3 RESULTS

3.1 Genetic diversity

In total, 162 high-quality sequences were obtained after alignment and trimmed to 618 bp. The average base composition was A = 22.3%, C = 28.8%, G = 18.8%, T = 30.1%. In total, we found 44 different haplotypes in our 11 sampling sites (Table 1, Fig. 2). All haplotype sequences were deposited in GenBank (accession numbers MW881382–MW881425). Overall, the nucleotide diversity was low (average, 0.00232; range, 0.00185–0.00277), whereas the haplotype diversity was relatively high and heterogeneous (average, 0.788; range, 0.657–0.886) (Table 1).
The haplotype network analyses of the mtDNA from E. cardinalis in Beibu Gulf showed a typical star-like pattern, with the most frequent haplotype, H1, located in the central position of the haplotype network and surrounded by many low-frequency haplotypes that were divergent from H1 by only one or two mutations (Fig. 2). Most of the haplotypes were low-frequency, and 27 haplotypes were unique to only one sampling site. Only 11 out of the 44 haplotypes were observed at more than two sampling sites. However, several of the abundant haplotypes were found at multiple sampling sites. For example, the dominant widespread haplotype H1 was found in all 11 sampling sites (Fig. 3); the largest distance between two sampling sites harboring this haplotype was more than 300 km. H6 and H8 were distributed at eight and seven sampling sites, respectively. Moreover, between six and 10 haplotypes were found per sampling site, but there was no clear pattern of geographical variation (Fig. 3). The highest number of haplotypes (H = 10) was observed at sites 8 and 10 (Table 1).
The average genetic differentiation, ΦST, of E. cardinalis within Beibu Gulf was 0.031 (range, −0.0657 to 0.0671). All pairwise ΦST values among the sampling sites were small and not significant (Table 2). The effective number of migrants per generation among 11 sampling sites was from 5.98 to 45.76. The migration rates from S7 to S1 were the lowest, whereas those from S1 to S3 were the highest (Table 3).

3.2 Demographic history

The Tajima’s D and Fu’s Fs tests of E. cardinalis in Beibu Gulf were significantly negative (Tajima’s D = −2.446, P < 0.01; Fu’s Fs = −28.378, P < 0.01); this showed that E. cardinalis may have experienced population expansion (Table 4). The mismatch distribution appeared to be unimodal (Fig. 4), which was consistent with the expected distribution under a sudden expansion model (R index = 0.055, P = 0.26).
On the basis of the mutation rate of 1%–3% per million years for mitochondrial genes (Cantatore et al., 1994) and τ value of all data (1.531, 95% confidence intervals: 1.281–1.941), the expansion time forE. cardinalis in Beibu Gulf was estimated to have occurred from approximately 62–21 ka.
The BSP analysis indicated that the E. cardinalis haplotypes in Beibu Gulf coalesced approximately 40 ka when a mutation rate of 2% per million years was used for analysis. However, the BSP pattern revealed a coalescence time of 30–70 ka when using a mutation rate of 1%–3% per million years (Fig. 5). Despite these different coalescence times, the BSP patterns showed similar tendencies and indicated that a steady population expansion took place between 5–30 ka.