Data from: Analysis of phylogenomic tree space resolves relationships among marsupial families

A fundamental challenge in resolving evolutionary relationships across the Tree of Life is to account for heterogeneity in the evolutionary signal across loci. Studies of marsupial mammals have demonstrated that this heterogeneity can be substantial, leaving considerable uncertainty in the evolutionary timescale and relationships within the group. Using simulations and a new phylogenomic data set comprising nucleotide sequences of 1550 loci from 18 of the 22 extant marsupial families, we demonstrate the power of a method for identifying clusters of loci that support different phylogenetic trees. We find two distinct clusters of loci, each providing an estimate of the species tree that matches previously proposed resolutions of the marsupial phylogeny. We also identify a well supported placement for the enigmatic marsupial moles (Notoryctes) that contradicts previous molecular estimates but is consistent with morphological evidence. The pattern of gene-tree variation across tree-space is characterized by changes in information content, GC content, substitution-model adequacy, and signatures of purifying selection in the data. In a simulation study, we show that incomplete lineage sorting can explain the division of loci into the two tree-topology clusters, as found in our phylogenomic analysis of marsupials. We also demonstrate the potential benefits of minimizing uncertainty from phylogenetic conflict for molecular dating. Our analyses reveal that Australasian marsupials appeared in the early Paleocene, whereas the diversification of present-day families occurred primarily during the late Eocene and early Oligocene. Our methods provide an intuitive framework for improving the accuracy and precision of phylogenetic inference and molecular dating using genome-scale data.

重建生命之树（Tree of Life）跨类群演化关系的核心挑战之一，是如何解释不同基因座（loci）间演化信号的异质性。针对有袋类哺乳动物的相关研究已表明，此类异质性程度往往较高，致使该类群的演化时间树与系统发育关系存在显著不确定性。本研究借助模拟实验，并基于一套全新的系统基因组学数据集——该数据集涵盖22个现生有袋类科中的18个科的1550个基因座的核苷酸序列——验证了一种可识别支持不同系统发育树的基因座簇的方法的效能。我们鉴定出两个截然不同的基因座簇，二者各自得到的物种树估计结果，均与此前提出的有袋类系统发育重建方案一致。此外，我们为神秘的袋鼹（Notoryctes，marsupial moles）确定了一个支持度优异的系统发育位置，该结果与既往分子估算相悖，但契合形态学证据。基因树在树空间中的变异模式，可通过数据的信息含量、GC含量（GC content）、替换模型适配性以及纯化选择（purifying selection）特征加以表征。模拟实验结果显示，不完全谱系分选（incomplete lineage sorting）能够解释本研究针对有袋类的系统基因组学分析中，基因座被划分为两个拓扑结构簇的现象。我们还证实，最小化系统发育冲突带来的不确定性，可有效提升分子定年的准确性。本研究的分析表明，澳新界有袋类起源于古新世早期，而现生有袋类各科的多样化过程主要发生在始新世晚期与渐新世早期。本研究提出的方法为利用基因组规模数据提升系统发育推断与分子定年的准确性与精确度提供了一套直观的分析框架。