Phylogeography And Population Genetic Structure Of The Chinese Cobra, Naja Atra

The Chinese cobra (Naja atra) is an oviparous elapid snake with a distribution covering southeastern China (including Taiwan, Hongkong and Hainan) and northern Vietnam. The cobra was one of the most commonly found snakes in China some thirty years ago. Largely because the cobra has been over hunted by local people for meat, skin, medicine and handiwork, it is currently regarded as a highly vulnerable species according to a published volume of China Red Data Book of Endangered Animals. To assess the genetic diversity within N. atra, and its population structure and evolutionary history, we sequenced 1029 bp of control region for 390 individuals collected from 27 localities covering almost the whole range of the snake. Forty variable sites were observed, and 52 haplotypes were defined. We identified two genetically distinct clades. one clade including haplotypes from Hekou and Miyi (western China), and the other clade from the whole distributional range except for Miyi.The Luoxiao mountain ranges and Nanling mountain ranges are important barriers limiting gene exchange between populations on the both sides of these two mountain series. Analysis of molecular variance indicated that a significant proportion (32.58%) of the total variation in the mitochondrial DNA data could be attributable to differences among groups:[Eastern China] [Southern China & Vietnam] [Western China]. A significant proportion of variation also occurred among populations within groups (43.18%) and within populations (24.25%). One plausible scenario to explain ourgenetic data is a historically widespread population that has been structured by vicariant factors such as the mountains and sea level fluctuations. Significantly large negative values of Fu's Fs test reject the null hypothesis of neutral evolution of the control region marker for the population group in Eastern China. This provides an inference for population expansion in Eastern China, which is supported by the mismatch distribution analysis and Rogers test of sudden population expansion. The value ofτfor the population group in Eastern China was 1.992. For the substitution rate for a variety of snakes were about 0.0065 site-1 myr-1, the expansion time was estimated to be 0.298 mya.We characterize thirteen polymorphic microsatellite loci isolated from N. atra genomic libraries, which enriched for AC-motif microsatellites. The thirteen loci were screened on a group of 48 individuals from two populations, one in Yong'an and the other in Ganzhou. These markers revealed a relatively high degree of genetic diversity (4-12 alleles per locus) and heterozygosity (Ho ranged from 0.213-0.854 and He ranged from 0.301-0.838). Four loci deviated from Hardy-Weinberg equilibrium. The high level of polymorphism revealed by these microsatellite markers will be useful for the study of gene flow, population structure and evolutionary history of N. atra.