Mol Biol Evol. 2011 Oct;28(10):2723-6. doi: 10.1093/molbev/msr099. Epub 2011 Apr 19.
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.
细菌中很大一部分蛋白质编码基因的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由水平转移引起的。在这里，通过进一步研究编码假单胞菌属主要表面蛋白的 oprF 基因的系统发育，我们发现观察到的不一致树拓扑结构是由长枝吸引（LBA）artifact 引起的，而不是由水平转移引起的。在 oprF 系统发育中，LBA 可以用适应根际的谱系的更快进化来解释，突出了意想不到的适应性辐射。我们认为，在其他不一致的细菌系统发育中分析这种假象可能是分子生态学中的一种有价值的工具，可以突出微生物中隐藏的适应性辐射。
