Bottom-up and top-down control of seagrass overgrazing by the sea urchin Tripneustes gratilla

The lack of top-down control on Tripneustes gratilla, a sea urchin commonly known to graze on seagrass, and the bottom-up control of its feeding preference, led to the overgrazing of seagrass meadows of the species Thalassodendron ciliatum in Changuu Island (Zanzibar Archipelago). The impact of overgrazing on seagrasses was assessed by mapping the presence of grazed versus non-grazed seagrass patches in the study site, while the top-down control on T. gratilla was assessed by measuring the abundance of its fish predators. The feeding preference and distribution of T. gratilla were characterized by calculating the electivity indexes for each seagrass species and measuring sea urchin density, respectively. Approximately half of the patches of T. ciliatum were overgrazed, while predatory fishes of T. gratilla were absent from the site. The Vanderploeg and Scavia's Relativized Electivity Index indicated that T. gratilla had a feeding preference for T. ciliatum, which was also supported by higher urchin densities within T. ciliatum dominated patches. Bottom-up control of grazing activity was observed by quantifying and analyzing morphological, nutritional, and the chemical defense traits of the seagrass in relation to feeding preference and urchin density. Feeding was positively correlated to the seagrass tissue C:P ratio (ρ = 0.9), whereas urchin density showed no correlations. The bottom-up control of the feeding preference and agglomeration of T. gratilla in T. ciliatum meadows, together with the lack of evidence of substantial top-down control and the long recovery time of T. ciliatum led to the overgrazing of this species at this site. Overgrazing, therefore, was shown to be the result of multiple factors ranging from the traits of the seagrass and feeding preference of T. gratilla, to the abundance of predators in this area.     

Evidence of deep genetic divergence between populations of an important recreational fishery species,Lichia amia L. 1758, around southern Africa

Lichia amia is an important coastal recreational fishery species with a cosmopolitan distribution in the eastern Atlantic. In southern Africa, it is distributed from southern Angola to northern KwaZulu-Natal in South Africa. A recent biological survey revealed differences between Angolan and South African individuals suggesting that they may represent separate stocks. As fishery management decisions should be based on accurate knowledge of population structure, an initial survey of the genetic substructuring of L. amia was conducted on samples collected in southern Angola and South Africa. Assessment of genetic diversity and population structure was conducted using a fragment of the mitochondrial Control Region. Obtained genetic diversity levels were within the expected range for marine teleosts (h = 0.867, π = 0.007), and two deeply divergent (southern Angolan and South African) populations were identified (average φ _ST = 0.78) across the Benguela Current system. These results suggest that Angolan and South African L. amia should be managed as two independent stocks. This work represents the first assessment of population genetic substructuring across the Benguela Current of a valuable coastal fishery resource, and has application for future fisheries management.     

Phylogeography of the pelagic fish Seriola lalandi at different scales: confirmation of inter-ocean population structure and evaluation of southern African genetic diversity

The study investigated the global and regional phylogeography of the yellowtail kingfish Seriola lalandi by examining genetic diversity and population genetic structure of this species at inter-and intra-ocean level and on a regional scale. DNA fragments of two mitochondrial genes, cytochrome b (Cytb) and cytochrome c oxidase subunit I (COI) and one nuclear gene, recombination activating gene 1 (RAG1), were sequenced to investigate the global-scale phylogeography of this species. The population genetic structure within the South Pacific, as well as along the South African coastline, was examined further using six microsatellite markers. Three distinct clades were identified for S. lalandi, which correspond with previously described subspecies of the North-East Pacific, North-West Pacific and the Southern Hemisphere. Within the latter, additional divergence was observed between the South Pacific and the South-East Atlantic regions. Divergence estimates were indicative of a Pacific origin for S. lalandi populations, because of Pleistocene vicariant events. Microsatellite analyses revealed overall significant genetic differentiation between South African and South Pacific samples. This corroborates recent findings on the global phylogeography of the species. No population differentiation was observed within South Africa, indicating high levels of gene flow.     

A comparison of genetic structure in two low-dispersal crabs from the Wild Coast,South Africa

The Wild Coast in south-eastern South Africa is strongly influenced by the warm, southward-flowing Agulhas Current. This current has a significant impact on dispersal in the coastal biota of the region, and facilitates high levels of connectivity among populations. However, it is not known how the region's high-velocity hydrology affects genetic population structure in endemic estuarine species, populations of which are frequently isolated from the sea. Here, we compared genetic structure in two estuarine crabs of the family Hymenosomatidae. Both are presumed to have low dispersal potential, but they differ in terms of their life histories. Hymenosoma longicrure has abbreviated larval development and can complete its entire life cycle within estuaries, whereas Neorhynchoplax bovis is a direct developer that lacks planktonic larvae. Using DNA sequence data from the mitochondrial COI gene and the intron of the nuclear ANT gene, we found that levels of genetic structure differ considerably between the species. Depending on the genetic marker used, H. longicrure is genetically homogeneous (COI) or displays low levels of genetic structure and minor evidence of recruitment near natal sites (ANT). In contrast, connectivity in N. bovis is much lower, as this species has a unique combination of alleles at each site, indicating that recruitment is mostly local. These results support previous findings suggesting that even a short larval dispersal phase is sufficient to maintain high levels of connectivity and prevent genetic divergence among populations.     

2022年夏季胶州湾致灾物种多棘海盘车的分子解析

多棘海盘车(Asterias amurensis)是海星纲的一个致灾物种,广泛分布于包括我国黄海、渤海海域、韩国、日本和俄罗斯海域在内的北太平洋海域,并作为入侵种分布于澳大利亚的塔斯马尼亚海域。多棘海盘车在多个海域发生过暴发性增殖导致的高密度、大规模聚集,对海洋生态系统和水产养殖造成严重的负面影响。自2006年以来在我国山东青岛海域多次发生大规模多棘海盘车聚集,对贝类养殖造成重大经济损失。日本、俄罗斯、澳大利亚等海域的多棘海盘车遗传多样性研究取得了显著进展,然而,迄今为止鲜有针对我国海域致灾物种多棘海盘车的分子生物学分析,阻碍了我国海域种群与全球种群间遗传进化关系的比较分析。研究重点分析了于2022年7月在胶州湾发生多棘海盘车暴发时采集的12个样本,系统组装了其线粒体基因组、核糖体基因簇以及多种通用分子标记。基于线粒体基因组和核糖体基因簇的系统发育分析表明多棘海盘车具有较高的种内遗传多样性。基于线粒体基因组的蛋白编码基因进行分化时间估算,多棘海盘车的种内遗传分化可能发生在1.7～4.2 Ma,表明多棘海盘车的扩布可能较早发生。与线粒体基因组相比,多棘海盘车核糖体基因簇序列在种内极为保守...     

Genetic architecture of three Turbinella pyrum varieties (Linnaeus, 1758) from the southeast coast of India

The genetic diversity and variation of three pseudo‐species of the commercially important Indian conch Turbinella pyrum from the southeast coast of India were studied. A total of 88 individuals was genotyped at 12 loci and differences in the genetic diversity among genetic groups were correlated with known population histories. The study identified 535 alleles and all the studied loci were highly polymorphic. The number of alleles ranged between four and 29 with a global mean of 14.861. The global means of the observed and expected heterozygosities were 0.774 and 0.891, respectively. The estimated within‐population inbreeding value (F_IS = 0.131) indicated a shortfall of heterozygosity in the populations. An analysis of molecular variance showed that 5% of the total variation was due to differences between genetic groups. The Bayesian approach revealed strong distinctiveness in the three genetic groups studied. Overall microsatellite analysis revealed less genetic diversity in all studied genetic groups and significant genetic variation among the three pseudo‐species. The study highlights the significant distinctiveness of the pseudo‐species of T. pyrum and the need for appropriate conservation efforts in order to prevent further losses of their genetic diversity.     

Decline of Terebralia palustris in South African mangroves

Terebralia palustris (Linnaeus, 1767), the giant mangrove whelk, is a prominent component of mangrove ecosystem malacofauna in the Indo-West-Pacific region. On the east coast of Africa, the range of T. palustris extends from Kenya to the south-eastern region of South Africa. Here we confirm reports that, in the past three decades, South African populations of T. palustris have declined. Terebralia palustris was recorded from only two estuarine mangrove forests during a survey conducted in 2013/2014, compared with six estuaries in the mid-20th century. At Kosi Bay, the average density was 186 ind. m^-2 (SD 106) in comparison to only 7.1 ind. m^-2 (SD 2.5) at Durban Bay. Additionally, the average shell height of individuals at Durban Bay (60.3 mm; SD 13.6) was larger than at Kosi Bay (31.84 mm; SD 16.09), indicating the absence of juvenile snails at Durban. In South Africa there have been no previous ecological assessments for T. palustris and, aside from one detailed survey in the early 1960s, most of the occurrence records are vague and incomplete. The ultimate causes for the decline of this charismatic gastropod in South Africa are unknown, although habitat loss and degradation are suspected. Further research is urgently required, particularly into aspects concerning its disappearance at the limit of its global distribution.     

Evidence for multiple paternity and confirmation of an Indo-Pacific origin of blacktip shark Carcharhinus limbatus occurring in South Africa

The blacktip shark Carcharhinus limbatus is a cosmopolitan species found in warm-temperate, subtropical and tropical waters around the world. The research here aimed to assess whether multiple paternity exists in South African C. limbatus and to confirm phylogeographic patterns previously observed within the species. A minimum and maximum frequency of 50% and 71% multiple paternity, respectively, were observed in 14 litters genotyped with five microsatellite markers. Based on the mitochondrial control region, relatively high nucleotide and haplotype diversity characterised the South African sampling population, and pairwise φ_ST values indicated that it significantly differed from the populations of the Pacific and the western Atlantic oceans. The haplotype network showed that the South African samples were grouped closely with the Australian, Indo-Pacific and West African C. limbatus samples, which is suggestive of an Indo-Pacific origin for this population. This study is the first to report multiple paternity in this species. Furthermore, the results reveal that C. limbatus from South Africa is genetically diverse and phylogeographically distinct from most other C. limbatus populations.     

Genetic variability of half-smooth tongue sole Cynoglossus semilaevis populations using microsatellite markers

Ten highly variable microsatellite loci were performed in order to evaluate the genetic variability of wild and hatchery samples of half-smooth tongue sole Cynoglossus semilaevis. A group of 200 genotypes belonging to four wild samples, Laizhou (LZ), Weihai (WH), Qingdao (QD), Rizhao (RZ) and one hatchery sample, Mingbo (MB), were screened. All of the ten microsatellite loci screened in this study showed marked polymorphism. A total of 70 different alleles were observed over all loci. The number of alleles per locus ranged from 4.2 to 10.6. The average of expected and observed heterozygosity ranged from 0.67 to 0.82, and from 0.77 to 0.87, respectively. A total of 10, 16, 10, 11 and 5 unique alleles each were found in LZ, WH, QD, RZ and MB populations. The effective number of alleles varied from 2.87 for HSTS_7 to 6.83 for HSTS-h. The number of average genotypes ranged from 6.0 for HSTS_a to 15.4 for HSTS_h. As compared with the wild populations, the hatchery population, MB, showed significant genetic changes such as fewer alleles per locus (P <0.05), a smaller number of low frequency alleles (P <0.05), a small number of unique alleles and a small number of genotypes (P <0.05), all indicative of a reduction in genetic diversity.     

中国黄渤海真江蓠(Agarophyton vermiculophyllum)群体遗传多样性研究

真江蓠是原产于西北太平洋的重要经济红藻。我们利用10对微卫星引物检测中国黄渤海地区真江蓠的群体遗传多样性和结构。10个微卫星位点在12个群体中共检测到65个等位基因,每个位点的等位基因（N_a）为1~28,有效等位基因（N_e）为1.0~9.6。每个群体的平均等位基因（N_a）、平均有效等位基因（N_e）、平均香浓指数（I）、平均观察杂合度（H_o）和平均预期杂合度（H_e）分别为2.4、1.6、0.419、0.133和0.227,显示较低的群体遗传多样性。中国黄渤海12个真江蓠群体间遗传分化较大（F_st=0.398 7）,基因流有限（N_m=0.377 1）,近交系数为正（F_is=0.391 3,F_it=0.634 0）,表明可能存在近交和杂合子缺失现象。Structure和UPGMA系统进化分析一致将12个群体分为两个遗传组,并在黑石礁群体（HS）和石岛群体（SD）中发现明显的遗传混杂现象。AMOVA分析显示遗传变异主要来自于群体内（73.27%）。该研究可为黄渤海地区真江蓠自然资源保护和管理提供科学依据。     

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.     

绿鳍马面鲀微卫星标记开发及在丝背细鳞鲀中的通用性检测

为充分挖掘绿鳍马面鲀(Thamnaconus modestus)基因组资源,开发可用于群体遗传学研究的分子标记,本研究利用NCBI数据库中公布的绿鳍马面鲀全基因组序列筛查微卫星位点并在野生群体中验证,在85个选取的位点中筛选得到30个新的多态性较高的微卫星标记。每个微卫星标记的等位基因数为4~16,平均为8.5个;观测杂合度范围为0.207~0.916,平均值为0.685;期望杂合度范围为0.315~0.971,平均值为0.756;多态信息含量范围为0.301~0.898,平均值为0.716,其中属于高度多态的位点有26个,占总位点数的86.67%;经过Bonferroni校正后,有7个位点显著偏离Hardy-Weinberg平衡。将30个绿鳍马面鲀多态性微卫星标记在丝背细鳞鲀(Stephanolepis cirrhifer)中进行通用性检测,其中13个位点成功扩增,9个位点具有多态性。本研究开发的微卫星标记可用于绿鳍马面鲀及相关物种的遗传多样性分析、QTL定位以及系统进化等研究。     

中国沿海不同地区泥蚶(Tegillarca granosa)的遗传多样性分析

以采自海南海口、广西防城港、广西北海、广东湛江、福建漳州、山东荣成、山东威海7个地理群体62个泥蚶个体为材料,获取592bp线粒体COI基因片段序列,并进行遗传多样性及分化分析。多态性遗传参数统计显示:62个个体共检测出103个多态性位点,定义了26个单倍型;总群体单倍型多样性指数为0.834,核苷酸多样性指数为0.01665,平均核苷酸差异数为9.85772。7个群体均显示出较丰富的遗传多样性,群体内遗传距离及群体内遗传多样性参数显示中国沿海泥蚶遗传多样性由北向南呈升高趋势,而群体内遗传分化系数也呈现升高的趋势。基于26个单倍型COI序列构建的NJ树和UPGMA树以及基于群体间遗传距离构建的UPGMA树显示,荣成群体和威海群体亲缘关系较近,聚成一小支,而后与漳州群体相聚,然而南方类群并没有聚为独立的一支。     

Intraspecific cleaning by juvenile Cape white seabream Diplodus capensis (Sparidae) off eastern South Africa

Juveniles of the Cape white seabream Diplodus capensis were observed cleaning adult conspecifics in a large tidepool off Sodwana Bay, South Africa. Although nine other tropical fish species were present and interacted with a nearby pair of Labroides cleaner wrasses, only adults of D. capensis posed for and were cleaned by the D. capensis juveniles. Such cleaning interactions have not been reported previously for this species or among marine fishes off South Africa, and thus add to the growing list of facultative cleaners globally.     

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.     

Abundance and degree of residency of humpback dolphins Sousa plumbea in Mossel Bay,South Africa

Indian Ocean humpback dolphins Sousa plumbea inhabit nearshore waters from South Africa to eastern India. Humpback dolphins are vulnerable to conservation threats due to their naturally small population sizes and use of nearshore habitats, where human activities are highest. We investigated the abundance and residency of this species inhabiting Mossel Bay, South Africa, using photographic mark-recapture. Data were collected during 81 surveys in Mossel Bay between 2011 and 2013. Open population modelling using the POPAN parameterisation produced a ‘super-population’ estimate of 125 individuals (95% CI: 61–260) and within-year estimates of between 33 and 86 individuals (2011: 71 [95% CI: 30–168]; 2012: 33 [15–73], 32 [15–70]; 2013: 46 [20–108]). Although less appropriate, closed capture models were also run for comparison with previous studies in the region and generated similar, but slightly smaller, population estimates within each year. We compared our catalogue with opportunistic data collected from East London, Plettenberg Bay, De Hoop and Gansbaai. The only catalogue matches attained were between Plettenberg Bay (n = 44 identified) and Mossel Bay (n = 67 identified), separated by 140?km. Population exchange was moderate, with nine individuals resighted in multiple years between these two areas. This study supports previous findings of long-range movements for this species and provides a baseline from which to assess future impacts on the population.     

Hierarchical analysis of the population genetic structure in Concholepas concholepas,a marine mollusk with a long‐lived dispersive larva

For most marine invertebrate species, dispersal is achieved mainly or exclusively by pelagic larvae. When the duration of the pelagic larval stage is long, genetic homogeneity over large geographic scales is expected. However, genetic structure has often been reported over small spatial scales, suggesting that more complex processes occur than a simple positive relationship between pelagic larval duration and gene flow. Concholepas concholepas has a larval stage that can last up to 3 months in the water column with a wide distributional range covering from 6°S to 56°S. We used a hierarchical sampling technique to test if the genetic homogeneity of this highly dispersive species is maintained throughout its total geographic range in spite of environmental heterogeneity. In the three studied regions (Antofagasta Bay, Valdivia and Patagonia), a spatial pattern of isolation by distance in conjunction with a spatial genetic structure was observed. Within each region, different spatial genetic patterns were detected. In Antofagasta Bay and Valdivia there was evidence of substantial gene flow among populations, whereas in Patagonia, populations showed genetic structure and a unique, genetically isolated location was identified. These results revealed the existence of spatial differences in the genetic patterns among regions with different coastal topographies in C. concholepas, and give us new insights into the inter‐relationships of larval dispersal potential, actual larval dispersal and physical processes. Regarding the sustainable management of C. concholepas, two important issues are derived from this study: (i) to highlight the need for a regional context in the management of C. concholepas, (ii) to determine the distinctiveness of the most austral population and to focus on the conservation efforts due to the relevance of this area.     

基于线粒体cox1片段序列的胶州湾浮游动物DNA条形码分析

采用cox1基因特异扩增测序的方法,分析了胶州湾45种常见海洋动物的DNA条形码序列82条,联合GenBank中28条cox1序列的分析结果表明：种内个体间遗传差异均值为0.013（0—0.11）;属内不同种间遗传差异均值为0.265（0.137—0.369）,是种内遗传差异的20多倍,条形码间隙明显。在分子系统树中,...     

基于微卫星(SSR)分子标记的中国对虾渤海湾增殖亲虾群体及回捕群体的遗传多样性分析

Eight microsatellite markers were used to analyze genetic diversity, level of inbreeding, and effective population size of spawner and recaptured populations of Chinese shrimp(Fenneropenaeus chinensis) during stock enhancement in the Bohai Bay in 2013. A total of 254 and 238 alleles were identified in the spawner and recaptured populations, respectively, and the numbers of alleles(N_a) were 8–63 and 6–60, respectively. The numbers of effective alleles(N_e) were 2.52–21.60 and 2.67–20.72, respectively. The polymorphism information content ranged from 0.529 to 0.952. The observed heterozygosity(H_o) values(0.638–0.910 and 0.712–0.927) were lower than the expected heterozygosity(H_e) values(0.603–0.954 and 0.625–0.952), which indicated that the two populations possessed a rich genetic diversity. In 16 tests(2 populations×8 loci), 13 tests deviated from the HardyWeinberg equilibrium. F_(is) values were positive at seven loci and the inbreeding coefficients(F) of the two populations estimated by trio ML were 13.234% and 11.603%, suggesting that there was a relatively high degree of inbreeding. A certain level of inbreeding depression had occurred in the Chinese shrimp population. F_(st) values ranged from 0 to 0.059, with a mean of 0.028, displaying a low level of genetic differentiation in the two populations. Effective population sizes(3 060.2 and 3 842.8) were higher than the minimum number suggested for retaining the evolutionary potential to adapt to new environmental conditions. For enhancement activity in 2014,the ideal number of captured shrimp spawners should have ranged from 7 686 to 19 214 to maintain genetic diversity and effective population size. Further strategies to adjust the balance of economic cost, fishing effort and ideal number of shrimp spawners to maintain a satisfactory effective population size for ensuring the sustainability of Chinese shrimp are proposed.     

三峡库区短颌鲚(Coilia brachygnathus)新建种群的年龄结构、生长特征及遗传多样性分析

2019~2020年在三峡库区巫山(WS)、万州(WZ)、丰都(FD)、涪陵(FL)4个采样点采集到新建短颌鲚(Coilia brachygnathus)种群153尾个体,基于鳞片和10个微卫星DNA标记进行年龄结构、生长特征与遗传多样性分析。结果显示,短颌鲚种群体长分布范围为102.1~301.6mm,平均体长(196.6±40.0)mm;体重分布范围为1.90~79.70g,平均体重(17.70±13.06)g。短颌鲚种群年龄组为1~5龄,其中2龄和3龄为优势年龄组,占总个体数的82.35%。体长-体重呈幂函数指数关系,属于正异速生长类型。微卫星DNA标记分析结果显示,10个微卫星位点共检测到82个等位基因,各群体平均等位基因数(N_a)为5.600 0~7.300 0,平均有效等位基因数(N_e)为3.541 4~3.831 5,平均观测杂合度(H_o)为0.617 7~0.700 0,平均期望杂合度(H_e)为0.682 3~0.702 9之间,平均多态信息含量(PIC)为0.628 5~0.648 4。4个群体的遗传多样性水平均较高,呈现出由三峡库区下游至上游逐渐减小的特点。遗传结构分析结果显示,群体间遗传分化水平很低,遗传变异主要来源于个体内部。结果表明,三峡库区短颌鲚种群处于快速扩张阶段,4个群体均具有较丰富的遗传多样性,遗传结构未发生显著群体分化,群体间基因交流频繁。由此提示,三峡库区短颌鲚很可能来源于三峡大坝下种群扩张迁入三峡库区水域而繁殖建群。