Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families
Analysis of Phylogenomic Tree Space Resolves Relationships Among Marsupial Families
复制标题
DOI：
10.1093/sysbio/syx076
复制
发表时间：
2018-05-01
影响因子：
6.5
通讯作者：
Eldridge, Mark D. B.
中科院分区：
文献类型：
--
作者：
Duchene, David A.;Bragg, Jason G.;Eldridge, Mark D. B.
在解决生命之树上的进化关系时，一个根本的挑战是解释跨基因进化信号的异质性。对有袋类哺乳动物的研究表明，这种异质性可能是巨大的，这给进化时间表和群体内的关系留下了相当大的不确定性。通过模拟和一个新的系统基因组数据集，包括来自22个现存有袋动物家族中18个家族的1550个基因座的核苷酸序列，我们展示了一种识别支持不同系统发育树的基因座簇的方法的威力。我们发现了两个不同的基因座簇，每个基因座都提供了一个物种树的估计，与先前提出的有袋类动物系统发育的解决方案相匹配。我们还确定了神秘的有袋鼹鼠(Notoryctes)的一个良好支持的位置，这与先前的分子估计相矛盾，但与形态证据一致。基因-树在树空间的变异模式表现为数据中信息含量、GC含量、替换模型充分性和净化选择特征的变化。在模拟研究中，我们发现，不完全谱系排序可以解释有袋类系统发育分析中发现的两个树状拓扑簇的基因座划分。我们还展示了最大限度地减少分子测年中系统发育冲突的不确定性的潜在好处。我们的分析表明，澳大拉西亚有袋类出现在古新世早期，而今天的科的多样化主要发生在始新世晚期和渐新世早期。我们的方法为使用基因组规模的数据提高系统发育推断和分子测年的准确性和精确度提供了一个直观的框架。
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.