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Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds

Citation

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]


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DOI: doi:10.1111/1755-0998.12372

Abstract

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.

Item Details

Item Type:Refereed Article
Keywords:cross-species transferability, genetic diversity, microsatellite, null alleles, Pachyptila, Procellariiformes
Research Division:Biological Sciences
Research Group:Ecology
Research Field:Population Ecology
Objective Division:Environment
Objective Group:Flora, Fauna and Biodiversity
Objective Field:Antarctic and Sub-Antarctic Flora, Fauna and Biodiversity
Author:Alderman, R (Ms Rachael Alderman)
ID Code:118580
Year Published:2015
Web of Science® Times Cited:5
Deposited By:IMAS - Directorate
Deposited On:2017-07-14
Last Modified:2017-07-14
Downloads:0

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