Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds
Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at...
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Online Access: | http://hdl.handle.net/10255/dryad.74003 https://doi.org/10.5061/dryad.rc917 |
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ftdryad:oai:v1.datadryad.org:10255/dryad.74003 2023-05-15T13:55:49+02:00 Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds Moodley, Yoshan Masello, Juan F. Munimanda, Gopi K. Cole, Theresa L. Thali, Marco R. Alderman, Rachael Cuthbert, Richard J. Marin, Manuel Massaro, Melanie Navarro, Joan Phillips, Richard A. Ryan, Peter G. Suazo, Cristián G. Cherel, Yves Weimerskirch, Henri Quillfeldt, Petra Calderon, Luciano Southern Ocean Subantarctic 10 million years 2015-01-15T20:19:28Z http://hdl.handle.net/10255/dryad.74003 https://doi.org/10.5061/dryad.rc917 unknown doi:10.5061/dryad.rc917/1 doi:10.5061/dryad.rc917/2 doi:10.5061/dryad.rc917/3 doi:10.5061/dryad.rc917/4 doi:10.1111/1755-0998.12372 PMID:25594938 doi:10.5061/dryad.rc917 Moodley Y, Masello JF, Cole TL, Calderon L, Munimanda GK, Thali MR, Alderman R, Cuthbert RJ, Marin M, Massaro M, Navarro J, Phillips RA, Ryan PG, Suazo CG, Cherel Y, Weimerskirch H, Quillfeldt P (2015) Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds. Molecular Ecology Resources 15(5): 1046–1058. http://hdl.handle.net/10255/dryad.74003 cross-species utility Birds genetic diversity microsatellite null alleles Article 2015 ftdryad https://doi.org/10.5061/dryad.rc917 https://doi.org/10.5061/dryad.rc917/1 https://doi.org/10.5061/dryad.rc917/2 https://doi.org/10.5061/dryad.rc917/3 https://doi.org/10.5061/dryad.rc917/4 https://doi.org/10.1111/1755-0998.12372 2020-01-01T15:13:22Z Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased nonamplification, or disruptions that may result in decreased polymorphism in nontarget species. Furthermore, high mutation rates and constraints on allele size may also with evolutionary time, promote an increase in convergently evolved allele size classes, biasing measures of interspecific genetic differentiation. Here, we used next-generation sequencing to develop microsatellite markers from a shotgun genome sequence of the sub-Antarctic seabird, the thin-billed prion (Pachyptila belcheri), that we tested for cross-species amplification in other Pachyptila and related sub-Antarctic species. We found that heterozygosity decreased and the proportion of nonamplifying loci increased with phylogenetic distance from the target species. Surprisingly, we found that species trees estimated from interspecific FST provided better approximations of mtDNA relationships among the studied species than those estimated using DC, even though FST was more affected by null alleles. We observed a significantly nonlinear second order polynomial relationship between microsatellite and mtDNA distances. We propose that the loss of linearity with increasing mtDNA distance stems from an increasing proportion of homoplastic allele size classes that are identical in state, but not identical by descent. Therefore, despite high cross-species amplification success and high polymorphism among the closely related Pachyptila species, we caution against the use of microsatellites in phylogenetic inference among distantly related taxa. Article in Journal/Newspaper Antarc* Antarctic Southern Ocean Dryad Digital Repository (Duke University) Antarctic Southern Ocean |
institution |
Open Polar |
collection |
Dryad Digital Repository (Duke University) |
op_collection_id |
ftdryad |
language |
unknown |
topic |
cross-species utility Birds genetic diversity microsatellite null alleles |
spellingShingle |
cross-species utility Birds genetic diversity microsatellite null alleles Moodley, Yoshan Masello, Juan F. Munimanda, Gopi K. Cole, Theresa L. Thali, Marco R. Alderman, Rachael Cuthbert, Richard J. Marin, Manuel Massaro, Melanie Navarro, Joan Phillips, Richard A. Ryan, Peter G. Suazo, Cristián G. Cherel, Yves Weimerskirch, Henri Quillfeldt, Petra Calderon, Luciano Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds |
topic_facet |
cross-species utility Birds genetic diversity microsatellite null alleles |
description |
Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased nonamplification, or disruptions that may result in decreased polymorphism in nontarget species. Furthermore, high mutation rates and constraints on allele size may also with evolutionary time, promote an increase in convergently evolved allele size classes, biasing measures of interspecific genetic differentiation. Here, we used next-generation sequencing to develop microsatellite markers from a shotgun genome sequence of the sub-Antarctic seabird, the thin-billed prion (Pachyptila belcheri), that we tested for cross-species amplification in other Pachyptila and related sub-Antarctic species. We found that heterozygosity decreased and the proportion of nonamplifying loci increased with phylogenetic distance from the target species. Surprisingly, we found that species trees estimated from interspecific FST provided better approximations of mtDNA relationships among the studied species than those estimated using DC, even though FST was more affected by null alleles. We observed a significantly nonlinear second order polynomial relationship between microsatellite and mtDNA distances. We propose that the loss of linearity with increasing mtDNA distance stems from an increasing proportion of homoplastic allele size classes that are identical in state, but not identical by descent. Therefore, despite high cross-species amplification success and high polymorphism among the closely related Pachyptila species, we caution against the use of microsatellites in phylogenetic inference among distantly related taxa. |
format |
Article in Journal/Newspaper |
author |
Moodley, Yoshan Masello, Juan F. Munimanda, Gopi K. Cole, Theresa L. Thali, Marco R. Alderman, Rachael Cuthbert, Richard J. Marin, Manuel Massaro, Melanie Navarro, Joan Phillips, Richard A. Ryan, Peter G. Suazo, Cristián G. Cherel, Yves Weimerskirch, Henri Quillfeldt, Petra Calderon, Luciano |
author_facet |
Moodley, Yoshan Masello, Juan F. Munimanda, Gopi K. Cole, Theresa L. Thali, Marco R. Alderman, Rachael Cuthbert, Richard J. Marin, Manuel Massaro, Melanie Navarro, Joan Phillips, Richard A. Ryan, Peter G. Suazo, Cristián G. Cherel, Yves Weimerskirch, Henri Quillfeldt, Petra Calderon, Luciano |
author_sort |
Moodley, Yoshan |
title |
Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds |
title_short |
Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds |
title_full |
Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds |
title_fullStr |
Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds |
title_full_unstemmed |
Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds |
title_sort |
data from: evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds |
publishDate |
2015 |
url |
http://hdl.handle.net/10255/dryad.74003 https://doi.org/10.5061/dryad.rc917 |
op_coverage |
Southern Ocean Subantarctic 10 million years |
geographic |
Antarctic Southern Ocean |
geographic_facet |
Antarctic Southern Ocean |
genre |
Antarc* Antarctic Southern Ocean |
genre_facet |
Antarc* Antarctic Southern Ocean |
op_relation |
doi:10.5061/dryad.rc917/1 doi:10.5061/dryad.rc917/2 doi:10.5061/dryad.rc917/3 doi:10.5061/dryad.rc917/4 doi:10.1111/1755-0998.12372 PMID:25594938 doi:10.5061/dryad.rc917 Moodley Y, Masello JF, Cole TL, Calderon L, Munimanda GK, Thali MR, Alderman R, Cuthbert RJ, Marin M, Massaro M, Navarro J, Phillips RA, Ryan PG, Suazo CG, Cherel Y, Weimerskirch H, Quillfeldt P (2015) Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds. Molecular Ecology Resources 15(5): 1046–1058. http://hdl.handle.net/10255/dryad.74003 |
op_doi |
https://doi.org/10.5061/dryad.rc917 https://doi.org/10.5061/dryad.rc917/1 https://doi.org/10.5061/dryad.rc917/2 https://doi.org/10.5061/dryad.rc917/3 https://doi.org/10.5061/dryad.rc917/4 https://doi.org/10.1111/1755-0998.12372 |
_version_ |
1766262716971876352 |