Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers

Population genetics and evolutionary history of the intertidal brittle star Ophiothrix (Ophiothrix) exigua in the northern China Sea

Ophiothrix (Ophiothrix) exigua is a common brittle star in the northwestern Pacific. As a dominant species, O. exigua inhabiting the intertidal rocky ecosystem are affected by multiple environmental stressors, but molecular insights into their genetic population structure remain poorly studied. In this study, we investigated the population genetics and evolutionary history of six O. exigua populations from the northern China Sea using mitochondrial (COI, NAD4) and nuclear (ITS2, 18S) gene markers. High haplotype diversity, low nucleotide diversity, and low rates of gene differentiation among the populations of O. exigua were detected. Pairwise genetic differentiation (ΦST) statistics between different localities were negative or low and insignificant, suggesting strong gene flow of this species over the study areas. The phylogenetic analyses showed that the populations exhibited high homogeneity between localities in our study area. Demographic analyses indicated that the populations experienced sustained expansion around 0.2 million years ago. This expansion was likely related to transgressions events in the Yellow Sea during the Pleistocene period. Additional samples of O. exigua from disparate geographical locations, especially the Japan Sea and the Korean Peninsula, will be needed to unravel the population genetic patterns and evolutionary history of this species.

The metabarcoding of Grubs: Traditional herbal medicine of Scarabaeidae larvae

Grubs, called Qicao in China, have a long tradition as herbal medicine in East Asia. These larvae belong to the diverse family Scarabaeidae and are typically harvested from the wild during their immature stage based on morphological characteristics. However, rapid and accurate identification becomes challenging when relying solely on external morphological features, as the lack of clarity on biological sources raises safety concerns for clinical applications. The application of DNA metabarcoding provides a solution by enabling the determination of the biological source of a large sample. In the current study, we collected 19 batches of Grubs, consisting of 11,539 individuals, from the market and analyzed their biological composition through metabarcoding. We identified 49 Amplicon Sequence Variants (ASVs), 21 of which were Grubs. The 21 ASVs were classified into seven Molecular Operational Taxonomic Units (MOTUs) through species delimitation, which revealed that commercially available Grubs are predominantly sourced from Protaetia brevitarsis seulensis, while species of Rutelinae, Anomala, and Holotrichia were also abundant in some commercial batches. Among the identified ASVs, 28 belonged to non-Grub species and indicated adulteration from different animal families; high abundances of these ASVs were detected for Bombycidae, Tabanidae, and Viviparidae. Our findings underscore the complexity of Grubs' species composition and advocate for a deeper understanding of the wildlife sources contributing to herbal products. This research contributes valuable insights into the molecular identification of Grubs, paving the way for enhanced quality assurance in traditional medicine applications to provide safe and effective medicines for humanity.

High genetic differentiation and moderate genetic diversity of the degenerative branching coral Pocillopora verrucosa in the tropical South China Sea

Global warming is causing rapid degradation of coral reefs, among which branching corals are degrading the fastest. An assessment of coral genetic diversity and adaptive potential provides a basis for coral reef protection. In this study, we selected the branching coral Pocillopora verrucosa, a widely distributed species in the tropical South China Sea (SCS), to carry out population genetic studies. To analyze the genetic diversity and structure of 319 P. verrucosa samples from 10 populations in 4 SCS regions, twelve pairs of microsatellite primers and two nuclear markers, ITS and β-tub, were selected. Microsatellite marker results showed moderate genetic diversity for P. verrucosa in the SCS, but relatively low diversity in Dazhou Island and Yongxing Island. The haplotype network showed that P. verrucosa in the SCS was derived from two ancestors, which may be linked to geographical isolation in the Pleistocene glacial period. AMOVA (Φ_ST = 0.3375) and F_ST pairwise analysis results based on β-tub showed that the populations were highly differentiated, with most F_ST values (21/45) > 0.25. Yongxing and Qilianyu Islands populations were significantly different from those in the Xisha area. Mantel test results showed that genetic differentiation among P. verrucosa populations was significantly and positively correlated with both mean sea surface temperature (SST) and SST variance, and was not correlated with distance, chlorophyll-a, or turbidity. The reproductive mode of brooding planulae was an important factor contributing to high genetic differentiation among populations. The moderate genetic diversity of SCS P. verrucosa indicates that this population has a certain genetic potential in the context of global changes, but the high genetic differentiation between populations increases the risk of local degradation or extinction. This study provides a theoretical basis for the protection and restoration of SCS coral reefs.

Insights into genetic variation and demographic history of sharpnose rays: Examinations of three species of Telatrygon (Elasmobranchii, Dasyatidae) from the Indo-West Pacific

Coastal and demersal chondrichthyans (sharks, rays, and skates) are expected to exhibit high levels of genetic differentiation in areas of complex geomorphology. Population genetic studies investigating the extent to which demographic history shapes the genetic structure of these fishes are rare. Here, we combination mitochondrial DNA (Cytb and ND2) and eight nuclear microsatellite loci from 244 individuals to examine the population genetic structure and demographic history of the three Indo-West Pacific species of sharpnose rays (Telatrygon zugei, Telatrygon biasa, and Trygon crozieri). High levels of genetic variation both within and between species was identified. Phylogenetic analysis partitioned haplotypes into two lineages supporting divergence of T. zugei from T. crozieri and T. biasa during the Pleistocene. Furthermore, microsatellite-based clustering analyses identified four genetic groups (i.e., T. zugei from Japan, T. zugei from coastal China, T. biasa from Gulf of Thailand, and T. crozieri from the Andaman Sea. Measurements of genetic differentiation also support these four groups. Additionally, Pleistocene demographic expansions were examined in all genetic groups. The climate oscillations and current hydrologic cycles in the Indo-West Pacific appear to be coincide with the hypothesis regarding speciation and the observed demographic history trends of the sharpnose rays. Considering the species group has, until recently, been thought to be one species, these results are critical for defining management units and guiding conservation efforts to preserve stingray biodiversity. This article is protected by copyright. All rights reserved.

Life-history features and oceanography drive phylogeographic patterns of the chiton Acanthochitona cf. rubrolineata (Lischke, 1873) in the northwestern Pacific

Chitons are a group of marine mollusks (class Polyplacophora) characterized by having eight articulating shell plates on their dorsal body surface. They represent suitable materials for studying the spatiotemporal processes that underlie population differentiation and speciation in ocean environments. Here we performed population genetic analyses on the northwestern Pacific chiton Acanthochitona cf. rubrolineata (Lischke, 1873) using two mitochondrial gene fragments (COI and 16S) from 180 individuals sampled from 11 populations among the coastal waters of Korea, Japan, and China. The phylogenetic network uncovered a reticulated relationship with several sub-haplogroups for all A. cf. rubrolineata haplotypes. SAMOVA analyses suggested the best grouping occurred at three groups (Φ_CT = 0.151, P < 0.0001), which geographically corresponds to hydrographic discontinuity among the coastal regions of Korea, Japan, and China. The assumed limited dispersal ability of A. cf. rubrolineata, coupled with northeasterly flowing, trifurcate warm currents, might have contributed to the genetic differentiation among the three groups. Meanwhile, a high level of within-group genetic homogeneity was detected, indicating extensive coastal currents might facilitate gene flow among the populations within each group. Bayesian skyline plots demonstrated significant population expansion after the Last Glacial Period (110-25 thousand years ago) for all studied populations except the Japan group. Together these results suggest that the present-day phylogeographic patterns of A. cf. rubrolineata are strongly affected by the interplay of historical and/or contemporary oceanography and species-specific life-history features.

Demographic history and population genetic analysis of Decapterus maruadsi from the northern South China Sea based on mitochondrial control region sequence

Late Pleistocene climate oscillations are believed to have greatly influenced the distribution, population dynamics, and genetic variation of many marine organisms in the western Pacific. However, the impact of the late Pleistocene climate cycles on the demographic history and population genetics of pelagic fish in the northern South China Sea (SCS) remains largely unexplored. In this study, we explored the demographic history, genetic structure, and genetic diversity of Decapterus maruadsi, a typical pelagic fish, over most of its range in the northern SCS. A 828–832 bp fragment of mitochondrial control region were sequenced in 241 individuals from 11 locations. High haplotype diversity (0.905–0.980) and low nucleotide diversity (0.00269–0.00849) was detected, revealing low levels of genetic diversity. Demographic history analysis revealed a pattern of decline and subsequent rapid growth in the effective population size during deglaciation, which showed that D. maruadsi experienced recent demographic expansion after a period of low effective population size. Genetic diversity, genetic structure, and phylogenetic relationship analysis all demonstrated that no significant genetic differentiation existed among the populations, indicating that D. maruadsi was panmictic throughout the northern SCS. Periodic sea-level changes, fluctuation of the East Asian Monsoon, and Kuroshio variability were responsible for the population decline and expansion of D. maruadsi. The demographic history was the primary reason for the low levels of genetic diversity and the lack of significant genetic structure. The life history characteristics and ocean currents also had a strong correlation with the genetic homogeneity of D. maruadsi. However, the genetic structure of the population (genetic homogeneity) is inconsistent with biological characteristics (significant difference), which is an important reminder to identify and manage the D. maruadsi population carefully.

Understanding genetic diversity and population genetic structure of three Cyprinidae fishes occupying the same habitat from Uttarakhand, India

Different pattern of genetic diversity and population genetic structure among the species are reported due to their different ecological requirements, adaptability and the evolutionary histories. Understanding such patterns in a species and between the populations is important to develop the effective conservation plans. Very limited studies are available, how different factors influencing the gene flow of a species especially in fish communities. Therefore, the present study is aimed to document the genetic diversity and population genetic structure of the three species of Cyprinidae fishes (Puntius sophore, Pethia ticto, and Pethia conchonius) sharing the same kind of habitat using the mitochondrial cytochrome c oxidase subunit 1 (CO1). We used 80 samples of the three species from different river/streams. In which we observed total 4–9 haplotypes in all three species with the intra-species sequenced divergence ranges between 0.002 and 0.019. The nucleotide and haplotype diversity was ranged from 0.002040 to 0.01007 and from 0.251 to 0.822, respectively. Neutrality test values were found to be positive only in the P. ticto but statistically non-significant. The AMOVA variation among the populations was 8.89–84.30% whereas, within the populations, it was ranged from 15.70 to 91.11%. The median-joining haplotype network suggests the stable population size over the time and haplotypes were clustered with respect to their geographic locations except the P. conchonius. Similar pattern observed in the phylogenetic tree.

Comprehensive analysis of population genetics of Phoxinus phoxinus ujmonensis in the Irtysh River: Abiotic and biotic factors

As a widely distributed species along the Irtysh River, Phoxinus phoxinus ujmonensis (Kaschtschenko, 1899) was used as a model to investigate genetic diversity and population structure as well as the influence of environmental factors on population genetics. In this study, we specifically developed 12 polymorphic microsatellite loci. The analysis of microsatellite and mtDNA markers revealed a high and a moderate genetic diversity across seven populations, respectively. Moderate differentiation was also detected among several populations, indicating the impact of habitat fragmentation and divergence. The absence of isolation by distance implied an extensive gene flow, while the presence of isolation by adaptation implied that these populations might be in the process of adapting to divergent habitats. Correlation analysis showed that abiotic factors like dissolved oxygen, pH, total dissolved solids, and conductivity in water as well as biotic factors like plankton diversity and fish species diversity had impact on genetic diversity and divergence in P. phoxinus ujmonensis populations. The results of this study will provide an insight into the effect of environmental factors on genetic diversity and contribute to the study of population genetics of sympatric species.

Genetic structure, phylogeography, and demography of Anadara tuberculosa (Bivalvia) from East Pacific as revealed by mtDNA: Implications to conservation

Wild populations of the pustulose ark, Anadara tuberculosa (Bivalvia), an emblematic species of the East Pacific mangrove ecosystem declined in South American countries (Colombia, Ecuador, and Peru) mainly due to overharvesting and habitat loss or degradation. Understanding the genetic aspects of geographic variations and population structure of A. tuberculosa, currently unknown, appears as a priority to fishery authorities in order to elaborate integrated and collaborative conservation policies for fishery management, aquaculture, and stock enhancement programs. We used mtDNA sequence data to investigate haplotype diversity, genetic structure, and demography of A. tuberculosa. Results indicate genetic homogeneity of populations distributed north and south of the equator, respectively. However, statistically significant differentiation emerged between northern and southern populations with pairwise ф ST values ranging between 0.036 and 0.092. The oceanic current system acting in the area (Panama Current and Humboldt Current) might play a role in limiting the larval dispersal of the species, still poorly understood. Demography reconstruction supported recent population expansion, possibly started after last glacial maximum. Our results would suggest separate and independent management of populations north and south of the equator.

Development of microsatellite markers and analysis of genetic diversity of Barbatia virescens in the southern coasts of China

BACKGROUND

The blood clam Barbatia virescens is an ecologically and economically important species in the southern coast of China. Understanding of the genetic structure of B. virescens populations is vital to breeding strategies and conservation programs.

OBJECTIVE

To develop and characterize a set of microsatellites loci primers for B. virescens, and provide helpful information for reasonable utilization and protection of B. virescens natural resources.

METHODS

The microsatellites of B. virescens were detected using a RAD-seq approach based on an Illumina sequencing platform. For the test of microsatellite development, we calculated the number of alleles (Na), observed heterozygosities (Ho), expected heterozygosities (He) and exact tests for deviations from Hardy-Weinberg equilibrium (HWE). Twelve polymorphic loci were used to access the genetic diversity and population structure of four B. virescens populations.

RESULTS

In this study, 50,729 microsatellites of B. virescens were detected. Twenty-two polymorphic microsatellite loci were developed for B. virescens. The number of alleles per locus ranged from 6 to 15, and expected heterozygosities varied from 0. 567 to 0.911. All the PIC values of the 22 loci were greater than 0.5, indicating that these markers were highly informative for further genetic analysis. Twelve loci were selected to analyze genetic diversity and population structure of four B. virescens populations collected from different geographical regions along the southern coast of China. The results showed moderate to high levels of genetic diversity in the four populations (mean Ar = 7.756-8.133; mean Ho = 0.575-0.639; mean He = 0.754-0.775). Pairwise F_ST estimates indicated that there was significant divergence among the four populations.

CONCLUSION

This study not only provides a large scale of sequence information of microsatellites which are valuable for future genetic mapping, trait association and kinship among B. virescens, but also offers useful information for the sustainable management of natural stocks and the development of breeding industry of B. virescens.

Araniella cucurbitina: the first molecular evidence of a Palearctic species of genus Araniella inhabiting India

The present study represents first genetic record of single spider species Araniella cucurbitina, genus Araniella from Uttarakhand, India. There are 12 identified species under Araniella genus and they are distributed in Palearctic region. Here, we used known N = 47 (2 from present study and 45 from GenBank) cytochrome oxidase 1 (CO1) sequences of A. cucurbitina representing seven different geographical groups, additionally 23 sequences of eight Araniella species were used for phylogenetic relationship. The CO1 (561 bp) sequences of A. cucurbitina consisted of n = 14 haplotypes, where haplotype 14 (Hap 14) represents Indian species, while all 13 haplotypes (Hap1-13) shared between six A. cucurbitina groups. The overall 'h' and 'π' diversities among seven groups of A. cucurbitina were 0.85291 and 0.00888, respectively, while overall evolutionary divergence was 0.04. The Indian Hap 14, showed minimum sequence divergence (0.02) from Italy and Czech Republic haplotypes (Hap 6), it means it is the closest group compared to others. Evolutionary divergence among eight species of Araniella ranges from 0.003 to 0.114. The maximum likelihood (ML) topology based on 14 haplotypes of A. cucurbitina was divided into two major clades and further two subclades. Furthermore, ML topology between eight species of Araniella was divided into three major clades, where A. cucurbitina and A. proxima clustered together in clade 'A', while six others were present together in clade 'B' and 'C'. This study helps to identify the Indian species from the rest of Araniella species and other cucurbitina population across the world. This study further needs to be on a large scale to know the exact status distribution and molecular phylogeography of this single species of genus Araniella from India.

Phylogeography of bivalve Meretrix petechialis in the Northwestern Pacific indicated by mitochondrial and nuclear DNA data

The marine clam Meretrix petechialis is an important economic shellfish species in Northwestern Pacific, but little is known about its phylogeographical pattern. Here, we analyzed 311 samples from 22 locations along the northwestern Pacific using combined profiling of one mitochondrial gene (the first subunit of cytochrome coxidase, COI) and one nuclear DNA marker (the internal transcribed spacer region 1, ITS-1) to investigate contemporary genetic structure and reconstruct phylogenetic history of this species. The results revealed that two distinct phylogeographic lineages dominated marginal seas-the East China Sea (ECS) and the South China Sea (SCS) respectively. The estimation of divergence time between two lineages was 2.1-3.8 Ma, corresponding to a period of the early Pleistocene to late Pliocene. The vicariance of the two lineages was connected to the historical isolation of marginal seas and sea surface temperature (SST) gradient, pointing that SST might play an important role in maintaining phylogeographical patterns of M. petachialis. Significant overlaps between two lineages were observed in 23° to 29° N, located at the adjacent area of the ECS and SCS, which might be promoted by the connectivity of China Coast Current. However, the influence of ocean currents on mixings between two lineages was limited. In comparison, significant relationships were found between genetic distances and geographic distances if the North and South populations were analyzed separately, result of which might be due to some small reciprocal, rotating flows along coastal areas and special geographical conditions.

Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species

Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity.

New insight into hybridization and unidirectional introgression between Ammodytes japonicus and Ammodytes heian (Trachiniformes, Ammodytidae)

Based on northern (NOL) and southern (SOL) mitochondrial lineages, recently, it proposed the new species Ammodytes heian and revived the species name Ammodytes japonicus to describe sand lances from the northwestern Pacific Ocean. This study used molecular methods to investigate genetic relationships between the two sand lance species in Korea and Japan. In total, 154 specimens were collected from four locations in Korea (Baengnyeongdo in the Yellow Sea, Tongyeong in the Korean Strait, and Jumunjin and Gijang in the East Sea), and 50 specimens were collected from a single location in Japan (Wakkanai in the Okhotsk Sea). Mitochondrial DNA analysis demonstrated that the individuals from Baengnyeongdo and Tongyeong all belonged to the SOL, whereas those from Gijang, Jumunjin, and Wakkanai included individuals from both the NOL and SOL (over 75% NOL). Population structure analyses were performed on the same individuals using seven microsatellite DNA markers. The population structure analysis based on 201 specimens identified two clusters (named as northern group and southern group), with the admixture proportion (q) of < 0.1 for the northern group in the Backyeongdo and Tongyeong sand lances and < 0.1 for the southern group in the Wakkanai sand lances. The high heterogeneity indicated that the former was probably A. japonicus and the latter probably A. heian. However, the admixture proportion in the Jumunjin and Gijang sand lances was 0.71–0.75 for the southern group, indicating that hybridization and unidirectional introgression from SOL to NOL occurs in southwestern margin of the East Sea. Our findings illustrate the speciation process based on different patterns of gene flow between Korean and Japanese sand lance, which is strongly influenced by both the paleo-climatic change and the contemporary local oceanic current pattern.

Phylogeography of freshwater fish Puntius sophore in India

Phylogeography and evolutionary history of the freshwater species are poorly known. We document the phylogeography of widely distributed Puntius sophore using cytochrome oxidase subunit I (COI) gene of 650 bp. In the present study, we used 61 individual sequences from known geographic locations across India whereas data are lacking from other parts of its distribution range. Total 20 haplotypes with the intra-species sequence divergence ranging from 0.004 to 0.025 were observed and they were split into two major clades (North and Northeastern to Central India). Two distant geographic (North and Northeastern to Central India) regions shared haplotype suggesting ancient river connectivity or introduction of species from Northeast and Central India. Overall nucleotide and haplotype diversities were 0.00971 and 0.915. The Tajima's D and Fu's Fs values were found negative but non-significant thus rejecting the population expansion model followed by the multimodal mode of mismatch distribution. Bayesian skyline plots from both the clade showed steady population history over time; and start of decline in recent years in the clade B (∼1000-1500 years). The present finding is in support to the 'Satpura hypothesis' proposed to explain species movement patterns from Southeast Asian countries to Indian subcontinent, seconded by P. sophore showing high genetic diversity within Northern India clade (high genetic splits) because of presence of high river network in comparison to other parts of the country.

Phylogeography of the Rock Shell Thais clavigera (Mollusca): Evidence for Long-Distance Dispersal in the Northwestern Pacific

The present-day genetic structure of a species reflects both historical demography and patterns of contemporary gene flow among populations. To precisely understand how these factors shape current population structure of the northwestern (NW) Pacific marine gastropod, Thais clavigera, we determined the partial nucleotide sequences of the mitochondrial COI gene for 602 individuals sampled from 29 localities spanning almost the whole distribution of T. clavigera in the NW Pacific Ocean (~3,700 km). Results from population genetic and demographic analyses (AMOVA, ΦST-statistics, haplotype networks, Tajima's D, Fu's FS, mismatch distribution, and Bayesian skyline plots) revealed a lack of genealogical branches or geographical clusters, and a high level of genetic (haplotype) diversity within each of studied population. Nevertheless, low but significant genetic structuring was detected among some geographical populations separated by the Changjiang River, suggesting the presence of geographical barriers to larval dispersal around this region. Several lines of evidence including significant negative Tajima's D and Fu's FS statistics values, the unimodally shaped mismatch distribution, and Bayesian skyline plots suggest a population expansion at marine isotope stage 11 (MIS 11; 400 ka), the longest and warmest interglacial interval during the Pleistocene epoch. The lack of genetic structure among the great majority of the NW Pacific T. clavigera populations may be attributable to high gene flow by current-driven long-distance dispersal of prolonged planktonic larval phase of this species.

Taxonomic status of the three color variants in sea cucumber (Apostichopus japonicus): evidence from mitochondrial phylogenomic analyses

Color variation in sea cucumber is one of the most crucial traits affecting price and taste in East Asian countries. However, the relationship and taxonomic status of the three color variants are still unclear. We used 14 samples that covered all three color variants and their geographic distributions, to construct the first phylogeny for the color variants based on the complete mitochondrial genome sequence and a number of tree-building methods (maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference (BI)). The divergence times within color variants were estimated by the Bayesian molecular clock approach using the BEAST program. Our results showed that the color variants were not monophyletic in the well-resolved phylogenetic tree, which strongly refuted their separate species status. The molecular dating estimate revealed that the sea cucumber was a young group, which originated in the early Miocene period (22.03 mya) and rapidly diverged after the late Miocene period. It is interesting that individuals within each variant or geographic distribution were not always closely related and thus did not share a common origin. We propose that although they differ in body color, the three color morphs all belong to a single species of Apostichopus japonicus and the historical marine climate and the hydrographic complexity of the ocean currents could be responsible for their present distribution patterns.

Postglacial range shift and demographic expansion of the marine intertidal snail Batillaria attramentaria

To address the impacts of past climate changes, particularly since the last glacial period, on the history of the distribution and demography of marine species, we investigated the evolutionary and demographic responses of the intertidal batillariid gastropod, Batillaria attramentaria, to these changes, using the snail as a model species in the northwest Pacific. We applied phylogeographic and divergence population genetic approaches to mitochondrial COI sequences from B. attramentaria. To cover much of its distributional range, 197 individuals collected throughout Korea and 507 publically available sequences (mostly from Japan) were used. Finally, a Bayesian skyline plot (BSP) method was applied to reconstruct the demographic history of this species. We found four differentiated geographic groups around Korea, confirming the presence of two distinct, geographically subdivided haplogroups on the Japanese coastlines along the bifurcated routes of the warm Tsushima and Kuroshio Currents. These two haplogroups were estimated to have begun to split approximately 400,000 years ago. Population divergence analysis supported the hypothesis that the Yellow Sea was populated by a northward range expansion of a small fraction of founders that split from a southern ancestral population since the last glacial maximum (LGM: 26,000-19,000 years ago), when the southern area became re-submerged. BSP analyses on six geographically and genetically defined groups in Korea and Japan consistently demonstrated that each group has exponentially increased approximately since the LGM. This study resolved the phylogeography of B. attramentaria as a series of events connected over space and time; while paleoceanographic conditions determining the connectivity of neighboring seas in East Asia are responsible for the vicariance of this species, the postglacial sea-level rise and warming temperatures have played a crucial role in rapid range shifts and broad demographic expansions of its populations.