1
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Weise EM, Scribner KT, Adams JV, Boeberitz O, Jubar A, Bravener G, Johnson NS, Robinson JD. Pedigree analysis and estimates of effective breeding size characterize sea lamprey reproductive biology. Evol Appl 2022; 15:484-500. [PMID: 35386399 PMCID: PMC8965388 DOI: 10.1111/eva.13364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 12/02/2022] Open
Abstract
The sea lamprey (Petromyzon marinus) is an invasive species in the Great Lakes and the focus of a large control and assessment program. Current assessment methods provide information on the census size of spawning adult sea lamprey in a small number of streams, but information characterizing reproductive success of spawning adults is rarely available. We used RAD-capture sequencing to genotype single nucleotide polymorphism (SNP) loci for ~1600 sea lamprey larvae collected from three streams in northern Michigan (Black Mallard, Pigeon, and Ocqueoc Rivers). Larval genotypes were used to reconstruct family pedigrees, which were combined with Gaussian mixture analyses to identify larval age classes for estimation of spawning population size. Two complementary estimates of effective breeding size (N b), as well as the extrapolated minimum number of spawners (N s), were also generated for each cohort. Reconstructed pedigrees highlighted inaccuracies of cohort assignments from traditionally used mixture analyses. However, combining genotype-based pedigree information with length-at-age assignment of cohort membership greatly improved cohort identification accuracy. Population estimates across all three streams sampled in this study indicate a small number of successfully spawning adults when barriers were in operation, implying that barriers limited adult spawning numbers but were not completely effective at blocking access to spawning habitats. Thus, the large numbers of larvae present in sampled systems were a poor indicator of spawning adult abundance. Overall, pedigree-based N b and N s estimates provide a promising and rapid assessment tool for sea lamprey and other species.
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Affiliation(s)
- Ellen M. Weise
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
| | - Kim T. Scribner
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
- Department of Integrative BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Jean V. Adams
- US Geological Survey ‐ Great Lakes Science CenterAnn ArborMichiganUSA
| | - Olivia Boeberitz
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
| | | | - Gale Bravener
- Fisheries and Oceans CanadaSea Lamprey Control CentreSault Ste. MarieOntarioCanada
| | - Nicholas S. Johnson
- US Geological SurveyGreat Lakes Science CenterHammond Bay Biological StationMillersburgMichiganUSA
| | - John D. Robinson
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
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2
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Gwak WS, Roy A. Genetic Diversity and Variation in Mitochondrial COI Gene in Wild and Hatchery Populations of Saxidomus purpuratus. Biochem Genet 2021; 60:969-986. [PMID: 34611791 DOI: 10.1007/s10528-021-10137-9] [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: 06/10/2021] [Accepted: 09/23/2021] [Indexed: 11/25/2022]
Abstract
To investigate the genetic diversity and genetic variations of four wild (Geoje, Jinhae, Yeosu, and Boryeong) and two hatchery (Goheung and Geoje) populations of purplish Washington clam (Saxidomus purpuratus), 421 bp sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene were analyzed. A total of 149 haplotypes were identified from 358 individuals from the four wild and two hatchery populations with 109 substitutions. The genetic diversity of the wild populations and Geoje hatchery population were high, whereas the total number of haplotypes, population-specific haplotypes, and haplotype diversity were comparatively low in the Goheung hatchery population. The fixation index (FST) indicated that there was no significant genetic difference between the four wild populations. However, the Goheung hatchery population was significantly different from that of the Geoje hatchery, exhibiting the most pronounced difference, and two wild populations (Jinhae and Yeosu). The low genetic diversity indices exhibited by the Goheung hatchery population might have resulted from farm propagation using a limited parental stock. Therefore, to maintain genetic diversity, a proper breeding management program using more progenitors is required in hatcheries, in addition to regular monitoring of both hatchery and wild populations.
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Affiliation(s)
- Woo-Seok Gwak
- Marine Bio-Education and Research Center, Gyeongsang National University, Tongyeong, 53064, Korea.
- Marine Bio-Education and Research Center, Gyeongsang National University, Tongyeong, 53064, Korea.
| | - Animesh Roy
- Marine Bio-Education and Research Center, Gyeongsang National University, Tongyeong, 53064, Korea
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3
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Yates MC, Cristescu ME, Derry AM. Integrating physiology and environmental dynamics to operationalize environmental DNA (eDNA) as a means to monitor freshwater macro-organism abundance. Mol Ecol 2021; 30:6531-6550. [PMID: 34592014 DOI: 10.1111/mec.16202] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/03/2021] [Accepted: 09/17/2021] [Indexed: 12/14/2022]
Abstract
Research has demonstrated consistent positive correlations between organism abundance and absolute environmental DNA (eDNA) concentrations. Robust correlations in laboratory experiments indicate strong functional links, suggesting the potential for eDNA to monitor organism abundance in nature. However, correlations between absolute eDNA concentrations and organism abundance in nature tend to be weaker because myriad biotic and abiotic factors influence steady-state eDNA concentrations, decoupling its direct functional link with abundance. Additional technical challenges can also weaken correlations between relative organism abundance and relative eDNA data derived from metabarcoding. Future research must account for these factors to improve the inference of organism abundance from eDNA, including integrating the effects of organism physiology on eDNA production, eDNA dynamics in lentic/lotic systems, and key environmental parameters that impact estimated steady-state concentrations. Additionally, it is critical to manage expectations surrounding the accuracy and precision that eDNA can provide - eDNA, for example, cannot provide abundance estimates comparable to intensively managed freshwater fisheries that enumerate every individual fish. Recent developments, however, are encouraging. Current methods could provide meaningful information regarding qualitative conservation thresholds and emergent research has demonstrated that eDNA concentrations in natural ecosystems can provide rough quantitative estimates of abundance, particularly when models integrate physiology and/or eDNA dynamics. Operationalizing eDNA to infer abundance will probably require more than simple correlations with organism biomass/density. Nevertheless, the future is promising - models that integrate eDNA dynamics in nature could represent an effective means to infer abundance, particularly when traditional methods are considered too "costly" or difficult to obtain.
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Affiliation(s)
| | | | - Alison M Derry
- Université du Québec à Montréal, Montréal, Québec, Canada
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4
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Gajdzik L, Green AL, Cochran JEM, Hardenstine RS, Tanabe LK, Berumen ML. Using species connectivity to achieve coordinated large-scale marine conservation efforts in the Red Sea. MARINE POLLUTION BULLETIN 2021; 166:112244. [PMID: 33740655 DOI: 10.1016/j.marpolbul.2021.112244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 02/28/2021] [Accepted: 03/02/2021] [Indexed: 05/12/2023]
Abstract
In the face of increasing anthropogenic threats, coastal nations need to reach common ground for effective marine conservation. Understanding species' connectivity can reveal how nations share resources, demonstrating the need for cooperative protection efforts. Unfortunately, connectivity information is rarely integrated into the design of marine protected areas (MPAs). This is exemplified in the Red Sea where biodiversity is only nominally protected by a non-cohesive network of small-sized MPAs, most of which are barely implemented. Here, we showcase the potential of using connectivity patterns of flagship species to consolidate conservation efforts in the Red Sea. We argue that a large-scale MPA (LSMPA) would more effectively preserve Red Sea species' multinational migration routes. A connectivity-informed LSMPA approach provides thus one avenue to unite coastal nations toward acting for the common good of conservation and reverse the global decline in marine biodiversity.
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Affiliation(s)
- Laura Gajdzik
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, 23955 Thuwal, Saudi Arabia.
| | - Alison L Green
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, 23955 Thuwal, Saudi Arabia
| | - Jesse E M Cochran
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, 23955 Thuwal, Saudi Arabia
| | - Royale S Hardenstine
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, 23955 Thuwal, Saudi Arabia
| | - Lyndsey K Tanabe
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, 23955 Thuwal, Saudi Arabia
| | - Michael L Berumen
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), 4700 KAUST, 23955 Thuwal, Saudi Arabia
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5
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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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6
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Pirog A, Ravigné V, Fontaine MC, Rieux A, Gilabert A, Cliff G, Clua E, Daly R, Heithaus MR, Kiszka JJ, Matich P, Nevill JEG, Smoothey AF, Temple AJ, Berggren P, Jaquemet S, Magalon H. Population structure, connectivity, and demographic history of an apex marine predator, the bull shark Carcharhinus leucas. Ecol Evol 2019; 9:12980-13000. [PMID: 31871624 PMCID: PMC6912899 DOI: 10.1002/ece3.5597] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 07/23/2019] [Accepted: 07/28/2019] [Indexed: 01/16/2023] Open
Abstract
Knowledge of population structure, connectivity, and effective population size remains limited for many marine apex predators, including the bull shark Carcharhinus leucas. This large-bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark likely plays a vital ecological role within marine food webs, but is at risk due to inshore habitat degradation and various fishing pressures. We investigated the bull shark's global population structure and demographic history by analyzing the genetic diversity of 370 individuals from 11 different locations using 25 microsatellite loci and three mitochondrial genes (CR, nd4, and cytb). Both types of markers revealed clustering between sharks from the Western Atlantic and those from the Western Pacific and the Western Indian Ocean, with no contemporary gene flow. Microsatellite data suggested low differentiation between the Western Indian Ocean and the Western Pacific, but substantial differentiation was found using mitochondrial DNA. Integrating information from both types of markers and using Bayesian computation with a random forest procedure (ABC-RF), this discordance was found to be due to a complete lack of contemporary gene flow. High genetic connectivity was found both within the Western Indian Ocean and within the Western Pacific. In conclusion, these results suggest important structuring of bull shark populations globally with important gene flow occurring along coastlines, highlighting the need for management and conservation plans on regional scales rather than oceanic basin scale.
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Affiliation(s)
- Agathe Pirog
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint DenisFrance
| | | | - Michaël C. Fontaine
- Laboratoire MIVEGEC (Université de Montpellier UMR CNRS 5290, IRD 229)Centre IRD de MontpellierMontpellierFrance
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | | | | | - Geremy Cliff
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- School of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Eric Clua
- EPHECNRS UPVDUSR 3278 CRIOBEPSL Research UniversityPerpignanFrance
- Laboratoire d'Excellence CORAILPerpignanFrance
| | - Ryan Daly
- Oceanographic Research InstituteDurbanSouth Africa
- South African Institute for Aquatic BiodiversityGrahamstownSouth Africa
| | - Michael R. Heithaus
- Department of Biological SciencesFlorida International UniversityNorth MiamiFLUSA
| | - Jeremy J. Kiszka
- Department of Biological SciencesFlorida International UniversityNorth MiamiFLUSA
| | - Philip Matich
- Department of Biological SciencesFlorida International UniversityNorth MiamiFLUSA
| | | | - Amy F. Smoothey
- NSW Department of Primary IndustriesSydney Institute of Marine ScienceMosmanNSWAustralia
| | - Andrew J. Temple
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Per Berggren
- School of Natural and Environmental SciencesNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Sébastien Jaquemet
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint DenisFrance
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion/IRD/CNRS)Université de La RéunionSaint DenisFrance
- Laboratoire d'Excellence CORAILPerpignanFrance
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7
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Sandoval-Castillo J. Conservation genetics of elasmobranchs of the Mexican Pacific Coast, trends and perspectives. ADVANCES IN MARINE BIOLOGY 2019; 83:115-157. [PMID: 31606069 DOI: 10.1016/bs.amb.2019.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
One of the most critical threats to biodiversity is the high extinction rate driven by human activities. Reducing extinction rates requires the implementation of conservation programmes based on robust scientific data. Elasmobranchs are important ecological components of the ocean, and several species sustain substantial economic activities. Unfortunately, elasmobranchs are one of the most threatened and understudied animal taxa. The Mexican Pacific Coast (MPC) is a region with high elasmobranch diversity and is the seat of major elasmobranch fisheries. But it is also a developing region with several conservation and management challenges which require national and international attention. Here, we review the conservation genetics literature of elasmobranchs from the MPC. We present a synthesis of the works using samples from the region and emphasize the main gaps and biases in these data. In addition, we discuss the benefits and challenges of generating genomic information to improve the management and conservation of an elasmobranch biodiversity hotspot in a developing country. We found 47 elasmobranch genetic articles that cover <30% of the elasmobranch diversity in the region. These studies mainly used mitochondrial DNA sequences to analyse the genetic structure of commercially important and abundant species of the order Carcharhiniformes. Some of these papers also assessed mating systems, demographic parameters, and taxonomic uncertainties, all of which are important topics for efficient management decisions. In terms of conservation genetics, elasmobranchs from the MPC remain understudied. However, high-throughput sequencing technologies have increased the power and accessibility of genomic tools, even in developing countries such as Mexico. The tools described here provide information relevant for biodiversity conservation. Therefore, we strongly suggest that investment in genomic research will assist implementation of efficient management strategies. In time, this will reduce the extinction risk of the unique elasmobranch biodiversity from the MPC.
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Affiliation(s)
- Jonathan Sandoval-Castillo
- Molecular Ecology Lab, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.
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8
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Oosting T, Star B, Barrett JH, Wellenreuther M, Ritchie PA, Rawlence NJ. Unlocking the potential of ancient fish DNA in the genomic era. Evol Appl 2019; 12:1513-1522. [PMID: 31462911 PMCID: PMC6708421 DOI: 10.1111/eva.12811] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 04/11/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022] Open
Abstract
Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.
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Affiliation(s)
- Tom Oosting
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Bastiaan Star
- Department of Biosciences, Centre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | - James H. Barrett
- Department of ArchaeologyUniversity of CambridgeCambridgeUK
- Department of Archaeology and Cultural HistoryNTNU University MuseumTrondheimNorway
- Trinity Centre for Environmental HumanitiesTrinity College DublinDublinIreland
| | - Maren Wellenreuther
- Nelson Seafood Research UnitPlant and Food ResearchNelsonNew Zealand
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | - Peter A. Ritchie
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Nicolas J. Rawlence
- Otago Palaeogenetics Laboratory, Department of ZoologyUniversity of OtagoDunedinNew Zealand
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9
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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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10
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Gajdzik L, Bernardi G, Lepoint G, Frédérich B. Genetic diversity mirrors trophic ecology in coral reef fish feeding guilds. Mol Ecol 2018; 27:5004-5018. [DOI: 10.1111/mec.14936] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 10/16/2018] [Accepted: 10/24/2018] [Indexed: 11/26/2022]
Affiliation(s)
- Laura Gajdzik
- Laboratory of Functional and Evolutionary Morphology FOCUS, University of Liège Liège Belgium
| | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz California
| | - Gilles Lepoint
- Laboratory of Oceanology FOCUS, University of Liège Liège Belgium
| | - Bruno Frédérich
- Laboratory of Functional and Evolutionary Morphology FOCUS, University of Liège Liège Belgium
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11
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Blower DC, Riginos C, Ovenden JR. neogen: A tool to predict genetic effective population size (N e ) for species with generational overlap and to assist empirical N e study design. Mol Ecol Resour 2018; 19:260-271. [PMID: 30194750 DOI: 10.1111/1755-0998.12941] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 08/21/2018] [Accepted: 08/28/2018] [Indexed: 12/17/2022]
Abstract
Molecular genetic estimates of population effective size (Ne ) lose accuracy and precision when insufficient numbers of samples or loci are used. Ideally, researchers would like to forecast the necessary power when planning their project. neogen (genetic Ne for Overlapping Generations) enables estimates of precision and accuracy in advance of empirical investigation and allows exploration of the power available in different user-specified age-structured sampling schemes. neogen provides a population simulation and genetic power analysis framework that simulates the demographics, genetic composition, and Ne , from species-specific life history, mortality, population size, and genetic priors. neogen guides the user to establish a tractable sampling regime and to determine the numbers of samples and microsatellite or SNP loci required for accurate and precise genetic Ne estimates when sampling a natural population. neogen is useful at multiple stages of a study's life cycle: when budgeting, as sampling and locus development progresses, and for corroboration when empirical Ne estimates are available. The underlying model is applicable to a wide variety of iteroparous species with overlapping generations (e.g., mammals, birds, reptiles, long-lived fishes). In this paper, we describe the neogen model, detail the workflow for the point-and-click software, and explain the graphical results. We demonstrate the use of neogen with empirical Australian east coast zebra shark (Stegostoma fasciatum) data. For researchers wishing to make accurate and precise genetic Ne estimates for overlapping generations species, neogen facilitates planning for sample and locus acquisition, and with existing empirical genetic Ne estimates neogen can corroborate population demographic and life history properties.
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Affiliation(s)
- Dean C Blower
- School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, Australia.,Molecular Fisheries Laboratory, The University of Queensland, St. Lucia, Queensland, Australia
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Jennifer R Ovenden
- Molecular Fisheries Laboratory, The University of Queensland, St. Lucia, Queensland, Australia.,School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia
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12
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Sahoo L, Mohanty M, Meher PK, Murmu K, Sundaray JK, Das P. Population structure and genetic diversity of hatchery stocks as revealed by combined mtDNA fragment sequences in Indian major carp, Catla catla. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:289-295. [PMID: 29989460 DOI: 10.1080/24701394.2018.1484120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Catla catla is the second most important Indian major carp due to high growth rate and acceptance to consumers for food value. It is widely cultured in the Indian subcontinent as monoculture or polyculture. In the present study, genetic diversity among hatchery stocks (total 218 samples of catla) collected from different geographical regions of India was examined using mtDNA fragment sequence of Cyt b (306 bp) and D loop (710 bp). High numbers (57) of population specific haplotypes were observed in the present study. The results revealed significant genetic heterogeneity for the sequence data (FST = 0.27546, p < .05). Analysis of molecular variance revealed significant genetic differentiation among different catla populations. The information generated in present study could be useful to develop broad genetic base populations of catla.
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Affiliation(s)
- L Sahoo
- a Fish Genetics and Biotechnology Division , ICAR-CIFA , Kausalyaganga, Bhubaneswar , Odisha , India
| | - M Mohanty
- a Fish Genetics and Biotechnology Division , ICAR-CIFA , Kausalyaganga, Bhubaneswar , Odisha , India
| | - P K Meher
- a Fish Genetics and Biotechnology Division , ICAR-CIFA , Kausalyaganga, Bhubaneswar , Odisha , India
| | - K Murmu
- a Fish Genetics and Biotechnology Division , ICAR-CIFA , Kausalyaganga, Bhubaneswar , Odisha , India
| | - J K Sundaray
- a Fish Genetics and Biotechnology Division , ICAR-CIFA , Kausalyaganga, Bhubaneswar , Odisha , India
| | - P Das
- a Fish Genetics and Biotechnology Division , ICAR-CIFA , Kausalyaganga, Bhubaneswar , Odisha , India
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Crane NL, Tariel J, Caselle JE, Friedlander AM, Robertson DR, Bernardi G. Clipperton Atoll as a model to study small marine populations: Endemism and the genomic consequences of small population size. PLoS One 2018; 13:e0198901. [PMID: 29949612 PMCID: PMC6021044 DOI: 10.1371/journal.pone.0198901] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/29/2018] [Indexed: 01/05/2023] Open
Abstract
Estimating population sizes and genetic diversity are key factors to understand and predict population dynamics. Marine species have been a difficult challenge in that respect, due to the difficulty in assessing population sizes and the open nature of such populations. Small, isolated islands with endemic species offer an opportunity to groundtruth population size estimates with empirical data and investigate the genetic consequences of such small populations. Here we focus on two endemic species of reef fish, the Clipperton damselfish, Stegastes baldwini, and the Clipperton angelfish, Holacanthus limbaughi, on Clipperton Atoll, tropical eastern Pacific. Visual surveys, performed over almost two decades and four expeditions, and genetic surveys based on genomic RAD sequences, allowed us to estimate kinship and genetic diversity, as well as to compare population size estimates based on visual surveys with effective population sizes based on genetics. We found that genetic and visual estimates of population numbers were remarkably similar. S. baldwini and H. limbaughi had population sizes of approximately 800,000 and 60,000, respectively. Relatively small population sizes resulted in low genetic diversity and the presence of apparent kinship. This study emphasizes the importance of small isolated islands as models to study population dynamics of marine organisms.
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Affiliation(s)
- Nicole L. Crane
- Department of Biology, Cabrillo College, Aptos, CA, United States of America
| | - Juliette Tariel
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Jennifer E. Caselle
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, United States of America
| | - Alan M. Friedlander
- Pristine Seas, National Geographic Society, Washington, DC, United States of America
- Fisheries Ecology Research Lab, Department of Biology, University of Hawaii, Honolulu, HI, United States of America
| | | | - Giacomo Bernardi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California, United States of America
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Couvray S, Coupé S. Three-year monitoring of genetic diversity reveals a micro-connectivity pattern and local recruitment in the broadcast marine species Paracentrotus lividus. Heredity (Edinb) 2017; 120:110-124. [PMID: 29180717 DOI: 10.1038/s41437-017-0013-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 09/14/2017] [Accepted: 09/23/2017] [Indexed: 12/20/2022] Open
Abstract
In conservation and management of marine biological resources, a knowledge of connectivity is necessary to understand how local populations are naturally replenished by the arrival of new recruits from source populations. At small geographical scales, species experiencing moderate to long pelagic larval phases are mostly genetically homogeneous, which hinders inferences about local connectivity. Recent studies demonstrated that assessing genetic relatedness and kinship could provide information about local connectivity in populations with high levels of gene flow. Here, we were interested in deciphering the structure and connectivity of populations of the sea urchin Paracentrotus lividus, by monitoring populations at 11 localities distributed along a 225-km coast-line in the south-eastern French Mediterranean Sea. Using 12 microsatellite loci, we found a weak but significant genetic differentiation and observed a transient genetic differentiation among locations within temporal cohorts, without any correlation with the distance between locations, interpreted as unexplainable chaotic genetic patchiness. Among temporal cohorts, the more related individuals were mainly found within locations and the observed local differentiation (FST) correlated with the proportion of kin within locations, suggesting that larvae dispersed cohesively. Specifically, we could also reveal that populations flanking Cape Sicié were influenced by eastern populations and that local recruitment was a frequent occurrence. Overall, our results contribute to the growing number of studies showing that connectivity can be reliably assessed at a fine spatial scale even in genetically homogenous populations.
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Affiliation(s)
- Sylvain Couvray
- Institut Océanographique Paul Ricard, Ile des Embiez, 83140, Six-Fours-Les-Plages, France
| | - Stéphane Coupé
- Univ Toulon, Aix Marseille Univ, CNRS/INSU, IRD, MIO UM 110, Mediterranean Institute of Oceanography, La Garde, France.
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Yates MC, Bernos TA, Fraser DJ. A critical assessment of estimating census population size from genetic population size (or vice versa) in three fishes. Evol Appl 2017; 10:935-945. [PMID: 29151884 PMCID: PMC5680432 DOI: 10.1111/eva.12496] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/22/2017] [Indexed: 12/25/2022] Open
Abstract
Technological and methodological advances have facilitated the use of genetic data to infer census population size (Nc) in natural populations, particularly where traditional mark-and-recapture is challenging. The effective number of breeders (Nb) describes how many adults effectively contribute to a cohort and is often correlated with Nc. Predicting Nc from Nb or vice versa in species with overlapping generations has important implications for conservation by permitting (i) estimation of the more difficult to quantify variable and (ii) inferences of Nb/Nc relationships in related species lacking data. We quantitatively synthesized Nb/Nc relationships in three salmonid fishes where sufficient data have recently accumulated. Mixed-effects models were analysed in which each variable was included as a dependent variable or predictor term (Nb from Nc and vice versa). Species-dependent Nb/Nc slope estimates were significantly positive in two of three species. Variation in species slopes was likely due to varying life histories and reinforce caution when inferring Nb/Nc from taxonomically related species. Models provided maximum probable estimates for Nb and Nc for two species. However, study, population and year effects explained substantial amounts of variation (39%-57%). Consequently, prediction intervals were wide and included or were close to zero for all population sizes and species; model predictive utility was limited. Cost-benefit trade-offs when estimating Nb and/or Nc were also discussed using a real-world system example. Our findings based on salmonids suggest that no short cuts currently exist when estimating population size and researchers should focus on quantifying the variable of interest or be aware of caveats when inferring the desired variable because of cost or logistics. We caution that the salmonid species examined share life-history traits that may obscure relationships between Nb and Nc. Sufficient data on other taxa were unavailable; additional research examining Nb/Nc relationships in species with potentially relevant life-history trait differences (e.g., differing survival curves) is needed.
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Affiliation(s)
- Matthew Carl Yates
- Department of BiologyConcordia UniversityMontrealQCCanada
- Group for Interuniversity Research in Limnology and Aquatic Environments (GRIL)Universite du QuebecTrois‐RivieresQCCanada
| | | | - Dylan J. Fraser
- Department of BiologyConcordia UniversityMontrealQCCanada
- Group for Interuniversity Research in Limnology and Aquatic Environments (GRIL)Universite du QuebecTrois‐RivieresQCCanada
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Carvalho GR, Hauser L, Martinsohn J, Naish K. Fish, genes and genomes: contributions to ecology, evolution and management. JOURNAL OF FISH BIOLOGY 2016; 89:2471-2478. [PMID: 27921308 DOI: 10.1111/jfb.13228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- G R Carvalho
- Molecular Ecology & Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, U.K
| | - L Hauser
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, U.S.A
| | - J Martinsohn
- European Commission, Joint Research Centre (JRC), Directorate D - Sustainable Resources, Water and Marine Resources, Via E. Fermi 2749, I-21027, Ispra, VA, Italy
| | - K Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98195-5020, U.S.A
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