Genetic structure of the reef grouper Epinephelus merra in the West Indian Ocean appears congruent with biogeographic and oceanographic boundaries

The reef fauna connectivity of the West Indian Ocean (WIO) is one of the least studied globally. Here we use genetic analyses of the grouper Epinephelus merra (Bloch 1793) to determine patterns of connectivity and to identify barriers to dispersal in this WIO marine area. Phylogeographic and population‐level analyses were conducted on cytochrome b sequences and microsatellites (13 loci) from 557 individuals sampled in 15 localities distributed across the West Indian Ocean. Additional samples from the Pacific Ocean were used to benchmark the WIO population structure. The high level of divergence revealed between Indian and Pacific localities (of about 4.5% in sequences) might be the signature of the major tectonic and climatic changes operating at the Plio‐Pleistocene transition, congruently with numerous examples of Indo‐Pacific speciation. In comparison, the E. merra sequences from the Indian Ocean constitute a monophyletic clade with a low average genetic distance (d < 0.5%). However both genetic markers indicated some structure within this ocean. The main structure revealed was the isolation of the Maldives from the WIO localities (a different group signature identified by clustering analysis, great values of differentiation). Both marker types reveal further significant structure within the WIO, mainly the isolation of the Mascarene Islands (significant AMOVA and isolation‐by‐distance patterns) and some patchy structure between the northernmost localities and within the Mozambique Channel. The WIO genetic structure of E. merra appeared congruent with main biogeographic boundaries and oceanographic currents.     

印度洋-西太平洋海洋动物谱系地理演化格局

印度洋和西太平洋海域,拥有大量浅海大陆架、边缘海和岛屿,孕育了全球最丰富的初级生产力和渔业资源,尤其是作为该区域陆源物质输入、两大洋能量汇聚中心和生物多样性中心的东印度三角,在全球海洋生物分布和进化中扮演了重要角色。本文结合物理海洋和化学海洋环境,通过线粒体基因和核基因等分子标记研究结果,归纳分析了印度洋和西太平洋区域海洋动物谱系生物地理演化格局及其可能的成因。具体结果如下:(1)雷州半岛-海南岛、冰期暴露的台湾海峡和长江冲淡水等沿岸海区,阻碍了海洋动物在海区间的扩散,南海、东海和黄、渤海广布类群,多由一个星状辐射谱系组成,种群经历最近的数量扩张和区域扩散,而仅分布于南海的物种,一般具有多个深度分歧的遗传谱系,种群呈现出数量平衡状态,同一广布物种的南海和东海种群,因区域海洋环境差异,种群数量动态演化历史不同;(2)黑潮影响区的沿岸广布类群,黑潮海流促进了顺流扩散、限制了跨海流基因交流;(3)东印度三角区,存在"华莱士线"、"赫胥黎线"和"印度洋-太平洋线"等生物地理边界,该区域海洋或咸淡水溯河洄游动物多呈现为分布在生物地理边界两侧的2个遗传谱系;(4)西太平洋,存在与目前东西向大洋环流垂直的南北向跨赤道扩散和基因流现象,可能受到目前南北向随季节反转的沿岸流和深层海流影响;(5)印度洋东西海岸共享物种,受印度洋西向赤道流影响,海洋动物多由东印度洋向西印度洋跨洋扩散;(6)西印度洋广布物种/类群,呈现了两种不同种群分化格局——遗传同质均一种群和深度分化的遗传谱系;(7)东、北印度洋和南海区域共享大量物种,可能是海盆间双向扩散的结果;(8)海洋生物谱系生物地理进化史信息,可以用于地质事件、海洋环流和古气候重建。     

Mitochondrial DNA variation reveals distinct lineages in Penaeus semisulcatus (Decapoda,Penaeidae) from the Indo‐West Pacific Ocean

Penaeus semisulcatus, the green tiger prawn, is an ecologically and economically important penaeid shrimp in the Indo‐West Pacific region, especially in rice‐shrimp farming and capture fisheries in Bangladesh and Sri Lanka, respectively. Genetic variation and phylogeography of samples of this species from Bangladesh and Sri Lanka were studied utilizing different mitochondrial DNA markers, i.e. cytochrome oxidase subunit 1 (CO1), control region (CR) and 16S rRNA genes. No evidence of population structure was observed in Bangladesh, but distinct variations were found among the Sri Lankan samples (Φ_ST = 0.04, p = .002; F_ST = 0.07, p = .001), with the western sample differing from the northwestern and southern samples. The Bangladesh population had lower genetic diversity than two of the three Sri Lanka populations. The phylogeography of P. semisulcatus revealed two distinct mitochondrial DNA (mtDNA) lineages, one in the Western Pacific Ocean and second in the Indian Ocean. The Bangladesh samples showed highest levels of similarity with samples from Sri Lanka, India and Malaysia, with the Bangladesh and Sri Lanka populations sharing the most common recent ancestry. Among the Indian Ocean samples, high levels of variation were observed in the samples from Iran, indicating admixture of two distinct mtDNA lineages, one shared by the populations from the Bay of Bengal and the other possibly originating from Eastern Africa. The genetic and phylogeographic information obtained in this study will be useful in appropriate planning for management and conservation of shrimp fisheries in Bangladesh and Sri Lanka, and in the Indo‐West Pacific region.     

Matrilineal evidence for genetic structure and Late Pleistocene demographic expansion of the Ornate goby Istigobius ornatus (Teleostei: Gobiidae) in the Persian Gulf and Oman Sea

The Persian Gulf and Oman Sea are characterized by an interesting paleoclimatic history and different ecological settings, and offer a unique study area to investigate the genetic structure of marine organisms including fishes. The Ornate goby Istigobius ornatus is widely distributed throughout the tropical Indo‐West Pacific including the Persian Gulf and Oman Sea. Here, we present the population structure, genetic diversity, and demographic history of four populations of I. ornatus from the latter two regions using the D‐loop marker of mitochondrial DNA. The results reveal a shallow genealogy, a star‐like haplotype network, significance of neutrality tests, and unimodal mismatch distribution. This is concordant with a recent demographic expansion of I. ornatus in the Persian Gulf and Oman Sea at about 63,000–14,000 years ago, which appears to be related to Late Pleistocene sea level fall and rise. The results of the pairwise Fst estimates imply high gene flow along the coast of the Persian Gulf, which is probably due to larval dispersion, whereas the Oman Sea population clearly differs from all Persian Gulf populations. The AMOVA result indicates that 7.74% of the variation is related to differences among ecoregions, while inter‐ and intra‐population differences explained ?3.20% and 95.47% of the variation, respectively. The haplotype network depicts two groups of haplotypes, most of them were specific to the Persian Gulf. No further evidence for geographic lineage substructuring was evident. The Mantel test result indicates that isolation by distance is not the main mechanism that promoted the genetic differentiation among the studied populations of I. ornatus. We suggest that cumulative effects of ecological and geographic barriers such as salinity, oceanographic conditions, and the presence of the Strait of Hormuz have shaped the genetic structure of I. ornatus in the Persian Gulf and Oman Sea.     

Lack of mitochondrial genetic structure in the endangered giant clam populations of Tridacna maxima (Bivalvia: Cardiidae: Tridacninae) across the Saudi Arabian coast

The present investigation focuses on population genetic structure analysis of the endangered giant clam species Tridacna maxima across part of the Red Sea,with the main aim of assessing the influence of postulated potential barriers to gene flow(i.e.,particular oceanographic features and marked environmental heterogeneity)on genetic connectivity among populations of this poorly dispersive bivalve species.For this purpose,a total of 44 specimens of T.maxima were collected from five sampling locations along the Saudi Arabian coast and examined for genetic variability at the considerably variable mitochondrial gene cytochrome c oxidase I(COI).Our results revealed lack of population subdivision and phylogeographic structure across the surveyed geographic spectrum,suggesting that neither the short pelagic larval dispersal nor the various postulated barriers to gene flow in the Red Sea can trigger the onset of marked genetic differentiation in T.maxima.Furthermore,the discerned shallow COI haplotype genealogy(exhibiting high haplotype diversity and low nucleotide diversity),associated with recent demographic and spatial expansion events,can be considered as residual effect of a recent evolutionary history of the species in the Red Sea.     

Concordance of microsatellite and mitochondrial DNA markers in detecting genetic population structure in the boring giant clam Tridacna crocea across the Indo‐Malay Archipelago

Mitochondrial DNA (mtDNA) is a single, usually non‐recombining locus, and often uniparentally inherited. Therefore, its ability to reveal recent gene flow among populations is usually questioned. In this study, the genetic population structure of 16 populations of Tridacna crocea (n = 366) from the Indo‐Malay Archipelago (IMA) was examined with 10 microsatellite markers and compared to previous studies using mtDNA, in order to test if the revealed population structure was congruent between the two marker systems. The results showed that the genetic population structure revealed by the two marker systems was mostly congruent, with a high correlation between cytochrome c oxidase subunit I (COI) and microsatellites. The studied populations could be divided by both marker systems as follows: (i) Eastern Indian Ocean, (ii) Central IMA, and (iii) Western Pacific. Populations in the Central IMA showed high gene flow. However, populations in the Java Sea (Karimunjava, Pulau Seribu) were grouped into a separate cluster by mtDNA analysis, while this grouping was not detected by microsatellites. It was also noteworthy that there is obvious heterozygosity deficiency in most of the populations, which may be caused by null alleles, inbreeding or population expansion. Overall, these results indicate that the mitochondrial COI gene is applicable for population genetic analysis and precise recovery of connectivity patterns of giant clams. Therefore, the combination of mtDNA and nuclear DNA markers can lead to a more complete understanding of population genetics. Moreover, this study is expected to facilitate fully displaying the population genetic structure of giant clams combining with other researchers' results.     

Genetic differentiation of the soft shore barnacle Fistulobalanus albicostatus (Cirripedia: Thoracica: Balanomorpha) in the West Pacific

This study examined the phylogeography of the barnacle Fistulobalanus albicostatus, which inhabits mangroves and estuarine shores in the West Pacific. Differentiation in the mitochondrial cytochrome c oxidase subunit I (COI) and 12S ribosomal RNA (12S) genes of 401 specimens of F. albicostatus was examined in samples from 16 locations in the West Pacific, ranging from Honshu to Southern China. Our results revealed that F. albicostatus comprises two major clades exhibiting a COI divergence ranging from 1.25% to 2.8%. Clade A demonstrated the widest distribution, ranging from Japan to China, and was divided into three subclades occurring in the South China Sea (A1), Okinawa (A2), and Honshu, Korea and Qingdao (A3). Clade B was determined to be endemic to Okinawa; i.e. two endemic lineages occur in this island. Thus, F. albicostatus resembles several inter‐tidal species in having clades that are endemic to Okinawan waters. Nevertheless, in contrast to the rocky inter‐tidal barnacles Tetraclita spp. and Chthamalus malayensis, F. albicostatus was not found to be separated into continental and oceanic populations, but instead is divided into northern and southern clades, probably because of the Yangtze River discharge, which limits gene flow between the northern and southern populations.     

Mesopelagic fishes of the Bering Sea and adjacent northern North Pacific Ocean

Fourteen midwater trawl collections to depths of 450 m to 1,400 m were taken at eleven stations in the Bering Sea and adjoining regions of the northern North Pacific by the R/V Hakuho Maru during the summer of 1975. A total of 29 kinds of fishes were identified. Mesopelagic fishes of the families Myctophidae, Gonostomatidae and Bathylagidae predominated in the catches, contributing 14 species (94%) of the fishes caught.Seventeen species of fishes were caught in the Bering Sea, and all of these are known from nearby areas. The mesopelagic fish fauna of the Bering Sea is similar to that in adjoining regions of the northern North Pacific Ocean: endemic species are rare or absent. Stenobrachius nannochir was usually the most common mesopelagic fish in our catches.Stenobrachius leucopsarus is a diel vertical migrant that is usually the dominant mesopelagic fish in modified Subarctic waters of the northeastern Pacific. The change in dominance fromS. nannochir in the western Bering Sea toS. leucopsarus in the eastern Bering Sea is related to differences in oceanographic conditions.     

北太平洋西部和印度洋东部及其邻近海域表层水体中137Cs的分布

对北太平洋西部海域、苏禄海及印尼海、中国南海、印度洋东部海域、孟加拉湾及安达曼海等表层水体中放射性核素137Cs的活度进行了测定。结果表明,上述海域表层水体中137Cs活度显示了较大的变化范围,最低值出现在南极附近的南大洋(1.1Bqm-3),较高的活度值则出现在北太平洋西部海域及中国南海(3Bqm-3)。在所研究水域范围内,137Cs活度的纬度分布特征并没有完全有效地反映出137Cs的全球理论大气沉降趋势及其纬度效应。综合本研究及Miyake等人(1988)的测定结果,我们计算出137Cs自表层海水中的析出速率在苏禄海及印尼海约为0.016/a,在孟加拉湾及安达曼海约为0.033/a,在中国南海约为0.029/a,这一结果明显低于西北太平洋日本沿海表层水体中137Cs的析出速率。这可能是因为在这些海域,横向及纵向的水体混合过程相对都较慢,而且颗粒物对137Cs的吸附析出过程也比较弱所致。     

北半球热带中太平洋与印度洋海表温度梯度对夏季西北太平洋热带气旋生成频数变化的影响

基于1951—2018年哈德里中心海温资料、美国气象环境预报中心和美国国家大气研究中心再分析资料和第四代欧洲中心汉堡模式, 针对1994年、2018年等西北太平洋热带气旋(TC)生成异常多的年份, 研究了引起TC增加的海表温度异常(SSTA)模态及其影响机制。结果表明, 北半球热带中太平洋增暖与印度洋变冷是夏季西北太平洋TC生成频数增加的主要原因, 北大西洋负三极型式SSTA促使TC生成的进一步增加。热带中太平洋增暖与印度洋冷却在菲律宾以东激发出西风异常和气旋性环流异常。北大西洋负三极型式SSTA在我国南海、菲律宾至东南沿岸激发出气旋性环流异常。前者在西北太平洋中部, 后者在南海产生有利于TC生成的局地环境。1994年和2018年夏季热带中太平洋出现暖SSTA、印度洋为冷SSTA、北大西洋呈现负三极型式SSTA, 西北太平洋TC生成频数极端增多。近30年来, 当出现热带中太平洋增暖和印度洋冷却时, 北大西洋表现出比1989年以前更强的负三极型式SSTA, 使西北太平洋TC生成频数和北半球热带印度洋-太平洋SSTA梯度的线性相关更显著。     

First records of Scorpaena onaria (Scorpaeniformes: Scorpaenidae) from the southwestern Pacific Ocean,and comparisons with the Northern Hemisphere population

Scorpaena onaria Jordan & Snyder (Scorpaeniformes: Scorpaenidae), previously known only from the northwestern Pacific Ocean, is reported from the southwestern Pacific Ocean for the first time on the basis of 19 specimens. The southwestern Pacific specimens are regarded as a southern population of S. onaria, characterised by a shorter supraocular tentacle and larger body size compared with the northwestern Pacific specimens. The southern population is described in detail including comparisons with all known Indo‐Pacific species of the genus Scorpaena. Analyses of 37 measurements of the southern population of S. onaria found that relative orbit diameter and second anal‐fin spine length became significantly smaller with growth. Initially cycloid, the scales enclosed by the posterior tips of the upper and lower opercular spines and opercular margin change to ctenoid with growth at c. 160–170 mm standard length. A mature female differed from an immature female and males in having a longer upper jaw, steeper dorsal profile of the snout, and shorter nasal spine. As a consequence, the species previously reported as S. neglecta from the Andaman Sea and northwestern Australia was re‐identified as S. onaria.     

Stock structure and demographic history of the Indo-West Pacific mud crab Scylla serrata

The increasing exploitation of mangrove forests, without any sustainable planning, has been seriously compromising the survival of this ecosystem and of its exclusive resources. Scylla serrata is one of the most commercially exploited crabs inhabiting mangroves and estuaries of the Indo-Pacific region. This species is extensively harvested, mainly for selling to the tourist market, and, as a consequence, its populations are in constant decline. The aim of the present study was to assess the level of genetic exchange of S. serrata within the Western Indian Ocean (WIO), using a population genetic structure approach. To achieve this goal, we reconstructed the intra-specific geographic pattern of genetic variation by partial sequencing the mitochondrial DNA cytochrome oxidase subunit I, in samples from seven mangrove sites of the WIO. Our data set then encompassed all the sequences for the same genetic marker deposited in Genbank and corresponding to samples from South East Asia, Australia and some Pacific Islands: this allowed us to estimate the level of connectivity among S. serrata populations within its distribution area.     

Cryptic diversity of marine gastropod Monodonta labio (Trochidae): did the early Pleistocene glacial isolation and sea surface temperature gradient jointly drive diversification of sister species and/or subspecies in the Northwestern Pacific?

Formation of glacial refugia during the Pleistocene climatic oscillations has been put forward to elucidate the diversification of marine organisms in the north‐western Pacific. The marine gastropod Monodonta labio is one of the most common species in the Northwestern Pacific and possibly possesses cryptic diversity. Here, we investigate the phylogeographic pattern of this species to test the potential mechanisms driving its diversification in the Northwestern Pacific. Genetic information for two mitochondrial genes (Cytochrome oxidase subunit I and 16S rDNA) and one nuclear gene (internal transcribed spacer 1) was acquired to detect genetic structuring and to reconstruct the gastropod's phylogenetic history. Our results revealed that M. labio is comprised of five main clades, and divergence time estimates place their cladogenesis as corresponding to the initiation (c. 2.5 mya) and intensification (c. 0.9 mya) of large‐scale Northern Hemisphere ice sheets. The early and middle Pleistocene divergence times are consistent with the emergence times of the Dongshan land bridge, which would seperate the ancient East China Sea and the ancient South China Sea forming two potential refugia. In addition, the deep trough in the Qiongzhou Strait would possibly act as another potential refugium with the uplift of the Qiongzhou Strait at mid‐Pleistocene. This study suggests that the current genetic architecture of M. labio is probably correlated with glacial isolation and sea surface temperature gradient. We also put forward the possibility that these factors were probably an important driver for the diversification of sister species or subspecies of other taxa in the Northwestern Pacific.     

Difference of planktonic ciliate communities of the tropical West Pacific,the Bering Sea and the Arctic Ocean

Ciliates are important components in planktonic food webs,but our understanding of their community structures in different oceanic water masses is limited.We report pelagic ciliate community characteristics in three seas:the tropical West Pacific,the Bering Sea and the Arctic Ocean.Planktonic ciliate abundance had"bimodal-peak","surface-peak"and"DCM(deep chlorophyll a maximum layer)-peak"vertical distribution patterns in the tropical West Pacific,the Bering Sea and the Arctic Ocean,respectively.The abundance proportion of tintinnid to total ciliate in the Bering Sea(42.6%)was higher than both the tropical West Pacific(7.8%)and the Arctic Ocean(2.0%).The abundance proportion of small aloricate ciliates(10–20μm size-fraction)in the tropical West Pacific was highest in these three seas.The Arctic Ocean had higher abundance proportion of tintinnids in larger LOD(lorica oral diameter)size-class.Proportion of redundant species increased from the Arctic Ocean to the tropical West Pacific.Our result provided useful data to further understand ecology roles of planktonic ciliates in different marine habitats.     

Oceanographic Studies in the Northwest Pacific and Seas of Japan and Okhotsk on Cruise 73 of the R/V Professor Gagarinskiy and Cruise 53 of the R/V Akademik Oparin

Oceanology - During cruise 73 of the R/V Professor Gagarinskiy and cruise 53 of the R/V Akademik Oparin, oceanographic studies of the Sea of Japan and Sea of Okhotsk and the Northwest Pacific were...     

西北太平洋环境变化对柔鱼冬春生群体资源丰度年间变化的影响

The neon flying squid Ommastrephes bartramii is an economically important species in the Northwest Pacific Ocean. The life cycle of O. bartramii is highly susceptible to climatic and oceanic factors. In this study, we have examined the impacts of climate variability and local biophysical environments on the interannual variability of the abundance of the western winter-spring cohort of O. bartramii over the period of 1995–2011. The results showed that the squid had experienced alternant positive and negative Pacific Decadal Oscillation(PDO) over the past 17 years during which five El Ni?o and eight La Ni?a events occurred. The catch per unit effort(CPUE) was positively correlated with the PDO index(PDOI) at a one-year time lag. An abnormally warm temperature during the La Ni?a years over the positive PDO phase provided favorable oceanographic conditions for the habitats of O.bartramii, whereas a lower temperature on the fishing ground during the El Ni?o years over the negative PDO phase generally corresponded to a low CPUE. The same correlation was also found between CPUE and Chl a concentration anomaly. A possible explanation was proposed that the CPUE was likely related to the climateinduced variability of the large-scale circulation in the Northwest Pacific Ocean: high squid abundance often occurred in a year with a significant northward meander of the Kuroshio Current. The Kuroshio Current advected the warmer and food-rich waters into the fishing ground, and multiple meso-scale eddies arising from current instability enhanced the food retention on the fishing ground, all of which were favorable for the life stage development of the western squid stocks. Our results help better understand the potential process that the climatic and oceanographic factors affect the abundance of the winter-spring cohort of O. bartramii in the Northwest Pacific Ocean.     

卡里马塔海峡贯穿流与印尼贯穿流的相互作用

卡里马塔海峡贯穿流将中国南海的低盐水输运到爪哇海,与印度尼西亚贯穿流(印尼贯穿流)携带的西太平洋高盐水在印度尼西亚海(印尼海)交汇,二者通过混合、浮力强迫等过程相互作用。这改变了印度尼西亚海的水体热盐性质,影响局地海气交换和热带太平洋-印度洋之间的热盐交换。依据卡里马塔海峡、龙目海峡和望加锡海峡的实测表层海流数据,采用被动示踪法和数值模拟诊断实验,分析并研究了2支海流在季节尺度上的相关关系及其相互作用。观测结果表明,卡里马塔海峡贯穿流与印尼贯穿流的表层流季节变化存在负相关,且超前1个月达到相关系数最大值,其中印尼贯穿流下游的龙目海峡表层流与卡里马塔海峡贯穿流关系更密切。被动示踪结果显示,卡里马塔海峡释放的示踪粒子主要向南流入爪哇海,然后经巽他海峡、龙目海峡及班达海方向流出,但很难进入到望加锡海峡北部;望加锡海峡释放的表层示踪粒子主要经龙目海峡和班达海流入印度洋,但无法进入到爪哇海及卡里马塔海峡。数值诊断实验结果表明,卡里马塔海峡贯穿流在冬季阻挡了印尼贯穿流表层海水的南下,从而使其表层流产生明显的季节变化;而望加锡海峡贯穿流对卡里马塔海峡贯穿流的影响较小。在季节尺度上,卡里马塔海峡贯穿流对印尼贯穿流尤其是表层流,有着重要影响,但印尼贯穿流对卡里马塔海峡贯穿流的影响较小。     

西北太平洋围线海绵科(海绵动物门:六放海绵纲:双盘海绵目)一新种

本文记录了西太平洋深海围线海绵科1新种——扭形白须海绵。该海绵共含2个标本，其中1个采集于雅浦海山932米处，另1个采集于卡罗琳海山775.3米处。该新种含有椭圆形大双盘骨针、3种类型的双盘骨针、棒状骨针和节杖骨针，使其很容易与该属下的现有8种区分开。该种为西北太平洋报道的第4种白须海绵属的种。     

中国近海浮游桡足类中华哲水蚤（Calanussinicus Brodsky）的分子系统地理学和种群遗传结构研究

Planktonic copepod Calanus sinicus is the dominant meso-zooplankton in the Northwest Pacific Ocean. To better understand its population dynamics and phylogeographic patterns, 243 C. sinicus individuals were collected from seven locations across the shelf waters of China and its population genetics was studied by mitochondrial DNA cytochrome oxidase I(mtCOI) sequences analyses. Thirty-nine different sequences, or haplotypes, were detected with moderate haplotype diversity(h=0.749) and low nucleotide diversity(π=0.003) for all populations. The evolutionary divergence between geographic populations varied from 0.24% to 0.37%, indicative of very limited genetic differentiation. Visualized minimum spanning network(MSN) and phylogenetic analysis of all the detected haplotypes did not reveal any clear phylogeographic pattern. Furthermore, AMOVA data showed no significant spatial population differentiation existed among the individuals collected across China shelf waters. Pairwise FST values showed that population collected from northwest of the East China Sea(ECS) displayed a low difference to other populations. Mismatch distribution analyses and neutrality tests indicated that C. sinicus might undergo a demographic/population expansion. No significant population genetic structuring was detected, indicating an extensive gene flow among the C. sinicus populations. Our results provide molecular evidence for the hypothesis that C. sinicus in the northwestern South China Sea in winter is transported from the East China Sea and the Yellow Sea by the China Coastal Current during the northeast monsoon period.