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Background  The typical antbirds (Thamnophilidae) form a monophyletic and diverse family of suboscine passerines that inhabit neotropical forests. However, the phylogenetic relationships within this assemblage are poorly understood. Herein, we present a hypothesis of the generic relationships of this group based on Bayesian inference analyses of two nuclear introns and the mitochondrial cytochrome  b  gene. The level of phylogenetic congruence between the individual genes has been investigated utilizing Bayes factors. We also explore how changes in the substitution models affected the observed incongruence between partitions of our data set.    Results  The phylogenetic analysis supports both novel relationships, as well as traditional groupings. Among the more interesting novel relationship suggested is that the  Terenura  antwrens, the wing-banded antbird ( Myrmornis torquata ), the spot-winged antshrike ( Pygiptila stellaris ) and the russet antshrike ( Thamnistes anabatinus ) are sisters to all other typical antbirds. The remaining genera fall into two major clades. The first includes antshrikes, antvireos and the  Herpsilochmus  antwrens, while the second clade consists of most antwren genera, the  Myrmeciza  antbirds, the "professional" ant-following antbirds, and allied species. Our results also support previously suggested polyphyly of  Myrmotherula  antwrens and  Myrmeciza  antbirds. The tests of phylogenetic incongruence, using Bayes factors, clearly suggests that allowing the gene partitions to have separate topology parameters clearly increased the model likelihood. However, changing a component of the nucleotide substitution model had much higher impact on the model likelihood.    Conclusions  The phylogenetic results are in broad agreement with traditional classification of the typical antbirds, but some relationships are unexpected based on external morphology. In these cases their true affinities may have been obscured by convergent evolution and morphological adaptations to new habitats or food sources, and genera like  Myrmeciza  antbirds and the  Myrmotherula  antwrens obviously need taxonomic revisions. Although, Bayes factors seem promising for evaluating the relative contribution of components to an evolutionary model, the results suggests that even if strong evidence for a model allowing separate topology parameters is found, this might not mean strong evidence for separate gene phylogenies, as long as vital components of the substitution model are still missing.

Phylogenetic relationships of typical antbirds (Thamnophilidae) and test of incongruence based on Bayes factors.