Data from: Phylogenetic signal variation in the genomes of Medicago (Fabaceae)

Genome-scale data offer the opportunity to clarify phylogenetic relationships that are difficult to resolve with few loci, but they can also identify genomic regions with evolutionary history distinct from that of the species history. We collected whole-genome sequence data from 29 taxa in the legume genus Medicago, then aligned these sequences to the M. truncatula reference genome to confidently identify 87,596 variable homologous sites. We used this data set to estimate phylogenetic relationships among Medicago species, to investigate the number of sites needed to provide robust phylogenetic estimates, and to identify specific genomic regions supporting topologies in conflict with the genome-wide phylogeny. Our full genomic data set resolves relationships within the genus that were previously intractable. Sub-sampling the data reveals considerable variation in phylogenetic signal and power in smaller subsets of the data. Even when sampling 5,000 sites, no random sample of the data supports a topology identical to that of the genome-wide phylogeny. Phylogenetic relationships estimated from 500-site sliding windows revealed genome regions supporting several alternative species relationships among recently-diverged taxa, consistent with the expected effects of deep coalescence or introgression in the recent history of Medicago.

全基因组规模数据可为厘清通过少量基因座难以解析的系统发育关系提供契机，同时亦可识别进化历史与物种历史存在显著差异的基因组区域。本研究从豆科苜蓿属（Medicago）的29个分类单元中收集了全基因组测序数据，将这些序列比对至蒺藜苜蓿（M. truncatula）参考基因组，最终可靠鉴定出87596个可变同源位点。本研究利用该数据集对苜蓿属物种间的系统发育关系进行推断，探究了获得可靠系统发育估计所需的位点数量，并鉴定出与全基因组系统发育树拓扑结构存在冲突的特定基因组区域。本研究的全基因组数据集成功解析了该属内此前难以解析的演化关系。对数据集进行子采样分析显示，在较小的数据子集内，系统发育信号与统计效力存在显著差异。即便采样5000个位点，也没有任何一组随机采样的数据能够得到与全基因组系统发育树完全一致的拓扑结构。通过对500位点滑动窗口进行系统发育关系推断，发现基因组中存在多个区域支持新近分化类群间的不同物种关系，这与苜蓿属近期演化历史中预期的深度趋同或基因渐渗效应相符。