Abstract
An understanding of population structure and genetic diversity is crucial for wildlife conservation and for determining the integrity of wildlife populations. The vulnerable Chinese cobra (Naja atra) has a distribution from the mouth of the Yangtze River down to northern Vietnam and Laos, within which several large mountain ranges and water bodies may influence population structure. We combined 12 microsatellite loci and 1117 bp of the mitochondrial cytochrome b gene to explore genetic structure and demographic history in this species, using 269 individuals from various localities in Mainland China and Vietnam. High levels of genetic variation were identified for both mtDNA and microsatellites. mtDNA data revealed two main (Vietnam + southern China + southwestern China; eastern + southeastern China) and one minor (comprising only two individuals from the westernmost site) clades. Microsatellite data divided the eastern + southeastern China clade further into two genetic clusters, which include individuals from the eastern and southeastern regions, respectively. The Luoxiao and Nanling Mountains may be important barriers affecting the diversification of lineages. In the haplotype network of cytchrome b, many haplotypes were represented within a “star” cluster and this and other tests suggest recent expansion. However, microsatellite analyses did not yield strong evidence for a recent bottleneck for any population or genetic cluster. The three main clusters identified here should be considered as independent management units for conservation purposes. The release of Chinese cobras into the wild should cease unless their origin can be determined, and this will avoid problems arising from unnatural homogenization.
Highlights
The elapid genus Naja comprises 28 species of non-spitting and spitting cobras and was recently split into four subgenera
Microsatellite diversity in N. atra is slightly higher than, or similar to, those reported for other snakes such as E. subflavus (NA = 7.44 and HE = 0.64) [26], A. laevis (NA = 8.4 and HE = 0.263–0.881) [13] and S. c. catenatus (NA = 13.8 and HE = 0.49–0.77) [14]. These results suggest that despite a declining population, high genetic variation remains amongst wild populations of N. atra, perhaps because of a large effective population size, or because bottlenecks due to very recent ecological disturbance are unlikely to dramatically reduce genetic diversity within a handful of generations unless they lead to catastrophically low population sizes
Conclusions and conservation implications Phylogeography and population genetic studies can aid the identification of evolutionarily significant units and management units [38] and result in evidence-based conservation decisionmaking regarding endangered species [39]
Summary
The elapid genus Naja comprises 28 species of non-spitting and spitting cobras and was recently split into four subgenera. All 11 Asian species except N. naja and N. oxiana have some degree of adaptation to spitting [1,3]. Phylogenetic analysis of 1333 bp of mitochondrial DNA (606 for ND4 and 727 for cytochrome b) supports monophyly of the Asian cobras [2]. This result is consistent with that based on morphological data [4], but invalidates the hypothesis that spitting and non-spitting cobras in Asia are the outcome of two separate ancestral stocks migrating from Africa [5,6]
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