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Abbreviated Journal Title

Proc. Natl. Acad. Sci. U. S. A.

Keywords

Adaptation; Convergence; Phylogenetics; Reptile; Branch Attraction Artifacts; Phylogenetic Inference; Parallel Evolution; Foregut Fermenters; Stomach Lysozymes; Snakes; Amphisbaenians; Reconstruction; Adaptation; Reptiles; Multidisciplinary Sciences

Abstract

Documented cases of convergent molecular evolution due to selection are fairly unusual, and examples to date have involved only a few amino acid positions. However, because convergence mimics shared ancestry and is not accommodated by current phylogenetic methods, it can strongly mislead phylogenetic inference when it does occur. Here, we present a case of extensive convergent molecular evolution between snake and agamid lizard mitochondrial genomes that overcomes an otherwise strong phylogenetic signal. Evidence from morphology, nuclear genes, and most sites in the mitochondrial genome support one phylogenetic tree, but a subset of mostly amino acid-altering substitutions ( primarily at the first and second codon positions) across multiple mitochondrial genes strongly supports a radically different phylogeny. The relevant sites generally evolved slowly but converged between ancient lineages of snakes and agamids. We estimate that approximate to 44 of 113 predicted convergent changes distributed across all 13 mitochondrial protein-coding genes are expected to have arisen from nonneutral causes-a remarkably large number. Combined with strong previous evidence for adaptive evolution in snake mitochondrial proteins, it is likely that much of this convergent evolution was driven by adaptation. These results indicate that nonneutral convergent molecular evolution in mitochondria can occur at a scale and intensity far beyond what has been documented previously, and they highlight the vulnerability of standard phylogenetic methods to the presence of nonneutral convergent sequence evolution.

Journal Title

Proceedings of the National Academy of Sciences of the United States of America

Volume

106

Issue/Number

22

Publication Date

1-1-2009

Document Type

Article

Language

English

First Page

8986

Last Page

8991

WOS Identifier

WOS:000266580500039

ISSN

0027-8424

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