title: Unrecognized fine-scale recombination can mimic the effects of adaptive radiation.
abstract: 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.
authors: Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA. haow@wayne.edu
authors: Weilong
authors: W
authors: Hao
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D005075:Biological Evolution; D022761:Gene Transfer, Horizontal; D010802:Phylogeny; D011549:Pseudomonas / Q000235:genetics*; D011551:Pseudomonas fluorescens / Q000235:genetics; D011995:Recombination, Genetic
chemical_list: D001426:Bacterial Proteins; C547605:OprF protein, Pseudomonas aeruginosa