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（non-model organism）的比较遗传学研究正迎来快速变革。此类研究的一项核心限制因素，是在进化距离较远的一系列类群中鉴定与筛选直系同源位点（orthologous loci）。本研究针对超保守DNA元件（ultraconserved DNA elements, UCEs）靶向的基因组标记在浅进化时间尺度分析中的应用效能展开评估。本研究采用序列捕获（sequence capture）技术与大规模并行测序（massively parallel sequencing）手段，为5种同域分布的新热带界雨林鸟类生成UCE数据，最终在5个物种中共获得776~1516个UCE位点。跨物种分析显示，53%~77%的位点呈现多态性，每个多态位点平均包含2.0~3.2个变异位点。我们开展了物种树（species tree）构建、溯祖模型分析（coalescent modeling）与物种界定（species delimitation）工作，结果表明这5种同域分布鸟类呈现出不一致的系统地理历史（phylogeographic history）。此外，基于UCE数据估算得到的物种树与分化时间参数，与线粒体DNA（mtDNA）获取的结果高度相似。相较于栖息于林冠层的类群，栖息于林下层（understory）的物种跨地理屏障的分化时间更久、隐存物种（cryptic species）数量更多，且有效种群大小（effective population size）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。