Genetic structure of Onchidium “struma” (Mollusca: Gastropoda: Eupulmonata) from the coastal area of China based on mtCO I

ObjectivesAnopheles sinensis is a predominant malaria vector found throughout the Republic of Korea (ROK). Population genetic analysis can provide insights into the origins and migration patterns of malaria vectors by assessing genetic variation and distribution among populations.MethodsIn this study, we examined the population genetic structure of An. sinensis in the ROK using mitochondrial cytochrome c oxidase subunit I (COI) marker.ResultsA total of 903 specimens of An. sinensis were collected from 9 sampling regions, including malaria-endemic and non-endemic areas. All populations displayed characteristics typical of migrant populations, with high haplotype diversity (Hd) and low nucleotide diversity (Pi). Network analysis identified 124 haplotypes grouped into 2 clusters. Both clusters included haplotypes from malaria-endemic and non-endemic areas. Cluster I shared its most recent common ancestry with Chinese reference sequences, while cluster II had related with Japanese reference sequences. Pairwise genetic distance (FST) analysis indicated generally low genetic differentiation among populations. Furthermore, FST values tended to increase proportionally with geographical distance between regions. Analysis of molecular variance confirmed that individual mosquitoes within the population had a large effect on the overall variation. Neutrality tests using 4 methods (Tajima’s D, Fu’s Fs, Fu and Li’s D, and Fu and Li’s F) yielded negative values, suggesting that An. sinensis populations are expanding in all studied regions.ConclusionThis study characterizes the genetic attributes of An. sinensis in the ROK, providing valuable insights into the biology of this important malaria vector and contributing useful data for malaria control strategies.

BackgroundDespite the morphological characterization established in the 1950s and 1960s, the identity of extant taxa that make up Glossina fuscipes (s.l.) in the Congo remains questionable. Previous claims of overlap between G. fuscipes (believed to be G. f. quanzensis) and G. palpalis palpalis around Brazzaville city further complicate the taxonomic status and population dynamics of the two taxa. This study aimed to determine the phylogenetic relationships between G. fuscipes (s.l.) and G. p. palpalis and to assess genetic variation among G. fuscipes (s.l.) populations in Congo Brazzaville.MethodsWe collected 263 G. fuscipes (s.l.) from northern and central regions, and 65 G. p. palpalis from southern part of the country. The mitochondrial cytochrome c oxidase subunit 1 (cox1) gene was amplified using taxa-specific primer pairs. Sequence data were analyzed in DnaSP and Arlequin to assess the genetic diversity, differentiation and demographic history of G. fuscipes (s.l.) populations.ResultsThe general BLAST analysis yielded a similarity of 99% for G. fuscipes (s.l.) and G. p. palpalis. BLASTn analysis for G. fuscipes (s.l.) showed > 98% identity with GenBank sequences for G. fuscipes (s.l.), with BEMB population showing 100% similarity with G. f. fuscipes. Glossina fuscipes (s.l.) populations showed high haplotype diversity (H = 46, Hd = 0.884), moderate nucleotide diversity ( = 0.012) and moderate (FST = 0.072) to high (FST = 0.152) genetic differentiation. Most of the genetic variation (89.73%) was maintained within populations. The mismatch analysis and neutrality tests indicated recent tsetse population expansions.ConclusionsPhylogenetic analysis revealed minor differences between G. fuscipes (s.l.) and G. p. palpalis. Genetic diversity of G. fuscipes (s.l.) was high in the populations sampled except one. Genetic differentiation ranged from moderate to high among subpopulations. There was a restricted gene flow between G. fuscipes (s.l.) populations in the north and central part of the country. Genetic signatures based on cox1 showed recent expansion and recovery of G. fuscipes (s.l.) populations from previous bottlenecks. To fully understand the species distribution limits, we recommend further studies involving a wider sampling scheme including the swampy Mossaka focus for G. fuscipes (s.l.) and the entire range of G. p. palpalis in South Congo.

BackgroundThe black-lip rock oyster (Saccostrea echinata) has considerable potential for aquaculture throughout the tropics. Previous attempts to farm S. echinata failed due to an insufficient supply of wild spat; however, the prospect of hatchery-based aquaculture has stimulated renewed interest, and small-scale farming is underway across northern Australia and in New Caledonia. The absence of knowledge surrounding the population genetic structure of this species has raised concerns about the genetic impacts of this emerging aquaculture industry. This study is the first to examine population genetics of S. echinata and employs both mitochondrial cytochrome c oxidase subunit I gene (COI) and single nucleotide polymorphism (SNP) markers.ResultsThe mitochondrial COI data set included 273 sequences of 594 base pair length, which comprised 74 haplotypes. The SNP data set included 27,887 filtered SNPs for 272 oysters and of these 31 SNPs were identified as candidate adaptive loci. Data from the mitochondrial COI analyses, supports a broad tropical Indo-Pacific distribution of S. echinata, and showed high haplotype and nucleotide diversities (0.887–1.000 and 0.005–0.008, respectively). Mitochondrial COI analyses also revealed a ‘star-like’ haplotype network, and significant and negative neutrality tests (Tajima’s D = − 2.030, Fu’s Fs = − 25.638, P < 0.001) support a recent population expansion after a bottleneck. The SNP analyses showed significant levels of population subdivision and four genetic clusters were identified: (1) the Noumea (New Caledonia) sample location; (2) the Bowen (north Queensland, Australia) sample location, and remaining sample locations in the Northern Territory, Australia (n = 8) were differentiated into two genetic clusters. These occurred at either side of the Wessel Islands and were termed (3) ‘west’ and (4) ‘east’ clusters, and two migrant individuals were detected between them. The SNP data showed a significant positive correlation between genetic and geographic distance (Mantel test, P < 0.001, R2 = 0.798) and supported isolation by distance. Three candidate adaptive SNPs were identified as occurring within known genes and gene ontology was well described for the sex peptide receptor gene.ConclusionsData supports the existence of genetically distinct populations of S. echinata, suggesting that management of wild and farmed stocks should be based upon multiple management units. This research has made information on population genetic structure and connectivity available for a new aquaculture species.

The oak longhorned beetle (OLB), Massicus raddei (Blessig, 1872) (Coleoptera: Cerambycidae), is widely distributed in Asia (China, the Korean Peninsula, Japan, Vietnam and the Russian Far‐East), but pest outbreaks have occurred only in Liaoning Province and Jilin Province of China. In order to explore possible mechanisms of local population outbreaks and characterize the genetic diversity and genetic structure of M. raddei across its range in China, three mitochondrial genes (COI, Cytb, and COII) were sequenced and analyzed for seven M. raddei populations collected from six provinces in China. From these different populations, we found a high haplotype and nucleotide diversity. Haplotype networks and phylogenetic analyses both demonstrate apparent genetic diversification between SC (southern China) and NC (northern China) population groups. A set of 21 pairwise comparisons for Fst (pairwise fixation indices) and Nm (genetic flow index) showed significant genetic differentiation and limited gene flow except for two pairs, Shandong (SD) and Liaoning (LN), and Anhui (AH) and Henan (HN). This pattern suggested that the periodic outbreak of the LN population could not be attributed to the absence of genetic flow with other spatial populations and that regional environmental factors might be responsible. AMOVA (Analysis of molecular variance) showed that the greater molecular genetic variation was among populations. Based on Tajima's D statistic, Fu's Fs, and the mismatch distribution test, we determined that the seven populations sampled were stable and had not experienced any recent population expansion. The fact that all the sampled populations showed only unique haplotypes and lacked shared or ancestral haplotypes, as well as the nonstar‐like distribution of haplotype network for concatenated genes, collectively provided powerful evidence of the stable and isolated nature of most populations. The high genetic differentiation and spatial genetic structuring among populations are both likely related to the beetle's moderate flight capacity, regional variation in host tree species and microclimate, as well as the geographic distance between sampling sites.

Aim: To investigate genetic diversity, gene flow and demographic history of frigate tuna (Auxis thazard) populations found in Tanzanian marine waters.&#x0D; Study Design: The study used a descriptive research design whereby fish samples were randomly collected from four locations and the genetic variation within and among the four populations analyzed using mitochondrial DNA (mtDNA) control region.&#x0D; Place and Duration of the Study: Fish samples were collected from landing sites in Tanga, Dar es Salaam, Mtwara and Zanzibar, Tanzania. The study was conducted between July 2020 and June 2021.&#x0D; Methodology: A total of 100 frigate tuna were randomly sampled from small-scale fishermen at the landing sites of Dar-es-Salaam (20), Tanga (30), Mtwara (30), and Zanzibar (20). For each fish, 50 g muscle tissue was obtained and put in a vial containing 95% ethanol. DNA was extracted from the muscle using a commercial DNA Kit (Quick-DNATM Miniprep Plus Kit, Zymo Research Corp.) according to the instructions of the manufacturer and a fragment of 432 bp of the mtDNA control region was amplified and sequenced using ABI PRISIM™ 3100 Genetic Analyzer (Applied Biosystems). Haplotype and nucleotide diversity, gene flow and historic demographic were estimated from 92 fish samples.&#x0D; Results: A total of 88 haplotypes were identified in all fish samples. The highest haplotype diversity was found in Zanzibar (1.000 ± 0.017) and Mtwara (1.000 ± 0.010) populations while the lowest was observed in Tanga population (0.992 ± 0.012). Tanga population had the highest nucleotide diversity (0.078 ± 0.018) while Dar es Salaam had the lowest (0.016 ± 0.009). The highest genetic differentiation (FST) was found between Tanga and Dar-es-Salaam (0.178) and the lowest was observed between Mtwara and Zanzibar (0.016). The genetic distances between pairs of populations were small. The phylogenetic tree revealed two main clusters. Cluster 1 which consisted of nine haplotypes was dominated by Tanga population with seven haplotypes while the remaining two haplotypes were from Mtwara and the reference sequences of Euthynnus affinis (Kawakawa tuna). Cluster II had 84 haplotypes of individuals from all four populations, with no population specific subcluster. The number of immigrants per generation was highest between Mtwara and Zanzibar (Nm=18.310) and lowest between Tanga and Dar-es-Salaam (Nm=1.180). The neutrality test indicated negative values, suggesting a recent population expansion.&#x0D; Conclusion: There is high genetic diversity within the populations, but there is no significant genetic differentiation among the four frigate tuna populations, suggesting that the four populations comprise a single panmictic population.

Genetic diversity and population structure of Oncomelania hupensis in Sichuan Province, China: implications for schistosomiasis control.

PDF HTML阅读 XML下载 导出引用 引用提醒 基于COI序列的长江中上游鲢6个地理群体遗传多样性分析 DOI: 作者: 作者单位: 1. 中国水产科学研究院长江水产研究所, 湖北 武汉 430223;2. 农业农村部水生动物基因组学重点实验室, 湖北 武汉 430223 作者简介: 沙航(1991-),男,硕士,研究方向为水产动物种质资源与遗传育种.E-mail:ikriss@163.com 通讯作者: 中图分类号: S917 基金项目: 科技部科技基础性工作专项（2013FY110700）；中国水产科学研究院基本科研业务费项目（2014A11，2016HY-JC03）；现代农业产业技术体系建设专项（CARS-46-01）. Genetic diversity of six silver carp (Hypophthalmichthys molitrix) geographical populations based on mitochondrial COI sequences Author: Affiliation: 1. Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China;2. Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, Wuhan 430223, China Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:为了对长江中上游鲢（）种质资源现状进行监测和评价，本研究利用线粒体细胞色素C氧化酶I（cytochrome c oxidase subunit I）基因（COI）对长江中上游宜宾、忠县、万州、石首、监利、湘江6个鲢群体进行了遗传多样性分析。结果表明，在648 bp的COI序列中共检测到42个变异位点，其中单变异位点14个，简约信息位点28个。6个群体123个个体共定义了26个单倍型，单倍型多样性为0.0476~0.0945，核苷酸多样性为0.00196~0.00982。6个鲢群体总体遗传多样性丰富，万州群体单倍型多样性和核苷酸多样性均最高，忠县群体单倍型多样性最低，核苷酸多样性最低的为石首群体。遗传变异主要来自群体内个体间，单倍型网络图和系统进化树显示各群体的单倍型没有形成明显的地理格局。此外，上游宜宾群体和万州群体与中游的石首、监利和湘江群体具有明显的遗传分化，中游的监利群体与石首群体和湘江群体也有一定的遗传分化，上游群体和中游群体应该分属于长江水系两个不同的种群。 Abstract:The silver carp (), one of the four major Chinese carps, is widely distributed in the Yangtze, Pearl, and Heilongjiang River Basins of China. The wild silver carp populations in the Yangtze River, with an excellent production performance, is an important germplasm resource for artificial farming and breeding. Because of overfishing, habitat fragmentation, and water pollution, the natural carp populations have been continuously declining in recent years. The basic genetic background analysis of the silver carp would be theoretically and practically important for the conservation of germplasm resources and genetic improvement. In this study, mitochondrial cytochrome C oxidase subunit I gene (COI) was sequenced to determine the genetic diversity and variation of six geographical silver carp populations:Yibin, Zhongxian, Wanzhou, Shishou, Jianli, and Xiangjiang. The amplified fragment was 648 bp in length, and a total of 26 haplotypes were defined among 123 sequences of COI from the six silver carp populations. The haplotype and nucleotide diversity index of the six populations ranged from 0.0476 to 0.0945, and from 0.00196 to 0.00982, respectively. The six groups exhibited a high genetic diversity, of which the Wanzhou population showed the highest haplotype and nucleotide diversities; the lowest haplotype and nucleotide diversities were observed in the Zhongxian and Shishou populations, respectively. The molecular variance (AMOVA) analysis showed that the variation within populations (accounting for 88.72%) was the main source of variation, and only 11.28% of the variation was found among the groups. The haplotype network was radial, centering on the main haplotype. The neighbor-joining phylogenetic tree of haplotypes based on genetic distances were inconsistent with their geographical distances. According to the differentiation index (, there were high differences between the Yinbin, Wanzhou, and 3 populations from the middle reach ( < 0.05); meanwhile, the Jianli population showed a significant differentiation from the Shishou and Xiangjiang populations ( < 0.01). The results revealed that the upper-and middle-reach populations should have originated from different populations in the Yangtze River. This study could provide useful basic data for the scientific protection, and reasonable and sustainable utilization of this germplasm resource in the Yangtze River Basin. 参考文献 相似文献 引证文献

Elevational and climatic gradients shape the genetic structure of a typical Tibetan loach Triplophysa stenura (Cypriniformes: Nemacheilidae)

BackgroundStrongyllodes variegatus (Fairmaire) is a major insect pest of oilseed rape in China. Despite its economic importance, the contribution of its population genetics in the development of any suitable protection control strategy for the management of oilseed rape crops is poorly studied. It is a much urgent need to prevent its spread to the rest of the world.ResultsUsing the sequences of mitochondrial DNA cytochrome c oxidase subunit I (COI) and cytochrome b (Cytb) as genetic markers, we analyzed the population genetic diversity and structure of 437 individuals collected from 15 S. variegatus populations located in different oilseed rape production areas in China. In addition, we estimated the demographic history using neutrality test and mismatch distribution analysis. The high level of genetic diversity was detected among the COI and Cytb sequences of S. variegatus. The population structure analyses strongly suggested three distinct genetic and geographical regions in China with limited gene flow. The Mantel test showed that the genetic distance was greatly influenced by the geographical distance. The demographic analyses showed that S. variegatus had experienced population fluctuation during the Pleistocene Epoch, which was likely to be related to the climatic changes.ConclusionOverall, these results demonstrate that the strong genetic structure of S. variegatus populations in China, which is attributed by the isolation through the geographical distance among populations, their weak flight capacity and subsequent adaptation to the regional ecological conditions.

In the terrestrial environment, endemic species and isolated populations of widespread species have the highest rates of extinction partly due to their low genetic diversity. To determine if this pattern holds in the marine environment, we examined genetic diversity in endemic coral reef angelfishes and isolated populations of widespread species. Specifically, this study tested the prediction that angelfish (genus: Centropyge) populations at Christmas and Cocos Islands have low genetic diversity. Analyses of a 436 base pair fragment of the mtDNA control region revealed that the endemic C. joculator exhibited high haplotype (h &gt; 0.98 at both locations) and nucleotide (Christmas p% = 3.63, Cocos p% = 9.99) diversity. Similarly, isolated populations of widespread angelfishes (C. bispinosa and C. flavicauda) had high haplotype (h &gt; 0.98) and nucleotide (p% = 2.81 and p% = 5.78%, respectively) diversity. Therefore, in contrast to terrestrial patterns, endemic and isolated populations of widespread angelfishes do not have low genetic diversity, rather their haplotype and nucleotide diversities were among the highest reported for marine fishes. High genetic diversity should reduce extinction risk in these species as it could provide the evolutionary potential to adapt to the rapidly changing environmental conditions forecast for coral reefs.

Demographic inference from the mt-DNA COI gene and wing geometry of Culex gelidus (Diptera: Culicidae), an important vector of Japanese encephalitis in Thailand

Species belonging to the genus Caranx, locally known as “talakitok,” belong to the economically important fish in the Philippines. The popularity of these species makes them prone to overexploitation, which may result to a decline in their population in the wild. Despite these circumstances, stock assessment and population genetic variation studies are scarce. In this study, three species from this genus (C. ignobilis, C. papuensis, C. ignobilis) from the Batangas region were subjected to genetic diversity and population structure analyses using the cytochrome b (cyt b) gene of the mitochondrial DNA (mtDNA) to address these information gaps. High haplotype and high nucleotide diversity were noted in C. ignobilis, which may indicate that the population is still large and stable. However, C. papuensis and C. sexfasciatus populations had a low nucleotide diversity and high haplotype diversity, which could mean a possible genetic bottleneck in the recent past. Likewise, each of these three species showed no genetic differentiation between marine and freshwater specimens, which can be attributed to their life history and biology. Analysis of molecular variance (AMOVA) revealed weak genetic structure, indicated by low percentage value between populations. Based on neutrality tests and mismatch distribution analysis, the three species may have possibly undergone demographic expansion. This study provides the genetic profile of Caranx species found in the Batangas region before the recent Taal Volcano eruption (January 2020), which can be used to investigate the effects of this eruption on the population of this species. Likewise, results obtained from this study served as preliminary data for the population genetics of Caranx spp. found in Batangas, Philippines.

Spilostethus pandurus is a phytophagous insect widely distributed across Asia, Europe, and Africa, yet its genetic variation remains poorly understood. This study presents the first comprehensive analysis of the genetic diversity and structure of S. pandurus in Thailand using mitochondrial cytochrome c oxidase subunit 1 (CO1) sequences from 202 individuals across 27 localities. A total of 58 haplotypes were identified, with high haplotype and nucleotide diversity observed, suggesting substantial genetic variation. The haplotype network revealed a star-like topology, indicating recent population expansion or ongoing gene flow. Neutrality tests and mismatch distribution analyses showed no strong signal of recent demographic expansion. Phylogenetic analysis confirmed that all Thai specimens clustered within a well-supported S. pandurus clade along with sequences from India, Namibia, and Europe. Analysis of Molecular Variance (AMOVA) revealed significant genetic differentiation among four continental groups, indicating that geographic isolation and restricted gene flow have shaped genetic divergence at a broad biogeographic scale. Further research using highly polymorphic nuclear markers is recommended to better resolve the population structure and evolutionary history of S. pandurus in Thailand and beyond.

The freshwater sculpin Cottus koreanus is endemic to the Korean Peninsula and has a fluvial life history. However, its population has been greatly reduced and it is now listed as an endangered class II species. To obtain important information for its conservation, we examine the genetic diversity, population structure, and demographic history of C. koreanus through mitochondrial cytochrome c oxidase subunit I (CO1) gene sequence analysis. We analyzed the CO1 gene sequences of 430 individuals of C. koreanus from 23 populations in South Korea. In all, 32 haplotypes were defined by 124 variable nucleotide sites, of which 28 were unique haplotypes not shared with other regional populations. All sampled populations had high haplotype diversity (Hd = 0.941) and low nucleotide diversity (π = 0.0146). Median-joining network analysis identified two divergent clusters: cluster I that had unique haplotype patterns assigned to each population and cluster II that had a star-like pattern. Each was supported by pairwise FST values and hierarchical analysis of molecular variance. The results of the mismatch distribution, goodness-of-fit test, and extended Bayesian skyline plot analysis showed that cluster I has experienced a gradual population expansion since the last glacial maximum, while cluster II experienced a sudden one. The results of neutrality testing supported the results for cluster II but the signal was weak. C. koreanus inhabits the upper reaches of rivers and has extremely low dispersal ability, resulting in unique genetic structure patterns among populations. Therefore, all populations should be managed and conserved separately.

The genetic diversity and population history of the Asian shore crab, Hemigrapsus sanguineus, were investigated with a nucleotide sequence analysis of 536 base pairs (bp) of the mitochondrial cytochrome c oxidase subunit I gene (COI) in 111 samples collected from four populations in Korea and one in Japan. In total, 28 haplotypes were defined by 27 variable nucleotide sites in the COI region examined. The observed haplotypes had a shallow haplotype genealogy and no geographical associations. Most of the populations had high haplotype diversity (0.656–0.788) and low nucleotide diversity (0.00165–0.00244), and significant negative values for Fu's F S , suggesting rapid and recent population growth from an ancestral population and sudden population expansion. The pairwise fixation indices (F ST) estimated with the exact test and the migration rates indicate that substantial gene flow occurs among these populations as a result of sea currents, except between the Yellow Sea coast of Korea (BUA) and the Pacific Ocean coast of Japan (JPA). These two populations (BUA and JPA) showed significant genetic differentiation and low migration rate.