Data from: A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci
Estimation of contemporary effective population size (Ne) from linkage disequilibrium (LD) between unlinked pairs of genetic markers has become an important tool in the field of population and conservation genetics. If data pertaining to physical linkage or genomic position are available for genetic...
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ftdryad:oai:v1.datadryad.org:10255/dryad.112697 2023-05-15T18:06:07+02:00 Data from: A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci Hollenbeck, Christopher M. Portnoy, David S. Gold, John R. West Matagorda Bay Texas 2016-03-30T18:15:46Z http://hdl.handle.net/10255/dryad.112697 https://doi.org/10.5061/dryad.73s46 unknown doi:10.5061/dryad.73s46/1 doi:10.1038/hdy.2016.30 PMID:27165767 doi:10.5061/dryad.73s46 Hollenbeck CM, Portnoy DS, Gold JR (2016) A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci. Heredity 117(4): 207-216. http://hdl.handle.net/10255/dryad.112697 effective population size linkage disequilibrium red drum Article 2016 ftdryad https://doi.org/10.5061/dryad.73s46 https://doi.org/10.5061/dryad.73s46/1 https://doi.org/10.1038/hdy.2016.30 2020-01-01T15:33:06Z Estimation of contemporary effective population size (Ne) from linkage disequilibrium (LD) between unlinked pairs of genetic markers has become an important tool in the field of population and conservation genetics. If data pertaining to physical linkage or genomic position are available for genetic markers, estimates of recombination rate between loci can be combined with LD data to estimate contemporary Ne at various times in the past. We extend the well-known, LD-based method of estimating contemporary Ne to include linkage information and show via simulation that even relatively small, recent changes in Ne can be detected reliably with a modest number of SNP loci. We explore several issues important to interpretation of the results and quantify the bias in estimates of contemporary Ne associated with the assumption that all loci in a large SNP dataset are unlinked. The approach is applied to an empirical dataset of SNP genotypes from a population of a marine fish where a recent, temporary decline in Ne is known to have occurred. Article in Journal/Newspaper Red drum Dryad Digital Repository (Duke University) |
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Dryad Digital Repository (Duke University) |
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effective population size linkage disequilibrium red drum |
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effective population size linkage disequilibrium red drum Hollenbeck, Christopher M. Portnoy, David S. Gold, John R. Data from: A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci |
topic_facet |
effective population size linkage disequilibrium red drum |
description |
Estimation of contemporary effective population size (Ne) from linkage disequilibrium (LD) between unlinked pairs of genetic markers has become an important tool in the field of population and conservation genetics. If data pertaining to physical linkage or genomic position are available for genetic markers, estimates of recombination rate between loci can be combined with LD data to estimate contemporary Ne at various times in the past. We extend the well-known, LD-based method of estimating contemporary Ne to include linkage information and show via simulation that even relatively small, recent changes in Ne can be detected reliably with a modest number of SNP loci. We explore several issues important to interpretation of the results and quantify the bias in estimates of contemporary Ne associated with the assumption that all loci in a large SNP dataset are unlinked. The approach is applied to an empirical dataset of SNP genotypes from a population of a marine fish where a recent, temporary decline in Ne is known to have occurred. |
format |
Article in Journal/Newspaper |
author |
Hollenbeck, Christopher M. Portnoy, David S. Gold, John R. |
author_facet |
Hollenbeck, Christopher M. Portnoy, David S. Gold, John R. |
author_sort |
Hollenbeck, Christopher M. |
title |
Data from: A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci |
title_short |
Data from: A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci |
title_full |
Data from: A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci |
title_fullStr |
Data from: A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci |
title_full_unstemmed |
Data from: A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci |
title_sort |
data from: a method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci |
publishDate |
2016 |
url |
http://hdl.handle.net/10255/dryad.112697 https://doi.org/10.5061/dryad.73s46 |
op_coverage |
West Matagorda Bay Texas |
genre |
Red drum |
genre_facet |
Red drum |
op_relation |
doi:10.5061/dryad.73s46/1 doi:10.1038/hdy.2016.30 PMID:27165767 doi:10.5061/dryad.73s46 Hollenbeck CM, Portnoy DS, Gold JR (2016) A method for detecting recent changes in contemporary effective population size from linkage disequilibrium at linked and unlinked loci. Heredity 117(4): 207-216. http://hdl.handle.net/10255/dryad.112697 |
op_doi |
https://doi.org/10.5061/dryad.73s46 https://doi.org/10.5061/dryad.73s46/1 https://doi.org/10.1038/hdy.2016.30 |
_version_ |
1766177693707010048 |