Search for a 'Tree of Life' in the thicket of the phylogenetic forest.

Journal of Biology Pub Date : 2009-01-01 Epub Date: 2009-07-13 DOI:10.1186/jbiol159
Pere Puigbò, Yuri I Wolf, Eugene V Koonin
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引用次数: 261

Abstract

Background: Comparative genomics has revealed extensive horizontal gene transfer among prokaryotes, a development that is often considered to undermine the 'tree of life' concept. However, the possibility remains that a statistical central trend still exists in the phylogenetic 'forest of life'.

Results: A comprehensive comparative analysis of a 'forest' of 6,901 phylogenetic trees for prokaryotic genes revealed a consistent phylogenetic signal, particularly among 102 nearly universal trees, despite high levels of topological inconsistency, probably due to horizontal gene transfer. Horizontal transfers seemed to be distributed randomly and did not obscure the central trend. The nearly universal trees were topologically similar to numerous other trees. Thus, the nearly universal trees might reflect a significant central tendency, although they cannot represent the forest completely. However, topological consistency was seen mostly at shallow tree depths and abruptly dropped at the level of the radiation of archaeal and bacterial phyla, suggesting that early phases of evolution could be non-tree-like (Biological Big Bang). Simulations of evolution under compressed cladogenesis or Biological Big Bang yielded a better fit to the observed dependence between tree inconsistency and phylogenetic depth for the compressed cladogenesis model.

Conclusions: Horizontal gene transfer is pervasive among prokaryotes: very few gene trees are fully consistent, making the original tree of life concept obsolete. A central trend that most probably represents vertical inheritance is discernible throughout the evolution of archaea and bacteria, although compressed cladogenesis complicates unambiguous resolution of the relationships between the major archaeal and bacterial clades.

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在系统发育森林的丛林中寻找“生命之树”。
背景:比较基因组学揭示了原核生物之间广泛的水平基因转移,这一发展通常被认为破坏了“生命之树”的概念。然而,在系统发育的“生命森林”中仍然存在统计中心趋势的可能性仍然存在。结果:对6,901棵原核基因系统发育树的“森林”进行了全面的比较分析,发现了一致的系统发育信号,特别是在102棵几乎通用的树中,尽管拓扑结构高度不一致,可能是由于水平基因转移。横向转移似乎是随机分布的,并没有掩盖中心趋势。几乎普遍的树在拓扑结构上与许多其他树相似。因此,几乎普遍的树木可能反映了一个重要的集中趋势,尽管它们不能完全代表森林。然而,拓扑一致性主要出现在较浅的树深,而在古细菌和细菌门的辐射水平上突然下降,这表明进化的早期阶段可能不是树状的(生物大爆炸)。在压缩枝状发育或生物大爆炸下的进化模拟更符合压缩枝状发育模型中观察到的树不一致性与系统发育深度之间的相关性。结论:水平基因转移在原核生物中普遍存在,很少有基因树是完全一致的,使得原来的生命树概念过时。在古生菌和细菌的整个进化过程中,一个最可能代表垂直遗传的中心趋势是显而易见的,尽管压缩枝发生使主要古生菌和细菌枝之间关系的明确解决变得复杂。
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