Evolutionary factors affecting the cross‐species utility of newly developed microsatellite markers in seabirds. (29th January 2015)

• Record Type: Journal Article
• Authors: Moodley, Yoshan; Masello, Juan F.; Cole, Theresa L.; Calderon, Luciano; Munimanda, Gopi K.; 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
• Is Part Of: Molecular ecology resources. Volume 15:Number 5(2015:Sep.)
• Page Start: 1046
• Page End: 1058
• Publication Date: 2015-01-29
• Subjects: Molecular ecology -- Periodicals; 572.8
• DOI: 10.1111/1755-0998.12372
• Languages: English
• ISSNs: 1755-098X

Abstract

<abstract abstract-type="main" id="men12372-abs-0001"> <title>Abstract</title> <p>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 (<italic>Pachyptila belcheri</italic>), that we tested for cross‐species amplification in other <italic>Pachyptila</italic> 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 <italic>F</italic><sub>ST</sub> provided better approximations of mtDNA relationships among the studied species than those estimated using <italic>D</italic><sub>C</sub>, even though <italic>F</italic><sub>ST</sub> 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 <italic>Pachyptila</italic> species, we caution against the use of microsatellites in phylogenetic inference among distantly related taxa.</p> </abstract>