Mitochondrial DNA analyses of the golden snapper, Lutjanus johnii (Bloch, 1792), revealed two distinct population stocks in the South China Sea and the Strait of Malacca.

In this study, we analyzed mitochondrial COI gene sequences to reveal genetic diversity, population structure and demographic history of two Bangladeshi (BD) populations (SB and CK) of the orange mud crab Scylla olivacea of the Northern Bay of Bengal (BoB), and compared these two with other four populations in the Northern Indian Ocean region (Arabian Sea, Andaman Sea and Malacca strait) and South China Sea. For all of the populations, nucleotide diversities were low (0.005–0.01) while the haplotype diversities were as high as 0.70–0.96, indicating that the S. olivacea has undergone a recent population expansion after experiencing bottleneck. The pairwise population statistics (FST) revealed that no genetic variation was made between SB and CK populations of BD in BoB. However, these two BoB populations showed separate genetic structure with each of the Andaman Sea (Myanmar coast, MM) and Malacca strait (West coast of Malaysia, MS) populations. On the other hand, two BoB populations did not form separate genetic structure from the population of Arabian Sea (AS). Larval dispersal-based migration by the East and West India coastal currents probably caused this genetic homogeneity between BoB and AS populations.The MM population had separate genetic structure from all of the populations studied in the present study. The Hierarchical analysis of molecular variance (AMOVA) revealed four large population groups of S. olivacea within its distribution range in the Indo-west Pacific region namely, Arabian Sea, Bay of Bengal, Andaman Sea and South China Sea groups. Some geographical barriers (e.g. Indian peninsula, Andaman and Nicobar Islands) along with seasonally formed marine gyres in the Andaman Sea are responsible for separate genetic structure among different populations and also for establishing four population groups. Star-shaped patterns of haplotype network and neutrality test corroboratethe recent population expansion of all populations except MM and CK. Mismatch distribution analysis reveals that the demographic expansion of the species started during the late Pleistocene period approximately 125,000 to 365,000 years ago. These results will help to establish the conservation and management strategy for orange mud crab in the Northern Indian Ocean region including the Bay of Bengal.
 J. of Sci. and Tech. Res. 4(1): 101-118, 2022

BackgroundMangrove forests are ecologically important but globally threatened intertidal plant communities. Effective mangrove conservation requires the determination of species identity, management units, and genetic structure. Here, we investigate the genetic distinctiveness and genetic structure of an iconic but yet taxonomically confusing species complex Rhizophora mucronata and R. stylosa across their distributional range, by employing a suite of 20 informative nuclear SSR markers.ResultsOur results demonstrated the general genetic distinctiveness of R. mucronata and R. stylosa, and potential hybridization or introgression between them. We investigated the population genetics of each species without the putative hybrids, and found strong genetic structure between oceanic regions in both R. mucronata and R. stylosa. In R. mucronata, a strong divergence was detected between populations from the Indian Ocean region (Indian Ocean and Andaman Sea) and the Pacific Ocean region (Malacca Strait, South China Sea and Northwest Pacific Ocean). In R. stylosa, the genetic break was located more eastward, between populations from South and East China Sea and populations from the Southwest Pacific Ocean. The location of these genetic breaks coincided with the boundaries of oceanic currents, thus suggesting that oceanic circulation patterns might have acted as a cryptic barrier to gene flow.ConclusionsOur findings have important implications on the conservation of mangroves, especially relating to replanting efforts and the definition of evolutionary significant units in Rhizophora species. We outlined the genetic structure and identified geographical areas that require further investigations for both R. mucronata and R. stylosa. These results serve as the foundation for the conservation genetics of R. mucronata and R. stylosa and highlighted the need to recognize the genetic distinctiveness of closely-related species, determine their respective genetic structure, and avoid artificially promoting hybridization in mangrove restoration programmes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0331-3) contains supplementary material, which is available to authorized users.

Genetic diversity and population connectivity of the Asian green mussel Perna viridis in South China Sea, inferred from mitochondria DNA markers

Eleutheronema rhadinum is a potential commercial fisheries species and is subject to intense exploitation in China. Knowledge on the population structure of E. rhadinum in Chinese coastal waters, which is important for sustainable exploitation and proper resource management, is lacking. In the present study, the genetic diversity and population structure of E. rhadinum were evaluated using a 564-base pair fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of 76 specimens were collected from three localities around the East (Qidong and Zhoushan) and South China Seas (Zhuhai). Among these individuals, nine polymorphic sites were detected and 11 distinct haplotypes were defined. High levels of haplotype diversity (h =0.759±0.035) and low levels of nucleotide diversity (π= 0.001 98±0.003 26) were observed in these populations. Hierarchical analysis of molecular variance (AMOVA) indicated that 96.72% of the genetic variation occurred within the populations, whereas 3.28% occurred among populations. No significant genealogical branches or clusters were recognized on the neighbor-joining tree. Intra-group variation among populations was significant (φ st=0.032 85, P<0.01). These results suggest that E. rhadinum populations in the East and South China Seas have developed divergent genetic structures. Tests of neutral evolution and mismatch distribution suggest that E. rhadinum may have experienced a population expansion. The present study provides basic information for the conservation and sustainable exploitation of this species.

Understanding the genetic structure and diversity of marine fish is crucial for a sustainable management program. We examined the genetic diversity and historical demographics of the yellowfin snapper, Lutjanus xanthopinnis Iwatsuki, Tanaka et Allen, 2015, in the coastal waters of east Peninsular Malaysia which is bordered by the southern part of the South China Sea using the mitochondrial genes (mtDNA) D-loop and Cytochrome b (Cyt-b). A total of 99 (D-loop) and 78 (Cyt-b) specimens of L. xanthopinnis were successfully sequenced from six locations within the range of species distribution along the Malaysian South China Sea. In the presently reported study, the lack of genetic differentiation among populations can be attributed to historical demographic events, eggs and planktonic larvae’ ability to disperse, spawning patterns, and the absence of physical barriers in the geographical landscape. Maximum likelihood gene trees demonstrated that the populations under study had limited structuring and formed a panmictic population that lacks support for internal clades. The AMOVA (Analysis of Molecular Variance) and population pairwise ФST values indicated high genetic exchange between the study areas. A high level of haplotype diversity (D-loop: 0.948–1.000; Cyt-b: 0.542–0.928), low nucleotide diversity (D-loop: 0.0095–0.0159; Cyt-b: 0.0022–0.0049) and starlike haplotype network indicates a recent expansion of L. xanthopinnis populations in Malaysian South China Sea. However, neutrality and goodness of fit tests revealed non-significant values. Furthermore, the BSP (Bayesian skyline plot) analysis estimated population expansion events during the late Pleistocene. During this epoch, the fluctuation in sea level may have led to an increase in the abundance of resources and favorable habitats for the yellowfin snapper. The presently reported findings could initiate efficient management strategies for L. xanthopinnis along the coastal areas of the Malaysian South China Sea and other nearby nations that share the same waterways.

PDF HTML阅读 XML下载 导出引用 引用提醒 南海鸢乌贼的遗传差异: 种群分化还是种间分化 DOI: 作者: 作者单位: 中国水产科学研究院南海水产研究所, 农业农村部外海渔业开发重点实验室, 广东 广州 510300 作者简介: 李敏(1984-),男,博士,副研究员,从事海洋生物多样性和保护研究.E-mail:limin@scsfri.ac.cn 通讯作者: 中图分类号: S931 基金项目: 国家重点研发计划项目（2018YFC1406500）；农业农村部财政专项（NFZX2018）；广东省自然科学基金项目（2014A030310177）；国家重点基础研究发展计划项目（2014CB441500）. Genetic differentiation of the purpleback flying squid, Sthenoteuthis oualaniensis, in the South China Sea:population or species divergence Author: Affiliation: Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture and Rural Affairs;South China Sea Fisher-ies Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, 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:利用线粒体ND2、COI和16S rDNA序列，对2012年9月至2015年9月采自南海的鸢乌贼（）样本进行了种群遗传结构的分析。系统发育关系显示鸢乌贼中型群和微型群各自形成了单系群分支，而分支内没有形成与地理群体或季节群体对应的支系。分子方差分析同样表明，地理群体或季节群体之间不存在明显的遗传分化，而中型群和微型群之间具有极显著的遗传分化（<0.0001）。遗传多样性分析显示，鸢乌贼中型群和微型群均呈现出较高的单倍型多样性（0.9465和0.8545）和较低的核苷酸多样性（0.0051和0.0021），中型群的遗传多样性指数要高于微型群。基于ND2、COI和16S rDNA序列计算的中型群和微型群之间的遗传距离分别达到了14.0%、9.6%和8.8%，远大于类群内的遗传分化（平均<1%）。研究结果表明，南海鸢乌贼存在分布高度重合且有显著遗传分化的两个种群，即中型群和微型群。中型群和微型群之间的遗传差异达到了种间分化的水平，提示体型较大、具有背部发光器的中型群鸢乌贼（典型鸢乌贼）与体型较小、背部发光器缺失的微型群鸢乌贼可能是两个相互独立的种类。 Abstract:In the present study, the population differentiation of the purpleback flying squid () in the South China Sea was examined based on mitochondrial ND2, COI, and 16S rDNA sequences, using samples collected between September 2012 and September 2015. Phylogenetic analysis revealed two significantly divergent monophyletic groups corresponding to the "medium form" and the "dwarf form, " but no geographical lineages corresponding to the sampling localities or seasonal groups were found. The Analysis of Molecular Variance also revealed significant genetic differentiation between the "medium form" and the "dwarf form" (<0.0001), while no genetic variance between either geographic populations or seasonal groups was found. The genetic diversity analysis showed that both the "medium form" and the "dwarf form" of in the South China Sea were characterized by high haplotype diversity (0.9465 and 0.8545) and low nucleotide diversity (0.0051 and 0.0021). The genetic distance between the ‘medium form’ and the "dwarf form" based on ND2, COI, and 16S sequences were 14.0%, 9.6%, and 8.8%, respectively. The genetic distances between the two forms were considerably larger than the genetic distances within each of the two forms (<1%). It was demonstrated that two divergent populations of were sympatrically distributed in the South China Sea, i.e. the "medium form" and the "dwarf form." The genetic differentiation between these two populations was similar to that among separate species within Ommastrephidae, which indicated that the two morphologically distinct forms of the purpleback flying squid, namely the "medium form" (middle sized, with a photophore) and the "dwarf form" (small sized, without a photophore), are two distinct species. 参考文献 相似文献 引证文献

Population genetic structure and demographic history of Pampus argenteus in the Indo-West Pacific inferred from mitochondrial cytochrome b sequences

Various studies on population genetics in the Indo-Pacific that include the Coral Triangle region have revealed phylogeographic patterns in marine species populations. However, little is known about the population structure and connectivity pattern among the coral reefs in four seas surrounding Malaysia: the Strait of Malacca (Andaman Sea), the South China Sea, the Sulu Sea, and the Sulawesi Sea. In view of this, we examined the genetic population structure of two invertebrate species: the blue sea star (Linckia laevigata) and the boring clam (Tridacna crocea) from seven localities across Malaysia, including Pulau Layang-Layang in the Spratly Islands. Additional samples of L. laevigata were obtained from the Davao Gulf, the Philippines. The analyses were based on partial mitochondrial cytochrome oxidase I sequences of L. laevigata and T. crocea. Populations of L. laevigata and T. crocea showed departure from neutrality, indicating selection or population expansion. However, a mismatch analysis suggested population expansion. Lack of genetic population structure in L. laevigata (ΦST = − 0.001, P = 0.399) implies high connectivity among the sampled reef sites. There was subtle genetic structuring in populations of T. crocea (ΦST = 0.032, P = 0.009), but AMOVA did not detect any structure in the a priori groupings. The genetic population structure and scale in connectivity are most likely attributed to the life history traits of the sea star and giant clam species, and also to the geological history and seasonal current patterns of the region.

Summary The silver pomfret (Pampus argenteus) is a commercially important species native to the Indo-western Pacific area. In the present study, the genetic structure of five P. argenteus populations from the Arabian Sea, Bay of Bengal, and South China Sea were investigated using sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene. All populations showed high levels of haplotype diversity (h) and low levels of nucleotide diversity (π). Phylogenetic trees indicated that the haplotypes could be divided into three clusters, indicating the geographic distribution of the five populations. Analysis of molecular variance (amova) indicated the intra-region variation among these populations to be highly significant. The average pairwise differences and Fst values among the three regions were also found to be significant. These results suggest that P. argenteus in these regions has strong geographic genetic structure. The present results provide new information for the genetic assessment, fishery management, and conservation of this species.

For centuries, morphology-based fish identification has been applied without molecular evaluation. Many studies showed that specimens with a similar morphology are frequently found to be quite genetically distinct. One of the fish species that still remains taxonomically problematic is a commercial snapper species, Lutjanus johnii. Because of morphological ambiguities among local fish taxonomists in Malaysia, we examined the ability of the cytochrome oxidase I (COI) gene to genetically examine the taxonomic status of L. johnii. A 626-base pair COI region was successfully amplified and aligned with conspecific sequences that were retrieved from GenBank. The phylogenetic tree obtained showed two major clusters; the first cluster consists of L. johnii from Straits of Malacca, Thailand, Australia, and China while the second cluster comprises L. johnii from China and India. The latter group showed sequence divergence greater than 3.5%. After observing this, we suspected that there might be a cryptic species between the South China Sea and Indian Ocean. This is the first molecular report concerning the commercial species of snapper, L. johnii, in Malaysia, which had only gained provisional recognition from morphological examination.

Radiolarian biogeographic contrast between spring of 2017 and winter of 2017–2018 in the South China sea and Malacca Strait

A population genetics study of the commercially important Green Tiger Prawn (Penaeus semisulcatus) was conducted in the Indo-Pacific Ocean with a focus on the Indo-Malay Archipelago waters of the South China Sea (SCS), Sulu Sea (SLS), Celebes Sea (CLS) and the Strait of Malacca (SOM), the latter being the main waterway that connects the Indian Ocean with the Pacific Ocean. A 548-base-pair region of mitochondrial COI and 571 base pairs of the control region (CR) were analysed in 284 specimens from 15 locations. Genetic divergences (Tamura 3-parameter) for COI ranged from 0.1% to 7.2% and CR 2.3% to 21.7%, with Bagan Pasir (BGP) in central SOM being the most genetically different from other populations (COI: 3.3-4.2%; CR: 7.1-16.5%). All populations were differentiated into two lineages with a genetic break in the vicinity of BGP; Lineage I comprised populations south of this site (SCS, SLS, CLS and part of SOM) and Lineage II comprised populations north of BGP (part of the SOM). Specifically, most individuals of Bagan Pasir (BGP) and another site just south of it, Batu Pahat (BPT), clustered in Lineage I, while all SOM populations to the north of these sites clustered in Lineage II. The BGP population is believed to be a mixed gene pool between the two lineages. The results could be attributed to the fluctuations of Pleistocene sea levels and a possible influence of the One Fathom Bank in SOM. High genetic diversity was recorded, π (Lineage I: COI: 3.4%; CR: 7.4%) (Lineage II: COI: 3.8%; CR: 12.6%) and, h (Lineage I: COI: 0.81; CR: 1.0) (Lineage II: COI: 0.57; CR: 0.99). Demographic statistics revealed that both lineages underwent a sudden expansion and consequent stabilisation in genetic variability. The findings of this study have wide implications for fisheries in the Indo-Pacific. The increased sampling effort within a narrower geographical scale by the current study permitted a precise locality of the genetic break for this species within the Indo-Pacific Ocean to be identified. The substantial genetic diversity within both lineages should be considered in fishery management and aquaculture development programs of this species in this region.

Energy, Trade and Geopolitics in Asia: The Implications for Canada

Canada’s growing interest in trade with countries in the Indo-Pacific region corresponds with an ominous growth in geopolitical instability and insecurity in that part of the globe. With Indo-Pacific hunger for oil expected to soar – especially in China, where demand will translate to 80 per cent of imports in 10 years – Canada needs to develop policies to deal with the region’s turbulent realities. The Indo-Pacific comprises countries in South Asia and Southeast Asia, and includes such unstable and unpredictable players as North Korea and Pakistan, both of which have nuclear weapons and long-simmering border tensions. India is an emerging economic and military rival to China. In the next 20 years, China and India are expected to lead the global demand for gas as coal consumption continues to decline, and Canada has a stake in this prosperous future. Along with territorial squabbles in the region, Canada will have to deal with complex issues such as terrorism, human trafficking, transnational crime, piracy and cyber-crime, as well as the struggle for global dominance between China and the U.S. One key area for potential conflict is China’s recent construction and militarization of artificial islands in the South China Sea. The Canadian government’s new military strategy, Strong, Secure, Engaged does little more than make a plea for peace and the rule of law in the South China Sea. However, more trade crosses the Pacific Ocean from Canada than crosses the Atlantic. And with Canada signing on to the Comprehensive and Progressive Trans-Pacific Partnership (CPTPP), the region’s troubles will need to be resolved by more than good intentions on paper. Canada must shift more diplomatic, security and military resources to the Indo-Pacific; otherwise, its efforts will be spread too thinly to be effective in the region. Trade, especially through a major route like the Strait of Malacca, could easily be disrupted by any one of a number of disputes, such as a conflict between China and Taiwan or if historic resentments boil over among competing territorial claimants in the region. Thus, Canada needs to step up and reaffirm its security commitments to the Association of Southeast Asian Nations (ASEAN) as a partner in the region. Participating in maritime exercises and Freedom of Navigation (FON) operations would also help to reinforce to countries in the region the importance of abiding by international law. Meanwhile, Canada should set aside for now any intentions to negotiate a free trade agreement with China. China does not share some of Canada’s key trade and security goals and its aggressive behaviour in the South and East China Seas clearly signal that now is not the time to talk about a trade pact. China must demonstrate that it is willing to take a more cooperative approach to resolving trade and security issues in the Indo-Pacific and to support and respect the rule of law in the region. Canada has the potential to become a reliable, stable source of energy for Indo-Pacific countries. There is also an opportunity for provinces such as Alberta to strike their own strategic deals to provide energy resources to countries in that region, in return for trade and investment benefits. However, while investing at home in the necessary infrastructure and export capability to expand its role, Canada must also strive to bring its own unique approach to enhancing regional and energy security in the Indo-Pacific.

Contents: Part I Introduction: Maritime security in the South China Sea: cooperation and implications, Wu Shicun and Zou Keyuan. Part II Securing Navigation in the South China Sea: Good order at sea in the South China Sea, Sam Bateman Maritime trade development in Asia: a need for regional maritime security cooperation in the South China Sea, Hong Nong Maritime security cooperation in the South China Sea region, Andrew S. Erickson Myth and reality: the rise and fall of contemporary maritime piracy in the South China Sea, Xu Ke Commentary: a regional perspective on South China Sea passage security, Wu Shicun. Part III Regional Cooperation Combating Maritime Terrorism and Piracy: Regional maritime security initiative (RMSI) and enhancing security in the Straits of Malacca: littoral states' and regional responses, Yann-huei Song Crackdown on piracy in Southeast Asian seas: need a more effective legal regime?, Zou Keyuan Southeast Asian SLOC security, Joshua H. Ho The United States response to maritime terrorism, Kristen G. Juras Commentary: enhancing Sino-US maritime cooperation for regional security, Bao Hongjun and Zhu Huayou. Part IV Environmental Security and Maritime Rescue: The development of oil spill preparedness and response in China, Xu Shiming Regional cooperation for marine pollution contingency response in the South China Sea, Zhang Xiangjun International submarine rescue: a constructive role for China, Lyle J. Goldstein and William S. Murray Commentary: search and rescue in South China Sea and regional cooperation, Zhang Jie Index.