Integrative modeling of gene and genome evolution roots the archaeal tree of life
Integrative modeling of gene and genome evolution roots the archaeal tree of life
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DOI：
10.1073/pnas.1618463114
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发表时间：
2017-06-06
影响因子：
11.1
通讯作者：
Embley, T. Martin
中科院分区：
文献类型：
--
作者：
Williams, Tom A.;Szollosi, Gergely J.;Embley, T. Martin
古生菌树的根对于重建早期细胞的代谢和生态以及验证真核细胞核谱系起源于古生菌的假设是必不可少的;然而，基于外群生根的已发表研究不同意古生菌根的位置。在这里，我们使用蛋白质连接和基于3，242棵单基因树的多基因超树方法构建了一个共识无根古细菌拓扑结构，然后使用最近开发的基因组进化模型将该树扎根。该模型使用来自31，236个古细菌基因家族中包含的基因复制，水平转移和基因丢失的证据来确定树的最可能的根。我们的分析支持单系DPANN（Diapherotrites，Parvarchaeota，Aenigmarchaeota，Nanoarchaeota，Nanohaloarchaea），最近发现的世界性和遗传多样性的血统，并在以前的工作相比，DPANN和所有其他的根。DPANN的姐妹群包括Euryarchaeota和TACK古菌，包括Lokiarchaeum，我们的分析表明它们是单系姐妹谱系。根树上的代谢重建表明，早期的根树是厌氧微生物，可能有能力通过伍德-扬达尔途径将CO2还原为乙酸盐。与基因组减少是古细菌进化的主要模式的建议相反，我们的分析推断出一个相对较小的基因组古细菌祖先，随后通过基因复制和水平基因转移增加了复杂性。
A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood-Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.