Molecular Phylogeny Of Extant Crocodylia (Reptilia) Inferred From Nuclear DNA Sequences

Currently there are 23 recognized species within the extant Crocodylia. They are commonly grouped in three primarily families, eight genera: the Alligatoridae, Crocodylidae and Gavialidae. The intergenus and interspecies relationships of extant Crocodylia have became the focus of systematic biological studies. Present study employed DNA sequences from nuclear genome, i.e. brain-derived neurotrophic factor gene (BDNF) 600bp, neurotrophin-3 gene (NT-3) 623bp and proto-oncogene c-myc 758bp to discussed the phylogenetic relationships of extant crocodylia.Based on individual gene sequence and concatenated datasets, Maximun parsimony method, Maximum likelihood method and Bayesian inference were applied to reconstructed phylogenetic tree of crocodiles. The results supported controversial genus Gavialis and Tomistoma had closer relationship, they formed sister group and placed at the basal to Crocodylidae. The relationship between African slender-snouted crocodile (Crocodylus cataphractus) and dwarf crocodile (Osteolaemus tetraspis) was closer than other true crocodiles, which implied African slender-snouted crocodile should separate from genus Crocodylus for another single genus Mecistops. Thus, Crocodylidae should be composed of Crocodylus, Osteolaemus, Mecistops, and their relationships were (Crocodylus (Osteolaemus, Mecistops)).As for the intergenus relationship of Alligator, Caiman, Melanosuchus, Paleosuchus of Alligatoridae, results showed Melanosuchus was more related to Caiman than Paleosuchus, Alligator. Chinese alligator (Alligator sinensis) and American alligator (Alligator mississippiensis) were closely related, but they didn't group together in present study. This topology was not consistent with the results inferred from mitochondrial datasets. Howerer, because of high evolutionary conservation of BDNF,NT-3 and c-myc gene sequences, nuclear gene sequences dataset didn't have interspecies relationship of true crocodiles resolved. It's suggested that more fast evolution rate molecular marker should explored for further resolution of recently divergent species of Crocodylia.Our analyses of nucleotide and amino acid sequence of crocodilian neurotrophin showed very low dN/dS rate of protein mature region (BDNF: 0.057, NT-3: 0.034) and rather high rate of pro-region (BDNF: 0.13, NT-3: 0.97). Lower dN/dS rates of mature region indicated that they were subject to higher levels of selective constraint than pro-region. And neurotrophin acid sequence showed very high conservation through the evolution of vertebrate. The pattern across loci of differing variability in the pro and mature region was interesting because it provided evidence for differences in the functions of the protein sequences encoded by the two regions.