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 primer binding sites may lead to increased non-amplification, or disruptions that may lead to decreased polymorphism in non-target species. Furthermore, high mutation rates and constraints on allele size may also lead, with evolutionary time, to 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 non-amplifying 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 non-linear 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.

微卫星位点（Microsatellite loci）是检验精细时空尺度下遗传分离相关假说的理想工具。其在近缘物种间具有保守性，因而可用于阐明新近分化类群间的种间关系。然而，引物结合位点的突变可能加剧无扩增现象，或在非靶物种中导致多态性降低。此外，高突变率与等位基因大小限制也可能随进化时间推移，催生趋同演化的等位基因大小类群，从而对种间遗传分化的评估造成偏倚。
本研究借助下一代测序技术，从亚南极海鸟细嘴锯鹱（Pachyptila belcheri）的鸟枪基因组序列中开发微卫星标记，并在其他锯鹱属（Pachyptila）及相关亚南极物种中开展种间扩增验证。研究发现，随着与靶物种的系统发育距离增加，杂合度降低、无扩增位点的比例升高。
令人意外的是，尽管FST更易受无效等位基因（null alleles）的影响，基于种间FST构建的物种树，相较于基于DC估算所得的结果，能更准确地反映研究物种间的线粒体DNA（mtDNA）演化关系。我们还观察到，微卫星位点与线粒体DNA距离之间存在显著的非线性二阶多项式关系。
我们认为，随着线粒体DNA距离增加而出现的线性关系丧失，源于状态相同但非同源的同塑等位基因大小类群比例上升。因此，尽管在近缘锯鹱属物种中，微卫星位点的种间扩增成功率与多态性均较高，但我们仍提醒：在亲缘关系较远的类群的系统发育推断中，应谨慎使用微卫星标记。