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.

全基因组尺度的数据为解析此前难以通过少量基因座（loci）厘清的系统发育关系提供了可能，同时也可识别出进化历史与物种历史存在显著差异的基因组区域。本研究收集了豆科苜蓿属（Medicago）29个分类单元（taxon）的全基因组测序数据，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推断所需的位点数量，并鉴定出与全基因组系统发育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此前难以解决的苜蓿属内物种关系。对数据集进行亚采样分析后发现，较小的数据子集在系统发育信号强度与推断效能上存在显著差异。即便采样5000个位点，随机抽取的任一数据子集均无法得到与全基因组系统发育拓扑结构一致的系统发育树。基于500位点滑动窗口推断的系统发育关系显示，在近期分化的分类单元间，存在多个基因组区域支持不同的物种关系，这与苜蓿属近期演化历史中预期的深层溯祖（deep coalescence）或基因渐渗（introgression）效应相符。