSA
| | - Ben J. G. Sutherland
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
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16
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Black AN, Seears HA, Hollenbeck CM, Samollow PB. Rapid genetic and morphologic divergence between captive and wild populations of the endangered Leon Springs pupfish, Cyprinodon bovinus. Mol Ecol 2017; 26:2237-2256. [PMID: 28133827 DOI: 10.1111/mec.14028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 12/20/2016] [Accepted: 12/28/2016] [Indexed: 12/17/2022]
Abstract
The Leon Springs pupfish (Cyprinodon bovinus) is an endangered species currently restricted to a single desert spring and a separate captive habitat in southwestern North America. Following establishment of the captive population from wild stock in 1976, the wild population has undergone natural population size fluctuations, intentional culling to purge genetic contamination from an invasive congener (Cyprinodon variegatus) and augmentation/replacement of wild fish from the captive stock. A severe population decline following the most recent introduction of captive fish prompted us to examine whether the captive and wild populations have differentiated during the short time they have been isolated from one another. If so, the development of divergent genetic and/or morphologic traits between populations could contribute to a diminished ability of fish from one location to thrive in the other. Examination of genomewide single nucleotide polymorphisms and morphologic variation revealed no evidence of residual C. variegatus characteristics in contemporary C. bovinus samples. However, significant genetic and morphologic differentiation was detected between the wild and captive populations, some of which might reflect local adaptation. Our results indicate that genetic and physical characteristics can diverge rapidly between isolated subdivisions of managed populations, potentially compromising the value of captive stock for future supplementation efforts. In the case of C. bovinus, our findings underscore the need to periodically inoculate the captive population with wild genetic material to help mitigate genetic, and potentially morphologic, divergence between them and also highlight the utility of parallel morphologic and genomic evaluation to inform conservation management planning.
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Affiliation(s)
- Andrew N Black
- Hatfield Marine Science Center, Coastal Oregon Marine Experiment Station, Oregon State University, 2030 SE Marine Science Drive, Newport, OR, 97365, USA
| | - Heidi A Seears
- Department of Biology, University of Virginia, Gilmer Hall, Charlottesville, VA, 22904, USA
| | - Christopher M Hollenbeck
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University, Corpus Christi, TX, 78412, USA
| | - Paul B Samollow
- Department of Veterinary Integrative Biosciences and Program in Genetics, Texas A&M University, College Station, TX, 77843, USA
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17
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Waples RK, Larson WA, Waples RS. Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci. Heredity (Edinb) 2016; 117:233-40. [PMID: 27553452 PMCID: PMC5026758 DOI: 10.1038/hdy.2016.60] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 06/19/2016] [Accepted: 06/24/2016] [Indexed: 12/15/2022] Open
Abstract
Contemporary effective population size (Ne) can be estimated using linkage disequilibrium (LD) observed across pairs of loci presumed to be selectively neutral and unlinked. This method has been commonly applied to data sets containing 10-100 loci to inform conservation and study population demography. Performance of these Ne estimates could be improved by incorporating data from thousands of loci. However, these thousands of loci exist on a limited number of chromosomes, ensuring that some fraction will be physically linked. Linked loci have elevated LD due to limited recombination, which if not accounted for can cause Ne estimates to be downwardly biased. Here, we present results from coalescent and forward simulations designed to evaluate the bias of LD-based Ne estimates ([Ncirc ]e). Contrary to common perceptions, increasing the number of loci does not increase the magnitude of linkage. Although we show it is possible to identify some pairs of loci that produce unusually large r(2) values, simply removing large r(2) values is not a reliable way to eliminate bias. Fortunately, the magnitude of bias in [Ncirc ]e is strongly and negatively correlated with the process of recombination, including the number of chromosomes and their length, and this relationship provides a general way to adjust for bias. Additionally, we show that with thousands of loci, precision of [Ncirc ]e is much lower than expected based on the assumption that each pair of loci provides completely independent information.
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Affiliation(s)
- R K Waples
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - W A Larson
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - R S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
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18
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Gleason LU, Burton RS. Genomic evidence for ecological divergence against a background of population homogeneity in the marine snail Chlorostoma funebralis. Mol Ecol 2016; 25:3557-73. [PMID: 27199218 DOI: 10.1111/mec.13703] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 04/29/2016] [Accepted: 05/03/2016] [Indexed: 12/19/2022]
Abstract
The balance between natural selection, gene flow and genetic drift is difficult to resolve in marine invertebrates with extensive dispersal and fluctuating population sizes. The intertidal snail Chlorostoma funebralis has planktonic larvae and previous work using mtDNA polymorphism reported no genetic population structure. Nevertheless, recent studies have documented differences in thermal tolerance and transcriptomic responses to heat stress between northern and southern California, USA, populations. To gain insight into the dynamics influencing adaptive divergence, we used double-digest restriction site-associated DNA (ddRAD) sequencing to identify 1861 genomewide, quality-filtered single-nucleotide polymorphism (SNP) loci for C. funebralis collected from three northern and three southern California sites (15 individuals per population). Considering all SNPs, there was no evidence for genetic differentiation among populations or regions (average FST = 0.0042). However, outlier tests revealed 34 loci putatively under divergent selection between northern and southern populations, and structure and SNP tree analyses based on these outliers show clear genetic differentiation between geographic regions. Three of these outliers are known or hypothesized to be involved in stress granule formation, a response to environmental stress such as heat. Combined with previous work that found thermally tolerant southern populations show high baseline expression of stress response genes, these results further suggest that thermal stress is a strong selective pressure across C. funebralis populations. Overall, this study increases our understanding of the factors constraining local adaptation in marine organisms, while suggesting that ecologically driven, strong differentiation can occur at relevant loci in a species with planktonic larvae.
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Affiliation(s)
- Lani U Gleason
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093-0202, USA.,Department of Biology, Loyola Marymount University, Los Angeles, CA, 90045, USA
| | - Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093-0202, USA
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19
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A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci. Heredity (Edinb) 2016; 117:207-16. [PMID: 27165767 DOI: 10.1038/hdy.2016.30] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 03/14/2016] [Accepted: 03/29/2016] [Indexed: 12/29/2022] Open
Abstract
Estimation of contemporary effective population size (Ne) from linkage disequilibrium (LD) between unlinked pairs of genetic markers has become an important tool in the field of population and conservation genetics. If data pertaining to physical linkage or genomic position are available for genetic markers, estimates of recombination rate between loci can be combined with LD data to estimate contemporary Ne at various times in the past. We extend the well-known, LD-based method of estimating contemporary Ne to include linkage information and show via simulation that even relatively small, recent changes in Ne can be detected reliably with a modest number of single-nucleotide polymorphism (SNP) loci. We explore several issues important to interpretation of the results and quantify the bias in estimates of contemporary Ne associated with the assumption that all loci in a large SNP data set are unlinked. The approach is applied to an empirical data set of SNP genotypes from a population of a marine fish where a recent, temporary decline in Ne is known to have occurred.
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20
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The application of genomics to inform conservation of a functionally important reef fish (Scarus niger) in the Philippines. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0776-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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21
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Munguía-Vega A, Sáenz-Arroyo A, Greenley AP, Espinoza-Montes JA, Palumbi SR, Rossetto M, Micheli F. Marine reserves help preserve genetic diversity after impacts derived from climate variability: Lessons from the pink abalone in Baja California. Glob Ecol Conserv 2015. [DOI: 10.1016/j.gecco.2015.07.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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22
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Candy JR, Campbell NR, Grinnell MH, Beacham TD, Larson WA, Narum SR. Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (
Thaleichthys pacificus
, Osmeridae), an anadromous Pacific smelt. Mol Ecol Resour 2015; 15:1421-34. [DOI: 10.1111/1755-0998.12400] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/30/2015] [Accepted: 02/07/2015] [Indexed: 11/30/2022]
Affiliation(s)
- John R. Candy
- Fisheries and Oceans Canada Pacific Biological Station 3190 Hammond Bay Road Nanaimo BC V9T 6N7 Canada
| | - Nathan R. Campbell
- Columbia River Inter‐Tribal Fish Commission 3059‐F National Fish Hatchery Road Hagerman ID 83332 USA
| | - Matthew H. Grinnell
- Fisheries and Oceans Canada Pacific Biological Station 3190 Hammond Bay Road Nanaimo BC V9T 6N7 Canada
| | - Terry D. Beacham
- Fisheries and Oceans Canada Pacific Biological Station 3190 Hammond Bay Road Nanaimo BC V9T 6N7 Canada
| | - Wesley A. Larson
- School of Aquatic and Fishery Science University of Washington 1122 NE Boat Street, Box 355020 Seattle WA 98195 USA
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish Commission 3059‐F National Fish Hatchery Road Hagerman ID 83332 USA
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23
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Pante E, Abdelkrim J, Viricel A, Gey D, France SC, Boisselier MC, Samadi S. Use of RAD sequencing for delimiting species. Heredity (Edinb) 2014; 114:450-9. [PMID: 25407078 DOI: 10.1038/hdy.2014.105] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 09/12/2014] [Accepted: 09/16/2014] [Indexed: 11/10/2022] Open
Abstract
RAD-tag sequencing is a promising method for conducting genome-wide evolutionary studies. However, to date, only a handful of studies empirically tested its applicability above the species level. In this communication, we use RAD tags to contribute to the delimitation of species within a diverse genus of deep-sea octocorals, Chrysogorgia, for which few classical genetic markers have proved informative. Previous studies have hypothesized that single mitochondrial haplotypes can be used to delimit Chrysogorgia species. On the basis of two lanes of Illumina sequencing, we inferred phylogenetic relationships among 12 putative species that were delimited using mitochondrial data, comparing two RAD analysis pipelines (Stacks and PyRAD). The number of homologous RAD loci decreased dramatically with increasing divergence, as >70% of loci are lost when comparing specimens separated by two mutations on the 700-nt long mitochondrial phylogeny. Species delimitation hypotheses based on the mitochondrial mtMutS gene are largely supported, as six out of nine putative species represented by more than one colony were recovered as discrete, well-supported clades. Significant genetic structure (correlating with geography) was detected within one putative species, suggesting that individuals characterized by the same mtMutS haplotype may belong to distinct species. Conversely, three mtMutS haplotypes formed one well-supported clade within which no population structure was detected, also suggesting that intraspecific variation exists at mtMutS in Chrysogorgia. Despite an impressive decrease in the number of homologous loci across clades, RAD data helped us to fine-tune our interpretations of classical mitochondrial markers used in octocoral species delimitation, and discover previously undetected diversity.
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Affiliation(s)
- E Pante
- Laboratoire LIENSs, UMR 7266 CNRS-Université de La Rochelle, La Rochelle, France
| | - J Abdelkrim
- 1] Département Systématique et Evolution, UMS 2700 MNHN-CNRS, SSM, Muséum national d'Histoire naturelle, Paris, France [2] ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - A Viricel
- Laboratoire LIENSs, UMR 7266 CNRS-Université de La Rochelle, La Rochelle, France
| | - D Gey
- Département Systématique et Evolution, UMS 2700 MNHN-CNRS, SSM, Muséum national d'Histoire naturelle, Paris, France
| | - S C France
- Department of Biology, University of Louisiana at Lafayette, Lafayette, LA, USA
| | - M C Boisselier
- 1] Département Systématique et Evolution, UMS 2700 MNHN-CNRS, SSM, Muséum national d'Histoire naturelle, Paris, France [2] ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
| | - S Samadi
- ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, Paris, France
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24
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Larson WA, Seeb LW, Everett MV, Waples RK, Templin WD, Seeb JE. Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha). Evol Appl 2014; 7:355-69. [PMID: 24665338 PMCID: PMC3962296 DOI: 10.1111/eva.12128] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/02/2013] [Indexed: 12/14/2022] Open
Abstract
Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure.
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Affiliation(s)
- Wesley A Larson
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Meredith V Everett
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - Ryan K Waples
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
| | - William D Templin
- Gene Conservation Laboratory, Alaska Department of Fish and Game Anchorage, AK, USA
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington Seattle, WA, USA
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