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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ftzenodo:oai:zenodo.org:5014494 2024-09-15T17:44:55+00:00 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 2015-01-15 https://doi.org/10.5061/dryad.rc917 unknown Zenodo https://doi.org/10.1111/1755-0998.12372 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.rc917 oai:zenodo.org:5014494 info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode Halobaena caerulea Pachyptila turtur Pachyptila desolata Oceanites oceanicus Pachyptila belcheri Pachyptila vittata null alleles cross-species utility 10 million years Pachyptila salvini info:eu-repo/semantics/other 2015 ftzenodo https://doi.org/10.5061/dryad.rc91710.1111/1755-0998.12372 2024-07-27T05:24:00Z 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. NGS shotgun data from Pachytila belcheri These are the 454 sequencing reads generated from two Pachyptila belcheri individuals (Kerguelen Archepelago) from which the 26 ... Other/Unknown Material Antarc* Antarctic Pachyptila desolata Zenodo |
institution |
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collection |
Zenodo |
op_collection_id |
ftzenodo |
language |
unknown |
topic |
Halobaena caerulea Pachyptila turtur Pachyptila desolata Oceanites oceanicus Pachyptila belcheri Pachyptila vittata null alleles cross-species utility 10 million years Pachyptila salvini |
spellingShingle |
Halobaena caerulea Pachyptila turtur Pachyptila desolata Oceanites oceanicus Pachyptila belcheri Pachyptila vittata null alleles cross-species utility 10 million years Pachyptila salvini 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 |
Halobaena caerulea Pachyptila turtur Pachyptila desolata Oceanites oceanicus Pachyptila belcheri Pachyptila vittata null alleles cross-species utility 10 million years Pachyptila salvini |
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. NGS shotgun data from Pachytila belcheri These are the 454 sequencing reads generated from two Pachyptila belcheri individuals (Kerguelen Archepelago) from which the 26 ... |
format |
Other/Unknown Material |
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 |
publisher |
Zenodo |
publishDate |
2015 |
url |
https://doi.org/10.5061/dryad.rc917 |
genre |
Antarc* Antarctic Pachyptila desolata |
genre_facet |
Antarc* Antarctic Pachyptila desolata |
op_relation |
https://doi.org/10.1111/1755-0998.12372 https://zenodo.org/communities/dryad https://doi.org/10.5061/dryad.rc917 oai:zenodo.org:5014494 |
op_rights |
info:eu-repo/semantics/openAccess Creative Commons Zero v1.0 Universal https://creativecommons.org/publicdomain/zero/1.0/legalcode |
op_doi |
https://doi.org/10.5061/dryad.rc91710.1111/1755-0998.12372 |
_version_ |
1810492602260127744 |