Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life

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. While 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 (∼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...

首次基于基因序列数据的分析显示，真核生物生命树（eukaryotic tree of life）由一条漫长的微生物类群主干构成，其顶端冠群涵盖植物、动物、真菌及其微生物亲缘类群。尽管近年来的多基因串联分析已进一步厘清真核生物众多分支间的演化关系，但真核生物生命树的根部始终难以确定。推断现存真核生物的根部极具挑战：该类群演化年代久远（约17至21亿年），不同谱系间演化速率差异悬殊，且多数基因缺乏明确的外类群（outgroup）。本研究通过最小化一组基因树中的重复与丢失事件数量，重建了现存真核生物的带根系统发育树。该方法无需依赖外类群序列，也无需对序列间的直同源性（orthology）作出假设。本研究还探讨了类群与基因采样策略的影响，并评估了不同根部假说的支持强度。本研究采用20个基因……