Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies.
Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies.
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Covariion 转变导致长分支吸引伪影，将 EF-1alpha 系统发育中的小孢子虫和古细菌结合在一起。
DOI：
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发表时间：
2004
影响因子：
10.7
通讯作者：
A. Roger
中科院分区：
文献类型：
--
作者：
Y. Inagaki;E. Susko;N. M. Fast;A. Roger
根据翻译延伸因子 1α (EF-1α) 序列推断，微孢子虫分支位于真核系统发育的基础上。由于这些寄生真核生物是真菌（或真菌的近亲），因此人们普遍认为，快速进化的微孢子虫序列被人为地“吸引”到通向古细菌（外群）序列的长分支（“长分支吸引”或“LBA”）。然而，之前的研究还没有明确确定为什么所有系统发育方法（包括最大似然法，一种被认为对经典 LBA 具有抵抗力的方法）都能恢复微孢子虫和古细菌（“M + A”）的人为忠诚度。在这里，我们表明，M + A 亲和力可归因于与真核和古细菌子树之间进化位点率的巨大差异相关的那些比对位点。因此，未能对内群和外群序列之间的显着进化速率分布差异（协变变化）进行建模显然是造成 EF-1α 序列系统发育分析中微孢子虫基础位置的原因。目前，没有任何进化模型可以解释特定分支上位点速率分布的离散变化，可用于蛋白质或核苷酸水平的系统发育分析，因此相同的工件可能会影响许多其他“深层”系统发育。此外，考虑到小孢子虫和古细菌 EF-1α 蛋白位点速率模式的相对相似性（“平行位点速率变异”），我们认为小孢子虫直系同源物可能已经失去了一些真核 EF-1α 特异性非翻译功能，这说明了这种寄生谱系的极度减少。
Microsporidia branch at the base of eukaryotic phylogenies inferred from translation elongation factor 1alpha (EF-1alpha) sequences. Because these parasitic eukaryotes are fungi (or close relatives of fungi), it is widely accepted that fast-evolving microsporidian sequences are artifactually "attracted" to the long branch leading to the archaebacterial (outgroup) sequences ("long-branch attraction," or "LBA"). However, no previous studies have explicitly determined the reason(s) why the artifactual allegiance of microsporidia and archaebacteria ("M + A") is recovered by all phylogenetic methods, including maximum likelihood, a method that is supposed to be resistant to classical LBA. Here we show that the M + A affinity can be attributed to those alignment sites associated with large differences in evolutionary site rates between the eukaryotic and archaebacterial subtrees. Therefore, failure to model the significant evolutionary rate distribution differences (covarion shifts) between the ingroup and outgroup sequences is apparently responsible for the artifactual basal position of microsporidia in phylogenetic analyses of EF-1alpha sequences. Currently, no evolutionary model that accounts for discrete changes in the site rate distribution on particular branches is available for either protein or nucleotide level phylogenetic analysis, so the same artifacts may affect many other "deep" phylogenies. Furthermore, given the relative similarity of the site rate patterns of microsporidian and archaebacterial EF-1alpha proteins ("parallel site rate variation"), we suggest that the microsporidian orthologs may have lost some eukaryotic EF-1alpha-specific nontranslational functions, exemplifying the extreme degree of reduction in this parasitic lineage.
影响因子：
1.9
作者：
Arisue, N;Sáchez, LB;Hashimoto, T
通讯作者：
Hashimoto, T
影响因子：
10.7
作者：
Keeling, PJ;Luker, MA;Palmer, JD
通讯作者：
Palmer, JD
线粒体原生动物β-微管蛋白序列的系统发育分析。
DOI：
10.1006/mpev.1996.0031
发表时间：
1996
期刊：
Molecular phylogenetics and evolution.
影响因子：
--
作者：
Edlind,TD;Li,J;Visvesvara,GS;Vodkin,MH;McLaughlin,GL;Katiyar,SK
通讯作者：
Katiyar,SK