Protein sequences indicate that turtles branched off from the amniote tree after mammals

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Abstract
The phylogenetic relationships among the major groups of amniote vertebrates remain a matter of controversy. Various alternatives for the position of the turtles have been proposed, branching off either before or after the mammals. To discover the phylogenetic position of turtles in relation to mammals and birds, we have determined cDNA sequences for the eye lens proteins αA- and αB-crystallin of the red-eared slider turtle (Trachemys scripta elegans). In addition, databases were searched for turtle protein sequences, for which mammalian, avian, and outgroup orthologs were available. All sequences were analyzed by three phylogenetic tree reconstruction methods (neighbor-joining, maximum parsimony, and maximum likelihood). Including the α-crystallins, 7 out of 12 proteins support a sister-group relation of turtles and birds with all 3 methods. For each of the other five proteins no topology was consistently preferred by the three approaches. Analyses of the combined amino acid data (1,695 aligned sites) also give extremely strong evidence that turtles are nearer to birds, indicating that mammals branched off before the divergence between turtles and birds occurred.