Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA.
Gene. 2013 Apr 15;518(2):483-8. doi: 10.1016/j.gene.2012.12.107. Epub 2013 Jan 18.
Gene sequences can undergo accelerated nucleotide changes and rapid diversification. The rapid sequence changes can then potentially lead to phylogenetic incongruence. Recently, Bodilis et al. (2011) observed artificial phylogenetic incongruence using the Pseudomonas surface protein gene oprF, and hypothesized that it was the result of a long-branch attraction artifact ultimately caused by adaptive radiation. In this study, an alternative hypothesis, namely fine-scale recombination, was tested on the same dataset. The results reveal that regions in oprF are of different evolutionary origins, and the mosaic gene structure resulted in confounding phylogenetic signals. These findings demonstrate that unrecognized fine-scale recombination can confound the phylogenetic interpretation and emphasize the limitation of using whole genes as the unit of phylogenetic analysis.
基因序列可能会经历加速的核苷酸变化和快速多样化。这些快速的序列变化可能导致系统发育不一致。最近，Bodilis 等人（2011 年）观察到使用假单胞菌表面蛋白基因 oprF 导致的人为系统发育不一致，并假设这是由适应性辐射最终导致的长枝吸引artifact。在这项研究中，对同一数据集检验了另一种假设，即精细重组。结果表明，oprF 中的区域具有不同的进化起源，镶嵌基因结构导致了混淆的系统发育信号。这些发现表明，未被识别的精细重组可能会混淆系统发育解释，并强调了使用整个基因作为系统发育分析的单位的局限性。
