title: Morphological and molecular convergences in mammalian phylogenetics.
abstract: Phylogenetic trees reconstructed from molecular sequences are often considered more reliable than those reconstructed from morphological characters, in part because convergent evolution, which confounds phylogenetic reconstruction, is believed to be rarer for molecular sequences than for morphologies. However, neither the validity of this belief nor its underlying cause is known. Here comparing thousands of characters of each type that have been used for inferring the phylogeny of mammals, we find that on average morphological characters indeed experience much more convergences than amino acid sites, but this disparity is explained by fewer states per character rather than an intrinsically higher susceptibility to convergence for morphologies than sequences. We show by computer simulation and actual data analysis that a simple method for identifying and removing convergence-prone characters improves phylogenetic accuracy, potentially enabling, when necessary, the inclusion of morphologies and hence fossils for reliable tree inference.
authors: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA.
authors: Zhengting
authors: 0000-0003-1716-5090
authors: Z
authors: Zou
authors: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA.
authors: Jianzhi
authors: 0000-0001-6141-1290
authors: J
authors: Zhang
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D000818:Animals; D001483:Base Sequence / Q000235:genetics; D005075:Biological Evolution; D003198:Computer Simulation; D019143:Evolution, Molecular; D005580:Fossils; D008322:Mammals; D010802:Phylogeny