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Ollé-Vilanova J, Hajjej G, Macias D, Saber S, Lino PG, Muñoz-Lechuga R, Baibbat S, Sow FN, Diaha NC, Araguas RM, Sanz N, Vinas J. Atlantic bonito (Sarda) genomic analysis reveals population differentiation across Northeast Atlantic and mediterranean locations: Implications for fishery management. MARINE ENVIRONMENTAL RESEARCH 2024; 196:106408. [PMID: 38402010 DOI: 10.1016/j.marenvres.2024.106408] [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: 11/10/2023] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/26/2024]
Abstract
The Atlantic bonito (Sarda, family Scombridae) is a pelagic species and one of the most exploited small tuna species. Despite its economic importance, biological information is scarce with no associated management directives. In this study, using a population genomic approach resulted in a lack of panmixia of two genetic pools with different effective population sizes (east central-tropical Atlantic and northeast Atlantic-Mediterranean) and an intermixing zone in Atlantic Morocco. The absence of genetic heterogeneity between the locations in Atlantic - Mediterranean transitional zone adds new evidence that challenges the Strait of Gibraltar as a phylogeographic barrier for marine pelagic species. These results are proposed to the ICCAT Commission to establish management areas for this species, although they are not consistent with the recently adopted pelagic ecoregions. Finally, a panel of highly informative SNPs was developed for efficient and low-cost population assignment and the analysis of unresolved population structures.
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Affiliation(s)
- Judith Ollé-Vilanova
- Laboratori Ictiologia Genetica, Departament de Biologia, Universitat de Girona, 17003, Girona, Catalunya, Spain
| | - Ghailen Hajjej
- National Institute of Marine Science and Technology, Tunisia
| | - David Macias
- Centro Oceanográfico de Málaga. Instituto Espanol de Oceanografía (IEO-CSIC), Spain
| | - Sámar Saber
- Centro Oceanográfico de Málaga. Instituto Espanol de Oceanografía (IEO-CSIC), Spain
| | - Pedro G Lino
- Instituto Portugues Do Mar e da Atmosfera (IPMA), Avenida 5 de Outubro S/n, 8700-305, Olhão, Portugal
| | - Rubén Muñoz-Lechuga
- Instituto Portugues Do Mar e da Atmosfera (IPMA), Avenida 5 de Outubro S/n, 8700-305, Olhão, Portugal; Department of Biology, Faculty of Marine and Environmental Sciences, University of Cádiz, 11510, Puerto Real, Cádiz, Spain
| | | | | | | | - Rosa M Araguas
- Laboratori Ictiologia Genetica, Departament de Biologia, Universitat de Girona, 17003, Girona, Catalunya, Spain
| | - Núria Sanz
- Laboratori Ictiologia Genetica, Departament de Biologia, Universitat de Girona, 17003, Girona, Catalunya, Spain
| | - Jordi Vinas
- Laboratori Ictiologia Genetica, Departament de Biologia, Universitat de Girona, 17003, Girona, Catalunya, Spain.
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2
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Waples RS. Practical application of the linkage disequilibrium method for estimating contemporary effective population size: A review. Mol Ecol Resour 2024; 24:e13879. [PMID: 37873672 DOI: 10.1111/1755-0998.13879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/25/2023]
Abstract
The method to estimate contemporary effective population size (Ne ) based on patterns of linkage disequilibrium (LD) at unlinked loci has been widely applied to natural and managed populations. The underlying model makes many simplifying assumptions, most of which have been evaluated in numerous studies published over the last two decades. Here, these performance evaluations are reviewed and summarized, with a focus on information that facilitates practical application to real populations in nature. Potential sources of bias that are discussed include calculation of r2 (a measure of LD), adjustments for sampling error, physical linkage, age structure, migration and spatial structure, mutation and selection, mating systems, changes in abundance, rare alleles, missing data, genotyping errors, data filtering choices and methods for combining multiple Ne estimates. Factors that affect precision are reviewed, including pseudoreplication that limits the information gained from large genomics datasets, constraints imposed by small samples of individuals, and the challenges in obtaining robust estimates for large populations. Topics that merit further research include the potential to weight r2 values by allele frequency, lump samples of individuals, use genotypic likelihoods rather than called genotypes, prune large LD values and apply the method to species practising partial monogamy.
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Affiliation(s)
- Robin S Waples
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
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3
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Weise EM, Scribner KT, Boeberitz O, Bravener G, Johnson NS, Robinson JD. Evaluating the utility of effective breeding size estimates for monitoring sea lamprey spawning abundance. Ecol Evol 2023; 13:e10519. [PMID: 37745785 PMCID: PMC10511834 DOI: 10.1002/ece3.10519] [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: 06/05/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023] Open
Abstract
Sea lamprey (Petromyzon marinus) is an invasive species that is a significant source of mortality for populations of valued fish species across the North American Great Lakes. Large annual control programs are needed to reduce the species' impacts; however, the number of successfully spawning adults cannot currently be accurately assessed. In this study, effective breeding size (N b) and the minimum number of spawning adults (N s) were estimated for larval cohorts from 17 tributaries across all five Great Lakes using single nucleotide polymorphisms (SNP) genotyped via RAD-capture sequencing. Reconstructed larval pedigrees showed substantial variability in the size and number of full- and half-sibling groups, N b (<1-367), and N s (5-545) among streams. Generalized linear models examining the effects of stream environmental characteristics and aspects of sampling regimes on N b and N s estimates identified sample size, the number of sampling sites, and drainage area as important factors predicting N b and N s. Correlations between N b, N s, and capture-mark-recapture estimates of adult census size (N c) increased when streams with small sample sizes (n < 50) were removed. Results collectively indicate that parameters estimated from genetic data can provide valuable information on spawning adults in a river system, especially if sampling regimes are standardized and physical stream covariates are included.
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Affiliation(s)
- Ellen M. Weise
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
- Present address:
Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Kim T. Scribner
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
- Department of Integrative BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Olivia Boeberitz
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
- Present address:
Pacific States Marine Fisheries CommissionPortlandOregonUSA
| | - Gale Bravener
- Fisheries and Oceans CanadaSea Lamprey Control CentreSault Ste. MarieOntarioCanada
| | - Nicholas S. Johnson
- U.S. Geological SurveyGreat Lakes Science Center, Hammond Bay Biological StationMillersburgMichiganUSA
| | - John D. Robinson
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
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4
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Fitz KS, Montes HR, Thompson DM, Pinsky ML. Isolation-by-distance and isolation-by-oceanography in Maroon Anemonefish ( Amphiprion biaculeatus). Evol Appl 2023; 16:379-392. [PMID: 36793687 PMCID: PMC9923474 DOI: 10.1111/eva.13448] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/27/2022] [Accepted: 07/07/2022] [Indexed: 11/29/2022] Open
Abstract
Obtaining dispersal estimates for a species is key to understanding local adaptation and population dynamics and to implementing conservation actions. Genetic isolation-by-distance (IBD) patterns can be used for estimating dispersal, and these patterns are especially useful for marine species in which few other methods are available. In this study, we genotyped coral reef fish (Amphiprion biaculeatus) at 16 microsatellite loci across eight sites across 210 km in the central Philippines to generate fine-scale estimates of dispersal. All sites except for one followed IBD patterns. Using IBD theory, we estimated a larval dispersal kernel spread of 8.9 km (95% confidence interval of 2.3-18.4 km). Genetic distance to the remaining site correlated strongly with the inverse probability of larval dispersal from an oceanographic model. Ocean currents were a better explanation for genetic distance at large spatial extents (sites greater than 150 km apart), while geographic distance remained the best explanation for spatial extents less than 150 km. Our study demonstrates the utility of combining IBD patterns with oceanographic simulations to understand connectivity in marine environments and to guide marine conservation strategies.
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Affiliation(s)
- Kyra S Fitz
- Department of Ecology, Evolution and Natural Resources Rutgers University New Brunswick New Jersey USA
| | - Humberto R Montes
- Institute of Tropical Ecology and Environmental Management Visayas State University Baybay City Philippines
| | - Diane M Thompson
- Department of Geosciences University of Arizona Tucson Arizona USA
| | - Malin L Pinsky
- Department of Ecology, Evolution and Natural Resources Rutgers University New Brunswick New Jersey USA
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5
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Delaval A, Bendall V, Hetherington SJ, Skaug HJ, Frost M, Jones CS, Noble LR. Evaluating the suitability of close-kin mark-recapture as a demographic modelling tool for a critically endangered elasmobranch population. Evol Appl 2023; 16:461-473. [PMID: 36793682 PMCID: PMC9923483 DOI: 10.1111/eva.13474] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 06/17/2022] [Accepted: 08/09/2022] [Indexed: 11/04/2022] Open
Abstract
Estimating the demographic parameters of contemporary populations is essential to the success of elasmobranch conservation programmes, and to understanding their recent evolutionary history. For benthic elasmobranchs such as skates, traditional fisheries-independent approaches are often unsuitable as the data may be subject to various sources of bias, whilst low recapture rates can render mark-recapture programmes ineffectual. Close-kin mark-recapture (CKMR), a novel demographic modelling approach based on the genetic identification of close relatives within a sample, represents a promising alternative approach as it does not require physical recaptures. We evaluated the suitability of CKMR as a demographic modelling tool for the critically endangered blue skate (Dipturus batis) in the Celtic Sea using samples collected during fisheries-dependent trammel-net surveys that ran from 2011 to 2017. We identified three full-sibling and 16 half-sibling pairs among 662 skates, which were genotyped across 6291 genome-wide single nucleotide polymorphisms, 15 of which were cross-cohort half-sibling pairs that were included in a CKMR model. Despite limitations owing to a lack of validated life-history trait parameters for the species, we produced the first estimates of adult breeding abundance, population growth rate, and annual adult survival rate for D. batis in the Celtic Sea. The results were compared to estimates of genetic diversity, effective population size (N e ), and to catch per unit effort estimates from the trammel-net survey. Although each method was characterized by wide uncertainty bounds, together they suggested a stable population size across the time-series. Recommendations for the implementation of CKMR as a conservation tool for data-limited elasmobranchs are discussed. In addition, the spatio-temporal distribution of the 19 sibling pairs revealed a pattern of site fidelity in D. batis, and supported field observations suggesting an area of critical habitat that could qualify for protection might occur near the Isles of Scilly.
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Affiliation(s)
- Aurélien Delaval
- Faculty of Biosciences and Aquaculture Nord University Bodø Norway
| | - Victoria Bendall
- Centre for Environment Fisheries and Aquaculture Science (CEFAS) Lowestoft UK
| | | | - Hans J Skaug
- Department of Mathematics University of Bergen Bergen Norway
| | - Michelle Frost
- School of Biological Sciences University of Aberdeen Aberdeen UK
| | | | - Leslie R Noble
- Faculty of Biosciences and Aquaculture Nord University Bodø Norway.,School of Biological Sciences University of Aberdeen Aberdeen UK
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6
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Hoey JA, Able KW, Pinsky ML. Genetic decline and recovery of a demographically rebuilt fishery species. Mol Ecol 2022; 31:5684-5698. [PMID: 36114805 PMCID: PMC9828022 DOI: 10.1111/mec.16697] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
The demographic history of a population is important for conservation and evolution, but this history is unknown for many populations. Methods that use genomic data have been developed to infer demography, but they can be challenging to implement and interpret, particularly for large populations. Thus, understanding if and when genetic estimates of demography correspond to true population history is important for assessing the performance of these genetic methods. Here, we used double-digest restriction-site associated DNA (ddRAD) sequencing data from archived collections of larval summer flounder (Paralichthys dentatus, n = 279) from three cohorts (1994-1995, 1997-1998 and 2008-2009) along the U.S. East coast to examine how contemporary effective population size and genetic diversity responded to changes in abundance in a natural population. Despite little to no detectable change in genetic diversity, coalescent-based demographic modelling from site frequency spectra revealed that summer flounder effective population size declined dramatically in the early 1980s. The timing and direction of change corresponded well with the observed decline in spawning stock census abundance in the late 1980s from independent fish surveys. Census abundance subsequently recovered and achieved the prebottleneck size. Effective population size also grew following the bottleneck. Our results for summer flounder demonstrate that genetic sampling and site frequency spectra can be useful for detecting population dynamics, even in species with large effective sizes.
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Affiliation(s)
- Jennifer A. Hoey
- Ecology, Evolution, & Natural ResourcesRutgers UniversityNew BrunswickNew JerseyUSA,Institute for Biodiversity Science and SustainabilityCalifornia Academy of SciencesSan FranciscoCaliforniaUSA
| | - Kenneth W. Able
- Marine Field Station, Department of Marine and Coastal Sciences, Rutgers UniversityTuckertonNew JerseyUSA
| | - Malin L. Pinsky
- Ecology, Evolution, & Natural ResourcesRutgers UniversityNew BrunswickNew JerseyUSA
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7
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Hemstrom W, Dauwalter D, Peacock M, Leasure D, Wenger S, Miller M, Neville. Population genomic monitoring provides insight into conservation status but no correlation with demographic estimates of extinction risk in a threatened trout. Evol Appl 2022; 15:1449-1468. [PMID: 36187186 PMCID: PMC9488680 DOI: 10.1111/eva.13473] [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: 03/10/2021] [Accepted: 08/12/2022] [Indexed: 12/03/2022] Open
Abstract
The current extinction crisis requires effective assessment and monitoring tools. Genetic approaches are appealing given the relative ease of field sampling required to estimate genetic diversity characteristics assumed related to population size, evolutionary potential, and extinction risk, and to evaluate hybridization with non‐native species simultaneously. However, linkages between population genetic metrics of diversity from survey‐style field collections and demographic estimates of population size and extinction risk are still in need of empirical examples, especially for remotely distributed species of conservation concern where the approach might be most beneficial. We capitalized on an exceptional opportunity to evaluate congruence between genetic diversity metrics and demographic‐based estimates of abundance and extinction risk from a comprehensive Multiple Population Viability Analysis (MPVA) in a threatened fish, the Lahontan cutthroat trout (LCT). We sequenced non‐native trout reference samples and recently collected and archived tissue samples of most remaining populations of LCT (N = 60) and estimated common genetic assessment metrics, predicting minimal hybridization with non‐native trout, low diversity, and declining diversity over time. We further hypothesized genetic metrics would correlate positively with MPVA‐estimated abundance and negatively with extinction probability. We uncovered several instances of hybridization that pointed to immediate management needs. After removing hybridized individuals, cautious interpretation of low effective population sizes (2–63) suggested reduced evolutionary potential for many LCT populations. Other genetic metrics did not decline over time nor correlate with MPVA‐based estimates of harmonic mean abundance or 30‐year extinction probability. Our results demonstrate benefits of genetic monitoring for efficiently detecting hybridization and, though genetic results were disconnected from demographic assessment of conservation status, they suggest reduced evolutionary potential and likely a higher conservation risk than currently recognized for this threatened fish. We emphasize that genetic information provides essential complementary insight, in addition to demographic information, for evaluating species status.
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Affiliation(s)
- W. Hemstrom
- Department of Animal Science University of California Davis California U.S.A
| | | | - M. Peacock
- Department of Biology University of Nevada Reno Nevada U.S.A
| | - D. Leasure
- WorldPop, Geography and Environmental Science University of Southampton Southampton United Kingdom
| | - S. Wenger
- Odum School of Ecology University of Georgia Athens GA U.S.A
| | - M. Miller
- Department of Animal Science University of California Davis California U.S.A
| | - Neville
- Science Program, Trout Unlimited Boise ID U.S.A
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8
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Naaykens T, D’Aloia CC. Isolation‐by‐distance and genetic parentage analysis provide similar larval dispersal estimates. Mol Ecol 2022; 31:3072-3082. [DOI: 10.1111/mec.16465] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/10/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Affiliation(s)
- T. Naaykens
- Department of Biological Sciences University of New Brunswick – Saint John 100 Tucker Park Road NB E2L 4L5 Canada
| | - C. C. D’Aloia
- Department of Biology University of Toronto Mississauga 3359 Mississauga Road Mississauga ON L5L 1C6 Canada
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9
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Nadachowska‐Brzyska K, Konczal M, Babik W. Navigating the temporal continuum of effective population size. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13740] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | - Wieslaw Babik
- Jagiellonian University in Kraków Faculty of Biology Institute of Environmental Sciences Kraków Poland
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10
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Buffalo V. Quantifying the relationship between genetic diversity and population size suggests natural selection cannot explain Lewontin's Paradox. eLife 2021; 10:e67509. [PMID: 34409937 PMCID: PMC8486380 DOI: 10.7554/elife.67509] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/16/2021] [Indexed: 12/21/2022] Open
Abstract
Neutral theory predicts that genetic diversity increases with population size, yet observed levels of diversity across metazoans vary only two orders of magnitude while population sizes vary over several. This unexpectedly narrow range of diversity is known as Lewontin's Paradox of Variation (1974). While some have suggested selection constrains diversity, tests of this hypothesis seem to fall short. Here, I revisit Lewontin's Paradox to assess whether current models of linked selection are capable of reducing diversity to this extent. To quantify the discrepancy between pairwise diversity and census population sizes across species, I combine previously-published estimates of pairwise diversity from 172 metazoan taxa with newly derived estimates of census sizes. Using phylogenetic comparative methods, I show this relationship is significant accounting for phylogeny, but with high phylogenetic signal and evidence that some lineages experience shifts in the evolutionary rate of diversity deep in the past. Additionally, I find a negative relationship between recombination map length and census size, suggesting abundant species have less recombination and experience greater reductions in diversity due to linked selection. However, I show that even assuming strong and abundant selection, models of linked selection are unlikely to explain the observed relationship between diversity and census sizes across species.
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Affiliation(s)
- Vince Buffalo
- Institute for Ecology and Evolution, University of OregonEugeneUnited States
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11
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Cowles SA, Weeks BC, Perrin L, Chen N, Uy JAC. Comparison of adult census size and effective population size support the need for continued protection of two Solomon Island endemics. THE EMU 2021; 121:45-54. [PMID: 35264816 PMCID: PMC8903160 DOI: 10.1080/01584197.2021.1915163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/05/2021] [Indexed: 06/14/2023]
Abstract
Because a population's ability to respond to rapid change is dictated by standing genetic variation, we can better predict a population's long-term viability by estimating and then comparing adult census size (N) and effective population size (N e ). However, most studies only measure N or N e , which can be misleading. Using a combination of field and genomic sequence data, we here estimate and compare N and N e in two range-restricted endemics of the Solomon Islands. Two Zosterops White-eye species inhabit the small island of Kolombangara, with a high elevation species endemic to the island (Z. murphyi) and a low elevation species endemic to the Solomon Islands (Z. kulambangrae). Field observations reveal large values of N for both species with Z. kulambangrae numbering at 114,781 ± 32,233 adults, and Z. murphyi numbering at 64,412 ± 15,324 adults. In contrast, genomic analyses reveal that N e was much lower than N, with Z. kulambangrae estimated at 694.5 and Z. murphyi at 796.1 individuals. Further, positive Tajima's D values for both species suggest that they have experienced a demographic contraction, providing a mechanism for low values of N e . Comparison of N and N e suggests that Z. kulambangrae and Z. murphyi are not at immediate threat of extinction but may be at genetic risk. Our results provide important baseline data for long-term monitoring of these island endemics, and argue for measuring both population size estimates to better gauge long-term population viability.
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Affiliation(s)
- Sarah A. Cowles
- Department of Biology, University of Miami, Coral Gables, FL, USA
| | - Brian C. Weeks
- School for Environment & Sustainability, University of Michigan, Ann Arbor, MI, USA
| | - Lindsey Perrin
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - J. Albert C. Uy
- Department of Biology, University of Miami, Coral Gables, FL, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
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12
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Stahlke A, Bell D, Dhendup T, Kern B, Pannoni S, Robinson Z, Strait J, Smith S, Hand BK, Hohenlohe PA, Luikart G. Population Genomics Training for the Next Generation of Conservation Geneticists: ConGen 2018 Workshop. J Hered 2021; 111:227-236. [PMID: 32037446 PMCID: PMC7117792 DOI: 10.1093/jhered/esaa001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 01/06/2020] [Indexed: 12/30/2022] Open
Abstract
The increasing availability and complexity of next-generation sequencing (NGS) data sets make ongoing training an essential component of conservation and population genetics research. A workshop entitled “ConGen 2018” was recently held to train researchers in conceptual and practical aspects of NGS data production and analysis for conservation and ecological applications. Sixteen instructors provided helpful lectures, discussions, and hands-on exercises regarding how to plan, produce, and analyze data for many important research questions. Lecture topics ranged from understanding probabilistic (e.g., Bayesian) genotype calling to the detection of local adaptation signatures from genomic, transcriptomic, and epigenomic data. We report on progress in addressing central questions of conservation genomics, advances in NGS data analysis, the potential for genomic tools to assess adaptive capacity, and strategies for training the next generation of conservation genomicists.
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Affiliation(s)
- Amanda Stahlke
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Donavan Bell
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Tashi Dhendup
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Department of Forest and Park Services, Ugyen Wangchuck Institute for Conservation and Environmental Research, Bumthang, Bhutan
| | - Brooke Kern
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN
| | - Samuel Pannoni
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
| | - Zachary Robinson
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Jeffrey Strait
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Seth Smith
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI
| | - Brian K Hand
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Gordon Luikart
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
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13
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Prystupa S, McCracken GR, Perry R, Ruzzante DE. Population abundance in arctic grayling using genetics and close-kin mark-recapture. Ecol Evol 2021; 11:4763-4773. [PMID: 33976846 PMCID: PMC8093667 DOI: 10.1002/ece3.7378] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/29/2021] [Accepted: 02/16/2021] [Indexed: 11/10/2022] Open
Abstract
Arctic Grayling (Thymallus arcticus) are among the most widely distributed and abundant freshwater fish in the Yukon Territory of Canada, yet little information exists regarding their broad and fine-scale population structures or the number and size of these populations. The estimation of population abundance is fundamental for robust management and conservation, yet estimating abundance in the wild is often difficult. Here, we estimated abundance of an Arctic Grayling population using multiple genetic markers and the close-kin mark-recapture (CKMR) method. A total of N = 1,104 Arctic Grayling collected from two systems in Yukon were genotyped at 38 sequenced microsatellites. We first identified structure and assessed genetic diversity (effective population size,N ^ e ). Collections from one of the systems (Lubbock River) comprised adults and young-of-the-year sampled independently allowing the identification of parent-offspring pairs (POPs), and thus, the estimation of abundance using CKMR. We used COLONY and CKMRsim to identify POPs and both provided similar results leading to indistinguishable estimates (95% CI) of census size, that is,N ^ c ( C O L O N Y ) = 1858 (1259-2457) andN ^ c ( C K M R s i m ) = 1812 (1229-2389). The accuracy of the population abundance estimates can in the future be improved with temporal sampling and more precise age or size-specific fecundity estimates for Arctic Grayling. Our study demonstrates that the method can be used to inform management and conservation policy for Arctic Grayling and likely also for other fish species for which the assumption of random and independent sampling of adults and offspring can be assured.
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Affiliation(s)
- Samuel Prystupa
- Department of BiologyDalhousie UniversityHalifaxNSCanada
- Present address:
Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | | | - Robert Perry
- Fish and Wildlife DivisionDepartment of EnvironmentWhitehorse, YukonCanada
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14
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Wright PGR, Schofield H, Mathews F. Can effective population size estimates be used to monitor population trends of woodland bats? A case study of Myotis bechsteinii. Ecol Evol 2021; 11:2015-2023. [PMID: 33717438 PMCID: PMC7920762 DOI: 10.1002/ece3.7143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 12/01/2022] Open
Abstract
Molecular approaches to calculate effective population size estimates (Ne) are increasingly used as an alternative to long-term demographic monitoring of wildlife populations. However, the complex ecology of most long-lived species and the consequent uncertainties in model assumptions means that effective population size estimates are often imprecise. Although methods exist to incorporate age structure into Ne estimations for long-lived species with overlapping generations, they are rarely used owing to the lack of relevant information for most wild populations. Here, we performed a case study on an elusive woodland bat, Myotis bechsteinii, to compare the use of the parentage assignment Ne estimator (EPA) with the more commonly used linkage disequilibrium (LD) Ne estimator in detecting long-term population trends, and assessed the impacts of deploying different overall sample sizes. We used genotypic data from a previously published study, and simulated 48 contrasting demographic scenarios over 150 years using the life history characteristics of this species The LD method strongly outperformed the EPA method. As expected, smaller sample sizes resulted in a reduced ability to detect population trends. Nevertheless, even the smallest sample size tested (n = 30) could detect important changes (60%-80% decline) with the LD method. These results demonstrate that genetic approaches can be an effective way to monitor long-lived species, such as bats, provided that they are undertaken over multiple decades.
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Affiliation(s)
- Patrick G. R. Wright
- Department of Life SciencesUniversity of SussexFalmerUK
- Vincent Wildlife TrustLedburyUK
| | | | - Fiona Mathews
- Department of Life SciencesUniversity of SussexFalmerUK
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15
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Davenport D, Butcher P, Andreotti S, Matthee C, Jones A, Ovenden J. Effective number of white shark ( Carcharodon carcharias, Linnaeus) breeders is stable over four successive years in the population adjacent to eastern Australia and New Zealand. Ecol Evol 2021; 11:186-198. [PMID: 33437422 PMCID: PMC7790646 DOI: 10.1002/ece3.7007] [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: 09/23/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 11/08/2022] Open
Abstract
Population size is a central parameter for conservation; however, monitoring abundance is often problematic for threatened marine species. Despite substantial investment in research, many marine species remain data-poor presenting barriers to the evaluation of conservation management outcomes and the modeling of future solutions. Such is the case for the white shark (Carcharodon carcharias), a highly mobile apex predator for whom recent and substantial population declines have been recorded in many globally distributed populations. Here, we estimate the effective number of breeders that successfully contribute offspring in one reproductive cycle (Nb) to provide a snapshot of recent reproductive effort in an east Australian-New Zealand population of white shark. Nb was estimated over four consecutive age cohorts (2010, 2011, 2012, and 2013) using two genetic estimators (linkage disequilibrium; LD and sibship assignment; SA) based on genetic data derived from two types of genetic markers (single nucleotide polymorphisms; SNPs and microsatellite loci). While estimates of Nb using different marker types produced comparable estimates, microsatellite loci were the least precise. The LD and SA estimates of Nb within cohorts using SNPs were comparable; for example, the 2013 age cohort Nb(SA) was 289 (95% CI 200-461) and Nb(LD) was 208.5 (95% CI 116.4-712.7). We show that over the time period studied, Nb was stable and ranged between 206.1 (SD ± 45.9) and 252.0 (SD ± 46.7) per year using a combined estimate of Nb(LD+SA) from SNP loci. In addition, a simulation approach showed that in this population the effective population size (Ne) per generation can be expected to be larger than Nb per reproductive cycle. This study demonstrates how breeding population size can be monitored over time to provide insight into the effectiveness of recovery and conservation measures for the white shark, where the methods described here may be applicable to other data-poor species of conservation concern.
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Affiliation(s)
- Danielle Davenport
- Molecular Fisheries Laboratory and Schools of Biomedical SciencesUniversity of QueenslandSt. LuciaQLDAustralia
| | - Paul Butcher
- New South Wales Department of Primary IndustriesCoffs HarbourNSWAustralia
| | - Sara Andreotti
- Evolutionary Genomics GroupDepartment of Botany and ZoologyStellenbosch UniversityStellenboschSouth Africa
| | - Conrad Matthee
- Evolutionary Genomics GroupDepartment of Botany and ZoologyStellenbosch UniversityStellenboschSouth Africa
| | - Andrew Jones
- Molecular Fisheries Laboratory and Schools of Biomedical SciencesUniversity of QueenslandSt. LuciaQLDAustralia
| | - Jennifer Ovenden
- Molecular Fisheries Laboratory and Schools of Biomedical SciencesUniversity of QueenslandSt. LuciaQLDAustralia
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16
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Ribolli J, Zaniboni-Filho E, Machado CB, Guerreiro TCDS, Freitas PDD, Galetti Jr PM. Anthropogenic river fragmentation reduces long-term viability of the migratory fish Salminus brasiliensis (Characiformes: Bryconidae) populations. NEOTROPICAL ICHTHYOLOGY 2021. [DOI: 10.1590/1982-0224-2020-0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract Life-history, geographical barriers, and damming can shape the genetic diversity of freshwater migratory fish, which are particularly vulnerable to anthropogenic impacts. We investigated the genetic diversity of Salminus brasiliensis, a long-distance migratory species that is recognized as an important provider of ecosystem services. We implemented microsatellite analyses to assess genetic diversity and simulate future scenarios for evaluating the long-term viability of dammed and non-dammed populations from the Uruguay River. High levels of genetic diversity were detected for all sampled populations. However, effective population sizes were lower in the uppermost river stretches, where the landscape is highly fragmented. Population structure analysis indicated two spatial genetic populations. It is suggested that this genetic structure preserves populations partially isolated by an ancient natural barrier, instead of being a result of the presence of dams. The simulated genetic scenarios indicated that genetic variability of S. brasiliensis populations from upstream dams could collapse over the years, mainly due to the reduction in the number of alleles. Therefore, besides helping to better understand issues related to the influence of dams on the genetic diversity of migratory fish, our results are especially relevant for driving local fishery policies and management actions for the species conservation.
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Affiliation(s)
- Josiane Ribolli
- Universidade Federal de São Carlos, Brazil; Universidade Federal de Santa Catarina, Brazil; Universidade Federal de São Carlos, Brazil
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17
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Shen ZY, Yu D, Gao X, Zhang FT, Liu HZ. Genetic diversity and reproductive success of a wild population of Chinese sturgeon ( Acipenser sinensis) from the Yangtze River inferred from juveniles born in 2014. Zool Res 2020; 41:423-430. [PMID: 32521574 PMCID: PMC7340514 DOI: 10.24272/j.issn.2095-8137.2020.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Chinese sturgeon (Acipenser sinensis Gray, 1835) is a large anadromous fish species, which is under considerable threat due to dramatic declines in population numbers. In the current study, population genetic diversity and individual reproductive success were assessed using nuclear microsatellite markers (simple sequence repeat, SSR) and complete mitochondrial (mtDNA) genome analysis of juveniles born in 2014. Results showed the existence of size polymorphism in the mtDNA genome of Chinese sturgeon, which was caused by a repeat motif. Population genetic diversity was high based on both SSR (Ho: 0.728±0.211; He: 0.779±0.122) and mtDNA genome analyses (H: 0.876±0.0035; Pi: 0.0011±0.0010). A positive inbreeding coefficient (FIS: 0.066±0.143) was also found, indicating the occurrence of inbreeding. Reconstruction of sibling groups identified 11 mothers and 11 fathers involved in reproduction of Chinese sturgeons in 2014. Variance in individual reproductive success was not significant, with reproductive success of parent fish instead shown to be relatively even (P=0.997>0.05), thus suggesting the absence of sweepstakes reproductive success (SRS). These results indicate that, in regard to conservation, loss of genetic diversity due to the effects of SRS is not of particular concern. However, we must focus on having an adequate number of adults and suitable environmental conditions to ensure that fish can reproduce.
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Affiliation(s)
- Zhong-Yuan Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dan Yu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Xin Gao
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Fu-Tie Zhang
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Huan-Zhang Liu
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China. E-mail:
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18
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Klein JD, der Merwe AEBV, Dicken ML, Emami-Khoyi A, Mmonwa KL, Teske PR. A globally threatened shark, Carcharias taurus, shows no population decline in South Africa. Sci Rep 2020; 10:17959. [PMID: 33087802 PMCID: PMC7578018 DOI: 10.1038/s41598-020-75044-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/09/2020] [Indexed: 12/03/2022] Open
Abstract
Knowledge about the demographic histories of natural populations helps to evaluate their conservation status, and potential impacts of natural and anthropogenic pressures. In particular, estimates of effective population size obtained through molecular data can provide useful information to guide management decisions for vulnerable populations. The spotted ragged-tooth shark, Carcharias taurus (also known as the sandtiger or grey nurse shark), is widely distributed in warm-temperate and subtropical waters, but has suffered severe population declines across much of its range as a result of overexploitation. Here, we used multilocus genotype data to investigate the demographic history of the South African C. taurus population. Using approximate Bayesian computation and likelihood-based importance sampling, we found that the population underwent a historical range expansion that may have been linked to climatic changes during the late Pleistocene. There was no evidence for a recent anthropogenic decline. Together with census data suggesting a stable population, these results support the idea that fishing pressure and other threats have so far not been detrimental to the local C. taurus population. The results reported here indicate that South Africa could possibly harbour the last remaining, relatively pristine population of this widespread but vulnerable top predator.
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Affiliation(s)
- Juliana D Klein
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Aletta E Bester-van der Merwe
- Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, 7600, South Africa
| | - Matthew L Dicken
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, 4320, South Africa
- Department of Development Studies, School of Economics, Development and Tourism, Nelson Mandela University, Port Elizabeth, 6031, South Africa
| | - Arsalan Emami-Khoyi
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Kolobe L Mmonwa
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, 4320, South Africa
| | - Peter R Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park, 2006, South Africa.
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19
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Papa Y, Oosting T, Valenza-Troubat N, Wellenreuther M, Ritchie PA. Genetic stock structure of New Zealand fish and the use of genomics in fisheries management: an overview and outlook. NEW ZEALAND JOURNAL OF ZOOLOGY 2020. [DOI: 10.1080/03014223.2020.1788612] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yvan Papa
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Tom Oosting
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Noemie Valenza-Troubat
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
- New Zealand Institute for Plant and Food Research Ltd, Nelson, New Zealand
| | - Maren Wellenreuther
- New Zealand Institute for Plant and Food Research Ltd, Nelson, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Peter A. Ritchie
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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20
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Sato Y, Ogden R, Kishida T, Nakajima N, Maeda T, Inoue-Murayama M. Population history of the golden eagle inferred from whole-genome sequencing of three of its subspecies. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa068] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe application of evolutionary genetic research to investigate the potential for endangered species to adapt to changing environments is important for conservation biology. Effective population size (Ne) is informative for understanding adaptive potential as it refers to the genetic variation in breeding individuals who have contributed to contemporary and historic population diversity. We reconstruct fluctuations in Ne in three golden eagle subspecies (Japanese, Scottish, North American) using the pairwise sequential Markovian coalescent (PSMC) model based on whole-genome sequence data. Our results indicate the timing of subspeciation events and suggest significant ongoing demographic reductions since the start of the Last Glacial Period. Importantly, we find evidence for gene flow from continental populations into the ancestral Japanese population resulting in a short, sharp recovery in genetic diversity. Timing agrees with the palaeogeographic estimates of land bridge connections between the Japanese archipelago and Asian continent and matches a similar Ne spike in the Scottish population, but not in the North American population. Given contemporary declines in isolated Japanese and UK island populations, our study highlights a concerning loss of local genetic diversity, but also indicates the likely response of populations to genetic reinforcement from neighbouring subspecies, increasing management options and encouraging a range-wide species conservation approach.
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Affiliation(s)
- Yu Sato
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, Easter Bush Campus, University of Edinburgh, UK
| | - Takushi Kishida
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Museum of Natural and Environmental History, Shizuoka, Japan
| | - Nobuyoshi Nakajima
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Japan
| | - Taku Maeda
- Iwate Prefectural Research Institute for Environmental Sciences and Public Health, Morioka, Japan
| | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto, Japan
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Japan
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21
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Mamoozadeh NR, Graves JE, McDowell JR. Genome-wide SNPs resolve spatiotemporal patterns of connectivity within striped marlin ( Kajikia audax), a broadly distributed and highly migratory pelagic species. Evol Appl 2020; 13:677-698. [PMID: 32211060 PMCID: PMC7086058 DOI: 10.1111/eva.12892] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/23/2019] [Accepted: 10/16/2019] [Indexed: 01/04/2023] Open
Abstract
Genomic methodologies offer unprecedented opportunities for statistically robust studies of species broadly distributed in environments conducive to high gene flow, providing valuable information for wildlife conservation and management. Here, we sequence restriction site-associated DNA to characterize genome-wide single nucleotide polymorphisms (SNPs) in a broadly distributed and highly migratory large pelagic fish, striped marlin (Kajikia audax). Assessment of over 4,000 SNPs resolved spatiotemporal patterns of genetic connectivity throughout the species range in the Pacific and, for the first time, Indian oceans. Individual-based cluster analyses identified six genetically distinct populations corresponding with the western Indian, eastern Indian, western South Pacific, and eastern central Pacific oceans, as well as two populations in the North Pacific Ocean (F ST = 0.0137-0.0819). F ST outlier analyses identified a subset of SNPs (n = 59) putatively under the influence of natural selection and capable of resolving populations separated by comparatively high degrees of genetic differentiation. Temporal collections available for some regions demonstrated the stability of allele frequencies over three to five generations of striped marlin. Relative migration rates reflected lower levels of genetic connectivity between Indian Ocean populations (m R ≤ 0.37) compared with most populations in the Pacific Ocean (m R ≥ 0.57) and highlight the importance of the western South Pacific in facilitating gene flow between ocean basins. Collectively, our results provide novel insights into rangewide population structure for striped marlin and highlight substantial inconsistencies between genetically distinct populations and stocks currently recognized for fisheries management. More broadly, we demonstrate that species capable of long-distance dispersal in environments lacking obvious physical barriers to movement can display substantial population subdivision that persists over multiple generations and that may be facilitated by both neutral and adaptive processes. Importantly, surveys of genome-wide markers enable inference of population-level relationships using sample sizes practical for large pelagic fishes of conservation concern.
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Affiliation(s)
- Nadya R. Mamoozadeh
- Department of Fisheries ScienceVirginia Institute of Marine ScienceWilliam & MaryGloucester PointVirginia
| | - John E. Graves
- Department of Fisheries ScienceVirginia Institute of Marine ScienceWilliam & MaryGloucester PointVirginia
| | - Jan R. McDowell
- Department of Fisheries ScienceVirginia Institute of Marine ScienceWilliam & MaryGloucester PointVirginia
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22
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Ruzzante DE, McCracken GR, Førland B, MacMillan J, Notte D, Buhariwalla C, Mills Flemming J, Skaug H. Validation of close‐kin mark–recapture (CKMR) methods for estimating population abundance. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13243] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | | | - Brage Førland
- Department of Mathematics University of Bergen Bergen Norway
| | - John MacMillan
- Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture Halifax Nova Scotia Canada
| | - Daniela Notte
- Department of Biology Dalhousie University Halifax Nova Scotia Canada
| | - Colin Buhariwalla
- Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture Halifax Nova Scotia Canada
| | - Joanna Mills Flemming
- Department of Mathematics and Statistics Dalhousie University Halifax Nova Scotia Canada
| | - Hans Skaug
- Department of Mathematics University of Bergen Bergen Norway
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23
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Jones AT, Lavery SD, Le Port A, Wang YG, Blower D, Ovenden J. Sweepstakes reproductive success is absent in a New Zealand snapper (Chrysophrus auratus) population protected from fishing despite "tiny" N e /N ratios elsewhere. Mol Ecol 2019; 28:2986-2995. [PMID: 31087739 DOI: 10.1111/mec.15130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/30/2019] [Accepted: 05/01/2019] [Indexed: 01/07/2023]
Abstract
A landmark study published in 2002 estimated a very small Ne /N ratio (around 10-5 ) in a population of pink snapper (Chrysophrys auratus, Forster, 1801) in the Hauraki Gulf in New Zealand. It epitomized the tiny Ne /N ratios (<10-3 ) reported in marine species due to the hypothesized operation of sweepstakes reproductive success (SRS). Here we re-evaluate the occurrence of SRS in marine species and the potential effect of fishing on the Ne /N ratio by studying the same species in the same region, but in a population that has been protected from fishing since 1975. We combine empirical, simulation and model-based approaches to estimate Ne (and Nb ) from genotypes of 1,044 adult fish and estimate N using recapture-probabilities. The estimated Ne /N ratio was much larger (0.33, SE: 0.14) than expected. The magnitude of estimates of population-wide variance in individual lifetime reproductive success (10-18) suggested that the sweepstakes effect was negligible in the study population. After evaluating factors that could explain the contrast between studies - experimental design, life history differences, environmental effects and the influence of exploitation on the Ne /N ratio - we conclude that the low Ne of the Hauraki Gulf population is associated with demographic instability in the harvested compared to the protected population despite circumstantial evidence that the 2002 study may have underestimated Ne . This study has broad implications for the prevailing view that reproductive success in the sea is largely driven by chance, and for genetic monitoring of populations using the Ne /N ratio and Nb .
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Affiliation(s)
- Andrew T Jones
- School of Mathematics and Physics, University of Queensland, Brisbane, Queensland, Australia
| | - Shane D Lavery
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Agnès Le Port
- Institute of Marine Science, University of Auckland, Auckland, New Zealand.,Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, Queensland, Australia
| | - You-Gan Wang
- Science and Engineering Faculty, School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Dean Blower
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia.,Molecular Fisheries Laboratory and School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Jennifer Ovenden
- Molecular Fisheries Laboratory and School of Biomedical Sciences, University of Queensland, Brisbane, Queensland, Australia
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24
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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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