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）为探究影响种群分化、存续与随时间动态变化的因素提供了必要的研究框架。艾维斯（Avise）于2000年阐述了当数据呈现显著系统地理学信号时，可观测到的四类一致性特征：单个基因座内各核苷酸位点间的一致性、物种内多个基因座间的一致性、区域内多个物种间的一致性，以及遗传模式与已确立的生物地理省（biogeographic provinces）之间的一致性。 为全面探讨上述四类一致性维度，本研究将一套直系同源基因座（orthologous loci）的目标捕获测序（target capture）与多个物种的靶向地理采样相结合，从而消除了因使用不同遗传标记与异质性采样分布所引入的系统误差。本研究针对美国东南部沿海平原（Southeastern U.S. Coastal Plain）这一系统地理学经典研究区域内的36个重合采样点，对4种无尾两栖类（anuran）开展杂交富集（hybrid enrichment）与高通量测序（high-throughput sequencing）。 本研究共在各物种间获取了超过375个同源核基因座（nuclear loci），并组装得到线粒体基因组（mitochondrial genomes），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物种间的一致性，比较了各物种的遗传结构（genetic structure），并验证了该区域此前已被报道的生物地理特征，包括主要河流流域与生物地理缝合带（suture zones）。随后，本研究采用新近开发的分析框架，通过系统地理学一致性因子（phylogeographic concordance factors）量化了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与相对有限的遗传分化结构。即便核序列长度可达约1400 bp（碱基对），单个核基因树的解析度依然较差。然而，线粒体数据集与多位点核数据集在物种内呈现出相似的遗传模式，却表明物种间存在高度的遗传不一致性，同时提示遗传模式与推定的生物地理屏障（biogeographic barriers）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，可能与各物种的生活史特征差异相关：其中两种广适性生境物种（habitat generalists）的遗传分化结构相对较弱。 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，可用于量化历史演化复杂区域内不同类群间的系统地理学一致性水平。