Deep mitochondrial divergence
Recent molecular-based phylogeography studies in the NWP have uncovered some general patterns: marine species often harbor genetically divergent lineages in the SCS and ES (Cheang, Chu, & Ang Jr, 2010 [macroalga:Sargassum hemiphyllum ]; Shen et al., 2011 [flathead grey mullet: Mugil cephalus ]; Ni et al., 2012 [venus clam:Cyclina sinensis ]; Cheng & Sha, 2017 [Japanese mantis shrimp: Oratosquilla oratoria ]; Wang, Kong, Chen, Matsukuma, & Li, 2017 [spotted hard clam: Meretrix petechialis ]). Here, using phylogenetic and network analyses of mtDNA cox1 sequence data, we identified two distinct mitochondrial lineages within M. virgata: a northern lineage found in the cold surface-water temperature zone in the northern NWP (the Korean coast, the northern part of the ES/JS and the northern Pacific coast of Japan), and a southern lineage occupying the warm surface-water temperature zone in the NWP (ECS, SCS and the southern Pacific coast of Japan). The fixation index (F st) and AMOVA analysis both support the conclusion that these lineages are genetically distinct and display a different biogeographic pattern except for some Japanese populations (JSH, JSS, JKS, JOI, JKG, JNG; Fig. 1 and Table 1).
Sequence divergence between the two lineages is extremely high (7.4-9.2%), while within-lineage distance is low (a maximum of 0.6%). DNA barcoding analyses of other molluscan species using mtDNAcox1 have reported a mean intraspecific variation less than 2% (Meyer & Paulay, 2005; Zou, Li, & Kong, 2012). However, deeper intraspecific divergence (>2%) has also been detected in some Atlantic and Pacific molluscan species (gastropods and bivalve species); such deep divergence has been attributed to population subdivision by a biogeographic partition between geographic lineages (Layton, Martel, & Hebert, 2014). Very high levels of cox1divergence have also been reported in NWP bivalve species (Liu et al., 2011 [>4.3% in Atrina pectinata ]; Wang et al., 2017 [5.85% in Meretrix petechialis ]). Such divergence has been interpreted as molecular evidence of a physical barrier reducing gene flow. Historical isolation in marginal seas, caused by low sea level during past glaciations, might be the primary driver for deep intraspecific genetic splits in the NWP (Layton et al., 2014).