102 
Fishery Bulletin 119(2—3) 
© Goto Isls. Koshiki-jima Isls. 
oO Niigata 
@ Aomori 
© Korean Penin. 
*—— D. trachyderma 
| t— D. macrocauda 
— D. tengu 
©) Danjo Isls. 
@ Kyoto 
© Kochi 
@ Taiwan 
Figure 2 
Maximum likelihood tree of haplotypes based on phylogenetic analysis of the 
mitochondrial cytochrome 6 gene sequences (931 base pairs) of 214 polkadot 
skate (Dipturus chinensis). Sequences were obtained from specimens caught 
at 7 locations around Japan, in the East China Sea, Sea of Japan, and Pacific 
Ocean, during 2010-2017 or were obtained through the International Nucle- 
million years ago(MYA).The uncorrected 
p-distance between clade B1 and clade 
B2 was 0.008, and the divergence time 
was estimated to be 0.50—0.80 MYA. 
The minimum spanning network of 
the haplotypes is given in Figure 3. Hap- 
lotypes were divided into 2 groups, group 
A and group B, with the latter subdivided 
into 2 subgroups, group B1 and group 
B2, which correspond to clades A, B1, 
and B2 in the maximum likelihood tree, 
respectively (Fig. 2). The 10 haplotypes 
of group B are separated from those of 
group A by a minimum of 15 mutations. 
The 3 haplotypes of group B1 are sepa- 
rated from those of group B2 by a mini- 
mum of 5 mutations. Group A consists of 
the most dominant haplotype, al (n=74, 
44.8% of the group), 9 haplotypes that 
are shared with more than 2 individuals 
(haplotypes a2—al10), and 14 rare haplo- 
types that were found in only 1 or 2 indi- 
viduals. Group B1 includes 1 dominant 
haplotype, b1, and 2 rare haplotypes 
that connect with haplotype b1 by 1 and 
3 mutations. Group B2 consists of 2 non- 
rare haplotypes (b2 and b3) and of 5 rare 
haplotypes connected to each other by 
1 or 2 mutations. 
mo 
o) 
ne) 
ECG 
O 
i 
jaa) 
Oo) 
xo) 
& 
O 
otide Sequence Database Collaboration for populations in Taiwan or off the 
Korean Peninsula. The evolutionary distances were calculated by using the 
TN93+G model. Numerals at nodes indicate the bootstrap probability for 
clades A, B, B1, and B2. Numerals in circles indicate the number of individuals 
sharing the same haplotype. The roughskin skate (D. trachydermus), bigtail 
skate (D. macrocaudus), and acutenose skate (D. tengu) served as outgroups 
for phylogenetic analysis. The bar in the bottom-left corner indicates evolu- 
tionary distance. Isls.=Islands; Penin.=Peninsula. 
B, as indicated by high values of bootstrap probability 
(96% and 74%, respectively). Clade B is divided into 2 
subclades, clades B1 and B2, with high values of boot- 
strap probability (85% and 91%, respectively). Clades 
A, B1, and B2 consist of 24, 3, and 7 haplotypes, respec- 
tively. Clade A comprises the populations in the East 
China Sea (populations at the Danjo Islands and Goto 
Islands, as well as 1 individual from the Koshiki-jima 
Islands), the Sea of Japan (populations in the Kyoto and 
Niigata Prefectures), as well as 1 individual each from 
Taiwan and the Korean Peninsula (n=165, 77.1% of all 
samples). Clades B1 and B2 consist of the populations 
along the southern (Kochi Prefecture: n=23, 10.7% of all 
samples) and northern (Aomori Prefecture: n=26, 12.1% 
of all samples) Pacific coasts of Japan, respectively. The 
net average distance (uncorrected p-distance) between 
clade A and clade B was 0.021. Applying the divergence 
rate of 1.0-1.6% per million years, we estimated that 
clade A and clade B diverged from each other 1.31—2.10 
Geographic distribution of haplotypes 
Haplotype frequencies in the 9 locations 
are shown in Figure 4. The population 
in the Danjo Islands consists of 8 non- 
rare haplotypes (al, a2, a4~-a6, and 
a8—al0) and 5 rare haplotypes, with 
haplotype a2 being dominant (27.1% of 
samples). The population in the Goto 
Islands comprises 5 non-rare (al—a3, 
a5, and a6) and 3 rare haplotypes, with 
haplotype al as the dominant haplotype (38.9% of sam- 
ples). The population in Kyoto Prefecture includes 4 non- 
rare (al, a3, a4, and a7) and 2 rare haplotypes, with the 
dominant haplotype being al (59.6% of samples). The 
population in Niigata Prefecture consists of 3 non-rare 
(al, a3, and a7) and 3 rare haplotypes, with haplotype 
al as the dominant haplotype (65.3% of samples). In the 
East China Sea and the Sea of Japan, the frequency of 
haplotype al gradually increased from the Goto Islands 
(38.9% of samples) northward to Niigata Prefecture 
(65.3% of samples). The population in Kochi Prefecture 
includes 1 dominant (b1: 87.0% of samples) and 2 rare 
haplotypes. The population in Aomori Prefecture con- 
sists of 2 non-rare (b2 and b3) and 5 rare haplotypes, 
with haplotype b2 being the dominant haplotype (46.2% 
of samples). 
Genetic differentiation among populations Samples from the 
Koshiki-jima Islands, Taiwan, and the Korean Peninsula 
