Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds
Population increases over the past several decades provide natural settings in which to study the evolutionary processes that occur during bottleneck, growth, and spatial expansion. We used parallel natural experiments of historical decline and subsequent recovery in two sympatric pinniped species i...
Main Authors: | , , , , , , , , , |
---|---|
Format: | Dataset |
Language: | unknown |
Published: |
Dryad Digital Repository
2019
|
Subjects: | |
Online Access: | https://doi.org/10.5061/dryad.fg52075 |
id |
fttriple:oai:gotriple.eu:50|dedup_wf_001::f9956165e8e8449e019249a62c19e5ba |
---|---|
record_format |
openpolar |
spelling |
fttriple:oai:gotriple.eu:50|dedup_wf_001::f9956165e8e8449e019249a62c19e5ba 2023-05-15T16:33:05+02:00 Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds Cammen, Kristina M. Schultz, Thomas F. Bowen, W. Don Hammill, Michael O. Puryear, Wendy B. Runstadler, Jonathan Wenzel, Frederick W. Wood, Stephanie A. Kinnison, Michael Don Bowen, W. 2019-01-01 https://doi.org/10.5061/dryad.fg52075 undefined unknown Dryad Digital Repository https://dx.doi.org/10.5061/dryad.fg52075 http://dx.doi.org/10.5061/dryad.fg52075 lic_creative-commons 10.5061/dryad.fg52075 oai:easy.dans.knaw.nl:easy-dataset:104614 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:104614 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c restriction site-associated DNA sequencing gray seal Halichoerus grypus atlantica harbor seal Phoca vitulina vitulina approximate Bayesian computation Life sciences medicine and health care envir anthro-se Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2019 fttriple https://doi.org/10.5061/dryad.fg52075 2023-01-22T16:53:35Z Population increases over the past several decades provide natural settings in which to study the evolutionary processes that occur during bottleneck, growth, and spatial expansion. We used parallel natural experiments of historical decline and subsequent recovery in two sympatric pinniped species in the Northwest Atlantic, the gray seal (Halichoerus grypus atlantica) and harbor seal (Phoca vitulina vitulina), to study the impact of recent demographic change in genomic diversity. Using restriction site‐associated DNA sequencing, we assessed genomic diversity at over 8,700 polymorphic gray seal loci and 3,700 polymorphic harbor seal loci in samples from multiple cohorts collected throughout recovery over the past half‐century. Despite significant differences in the degree of genetic diversity assessed in the two species, we found signatures of historical bottlenecks in the contemporary genomes of both gray and harbor seals. We evaluated temporal trends in diversity across cohorts, as well as compared samples from sites at both the center and edge of a recent gray seal range expansion, but found no significant change in genomewide diversity following recovery. We did, however, find that the variance and degree of allele frequency change measured over the past several decades were significantly different from neutral expectations of drift under population growth. These two cases of well‐described demographic history provide opportunities for critical evaluation of current approaches to simulating and understanding the genetic effects of historical demographic change in natural populations. Gray seal RAD lociCatalog of 244,822 RAD loci consensus sequences resulting from ddRAD sequencing of genomic DNA from 56 gray seals sampled in the Northwest Atlantic. The gray seals selected to build the RAD catalog included 7 individuals from each of the following sampling locations and cohorts - Gulf of St Lawrence, Canada: 2015; Sable Island, NS, Canada: 1973-74, 1985, 1998, 2004, and 2015; Muskeget Island, MA, USA: 2002 and ... Dataset harbor seal Northwest Atlantic Phoca vitulina Unknown Canada |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
restriction site-associated DNA sequencing gray seal Halichoerus grypus atlantica harbor seal Phoca vitulina vitulina approximate Bayesian computation Life sciences medicine and health care envir anthro-se |
spellingShingle |
restriction site-associated DNA sequencing gray seal Halichoerus grypus atlantica harbor seal Phoca vitulina vitulina approximate Bayesian computation Life sciences medicine and health care envir anthro-se Cammen, Kristina M. Schultz, Thomas F. Bowen, W. Don Hammill, Michael O. Puryear, Wendy B. Runstadler, Jonathan Wenzel, Frederick W. Wood, Stephanie A. Kinnison, Michael Don Bowen, W. Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds |
topic_facet |
restriction site-associated DNA sequencing gray seal Halichoerus grypus atlantica harbor seal Phoca vitulina vitulina approximate Bayesian computation Life sciences medicine and health care envir anthro-se |
description |
Population increases over the past several decades provide natural settings in which to study the evolutionary processes that occur during bottleneck, growth, and spatial expansion. We used parallel natural experiments of historical decline and subsequent recovery in two sympatric pinniped species in the Northwest Atlantic, the gray seal (Halichoerus grypus atlantica) and harbor seal (Phoca vitulina vitulina), to study the impact of recent demographic change in genomic diversity. Using restriction site‐associated DNA sequencing, we assessed genomic diversity at over 8,700 polymorphic gray seal loci and 3,700 polymorphic harbor seal loci in samples from multiple cohorts collected throughout recovery over the past half‐century. Despite significant differences in the degree of genetic diversity assessed in the two species, we found signatures of historical bottlenecks in the contemporary genomes of both gray and harbor seals. We evaluated temporal trends in diversity across cohorts, as well as compared samples from sites at both the center and edge of a recent gray seal range expansion, but found no significant change in genomewide diversity following recovery. We did, however, find that the variance and degree of allele frequency change measured over the past several decades were significantly different from neutral expectations of drift under population growth. These two cases of well‐described demographic history provide opportunities for critical evaluation of current approaches to simulating and understanding the genetic effects of historical demographic change in natural populations. Gray seal RAD lociCatalog of 244,822 RAD loci consensus sequences resulting from ddRAD sequencing of genomic DNA from 56 gray seals sampled in the Northwest Atlantic. The gray seals selected to build the RAD catalog included 7 individuals from each of the following sampling locations and cohorts - Gulf of St Lawrence, Canada: 2015; Sable Island, NS, Canada: 1973-74, 1985, 1998, 2004, and 2015; Muskeget Island, MA, USA: 2002 and ... |
format |
Dataset |
author |
Cammen, Kristina M. Schultz, Thomas F. Bowen, W. Don Hammill, Michael O. Puryear, Wendy B. Runstadler, Jonathan Wenzel, Frederick W. Wood, Stephanie A. Kinnison, Michael Don Bowen, W. |
author_facet |
Cammen, Kristina M. Schultz, Thomas F. Bowen, W. Don Hammill, Michael O. Puryear, Wendy B. Runstadler, Jonathan Wenzel, Frederick W. Wood, Stephanie A. Kinnison, Michael Don Bowen, W. |
author_sort |
Cammen, Kristina M. |
title |
Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds |
title_short |
Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds |
title_full |
Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds |
title_fullStr |
Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds |
title_full_unstemmed |
Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds |
title_sort |
data from: genomic signatures of population bottleneck and recovery in northwest atlantic pinnipeds |
publisher |
Dryad Digital Repository |
publishDate |
2019 |
url |
https://doi.org/10.5061/dryad.fg52075 |
geographic |
Canada |
geographic_facet |
Canada |
genre |
harbor seal Northwest Atlantic Phoca vitulina |
genre_facet |
harbor seal Northwest Atlantic Phoca vitulina |
op_source |
10.5061/dryad.fg52075 oai:easy.dans.knaw.nl:easy-dataset:104614 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:104614 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
https://dx.doi.org/10.5061/dryad.fg52075 http://dx.doi.org/10.5061/dryad.fg52075 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.fg52075 |
_version_ |
1766022802109890560 |