Psymbionts a touchstone of molecular phylogenetics

The most interesting and debated node in the whole tree of symbiotic bacteria is undoubtedly the putative origin of many symbiotic lineages within Enterobacteriaceae (Charles et al , 2001). In Figure 1 .1, this node is presented in its "maximal" version, encompassing several major P-symbionts and many minor lineages (node P). However, in the published studies, the whole issue has mostly been addressed by analyzing phylogenetic relationships of the two most popular groups, Buchnera and Wigglesworthia. Although retrieved by a majority of phylogenetic studies, the monophyly of the symbiotic cluster containing these two P-sym-biont lineages has been legitimately questioned This doubt arises because the genomes of P-symbionts meet typical conditions leading to phylogenetic artifacts Compared to their free-living relatives, P-symbiotic lineages display remarkably high frequency of AT in their sequences This bias is considered one of the most significant symptoms of genome degradation in symbiotic bacteria . For the first time it has been detected within 16S rDNA and is usually attributed to relaxed selection together with Muller's ratchet occurring in small asexual populations (Moran, 1996; Heddi et al ., 1998; Lambert and Moran, 1998; but see Itoh et al , 2002, for alternative explanation) The statistical significance of this compositional shift was later confirmed by Haywood-Farmer and Otto (2003)

Because the difference in nucleotide composition among the lineages seriously violates assumptions implemented in the majority of phylogenetic methods, it results in more or less predictable artifacts Currently, the most common approach to this problem is an employment of techniques designed to eliminate or at least suppress the effect of compositional heterogeneity Several such methods have been proposed and this area is undergoing fast advancement An alternative approach does not rely on extraction of phylogenetic signal by tuning the assumptions to (supposedly) real evolutionary process, but rather to extend the dataset and/or to find alternative sources of information. Genome-wide concatenation of protein-coding genes and extraction of a phylogenetic signal from genome structure are such techniques

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