Rooting for the root of elongation factor-like protein phylogeny
Rooting for the root of elongation factor-like protein phylogeny
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DOI：
10.1016/j.ympev.2010.04.040
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发表时间：
2010-09-01
影响因子：
4.1
通讯作者：
Inagaki, Yuji
中科院分区：
文献类型：
--
作者：
Kamikawa, Ryoma;Sakaguchi, Miako;Inagaki, Yuji
侧向基因转移(LGT)可能在真核生物中延伸因子样(EFL)基因的进化中起着关键作用。到目前为止，EFL基因横向转移的推定病例的数量是基于未扎根的EFL系统发育。然而，根在EFL系统发育中的位置对于验证横向EFL基因转移是重要的：例如，来自无根EFL树中遥远亲缘生物的两个EFL同源物的分支不一定证实LGT，因为不能排除根可能位于这个分支中的可能性。Cocquyt等人。(2009，第39页)最近证明，最初基于未扎根的系统发展史提出的横向EFL基因转移的推定案例，不能得到相应的根基分析的支持。虽然生根EFL的系统发育对于阐明EFL基因进化的各个方面是必不可少的，但我们怀疑外群分支由Ef-1α和真核生物特异性的EF-1α旁系错误地附着在Cocquyt等人的EFL长分支上。(2009)一个典型的长枝吸引物(LBA)文物。在这里，我们通过分析Cocquyt等人使用的原始数据集，系统地评估了导致外群分支的分支和较长的内群分支之间的假定LBA伪影。(2009)在修改组序列抽样和不修改组序列抽样的情况下。一系列扎根的EFL分析表明，根推理非常容易受到长分支内群序列的存在和缺失的影响，这表明扎根的EFL系统发育不可能没有严重的LBA伪影。我们还讨论了在上述EFL分析过程中发现的禁闭症患者EFL基因进化的一个新方面。最后，根据目前的EF-1α/EFL分布，推测了EFL基因在真核生物中首次出现的相对时间。(C)2010 Elsevier Inc.保留所有权利。
Lateral gene transfer (LGT) may play a pivotal role in the evolution of elongation factor-like (EFL) genes in eukaryotes. To date, numbers of putative cases for lateral transfer of EFL genes have been postulated based on unrooted EFL phylogenies. Nevertheless, the root position in EFL phylogeny is important to validate lateral EFL gene transfer: for instance, a clade of two EFL homologs from distantly related organisms in an unrooted EFL tree does not necessarily confirm the LGT, since the possibility that the root may locate in this clade cannot be excluded. Cocquyt et al. (2009, p. 39) recently demonstrated that a putative case of lateral EFL gene transfer, which was originally proposed based on an unrooted phylogeny, could not be endorsed by the corresponding rooted analysis. Although rooting EFL phylogeny is indispensable to elucidate various aspects in EFL gene evolution, we suspected that the outgroup clade comprised of EF-1 alpha and eukaryote-specific EF-1 alpha paralogs erroneously attached to long EFL branches in Cocquyt et al. (2009) a typical long branch attraction (LBA) artifact. Here, we systematically assessed the putative LBA artifact between the branch leading to the outgroup clade and long ingroup branches by analyzing the original dataset used in Cocquyt et al. (2009) with and without modifying ingroup-sequence sampling. A series of the rooted EFL analyses indicated that the root inference was highly susceptible to presence and absence of long-branched ingroup-sequences, suggesting that the rooted EFL phylogenies cannot be free from severe LBA artifact. We also discussed a new aspect in EFL gene evolution in stramenopiles identified in the course of the EFL analyses described above. Finally, the relative timing of the first emergence of EFL gene in eukaryotes was contemplated based on the current EF-1 alpha/EFL distribution. (C) 2010 Elsevier Inc. All rights reserved.