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.     

Reproduction and recruitment patterns of the surf clam Donax serra (Bivalvia,Donacidae) on two Namibian sandy beaches

Reproduction and recruitment of the surf clam Donax serra on two Namibian beaches were studied over a period of two years. Histological examination of the gonads indicated a discontinous annual reproductive cycle, related to monthly mean sea surface temperature. The spawning season lasted from August/September to February, but juveniles (2 – 6 mm anterior-posterior shell length) were only present for three months in the intertidal zone. The condition index indicates that the species spawns during autumn and summer, but histological validation is needed. The period when juveniles are abundant is decoupled from the spawning period and therefore cannot be predicted clearly, even if the spawning period is known. Starvation, hydrodynamic processes, chemical parameters and different release times during the spawning period are thought to cause the differences in settlement time and recruitment strength between locations.     

Long‐term comparison of structure and dynamics of the red coral metapopulation of the Portofino Promontory (Ligurian Sea): a case‐study for a Marine Protected Area in the Mediterranean Sea

A large amount of data on the precious coral Corallium rubrum has attested to a dramatic shift in the size structure of its over‐harvested Mediterranean populations in recent decades. One of the main problems for the conservation of this species is the substantial lack of data concerning the time span necessary for a population subjected to pluri‐decennial harvesting pressure to return to its pristine status. Here, we present a multi‐annual data set gathered from the Marine Protected Area (MPA) of Portofino, which hosts the most important shallow‐water coral populations in the Ligurian Sea and was subjected to strong harvesting pressure from the 1950s to the early 1970s. Quantitative comparison of the population structure data recorded in 1964, 1990 and 2012 indicated a strong size increase of the colonies (from 3 to 8 g mean weight), resulting in an increase in colony biomass from 300 to the current 1500 g·m^?2. As a consequence, over the same span of time, the density of colonies has slightly decreased. The role of mass mortality phenomena, like that occurred in this area during 1999, as possible biological features triggering the switch of red coral populations from a ‘grass plain‐like’ towards a ‘forest‐like’ structure, is discussed. All these data indicate that the instigation of MPAs is a winning strategy in the conservation of this precious species and similar management plans should also be evaluated for the protection of the deep benthic communities thriving on off‐shore banks.     

Large‐scale connectivity of Grapsus grapsus (Decapoda) in the Southwestern Atlantic oceanic islands: integrating genetic and morphometric data

The degree of connectivity among island populations can influence their demography and affect their level of genetic differentiation. In this study we investigated genetic and morphometric differences among four populations of Grapsus grapsus (Linnaeus 1758), in Saint Peter and Saint Paul Archipelago (0°55′ N, 29°20′ W), Fernando de Noronha Archipelago (3°50′ S, 32°24′ W), Rocas Atoll (3°50′ S, 33°49′ W) and Trindade Island (20°30′ S, 29°20′ W) from 2003 to 2011. Morphometric results indicated the existence of two distinct groups based on the morphology of their chelae (Trindade Island/Saint Peter and Saint Paul Archipelago versus Fernando de Noronha/Rocas Atoll). In addition, genetic variation in a fragment of the mitochondrial control region revealed substantial differentiation between Trindade and the other islands, with Trindade Island showing only exclusive haplotypes. The congruence of the genetic and morphologic analyses suggests the occurrence of a divergent population in Trindade Island as well as high connectivity among the three remaining equatorial islands. This is the first study to assess the level of morphologic differentiation and genetic connectivity of a species among all four Southwestern Atlantic oceanic islands. Our results provide valuable insight into understanding connectivity through surface ocean currents and suggest that the unstable current system of this area could be responsible for different dispersal patterns. We also suggest that the design of Brazilian marine protected areas should be adjusted to provide stronger protection for Trindade Island as it harbors unique genetic and morphologic variation in G. grapsus.     

Population dynamics and condition index of natural stock of blood cockle,Tegillarca granosa(Mollusca,Bivalvia,Arcidae) in the Marudu Bay,Malaysia

The population parameters of blood cockles, Tegillarca granosa in the intertidal zone of Marudu Bay, Sabah,Malaysia were investigated based on monthly length-weight frequency data(July 2017 to June 2018). A total of 279 cockle individuals with shell length and weight ranging from 27.7 mm to 82.2 mm and 13.11 g to 192.7 g were subjected to analysis. T. granosa in Marudu Bay showed a consistent moderately high condition index 4.98±0.86 throughout the year. The exponent b of the length-weight relationship was 2.6 demonstrating negative allometric growth. The estimated asymptotic length(L_∞), growth coefficient(K) and growth performance(?) of the T.granosa population in Marudu Bay were estimated at 86.68 mm, 0.98 a~(-1) and 3.87, respectively. The observed maximum shell length was 82.55 mm and the predicted maximum shell length was 84.44 mm with estimated maximum life span(t_(max)) of 3.06 years. The estimated mean lengths at the end of 2, 4, 6, 8, 10 and 12 months of age were 21.31 mm, 31.16 mm, 39.53 mm, 46.63 mm, 52.67 mm and 57.79 mm. Total, natural, and fishing mortalities were estimated at 2.39 a~(-1), 1.32 a~(-1) and 1.07 a~(-1). The exploitation level(E) was 0.45. Results of the current study also demonstrated that T. granosa in the Marudu Bay has two major recruitment peaks; one in March and another in October. The exploitation level revealed that natural stock of T. granosa in the Marudu Bay was approaching the maximum exploitation level. If such trend continues or demand for T. granosa is increasing,coupled with no effective fisheries management in place, possibility of the T. granosa population in the Marudu Bay to collapse is likely to elevate.     

AFLP analysis revealed differences in genetic diversity of four natural populations of Manila clam(Ruditapes philippinarum) in China

1 IntroductionManila clam (Ruditapes philippinarum) is aworldwide distributed species. In China, it is foundfrom the northern to southern seashores (Wang etal., 1993; Zhuang, 2001). This species is eura-line with the salinity tolerance ranging from 20 to4…     

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.     

Population biology and secondary production of the harvested clam Tivela mactroides (Born, 1778) (Bivalvia,Veneridae) in Southeastern Brazil

The population structure, growth and production of the trigonal clam Tivela mactroides were investigated by monthly sampling between January 2003 and October 2004 in two areas (southern and northern) of the intertidal and subtidal zones of Caraguatatuba Bay, Southeastern Brazil. Intertidal sampling was carried out in each area along eight transects perpendicular to the shoreline. In the subtidal zone of both areas, one 50‐m dredging was performed along five sampling stations arranged on three transects perpendicular to the coast. The intertidal abundance of T. mactroides was higher in the southern (more dissipative conditions) than in the northern area. High abundances occurred in February–March 2004 in the south and in September 2004 in the north. The size structure showed that younger individuals dominated in the sublittoral, indicating that recruitment occurs in this zone, followed by the migration of these individuals to the intertidal, where they complete their life cycle. Tivela mactroides showed continuous reproduction, with 26 cohorts detected in the study period. The lower estimates for the growth index (?′ = 3.22), mortality rate (Z = 2.10 year^?1) and turnover rate (P/B = 1.21 year^?1), and conversely the longer life span (2.5 years) of T. mactroides in Caraguatatuba Bay (24°S) compared with Venezuelan populations (10°N) suggests a latitudinal pattern of these life‐history traits. The high production of T. mactroides in Caraguatatuba Bay was due to continuous recruitment and rapid and continuous growth, and demonstrates the importance of T. mactroides as a biological resource for many marine species and for the local residents.     

Spatial and temporal variations in the population structure of the soft-shell clam Mya arenaria in the Pomeranian Bay (southern Baltic Sea)

The population structure of Mya arenaria has been investigated in the sublittoral zone of the Pomeranian Bay (southern Baltic Sea). Box-corer samples were collected during a 1.5-year period in 1993/94 to follow changes in size and age structure of the clam populations in different parts of the study area. Large spatial differences in population structure were found between the sheltered southwest of the Bay and the shallow and exposed Oder Bank in the centre. The stock of the Oder Bank consisted of two different clam types. A slow-growing cohort was assumed to be autochtonous on the Oder Bank, whereas a fast-growing one was assumed to have immigrated from the surrounding area. The contribution of the two cohorts to the total density varied seasonally. Because of bedload transport of clams, the contribution to the reduction of the clam stock by wintering sea ducks could not be quantified. In the southwest of the Pomeranian Bay erosion was of minor importance. High mortality rates during the first two years of life were assumed to be caused by predation. Mortality rates of older cohorts remained stable until old age. Variations in cohort strength were related to interannual differences in the reproductive success. A mild winter presumably lowers the reproductive success in the subsequent summer. Severe oxygen depletion in summer 1994 caused a strong reduction in the clam stock at stations deeper than 10 m.     

Biochemical genetic structure and identification of hairtail fish (Trichiurus) populations in Chinese coastal waters

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The genetic structure of the exotic ascidian Styela plicata (Tunicata) from Italian ports,with a re‐appraisal of its worldwide genetic pattern

The pleated ascidian Styela plicata (Lesueur, 1823) is a solitary species commonly found in ports and marinas around the world. It has been recorded in the Mediterranean region since the mid‐19th century. In the present work, the species’ genetic diversity was analysed, employing a 613‐bp portion of the mitochondrial cytochrome c oxidase subunit I (COI) gene from 149 individuals collected in 14 ports along Italian coasts at spatial scales ranging from 1 to approximately 2200 km. Haplotype and nucleotide diversity values were h = 0–0.933 (total h = 0.789) and π = 0–0.145 (total π = 0.0094), respectively. A general southward trend of increasing within‐population genetic diversity was observed. Analysis of molecular variance revealed significant genetic structuring but no significant differences were detected among basins, and no isolation by distance was found. Our data were integrated with the COI sequences available from previous studies and re‐analysed in order to investigate the possible routes of introduction of this ascidian into the Mediterranean Sea. The presence of the two COI haplogroups detected in previous molecular investigations on S. plicata at intercontinental spatial scale was confirmed in the Mediterranean Sea. The results revealed multiple introductions of S. plicata, although some locations appear to have experienced rapid expansion from few founding individuals with reduced genetic diversity. However, continuous introductions would confound the pattern deriving from single founder events and make it difficult to estimate the time needed for gene diffusion into established populations. This mixing of effects creates difficulties in understanding the past and current dynamics of this introduction, and managing this alien invasive ascidian whose genetic structure is continuously shuffled by vessel‐mediated transport.     

基于线粒体控制区序列的黄海日本鳀(Engraulis japonicus)的群体遗传结构*

遗传多样性和群体遗传结构是研究群体动态变化的重要内容, 也是种质资源评估与保护的基础。日本鳀(Engraulis japonicus)是我国东部近海的重要鱼种, 具有重要的生态价值和经济价值。文章利用线粒体控制区全序列分析了黄海海域4个地理群体(北黄海北部、北黄海南部、南黄海北部和南黄海中部)日本鳀的遗传多样性、种群遗传结构和历史动态变化。结果显示, 131个样品检测到了126个单倍型, 且4个群体的单倍型多样性均很高, 其中北黄海南部群体的最低(0.995±0.009), 南黄海中部群体的最高(1.000±0.014)。而核苷酸多样性均较低, 为0.010±0.005 ~ 0.011±0.006。主成分判别分析(DAPC)和遗传分化系数F_st表明4个群体无明显的群体分化现象, 群体间的遗传同质性水平高, 分子方差分析(AMOVA)也显示分子变异基本来自于群体内, 并且没有明显的群体遗传结构。贝叶斯系统发育树分析发现, 黄海日本鳀有2个谱系, 谱系1和谱系2的分化时间为0.701Ma前, 可以追溯到更新世期间; 进一步中性检验和核苷酸错配分布分析表明这2个谱系可能发生过群体扩张。贝叶斯天际线图则显示黄海鳀鱼的有效群体数量在0.150Ma前发生了明显的下降。     

基于鳃的microRNA转录组研究中国蛤蜊对重金属镉的响应

中国蛤蜊（Mactra chinensis）是一种重要的经济贝类,分布于我国的辽宁和山东。近年来,生境恶化和过度捕捞导致我国蛤蜊资源量减少。我们利用Illumina Hiseq-2500平台对中国蛤蜊鳃的microRNA转录组进行测序,运用差异表达寻找对镉刺激有响应的功能microRNA。结果显示对照组获得了14 415 256条clean reads,实验组获得了15 570 111条clean reads。在这些reads中一共存在14 584 077小RNA,包括1 898 035条unique小RNA,其中对照组和实验组共有187 859条unique小RNA。两个组的小RNA文库的片段长度分布是相似的,大部分小RNA长度分布在26~27 nt。在对照组文库中最丰富的片段长度是27 nt,其次是28 nt、26 nt和23 nt。在实验组文库中,数量最丰富的片段长度是26 nt,其次是27 nt、28 nt和23 nt。经过对序列前体以及结构特征的分析,发现这两个组中一共有50个microRNA,其中已知的是38个,新发现的是12个。对照组和实验组microRNA含量最丰富的片段长度是23 nt。通过差异表达分析,5个microRNA基因具有显著性差异且从对照组到实验组的表达量是上调的,其余45个没有显著性的差异。把这50个序列与中国蛤蜊转录组进行比对,一共找到了542个靶基因。5个具有表达差异的基因一共比对到11个靶基因。把这11个靶基因与NCBI数据库比对,4个靶基因在COG中得到注释,1个靶基因在GO中得到注释,6个靶基因在KEGG中得到注释,11个靶基因在nr数据库中得到注释,注释到的基因有泛素蛋白连接酶E3,Wnt信号通路,G蛋白信号调控等。     

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.