Long-branch attraction phenomenon and the impact of among-site rate variation on rodent phylogeny

The phylogenetic relationships among major lineages of rodents is one of th e issues most debated by both paleontologists and molecular biologists. In the present study, we have analyzed all complete mammalian mitochondrial ge nomes available in the databases. including five rodent species (rat, mouse , dormouse, squirrel and guinea-pig). Phylogenetic analyses were performed on H-strand amino acid sequences by means of maximum-likelihood and on H-st rand protein-coding and ribosomal genes by means of distance methods. Also, log-likelihood ratio tests were applied to different tree topologies under the assumption of rodent monophyly, paraphyly or polyphyly. The analyses s ignificantly rejected rodent monophyly and showed the existence of two diff erentiated clades, one containing non-murids (dormouse, squirrel and guinea -pig) and the other containing murids (rat and mouse). Long-branch attracti on between murids and the outgroups could not be responsible for the existe nce of two different rodent clades, as no significant differences in evolut ionary rate have been observed, except in the case of the squirrel, which s hows a lower rate. The impact of among-site rate variation models on the ph ylogeny of rodents has been evaluated using the gamma distribution model. R esults have shown that relationships among rodents remained unchanged, and the general topology of the tree was not affected, even though some branche s were not properly resolved, most likely due to a lack of fit between esti mated and real late heterogeneity parameters. (C) 2000 Elsevier Science B.V . All rights reserved.