Sample collection and DNA extraction
A total of 280 adult individuals of seaweed pipefish were collected from
9 sites along the coastal waters of China ranging from the Yellow Sea
(YS) to the South China Sea (SCS) (Table 1, Figure S1). We derived
morphological data from 163 seaweed pipefish specimens: 63 from the YS,
34 from the East China Sea (ECS), and 66 from the SCS. The body of the
remaining 117 specimens was damaged, preventing to obtain reliable
morphological measures. The total length (TL) of sampled specimens ofS. schlegeli ranged 18.1–21.6 cm, and no significant differences
in fish sizes existed among sampled localities (ANOVA, Duncan’s multiple
range tests, p > 0.05). Genomic DNA was extracted
from muscle samples and then treated with RNase A to digest any RNAs
present in the samples. The quality and integrity of the DNA samples
were checked by agarose gel electrophoresis, and DNA concentrations were
quantified using a Qubit 2.0 fluorometer.
We performed RAD-sequencing for 69 individuals (31 from the Yellow Sea,
22 from the East China Sea, and 16 from the South China Sea) (Table 1,
Figure S1). The mitochondrial Cytochrome b (cytb ) and nuclear
Sorting nexin 33 (snx33 ) amplificated from 270 pipefish
individuals, and we obtained 248 and 265 valid sh3 andcytb sequences after data correction (Table 1). All experimental
procedures performed in this study were in accordance with relevant
animal ethics guidelines and approved by the Ethical Committee of South
China Sea Institute of Oceanology, Chinese Academy of Sciences.