| Chinese giant salamander (Andrias davidianus) is a rare endemic amphibian, which exists widely in China concerning about 17 proviences and cities around Yangtze River, Yellow River and Pearl River. In a long time, as a result of many kinds of reasons, its number droped sharply and habitat was destroyed excessively, which presented serious loss and fragmentation.In order to identify the relationship between geographic subdivision and population genetic structure due to habitat loss and fragmentation, the mitochondrial complete cytochrome b genes of 13 Chinese giant salamanders and D-loop genes of 28 Chinese giant salamanders collected from Yangtze River Region (Hunan and Shanxi), Yellow River Region (Henan) and Pearl River Region (Guangxi) were amplified and sequenced. According to the analysis of Clustal X, MEGA2.0, PAUP4.01, DnaSP4.0 and Arlequinl.l, the research results show that 11 hapotypes are found and 44 sites were variable (23 parsim-informative sites) among 13 cyt b gene sequences. The content of A+G is 60.2% (66.5% at the third codon position) and transitions are obviously abundant 6.5 times than transversions. Based on the phylogenetic trees, it is concluded that the genetic differentiation of Chinese giant salamander is successional among the different geographical population, which mainly means that there are less variations in geographical populations from Yellow river (Henan population) and Yangtze river (Sichuan population), those from Pearl river (Gangxi population) and Yangtze river (Shanxi population and Hunan population). However, the geographical populations from Pearl river (Gangxi population) are more different from those from Yellow river (Henan population) in genetics. However, 64 nucleotide sites were variable, including 6 transitions, 2 transversions and 11 insertions /deletions in the 28 complete D-loop gene sequences (abdut 771bp). A total of 27 haplotypes were identified and the average genetic distance among all these haplotypes was 1.32%. Furthermore, the results showed that all three geographic regions exhibited low levels of nucleotide diversity and haplotypediversity, in which the two indexes of Yangtze River were the lowest. The results also presented there was significantly distinctive geographic phylogeography between Pearl River Region and Yangtze River Region, between Pearl River Region and Yellow River Region (P<0.001), but no obvious subdivision between Yangtze River Region and Yellow River Region (P>0.05). In addition, and the genetic variation within and between regions was 99.31% and 0.69% respectively, which means the genetic variation mainly happens within the geographic region and gene flow among the geographic regions is comparatively frequent.China giant salamander is a typical aquatic amphibian. The mutation of complete cyt b genes from different local population does not reach saturated state. Furthermore, its bias will drop sharply with the increase of evolution time and the separate of habitat, and the mutation will be saturated by the multiple substitution and saturated response. Moreover, the low and the distribution pattern of genetic diversity were mainly caused by some results in the evolution process as fallow. Firstly, variation of climate and geographical obstruction had an important effect on shaping the infraspecific geography construction. Secondly, historical geological succession had a great relationship with the phylogenesis of local populations. At last, habitat loss, fragmentation and reducing caused by many kinds of disturbance made it difficult in gene flow among different local populations.
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