Genetic structure and demographic history should inform conservation: Chinese cobras currently treated as homogenous show population divergence - PubMed (original) (raw)

Genetic structure and demographic history should inform conservation: Chinese cobras currently treated as homogenous show population divergence

Long-Hui Lin et al. PLoS One. 2012.

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Three genetic clusters of Naja atra in China and Vietnam based on the admixture model in Structure.

Individuals are represented by a point which is colored to reflect the cluster to which it was assigned with the highest membership coefficient. Large points represent individuals with membership coefficient _q_≥0.90 and small ones q<0.90. Ellipses show the three main genetic clusters. See Table 1 for sample site abbreviations.

Figure 2

Figure 2. Network of 39 mitochondrial cytochrome b haplotypes from 269 individual Naja atra.

The size of the circles is proportional to haplotype frequency; small open circles represent intermediate haplotypes that are not in our study. See Table 1 for sample sites abbreviations. Sites where most individuals were assigned to the same cluster on the basis of microsatellite data have gradations of the same color (s).

Figure 3

Figure 3. Maximum-likelihood tree for all 39 haplotypes of Naja atra and for one outgroup taxon.

Labels are haplotype identification numbers. Values above branches indicate support for each node based on maximum likelihood. Bootstrap values below 70% are not shown.

Figure 4

Figure 4. Admixture analysis of individual genotypes using Structure.

Colors correspond to one of three clusters (see also Fig. 1), and each bar represents a single sample. See Table 1 for sample site abbreviations.

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