Morphological and molecular convergences in mammalian phylogenetics
Zhengting Zou & Jianzhi Zhang
Nature Communications 7, Article number: 12758 (2016)
Evolutionary theory Phylogenetics
Received: 02 March 2016 Accepted: 29 July 2016 Published online: 02 September 2016
Source/Fonte: Molecular Cytogenetics
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.
We thank Wei-Chin Ho, Bryan Moyers and Jian-Rong Yang for constructive comments. This work was supported in part by a research grant from the U.S. National Institutes of Health (GM103232) to J.Z.
Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
J.Z. conceived the project; Z.Z. and J.Z. designed the project; Z.Z. conducted the experiments and analysed the data; Z.Z. and J.Z. wrote the manuscript.
The authors declare no competing financial interests.
Correspondence to Jianzhi Zhang.