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: | https://doi.org/10.1111/1755-0998.12372 http://www.ncbi.nlm.nih.gov/pubmed/25594938 http://ecite.utas.edu.au/118580 |
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ftunivtasecite:oai:ecite.utas.edu.au:118580 2023-05-15T13:49:03+02:00 Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds Moodely, 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 Cherl, Y Weimerskirch, H Quillfeldt, P 2015 https://doi.org/10.1111/1755-0998.12372 http://www.ncbi.nlm.nih.gov/pubmed/25594938 http://ecite.utas.edu.au/118580 en eng Wiley-Blackwell Publishing Ltd. http://dx.doi.org/10.1111/1755-0998.12372 Moodely, Y and Masello, JF and Cole, TL and Calderon, L and Munimanda, GK and Thali, MR and Alderman, R and Cuthbert, RJ and Marin, M and Massaro, M and Navarro, J and Phillips, RA and Ryan, PG and Suazo, CG and Cherl, Y and Weimerskirch, H and Quillfeldt, P, Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds, Molecular Ecology Resources, 15, (5) pp. 1046-1058. ISSN 1755-098X (2015) [Refereed Article] http://www.ncbi.nlm.nih.gov/pubmed/25594938 http://ecite.utas.edu.au/118580 Biological Sciences Ecology Population Ecology Refereed Article PeerReviewed 2015 ftunivtasecite https://doi.org/10.1111/1755-0998.12372 2019-12-13T22:17:50Z 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 F ST provided better approximations of mtDNA relationships among the studied species than those estimated using D C , even though F ST 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 eCite UTAS (University of Tasmania) Antarctic Molecular Ecology Resources 15 5 1046 1058 |
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collection |
eCite UTAS (University of Tasmania) |
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ftunivtasecite |
language |
English |
topic |
Biological Sciences Ecology Population Ecology |
spellingShingle |
Biological Sciences Ecology Population Ecology Moodely, 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 Cherl, Y Weimerskirch, H Quillfeldt, P Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds |
topic_facet |
Biological Sciences Ecology Population Ecology |
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 F ST provided better approximations of mtDNA relationships among the studied species than those estimated using D C , even though F ST 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 |
Moodely, 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 Cherl, Y Weimerskirch, H Quillfeldt, P |
author_facet |
Moodely, 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 Cherl, Y Weimerskirch, H Quillfeldt, P |
author_sort |
Moodely, Y |
title |
Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds |
title_short |
Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds |
title_full |
Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds |
title_fullStr |
Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds |
title_full_unstemmed |
Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds |
title_sort |
evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds |
publisher |
Wiley-Blackwell Publishing Ltd. |
publishDate |
2015 |
url |
https://doi.org/10.1111/1755-0998.12372 http://www.ncbi.nlm.nih.gov/pubmed/25594938 http://ecite.utas.edu.au/118580 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_relation |
http://dx.doi.org/10.1111/1755-0998.12372 Moodely, Y and Masello, JF and Cole, TL and Calderon, L and Munimanda, GK and Thali, MR and Alderman, R and Cuthbert, RJ and Marin, M and Massaro, M and Navarro, J and Phillips, RA and Ryan, PG and Suazo, CG and Cherl, Y and Weimerskirch, H and Quillfeldt, P, Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds, Molecular Ecology Resources, 15, (5) pp. 1046-1058. ISSN 1755-098X (2015) [Refereed Article] http://www.ncbi.nlm.nih.gov/pubmed/25594938 http://ecite.utas.edu.au/118580 |
op_doi |
https://doi.org/10.1111/1755-0998.12372 |
container_title |
Molecular Ecology Resources |
container_volume |
15 |
container_issue |
5 |
container_start_page |
1046 |
op_container_end_page |
1058 |
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1766250709767946240 |