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      The Structure of Genetic Diversity in Eelgrass ( Zostera marina L.) along the North Pacific and Bering Sea Coasts of Alaska

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          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: R 2 = 0.738, P < 0.001; allelic richness: R 2 = 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 (θ p = 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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          TreeView: an application to display phylogenetic trees on personal computers.

          R D Page (1996)
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            Arlequin (version 3.0): An integrated software package for population genetics data analysis

            Arlequin ver 3.0 is a software package integrating several basic and advanced methods for population genetics data analysis, like the computation of standard genetic diversity indices, the estimation of allele and haplotype frequencies, tests of departure from linkage equilibrium, departure from selective neutrality and demographic equilibrium, estimation or parameters from past population expansions, and thorough analyses of population subdivision under the AMOVA framework. Arlequin 3 introduces a completely new graphical interface written in C++, a more robust semantic analysis of input files, and two new methods: a Bayesian estimation of gametic phase from multi-locus genotypes, and an estimation of the parameters of an instantaneous spatial expansion from DNA sequence polymorphism. Arlequin can handle several data types like DNA sequences, microsatellite data, or standard multi-locus genotypes. A Windows version of the software is freely available on http://cmpg.unibe.ch/software/arlequin3.
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              Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach.

              A maximum likelihood estimator based on the coalescent for unequal migration rates and different subpopulation sizes is developed. The method uses a Markov chain Monte Carlo approach to investigate possible genealogies with branch lengths and with migration events. Properties of the new method are shown by using simulated data from a four-population n-island model and a source-sink population model. Our estimation method as coded in migrate is tested against genetree; both programs deliver a very similar likelihood surface. The algorithm converges to the estimates fairly quickly, even when the Markov chain is started from unfavorable parameters. The method was used to estimate gene flow in the Nile valley by using mtDNA data from three human populations.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                22 April 2016
                2016
                : 11
                : 4
                : e0152701
                Affiliations
                [1 ]Alaska Science Center, U.S. Geological Survey, Anchorage, Alaska, United States of America
                [2 ]Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
                [3 ]Escuela de Ciencias de la Salud, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
                [4 ]Biological Sciences, Humboldt State University, Arcata, California, United States of America
                [5 ]Friday Harbor Laboratories, University of Washington, Friday Harbor, Washington, United States of America
                [6 ]Center for Marine and Environmental Studies, University of Virgin Islands, St. Thomas, Virgin Islands, United States of America
                [7 ]Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, California, Mexico
                Chinese Academy of Sciences, CHINA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: SLT GKS DHW. Performed the experiments: SLT GKS JRR MCF RMS. Analyzed the data: SLT GKS JRR MCF. Contributed reagents/materials/analysis tools: SLT RMS BB SWE ACP DHW. Wrote the paper: SLT GKS JRR MCF RMS BB SWE ACP DHW.

                Article
                PONE-D-15-37058
                10.1371/journal.pone.0152701
                4841600
                27104836
                15e338eb-c9ff-42ec-8699-0fdb1e3da834

                This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

                History
                : 28 September 2015
                : 17 March 2016
                Page count
                Figures: 6, Tables: 1, Pages: 31
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000203, U.S. Geological Survey;
                Award Recipient :
                Funded by: Ramsar Convention on Wetlands
                Award ID: WFF/00-2/MEX/3
                Award Recipient :
                Funded by: Universidad Autónoma de Baja California
                Award Recipient :
                Funding for this research was provided by the Alaska Science Center, U.S. Geological Survey to SLT, the Universidad Autónoma de Baja California (#4033, #4023) to RMS and ACP and Ramsar Convention on Wetlands (WFF/00-2/MEX/3) to DHW.
                Categories
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                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Biology and Life Sciences
                Genetics
                Population Genetics
                Biology and Life Sciences
                Population Biology
                Population Genetics
                People and places
                Geographical locations
                North America
                United States
                Alaska
                Biology and Life Sciences
                Genetics
                Heredity
                Gene Flow
                Biology and Life Sciences
                Evolutionary Biology
                Population Genetics
                Gene Flow
                Biology and Life Sciences
                Genetics
                Population Genetics
                Gene Flow
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                Population Biology
                Population Genetics
                Gene Flow
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                Biology and Life Sciences
                Population Biology
                Population Genetics
                Phylogeography
                Earth Sciences
                Geography
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                Geographical locations
                North America
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                North America
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                Custom metadata
                All nucleotide sequence data are archived in GenBank (accession numbers are now listed in the manuscript), and all microsatellite data are archived at the USGS ASC data server ( http://dx.doi.org/10.5066/F7GQ6VTK).

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