The fate of terrestrial organic matter in two Scottish sea lochs

Sea lochs are zones of rapid organic matter (OM) turnover. Most of this OM is of allochthonous origin, being introduced into the lochs via freshwater input. In this study the behaviour of terrestrially derived OM was elucidated using a combination of parameters which indicate OM diagenesis in the near surface sediments from two Scottish sea lochs, Loch Creran and Loch Etive. Alkaline CuO oxidation was used to determine lignin phenols which serve as biomarkers for terrestrial OM in sediments. Stable carbon isotope, total carbon and nitrogen and total OM (including the labile and refractory fractions) compositions were also determined.     

Genetic stock structure of white steenbras Lithognathus lithognathus (Cuvier, 1829), an overexploited fishery species in South African waters

White steenbras Lithognathus lithognathus (Teleostei: Sparidae) is an overexploited marine fish species endemic to South Africa. Overexploitation in recreational, subsistence and commercial fisheries has resulted in stock collapse and the need for improved management of the species. Adults are thought to undertake large-scale annual spawning migrations, yet studies of their movement indicate low levels of connectivity among coastal regions. To address this, mitochondrial DNA sequencing and genotyping of microsatellite loci in the nuclear genome were conducted to determine the genetic stock structure and level of gene flow in this species. Genetic diversity was high throughout the species’ core distribution, with no evidence of isolation by way of distance or localised spawning. Low, non-significant pairwise fixation indices (F_ST, R_ST and Jost’s D_est) indicated low genetic differentiation and high levels of gene flow. The observed results, and agreement between mitochondrial and microsatellite DNA, confirm that white steenbras exists as a single genetic stock with high levels of gene flow throughout its distribution.     

Genetic diversity and population structure of the size‐selectively harvested owl limpet,Lottia gigantea

Size‐selective harvesting can elicit a genetic response in target species through changes in population genetic subdivision, genetic diversity and selective regimes. While harvest‐induced genetic change has been documented in some commercially important species through the use of historic samples, many commonly harvested species, such as coastal molluscs, lack historic samples and information on potential harvest induced genetic change. In this study, we have genotyped six microsatellite markers from populations across much of the California mainland range of the size‐selectively harvested owl limpet (Lottia gigantea) to explore the genetic structure and diversity of this species. We found no significant genetic structure or differences in genetic diversity among populations of L. gigantea. Our results suggest high gene flow among populations and that differences in life history, demography, and body size previously observed between protected and exploited populations is largely due to phenotypic plasticity. From a conservation perspective, if proper actions are taken to curb harvesting, then exploited populations should be able to return to their pre‐impact state given sufficient time.     

蟹类微卫星DNA标记的筛选及其在遗传学研究中的应用

微卫星DNA标记是近年来最受研究者青睐的分子标记之一.由于其具有高度多态性、共显性遗传、基因组中含量丰富且随机分布等特点,已被应用于种群分化研究、亲缘分析、基因连锁分析、进化以及生态学研究等许多领域.近年来,蟹类微卫星的研究报道日益增多.文中对蟹类微卫星分离方法、引物设计、遗传学特性以及在种群遗传、家系分析、遗传多样性评价等方面的最新研究进展进行综述,并分析微卫星分析中无效等位基因(null allele)、"结巴"带(stutter bands)和上游等位基因"扩增丢失"现象(upper allelic dropout)的产生原因以及对微卫星基因型判读带来的影响.     

Genetic diversity and population connectivity of the sea urchin Tripneustes gratilla along the South African coast

The collector sea urchin Tripneustes gratilla has been identified as a species with potential for aquaculture production in South Africa. The species’ roe is considered a culinary delicacy in Asia and Europe. However, T. gratilla remains genetically uncharacterised in South Africa. Therefore, the purpose of this study was to provide baseline genetic information consisting of estimates of genetic diversity and population stratification, which may aid in future sustainable use of this urchin resource. A total of 22 species-specific microsatellite markers were used for the genetic characterisation of T. gratilla samples from along the South African coast, at Haga Haga, Coffee Bay, Hibberdene, Ballito Bay and Sodwana Bay. A moderate level of genetic diversity was observed, with an average number of alleles of 7.89 and an average effective number of alleles of 6.57, as well as an average observed heterozygosity of 0.55. Population differentiation tests suggest that the geographically representative samples form part of a single, large interbreeding population, with a global F_st estimate of 0.02 (p > 0.05). This finding is likely explained by high levels of gene flow between these locations caused by extensive larval dispersal during the planktonic larval stage. The panmixia observed within these natural populations of T. gratilla indicate that they could be managed as a single genetic stock.     

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 connectivity of the coral‐eating sea star Acanthaster planci during the severe outbreak of 2006–2009 in the Society Islands,French Polynesia

Occasional population outbreaks of the crown‐of‐thorns sea star, Acanthaster planci, are a major threat to coral reefs across the Indo‐Pacific. The presumed association between the serial nature of these outbreaks and the long larval dispersal phase makes it important to estimate larval dispersal; many studies have examined the population genetic structure of A. planci for this purpose using different genetic markers. However, only a few have focused on reef‐scale as well as archipelago‐scale genetic structure and none has used a combination of different genetic markers with different effective population sizes. In our study, we used both mtDNA and microsatellite loci to examine A. planci population genetic structure at multiple spatial scales (from <2 km to almost 300 km) within and among four islands of the Society Archipelago, French Polynesia. Our analysis detected no significant genetic structure based on mtDNA (global F_ST = ?0.007, P = 0.997) and low levels of genetic structure using microsatellite loci (global F_ST = 0.006, P = 0.005). We found no significant isolation by distance patterns within the study area for either genetic marker. The overall genetically homogenized pattern found in both the mitochondrial and nuclear loci of A. planci in the Society Archipelago underscores the significant role of larval dispersal that may cause secondary outbreaks, as well as possible recent colonization in this area.     

Microsatellites reveal fine‐scale genetic structure of the Chinese surf clam Mactra chinensis (Mollusca,Bivalvia, Mactridae) in Northern China

As a commercially important fisheries resource in East Asia, the Chinese surf clam Mactra chinensis has experienced severe population declines in the past decades, probably due to over‐exploitation. To provide scientific bases for fisheries management and artificial breeding, we investigated genetic variation and population structure of Mactra chinensis in Northern China using microsatellites. Samples collected from eight localities throughout natural habitats of the species in Northern China were genotyped. Nine microsatellites revealed high allelic diversity with 14–36 alleles per locus. Observed and expected heterozygosity varied from 0.593 to 0.945 and from 0.638 to 0.958, respectively. Pairwise F_ST values indicated that all population pairs had small but significant genetic differentiation. A Mantel test showed statistically significant correlations between genetic distance and geographical distance, indicating that genetic differentiation of the Chinese surf clam conformed to a pattern of isolation‐by‐distance. Cluster analysis using neighbor‐joining separated the eight populations into three groups. The three areas of low gene flow identified by barrier analysis corresponded with local oceanographic features, suggesting that marine currents and peninsulas play an important role in population structuring of this species.     

The influence of environmental variability of a coastal lagoon ecosystem on genetic diversity and structure of white seabream [Diplodus sargus (Linnaeus 1758)] populations

As coastal lagoons serve as nursery areas for some marine and estuarine fish, selective pressures of these brackish or hypersaline lagoons may influence the genetic structure of species and populations. We examined spatial and temporal genetic patterns at eight microsatellite loci in white seabream [Diplodus sargus (Linnaeus 1758)] recruits from the Mar Menor (Southeast Spain) and compared these loci with those in coastal populations from the open sea, observing a high degree of genetic diversity and spatio‐temporal genetic stability. However, the results suggest the presence of subpopulations or genetic substructures in the Mar Menor D. sargus population that could be interpreted as a homogeneous mixture of individuals from three differentiated subpopulations in the Mediterranean and evidence of the Wahlund effect. It also suggests that D. sargus adults return to their original spawning habitat, thus conserving the genetic differences among the respective populations over time. Overall, this study demonstrates the importance of the Mar Menor coastal lagoon as a nursery area for the conservation of genetic diversity of D. sargus populations.     

Population genetics of cold‐water coral associated Pleustidae (Crustacea,Amphipoda) reveals cryptic diversity and recent expansion off Iceland

Amphipoda are a diverse and important faunal component of deep‐sea habitats worldwide. However, relatively little is known about species that are associated with cold‐water corals, in particular concerning their genetic diversity, population genetic processes, population differentiation, and potential host specificity. We exemplarily investigate these questions studying three pleustid species—Stenopleustes aff. malmgreni (Boeck, 1871), Stenopleustes aff. nodifera (Sars, 1883) and Neopleustes aff. boecki (Hansen, 1888)—that are associated with cold‐water corals and polychaete assemblages along the Reykjanes Ridge southwest of Iceland. We sequenced mitochondrial COI and performed ddRAD to study thousands of nuclear loci. These species and a pair of morphologically cryptic species within Stenopleustes aff. nodifera were consistently delimited by COI and ddRAD. We conclude that all of our studied species are new to science, raising the number of pleustids reported from cold‐water corals to six. Two species were collected only once, and these species exhibited high levels of inbreeding, suggesting little exchange with other populations, which might be a result of strong host specificity. The other two species were wider distributed, with very low differentiation among populations, even between populations separated by 130 km. These species showed signs of recent population expansions, possibly in relation to changes in the cold‐water coral associated ecosystem (e.g., due to glacial cycles and/or volcanic or geothermal activities). They had lower levels of inbreeding and were each associated with three different host coral species, which might facilitate dispersal and gene flow. Our results show divergent population genetic patterns for the studied pleustid species. These might be attributed to the species’ host specificity and highlight important differences among species with seemingly similar life‐styles. Species diversities appear to be greatly underestimated, limiting our abilities to truly assess the vulnerability of the fauna living in these threatened cold‐water coral habitats.     

Ocean currents determine functional connectivity in an Antarctic deep‐sea shrimp

The coherency among larval stages of marine taxa, ocean currents and population connectivity is still subject to discussion. A common view is that organisms with pelagic larval stages have higher dispersal abilities and therefore show a relatively homogeneous population genetic structure. Contrary to this, local genetic differentiation is assumed for many benthic direct developers. Specific larval or adult migratory behavior and hydrographic effects may significantly influence distribution patterns, rather than passive drifting abilities alone. The Southern Ocean is an ideal environment to test for the effects of ocean currents on population connectivity as it is characterized by several well‐defined and strong isolating current systems. In this study we studied the genetic structure of the decapod deep‐sea shrimp Nematocarcinus lanceopes, which has planktotrophic larval stages. We analysed 194 individuals from different sample localities around the Antarctic continent using nine microsatellite markers. Consistent with a previous study based on mitochondrial DNA markers, primarily weak genetic patterns among N. lanceopes populations around the continent were found. Using ocean resistance modeling approaches we were able to show that subtle genetic differences among populations are more likely explained by ocean currents rather than by geographic distance for the Atlantic Sector of the Southern Ocean.     

Attainment of ecosystem based governance in European waters—A State property rights regime approach for Ireland

On Ireland's continental shelf, as well as within its Exclusive Economic Zone (EEZ), there are significant biodiversity hotspots including those associated with Cold Water Corals (CWC). Some of these ecosystems enjoy little or no actual protection and are subject to the effects of open access. Sectorally driven initiatives, a recalcitrant attitude to environmental law and inadequate governance, have added to the conditions that have facilitated years of damage by fishers and other actors from many States. A review of the current governance regime, influenced primarily by the Common Fisheries Policy (CFP), is presented. Failings of this regime are highlighted by the destruction of some biodiversity hotspots associated with vulnerable marine ecosystems (VMEs), an externality primarily arising from the effects of deepwater fishing. While exploring some of the principles relating to the institution of property rights, this paper makes a link between property rights, the public trust doctrine and sovereign rights. The paper suggests that such biodiversity systems are the property of citizens of the individual States in whose area of jurisdiction they occur. The paper argues for an Irish State property rights regime as part of an ecosystem approach within a nested institutional architecture. This has important implications for the governance of biodiversity such as that associated with CWC and for the development of an Irish National Oceans Policy.     

厦金海域珊瑚体内重金属水平和分布特征

采用电感耦合等离子体质谱仪测定了厦金海域8种珊瑚中Cr、Mn、Co、Ni、Cu、Zn、As、Cd、Sn、Sb、Pb重金属的含量,通过数据处理、主成分分析方法,分析了重金属分布特征和其主要来源。采用单因子污染指数法对珊瑚重金属的污染水平进行了评价。结果表明,其平均浓度水平从大到小依次为:ZnMnSnCrCuAsNiPbSbCdCo。在8种珊瑚中,星柳珊瑚(Astrogrogia sp.)、等柳珊瑚(Paris fruticosa)、Paraplexaura sp.的重金属含量较高,花柳珊瑚(Anthogorgia sp.)和Guaiagorgia anas的含量较低。台湾海域珊瑚中Cu、Zn、Pb、Ni的含量、委内瑞拉海域珊瑚中Zn、Pb、Ni的含量远高于厦金海域珊瑚体内相同重金属含量,大堡礁珊瑚中Cu含量较厦金海域的略高。通过相关性分析发现,Cr、Co、Ni、Zn和Sn的种间差异较为显著。根据主成分分析,厦金海域珊瑚体内重金属元素可能的污染来源有:农业污染、港口生活污水和工业污水的排放、船舶油漆、涂料侵蚀、电镀工业。单因子污染指数法评价结果表明,6种重金属元素中,大佰屿、白哈礁和角屿的主要污染物是Mn。白哈礁、大佰屿站位的珊瑚体内重金属Mn处于重度污染水平,角屿站位的处于中度污染水平。     

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.     

皱纹盘鲍野生与养殖群体遗传多样性的研究

用随机扩增多态DNA（RAPD）技术,对山东长岛（CW）、辽宁大连（DW）两个野生群体和山东崆峒岛（KC）一个养殖群体的皱纹盘鲍遗传多样性进行了分析.结果表明,CW和DW群体间的遗传距离为0.170 3,CW和KC群体间的遗传距离为0.367 3,DW和KC群体间的遗传距离为0.347 7,显示野生群体与养殖群体之间的亲缘关系已发生了变化.CW,DW和KC三个群体的多态位点比例分别为49.22%、50.78%和43.75%;平均杂合度分别为0.350 6,0.340 8和0.307 9.与野生群体相比,养殖群体的多态位点比例和杂合度都有不同程度的降低.     

Biogeographic variability in the physiological response of the cold‐water coral Lophelia pertusa to ocean acidification

While ocean acidification is a global issue, the severity of ecosystem effects is likely to vary considerably at regional scales. The lack of understanding of how biogeographically separated populations will respond to acidification hampers our ability to predict the future of vital ecosystems. Cold‐water corals are important drivers of biodiversity in ocean basins across the world and are considered one of the most vulnerable ecosystems to ocean acidification. We tested the short‐term physiological response of the cold‐water coral Lophelia pertusa to three pH treatments (pH = 7.9, 7.75 and 7.6) for Gulf of Mexico (USA) and Tisler Reef (Norway) populations, and found that reductions in seawater pH elicited contrasting responses. Gulf of Mexico corals exhibited reductions in net calcification, respiration and prey capture rates with decreasing pH. In contrast, Tisler Reef corals showed only slight reductions in net calcification rates under decreased pH conditions while significantly elevating respiration and capture rates. These differences are likely the result of environmental differences (depth, pH, food supply) between the two regions, invoking the potential for local adaptation or acclimatization to alter their response to global change. However, it is also possible that variations in the methodology used in the experiments contributed to the observed differences. Regardless, these results provide insights into the resilience of L. pertusa to ocean acidification as well as the potential influence of regional differences on the viability of species in future oceans.     

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.     

海洋动物群体遗传学的研究进展

近年来，海洋动物群体遗传学已经成为海洋生态研究的热点和重要研究领域。介绍了影响海洋动物群体遗传结构的因素，阐述了海洋动物群体遗传的变化规律，概括了多年来国内外海洋动物群体遗传学的研究成果和研究进展，详细介绍了海洋动物群体遗传类型和海洋动物群体遗传学常用的遗传标记，并对今后海洋动物群体遗传学的研究方向进行了展望。