Turning the Crown Upside Down: Gene Tree Parsimony Roots the Eukaryotic Tree of Life
Turning the Crown Upside Down: Gene Tree Parsimony Roots the Eukaryotic Tree of Life
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DOI：
10.1093/sysbio/sys026
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发表时间：
2012-07-01
影响因子：
6.5
通讯作者：
Burleigh, J. Gordon
中科院分区：
文献类型：
--
作者：
Katz, Laura A.;Grant, Jessica R.;Burleigh, J. Gordon
基因序列数据的第一次分析表明，真核生物的生命树由一个长茎的微生物群体组成，“顶端”是一个冠状的植物，动物和真菌及其微生物亲属。虽然最近的多基因串联分析已经完善了真核生物的许多分支之间的关系，真核生物生命树的根仍然难以捉摸。推断现存真核生物的根源是具有挑战性的，因为该组的年龄（类似于17 - 21亿年），谱系之间进化速度的巨大异质性，以及许多基因缺乏明显的外群。在这里，我们重建了一个根深蒂固的现存真核生物的基础上最大限度地减少重复和损失的基因树的集合。这种方法不需要外群序列或假设序列之间的同源性。我们还探讨了分类群和基因采样的影响，并评估支持替代假设的根源。使用来自84个不同真核生物谱系的20个基因树，这种方法恢复了强大的真核生物分支，并揭示了位于后鞭毛纲（动物，真菌及其微生物亲属）和所有剩余真核生物之间的真核生物根的证据。
The first analyses of gene sequence data indicated that the eukaryotic tree of life consisted of a long stem of microbial groups "topped" by a crown-containing plants, animals, and fungi and their microbial relatives. Although more recent multigene concatenated analyses have refined the relationships among the many branches of eukaryotes, the root of the eukaryotic tree of life has remained elusive. Inferring the root of extant eukaryotes is challenging because of the age of the group (similar to 1.7-2.1 billion years old), tremendous heterogeneity in rates of evolution among lineages, and lack of obvious outgroups for many genes. Here, we reconstruct a rooted phylogeny of extant eukaryotes based on minimizing the number of duplications and losses among a collection of gene trees. This approach does not require outgroup sequences or assumptions of orthology among sequences. We also explore the impact of taxon and gene sampling and assess support for alternative hypotheses for the root. Using 20 gene trees from 84 diverse eukaryotic lineages, this approach recovers robust eukaryotic clades and reveals evidence for a eukaryotic root that lies between the Opisthokonta (animals, fungi and their microbial relatives) and all remaining eukaryotes.