Data from: Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales

Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an evolutionarily distant set of taxa. Here, we evaluate the efficacy of genomic markers targeting ultraconserved DNA elements (UCEs) for analyses at shallow evolutionary timescales. Using sequence capture and massively parallel sequencing to generate UCE data for five co-distributed Neotropical rainforest bird species, we recovered 776–1516 UCE loci across the five species. Across species, 53–77% of the loci were polymorphic, containing between 2.0 and 3.2 variable sites per polymorphic locus, on average. We performed species tree construction, coalescent modeling, and species delimitation, and we found that the five co-distributed species exhibited discordant phylogeographic histories. We also found that species trees and divergence times estimated from UCEs were similar to the parameters obtained from mtDNA. The species that inhabit the understory had older divergence times across barriers, contained a higher number of cryptic species, and exhibited larger effective population sizes relative to the species inhabiting the canopy. Because orthologous UCEs can be obtained from a wide array of taxa, are polymorphic at shallow evolutionary timescales, and can be generated rapidly at low cost, they are an effective genetic marker for studies investigating evolutionary patterns and processes at shallow timescales.

随着测序技术的重大突破，非模式生物的比较遗传学研究正快速发展。此类研究长期面临的一项限制因素，是在进化距离较远的类群集合中鉴定并筛选直系同源基因座（orthologous loci）。本研究针对浅进化时间尺度下的分析需求，评估了靶向超保守DNA元件（ultraconserved DNA elements, UCEs）的基因组标记的应用效能。我们通过序列捕获与大规模并行测序技术，为5种同分布的新热带雨林鸟类生成UCE数据，最终在5个物种中成功获取776至1516个UCE基因座。跨物种分析显示，53%至77%的基因座存在多态性，每个多态性基因座平均包含2.0至3.2个变异位点。我们开展了物种树构建、溯祖模型（coalescent modeling）分析与物种界定工作，结果发现5种同分布鸟类的系统地理历史存在显著不一致性。同时，研究发现基于UCE数据估算得到的物种树与分化时间，与线粒体DNA（mtDNA）获取的参数结果高度相似。相较于栖息于林冠层的物种，林下层栖息物种的跨屏障分化时间更早，隐存物种数量更多，且有效种群规模更大。由于直系同源UCE可从广泛的类群中获取、在浅进化时间尺度下仍具备多态性，且可低成本快速生成，因此其是开展浅进化时间尺度下进化模式与过程研究的高效遗传标记。