Genetic diversity of A. corniculatum at the population and species levels
Using next-generation sequencing techniques, we obtained 63 to 75 kb of DNA sequences covering 69 to 82 genes in the 11 populations (Table 2), ranging in length from 197 to 2301 bp. The average sequencing depth of the Sanya, Wenchang, and Yalong populations was more than 2200 x, whereas that of the other eight populations was more than 4400 x. By mapping short reads to reference sequences, we identified 91 to 761 segregating sites within each population (Table 2). The π and θ for each Illumina-sequenced gene indicated a high level of genetic variation at the species level but relatively low genetic diversity within populations and regions (Figure 1b&c). Extremely low π and θ were observed in the populations Chai-ya and Kuching from the southern South China Sea, significantly lower than those in the Gulf of Bengal (La-un and Ngao, P-value < 0.001, Wilcoxon test) and in Australasia (Sorong, Darwin, and U-Daintree, P<0.001, Wilcoxon test) (Figure 1, Table 2). The genetic diversity of Chai-ya and Kuching are also lower than those in Hainan Island, though not that significant (P-value=0.026 for π and P-value < 0.001 for θ, Wilcoxon test). The genetic diversity of populations without Illumina data was evaluated from the six nuclear genes sequenced by the Sanger method. Most of the populations from the northern South China Sea and Australasia have medium values of π and θ, and the two marginal populations in Siri Lanka composite a relatively low level of genetic variation (Figure 1, Table 2).