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Emerald Basin on the Scotian Shelf off Nova Scotia, Canada, is home to a globally unique population of the glass sponge Vazella pourtalesi. Through the analysis of both in situ photographs and trawl catch data from annual multispecies bottom-trawl surveys, we examined community composition, species density, and abundance of epibenthos and fish associated with V. pourtalesi compared to locations without this sponge. Using generalized linear models and analysis of similarities, the importance of V. pourtalesi in enhancing species density and abundance of the associated epibenthic community was assessed against that of the hard substrate on which it settles. Our results indicated that the megafaunal assemblage associated with V. pourtalesi was significantly different in composition and higher in species density and abundance compared to locations without V. pourtalesi. Analysis of similarity of trawl catch data indicated that fish communities associated with the sponge grounds are significantly different from those without V. pourtalesi, although no species were found exclusively on the sponge grounds. Our study provides further evidence of the role played by sponge grounds in shaping community structure and biodiversity of associated deep-sea epibenthic and fish communities. The mechanism for biodiversity enhancement within the sponge grounds formed by V. pourtalesi is likely the combined effect of both the sponge itself and its attachment substrate, which together comprise the habitat of the sponge grounds. We also discuss the role of habitat provision between the mixed-species tetractinellid sponges of the Flemish Cap and the monospecific glass sponge grounds of Emerald Basin.

The first living sample of Lophelia pertusa from Greenlandic waters was inadvertently collected at 60.3675°, −48.45528°, entangled together with other corals to a seawater sampler and property sensor (CTD) package. We collected in situ photographs taken at two sites in the same area in order to determine whether a reef was present. We identified reef-like structures formed by living and dead L. pertusa at 886–932 m depth on a steep slope. We assembled and analyzed hydrographic data to characterize the reef environment in order to facilitate future localization of other reefs and predictions of the impacts of climate change. We showed that the reef was located in a layer of modified Atlantic Water of relatively stable bottom temperature (4.1–5.0 °C) and salinity (34.90–34.98) with density slightly higher (27.62–27.71 kg m−3) than that reported for the occurrence of reefs in the northeast Atlantic, and in an area with exceptionally and persistently high currents of >15 cm s−1 at 1000 m. The intermediate-depth salinity maximum was found in the depth range where the corals were found. We discovered signals of consistent vertical and horizontal transports at 700–900 m over the reef area. Although this area is not directly influenced by intermediate and deep convection in the Labrador Sea, the seasonal evolution of near-bottom temperature, salinity and density for the 700–900 m depth range revealed strong seasonal patterns with both temperature and salinity reducing to their annual minimal values at the end of March and staying low for 1 month with an indication of a second minimum in June, 3 months later. The occurrence and temporal extent of these minima likely arose through a combination of local convection from the surface and advection of cooled and freshened waters at depth from the Irminger Sea. A diversified associated fauna was described; the short list of species compiled from our limited sample comprised species common in the area, as well as rare species, species new to Greenland, and species new to science

The structure, composition and distribution of epibenthic invertebrate assemblages on the Tail of the Grand Bank of Newfoundland and Flemish Cap (northwest Atlantic) were sampled using depth-stratified trawls. Faunal analysis of 152 uniquely identified taxa produced hierarchical synoptic tables of species associations with diagnostic indicators based on species fidelity. Twelve spatially coherent epibenthic megafaunal assemblages were identified, each with relatively sharp faunal boundaries and unique species attributes. These assemblages were shown a posteriori through ANOSIM to have statistically different species compositions, and were nested within three major regional-scale faunal groups: (I) the continental shelf of the Tail of the Grand Bank, typified by the sea cucumber Cucumaria frondosa and the sand dollar Echinarachnius parma ; (II) the upper slope of the Grand Bank and top of Flemish Cap, typified by the sponges Radiella hemisphaerica and Iophon piceum and the sea star Ceramaster granularis ; and (III) the lower slope of the Grand Bank and Flemish Cap, typified by the sea urchin Phormosoma placenta , and the sea pens Anthoptilum grandiflorum and Funiculina quadrangularis. Comparisons with literature on benthic species associations from a half century ago suggest that the assemblages identified herein have persisted in the area at least for decades. Detrended correspondence analysis (DCA) identified a well-defined biological gradient along the first axis with very high species turn-over. Ten environmental variables (including Trawling Intensity) were significantly correlated with the ordinated data. At one extreme the continental shelf faunal group (I) was associated with shallow depth (mostly, less than 200 m), coarse sediments and cold and fresh water associated with the Labrador Current. At the other extreme the lower slope faunal group (III; stations below 500–600 m throughout the study area) was strongly associated with deep water, muddy sediments, and warmer and saltier water. Conditional tests under a step-wise model identified the percentage of mud as having the greatest explanatory power (40%) of the tested environmental variables. Trawling Intensity explained 11% of the variation in the full data set in marginal tests. Species richness in the deep water assemblages (Cluster III) was significantly and negatively correlated with fishing intensity. The species most directly associated with high trawling intensity in the DCA were the hard-shelled scavenging and predatory gastropods and a thick-shelled bivalve, consistent with expectations based on the trawling impact literature. Our study fills a critical knowledge gap in this important fishing area, and our novel regional-scale maps of the epibenthic assemblages will facilitate the development of ecosystem-based models linking benthic and pelagic systems and inform biodiversity conservation.

Deep-sea coral aggregations represent important ecosystems in the Flemish Cap, where some areas have been closed to bottom fisheries by the Northwest Atlantic Fisheries Organization in order to implement conservation and management measures and prevent significant adverse impacts on Vulnerable Marine Ecosystems (VMEs). Flemish Cap is an offshore Bank located about 600 km to the east of Newfoundland, separated from the Grand Banks by the Flemish Pass, a channel approximately 1200 m deep. 40 taxa of corals were identified in the area from bottom trawl research vessel surveys (2006-2015) and rock dredges (2009-2010). They included 22 Alcyonacea, 11 Pennatulacea, 3 Antipatharia and 4 Scleractinia. Corals identified were classified according to their biological traits in an attempt to better understand their function in the ecosystem. This study analyzes which biological traits were useful to classify corals in the Flemish Cap and Flemish Pass prioritizing traits where information is available and that capture variation for a range of biological or ecological processes. This study represents a baseline classification, quantifying trait variation among species, for further studies such as habitat suitability models or impact studies from trawl fisheries and oil and gas exploitation, which represent the main potential human activities in the area.

We examined four species of sea pen (Anthoptilum grandiflorum, Halipteris finmarchica, Pennatula aculeata and Pennatula grandis) collected from the Gulf of St. Lawrence and mouth of the Laurentian Channel, eastern Canada. An exponential length–weight relationship was found for all four species, where growth in weight was progressively greater than growth in length with increasing colony size. Halipteris finmarchica, P. grandis and P. aculeata presented the better allometric fits, explaining over 80% of the variance. In addition, a count of growth increments visible in transverse sections in 86 A. grandiflorum and 80 P. aculeata samples was made. Presumed ages ranged between 5 and 28 years for A. grandiflorum and 2 and 21 years for P. aculeata. Radiocarbon assays were inconclusive and could not be used to confirm these ages; further age validation is required. Radial growth of the rod is slow during the first years, increasing at intermediate sizes of the colony and slowing down again for large colonies. Similar results were obtained from the relationship between colony length and number of growth increments where a logistic model was the best fit to the data. On average Spearman’s rank correlations showed 11% of shared variance between sea pen length or weight and environmental variables. Bottom temperature and salinity, depth and summer primary production were significantly correlated to sea pen size for most species., This project was funded by Fisheries and Oceans Canada through an International Governance Strategy (IGS) project awarded to EK. FJM was funded by the Natural Sciences and Engineering Research Council of Canada (Visiting Fellowship Programme).

Emerald Basin on the Scotian Shelf off Nova Scotia, Canada, is home to a globally unique aggregation of the glass sponge Vazella pourtalesi, first documented in the region in 1889. In 2009, Fisheries and Oceans Canada (DFO) implemented two Sponge Conservation Areas to protect these sponge grounds from bottom fishing activities. Together, the two conservation areas encompass 259 km2. In order to ascertain the degree to which the sponge grounds remain unprotected, we modelled the presence probability and predicted range distribution of V. pourtalesi on the Scotian Shelf using random forest modelling on presence-absence records. With a high degree of accuracy the random forest model predicted the highest probability of occurrence of V. pourtalesi in the inner basins on the central Scotian Shelf, with lower probabilities at the shelf break and in the Fundian and Northeast Channels. Bottom temperature was the most important determinant of its distribution in the model. Although the two DFO Sponge Conservation Areas protect some of the more significant concentrations of V. pourtalesi, much of its predicted distribution remains unprotected (over 99%). Examination of the hydrographic conditions in Emerald Basin revealed that the V. pourtalesi sponge grounds are associated with a warmer and more saline water mass compared to the surrounding shelf. Reconstruction of historical bottom temperature and salinity in Emerald Basin revealed strong multi-decadal variability, with average bottom temperatures varying by 8 ̊C. We show that this species has persisted in the face of this climatic variability, possibly indicating how it will respond to future climate change. &nbsp

A task of the EU ATLAS project is to review the current and likely future status of North Atlantic Area-Based Management Tools (ABMTs) in Areas Beyond National Jurisdiction (ABNJ) informed by predicted shifts in ecosystem dynamics. The effectiveness of these ABMTs, established by multi-lateral environmental agreements, needs to be assessed in terms of the spatial and temporal dimensions of those components of biodiversity which they identify as significant and/or which they are intended to protect, against predicted shifts in ecosystem dynamics. ABMTs under consideration are currently subject to review and scrutiny, through evaluations largely taking place independently of one another in line with the aims and obligations of the organisations responsible for their designation. This report contributes to an evaluation of priorities for an expert assessment of OSPAR Marine Protected Areas (MPAs), CBD Ecologically or Biologically Significant Marine Areas (EBSAs), and FAO Vulnerable Marine Ecosystems (VMEs) as identified or currently proposed for the North Atlantic ABNJ and will inform an expert workshop in 2018.

A previous study on the effects of experimental hydraulic clam dredging on seabed habitat and commercial bivalve populations revealed a lack of recovery after a 3-year post-dredging period (1998–2001) on a deep (65–75 m) offshore sandy bank on the Scotian Shelf, Canada. Follow-up sidescan sonar surveys were carried out 5 and 10 years after dredging (2003, 2008) in order to identify long-term processes of seabed recovery. Grab sampling was carried out 10 years after dredging to identify post-dredging commercial bivalve recruitment. Changes in the seafloor, including dredge tracks, were documented with a series of 7 sidescan sonar surveys between 1998 and 2008. A sediment mobility model was constructed based on modeled tidal current and hindcast wave data over this time period to quantify natural seabed disturbance and interpret changes to the dredge tracks mapped by sidescan sonar surveys. The model indicated that tidal currents had minimal effect on sediment mobilization. The main driving force associated with re-working of surficial sediments as evidenced by deterioration of dredge tracks in sonograms was annual fall/winter storms. While the annual frequency of storms and associated wave heights was variable, the observations and sediment mobility calculations suggest that the most influential variable is the magnitude of individual large storms, specifically storms with a significant wave height of ∼11 m. These storms are capable of generating mobile sediment layers of 20–30 cm thickness, equivalent to the dredge blade cutting depth. It appears that, with minor exceptions, sediment properties have returned to pre-dredging conditions 10 years after dredging in this habitat. Based on known age-length relationships, the four commercial bivalve species showed very low recruitment at the experimental site over the 10-year post-dredging period. However, this is unlikely due to a dredging effect since a similar pattern was observed in non-dredged areas.

This chapter reviews the major known monospecific and multispecific sponge aggregations in the world’s oceans. They are shown to occur from the intertidal to abyssal depths, in tropical, temperate, and high latitudes and sometimes to create spectacular formations, such as glass sponge reefs, lithistid reef-like fields, and carnivorous sponge grounds. Sponge aggregations are recognized as singular vulnerable habitats that deserve special research attention and legal protection. However, this review reveals that there is only a poor and fragmentary understanding of the main biological, environmental, and geochemical factors that favor and maintain these systems, including the food supply, which is fundamental knowledge. There is also a particular lack of information regarding reproductive biology, growth rates, life spans, and the main factors causing mortality, all crucial drivers for understanding population and community dynamics and for developing conservation strategies. The sponge aggregations have been shown to increase the structural complexity of the habitats, attracting a larger variety of organisms and locally enhancing biodiversity. From the very few cases in which sponge biomass and sponge physiology have been reliably approached jointly, phenomenal fluxes of matter and energy have been inferred. Through their benthic-pelagic coupling, some of the densest sponge aggregations have a significant local or regional impact on major biogeochemical cycles and food webs. Physical damage and habitat destruction derived from man-driven activities along with epidemic diseases facilitated by global environmental alterations emerge as major threats to the future of the sponge aggregations., This study has benefitted from funding by the Spanish Ministry of Economy and Competitiveness (CTM2012-37787) to MM; from the Caribbean Coral Reef Ecosystems Program and the National Museum of Natural History, Washington to KR, CD, and MM (Contribution Number 986); from Stiftung Drittes Millennium, Fundación Biodiversidad, and the Ministerio de Agricultura, Alimentación y Medio Ambiente to Oceana and RA; from NIWA, New Zealand Foundation for Research, Science and Technology, and CSIRO’s Division of Marine and Atmospheric Research to MK; the Natural Sciences and Engineering Council of Canada for Discovery and Ship Time grants to SPL; from the Norwegian Research Council to RJB and HTR; from The Norwegian Oil and Gas and the Norwegian Biodiversity Information Centre to HTR; and from the Natural Sciences and Engineering Council of Canada for Discovery and Ship Time grants to SPL.

International audience; The Canadian Arctic shelters millions of seabirds each year during the breeding season. By the excretion of important quantities of guano, seabirds locally concentrate nutrient-rich organic matter in the marine areas surrounding colonies. Seabirds, acting as biological vectors of nutrients, can markedly affect terrestrial ecosystems, but their influence on the structure of marine benthic communities is still under-studied. Sessile and long-lived megabenthic species can integrate environmental variation into marine food webs over long time frames. The objectives of this study were (1) to characterize the epifaunal and infaunal communities of the Lancaster Sound Region (LSR) and (2) to test the influence of the presence of seabird colonies and other environmental parameters on the structure of those benthic communities. Our prediction was that benthic diversity, number of taxa, total biomass of infauna and total density of epifauna and infauna, would be higher in areas with colonies present. Photos of the seafloor (data on epifauna) and grab samples (data on infauna) were taken at three control areas and at five areas near seabird colonies, within a depth range of 122 to 442 m. A database of 26 environmental parameters was built to study the environment-benthos relationships. Infauna, which was relatively uniform across the LSR, was numerically dominated by Annelida. Epifauna was much patchier, with each study area having unique epibenthic assemblages. Brittle stars were highly abundant in epifaunal communities, reaching 600 individuals per square meter. The presence of seabird colonies was not a major driver of benthic community structure in the LSR at the depths studied. Negative effects of colonies were detected on the density and number of taxa of infauna, perhaps due to top-down effects transmitted by the seabirds which feed in the water column and can directly reduce the quantity of food reaching the seabed. Sediment concentration of pigment, percent cover of gravel and boulders, depth, temperature and duration of open water explained a substantial part of the observed variation across the LSR. Food availability, as expressed by sediment pigment concentration, is a factor driving benthic communities, even if potential pathways through seabirds did not broadly affect the benthos at the point source.

We describe the trawl-vulnerable crustacean micronekton and macrozooplankton of the Gully, a large, shelf-incising submarine canyon off Nova Scotia, Canada, and a Marine Protected Area. Over 68 species of pelagic crustacea were collected with an International Young Gadoid Pelagic Trawl during three annual summer surveys at one fixed station in the canyon. Depths sampled ranged from the surface to the upper bathypelagic zone, concentrated in the upper 1250 m, with a maximum depth of 1500 m. The crustacean fauna was dominated by cold temperate species typical of mid- to higher-latitudes in the North Atlantic. Meganyctiphanes norvegica and Eusergestes arcticus were particularly dominant in terms of both observed biomass and abundance above 750 m depth. At least 17 species were new records for Canadian waters. The species assemblage of the station varied primarily with depth and diel cycle, the only dominant members of the assemblage showing pronounced inter-annual variations in catch being M. norvegica and Themisto gaudichaudii , both relatively shallow living species.

The world's oceans are subject to the influence of climate change at all latitudes and depths. There is a growing body of literature on the responses of species to climate change, which has a strong deterministic component indicating that responses can be predicted. At the same time, advances in oceanographic data acquisition and modeling have facilitated the identification of potential climate change refugia. The Convention on Biological Diversity's “Voluntary Specific Workplan on Biodiversity in Cold‐Water Areas within the Jurisdictional Scope of the Convention” explicitly calls for the identification and protection of refugia in cold‐water areas. We propose adding “Climate Change Refugium” as an integral consideration for identification of Ecologically or Biologically Significant Marine Areas (EBSAs). We provide a description of this as a potential eighth criterion. We then briefly discuss the pros and cons of introducing this eighth criterion, or an alternative strategy to develop guidelines that explicitly link refugia to the rationale of existing EBSA criteria, in the hope that this opinion piece will launch further discussion on this notion.

Association of demersal fish taxa with Geodia-dominated temperate sponge grounds was examined in 104 research vessel survey trawl sets from 500 to 1500 m depth along the conti- nental slopes of the Grand Banks and Flemish Cap, northwest Atlantic. The total number of fish taxa and their total biomass were negatively correlated with sponge biomass and catch depth, and sponge biomass increased with depth. ANOSIM identified significantly different fish communities (biomass and abundance composition) associated with 3 sponge catch weight classes, and multi- dimensional scaling plots showed separation of trawl sets labelled by this factor to be strongest for abundance. SIMPER analysis identified the fish assemblage associated with the sponge grounds (≥250 kg km �1 ): roughhead grenadier Macrourus berglax, roundnose grenadier Coryphaenoides rupestris, blue hake Antimora rostrata, longnose eel Synaphobranchus kaupii, turbot Reinhardtius hippoglossoides, black dogfish Centroscyllium fabricii and deep-sea cat shark Apristurus profun- dorum. These contributed to 92 and 81% of the similarity (~50%) among trawl set catches using biomass and abundance data, respectively. Four additional taxa contributed to 92% similarity in abundance: common grenadier Nezumia bairdii, shortnose snipe eel Serrivomer beanii, lantern- fish (Myctophidae) and goitre blacksmelts Bathylagus euryops. SIMPER dissimilarity identified 6 fish taxa with larger biomass in catches with high sponge catch weight: shortnose snipe eel, deep- sea cat shark, eelpout Lycodes spp., spinytail skate Bathyraja spinicauda, white skate Dipturus linteus and deepwater chimaeras Hydrolagus affinis. The first 3 species were also more abundant in those catches and are considered to be strongly associated with the sponge grounds. Future research focussing on these species identified as being associated with the sponge grounds may provide greater insight into the strength of the associations and the ecological linkages between these benthic and pelagic communities.

Marine fishes from the northwest Atlantic Ocean were analysed to determine whether barcoding was effective at identifying species. Our data included 177 species, 136 genera, 81 families and 28 orders. Overall, 88% of nominal species formed monophyletic clusters based on >500 bp of the CO1 region, and the average bootstrap value for these species was 98%. Although clearly effective, the percentage of species that were distinguishable with barcoding based on the criterion of reciprocal monophyletic clusters was slightly lower than has been documented in other studies of marine fishes. Eelpouts, sculpins and rocklings proved to be among the most challenging groups for barcoding, although we suspect that difficult identifications based on traditional (morphology based) taxonomy played a role. Within several taxa, speciation may have occurred too recently for barcoding to be effective (e.g. within Sebastes, Thunnus and Ammodytes) or the designation of distinct species may have been erroneous (e.g. within Antimora and Macrourus). Results were consistent with previous work recognizing particularly high levels of divergence within certain taxa, some of which have been recognized as distinct species (e.g. Osmerus mordax and Osmerus dentex; and Liparis gibbus and Liparis bathyarcticus), and some of which have not (e.g. within Halargyreus johnsonii and within Mallotus villosus). The results from this study suggest that morphology-based identification and taxonomy can be challenging in marine fishes, even within a region as well characterized as Atlantic Canada. Barcoding proved to be a very useful tool for species identification that will likely find a wide range of applications, including the fisheries trade, studies of range expansion, ecological analyses and population assessments.

Acanthephyra pelagica is a deep-sea pelagic shrimp with a global distribution. Mating has never been observed in this species as its pelagic lifestyle makes direct observations difficult. Multiple paternity has been reported for many other crustaceans, although not for deep-sea shrimp species like A. pelagica. Here we used four polymorphic microsatellite loci to test for multiple paternity. We genotyped the mother and a maximum of 63 of her brooded embryos in 19 ovigerous females, all of which exhibited evidence of multiple paternity; the frequency of multiple paternity is thus deemed to be close to 100 % in this species. The number of males contributing to each brood varied between 2 and 4 with evidence of pronounced reproductive skew suggesting the potential importance of mating order, different sperm contribution, the existence of pre-copulatory female choice, or post-copulatory sperm competition or selection. Our results with respect to multiple paternity, together with the size patterns, suggest a pure-search mating system. Our findings on the mating system of A. pelagica contribute to a better understanding of the reproductive behavior of this species.

We examined the habitat of juvenile haddock on the eastern Scotian Shelf (off Nova Scotia, Canada) in relation to grab-sampled benthic macrofaunal invertebrate species assemblages in order to determine whether there were significant differences in benthic macrofauna between areas of historically persistent high and low juvenile haddock abundance. Our analyses were conducted over two spatial scales in each of two years: among banks (Emerald, Western and Sable Island), approximately 60 km distant from each other, and between areas of high and low juvenile haddock abundance at distances of 10 to 30 km-all in an area that had not experienced groundfishing in the decade prior to sampling. We also examined fine-scale (10s of metres) within-site variability in the macrofauna and used surficial sediment characteristics, along with hydrographic variables, to identify environmental correlates. PERMANOVA identified statistically significant differences in biomass, density and composition of the benthos associated with juvenile haddock abundance; however it was difficult to determine whether the results had biological relevance. Post hoc tests showed that these differences occurred only on Sable Island Bank where both fish and benthos may have been independently responding to sediment type which was most different there (100% sand in the area of low haddock abundance vs. 22% gravel in the area of high haddock abundance). In total, 383 benthic taxa representing 13 phyla were identified. Annelida was the most specious phylum (36.29% of taxa, representing 33 families), followed by Arthropoda (with Crustaceans, mostly Amphipoda, accounting for 25.07% of the total number of taxa). The strongest pattern in the macrofauna was expressed at the largest scale, between banks, accounting for approximately 25% of the variation in the data. Emerald Bank, deeper, warmer and saltier than the Western and Sable Island Banks, had a distinctive fauna.

Knowledge of the reproductive life-history of deep-water corals is important for assessing their vulnerability to anthropogenic impacts. Yet, the reproductive biology of many deep-water corals, especially members of the subclass Octocorallia, has not been examined. We used histological techniques to describe the reproductive biology of the deep-water gorgonian coral Acanella arbuscula from the northwest Atlantic. All colonies examined were gonochoric, and no embryos or planula larvae were observed in the polyps. Mean polyp-level fecundity (females: 21.07 17.5 oocytes polyp

Acanthephyra pelagica is a widespread deep- sea decapod crustacean that is highly abundant and thus, of high ecological significance, within the Sable Gully marine protected area. Despite its importance no genetic analyses have previously been conducted on this species. Here we present a total of 26 novel species-specific microsatellites isolated and characterized in 132 individuals collected from one wild population within the Sable Gully. The number of alleles observed in polymorphic loci ranged from 6 to 18 with an average of 8.1. The observed and expected heterozygosities varied from 0.156 to 0.723 and from 0.156 to 0.913 respectively. These novel microsatel- lites are a contribution to future studies on A. pelagica and will have a positive impact on the future studies on biology and ecology of this deep-sea species.

Canada, the European Union, and the United States, amongst others, recognize the importance of habitat-forming biota such as cold-water corals to a host of associated ecologically and/or commercially important species including fish, crustaceans, and mollusks. These species and the ecological services they provide are important to the peoples surrounding the North Atlantic (i.e. the Atlantic Ocean north of the equator). There are several different legal and/or regulatory tools available to ensure that cold-water corals in the North Atlantic are protected along with the ecological services they provide. Through such tools, many protected areas have been designated or are under consideration in the North Atlantic to protect cold-water coral habitats. Although the designation and labeling varies, e.g. National Marine Conservation Area (Canada), Special Area of Conservation (European Union), or Habitat Area of Particular Concern (USA), all of these designations aim to provide protection into the future to vulnerable habitats like cold-water corals.

Ophiura sarsii was collected in May/June from Banquereau Bank off Nova Scotia, Canada as part of the benthic fauna analyzed in a 2 year clam dredging-impact experiment. In total, 529 O. sarsii specimens were analyzed; 174 (33%) had stomach contents while the rest were empty. Ophiura sarsii is a trophic generalist feeding on at least 31 taxa (52% identified to species) drawn from four phyla: Arthropoda (81.8%), Annelida (13.2%), Mollusca (3%), and Cnidaria (1.5%). However, the diet was largely restricted to two amphipod families (Ampeliscidae and Lysianassidae), accounting for 54–70% of stomach contents at any one sampling period. This diet provides indirect evidence for carnivory. Limited spatial and temporal heterogeneity in the proportion of animals feeding showed no consistent pattern. Where diet composition differed (ANOSIM) it was attributed to the proportion of lysianassid and ampeliscid amphipods consumed. Dredging introduced new dietary items, although diet composition was not significantly altered.

A north/south discontinuity along the northeastern coast of North America in the genetic structure of the American lobster (Homarus americanus) was detected using a suite of 13 microsatellite loci assessed using spatial analyses. Population genetic data laid over existing data on physiographic changes and sea-surface temperatures were used to reconstruct the Pleistocene distribution of this species. A postglacial northern-edge colonization model best explains the relative genetic homogeneity of the northern region compared to the southern region centred in the Gulf of Maine. Population genetic analyses identified significant structure (range of standardized theta 0-0.02) but no significant evidence for isolation by distance. The novel application of spatial genetic analyses to a marine species allowed us to interpret these results by providing a greater insight into the evolutionary factors responsible for shaping the genetic structure of this species throughout is natural range.

13 pages, 2 figures, 5 tables.-- PMID: 18794572 [PubMed].-- PMCID: PMC2635125.-- Available online Sep15, 2008., Study of the genetic basis of gene expression variation is central to attempts to understand the causes of evolutionary change. Although there are many transcriptomics studies estimating genetic variance and heritability in model organisms such as humans there is a lack of equivalent proteomics studies. In the present study, the heritability underlying egg protein expression was estimated in the marine mussel Mytilus. We believe this to be the first such measurement of genetic variation for gene expression in eggs of any organism. The study of eggs is important in evolutionary theory and life history analysis because maternal effects might have profound effects on the rate of evolution of offspring traits. Evidence is presented that the egg proteome varies significantly between individual females and that heritability of protein expression in mussel eggs is moderate to high suggesting abundant genetic variation on which natural selection might act. The study of the mussel egg proteome is also important because of the unusual system of mitochondrial DNA inheritance in mussels whereby different mitochondrial genomes are transmitted independently through female and male lineages (doubly uniparental inheritance). It is likely that the mechanism underlying this system involves the interaction of specific egg factors with sperm mitochondria following fertilization, and its elucidation might be advanced by study of the proteome in females having different progeny sex ratios. Putative identifications are presented here for egg proteins using MS/MS in Mytilus lines differing in sex ratio. Ontology terms relating to stress response and protein folding occur more frequently for proteins showing large expression differences between the lines. The distribution of ontology terms in mussel eggs was compared with those for previous mussel proteomics studies (using other tissues) and with mammal eggs. Significant differences were observed between mussel eggs and mussel tissues but not between the two types of eggs., This work was supported by a Marine Genomics Europe Network grant (European Union FP6 Contract GOCE-CT-2004-505403) and postdoctoral fellowship (to A. P. D.).

Analysis of presence / absence records from two comparable megabenthic surveys of scallop grounds in the Bay of Fundy, Canada, in 1966–67 and 1997 showed profound change over three decades. There were no indications that any species were lost and the average number of taxa per station remained steady. However, spatial heterogeneities in the community were reduced and species composition changed significantly. Some taxa widespread in 1966–67 declined while others expanded, with frequencies of occurrence of individual taxa changing by up to 71%. The whelks Buccinum undatum and Colus spp., the bivalves Astarte spp. and Cyclocardia borealis, the toad crabs Hyas spp., the sea urchin Strongylocentrotus droebachiensis and the brittle stars (Ophiurida) showed particular increases. Corresponding declines were seen in the boring sponges Cliona spp., the horse mussel Modiolus modiolus, the scallop Chlamys islandica, the fan worm Pseudopotamilla reniformis and the stalked tunicate Boltenia ovifera. Replacement of attached, fragile, epifaunal, filter-feeding taxa by a combination of motile scavengers, motile filter-feeders and robust, burrowing filter-feeders suggests that the primary cause of the temporal change was physical impacts by fishing gear, even though trawling and scallop dragging in the area were neither intense nor new developments. Secondary causes of change may have included other ecosystem effects of fishing (supply of discards and bait), a mass mortality of scallops and a range expansion of a bryozoan (Flustra foliacea).

Several studies have shown that in vertebrate mtDNAs the nucleotide content at fourfold degenerate sites is well correlated with the site's time of exposure to the single-strand state, as predicted from the asymmetrical model of mtDNA replication. Here we examine whether the same explanation may hold for the regional variation in nucleotide content in the maternal and paternal mtDNAs of the mussel Mytilus galloprovincialis. The origin of replication of the heavy strand (O(H)) of these genomes has been previously established. A systematic search of the two genomes for sequences that are likely to act as the origin of replication of the light strand (O(L)) suggested that the most probable site lies within the ND3 gene. By adopting this O(L) position we calculated times of exposure for 0(FD) (nondegenerate), 2(FD) (twofold degenerate), and 4(FD) (fourfold degenerate) sites of the protein-coding part of the genome and for the rRNA, tRNA and noncoding parts. The presence of thymine and absence of guanine at 4(FD) sites was highly correlated with the presumed time of exposure. Such an effect was not found for the 2(FD) sites, the rRNA, the tRNA, or the noncoding parts. There was a trend for a small increase in cytosine at 0(FD) sites with exposure time, which is explicable as the result of biased usage of 4(FD) codons. The same analysis was applied to a recently sequenced mitochondrial genome of Mytilus trossulus and produced similar results. These results are consistent with the asymmetrical model of replication and suggest that guanine oxidation due to single-strand exposure is the main cause of regional variation of nucleotide content in Mytilus mitochondrial genomes.

This article presents the results from the analysis of data acquired during the NEREIDA survey programme (2009-2010) around the Flemish Cap and the tail of the Grand Banks of Newfoundland (NAFO Regulatory Area). Biological samples were collected using a mega box-core, which were processed for the extraction and identification of benthic macrofauna. A suite of physical samples and environmental measurements was also collected for evaluation. Analyses revealed the presence of benthic assemblages that were indicative of Vulnerable Marine Ecosystems (VME). VME indicative assemblages were present mostly outside of the fishing footprint. A simple habitat suitability model identified areas that are likely to accommodate VME indicative assemblages. Areas with the greatest potential to accommodate VME assemblages closely correspond with areas already managed for the protection of VME, where bottom-contact fishing practices are presently excluded. Such results support the notion that existing bottom-fishery exclusion zones should continue to be enforced for the long-term protection of VME. En prensa 2,2770

We analyze the morphological and genetic variability within and between seven species of Acesta and specimens recently collected in the northwest Atlantic using traditional morphological measurements, landmark-based geometric morphometrics, and the cytochrome oxidase subunit I (COI) gene sequences, with particular emphasis on North Atlantic species. Shell morphology and external shell appearance do not allow reliable distinction between the widely recognized northeastern Atlantic A. excavata and other northwest Atlantic species or populations of Acesta, with the exception of A. oophaga. Similarly, shape analysis reveals a wide variability within northeastern Atlantic A. excavata, and significant morphological overlap with A. bullisi from the Gulf of Mexico and A. rathbuni from the southwestern Pacific and South China Sea. Specimens from the northwestern and Mid-Atlantic display shell shapes marginally similar to that of A. excavata. These differences are at least partly related to anterior or posterior shifting of the shell body and to the opposite shifting of the hinge line/dorsal region and upper lunule. These morphological variations, along with the midline-width-ratio, explain much of the variability extracted by principal component analysis. Results from a mitochondrial DNA barcode approach (COI), however, suggest that the northwest Atlantic specimens belong to a new species for which we propose the name Acesta cryptadelphe sp. nov. Differences in larval shell sizes between northeastern and northwestern Atlantic specimens are consistent with this result.

Capelin (Mallotus villosus) is a commercially exploited, key forage-fish species found in the boreal waters of the North Pacific and North Atlantic Oceans. We examined the population structure of capelin throughout their range in the Canadian northwest Atlantic Ocean using genetic-based methods. Capelin collected at ten beach and five demersal spawning locations over the period 2002 through 2008 (N = 3,433 fish) were genotyped using six polymorphic microsatellite loci. Temporally distinct samples were identified at three beach spawning locations: Chance Cove, Little Lawn and Straitsview, Newfoundland. Four capelin stocks are assumed for fisheries management in the northwest Atlantic Ocean based on meristics, morphometrics, tag returns, and seasonal distribution patterns. Our results suggested groupings that were somewhat different than the assumed structure, and indicate at least seven genetically defined populations arising from two ancestral populations. The spatial mosaic of capelin from each of the two basal cluster groups explains much of the observed geographic variability amongst neighbouring samples. The genetic-defined populations were resolved at Jost’s D est ≥ 0.01 and were composed of fish collected 1) in the Gulf of St. Lawrence, 2) along the south and east coasts of Newfoundland, 3) along coastal northern Newfoundland and southern Labrador, 4) along coastal northern Labrador, 5) near the Saguenay River, and at two nearshore demersal spawning sites, 6) one at Grebes Nest off Bellevue Beach on the east coast of Newfoundland, and 7) one off the coast of Labrador at Domino Run. Moreover, the offshore demersal spawners on the Scotian Shelf and Southeast Shoal appeared to be related to the inshore demersal spawners at Grebes Nest and in Domino Run and to beach spawners from the Gulf of St. Lawrence.

The effects of otter trawling on a hard-bottom ecosystem on Western Bank on Canada's Scotian Shelf were examined experimentally from 1997 to 1999 with an asymmetrical BACI design. The site was located within an area that had been closed to fishing since 1987 to protect juvenile haddock. An experimental line was trawled 12–14 times on three separate occasions over a 20 month period. The benthic macrofauna and megafauna were sampled before and after trawling on both impact and control lines with both a grab and a photographic system. The 100 grab samples collected contained 341 taxa, primarily polychaetes, amphipods and molluscs, the majority (60%) of which were epifaunal. Biomass was dominated by the horse-mussel Modiolus modiolus , a long-lived bivalve, while the tube-building amphipod Ericthonius fasciatus was the most abundant species. Through the study period the benthos on the control lines showed little qualitative or quantitative change in individual taxa or community metrics. However, the abundance of 24 individual taxa (polychaetes, amphipods, echinoderms and molluscs) changed significantly, with the majority of these increasing. This resulted in a significantly different relative abundance of taxa between years as detected through ANOSIM. A significant change in relative biomass amongst the taxa was also observed. Trawling had few detectable immediate effects on the abundance or biomass of individual taxa and none on community composition. A few taxa, primarily a mixture of polychaetes and amphipods, decreased significantly after trawling and data from fish stomachs collected during the experiment (Kenchington, E.L., Gordon Jr., D.C., Bourbonnais-Boyce, C., MacIsaac, K.G., Gilkinson, K.D., McKeown, D.L., Vass, W.P., 2005. Effects of experimental otter trawling on the feeding of demersal fish on Western Bank, Nova Scotia. Amer. Fish. Soc. Symp. 41, 391–409) showed that some of these were scavenged by demersal fish. Fifteen taxa showed significant decreases after trawling when the cumulative effects of trawling were considered. As in the analyses of individual years the species affected were primarily high turn-over species such as polychaetes and amphipods. Dominance curves prepared for both control and impact samples before trawling in 1997 and after trawling in 1999 showed a marked decrease in the biomass values of the highest ranking taxa, particularly of the first species, M. modiolus , only on the impact line at the conclusion of the experiment. The proportion of epifaunal biomass also declined significantly from 90% to 77% on the impact line by the conclusion of the experiment. These changes are in part due to trawl-induced damage and subsequent predation by demersal fish of the top ranking species. Analysis of the photographic images showed that the three top-ranking species in terms of biomass, M. modiolus , the tube-building polychaete Thelepus cincinnatus , and the brachiopod Terebratulina septentrionalis , were visibly damaged more than other species by the trawl gear. Two of these species, M. modiolus and T. cincinnatus , were preyed upon by scavenging demersal fish. The use of multiple sampling devices at the experimental site (grab, photographic system reported here and trawl and fish stomachs reported by Kenchington, E.L., Gordon Jr., D.C., Bourbonnais-Boyce, C., MacIsaac, K.G., Gilkinson, K.D., McKeown, D.L., Vass, W.P., 2005. Effects of experimental otter trawling on the feeding of demersal fish on Western Bank, Nova Scotia. Amer. Fish. Soc. Symp. 41, 391–409) enabled us to link trawl-induced changes to the benthos to predation by demersal fish.

The micro-phytoplankton Navicula pelliculosa, Chaetoceros septentrionalis and Prymnesium sp., indigenous to the coastal waters of Nova Scotia, Canada were isolated, cultured and used in laboratory feeding experiments with larvae of the giant sea scallop (Placopecten magellanicus) to evaluate their dietary benefits. The effects of these micro-phytoplankton on larval growth and survival were compared with three species of micro-algae commonly used as commercial feed for bivalve larvae: Tahitian Isochrysis sp., Pavlova lutheri and Chaetoceros calcitrans. The experiments were conducted at 14 °C over approximately one month. Larvae were fed at concentrations of 25,000 cells ml−1 from Day 3 to Day 9 and 35,000 cells ml−1 from Day 10 to Day 35. Total growth and survival were determined by sampling the larvae at intervals of 4 to 5 days. Eight dietary formulations were compared for larval survival and growth. Two way, repeated measures ANOVA using both larval shell height and percent larval survival as dependent variables and diet and time as factors resulted in significant variation (p

Species of the family Mytilidae have 2 mitochondrial genomes, one that is transmitted through the egg and one that is transmitted through the sperm. In the Mytilus edulis species complex (M. edulis, M. galloprovincialis, and M. trossulus) there is also a strong mother-dependent sex-ratio bias in favor of one or the other sex among progeny from pair matings. In a previous study, we have shown that sperm mitochondria enter the egg and that their behavior during cell division is different depending on whether the egg originated from a female- or male-biased mother. Specifically, in eggs from females that produce mostly or exclusively daughters, sperm mitochondria disperse randomly among cells after egg division. In eggs from females that produce predominantly sons, sperm mitochondria tend to stay together in the same cell. Here, we extend these observations and show that in 2- and 4-cell embryos from male-biased mothers most sperm mitochondria are located near or at the cleavage furrow of the major cell, in contrast to embryos from female-biased mothers where there is no preferential association of sperm mitochondria with the cleavage furrow. This observation provides evidence for an early developmental mechanism through which sperm mitochondria are preferentially channeled into the primordial cells of male embryos, thus making the paternal mitochondrial genome the dominant mtDNA component of the male germ line.Key words: mussels, doubly uniparental inheritance of mtDNA, sperm mitochondria.

Marine bivalves are sessile or sedentary as adults but have planktonic larvae which can potentially disperse over large distances. Consequently larval transport is expected to play a prominent role in facilitating gene flow and determining population structure. The sea scallop (Placopecten magellanicus) is a dioecious species with high fecundity, broadcast spawning and a c. 30-day planktonic larval stage, yet it forms discrete populations or 'beds' which have significantly different dynamics and characteristics. We analysed variation at six microsatellite loci in 12 locations throughout the geographic range of the species from Newfoundland, Canada, to New Jersey, USA. Significant differentiation was present and the maximum pairwise theta value, between one of the Newfoundland samples in the north and a sample from the southern portion of the range, was high at 0.061. Other proximate pairs of samples had no detectable genetic differentiation. Mantel tests indicated a significant isolation by distance, but only when one of the populations was excluded. A landscape genetic approach was used to detect areas of low gene flow using a joint analysis of spatial and genetic information. The two major putative barriers inferred by Monmonier's algorithm were then used to define regions for an analysis of molecular variance (amova). That analysis showed a significant but low percentage (1.2%) of the variation to be partitioned among regions, negligible variation among populations within regions, and the majority of the variance distributed between individuals within populations. Prominent currents were concordant with the demarcation of the regions, while a novel approach of using particle tracking software to mimic scallop larval dispersal was employed to interpret within-region genetic patterns.

A hydraulic clam dredging experiment, designed to mimic offshore commercial dredging practices, was carried out at a depth of approximately 70 m on a sandy seabed on Banquereau, on the Scotian Shelf, eastern Canada. The experiment was designed to study the separate and combined effects of dredging through three treatment boxes (Dredging Only, Dredging and Discarding, Discarding Only) and two spatially separated reference boxes. In all, 270 taxa were identified from grab samples. Of these, four bivalves are targeted in the commercial fishery (Arctica islandica, Cyrtodaria siliqua, Mactromeris polynyma, and Serripes groenlandicus) while 266 taxa were non-target species. Sample biomass was dominated by the propellerclam, C. siliqua, and the echinoderm, Echinarachnius parma, while the polychaete, Spiophanes bombyx, was the numerical dominant. The dredges captured 33 invertebrate and two fish taxa, although >80% of the catch biomass comprised propellerclams and echinoderms. Immediately after dredging, most macrofaunal species decreased in abundance, with the greatest declines inside dredge furrows (which covered 53–68% of the area inside the dredged boxes). Large numbers of propellerclams were excavated to the seabed surface, with a large proportion showing massive damage. There were few signs of discards on the sediment surface. Recovery trajectories of target and non-target species were followed for 2 years. Following initial declines in abundance and biomass of most taxa immediately after dredging, there were marked increases in abundance of polychaetes and amphipods after 1 year. Two years after dredging, abundances of opportunistic species were generally elevated by ≫100% relative to pre-dredging levels. Two years after dredging, average taxonomic distinctness had decreased (i.e. taxonomic relatedness between species had increased) due, in part, to increased numbers of species of certain polychaetes and amphipods, while communities had become numerically dominated (50–70%) by S. bombyx. It is concluded that the disturbed community was still in the colonizing phase 2 years after dredging. The mobile brittlestar, Ophiura sarsi, displayed increases in abundance ranging from 200% to 300% in the dredged and reference boxes over the 2-year post-dredging. A similar response of non-target macrofauna in the reference boxes suggests, possibly, a coincident natural recruitment pulse. Dredging resulted in pronounced, sustained reductions in biomass (up to 67%) of the target bivalves with no signs of recovery after 2 years. Recruitment of target bivalves (>1-mm shell length) was very low throughout the experimental area during this interval.

Colonial epifauna are vulnerable to the effects of bottom fishing, but impacts on the life histories of these non-target animals have not been examined extensively. Dredging potentially impairs sexual reproduction by invoking regeneration and induces clonality by severing colonies or through the abortion of damaged modules. This study investigated the potential for commercial-scale scallop dredging to alter sexual and asexual (“clonal”) reproduction in the hydroid Sertularia cupressina. In total, 1,071 colonies from 104 epizoic microhabitats (upper valves of live scallops relatively undisturbed by fishing) and 75 epilithic microhabitats (cobbles more severely disturbed by fishing) were collected from 53 to 94-m depths in the Bay of Fundy (Atlantic Canada). Colony abundance, injury frequency (proportion of colonies with sealed, snapped off stems), percentage of fertile colonies and sexual fecundity (number of gonophores and gonophore dimensions) were measured on all substrata. Ten randomly amplified polymorphic DNA (RAPD) primers were used to estimate clonal diversity. Field experiments found no significant effect of microhabitat differences between scallop and cobble substrata on fecundity and clonality in S. cupressina, while experimentally-induced injuries suppressed the percent of fertile colonies. On the fishing grounds, colonies on scallop valves were more abundant and sexually fertile than their counterparts on cobble, and all were sexually derived. In contrast, colonies on cobbles had a greater percentage of injury, were less fertile and were frequently clonally-derived. Impacts of fishing-related injuries on reproduction in colonial epifauna have been overlooked, yet the long-term consequences of such impacts could result in reduced adaptability, recruitment and recovery potential of these and dependent organisms.

Hydroid assemblages from the shells of 104 live scallops Placopecten magellanicus and 136 cobbles were sampled from 39 sites on heavily dredged commercial scallop grounds in the Bay of Fundy, northwest Atlantic. The scallop shells were considered pseudo-controls, representing undisturbed 'island habitats' naturally interspersed amongst the cobbles. Cobbles were expected to represent disturbed habitat. Samples yielded 51 taxa from 24 genera across substrata. The number of taxa was significantly lower on cobbles. Multidimensional scaling plots and statistical analyses on presence-absence data discriminated 2 divergent assemblages consistent with substratum. Cobble assemblages were characterized by Campanularia volubilis, Clytia hemisphaerica and Clytia sp., while those on the live scallop shells were characterized by the small auto-epizoite Calycella syringa and its hosts Sertularia cupressina and Obelia dichotoma. Species discriminating between the sub- strata are considered substrate generalists. Fishing effort was introduced as a factor in an analysis of similarity and accounted for a significant proportion of the variance within and between substrata, with larger R 2 values associated with the cobble assemblages, as expected. Runner-like forms with small, unbranched colonies and medusa life stages were more frequently found on cobbles than on live scallop shells. Assemblage and life history divergence associated with fishing effort, widespread substrate generalism amongst the principle taxa, and observations from other studies suggest that these observed differences could be related to chronic disturbance of cobbles caused by fishing.

Responses of delicate soft corals to mechanical injuries inflicted by bottom fishing (e.g., trawling, dredging) are not known. Effects of mechanical disturbance on the soft coral Gersemia rubiformis (Ehrenberg, 1834) were examined by experimentally simulating disturbances caused by bottom fishing. Eight colonies were collected in the Bay of Fundy and maintained in individual aquaria. Four colonies were rolled over and crushed 10 times, once every 2 weeks over 2 months, while four were left undisturbed. Colony response was recorded both 4 days and 1 week post disturbance in both treatments by assigning states reflecting colony and polyp physiognomy. Proportions of corals in different states did not differ between treatments over time. Crushing immediately induced complete colony retraction and daughter colonies were produced in crushed corals. Randomly amplified polymorphic DNA genetic markers demonstrated that daughter colonies were sexually derived. Despite initial fast growth, daughter colonies experienced high mortality. Premature larval expulsion may have been intrinsically initiated to dispose of resource-costly planulae during colony repair. Corals regenerated well from acute localized injuries, which, along with the ability to temporarily retract and survive repeated crushing, may benefit G. rubiformis in heavily disturbed habitats such as areas impacted by bottom fishing activities where the probability of mechanical disturbance is high.

A hydraulic clam dredging experiment was conducted on a deep (70–80 m) offshore sandy bank on the Scotian Shelf in order to examine the immediate impacts of hydraulic dredging on physical habitat and to follow processes of recovery over a 3-year period. Seabed structural complexity in this low-relief habitat consists of small-scale sedimentary features including pits and bivalve burrow openings as well as polychaete tubes and empty mollusc shells. The most obvious effect of dredging was a dramatic change in seabed topography due to the numerous deep (20 cm), wide (4 m) curvilinear furrows that were cut by the dredges. The loss of burrows, tubes, and shells through destruction or burial, and local sedimentation created a smooth surface. Both spatial scale and sampling resolution were critical in identifying longer-term impacts. Dredge furrows were no longer visible in video 1 year after dredging due to their low relief; however, they persisted, while undergoing changes, as evidenced in sidescan sonograms. The margins of furrows were gradually degraded, likely through the combined actions of slumping, sediment transport and bioturbation. Over time, dredge furrows act as traps for empty shells. Differences in patterns of acoustic reflectance between dredge furrows and the surrounding seabed indicate long-lasting effects on sediment structure. Densities of large burrows were reduced by up to 90% after dredging with no signs of recovery after 3 years due to the high mortalities of their architect, the propellerclam, Cyrtodaria siliqua . Dredging effects were detectable against a background of natural temporal (annual) and large-scale spatial variability in physical habitat.

Effective management of exploited species demands contemporary knowledge of population structure and mating patterns. Genetic markers can prove useful in providing this knowledge. Despite its commercial importance, genetic markers for American lobster (Homarus americanus) are limited. We developed 12 tetra- and 1 trinucleotide microsatellite loci for American lobster that exhibit little stuttering after PCR amplification. Gene diversity of these loci ranged from 0.516 to 0.929. A four-locus multiplex permits rapid genotyping of progeny in parentage experiments with a paternity exclusion probability over the four loci of 97.8%. We examined the loci for conformity to Hardy-Weinberg expectations (HWE) and linkage using individuals from one location and found that four loci deviated from HWE. We also tested inheritance and pairwise linkage using 48 embryos from each of two females. With the exception of two loci that were derived from the same clone and separated by 72 bp, no evidence of linkage was found. We, for the first time, demonstrate the occurrence of multiple paternity in American lobster. We also observed an apparent occurrence of dispermic androgenesis, possibly the first documentation of such an event within a species. Ten of the loci amplified in European lobster (Homarus gammarus), although two were monomorphic and one deviated significantly from HWE. We quantified mitochondrial DNA (mtDNA) sequence variation through the use of PCR amplification of two DNA fragments, followed by digestion with restriction enzymes; eight haplotypes were detected. One of the two fragments amplified in European lobster. Both sets of markers should prove useful for population discrimination purposes, and the microsatellites, in particular the four-locus multiplex, should prove highly amenable to rapidly addressing questions about mating patterns.Key Words: low-stutter microsatellites, mtDNA PCR–RFLP, multiple paternity, dispermic androgenesis, American lobster.

The 1992 Convention on Biological Diversity has established an international framework for broader conservation objectives for the management of ocean use activities (cf. Sainsbury and Sumaila, 2003). The Convention calls for preservation of biological diversity, including genetic, species and ecosystem diversity, thereby creating a demand for developing management forms that can cope with this issue. A number of initiatives have been developed to address this and other related international agreements. Notably, Ecosystem-Based Fishery Management (EBFM; cf. Brodziak and Link, 2002; Sainsbury and Sumaila, 2003) has emerged as a holistic approach to maintaining ecosystems and sustainable fisheries. EBFM should incorporate all levels of diversity, but in practice has focused on species and ecosystem diversity (e.g., Brodziak and Link, 2002). The application of EBFM must be broadened to include conservation of genetic diversity, including intraspecific diversity, which are not necessarily protected by maintaining diversity at higher levels (cf. Kenchington, 2003). Scientific justification for conserving genetic diversity stems from several sources including: (1) maintaining adaptability of natural populations; (2) the future utility of genetic resources for medical and other purposes; and (3) changes in life history traits and behaviour that influence the dynamics of fish populations, energy flows in the ecosystem, and ultimately, sustainable yield. The challenge is to formulate appropriate management actions for the preservation of genetic diversity (e.g., Sainsbury and Sumaila, 2003). This will require consensus on what it is we are trying to preserve (e.g., alleles, traits, population structure) and some means of assessing genetic status. This paper endeavours to outline a process to develop management advice for marine genetic diversity. We challenge fish conservation geneticists to consider their work in a more applied context so that management actions can be developed to preserve genetic resources.

Five tetranucleotide microsatellite loci developed from Atlantic haddock (Melanogrammus aeglefinus) are presented. Loci were isolated using a modified magnetic bead-hybridization selection procedure that enriched for tetranucleotide microsatellites. Loci were polymorphic (3-99 alleles per locus; mean, 33.2) and exhibited high levels of observed heterozygosity (0.07-0.99; mean, 0.73) in a sample of 70 haddock collected from the Scotian Shelf in the Northwest Atlantic Ocean. Primer sets for 5 tetranucleotide microsatellites, originally developed from cod (Gmo34), were also tested in Atlantic haddock; one pair yielded readily detectable product and was variable in the population assayed (29 alleles; heterozygosity, 0.96). These loci are suitable for kinship analyses in aquaculture-related applications, and are potentially useful for resolving population structure in the wild.

DNA barcode sequences were developed from 557 mesopelagic and upper bathypelagic teleost specimens collected in waters off Atlantic Canada. Confident morphological identifications were available for 366 specimens, of 118 species and 93 genera, which yielded 328 haplotypes. Five of the species were novel to the Barcode of Life Database (BOLD). Most of the 118 species conformed to expectations of monophyly and the presence of a “barcode gap”, though some known weaknesses in existing taxonomy were confirmed and a deficiency in published keys was revealed. Of the specimens for which no firm morphological identification was available, 156 were successfully identified to species, and a further 11 to genus, using their barcode sequences and a combination of distance- and character-based methods. The remaining 24 specimens were from species for which no reference barcode is yet available or else ones confused by apparent misidentification of publicly available sequences in BOLD. Addition of the new sequences to those previously in BOLD contributed support to recent taxonomic revisions of Chiasmodon and Poromitra, while it also revealed 18 cases of potential cryptic speciation. Most of the latter appear to result from genetic divergence among populations in different ocean basins, while the general lack of strong horizontal environmental gradients within the deep sea has allowed morphology to be conserved. Other examples of divergence appear to distinguish individuals living under the sub-tropical gyre of the North Atlantic from those under that ocean’s sub-polar gyre. In contrast, the available sequences for two myctophid species, Benthosema glaciale and Notoscopelus elongatus, showed genetic structuring on finer geographic scales. The observed structure was not consistent with recent suggestions that “resident” populations of myctophids can maintain allopatry despite the mixing of ocean waters. Rather, it indicates that the very rapid speciation characteristic of the Myctophidae is both on-going and detectable using barcodes.

The United Nations General Assembly Resolution 61/105, concerning sustainable fisheries in the marine ecosystem, calls for the protection of vulnerable marine ecosystems (VME) from destructive fishing practices. Subsequently, the Food and Agriculture Organization (FAO) produced guidelines for identification of VME indicator species/taxa to assist in the implementation of the resolution, but recommended the development of case-specific operational definitions for their application. We applied kernel density estimation (KDE) to research vessel trawl survey data from inside the fishing footprint of the Northwest Atlantic Fisheries Organization (NAFO) Regulatory Area in the high seas of the northwest Atlantic to create biomass density surfaces for four VME indicator taxa: large-sized sponges, sea pens, small and large gorgonian corals. These VME indicator taxa were identified previously by NAFO using the fragility, life history characteristics and structural complexity criteria presented by FAO, along with an evaluation of their recovery trajectories. KDE, a non-parametric neighbour-based smoothing function, has been used previously in ecology to identify hotspots, that is, areas of relatively high biomass/abundance. We present a novel approach of examining relative changes in area under polygons created from encircling successive biomass categories on the KDE surface to identify ‘‘significant concentrations’’ of biomass, which we equate to VMEs. This allows identification of the VMEs from the broader distribution of the species in the study area. We provide independent assessments of the VMEs so identified using underwater images, benthic sampling with other gear types (dredges, cores), and/or published species distribution models of probability of occurrence, as available. For each VME indicator taxon we provide a brief review of their ecological function which will be important in future assessments of significant adverse impact on these habitats here and elsewhere., SI

There has been increasing awareness of the vulnerability of marine organisms to population extirpation and species extinction. While very few documented cases of species extinction exist in the marine environment, it is anticipated that managers will face the dilemma of prioritizing populations of marine fish and shellfish for protection in the near future. Current prioritization procedures have been developed from salmonid models with the intent of applying them to all marine organisms, and in some cases to freshwater and terrestrial taxa. In this review we provide evidence for the relevance of such a process for marine species and further suggest five broad categories of marine organisms that have distinctive traits influencing their genetic structure. The current prioritization models have been adapted to account for each of these species groups. Emphasis is placed on ‘Classical Marine Species’ which represent the opposite end of the continuum from the salmon model, displaying high within-population genetic variance. From this category, three cod ( Gadus morhua ) stocks were selected to evaluate a revised scheme developed specifically for ‘Classical Marine Species’ that includes performance measures such as (i) reduction in number of spawning populations; (ii) reduction of Ne : Nc (ratio of effective to census population size); (iii) changes in life-history traits; (iv) critical density for spawning success; and (v) patchy vs. continuous distribution pattern. When the salmonid scheme was applied, the cod examples were allocated low values, indicating that they were not under threat. However, when the revised scheme was applied, all three cod stocks were allocated high values, indicating that the revised scheme was more reflective of the particular life-history traits of this category of organisms.

A 3-year otter trawling experiment was conducted on a deepwater (120-146 m) sandy bottom ecosystem on the Grand Banks of Newfoundland that had not experienced trawling for at least 12 years. The benthic macrofauna were sampled before and after trawling and in reference areas. The 200 grab samples collected contained 246 taxa, primarily polychaetes, crustaceans, echinoderms, and molluscs. Biomass was dominated by propeller clams (Cyrtodaria siliqua) and sand dollars (Echinarachnius parma), while abundance was dominated by the polychaete Prionospio steenstrupi and the mollusc Macoma calcarea. The most prominent feature of the data was a natural decline in the to- tal number of species, the total abundance, and the abundance and biomass of selected species between 1993 and 1995. The only immediate effect of trawling was seen in 1994 when the abundance of 13 species, the biomass of 11 species (mostly polychaetes), and the total abundance per grab were significantly lower. There was little evidence of long-term trawling effects. When trawling disturbance was indicated, it appeared to mimic natural disturbance, shifting the com - munity in the same direction in multidimensional scaling ordination; no distinctive trawling signature was observed. However, the results of this experiment should not be uncritically extrapolated to the impacts of commercial trawling. Resume : Pendant 3 ans, la peche au chalut a panneaux a ete pratiquee dans un ecosysteme profond (120-146 m) a fond sablonneux sur les Grands bancs de Terre-Neuve ou il n'y avait pas eu de chalutage depuis au moins 12 ans. Des recoltes de la macrofaune benthique ont ete faites avant et apres le chalutage, ainsi que dans des zones temoins. Les 200 echantillons recoltes a la benne contenaient 246 taxons, principalement des polychetes, des crustaces, des echino- dermes et des mollusques. Les Pitots (Cyrtodaria siliqua) et les Oursins plats de l'Atlantique (Echinarachnius parma) dominaient la biomasse, alors que le polychete Prionospio steenstrupi et le mollusque Macoma calcarea etaient les taxons les plus abondants. La caracteristique la plus evidente qui ressort de ces donnees est l'existence d'un declin na- turel dans le nombre d'especes, la densite totale et l'abondance et la biomasse d'especes particulieres entre 1993 et 1995. Le seul effet immediat du chalutage est apparu en 1994 lorsque la densite de 13 especes et la biomasse de 11 especes, surtout des polychetes, ainsi que la densite totale par echantillon de benne etaient significativement plus bas - ses. Il y a peu de signes d'effets a long terme du chalutage. Lorsqu'il y a une indication de perturbation, il s'agit d'un phenomene qui mime les perturbations naturelles et qui se reflete par un glissement de la communaute dans la meme direction sur une ordination de cadrage multidimensionnel; aucune signature particuliere reliee au chalutage n'est de - celee. Neanmoins, les resultats de notre experience ne doivent pas etre extrapoles de facon non critique dans l'evaluation des impacts du chalutage commercial.

New statistical developments combined with the use of highly polymorphic microsatellite DNA markers enable the determination of the population of origin of single fish, resulting in numerous new research possibilities and applications in practical management of fish populations. We first describe three main categories of methods available, i.e. (i) assignment tests and related methods, (ii) discriminant function analysis and (iii) artificial neural networks. In all these, individuals can be assigned to the population from which their multilocus genotypes are most likely to be derived. Assignment tests are based on calculations of the likelihood of multilocus genotypes in populations, based on allele frequencies. Discriminant function analysis is based on multivariate statistics, whereas artificial neural networks formulate predictions through exposure to correct solutions. Assignment tests are the methods of choice when considering genetic data alone, whereas discriminant function analysis and artificial neural networks may be useful when genetic data are combined with, for instance, morphological and ecological data. Assignment tests can be used to assess the genetic distinctness of populations, for discriminating among closely related species and to directly identify immigrants or individuals of immigrant ancestry, and thereby study patterns of dispersal among populations, including sex-biased dispersal. In a conservation context, assignment tests can be used to assess the genetic impact of domesticated fish on wild populations and for determining if extant fish populations are in fact indigenous or descendants from stocked fish or strayers, and they can be applied in forensics, for instance to reveal poaching. Assignment tests are at present most useful for studies of freshwater and anadromous fishes owing to stronger genetic differentiation among populations than in marine fishes. However, some genetically divergent populations of marine fishes have been discovered, which could be used as natural laboratories for studying dispersal and gene flow. It is foreseen that ongoing developments in statistical methods, combined with improved techniques for screening large numbers of loci, will permit assignment methods to become standard tools in studies on the biology of fishes.

Random amplified polymorphic DNA (RAPD) profiles were used in a preliminary investigation of the genetic relationships among American lobsters (Homarus americanus) from the ecologically disparate and geographically separate regions of the southern Gulf of St. Lawrence, a bay off southwestern Nova Scotia, and a deep-sea canyon off Georges Bank. Phenotypic analyses of the RAPD bands showed no significant difference between samples caught at these three geographic locations. Lobsters from the Gulf of Maine, collected inshore from Lobster Bay, Nova Scotia, and offshore from Georges Bank, were genetically the most similar (D = 0.002), whereas Gulf of St. Lawrence lobsters were about three times as genetically distant from these two subpopulations (D = 0.005-0.006). However, FSTvalues at each RAPD band ranged from

Deep-sea sponge grounds provide structurally complex habitat for fish and invertebrates and enhance local biodiversity. They are also vulnerable to bottom-contact fisheries and prime candidates for Vulnerable Marine Ecosystem designation and related conservation action. This study uses species distribution modeling, based on presence and absence observations of Geodia spp. and sponge grounds derived from research trawl catches, as well as spatially continuous data on the physical and biological ocean environment derived from satellite data and oceanographic models, to model the distribution of Geodia sponges and sponge grounds in the Northwest Atlantic. Most models produce excellent fits with validation data although fits are reduced when models are extrapolated to new areas, especially when oceanographic regimes differ between areas. Depth and minimum bottom salinity were important predictors in most models, and a Geodia spp. minimum bottom salinity tolerance threshold in the 34.3-34.8 psu range was hypothesized on the basis of model structure. The models indicated two currently unsampled regions within the study area, the deeper parts of Baffin Bay and the Newfoundland and Labrador slopes, where future sponge grounds are most likely to be found.

The influence of structure-forming deep-water sponge grounds on the composition, diversity, and abundance of the local epibenthic megafaunal community of the Flemish Pass area, Northwest Atlantic was statistically assessed. These habitats are considered vulnerable marine ecosystems and, therefore, warrant conservation measures to protect them from bottom fishing activities. The epibenthic megafauna were quantified from four photographic transects, three of which were located on the western slope of the Flemish Cap with an overall depth range of 444–940 m, and the fourth in the southern Flemish Pass between 1328 and 1411 m. We observed a diverse megafaunal community dominated by large numbers of ophiuroids and sponges. On the slope of the Flemish Cap, sponge grounds were dominated by axinellid and polymastid sponges, while the deeper sponge ground in the southern Flemish Pass was formed mainly by geodiids and Asconema sp. The presence of structure-forming sponges was associated with a higher biodiversity and abundance of associated megafauna compared with non-sponge habitat. The composition of megafauna significantly differed between sponge grounds and non-sponge grounds and also between different sponge morphologies. Surface chlorophyll a and near-bottom salinity were important environmental determinants in generalized linear models of megafaunal species richness and abundance., Sí

Many bivalves have an unusual mechanism of mitochondrial DNA (mtDNA) inheritance called doubly uniparental inheritance (DUI) in which distinctly different genomes are inherited through the female (F genome) and male (M genome) lineages. In fertilized eggs that will develop into male embryos, the sperm mitochondria remain in an aggregation, which is believed to be delivered to the primordial germ cells and passed to the next generation through the sperm. In fertilized eggs that will develop into female embryos, the sperm mitochondria are dispersed throughout the developing embryo and make little if any contribution to the next generation. The frequency of embryos with the aggregated or dispersed mitochondrial type varies among females. Previous models of DUI have predicted that maternal nuclear factors cause molecular differences among unfertilized eggs from females producing embryos with predominantly dispersed or aggregated mitochondria. We test this hypothesis using females of each of the two types from a natural population. We have found small, yet detectable, differences of the predicted type at the proteome level. We also provide evidence that eggs of females giving the dispersed pattern have consistently lower expression for different proteasome subunits than eggs of females giving the aggregated pattern. These results, combined with those of an earlier study in which we used hatchery lines of Mytilus, and with a transcriptomic study in a clam that has the DUI system of mtDNA transmission, reinforce the hypothesis that the ubiquitin-proteasome system plays a key role in the mechanism of DUI and sex determination in bivalves. We also report that eggs of females giving the dispersed pattern have higher expression for arginine kinase and enolase, enzymes involved in energy production, whereas ferritin, which is involved in iron homeostasis, has lower expression. We discuss these results in the context of genetic models for DUI and suggest experimental methods for further understanding the role of these proteins in DUI.