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.