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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fttriple:oai:gotriple.eu:50|dedup_wf_001::d32f2d13ba622cf2fed7d16080609511 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. 2017-01-01 https://doi.org/10.5061/dryad.73s46 undefined unknown http://dx.doi.org/10.5061/dryad.73s46 https://dx.doi.org/10.5061/dryad.73s46 lic_creative-commons oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:93929 oai:easy.dans.knaw.nl:easy-dataset:93929 10.5061/dryad.73s46 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Life sciences medicine and health care effective population size red drum Sciaenops ocellatus linkage disequilibrium West Matagorda Bay Texas demo envir Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2017 fttriple https://doi.org/10.5061/dryad.73s46 2023-01-22T16:51:41Z 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 Unknown |
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Open Polar |
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fttriple |
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topic |
Life sciences medicine and health care effective population size red drum Sciaenops ocellatus linkage disequilibrium West Matagorda Bay Texas demo envir |
spellingShingle |
Life sciences medicine and health care effective population size red drum Sciaenops ocellatus linkage disequilibrium West Matagorda Bay Texas demo envir 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 |
Life sciences medicine and health care effective population size red drum Sciaenops ocellatus linkage disequilibrium West Matagorda Bay Texas demo envir |
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 |
2017 |
url |
https://doi.org/10.5061/dryad.73s46 |
genre |
Red drum Sciaenops ocellatus |
genre_facet |
Red drum Sciaenops ocellatus |
op_source |
oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:93929 oai:easy.dans.knaw.nl:easy-dataset:93929 10.5061/dryad.73s46 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 re3data_____::r3d100000044 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.73s46 https://dx.doi.org/10.5061/dryad.73s46 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.73s46 |
_version_ |
1766177697701036032 |