Data

WAMSI Node 4.4.2-2b - Genetic (microsatellite) determination of the stock structures of Pink snapper (Pagrus auratus) and Baldchin groper (Choerodon rubescens) in Western Australian waters.

Australian Ocean Data Network
Gardner, Michelle (Principal investigator, Point of contact) Chaplin, Jennifer (Point of contact)
Viewed: [[ro.stat.viewed]] Cited: [[ro.stat.cited]] Accessed: [[ro.stat.accessed]]
ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rfr_id=info%3Asid%2FANDS&rft_id=https://catalogue.aodn.org.au:443/geonetwork/srv/api/records/c10912ec-b4e4-4c4f-a211-f2fad6cc1567&rft.title=WAMSI Node 4.4.2-2b - Genetic (microsatellite) determination of the stock structures of Pink snapper (Pagrus auratus) and Baldchin groper (Choerodon rubescens) in Western Australian waters.&rft.identifier=c10912ec-b4e4-4c4f-a211-f2fad6cc1567&rft.publisher=Australian Ocean Data Network&rft.description=The aim of the research is to use microsatellite markers to elucidate the stock structures of Pink snapper (Pagrus auratus) and Baldchin groper (Choerodon rubescens) in Western Australian waters. The research focused on analysing spatial patterns of genetic variation based on single samples from locations along the south-western Australian coast. The research was done in order to provide information to managers about the spatial scales that are relevant to the biology of these species and the appropriateness of the spatial units currently used for the management of these species, focussing on the West Coast Bioregion. This research is part of a PhD study being conducted by Michelle Gardner at Murdoch University. The actual data collected are patterns of variation at 12 microsatellite loci stored as Excel spreadsheetsStatement: Microsatellite markers are being used to assess the population structures of Pink snapper (Pagrus auratus) and Baldchin groper (Choerodon rubescens) in Western Australian waters. Genetic Identification Services (GIS, http://www. geneticidentificationservices.com) constructed microsatellite-enriched partial genomic libraries for C. rubescens and P. auratus, following the methods described by Jones et al. (2002). GIS was supplied with approximately 30 lg of high molecular weight DNA extracted from muscle tissue. The DNA was extracted using a MasterPureTM DNAPurificationKit following the manufacturer’s protocol for soft tissue, except that tissue and reagent quantities were significantly increased and a 5% sodium dodecyl sulfate (SDS) extraction buffer was substituted for the tissue and cell lysis solution. Four libraries, enriched for CA, ATG, TAGA, and CAGA motifs, were constructed and 36 recombinant clones from each library were randomly selected for sequencing, of which 34, 29, 34 and 30 contained microsatellites, respectively (GenBank accession numbers HM754266-392). Of the markers trialed 11 and 12 loci were considered ideal for population level analysis for P. auratus and C. rubescens respectively. In addition, the microsatellite marker PMA1 (Takagi et al, 1997) was also utilised for P. auratus. Microsatellite DNA data were generated for approximately 30 individuals of the P. auratus from each of 12 sites, namely Carnarvon, the western and eastern gulfs of Shark Bay, Kalbarri, Jurien Bay, Cockburn Sound, Augusta, Albany, Esperance, Gulf St Vincent and Sydney. Microsatellite DNA data were generated for 26-40 individuals of C. rubescens from five locations between Perth and Shark Bay, namely Monkey Rock, Jurien Bay, Abrolhos Islands north and south and Perth. Polymerase chain reaction (PCR) was used to amplify the 12 markers for each species and the resultant genotypes were determined using automated sequencing methods on an ABI 3730 DNA analyzer. The microsatellite data for individuals from all sites have been incorporated in a single data set for each species and subject to a range of analyses including exact tests for departures from Hardy-Weinberg equilibrium expectations (Raymond & Rousett, 1995), analysis of genetic variance (Weir and Cockerham, 1984; Jost, 2008), tests for isolation by distance (Slatkin, 1993), Bayesian clustering (Pritchard et al., 2000) and an analysis of statistical power (Ryman & Palm, 2006). The data interpretation is underway.&rft.creator=Gardner, Michelle&rft.date=2017&rft.coverage=westlimit=112.50; southlimit=-35.10; eastlimit=117.50; northlimit=-25.40&rft.coverage=westlimit=112.50; southlimit=-35.10; eastlimit=117.50; northlimit=-25.40&rft.coverage=westlimit=112.50; southlimit=-32.30; eastlimit=115.10; northlimit=-25.30&rft.coverage=westlimit=112.50; southlimit=-32.30; eastlimit=115.10; northlimit=-25.30&rft_rights= http://creativecommons.org/licenses/by-nc-sa/2.5/au/&rft_rights=http://i.creativecommons.org/l/by-nc-sa/2.5/au/88x31.png&rft_rights=WWW:LINK-1.0-http--related&rft_rights=License Graphic&rft_rights=Creative Commons Attribution-Noncommercial-Share Alike 2.5 Australia License&rft_rights=http://creativecommons.org/international/au/&rft_rights=WWW:LINK-1.0-http--related&rft_rights=WWW:LINK-1.0-http--related&rft_rights=License Text&rft_rights=Creative Commons Attribution-Noncommercial-Share Alike 2.5 Australia License&rft_rights= http://creativecommons.org/licenses/by-nc-sa/2.5/au/&rft_subject=oceans&rft_subject=biota&rft_subject=FISH&rft_subject=EARTH SCIENCE&rft_subject=BIOLOGICAL CLASSIFICATION&rft_subject=ANIMALS/VERTEBRATES&rft_subject=MARINE HABITAT&rft_subject=BIOSPHERE&rft_subject=AQUATIC ECOSYSTEMS&rft_subject=POPULATION DYNAMICS&rft_subject=ECOLOGICAL DYNAMICS&rft_subject=SPECIES/POPULATION INTERACTIONS&rft_subject=States, Territories (Australia) | Western Australia&rft_subject=Pagrus auratus&rft_subject=Sparidae&rft_subject=Choerodon rubescens&rft_subject=Labridae&rft_subject=Population Genetics&rft_subject=Gene Flow&rft_subject=Microsatellite Marker&rft.type=dataset&rft.language=English Access the data
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The aim of the research is to use microsatellite markers to elucidate the stock structures of Pink snapper (Pagrus auratus) and Baldchin groper (Choerodon rubescens) in Western Australian waters. The research focused on analysing spatial patterns of genetic variation based on single samples from locations along the south-western Australian coast. The research was done in order to provide information to managers about the spatial scales that are relevant to the biology of these species and the appropriateness of the spatial units currently used for the management of these species, focussing on the West Coast Bioregion. This research is part of a PhD study being conducted by Michelle Gardner at Murdoch University. The actual data collected are patterns of variation at 12 microsatellite loci stored as Excel spreadsheets

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Statement: Microsatellite markers are being used to assess the population structures of Pink snapper (Pagrus auratus) and Baldchin groper (Choerodon rubescens) in Western Australian waters. Genetic Identification Services (GIS, http://www. geneticidentificationservices.com) constructed microsatellite-enriched partial genomic libraries for C. rubescens and P. auratus, following the methods described by Jones et al. (2002). GIS was supplied with approximately 30 lg of high molecular weight DNA extracted from muscle tissue. The DNA was extracted using a MasterPureTM DNAPurificationKit following the manufacturer’s protocol for soft tissue, except that tissue and reagent quantities were significantly increased and a 5% sodium dodecyl sulfate (SDS) extraction buffer was substituted for the tissue and cell lysis solution. Four libraries, enriched for CA, ATG, TAGA, and CAGA motifs, were constructed and 36 recombinant clones from each library were randomly selected for sequencing, of which 34, 29, 34 and 30 contained microsatellites, respectively (GenBank accession numbers HM754266-392). Of the markers trialed 11 and 12 loci were considered ideal for population level analysis for P. auratus and C. rubescens respectively. In addition, the microsatellite marker PMA1 (Takagi et al, 1997) was also utilised for P. auratus. Microsatellite DNA data were generated for approximately 30 individuals of the P. auratus from each of 12 sites, namely Carnarvon, the western and eastern gulfs of Shark Bay, Kalbarri, Jurien Bay, Cockburn Sound, Augusta, Albany, Esperance, Gulf St Vincent and Sydney. Microsatellite DNA data were generated for 26-40 individuals of C. rubescens from five locations between Perth and Shark Bay, namely Monkey Rock, Jurien Bay, Abrolhos Islands north and south and Perth. Polymerase chain reaction (PCR) was used to amplify the 12 markers for each species and the resultant genotypes were determined using automated sequencing methods on an ABI 3730 DNA analyzer. The microsatellite data for individuals from all sites have been incorporated in a single data set for each species and subject to a range of analyses including exact tests for departures from Hardy-Weinberg equilibrium expectations (Raymond & Rousett, 1995), analysis of genetic variance (Weir and Cockerham, 1984; Jost, 2008), tests for isolation by distance (Slatkin, 1993), Bayesian clustering (Pritchard et al., 2000) and an analysis of statistical power (Ryman & Palm, 2006). The data interpretation is underway.

Notes

Credit
Brett Moloney
Credit
David Fairclough
Credit
Gary Jackson
Credit
Department of Fisheries (DoF)

Created: 11 08 2009

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117.5,-25.4 117.5,-35.1 112.5,-35.1 112.5,-25.4 117.5,-25.4

115,-30.25

115.1,-25.3 115.1,-32.3 112.5,-32.3 112.5,-25.3 115.1,-25.3

113.8,-28.8

text: westlimit=112.50; southlimit=-35.10; eastlimit=117.50; northlimit=-25.40

text: westlimit=112.50; southlimit=-32.30; eastlimit=115.10; northlimit=-25.30

Subjects
ANIMALS/VERTEBRATES | AQUATIC ECOSYSTEMS | BIOLOGICAL CLASSIFICATION | BIOSPHERE | Choerodon rubescens | EARTH SCIENCE | ECOLOGICAL DYNAMICS | Fish | Gene Flow | Labridae | Marine Habitat | Microsatellite Marker | Population Dynamics | Pagrus auratus | Population Genetics | SPECIES/POPULATION INTERACTIONS | Sparidae | States, Territories (Australia) | Western Australia | biota | oceans |

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