Abstract:
:Covarion processes allow changes in evolutionary rates at sites along the branches of a phylogenetic tree. Covarion-like evolution is increasingly recognized as an important mode of protein evolution. Several recent reports suggest that maximum likelihood estimation employing covarion models may support different optimal topologies than estimation using standard rates-across-sites (RAS) models. However, it remains to be demonstrated that ignoring covarion evolution will generally result in topological misestimation. In this study we performed analytical and theoretical studies of limiting distances under the covarion model and four-taxon tree simulations to investigate the extent to which the covarion process impacts on phylogenetic estimation. In particular, we assessed the limits of an RAS model-based maximum likelihood method to recover the phylogenies when the sequence data were simulated under the covarion processes. We find that, when ignored, covarion processes can induce systematic errors in phylogeny reconstruction. Surprisingly, when sequences are evolved under a covarion process but an RAS model is used for estimation, we find that a long branch repel bias occurs.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Wang HC,Susko E,Spencer M,Roger AJdoi
10.1007/s00239-007-9062-4subject
Has Abstractpub_date
2008-01-01 00:00:00pages
50-60issue
1eissn
0022-2844issn
1432-1432journal_volume
66pub_type
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