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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ftzenodo:oai:zenodo.org:4977006 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. 2016-03-30 https://zenodo.org/record/4977006 https://doi.org/10.5061/dryad.73s46 unknown doi:10.1038/hdy.2016.30 https://zenodo.org/communities/dryad https://zenodo.org/record/4977006 https://doi.org/10.5061/dryad.73s46 oai:zenodo.org:4977006 info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode red drum Sciaenops ocellatus info:eu-repo/semantics/other dataset 2016 ftzenodo https://doi.org/10.5061/dryad.73s4610.1038/hdy.2016.30 2023-03-10T19:16:57Z 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. Raw Data FilesGenepop files for simulated and empirical datasetsraw_data.tar.gz Dataset Red drum Sciaenops ocellatus Zenodo |
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red drum Sciaenops ocellatus |
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red drum Sciaenops ocellatus 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 |
red drum Sciaenops ocellatus |
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. Raw Data FilesGenepop files for simulated and empirical datasetsraw_data.tar.gz |
format |
Dataset |
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 |
https://zenodo.org/record/4977006 https://doi.org/10.5061/dryad.73s46 |
genre |
Red drum Sciaenops ocellatus |
genre_facet |
Red drum Sciaenops ocellatus |
op_relation |
doi:10.1038/hdy.2016.30 https://zenodo.org/communities/dryad https://zenodo.org/record/4977006 https://doi.org/10.5061/dryad.73s46 oai:zenodo.org:4977006 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.73s4610.1038/hdy.2016.30 |
_version_ |
1766177696022265856 |