Data from: Targeted sampling and target capture: assessing phylogeographic concordance with genome-wide data

Comparative phylogeography provides the necessary framework to examine the factors influencing population divergence, persistence, and change over time. Avise (2000) outlined four aspects of concordance that result when data exhibit significant phylogeographic signal: concordance among sites within a locus, among multiple loci within a species, among multiple species within a region, and between genetic patterns and established biogeographic provinces. To fully address each aspect of concordance, we combined target capture of a set of orthologous loci with targeted geographic sampling of multiple species, thus removing any variability introduced by using different genetic markers and heterogeneous sampling distributions. We used hybrid enrichment and high-throughput sequencing of four anuran species sampled from 36 congruent localities in the Southeastern U.S. Coastal Plain, a region that represents one of the classic systems in phylogeography. In total, we recovered >375 of the same nuclear loci across species and assembled mitochondrial genomes, resulting in one of the most comprehensive comparative phylogeographic datasets in any region or taxon to date. We used these data to evaluate concordance, compare genetic structure across species, and test previously described biogeographic features in the region including major river drainages and suture zones. We then applied a recently-developed framework to quantify concordance across species using phylogeographic concordance factors. For the four species examined, which have higher dispersal and potentially limited structure compared to many amphibians, we found poor resolution in individual nuclear gene trees even with long (~1400 bp) nuclear sequences. The mitochondrial and multi-locus nuclear datasets, however, produced similar patterns within species, indicated high discordance among species, and suggested little correspondence of genetic patterns with putative biogeographic barriers. Variation in the phylogeographic structure detected may be related to differences in natural history, in that the two habitat generalists exhibited less structure. Our study demonstrates the utility of combining target capture, which is highly repeatable and produces comparable datasets, with a targeted sampling strategy to quantify phylogeographic concordance across diverse taxa in a region with a complex history.比较系统地理学（Comparative phylogeography）为探究驱动种群随时间发生分化、存续与演变的各类因素提供了核心研究框架。Avise（2000）系统阐述了数据呈现显著系统地理学信号时所具备的四类一致性特征：同一位点内不同采样位点间的一致性、同一物种内不同基因座间的一致性、同一区域内不同物种间的一致性，以及遗传模式与既定生物地理分区间的一致性。为全面解析各类一致性特征，本研究将直系同源基因座（orthologous loci）的目标捕获测序（target capture）与多物种的靶向地理采样相结合，由此规避了因使用不同遗传标记以及异质性采样分布所引入的各类变异。本研究针对美国东南沿海平原（Southeastern U.S. Coastal Plain）——系统地理学经典研究区域之一——的36个一致采样点，对4种无尾类（anuran）开展了杂交富集（hybrid enrichment）与高通量测序（high-throughput sequencing）。本研究共从各物种中获取了超过375个同源核基因座，并组装得到线粒体基因组（mitochondrial genomes），由此构建了目前全球范围内针对任一区域或类群（taxon）的最全面的比较系统地理学数据集之一。本研究利用这些数据评估了系统地理学一致性特征，比较了不同物种间的遗传结构（genetic structure），并验证了该区域此前被报道的各类生物地理特征，包括主要河流流域（river drainages）与生物地理缝合带（suture zones）。随后，本研究采用新近开发的分析框架，利用系统地理学一致性因子（phylogeographic concordance factors）量化了不同物种间的一致性水平。相较于多数两栖动物，本次研究涉及的4个物种具有更强的扩散能力，种群遗传结构相对较弱；即便使用长达约1400 bp的核基因序列，单个核基因树的分辨率仍然较差。然而，线粒体数据集与多基因座核数据集在物种内部呈现出相似的遗传模式，同时显示出物种间极高的遗传不一致性，且表明遗传模式与推定的生物地理屏障之间几乎不存在对应关系。本研究检测到的系统地理学结构差异可能与物种的生态习性差异有关，其中2种广栖性物种的种群遗传结构相对更弱。本研究证实，将可重复性强且可生成标准化可比数据集的目标捕获测序技术，与靶向采样策略相结合，能够用于量化具有复杂演化历史区域内不同类群间的系统地理学一致性特征。