Sister Group Relationship of Turtles to the Bird-Crocodilian Clade Revealed by Nuclear DNA–Coded Proteins

Abstract

The phylogenetic position of turtles is a currently controversial issue. Recent molecular studies rejected a traditional view that turtles are basal living reptiles (Hedges, S. B., and L. L. Poling. 1999. A molecular phylogeny. Science 83:998-1001; Kumazawa, Y., and M. Nishida. 1999. Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink, statistical evidence for archosaurian affinity of turtles. Mol. Biol. Evol. 16:784-792). Instead, these studies grouped turtles with birds and crocodiles. The relationship among turtles, birds, and crocodiles remained unclear to date. To resolve this issue, we have cloned and sequenced two nuclear genes encoding the catalytic subunit of DNA polymerase alpha and glycinamide ribonucleotide synthetase-aminoimidazole ribonucleotide synthetase-glycinamide ribonucleotide formyltransferase from amniotes and an amphibian. The amino acid sequences of these proteins were subjected to a phylogenetic analysis based on the maximum likelihood method. The resulting tree showed that turtles are the sister group to a monophyletic cluster of archosaurs (birds and crocodiles). All other possible tree topologies were significantly rejected.

Molecular Cloning of Full-Length Dmrt1 cDNA of Reeves Turtle (Chinemys reevesii)

“…This result supports the hypothesis of Iwabe et al [12]. In the present study, RT-PCR using a Crdmrt1-specific primer pair was used to analyze the expression of dmrt1 in various tissues of the adult male turtles.…”

“…The phylogenetic position of turtles is a controversial issue. A recent phylogenetic analysis showed that turtles are a sister group to a monophyletic cluster of crocodiles and birds [12]. Previously reported Percentage identities and positives were calculated from comparisons of amino acid sequences of each species to the sequence of CrDMRT1.…”

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

“…Genomic-scale phylogenetic analysis of 1145 nuclear UCE loci agreed with most other molecular studies [4][5][6][7][8][9][10][11][12][13][14], supporting a sister relationship between turtles and archosaurs. We found no support for the turtleslepidosaur relationship predicted by the Ankylopoda hypothesis [15] (figure 2).…”

Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome

“…These results, based on higher-order homologies embedded in word counts, agree with a growing body of molecular and fossil evidence (4,27,28) in placing turtles in a derived position relative to lepidosaurs (lizards ϩ snakes) rather than in the traditional basal position within Reptilia. However, our topology conflicts with several recent analyses of aligned sequences that suggest a sister relationship of turtles to an archosaur clade (27,(29)(30)(31)(32)(33). Analysis of word frequencies is not expected to achieve the phylogenomic precision of aligned DNA sequences, yet we were surprised at the ability of genomic signatures to recover all but one node in the amniote tree congruent with aligned sequence analysis (27,(29)(30)(31)(32)(33).…”