The polymorphism of MHC class II B gene in 14 Chinese alligators was analyzed, which came from three different areas： a wild population from Xuancheng, Anhui, a captive population from Changxing, Zhejiang, and a captive population from Anhui Research Center for Reproduction of Chinese Alligators. The gene fragment was amplified using a pair of specific primers designed from the MHC gene sequence of the spectacled caiman. A total of 34 sequence haplotypes of exon 3 were detected in the sampled Chinese alligators. The numbers of haplotypes of the 3 Chinese alligator populations were 15, 10, and 9, respectively. The overall estimation of the MHC polymorphism in the Chinese alligator population was higher than those in mammals and in cypdnid fish, The rates of nonsynonymous substitutions （dN） occurred at a significantly lower frequency than that of synonymous substitutions （ds）, which were not consistent with the common rule. This result might suggest that the polymorphism of exon 3 seemed not to be maintained by the balancing selection. The neutrality test of Tajima excluded the null hypothesis that the polymorphism of exon 3 was generated by a random drift, and the fact that D = -0.401 indicated an excess of rare mutations in the Chinese alligator. The nucleotide diversity of the sequences and the phylogenetic relations were also analyzed, and the results suggested that there was no significant difference in genetic diversity among the 3 populations of Chinese alligator.
The nucleotide sequence of the complete mitochondrial DNA （mtDNA） molecule of the salt-water crocodile （Crocodylus porosus） was determined in this article. The molecule is 16,917 base pairs Cop） in length, and codes for 22 tRNAs, 13 protein-coding genes, 2 rRNAs, as well as a control region （D-loop）, as is characteristic for mitochondrial genomes of other metazoans. The gene order conforms to that of other crocodilians sequenced, but the arrangement of some tRNA genes differs from other vertebrates. It shows that the gene order of crocodilians is remarkably conserved. In this study, the relationships among crocodilians were examined in the phylogenetic analysis based on the control conserved regions of 17 crocodilians. The results suggest that the gharial （Gavialis gangeticus） joins the false gharial （Tomistoma schlegelii） on a common branch, and then constitutes a sister group to traditional Crocodylidae. Thus, the result supports that G gangeticus belongs to Crocodylidae. The analyses also suggest that the African slender-shouted crocodile （Crocodylus cataphractus） can be treated as an isolated genus, and constitutes a sister group to Crocodylus.
