Data for: The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats

A species tree is a central concept in evolutionary biology whereby a single-branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) – a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining recently published linked-read genome assemblies for seven murine species with other available rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that proximate chromosomal regions tended to have more similar phylogenetic histories. While we found no clear relationship between local tree similarity and recombination rates in house mice, we did observe a correlation between recombination rates and average similarity to the species tree. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.

物种树（species tree）是进化生物学中的核心概念，指以单分支系统发育结构反映物种种间亲缘关系的分析框架。然而，不同基因组区域的系统发育树往往与物种树存在分歧。尽管系统发育树不一致在系统基因组学研究中广泛存在，但我们仍未明确阐明：系统发育模式的变异是如何受基因组生物学塑造的，以及这种不一致在多大程度上会干扰比较研究。我们以鼠类啮齿动物（murine rodents）——一类规模庞大、生态多样性丰富且衍生出实验室小鼠与大鼠模型系统的类群——为研究对象，对其全基因组范围内的系统基因组不一致模式进行了刻画。我们将近期发表的7种鼠类啮齿动物的连锁读长基因组组装（linked-read genome assemblies）序列与其他现有啮齿类基因组数据相结合，首先利用超保守元件（ultra-conserved elements, UCEs）推断出一棵可靠性较高的物种树。随后，我们借助全基因组数据分析了更精细尺度上的不一致模式，发现相邻染色体区域往往具有更为相似的系统发育历史。尽管我们未在家小鼠中发现局部树结构相似度与重组率之间存在明确关联，但却观察到重组率与各区域对物种树的平均相似度之间存在相关性。我们还检测到连锁选择（linked selection）的强烈影响：超保守元件上的纯化选择（purifying selection）会降低系统发育树的不一致程度。最后，我们证实，在不同模型下开展正选择（positive selection）检验时，若假设仅存在单一物种树，会导致较高的错误率。综上，我们的研究结果揭示了系统发育推断与基因组生物学之间的复杂关联，并强调了若未考虑这种复杂性，可能会对比较基因组学研究造成误导。