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Dolan TE, Feldheim KA, O'Leary SJ, Fede CM, McElroy AE, Frisk MG. Patterns of persistence: Genetic and behavioral population complexity of winter flounder amid population declines. JOURNAL OF FISH BIOLOGY 2024; 105:1280-1297. [PMID: 39109654 DOI: 10.1111/jfb.15890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 10/09/2024]
Abstract
Winter flounder Pseudopleuronectes americanus (Walbaum 1792) are a coastal flatfish species of economic and cultural importance that have dwindled to <15, % of their historic abundance in the southern New England/Mid-Atlantic region of the United States, with evidence indicating near-extirpation of certain local populations. This species exhibits intricate behaviors in spawning and migration that contribute to population complexity and resilience. These behaviors encompass full or partial philopatry to natal estuaries, the generation of multiple pulses of larval delivery, and partial migration. The patterns of genetic diversity within and among estuaries and cohorts presented here carry important implications in understanding the susceptibility to demographic shocks, even if the full extent of genetic diversity within and among winter flounder stocks on the US East Coast remains unresolved. Our findings reveal connectivity between estuaries in Long Island, New York, suggesting the potential for genetic rescue of depleted subpopulations. Family reconstruction and relatedness analysis indicate that split cohorts and migration contingents are not the result of genetically distinct lineages. We found no evidence for genetic structure separating these groups, and in some instances, we were able to detect closely related individuals that belonged to different migratory contingents or cohorts. Characterizing the spatial and behavioral organization of this species at the population level is crucial for comprehending its potential for recovery, not only in terms of biomass but also in reinstating the complex population structure that supports resilience. The search for generality in winter flounder spawning and migration behavior remains elusive, but perhaps the lack of generalities within this species is what has allowed it to persist in the face of decades of environmental and anthropogenic stressors.
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Affiliation(s)
- Tara E Dolan
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
- Massachusetts Division of Marine Fisheries, Salem, Massachusetts, USA
| | - Kevin A Feldheim
- Prizker Laboratory for Molecular Systematics and Evolution, The Field Museum, Chicago, Illinois, USA
| | - Shannon J O'Leary
- Department of Biological Sciences, St Anselm College, Goffstown, New Hampshire, USA
| | - Catherine M Fede
- Marine Resources Division, New York State Department of Environmental Conservation, Kings Park, New York, USA
| | - Anne E McElroy
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
| | - Michael G Frisk
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
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EST-Microsatellite Types and Structural Scenarios in European Hake Fisheries. Animals (Basel) 2022; 12:ani12111462. [PMID: 35681926 PMCID: PMC9179439 DOI: 10.3390/ani12111462] [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: 05/06/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 11/17/2022] Open
Abstract
A fishery’s structure and connectivity are priors to its effective management. A successful description of such processes depends on both the sampling design and the choice of adequate genetic markers. EST markers are perfusing the studies of marine metapopulations and are believed to provide access to functional polymorphisms. However, the assumed adaptive role of outlier EST loci might not be generalizable. EST-microsatellites represent the upper polymorphic boundary in these regions because of their high mutation rate. We have subclassified the polymorphisms of EST-microsatellites to assess their structural contribution in the European hake, a paradigmatic and highly mobile marine species (HMMS). Because of the counterbalanced forces between directional markers (15%) and balanced markers (23%), the whole marker set offers the same structural situation as the one observed with neutral markers (62%), i.e., k = 2 gene pools. In contrast to outlier EST- microsatellites, neutral EST subsets allow one to measure crucial population phenomena for fisheries’ management. The high inter-population divergence of outlier EST-microsatellites is compatible with drifted post-selection genomic regions rather than with ongoing local selective pressures. The structural scenario in hake is explainable by a limited gene flow across the Almería-Oran Front (AOF) and by the within-basin IBD pattern of connectivity plus drift-related demographic events. This study highlights how polymorphic properties of EST-microsatellite types can be useful to address mutually excluding research tasks in fisheries, i.e., to address its evolutionary history (directional markers or FAPS: Fossil Adaptive Polymorphic Systems); to delineate management units (neutral markers or NAPS: Non Adaptive Polymorphic Systems); or to ensure sustainability (balanced markers or APS: Adaptive Polymorphic Systems).
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Maes SM, Christiansen H, Mark FC, Lucassen M, Van de Putte A, Volckaert FAM, Flores H. High gene flow in polar cod (Boreogadus saida) from West-Svalbard and the Eurasian Basin. JOURNAL OF FISH BIOLOGY 2021; 99:49-60. [PMID: 33559136 DOI: 10.1111/jfb.14697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/24/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
The current and projected environmental change of the Arctic Ocean contrasts sharply with the limited knowledge of its genetic biodiversity. Polar cod Boreogadus saida (Lepechin, 1774) is an abundant circumpolar marine fish and ecological key species. The central role of polar cod in the Arctic marine food web warrants a better understanding of its population structure and connectivity. In this study, the genetic population structure of 171 juveniles, collected from several fjords off West-Svalbard (Billefjorden, Hornsund and Kongsfjorden), the northern Sophia Basin and the Eurasian Basin of the Arctic Ocean, was analysed using nine DNA microsatellite loci. Genetic analyses indicated moderate to high genetic diversity, but absence of spatial population structure and isolation-by-distance, suggesting ongoing gene flow between the studied sampling regions. High levels of connectivity may be key for polar cod to maintain populations across wide spatial scales. The adaptive capacity of the species will be increasingly important to face challenges such as habitat fragmentation, ocean warming and changes in prey composition. In view of a limited understanding of the population dynamics and evolution of polar cod, a valuable next step to predict future developments should be an integrated biological evaluation, including population genomics, a life-history approach, and habitat and biophysical dispersal modelling.
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Affiliation(s)
- Sarah M Maes
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Felix C Mark
- Alfred-Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Magnus Lucassen
- Alfred-Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Anton Van de Putte
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Hauke Flores
- Alfred-Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
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Tempestini A, Pinchuk AI, Dufresne F. Spatial genetic structure in Themisto libellula (Amphipoda: Hyperiidae) from the coastal Gulf of Alaska, Bering and Chukchi seas. Polar Biol 2020. [DOI: 10.1007/s00300-020-02745-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Zhang S, Cai Y, Guo J, Li K, Peng R, Liu F, Roberts JA, Miao Y, Zhang X. Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints. Evol Bioinform Online 2019; 15:1176934319889948. [PMID: 31798299 PMCID: PMC6868568 DOI: 10.1177/1176934319889948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 10/30/2019] [Indexed: 11/16/2022] Open
Abstract
Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.
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Affiliation(s)
- Shulin Zhang
- College of Biology and Food Engineering, Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Yaling Cai
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Jinggong Guo
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Kun Li
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Renhai Peng
- College of Biology and Food Engineering, Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, China
| | - Jeremy A Roberts
- School of Biological and Marine Sciences, Faculty of Science and Engineering, University of Plymouth, Devon, UK
| | - Yuchen Miao
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
| | - Xuebin Zhang
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Kaifeng, China
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Deli Antoni MY, Delpiani SM, González-Castro M, Blasina GE, Spath MC, Depiani GE, Ashikaga FY, Cruz VP, Oliveira C, de Astarloa JMD. Comparative populational study of Lepidonotothen larseni and L. nudifrons (Teleostei: Nototheniidae) from the Antarctic Peninsula and the South Shetland Islands, Antarctica. Polar Biol 2019. [DOI: 10.1007/s00300-019-02540-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Inferring genetic connectivity in real populations, exemplified by coastal and oceanic Atlantic cod. Proc Natl Acad Sci U S A 2018; 115:4945-4950. [PMID: 29674450 PMCID: PMC5948993 DOI: 10.1073/pnas.1800096115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Estimates of migration are important for understanding the dynamics of natural populations. A statistic known as FST is often used to measure levels of genetic differentiation among natural populations. Equations that translate FST into estimates of migration are based on “ideal” populations, which are subject to many simplifying assumptions compared with real populations. Therefore, theoretical estimates of migration might not be realistic. We modeled populations of Atlantic cod in the North Sea and the adjacent Skagerrak region to compare how migration is related to the complexities of real populations, and how actual migration compares with predictions based on theory. Results are intended to help apply population genetic theory to practical situations. Genetic data are commonly used to estimate connectivity between putative populations, but translating them to demographic dispersal rates is complicated. Theoretical equations that infer a migration rate based on the genetic estimator FST, such as Wright’s equation, FST ≈ 1/(4Nem + 1), make assumptions that do not apply to most real populations. How complexities inherent to real populations affect migration was exemplified by Atlantic cod in the North Sea and Skagerrak and was examined within an age-structured model that incorporated genetic markers. Migration was determined under various scenarios by varying the number of simulated migrants until the mean simulated level of genetic differentiation matched a fixed level of genetic differentiation equal to empirical estimates. Parameters that decreased the Ne/Nt ratio (where Ne is the effective and Nt is the total population size), such as high fishing mortality and high fishing gear selectivity, increased the number of migrants required to achieve empirical levels of genetic differentiation. Higher maturity-at-age and lower selectivity increased Ne/Nt and decreased migration when genetic differentiation was fixed. Changes in natural mortality, fishing gear selectivity, and maturity-at-age within expected limits had a moderate effect on migration when genetic differentiation was held constant. Changes in population size had the greatest effect on the number of migrants to achieve fixed levels of FST, particularly when genetic differentiation was low, FST ≈ 10−3. Highly variable migration patterns, compared with constant migration, resulted in higher variance in genetic differentiation and higher extreme values. Results are compared with and provide insight into the use of theoretical equations to estimate migration among real populations.
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Booth Jones KA, Nicoll MAC, Raisin C, Dawson DA, Hipperson H, Horsburgh GJ, Groombridge JJ, Ismar SMH, Sweet P, Jones CG, Tatayah V, Ruhomaun K, Norris K. Widespread gene flow between oceans in a pelagic seabird species complex. Mol Ecol 2017; 26:5716-5728. [PMID: 28833786 DOI: 10.1111/mec.14330] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 08/02/2017] [Accepted: 08/07/2017] [Indexed: 12/15/2022]
Abstract
Global-scale gene flow is an important concern in conservation biology as it has the potential to either increase or decrease genetic diversity in species and populations. Although many studies focus on the gene flow between different populations of a single species, the potential for gene flow and introgression between species is understudied, particularly in seabirds. The only well-studied example of a mixed-species, hybridizing population of petrels exists on Round Island, in the Indian Ocean. Previous research assumed that Round Island represents a point of secondary contact between Atlantic (Pterodroma arminjoniana) and Pacific species (Pterodroma neglecta and Pterodroma heraldica). This study uses microsatellite genotyping and tracking data to address the possibility of between-species hybridization occurring outside the Indian Ocean. Dispersal and gene flow spanning three oceans were demonstrated between the species in this complex. Analysis of migration rates estimated using bayesass revealed unidirectional movement of petrels from the Atlantic and Pacific into the Indian Ocean. Conversely, structure analysis revealed gene flow between species of the Atlantic and Pacific oceans, with potential three-way hybrids occurring outside the Indian Ocean. Additionally, geolocation tracking of Round Island petrels revealed two individuals travelling to the Atlantic and Pacific. These results suggest that interspecific hybrids in Pterodroma petrels are more common than was previously assumed. This study is the first of its kind to investigate gene flow between populations of closely related Procellariiform species on a global scale, demonstrating the need for consideration of widespread migration and hybridization in the conservation of threatened seabirds.
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Affiliation(s)
- Katherine A Booth Jones
- Institute of Zoology, Zoological Society London, London, UK.,Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield, Sheffield, UK
| | | | - Claire Raisin
- Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield, Sheffield, UK.,Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, UK
| | - Deborah A Dawson
- Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield, Sheffield, UK
| | - Helen Hipperson
- Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield, Sheffield, UK
| | - Gavin J Horsburgh
- Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield, Sheffield, UK
| | - Jim J Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, UK
| | - Stefanie M H Ismar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paul Sweet
- Division of Vertebrate Zoology - Ornithology, American Museum of Natural History, New York, NY, USA
| | - Carl G Jones
- Mauritian Wildlife Foundation, Vacoas, Mauritius.,Durrell Wildlife Conservation Trust, Channel Islands, UK
| | | | - Kevin Ruhomaun
- National Parks and Conservation Service (Government of Mauritius), Reduit, Mauritius
| | - Ken Norris
- Institute of Zoology, Zoological Society London, London, UK
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9
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Genetic population structure of Indian oil sardine, Sardinella longiceps assessed using microsatellite markers. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0946-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Ely CR, Wilson RE, Talbot SL. Genetic structure among greater white-fronted goose populations of the Pacific Flyway. Ecol Evol 2017; 7:2956-2968. [PMID: 28479995 PMCID: PMC5415542 DOI: 10.1002/ece3.2934] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 02/23/2017] [Accepted: 03/03/2017] [Indexed: 01/13/2023] Open
Abstract
An understanding of the genetic structure of populations in the wild is essential for long-term conservation and stewardship in the face of environmental change. Knowledge of the present-day distribution of genetic lineages (phylogeography) of a species is especially important for organisms that are exploited or utilize habitats that may be jeopardized by human intervention, including climate change. Here, we describe mitochondrial (mtDNA) and nuclear genetic (microsatellite) diversity among three populations of a migratory bird, the greater white-fronted goose (Anser albifrons), which breeds discontinuously in western and southwestern Alaska and winters in the Pacific Flyway of North America. Significant genetic structure was evident at both marker types. All three populations were differentiated for mtDNA, whereas microsatellite analysis only differentiated geese from the Cook Inlet Basin. In sexual reproducing species, nonrandom mate selection, when occurring in concert with fine-scale resource partitioning, can lead to phenotypic and genetic divergence as we observed in our study. If mate selection does not occur at the time of reproduction, which is not uncommon in long-lived organisms, then mechanisms influencing the true availability of potential mates may be obscured, and the degree of genetic and phenotypic diversity may appear incongruous with presumed patterns of gene flow. Previous investigations revealed population-specific behavioral, temporal, and spatial mechanisms that likely influence the amount of gene flow measured among greater white-fronted goose populations. The degree of observed genetic structuring aligns well with our current understanding of population differences pertaining to seasonal movements, social structure, pairing behavior, and resource partitioning.
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Affiliation(s)
- Craig R. Ely
- U.S. Geological SurveyAlaska Science CenterAnchorageAKUSA
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11
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Population genomics of an endemic Mediterranean fish: differentiation by fine scale dispersal and adaptation. Sci Rep 2017; 7:43417. [PMID: 28262802 PMCID: PMC5338269 DOI: 10.1038/srep43417] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/24/2017] [Indexed: 12/04/2022] Open
Abstract
The assessment of the genetic structuring of biodiversity is crucial for management and conservation. For species with large effective population sizes a low number of markers may fail to identify population structure. A solution of this shortcoming can be high-throughput sequencing that allows genotyping thousands of markers on a genome-wide approach while facilitating the detection of genetic structuring shaped by selection. We used Genotyping-by-Sequencing (GBS) on 176 individuals of the endemic East Atlantic peacock wrasse (Symphodus tinca), from 6 locations in the Adriatic and Ionian seas. We obtained a total of 4,155 polymorphic SNPs and we observed two strong barriers to gene flow. The first one differentiated Tremiti Islands, in the northwest, from all the other locations while the second one separated east and south-west localities. Outlier SNPs potentially under positive selection and neutral SNPs both showed similar patterns of structuring, although finer scale differentiation was unveiled with outlier loci. Our results reflect the complexity of population genetic structure and demonstrate that both habitat fragmentation and positive selection are on play. This complexity should be considered in biodiversity assessments of different taxa, including non-model yet ecologically relevant organisms.
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12
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Antoniou A, Kasapidis P, Kotoulas G, Mylonas CC, Magoulas A. Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: insights from genome-wide SNPs and microsatellites. ACTA ACUST UNITED AC 2017; 24:3. [PMID: 28239596 PMCID: PMC5314471 DOI: 10.1186/s40709-017-0062-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/28/2017] [Indexed: 11/25/2022]
Abstract
Background Elucidating the patterns of the Atlantic Bluefin tuna [ABFT, Thunnus thynnus (Linnaeus, 1758)] population structure constitutes a challenging task of great importance. Most of the unique challenges stem from its biology, as well as the attributes of the marine realm in which it disperses. Accurate information is urgently needed for stock assessment, and the identification of critical features to the persistence and adaptation of populations in order to formulate and adopt effective strategies for ABFT conservation and management. Conclusions of a great number of ABFT genetic studies on the Mediterranean Sea stock structure are rather controversial and not yet conclusive. In this study, ABFT genomic diversity was investigated in the Mediterranean Sea, which is the most important area for the species’ reproduction. Results Analyzing genome-wide SNPs and microsatellites from ABFT samples collected throughout the Mediterranean Sea did not provide strong evidence of genetic structure, pointing towards the existence of a single panmictic unit. An alternative view would recognize a failure to reject the null hypothesis of a panmictic unit as an effect of the study’s sampling design, the type of markers used, and the effectiveness/suitability of analysis methods in respect to the species biological characteristics or any combination of the above. Conclusions Unravelling the drivers of ABFT population diversity would require the consideration of important aspects of the species spawning behavior for the determination of the appropriate sampling design. Novel approaches and methods of analysis that will bring together experts in genetics/-omics, ecology and oceanography are deemed necessary. Analyzing ABFT genetic data under the discipline of seascape genetics could provide the analysis framework under which major abiotic and biotic forces controlling ABFT recruitment could be identified, elucidating the complicated population dynamics of the species, while multiple and continuous fisheries monitoring should in all cases be considered as a prerequisite in order to achieve efficient and long-term ABFT conservation.
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Affiliation(s)
- Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Panagiotis Kasapidis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Constantinos C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
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Khimoun A, Ollivier A, Faivre B, Garnier S. Level of genetic differentiation affects relative performances of expressed sequence tag and genomic SSRs. Mol Ecol Resour 2017; 17:893-903. [PMID: 27978606 DOI: 10.1111/1755-0998.12642] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 10/26/2016] [Accepted: 12/06/2016] [Indexed: 12/12/2022]
Abstract
Microsatellites, also called simple sequence repeats (SSRs), are markers of choice to estimate relevant parameters for conservation genetics, such as migration rates, effective population size and kinship. Cross-amplification of SSRs is the simplest way to obtain sets of markers, and highly conserved SSRs have recently been developed from expressed sequence tags (EST) to improve SSR cross-species utility. As EST-SSRs are located in coding regions, the higher stability of their flanking regions reduces the frequency of null alleles and improves cross-species amplification. However, EST-SSRs have generally less allelic variability than genomic SSRs, potentially leading to differences in estimates of population genetic parameters such as genetic differentiation. To assess the potential of EST-SSRs in studies of within-species genetic diversity, we compared the relative performance of EST- and genomic SSRs following a multispecies approach on passerine birds. We tested whether patterns and levels of genetic diversity within and between populations assessed from EST- and from genomic SSRs are congruent, and we investigated how the relative efficiency of EST- and genomic SSRs is influenced by levels of differentiation. EST- and genomic SSRs ensured comparable inferences of population genetic structure in cases of strong genetic differentiation, and genomic SSRs performed slightly better than EST-SSRs when differentiation is moderate. However and interestingly, EST-SSRs had a higher power to detect weak genetic structure compared to genomic SSRs. Our study attests that EST-SSRs may be valuable molecular markers for conservation genetic studies in taxa such as birds, where the development of genomic SSRs is impeded by their low frequency.
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Affiliation(s)
- Aurélie Khimoun
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Anthony Ollivier
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Bruno Faivre
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
| | - Stéphane Garnier
- Biogéosciences UMR6282, CNRS, Univ. Bourgogne Franche-Comté, Equipe BIOME, 6 bd Gabriel, 21000, Dijon, France
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Kumar S, Kirk C, Deng C, Wiedow C, Knaebel M, Brewer L. Genotyping-by-sequencing of pear ( Pyrus spp.) accessions unravels novel patterns of genetic diversity and selection footprints. HORTICULTURE RESEARCH 2017; 4:17015. [PMID: 28451438 PMCID: PMC5389204 DOI: 10.1038/hortres.2017.15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/22/2017] [Accepted: 02/22/2017] [Indexed: 05/06/2023]
Abstract
Understanding of genetic diversity and marker-trait relationships in pears (Pyrus spp.) forms an important part of gene conservation and cultivar breeding. Accessions of Asian and European pear species, and interspecific hybrids were planted in a common garden experiment. Genotyping-by-sequencing (GBS) was used to genotype 214 accessions, which were also phenotyped for fruit quality traits. A combination of selection scans and association analyses were used to identify signatures of selection. Patterns of genetic diversity, population structure and introgression were also investigated. About 15 000 high-quality SNP markers were identified from the GBS data, of which 25% and 11% harboured private alleles for European and Asian species, respectively. Bayesian clustering analysis suggested negligible gene flow, resulting in highly significant population differentiation (Fst=0.45) between Asian and European pears. Interspecific hybrids displayed an average of 55% and 45% introgression from their Asian and European ancestors, respectively. Phenotypic (firmness, acidity, shape and so on) variation between accessions was significantly associated with genetic differentiation. Allele frequencies at large-effect SNP loci were significantly different between genetic groups, suggesting footprints of directional selection. Selection scan analyses identified over 20 outlier SNP loci with substantial statistical support, likely to be subject to directional selection or closely linked to loci under selection.
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Affiliation(s)
- Satish Kumar
- The New Zealand Institute for Plant & Food Research Limited, Hawke’s Bay Research Centre, Havelock North, New Zealand
- ()
| | - Chris Kirk
- Palmerston North Research Centre, Palmerston North, New Zealand
| | - Cecilia Deng
- Mount Albert Research Centre, Auckland, New Zealand
| | - Claudia Wiedow
- Palmerston North Research Centre, Palmerston North, New Zealand
| | - Mareike Knaebel
- Palmerston North Research Centre, Palmerston North, New Zealand
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Taillebois L, Dudgeon C, Maher S, Crook DA, Saunders TM, Barton DP, Taylor JA, Welch DJ, Newman SJ, Travers MJ, Saunders RJ, Ovenden J. Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification. PeerJ 2016; 4:e2418. [PMID: 27635362 PMCID: PMC5012413 DOI: 10.7717/peerj.2418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/06/2016] [Indexed: 11/20/2022] Open
Abstract
Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.
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Affiliation(s)
- Laura Taillebois
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia; North Australia Marine Research Alliance, Arafura Timor Research Facility, Darwin, Northern Territory, Australia
| | - Christine Dudgeon
- Molecular Fisheries Laboratory, School of Biomedical Sciences, University of Queensland , Brisbane , Queensland , Australia
| | - Safia Maher
- Molecular Fisheries Laboratory, School of Biomedical Sciences, University of Queensland , Brisbane , Queensland , Australia
| | - David A Crook
- Research Institute for the Environment and Livelihoods, Charles Darwin University , Darwin , Northern Territory , Australia
| | - Thor M Saunders
- Fisheries Research, Northern Territory Department of Primary Industries and Fisheries , Berrimah , Northern Territory , Australia
| | - Diane P Barton
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia; Fisheries Research, Northern Territory Department of Primary Industries and Fisheries, Berrimah, Northern Territory, Australia
| | - Jonathan A Taylor
- Fisheries Research, Northern Territory Department of Primary Industries and Fisheries , Berrimah , Northern Territory , Australia
| | | | - Stephen J Newman
- Western Australian Fisheries and Marine Research Laboratories, Department of Fisheries, Government of Western Australia , North Beach , Western Australia , Australia
| | - Michael J Travers
- Western Australian Fisheries and Marine Research Laboratories, Department of Fisheries, Government of Western Australia , North Beach , Western Australia , Australia
| | - Richard J Saunders
- Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Douglas, Queensland, Australia; Animal Science, Queensland Department of Agriculture and Fisheries, Brisbane, Queensland, Australia
| | - Jennifer Ovenden
- Molecular Fisheries Laboratory, School of Biomedical Sciences, University of Queensland , Brisbane , Queensland , Australia
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Reid K, Hoareau TB, Graves JE, Potts WM, Dos Santos SMR, Klopper AW, Bloomer P. Secondary contact and asymmetrical gene flow in a cosmopolitan marine fish across the Benguela upwelling zone. Heredity (Edinb) 2016; 117:307-315. [PMID: 27436525 DOI: 10.1038/hdy.2016.51] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 05/09/2016] [Accepted: 05/12/2016] [Indexed: 12/16/2022] Open
Abstract
The combination of oceanographic barriers and habitat heterogeneity are known to reduce connectivity and leave specific genetic signatures in the demographic history of marine species. However, barriers to gene flow in the marine environment are almost never impermeable which inevitably allows secondary contact to occur. In this study, eight sampling sites (five along the South African coastline, one each in Angola, Senegal and Portugal) were chosen to examine the population genetic structure and phylogeographic history of the cosmopolitan bluefish (Pomatomus saltatrix), distributed across a large South-east Atlantic upwelling zone. Molecular analyses were applied to mtDNA cytochrome b, intron AM2B1 and 15 microsatellite loci. We detected uncharacteristically high genetic differentiation (FST 0.15-0.20; P<0.001) between the fish sampled from South Africa and the other sites, strongly influenced by five outlier microsatellite loci located in conserved intergenic regions. In addition, differentiation among the remaining East Atlantic sites was detected, although mtDNA indicated past isolation with subsequent secondary contact between these East Atlantic populations. We further identified secondary contact, with unidirectional gene flow from South Africa to Angola. The directional contact is likely explained by a combination of the northward flowing offshore current and endogenous incompatibilities restricting integration of certain regions of the genome and limiting gene flow to the south. The results confirm that the dynamic system associated with the Benguela current upwelling zone influences species distributions and population processes in the South-east Atlantic.
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Affiliation(s)
- K Reid
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - T B Hoareau
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - J E Graves
- Department of Fisheries Science, Virginia Institute of Marine Science, College of William & Mary, Williamsburg, VA, USA
| | - W M Potts
- Department of Ichthyology and Fisheries Science, Rhodes University, Grahamstown, South Africa
| | - S M R Dos Santos
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - A W Klopper
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - P Bloomer
- Molecular Ecology and Evolution Programme, Department of Genetics, University of Pretoria, Pretoria, South Africa
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Cooke GM, Schlub TE, Sherwin WB, Ord TJ. Understanding the Spatial Scale of Genetic Connectivity at Sea: Unique Insights from a Land Fish and a Meta-Analysis. PLoS One 2016; 11:e0150991. [PMID: 27195493 PMCID: PMC4873183 DOI: 10.1371/journal.pone.0150991] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/21/2016] [Indexed: 11/19/2022] Open
Abstract
Quantifying the spatial scale of population connectivity is important for understanding the evolutionary potential of ecologically divergent populations and for designing conservation strategies to preserve those populations. For marine organisms like fish, the spatial scale of connectivity is generally set by a pelagic larval phase. This has complicated past estimates of connectivity because detailed information on larval movements are difficult to obtain. Genetic approaches provide a tractable alternative and have the added benefit of estimating directly the reproductive isolation of populations. In this study, we leveraged empirical estimates of genetic differentiation among populations with simulations and a meta-analysis to provide a general estimate of the spatial scale of genetic connectivity in marine environments. We used neutral genetic markers to first quantify the genetic differentiation of ecologically-isolated adult populations of a land dwelling fish, the Pacific leaping blenny (Alticus arnoldorum), where marine larval dispersal is the only probable means of connectivity among populations. We then compared these estimates to simulations of a range of marine dispersal scenarios and to collated FST and distance data from the literature for marine fish across diverse spatial scales. We found genetic connectivity at sea was extensive among marine populations and in the case of A. arnoldorum, apparently little affected by the presence of ecological barriers. We estimated that ~5000 km (with broad confidence intervals ranging from 810-11,692 km) was the spatial scale at which evolutionarily meaningful barriers to gene flow start to occur at sea, although substantially shorter distances are also possible for some taxa. In general, however, such a large estimate of connectivity has important implications for the evolutionary and conservation potential of many marine fish communities.
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Affiliation(s)
- Georgina M. Cooke
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052 NSW, Australia
- The Australian Museum, Australian Museum Research Institute, Ichthyology, 6 College Street, Sydney NSW 2010, Australia
| | - Timothy E. Schlub
- Sydney School of Public Health, Sydney Medical School, University of Sydney, 2006 NSW, Australia
| | - William B. Sherwin
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052 NSW, Australia
| | - Terry J. Ord
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington 2052 NSW, Australia
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18
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Khalili Samani N, Esa Y, Amin SMN, Fatin Mohd Ikhsan N. Phylogenetics and population genetics of Plotosus canius (Siluriformes: Plotosidae) from Malaysian coastal waters. PeerJ 2016; 4:e1930. [PMID: 27231645 PMCID: PMC4878373 DOI: 10.7717/peerj.1930] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 03/22/2016] [Indexed: 11/20/2022] Open
Abstract
Plotosus canius (Hamilton, 1822) is a significant marine species in Malaysia from nutritional and commercial perspectives. Despite numerous fundamental research on biological characteristics of P. canius, there are various concerns on the level of population differentiation, genomic structure, and the level of genetic variability among their populations due to deficiency of genetic-based studies. Deficiency on basic contexts such as stock identification, phylogenetic relationship and population genetic structure would negatively impact their sustainable conservation. Hence, this study was conducted to characterize the genetic structure of P. canius for the first time through the application of mitochondrial Cytochrome Oxidase I (COI) gene, cross amplification of Tandanus tandanus microsatellites, and a total of 117 collected specimens across five selected populations of Malaysia. The experimental results of the mitochondrial analysis revealed that the haplotype diversity and nucleotide diversity varied from 0.395–0.771 and 0.033–0.65 respectively. Moreover, the statistical analysis of microsatellites addressed a considerable heterozygote insufficiency in all populations, with average observed heterozygosity (Ho) value of 0.2168, which was lower than the standard heterozygosity in marine populations (Ho = 0.79). This alongside the high Fis values estimation, high pairwise differentiation among populations and low within population variations are supposed to be associated with small sample size, and inbreeding system. Besides, the significant finding of this study was the sharing of common haplotype KR086940, which reflects a historical genetic connectivity between Peninsular Malaysia and Borneo populations due to the geological history of Southeast Asia during Pleistocene era. Demographic analyses showed that all populations were in an equilibrium state with no significant evidence of population expansion. To put it briefly, the current study has managed to provide an initial genomic database toward understanding of the genetic characterization, phylogenetic, molecular diversification and population structure in P. canius, and should be necessary highlighted for appropriate management and conservation of species. Further studies must be carried out involving more geographical and sampling sites, larger population size per site, and utilization of species specific microsatellites loci.
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Affiliation(s)
- Nima Khalili Samani
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia , Serdang, Selangor , Malaysia
| | - Yuzine Esa
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia , Serdang, Selangor , Malaysia
| | - S M Nurul Amin
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia , Serdang, Selangor , Malaysia
| | - Natrah Fatin Mohd Ikhsan
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia , Serdang, Selangor , Malaysia
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19
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Škute N, Oreha J. Evaluation of some microsatellite markers variability in the study of genetic structure of vendace (Coregonus albula (L.)) populations from Latvian lakes. CONTEMP PROBL ECOL+ 2016. [DOI: 10.1134/s1995425516020074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Boissin E, Micu D, Janczyszyn-Le Goff M, Neglia V, Bat L, Todorova V, Panayotova M, Kruschel C, Macic V, Milchakova N, Keskin Ç, Anastasopoulou A, Nasto I, Zane L, Planes S. Contemporary genetic structure and postglacial demographic history of the black scorpionfish, Scorpaena porcus, in the Mediterranean and the Black Seas. Mol Ecol 2016; 25:2195-209. [PMID: 26989881 DOI: 10.1111/mec.13616] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 02/09/2016] [Accepted: 03/11/2016] [Indexed: 12/24/2022]
Abstract
Understanding the distribution of genetic diversity in the light of past demographic events linked with climatic shifts will help to forecast evolutionary trajectories of ecosystems within the current context of climate change. In this study, mitochondrial sequences and microsatellite loci were analysed using traditional population genetic approaches together with Bayesian dating and the more recent approximate Bayesian computation scenario testing. The genetic structure and demographic history of a commercial fish, the black scorpionfish, Scorpaena porcus, was investigated throughout the Mediterranean and Black Seas. The results suggest that the species recently underwent population expansions, in both seas, likely concomitant with the warming period following the Last Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic differentiation was identified between the Black Sea and the Mediterranean Sea. However, the genetic diversity was similar for populations of the two seas, suggesting a high number of colonizers entered the Black Sea during the interglacial period and/or the presence of a refugial population in the Black Sea during the glacial period. Finally, within seas, an east/west genetic differentiation in the Adriatic seems to prevail, whereas the Black Sea does not show any structured spatial genetic pattern of its population. Overall, these results suggest that the Black Sea is not that isolated from the Mediterranean, and both seas revealed similar evolutionary patterns related to climate change and changes in sea level.
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Affiliation(s)
- E Boissin
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, F-66360, France.,Laboratoire d'Excellence CRIOBE, BP 1013, 98729, Papetoai, Moorea, Polynésie Française
| | - D Micu
- National Institute of Marine Research and Development, Grigore Antipa, Constanta, 900581, Romania
| | - M Janczyszyn-Le Goff
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, F-66360, France.,Laboratoire d'Excellence CRIOBE, BP 1013, 98729, Papetoai, Moorea, Polynésie Française
| | - V Neglia
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, F-66360, France.,Laboratoire d'Excellence CRIOBE, BP 1013, 98729, Papetoai, Moorea, Polynésie Française
| | - L Bat
- Department of Marine Biology and Ecology, Faculty of Fisheries, Sinop University, Sinop, TR57000, Turkey
| | - V Todorova
- IO-BAS - Institute of Oceanology, PO Box 152, Varna, 9000, Bulgaria
| | - M Panayotova
- IO-BAS - Institute of Oceanology, PO Box 152, Varna, 9000, Bulgaria
| | - C Kruschel
- University of Zadar, Ul. Mihovila Pavlinovića, Zadar, 23000, Croatia
| | - V Macic
- Institute of Marine Biology Kotor (IBMK), Dobrota bb, PO Box 69, Kotor, 85330, Montenegro
| | - N Milchakova
- Institute of Marine Biological Research (IMBR), 2 Nakhimov ave., Sevastopol, 299011, Russia
| | - Ç Keskin
- Faculty of Fisheries, Istanbul University, Ordu St 200, Istanbul, TR-34470, Turkey
| | - A Anastasopoulou
- Hellenic Centre for Marine Research, 46.7 km Athinon-Souniou Av., Anavyssos, 19013, Greece
| | - I Nasto
- Department of Biology, Faculty of Technical Sciences, Vlora University, Vlora, 9401, Albania
| | - L Zane
- Department of Biology, University of Padova, via U. Bassi/58B, Padova, I-35121, Italy
| | - S Planes
- EPHE, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, Perpignan, F-66360, France.,Laboratoire d'Excellence CRIOBE, BP 1013, 98729, Papetoai, Moorea, Polynésie Française
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21
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Tusso S, Morcinek K, Vogler C, Schupp PJ, Caballes CF, Vargas S, Wörheide G. Genetic structure of the crown-of-thorns seastar in the Pacific Ocean, with focus on Guam. PeerJ 2016; 4:e1970. [PMID: 27168979 PMCID: PMC4860296 DOI: 10.7717/peerj.1970] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 04/04/2016] [Indexed: 11/20/2022] Open
Abstract
Population outbreaks of the corallivorous crown-of-thorns seastar (COTS), Acanthaster 'planci' L., are among the most important biological disturbances of tropical coral reefs. Over the past 50 years, several devastating outbreaks have been documented around Guam, an island in the western Pacific Ocean. Previous analyses have shown that in the Pacific Ocean, COTS larval dispersal may be geographically restricted to certain regions. Here, we assess the genetic structure of Pacific COTS populations and compared samples from around Guam with a number of distant localities in the Pacific Ocean, and focused on determining the degree of genetic structure among populations previously considered to be isolated. Using microsatellites, we document substantial genetic structure between 14 localities from different geographical regions in the Pacific Ocean. Populations from the 14 locations sampled were found to be structured in three significantly differentiated groups: (1) all locations immediately around Guam, as well as Kingman Reef and Swains Island; (2) Japan, Philippines, GBR and Vanuatu; and (3) Johnston Atoll, which was significantly different from all other localities. The lack of genetic differentiation between Guam and extremely distant populations from Kingman Reef and Swains Island suggests potential long-distance dispersal of COTS in the Pacific.
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Affiliation(s)
- Sergio Tusso
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München , München , Germany
| | - Kerstin Morcinek
- Department of Anatomy (Neuroanatomy), University of Cologne , Köln , Germany
| | - Catherine Vogler
- Environment Department, Pöyry Switzerland Ltd. , Zurich , Switzerland
| | - Peter J Schupp
- Environmental Biochemistry, Carl-von-Ossietzky University Oldenburg, ICBM-Terramare , Wilhelmshaven , Germany
| | - Ciemon F Caballes
- ARC Centre of Excellence for Coral Reef Studies, James Cook University , Townsville, Queensland , Australia
| | - Sergio Vargas
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München , München , Germany
| | - Gert Wörheide
- Department of Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, München, Germany; SNSB-Bavarian State Collections of Palaeontology and Geology, München, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, München, Germany
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22
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Talbot SL, Sage GK, Rearick JR, Fowler MC, Muñiz-Salazar R, Baibak B, Wyllie-Echeverria S, Cabello-Pasini A, Ward DH. The Structure of Genetic Diversity in Eelgrass (Zostera marina L.) along the North Pacific and Bering Sea Coasts of Alaska. PLoS One 2016; 11:e0152701. [PMID: 27104836 PMCID: PMC4841600 DOI: 10.1371/journal.pone.0152701] [Citation(s) in RCA: 12] [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: 09/28/2015] [Accepted: 03/17/2016] [Indexed: 11/25/2022] Open
Abstract
Eelgrass (Zostera marina) populations occupying coastal waters of Alaska are separated by a peninsula and island archipelago into two Large Marine Ecosystems (LMEs). From populations in both LMEs, we characterize genetic diversity, population structure, and polarity in gene flow using nuclear microsatellite fragment and chloroplast and nuclear sequence data. An inverse relationship between genetic diversity and latitude was observed (heterozygosity: R2 = 0.738, P < 0.001; allelic richness: R2 = 0.327, P = 0.047), as was significant genetic partitioning across most sampling sites (θ = 0.302, P < 0.0001). Variance in allele frequency was significantly partitioned by region only in cases when a population geographically in the Gulf of Alaska LME (Kinzarof Lagoon) was instead included with populations in the Eastern Bering Sea LME (θp = 0.128-0.172; P < 0.003), suggesting gene flow between the two LMEs in this region. Gene flow among locales was rarely symmetrical, with notable exceptions generally following net coastal ocean current direction. Genetic data failed to support recent proposals that multiple Zostera species (i.e. Z. japonica and Z. angustifolia) are codistributed with Z. marina in Alaska. Comparative analyses also failed to support the hypothesis that eelgrass populations in the North Atlantic derived from eelgrass retained in northeastern Pacific Last Glacial Maximum refugia. These data suggest northeastern Pacific populations are derived from populations expanding northward from temperate populations following climate amelioration at the terminus of the last Pleistocene glaciation.
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Affiliation(s)
- Sandra L. Talbot
- Alaska Science Center, U.S. Geological Survey, Anchorage, Alaska, United States of America
| | - George K Sage
- Alaska Science Center, U.S. Geological Survey, Anchorage, Alaska, United States of America
| | - Jolene R. Rearick
- Alaska Science Center, U.S. Geological Survey, Anchorage, Alaska, United States of America
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Meg C. Fowler
- Alaska Science Center, U.S. Geological Survey, Anchorage, Alaska, United States of America
| | - Raquel Muñiz-Salazar
- Escuela de Ciencias de la Salud, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
| | - Bethany Baibak
- Biological Sciences, Humboldt State University, Arcata, California, United States of America
| | - Sandy Wyllie-Echeverria
- Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington, United States of America
- Center for Marine and Environmental Studies, University of Virgin Islands, St. Thomas, Virgin Islands, United States of America
| | - Alejandro Cabello-Pasini
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, California, Mexico
| | - David H. Ward
- Alaska Science Center, U.S. Geological Survey, Anchorage, Alaska, United States of America
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Ding Y, Zhang J, Lu Y, Lin E, Lou L, Tong Z. Development of EST-SSR markers and analysis of genetic diversity in natural populations of endemic and endangered plant Phoebe chekiangensis. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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24
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Aykanat T, Johnston SE, Orell P, Niemelä E, Erkinaro J, Primmer CR. Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population. Mol Ecol 2015; 24:5158-74. [DOI: 10.1111/mec.13383] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 09/04/2015] [Accepted: 09/09/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Tutku Aykanat
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
| | - Susan E. Johnston
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
- Institute of Evolutionary Biology; University of Edinburgh; Charlotte Auerbach Road Edinburgh EH9 3FL UK
| | - Panu Orell
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Eero Niemelä
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Jaakko Erkinaro
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Craig R. Primmer
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
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25
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Andrews KR, Norton EL, Fernandez-Silva I, Portner E, Goetze E. Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod. Mol Ecol 2015; 23:5462-79. [PMID: 25283587 DOI: 10.1111/mec.12950] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 11/29/2022]
Abstract
Zooplanktonic taxa have a greater number of distinct populations and species than might be predicted based on their large population sizes and open-ocean habitat, which lacks obvious physical barriers to dispersal and gene flow. To gain insight into the evolutionary mechanisms driving genetic diversification in zooplankton, we developed eight microsatellite markers to examine the population structure of an abundant, globally distributed mesopelagic copepod, Haloptilus longicornis, at 18 sample sites across the Atlantic and Pacific Oceans (n = 761). When comparing our microsatellite results with those of a prior study that used a mtDNA marker (mtCOII, n = 1059, 43 sample sites), we unexpectedly found evidence for the presence of a cryptic species pair. These species were globally distributed and apparently sympatric, and were separated by relatively weak genetic divergence (reciprocally monophyletic mtCOII lineages 1.6% divergent; microsatellite FST ranging from 0.28 to 0.88 across loci, P < 0.00001). Using both mtDNA and microsatellite data for the most common of the two species (n = 669 for microsatellites, n = 572 for mtDNA), we also found evidence for allopatric barriers to gene flow within species, with distinct populations separated by continental landmasses and equatorial waters in both the Atlantic and Pacific Ocean basins. Our study shows that oceanic barriers to gene flow can act as a mechanism promoting allopatric diversification in holoplanktonic taxa, despite the high potential dispersal abilities and pelagic habitat for these species.
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Affiliation(s)
- Kimberly R Andrews
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA; School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE, UK
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26
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Smith BL, Lu CP, García-Cortés B, Viñas J, Yeh SY, Alvarado Bremer JR. Multilocus Bayesian Estimates of Intra-Oceanic Genetic Differentiation, Connectivity, and Admixture in Atlantic Swordfish (Xiphias gladius L.). PLoS One 2015; 10:e0127979. [PMID: 26057382 PMCID: PMC4461265 DOI: 10.1371/journal.pone.0127979] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Accepted: 04/21/2015] [Indexed: 12/03/2022] Open
Abstract
Previous genetic studies of Atlantic swordfish (Xiphias gladius L.) revealed significant differentiation among Mediterranean, North Atlantic and South Atlantic populations using both mitochondrial and nuclear DNA data. However, limitations in geographic sampling coverage, and the use of single loci, precluded an accurate placement of boundaries and of estimates of admixture. In this study, we present multilocus analyses of 26 single nucleotide polymorphisms (SNPs) within 10 nuclear genes to estimate population differentiation and admixture based on the characterization of 774 individuals representing North Atlantic, South Atlantic, and Mediterranean swordfish populations. Pairwise FST values, AMOVA, PCoA, and Bayesian individual assignments support the differentiation of swordfish inhabiting these three basins, but not the current placement of the boundaries that separate them. Specifically, the range of the South Atlantic population extends beyond 5°N management boundary to 20°N-25°N from 45°W. Likewise the Mediterranean population extends beyond the current management boundary at the Strait of Gibraltar to approximately 10°W. Further, admixture zones, characterized by asymmetric contributions of adjacent populations within samples, are confined to the Northeast Atlantic. While South Atlantic and Mediterranean migrants were identified within these Northeast Atlantic admixture zones no North Atlantic migrants were identified respectively in these two neighboring basins. Owing to both, the characterization of larger number of loci and a more ample spatial sampling coverage, it was possible to provide a finer resolution of the boundaries separating Atlantic swordfish populations than previous studies. Finally, the patterns of population structure and admixture are discussed in the light of the reproductive biology, the known patterns of dispersal, and oceanographic features that may act as barriers to gene flow to Atlantic swordfish.
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Affiliation(s)
- Brad L. Smith
- Department of Marine Biology, Texas A&M University at Galveston, OCSB 3029, Galveston, TX 77553, United States of America
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 210 Nagle Hall, TAMU 2258, College Station, TX, 75044, United States of America
- * E-mail:
| | - Ching-Ping Lu
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 210 Nagle Hall, TAMU 2258, College Station, TX, 75044, United States of America
| | - Blanca García-Cortés
- Centro Oceanográphico A Coruña, Instituto Español de Oceanografia, Muelle de las Animas s/n P.O. Box 130, 15080 A Coruña, Spain
| | - Jordi Viñas
- Department de Biologia, Universitat de Girona, Campus Montilivi, E-17071 Girona, Spain
| | - Shean-Ya Yeh
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
| | - Jaime R. Alvarado Bremer
- Department of Marine Biology, Texas A&M University at Galveston, OCSB 3029, Galveston, TX 77553, United States of America
- Department of Wildlife and Fisheries Sciences, Texas A&M University, 210 Nagle Hall, TAMU 2258, College Station, TX, 75044, United States of America
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Akib NAM, Tam BM, Phumee P, Abidin MZ, Tamadoni S, Mather PB, Nor SAM. High connectivity in Rastrelliger kanagurta: influence of historical signatures and migratory behaviour inferred from mtDNA cytochrome b. PLoS One 2015; 10:e0119749. [PMID: 25786216 PMCID: PMC4365000 DOI: 10.1371/journal.pone.0119749] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 02/03/2015] [Indexed: 11/18/2022] Open
Abstract
Phylogeographic patterns and population structure of the pelagic Indian mackerel, Rastrelliger kanagurta were examined in 23 populations collected from the Indonesian-Malaysian Archipelago (IMA) and the West Indian Ocean (WIO). Despite the vast expanse of the IMA and neighbouring seas, no evidence for geographical structure was evident. An indication that R. kanagurta populations across this region are essentially panmictic. This study also revealed that historical isolation was insufficient for R. kanagurta to attain migration drift equilibrium. Two distinct subpopulations were detected between the WIO and the IMA (and adjacent populations); interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the IMA and WIO regions suggest historical isolation as a result of fluctuations in sea levels during the late Pleistocene. This occurrence resulted in the evolution of a phylogeographic break for this species to the north of the Andaman Sea.
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Affiliation(s)
| | - Bui Minh Tam
- College of Aquaculture and Fisheries, Can Tho University, Can Tho city, Vietnam
| | - Preeda Phumee
- Faculty of Science and Fisheries and Technology, Rajamangala University of Technology Srivijaya Trang Campus, Trang, Thailand
| | - Muchlisin Zainal Abidin
- Department of Aquaculture, Faculty of Marine and Fishery, Universitas Syiah Kuala, Jl. T. Nyak Arief Darussalam, Banda Aceh, Indonesia
| | - Saied Tamadoni
- Persian Gulf and Oman Sea Ecological Research Institute, Bandar Abbass, Iran
| | - Peter B. Mather
- Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Siti Azizah Mohd Nor
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- Centre for Marine & Coastal Studies, Universiti Sains Malaysia, Penang, Malaysia
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Schilling MP, Wolf PG, Duffy AM, Rai HS, Rowe CA, Richardson BA, Mock KE. Genotyping-by-sequencing for Populus population genomics: an assessment of genome sampling patterns and filtering approaches. PLoS One 2014; 9:e95292. [PMID: 24748384 PMCID: PMC3991623 DOI: 10.1371/journal.pone.0095292] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 03/25/2014] [Indexed: 12/19/2022] Open
Abstract
Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS) protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging as a target for population genomic studies. We estimate the proportions and patterns of genomic sampling by examining the Populus trichocarpa genome (Nisqually-1), and demonstrate a pronounced bias towards coding regions when using the methylation-sensitive ApeKI restriction enzyme in this species. Using population-level data from a closely related species (P. tremuloides), we also investigate various approaches for filtering GBS data to retain high-depth, informative SNPs that can be used for population genetic analyses. We find a data filter that includes the designation of ambiguous alleles resulted in metrics of population structure and Hardy-Weinberg equilibrium that were most consistent with previous studies of the same populations based on other genetic markers. Analyses of the filtered data (27,910 SNPs) also resulted in patterns of heterozygosity and population structure similar to a previous study using microsatellites. Our application demonstrates that technically and analytically simple approaches can readily be developed for population genomics of natural populations.
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Affiliation(s)
- Martin P. Schilling
- Department of Biology, Utah State University, Logan, Utah, United States of America
- Ecology Center, Utah State University, Logan, Utah, United States of America
| | - Paul G. Wolf
- Department of Biology, Utah State University, Logan, Utah, United States of America
- Ecology Center, Utah State University, Logan, Utah, United States of America
| | - Aaron M. Duffy
- Department of Biology, Utah State University, Logan, Utah, United States of America
| | - Hardeep S. Rai
- Department of Wildland Resources, Utah State University, Logan, Utah, United States of America
| | - Carol A. Rowe
- Department of Wildland Resources, Utah State University, Logan, Utah, United States of America
| | - Bryce A. Richardson
- Rocky Mountain Research Station, USDA Forest Service, Provo, Utah, United States of America
| | - Karen E. Mock
- Department of Wildland Resources, Utah State University, Logan, Utah, United States of America
- Ecology Center, Utah State University, Logan, Utah, United States of America
- * E-mail:
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Cao L, Liang XF, Du Y, Zheng H, Yang M, Huang W. Genetic population structure in Siniperca scherzeri (Perciformes: Siniperca) in China inferred from mitochondrial DNA sequences and microsatellite loci. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2013.08.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Jackson ND, Austin CC. Testing the role of meander cutoff in promoting gene flow across a riverine barrier in ground skinks (Scincella lateralis). PLoS One 2013; 8:e62812. [PMID: 23658778 PMCID: PMC3642178 DOI: 10.1371/journal.pone.0062812] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 03/26/2013] [Indexed: 11/18/2022] Open
Abstract
Despite considerable attention, the long-term impact of rivers on species diversification remains uncertain. Meander loop cutoff (MLC) is one river phenomenon that may compromise a river's diversifying effects by passively transferring organisms from one side of the river to the other. However, the ability of MLC to promote gene flow across rivers has not been demonstrated empirically. Here, we test several predictions of MLC-mediated gene flow in populations of North American ground skinks (Scincella lateralis) separated by a well-established riverine barrier, the Mississippi River: 1) individuals collected from within meander cutoffs should be more closely related to individuals across the river than on the same side, 2) individuals within meander cutoffs should contain more immigrants than individuals away from meander cutoffs, 3) immigration rates estimated across the river should be highest in the direction of the cutoff event, and 4) the distribution of alleles native to one side of the river should be better predicted by the historical rather than current path of the river. To test these predictions we sampled 13 microsatellite loci and mitochondrial DNA from ground skinks collected near three ancient meander loops. These predictions were generally supported by genetic data, although support was stronger for mtDNA than for microsatellite data. Partial support for genetic divergence of samples within ancient meander loops also provides evidence for the MLC hypothesis. Although a role for MLC-mediated gene flow was supported here for ground skinks, the transient nature of river channels and morphologies may limit the long-term importance of MLC in stemming population divergence across major rivers.
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Affiliation(s)
- Nathan D Jackson
- Department of Biological Sciences, Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, United States of America.
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Genetic diversity and population structure of the endangered alpine quillwort Isoetes hypsophila (Isoetaceae) revealed by SSR analysis. BIOCHEM SYST ECOL 2013. [DOI: 10.1016/j.bse.2012.10.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Quéré N, Desmarais E, Tsigenopoulos CS, Belkhir K, Bonhomme F, Guinand B. Gene flow at major transitional areas in sea bass (Dicentrarchus labrax) and the possible emergence of a hybrid swarm. Ecol Evol 2012; 2:3061-78. [PMID: 23301173 PMCID: PMC3539001 DOI: 10.1002/ece3.406] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/18/2012] [Accepted: 09/25/2012] [Indexed: 11/08/2022] Open
Abstract
The population genetic structure of sea bass (Dicentrarchus labrax) along a transect from the Atlantic Ocean (AO) to the Eastern Mediterranean (EM) Sea differs from that of most other marine taxa in this area. Three populations (AO, Western Mediterranean [WM], EM) are recognized today, which were originally two allopatric populations. How two ancestral genetic units have evolved into three distinct units has not been addressed yet. Therefore, to investigate mechanisms that lead to the emergence of the central WM population, its current status, and its connectivity with the two parental populations, we applied 20 nuclear loci that were either gene associated or gene independent. Results confirmed the existence of three distinct gene pools, with higher differentiation at two transitional areas, the Almeria-Oran Front (AOF) and of the Siculo-Tunisian Strait (STS), than within any population. Significant linkage disequilibrium and heterozygote excess indicated that the STS is probably another tension zone, as already described for the AOF. Neutrality tests fail to reveal marker loci that could be driven by selection within or among metapopulations, except for locus DLA0068. Collectively, results support that the central WM population arose by trapping two tensions zones at distinct geographic locations of limited connectivity. Population assignment further revealed that WM individuals were more introgressed than individuals from the other two metapopulations. This suggests that this population might result from hybrid swarming, and was or is still seeded by genes received through the filter of each tension zone.
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Affiliation(s)
- Nolwenn Quéré
- Institut des Sciences de l'Évolution de Montpellier, CNRS-UMR 5554, Université Montpellier 2cc63, 34095, Montpellier Cedex 5, France
- Station Méditerranéenne de l'Environnement Littoral2 Avenue des chantiers, 34200, Sète, France
| | - Erick Desmarais
- Institut des Sciences de l'Évolution de Montpellier, CNRS-UMR 5554, Université Montpellier 2cc63, 34095, Montpellier Cedex 5, France
- LabEx CeMEB, Université Montpellier IIplace E. Bataillon, cc63, 34095, Montpellier Cedex 5, France
| | - Costas S Tsigenopoulos
- Hellenic Center for Marine Research, Institute of Marine Biology and GeneticsPO Box 2214, Gournes Pediados, 71500, Heraklion, Crete, Greece
| | - Khalid Belkhir
- Institut des Sciences de l'Évolution de Montpellier, CNRS-UMR 5554, Université Montpellier 2cc63, 34095, Montpellier Cedex 5, France
| | - François Bonhomme
- Institut des Sciences de l'Évolution de Montpellier, CNRS-UMR 5554, Université Montpellier 2cc63, 34095, Montpellier Cedex 5, France
- Station Méditerranéenne de l'Environnement Littoral2 Avenue des chantiers, 34200, Sète, France
| | - Bruno Guinand
- Institut des Sciences de l'Évolution de Montpellier, CNRS-UMR 5554, Université Montpellier 2cc63, 34095, Montpellier Cedex 5, France
- Station Méditerranéenne de l'Environnement Littoral2 Avenue des chantiers, 34200, Sète, France
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Van de Putte AP, Janko K, Kasparova E, Maes GE, Rock J, Koubbi P, Volckaert FA, Choleva L, Fraser KP, Smykla J, Van Houdt JK, Marshall C. Comparative phylogeography of three trematomid fishes reveals contrasting genetic structure patterns in benthic and pelagic species. Mar Genomics 2012. [DOI: 10.1016/j.margen.2012.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Yanagimoto T, Kitamura T, Kobayashi T. Genetic stock structure of walleye pollock (Theragra chalcogramma) inferred by PCR-RFLP analysis of the mitochondrial DNA and SNP analysis of nuclear DNA. Mar Genomics 2012; 7:17-25. [PMID: 22897958 DOI: 10.1016/j.margen.2012.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 03/30/2012] [Accepted: 04/10/2012] [Indexed: 11/28/2022]
Abstract
Walleye pollock, Theragra chalocogramma, is one of the most important species in the North Pacific and Bering Sea ecosystems. However genetic population structuring of walleye pollock is uncertain. In the present study, genetic variation of walleye pollock collected in several spawning areas ranging from the Japan Sea to the Gulf of Alaska was investigated by DNA analysis. Three regions of the spacer control region, the ND5 and ND6 region (ND complex), and the ND1 and 16S rRNA region (rDNA complex) were amplified using the polymerase chain reaction (PCR). Restriction fragment length polymorphism (RFLP) was conducted on these PCR products and composite haplotypes were calculated. Furthermore, several nuclear DNA regions (actin, Calmodulin, S7 ribosomal protein, creatin kinase, and SypI gene) were investigated to study the stock structure of walleye pollock. It was considered that Calmodulin gene was one of good genetic marker, therefore we conducted SNP analysis for Calmodulin gene by SnaPshot kits. In RFLP analyses, there were no area-specific fragment patterns in the three regions, control region, ND complex and rDNA complex of mtDNA. However compositions of the fragment patterns for the three digested sets, control region/HinfI, rDNA complex/MspI and ND complex/MspI indicated that there are significant differences between around the Japan (Sado-Funka Bay-Wakkanai-Rausu) and the Bering Sea (Western Bering Sea-Nabarin-Atka I.-Bogoslof I). Furthermore, in the case of haplotype frequency, composition showed also significant genetic difference between two areas. Moreover, in Calmodulin analyses, haplotype compositions were changing from western area to eastern area gradually and the results of AMOVA analysis showed that there are interesting differences between western Pacific, western Bering Sea, and eastern Bering Sea. Judging from these results, it was considered that there are three populations of walleye pollock in the Northern Ocean. However, area-specific pattern was not found in some populations in the Northern Ocean. Therefore, we suggested that these populations were related by weak gene flow, and the walleye pollock was formed with meta-population around the Japan and the Bering Sea.
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Affiliation(s)
- Takashi Yanagimoto
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan.
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DiBattista JD, Rocha LA, Craig MT, Feldheim KA, Bowen BW. Phylogeography of two closely related Indo-Pacific butterflyfishes reveals divergent evolutionary histories and discordant results from mtDNA and microsatellites. ACTA ACUST UNITED AC 2012; 103:617-29. [PMID: 22888133 DOI: 10.1093/jhered/ess056] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Marine biogeographic barriers can have unpredictable consequences, even among closely related species. To resolve phylogeographic patterns for Indo-Pacific reef fauna, we conducted range-wide surveys of sister species, the scrawled butterflyfish (Chaetodon meyeri; N = 134) and the ornate butterflyfish (Chaetodon ornatissimus; N = 296), using mitochondrial DNA cytochrome b sequences and 10 microsatellite loci. The former is distributed primarily in the Indian Ocean but also extends to the Line Islands in the Central Pacific, whereas the latter is distributed primarily in the Central-West Pacific (including Hawaii and French Polynesia) but extends to the eastern margin of the Indian Ocean. Analyses of molecular variance and Bayesian STRUCTURE results revealed 1 range-wide group for C. meyeri and 3 groups for C. ornatissimus: 1) eastern Indian Ocean and western Pacific, 2) Central Pacific, and 3) Hawaii. Estimates of the last population expansion were much more recent for C. meyeri (61 500 to 95 000 years) versus C. ornatissimus (184 700 to 286 300 years). Despite similarities in ecology, morphology, life history, and a broadly overlapping distribution, these sister species have divergent patterns of dispersal and corresponding evolutionary history. The mtDNA and microsatellite markers did not provide concordant results within 1 of our study species (C. meyeri), or in 7 out of 12 other cases of marine fishes in the published literature. This discordance renews caution in relying on one or a few markers for reconstructing historical demography.
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Karl SA, Toonen RJ, Grant WS, Bowen BW. Common misconceptions in molecular ecology: echoes of the modern synthesis. Mol Ecol 2012; 21:4171-89. [PMID: 22574714 DOI: 10.1111/j.1365-294x.2012.05576.x] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The field of molecular ecology has burgeoned into a large discipline spurred on by technical innovations that facilitate the rapid acquisition of large amounts of genotypic data, by the continuing development of theory to interpret results, and by the availability of computer programs to analyse data sets. As the discipline grows, however, misconceptions have become enshrined in the literature and are perpetuated by routine citations to other articles in molecular ecology. These misconceptions hamper a better understanding of the processes that influence genetic variation in natural populations and sometimes lead to erroneous conclusions. Here, we consider eight misconceptions commonly appearing in the literature: (i) some molecular markers are inherently better than other markers; (ii) mtDNA produces higher F(ST) values than nDNA; (iii) estimated population coalescences are real; (iv) more data are always better; (v) one needs to do a Bayesian analysis; (vi) selective sweeps influence mtDNA data; (vii) equilibrium conditions are critical for estimating population parameters; and (viii) having better technology makes us smarter than our predecessors. This is clearly not an exhaustive list and many others can be added. It is, however, sufficient to illustrate why we all need to be more critical of our own understanding of molecular ecology and to be suspicious of self-evident truths.
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Affiliation(s)
- Stephen A Karl
- Hawai'i Institute of Marine Biology, University of Hawai'i, Mānoa, Kāne'ohe, HI 96744, USA.
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Spice EK, Goodman DH, Reid SB, Docker MF. Neither philopatric nor panmictic: microsatellite and mtDNA evidence suggests lack of natal homing but limits to dispersal in Pacific lamprey. Mol Ecol 2012; 21:2916-30. [PMID: 22564149 DOI: 10.1111/j.1365-294x.2012.05585.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Most species with lengthy migrations display some degree of natal homing; some (e.g. migratory birds and anadromous salmonids) show spectacular feats of homing. However, studies of the sea lamprey (Petromyzon marinus) indicate that this anadromous species locates spawning habitat based on pheromonal cues from larvae rather than through philopatry. Previous genetic studies in the anadromous Pacific lamprey (Entosphenus tridentatus) have both supported and rejected the hypothesis of natal homing. To resolve this, we used nine microsatellite loci to examine the population structure in 965 Pacific lamprey from 20 locations from central British Columbia to southern California and supplemented this analysis with mitochondrial DNA restriction fragment length polymorphism analysis on a subset of 530 lamprey. Microsatellite analysis revealed (i) relatively low but often statistically significant genetic differentiation among locations (97% pairwise F(ST) values were <0.04 but 73.7% were significant); and (ii) weak but significant isolation by distance (r(2) = 0.0565, P = 0.0450) but no geographic clustering of samples. The few moderate F(ST) values involved comparisons with sites that were geographically distant or far upstream. The mtDNA analysis--although providing less resolution among sites (only 4.7%F(ST) values were significant)--was broadly consistent with the microsatellite results: (i) the southernmost site and some sites tributary to the Salish Sea were genetically distinct; and (ii) southern sites showed higher haplotype and private haplotype richness. These results are inconsistent with philopatry, suggesting that anadromous lampreys are unusual among species with long migrations, but suggest that limited dispersal at sea precludes panmixia in this species.
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Affiliation(s)
- Erin K Spice
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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Flight PA, O'Brien MA, Schmidt PS, Rand DM. Genetic structure and the North American postglacial expansion of the barnacle, Semibalanus balanoides. ACTA ACUST UNITED AC 2011; 103:153-65. [PMID: 21885571 DOI: 10.1093/jhered/esr083] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Population genetic characteristics are shaped by the life-history traits of organisms and the geologic history of their habitat. This study provides a neutral framework for understanding the population dynamics and opportunities for selection in Semibalanus balanoides, a species that figures prominently in ecological and evolutionary studies in the Atlantic intertidal. We used mitochondrial DNA (mtDNA) control region (N = 131) and microsatellite markers (∼40 individuals/site/locus) to survey populations of the broadly dispersing acorn barnacle from 8 sites spanning 800 km of North American coast and 1 site in Europe. Patterns of mtDNA sequence evolution were consistent with larger population sizes in Europe and population expansion at the conclusion of the last ice age, approximately 20 000 years ago, in North America. A significant portion of mitochondrial diversity was partitioned between the continents (ϕ(ST) = 0.281), but there was only weak structure observed from mtDNA within North America. Microsatellites showed significant structuring between the continents (F(ST) = 0.021) as well as within North America (F(ST) = 0.013). Isolation by distance in North America was largely driven by a split between populations south of Cape Cod and all others (P < 10(-4)). The glacial events responsible for generating allelic diversity at mtDNA and microsatellites may also be responsible for generating selectable variation at metabolic enzymes in S. balanoides.
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Affiliation(s)
- Patrick A Flight
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA.
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MEIRMANS PATRICKG, HEDRICK PHILIPW. Assessing population structure:
F
ST
and related measures. Mol Ecol Resour 2010; 11:5-18. [PMID: 21429096 DOI: 10.1111/j.1755-0998.2010.02927.x] [Citation(s) in RCA: 659] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- PATRICK G. MEIRMANS
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, PO Box 94248, 1090GE, Amsterdam, The Netherlands
| | - PHILIP W. HEDRICK
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
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YU HUI, NASON JOHND, GE XUEJUN, ZENG JIQING. Slatkin’s Paradox: when direct observation and realized gene flow disagree. A case study in Ficus. Mol Ecol 2010; 19:4441-53. [DOI: 10.1111/j.1365-294x.2010.04777.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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42
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An HS, Lee JH, Noh JK, Kim HC, Park CJ, Min BH, Myeong JI. Ten new microsatellite markers in cutlassfishTrichiurus lepturusderived from an enriched genomic library. Anim Cells Syst (Seoul) 2010. [DOI: 10.1080/19768354.2010.504347] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Noble DWA, Qi Y, Fu J. Species delineation using Bayesian model-based assignment tests: a case study using Chinese toad-headed agamas (genus Phrynocephalus). BMC Evol Biol 2010; 10:197. [PMID: 20579368 PMCID: PMC2904330 DOI: 10.1186/1471-2148-10-197] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 06/25/2010] [Indexed: 11/11/2022] Open
Abstract
Background Species are fundamental units in biology, yet much debate exists surrounding how we should delineate species in nature. Species discovery now requires the use of separate, corroborating datasets to quantify independently evolving lineages and test species criteria. However, the complexity of the speciation process has ushered in a need to infuse studies with new tools capable of aiding in species delineation. We suggest that model-based assignment tests are one such tool. This method circumvents constraints with traditional population genetic analyses and provides a novel means of describing cryptic and complex diversity in natural systems. Using toad-headed agamas of the Phrynocephalus vlangalii complex as a case study, we apply model-based assignment tests to microsatellite DNA data to test whether P. putjatia, a controversial species that closely resembles P. vlangalii morphologically, represents a valid species. Mitochondrial DNA and geographic data are also included to corroborate the assignment test results. Results Assignment tests revealed two distinct nuclear DNA clusters with 95% (230/243) of the individuals being assigned to one of the clusters with > 90% probability. The nuclear genomes of the two clusters remained distinct in sympatry, particularly at three syntopic sites, suggesting the existence of reproductive isolation between the identified clusters. In addition, a mitochondrial ND2 gene tree revealed two deeply diverged clades, which were largely congruent with the two nuclear DNA clusters, with a few exceptions. Historical mitochondrial introgression events between the two groups might explain the disagreement between the mitochondrial and nuclear DNA data. The nuclear DNA clusters and mitochondrial clades corresponded nicely to the hypothesized distributions of P. vlangalii and P. putjatia. Conclusions These results demonstrate that assignment tests based on microsatellite DNA data can be powerful tools for distinguishing closely related species and support the validity of P. putjatia. Assignment tests have the potential to play a significant role in elucidating biodiversity in the era of DNA data. Nonetheless, important limitations do exist and multiple independent datasets should be used to corroborate results from assignment programs.
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Affiliation(s)
- Daniel W A Noble
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Kronholm I, Loudet O, de Meaux J. Influence of mutation rate on estimators of genetic differentiation--lessons from Arabidopsis thaliana. BMC Genet 2010; 11:33. [PMID: 20433762 PMCID: PMC2888750 DOI: 10.1186/1471-2156-11-33] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2009] [Accepted: 05/01/2010] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The analysis of molecular variation within and between populations is crucial to establish strategies for conservation as well as to detect the footprint of spatially heterogeneous selection. The traditional estimator of genetic differentiation (F(ST)) has been shown to be misleading if genetic diversity is high. Alternative estimators of F(ST) have been proposed, but their robustness to variation in mutation rate is not clearly established. We first investigated the effect of mutation and migration rate using computer simulations and examined their joint influence on Q(ST), a measure of genetic differentiation for quantitative traits. We further used experimental data in natural populations of Arabidopsis thaliana to characterize the effect of mutation rate on various estimates of population differentiation. Since natural species exhibit various degrees of self-fertilisation, we also investigated the effect of mating system on the different estimators. RESULTS If mutation rate is high and migration rate low, classical measures of genetic differentiation are misleading. Only Phi(ST), an estimator that takes the mutational distances between alleles into account, is independent of mutation rate, for all migration rates. However, the performance of Phi(ST) depends on the underlying mutation model and departures from this model cause its performance to degrade. We further show that Q(ST) has the same bias. We provide evidence that, in A. thaliana, microsatellite variation correlates with mutation rate. We thereby demonstrate that our results on estimators of genetic differentiation have important implications, even for species that are well established models in population genetics and molecular biology. CONCLUSIONS We find that alternative measures of differentiation like F'(ST) and D are not suitable for estimating effective migration rate and should not be used in studies of local adaptation. Genetic differentiation should instead be measured using an estimator that takes mutation rate into account, such as Phi(ST). Furthermore, in systems where migration between populations is low, such as A. thaliana, Q(ST) < F(ST) cannot be taken as evidence for homogenising selection as has been traditionally thought.
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Affiliation(s)
- Ilkka Kronholm
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, F-78000 Versailles, France
| | - Juliette de Meaux
- Department of Plant Breeding and Genetics, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
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45
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Larmuseau MHD, Raeymaekers JAM, Hellemans B, Van Houdt JKJ, Volckaert FAM. Mito-nuclear discordance in the degree of population differentiation in a marine goby. Heredity (Edinb) 2010; 105:532-42. [PMID: 20145668 DOI: 10.1038/hdy.2010.9] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
An increasing number of phylogeographic studies on marine species shows discordant patterns in the degree of population differentiation between nuclear and mitochondrial markers. To understand better which factors have the potential to cause these patterns of discordance in marine organisms, a population genetic study was realized on the sand goby Pomatoschistus minutus (Pallas 1770; Gobiidae, Teleostei). Sand gobies from eight European locations were genotyped at eight microsatellite markers. Microsatellites confirmed the global phylogeographical pattern of P. minutus observed with mitochondrial DNA (mtDNA) markers and nuclear allozyme markers. Three groups consistent with the mitochondrial lineages were defined (the Mediterranean, Iberian and North Atlantic groups) and indications of a recent founder event in the northern Baltic Sea were found. Nevertheless, differences in the degree of population differentiation between the nuclear and mitochondrial markers were large (global F(ST)-values for microsatellites=0.0121; for allozymes=0.00831; for mtDNA=0.4293). Selection, sex-biased dispersal, homoplasy and a high effective population size are generally accepted as explanations for this mitonuclear discrepancy in the degree of population differentiation. In this study, selection on mtDNA and microsatellites, male-biased dispersal and homoplasy on microsatellite markers are unlikely to be a main cause for this discrepancy. The most likely reason for the discordant pattern is a recent demographical expansion of the sand goby, resulting in high effective population sizes slowing down the differentiation of nuclear DNA.
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Affiliation(s)
- M H D Larmuseau
- Laboratory of Animal Diversity and Systematics, Katholieke Universiteit Leuven, Leuven, Belgium
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46
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Shubina EA, Ponomareva EV, Glubokov AI. Population genetic structure of walleye pollock Theragra chalcogramma (Gadidae, Pisces) from the Bering Sea and Sea of Okhotsk. Mol Biol 2009. [DOI: 10.1134/s0026893309050161] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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Bradbury IR, Snelgrove PVR, Bentzen P, de Young B, Gregory RS, Morris CJ. Structural and functional connectivity of marine fishes within a semi-enclosed Newfoundland fjord. JOURNAL OF FISH BIOLOGY 2009; 75:1393-1409. [PMID: 20738621 DOI: 10.1111/j.1095-8649.2009.02391.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The interplay between structural connectivity (i.e. habitat continuity) and functional connectivity (i.e. dispersal probability) in marine fishes was examined in a coastal fjord (Holyrood Pond, Newfoundland, Canada) that is completely isolated from the North Atlantic Ocean for most of the year. Genetic differentiation was described in three species (rainbow smelt Osmerus mordax, white hake Urophycis tenuis and Atlantic cod Gadus morhua) with contrasting life histories using seven to 10 microsatellite loci and a protein-coding locus, PanI (G. morhua). Analysis of microsatellite differentiation indicated clear genetic differences between the fjord and coastal regions; however, the magnitude of difference was no more elevated than adjacent bays and was not enhanced by the fjord's isolation. Osmerus mordax was characterized by the highest structure overall with moderate differentiation between the fjord and St Mary's Bay (F(ST)c.0.047). In contrast, U. tenuis and G. morhua displayed weak differentiation (F(ST) < 0.01). Nonetheless, these populations did demonstrate high rates (< 75%) of Bayesian self-assignment. Furthermore, elevated differentiation was observed at the PanI locus in G. morhua between the fjord and other coastal locations. Interestingly, locus-specific genetic differentiation and expected heterozygosity were negatively associated in O. mordax, in contrast to the positive associations observed in U. tenuis and G. morhua. Gene flow in these species is apparently unencumbered by limited structural connectivity, yet the observed differentiation suggests that population structuring exists over small scales despite high dispersal potential.
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Affiliation(s)
- I R Bradbury
- Marine Gene Probe Laboratory, Biology Department, Life Sciences Centre Dalhousie University, 1355 Oxford Street Halifax, Nova Scotia B3H4J1, Canada.
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Pires AE, Amorim IR, Ginja C, Gomes M, Godinho I, Simões F, Oom M, Petrucci-Fonseca F, Matos J, Bruford MW. Molecular structure in peripheral dog breeds: Portuguese native breeds as a case study. Anim Genet 2009; 40:383-92. [DOI: 10.1111/j.1365-2052.2009.01849.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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NIELSEN EINARE, HEMMER-HANSEN JAKOB, LARSEN PETERFOGED, BEKKEVOLD DORTE. Population genomics of marine fishes: identifying adaptive variation in space and time. Mol Ecol 2009; 18:3128-50. [DOI: 10.1111/j.1365-294x.2009.04272.x] [Citation(s) in RCA: 236] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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50
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