A Long-Branch Attraction Artifact Reveals an Adaptive Radiation in Pseudomonas
A Long-Branch Attraction Artifact Reveals an Adaptive Radiation in Pseudomonas
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DOI：
10.1093/molbev/msr099
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发表时间：
2011-10-01
影响因子：
10.7
通讯作者：
Barray, Sylvie
中科院分区：
文献类型：
--
作者：
Bodilis, Josselin;Meilo, Sandrine Nsigue;Barray, Sylvie
细菌中很大一部分蛋白质编码基因系统发育与物种系统发育不一致。人们通常认为这种不一致是横向转移造成的。在这里，通过进一步研究细菌假单胞菌属中编码主要表面蛋白的 oprF 基因的系统发育，我们发现观察到的不一致的树拓扑是长分支吸引（LBA）伪影的结果，而不是横向转移的结果。 oprF 系统发育中的 LBA 可以用适应根际的谱系更快的进化来解释，突出了意想不到的适应性辐射。我们认为，对其他不一致的细菌系统发育中的此类伪影进行分析可能是分子生态学中强调微生物中隐秘的适应性辐射的一个有价值的工具。
A significant proportion of protein-encoding gene phylogenies in bacteria is inconsistent with the species phylogeny. It was usually argued that such inconsistencies resulted from lateral transfers. Here, by further studying the phylogeny of the oprF gene encoding the major surface protein in the bacterial Pseudomonas genus, we found that the incongruent tree topology observed results from a long-branch attraction (LBA) artifact and not from lateral transfers. LBA in the oprF phylogeny could be explained by the faster evolution in a lineage adapted to the rhizosphere, highlighting an unexpected adaptive radiation. We argue that analysis of such artifacts in other inconsistent bacterial phylogenies could be a valuable tool in molecular ecology to highlight cryptic adaptive radiations in microorganisms.