Population Genetic Structure and Demographic History of Atrina pectinata Based on Mitochondrial DNA and Microsatellite Markers

The pen shell, Atrina pectinata, is one of the commercial bivalves in East Asia and thought to be recently affected by anthropogenic pressure (habitat destruction and/or fishing pressure). Information on its population genetic structure is crucial for the conservation of A. pectinata. Considering its long pelagic larval duration and iteroparity with high fecundity, the genetic structure for A. pectinata could be expected to be weak at a fine scale. However, the unusual oceanography in the coasts of China and Korea suggests potential for restricted dispersal of pelagic larvae and geographical differentiation. In addition, environmental changes associated with Pleistocene sea level fluctuations on the East China Sea continental shelf may also have strongly influenced historical population demography and genetic diversity of marine organisms. Here, partial sequences of the mitochondrial Cytochrome c oxidase subunit I (COI) gene and seven microsatellite loci were used to estimate population genetic structure and demographic history of seven samples from Northern China coast and one sample from North Korea coast. Despite high levels of genetic diversity within samples, there was no genetic differentiation among samples from Northern China coast and low but significant genetic differentiation between some of the Chinese samples and the North Korean sample. A late Pleistocene population expansion, probably after the Last Glacial Maximum, was also demonstrated for A. pectinata samples. No recent genetic bottleneck was detected in any of the eight samples. We concluded that both historical recolonization (through population range expansion and demographic expansion in the late Pleistocene) and current gene flow (through larval dispersal) were responsible for the weak level of genetic structure detected in A. pectinata.     

Phylogeography of Quercus variabilis Based on Chloroplast DNA Sequence in East Asia: Multiple Glacial Refugia and Mainland-Migrated Island Populations

The biogeographical relationships between far-separated populations, in particular, those in the mainland and islands, remain unclear for widespread species in eastern Asia where the current distribution of plants was greatly influenced by the Quaternary climate. Deciduous Oriental oak (Quercus variabilis) is one of the most widely distributed species in eastern Asia. In this study, leaf material of 528 Q. variabilis trees from 50 populations across the whole distribution (Mainland China, Korea Peninsular as well as Japan, Zhoushan and Taiwan Islands) was collected, and three cpDNA intergenic spacer fragments were sequenced using universal primers. A total of 26 haplotypes were detected, and it showed a weak phylogeographical structure in eastern Asia populations at species level, however, in the central-eastern region of Mainland China, the populations had more haplotypes than those in other regions, with a significant phylogeographical structure (N _ST =0.751> G _ST =0.690, P<0.05). Q. variabilis displayed high interpopulation and low intrapopulation genetic diversity across the distribution range. Both unimodal mismatch distribution and significant negative Fu’s F_S indicated a demographic expansion of Q. variabilis populations in East Asia. A fossil calibrated phylogenetic tree showed a rapid speciation during Pleistocene, with a population augment occurred in Middle Pleistocene. Both diversity patterns and ecological niche modelling indicated there could be multiple glacial refugia and possible bottleneck or founder effects occurred in the southern Japan. We dated major spatial expansion of Q. variabilis population in eastern Asia to the last glacial cycle(s), a period with sea-level fluctuations and land bridges in East China Sea as possible dispersal corridors. This study showed that geographical heterogeneity combined with climate and sea-level changes have shaped the genetic structure of this wide-ranging tree species in East Asia.     

Phylogeography of the Asian lesser white-toothed shrew, <Emphasis Type="Italic">Crocidura shantungensis</Emphasis>, in East Asia: role of the Korean Peninsula as refugium for small mammals

Many peninsulas in the temperate zone played an important role as refugia of various flora and fauna, and the southern Korean Peninsula also served as a refugium for many small mammals in East Asia during the Pleistocene. The Asian lesser white-toothed shrew, Crocidura shantungensis, is a widely distributed species in East Asia, and is an appropriate model organism for exploring the role of the Korean Peninsula as a refugium of small mammals. Here, we investigated phylogenetic relationships and genetic diversity based on the entire sequence of the mitochondrial cytochrome b gene (1140 bp). A Bayesian tree for 98 haplotypes detected in 228 C. shantungensis specimens from East Asia revealed the presence of three major groups with at least 5 subgroups. Most haplotypes were distributed according to their geographic proximity. Pairwise F_ST’s and analysis of molecular variance (AMOVA) revealed a high degree of genetic differentiation and variance among regions as well as among populations within region, implying little gene flow among local populations. Genetic evidence from South Korean islands, Jeju-do Island of South Korea, and Taiwan leads us to reject the hypothesis of recent population expansion. We observed unique island-type genetic characteristics consistent with geographic isolation and resultant genetic drift. Phylogeographic inference, together with estimates of genetic differentiation and diversity, suggest that the southern most part the Korean Peninsula, including offshore islands, played an important role as a refugium for C. shantungensis during the Pleistocene. However, the presence of several refugia on the mainland of northeast Asia is also proposed.     

中国近海银鲳线粒体COⅠ基因序列变异分析

对采自黄海、东海和南海的7个银鲳群体的线粒体COⅠ基因序列变异进行分析,研究银鲳的遗传多样性、遗传结构和群体历史动态。在所分析的111个个体中检测到16个单倍型。7个群体呈现出高的单倍型多样性（h=0.564～0.688） 和低的核苷酸多样性（π=0.001～0.003）。单倍型遗传学关系、两两群体间的F_ST值和分子方差分析均表明中国近海7个银鲳群体间的遗传分化不显著。中性检验和核苷酸不配对分析均表明中国近海银鲳经历了晚更新世的群体扩张事件,扩张时间约为6.0×10⁴～1.04×10⁵ 年前。研究结果表明,银鲳的卵和幼体具有较强的扩散能力、中国近海的海洋环流以及近期的群体扩张可能是造成中国近海银鲳群体在线粒体COⅠ基因序列上存在较高的遗传同质性的原因。     

Molecular data and ecological niche modelling reveal the Pleistocene history of a semi‐aquatic bug (Microvelia douglasi douglasi) in East Asia

This study investigated the Pleistocene history of a semi‐aquatic bug, Microvelia douglasi douglasi Scott, 1874 (Hemiptera: Veliidae) in East Asia. We used M. douglasi douglasi as a model species to explore the effects of historical climatic fluctuations on montane semi‐aquatic invertebrate species. Two hypotheses were developed using ecological niche models (ENMs). First, we hypothesized that M. douglasi douglasi persisted in suitable habitats in southern Guizhou, southern Yunnan, Hainan, Taiwan and southeast China during the LIG. After that, the populations expanded (Hypothesis 1). As the spatial prediction in the LGM was significantly larger than in the LIG, we then hypothesized that the population expanded during the LIG to LGM transition (Hypothesis 2). We tested these hypotheses using mitochondrial data (COI+COII) and nuclear data (ITS1 + 5.8S+ITS2). Young lineages, relatively deep splits, lineage differentiation among mountain ranges in central, south and southwest China and high genetic diversities were observed in these suitable habitats. Evidence of mismatch distributions and neutrality tests indicate that a population expansion occurred in the late Pleistocene. The Bayesian skyline plot (BSP) revealed an unusual population expansion that likely happened during the cooling transition between LIG and LGM. The results of genetic data were mostly consistent with the spatial predictions from ENM, a finding that can profoundly improve phylogeographic research. The ecological requirements of M. douglasi douglasi, together with the geographical heterogeneity and climatic fluctuations of Pleistocene in East Asia, could have shaped this unusual demographic history. Our study contributes to our knowledge of semi‐aquatic bug/invertebrate responses to Pleistocene climatic fluctuations in East Asia.     

Genetic variation and population structure of swimming crab (Portunus trituberculatus) inferred from mitochondrial control region

Genetic variation and population structure in Portunus trituberculatus along the coast of China were revealed according to 617 bp of mitochondrial DNA control region. 90 polymorphic sites defined 53 distinct haplotypes, showing a moderately high diversity among 72 individuals sampled from eight localities. Neighbor-joining tree, statistics analyses of gene flow and genetic differentiation index indicated two populations from Beihai and Laizhou had differentiated. The population from Yingkou, Dandong, Laizhou and Beihai had smaller genetic diversity compared to that from Ningbo, Lianyungang, Qingdao and Japan according to the genetic distance. And mantel test showed significant positive correlation between genetic distance and geographic distance for P. trituberculatus. TCS parsimony network suggested that all the animals sampled were probably the result of recent divergence from a common ancestral haplotype but for Laizhou population. Moreover, the haplotype distribution appeared to correlate with a recent colonization followed by localized genetic differentiation. Mismatch distribution results suggested that Ningbo, Yingkou, Qingdao, Lianyungang and Japan populations, particularly Dandong population had experienced a sudden demographic or spatial expansion. The Pleistocene glaciations might contribute to this process.     

Genetic structure and demographic history of Lymantria dispar (Linnaeus, 1758) (Lepidoptera: Erebidae) in its area of origin and adjacent areas

We analyzed the population genetic structure and demographic history of 20 Lymantria dispar populations from Far East Asia using microsatellite loci and mitochondrial genes. In the microsatellite analysis, the genetic distances based on pairwise F_ST values ranged from 0.0087 to 0.1171. A NeighborNet network based on pairwise F_ST genetic distances showed that the 20 regional populations were divided into five groups. Bayesian clustering analysis (K = 3) demonstrated the same groupings. The populations in the Korean Peninsula and adjacent regions, in particular, showed a mixed genetic pattern. In the mitochondrial genetic analysis based on 98 haplotypes, the median‐joining network exhibited a star shape that was focused on three high‐frequency haplotypes (Haplotype 1: central Korea and adjacent regions, Group 1; Haplotype 37: southern Korea, Group 2; and Haplotype 90: Hokkaido area, Group 3) connected by low‐frequency haplotypes. The mismatch distribution dividing the three groups was unimodal. In the neutral test, Tajima's D and Fu's FS tests were negative. We can thus infer that the Far East Asian populations of L. dispar underwent a sudden population expansion. Based on the age expansion parameter, the expansion time was inferred to be approximately 53,652 years before present (ybp) for Group 1, approximately 65,043 ybp for Group 2, and approximately 76,086 ybp for Group 3. We propose that the mixed genetic pattern of the inland populations of Far East Asia is due to these expansions and that the inland populations of the region should be treated as valid subspecies that are distinguishable from other subspecies by genetic traits.     

Phylogeography and demographic history of Gyrodactylus konovalovi (Monogenoidea: Gyrodactylidae), an ectoparasite on the East Asia Amur minnow (Cyprinidae) in Central China

Gyrodactylus konovalovi is an ectoparasite on the Amur minnow (Rhynchocypris lagowskii) that is widely distributed in the cold fresh waters of East Asia. In the present study, the phylogeography and demographic history of G. konovalovi and the distribution of its host in the Qinling Mountains are examined. A total of 79 individual parasites was sequenced for a 528 bp region of the mitochondrial NADH dehydrogenase subunit 5 (ND5) gene, and 25 haplotypes were obtained. The substitution rate (dN/dS) was 0.068 and indicated purifying selection. Haplotype diversity (h) and nucleotide diversity (π) varied widely in the Qinling Mountains. Phylogenetic trees based on Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods and network analysis revealed that all haplotypes were consistently well‐supported in three different lineages, indicating a significant geographic distribution pattern. There was a significant positive correlation between genetic differentiation (F_st) and geographic distance. The results of mismatch distribution, neutrality test and Bayesian skyline plot analyses showed that whole populations underwent population contraction during the Pleistocene. Based on the molecular clock calibration, the most common ancestor was estimated to have emerged in the middle Pleistocene. Our study suggests for the first time that a clearly phylogeography of G. konovalovi was shaped by geological events and climate fluctuations, such as orogenesis, drainage capture changes, and vicariance, during the Pleistocene in the Qinling Mountains.     

Genetic diversification of the Kanehira bitterling Acheilognathus rhombeus inferred from mitochondrial DNA,with comments on the phylogenetic relationship with its sister species Acheilognathus barbatulus

The Kanehira bitterling, Acheilognathus rhombeus, is a freshwater fish, discontinuously distributed in western Japan and the Korean Peninsula. Unusually among bitterling it is an autumn-spawning species and shows developmental diapause. Consequently, the characterization of its evolutionary history is significant not only in the context of the fish assemblage of East Asia, but also for understanding life-history evolution. This study aimed to investigate the phylogeography of A. rhombeus and its sister species Acheilognathus barbatulus, distributed in China, using a mitochondrial analysis of the ND1 gene from 311 samples collected from 50 localities in Japan and continental Asia. Phylogenetic analysis revealed that A. barbatulus is included in A. rhombeus and genetically closer to Japanese A. rhombeus than to Korean A. rhombeus. Divergence of Korean A. rhombeus and A. barbatulus from Japanese A. rhombeus was estimated to be from the late Pliocene (3.44 Mya) and the early Pleistocene (1.98 Mya), respectively. Each event closely coincided with the time of the Japan Sea opening. Japanese A. rhombeus comprised seven lineages: three in Honshu and four in Kyushu. One lineage in central Kyushu was genetically closer to the Honshu lineages than to other lineages in northern Kyushu. Divergence of Japanese lineages was estimated to be from the early to middle Pleistocene (0.55–0.93 Mya), during a period of geological and paleoclimatic change, including volcanic activity. Population expansion in the late Pleistocene (<0.10 Ma) was suggested in many of the lineages, which accords with other freshwater fishes. Biogeographically the ancestral A. rhombeus/A. barbatulus was likely to have repeatedly colonized Japan from the continent through land bridges in the late Pliocene and the early Pleistocene. However, the close genetic relationship between Japanese A. rhombeus and A. barbatulus suggests another possibility, with the second colonization occurring in reverse, from Japan to China. The small genetic distance between them indicates that the colonization occurred later than colonization events of other freshwater fishes, including other bitterling species.     

Genetic Variation Analysis of Mugil cephalus in China Sea Based on Mitochondrial COI Gene Sequences

In this study, genetic diversity and population genetic structure of flathead grey mullet, Mugil cephalus, among four China Sea populations were investigated by COI sequences. All the populations studied had high values of haplotype and nucleotide diversity, except for the Yellow Sea population. In the phylogenetic tree, these haplotypes clustered in two groups, one for the populations from the Bohai and East China seas, and the other from the Yellow and South China seas. Analysis of molecular variance indicated that the northern populations (Bohai and East China) had lower genetic divergence (0.0725, P > 0.05) than that of the southern population (South China) (0.4530-0.6827, P < 0.001), suggesting that two distinct genetic groups exist in Chinese waters. Tests of neutral evolution and mismatch distribution indicated that no historical demographic expansion occurred in these populations. The results provide new information for genetic assessment, fishery management, and conservation of this species.