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A global horizon scan of issues impacting marine and coastal biodiversity conservation. Nat Ecol Evol 2022; 6:1262-1270. [PMID: 35798839 DOI: 10.1038/s41559-022-01812-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/24/2022] [Indexed: 11/09/2022]
Abstract
The biodiversity of marine and coastal habitats is experiencing unprecedented change. While there are well-known drivers of these changes, such as overexploitation, climate change and pollution, there are also relatively unknown emerging issues that are poorly understood or recognized that have potentially positive or negative impacts on marine and coastal ecosystems. In this inaugural Marine and Coastal Horizon Scan, we brought together 30 scientists, policymakers and practitioners with transdisciplinary expertise in marine and coastal systems to identify new issues that are likely to have a significant impact on the functioning and conservation of marine and coastal biodiversity over the next 5-10 years. Based on a modified Delphi voting process, the final 15 issues presented were distilled from a list of 75 submitted by participants at the start of the process. These issues are grouped into three categories: ecosystem impacts, for example the impact of wildfires and the effect of poleward migration on equatorial biodiversity; resource exploitation, including an increase in the trade of fish swim bladders and increased exploitation of marine collagens; and new technologies, such as soft robotics and new biodegradable products. Our early identification of these issues and their potential impacts on marine and coastal biodiversity will support scientists, conservationists, resource managers and policymakers to address the challenges facing marine ecosystems.
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Abstract
Implementation of marine conservation strategies, such as increasing the numbers, extent, and effectiveness of protected areas (PAs), can help achieve conservation and restoration of ocean health and associated goods and services. Despite increasing recognition of the importance of including aspects of ecological functioning in PA design, the physical characteristics of habitats and simple measures of species diversity inform most PA designations. Marine and terrestrial ecologists have recently been using biological traits to assess community dynamics, functioning, and vulnerability to anthropogenic impacts. Here, we explore potential trait-based marine applications to advance PA design. We recommend strategies to integrate biological traits into (a) conservation objectives (e.g., by assessing and predicting impacts and vulnerability), (b) PA spatial planning (e.g., mapping ecosystem functions and functional diversity hot spots), and (c) time series monitoring protocols (e.g., using functional traits to detect recoveries). We conclude by emphasizing the need for pragmatic tools to improve the efficacy of spatial planning and monitoring efforts.
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Climate change considerations are fundamental to management of deep-sea resource extraction. GLOBAL CHANGE BIOLOGY 2020; 26:4664-4678. [PMID: 32531093 PMCID: PMC7496832 DOI: 10.1111/gcb.15223] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/12/2020] [Indexed: 05/19/2023]
Abstract
Climate change manifestation in the ocean, through warming, oxygen loss, increasing acidification, and changing particulate organic carbon flux (one metric of altered food supply), is projected to affect most deep-ocean ecosystems concomitantly with increasing direct human disturbance. Climate drivers will alter deep-sea biodiversity and associated ecosystem services, and may interact with disturbance from resource extraction activities or even climate geoengineering. We suggest that to ensure the effective management of increasing use of the deep ocean (e.g., for bottom fishing, oil and gas extraction, and deep-seabed mining), environmental management and developing regulations must consider climate change. Strategic planning, impact assessment and monitoring, spatial management, application of the precautionary approach, and full-cost accounting of extraction activities should embrace climate consciousness. Coupled climate and biological modeling approaches applied in the water and on the seafloor can help accomplish this goal. For example, Earth-System Model projections of climate-change parameters at the seafloor reveal heterogeneity in projected climate hazard and time of emergence (beyond natural variability) in regions targeted for deep-seabed mining. Models that combine climate-induced changes in ocean circulation with particle tracking predict altered transport of early life stages (larvae) under climate change. Habitat suitability models can help assess the consequences of altered larval dispersal, predict climate refugia, and identify vulnerable regions for multiple species under climate change. Engaging the deep observing community can support the necessary data provisioning to mainstream climate into the development of environmental management plans. To illustrate this approach, we focus on deep-seabed mining and the International Seabed Authority, whose mandates include regulation of all mineral-related activities in international waters and protecting the marine environment from the harmful effects of mining. However, achieving deep-ocean sustainability under the UN Sustainable Development Goals will require integration of climate consideration across all policy sectors.
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The BenBioDen database, a global database for meio-, macro- and megabenthic biomass and densities. Sci Data 2020; 7:206. [PMID: 32601290 PMCID: PMC7324384 DOI: 10.1038/s41597-020-0551-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/05/2020] [Indexed: 11/30/2022] Open
Abstract
Benthic fauna refers to all fauna that live in or on the seafloor, which researchers typically divide into size classes meiobenthos (32/64 µm-0.5/1 mm), macrobenthos (250 µm-1 cm), and megabenthos (>1 cm). Benthic fauna play important roles in bioturbation activity, mineralization of organic matter, and in marine food webs. Evaluating their role in these ecosystem functions requires knowledge of their global distribution and biomass. We therefore established the BenBioDen database, the largest open-access database for marine benthic biomass and density data compiled so far. In total, it includes 11,792 georeferenced benthic biomass and 51,559 benthic density records from 384 and 600 studies, respectively. We selected all references following the procedure for systematic reviews and meta-analyses, and report biomass records as grams of wet mass, dry mass, or ash-free dry mass, or carbon per m2 and as abundance records as individuals per m2. This database provides a point of reference for future studies on the distribution and biomass of benthic fauna.
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Resolving fine-scale population structure and fishery exploitation using sequenced microsatellites in a northern fish. Evol Appl 2020; 13:1055-1068. [PMID: 32431752 PMCID: PMC7232759 DOI: 10.1111/eva.12922] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/02/2020] [Indexed: 12/11/2022] Open
Abstract
The resiliency of populations and species to environmental change is dependent on the maintenance of genetic diversity, and as such, quantifying diversity is central to combating ongoing widespread reductions in biodiversity. With the advent of next-generation sequencing, several methods now exist for resolving fine-scale population structure, but the comparative performance of these methods for genetic assignment has rarely been tested. Here, we evaluate the performance of sequenced microsatellites and a single nucleotide polymorphism (SNP) array to resolve fine-scale population structure in a critically important salmonid in north eastern Canada, Arctic Charr (Salvelinus alpinus). We also assess the utility of sequenced microsatellites for fisheries applications by quantifying the spatial scales of movement and exploitation through genetic assignment of fishery samples to rivers of origin and comparing these results with a 29-year tagging dataset. Self-assignment and simulation-based analyses of 111 genome-wide microsatellite loci and 500 informative SNPs from 28 populations of Arctic Charr in north-eastern Canada identified largely river-specific genetic structure. Despite large differences (~4X) in the number of loci surveyed between panels, mean self-assignment accuracy was similar with the microsatellite loci and the SNP panel (>90%). Subsequent analysis of 996 fishery-collected samples using the microsatellite panel revealed that larger rivers contribute greater numbers of individuals to the fishery and that coastal fisheries largely exploit individuals originating from nearby rivers, corroborating results from traditional tagging experiments. Our results demonstrate the efficacy of sequence-based microsatellite genotyping to advance understanding of fine-scale population structure and harvest composition in northern and understudied species.
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Seafloor biodiversity of Canada's three oceans: Patterns, hotspots and potential drivers. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.13013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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A climate-associated multispecies cryptic cline in the northwest Atlantic. SCIENCE ADVANCES 2018; 4:eaaq0929. [PMID: 29600272 PMCID: PMC5873842 DOI: 10.1126/sciadv.aaq0929] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/14/2018] [Indexed: 06/08/2023]
Abstract
The spatial genetic structure of most species in the open marine environment remains largely unresolved. This information gap creates uncertainty in the sustainable management, recovery, and associated resilience of marine communities and our capacity to extrapolate beyond the few species for which such information exists. We document a previously unidentified multispecies biogeographic break aligned with a steep climatic gradient and driven by seasonal temperature minima in the northwest Atlantic. The coherence of this genetic break across our five study species with contrasting life histories suggests a pervasive macroecological phenomenon. The integration of this genetic structure with habitat suitability models and climate forecasts predicts significant variation in northward distributional shifts among populations and availability of suitable habitat in future oceans. The results of our integrated approach provide new perspective on how cryptic intraspecific diversity associated with climatic variation influences species and community response to climate change beyond simple poleward shifts.
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Oceanographic variation influences spatial genomic structure in the sea scallop, Placopecten magellanicus. Ecol Evol 2018; 8:2824-2841. [PMID: 29531698 PMCID: PMC5838053 DOI: 10.1002/ece3.3846] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 01/03/2023] Open
Abstract
Environmental factors can influence diversity and population structure in marine species and accurate understanding of this influence can both improve fisheries management and help predict responses to environmental change. We used 7163 SNPs derived from restriction site-associated DNA sequencing genotyped in 245 individuals of the economically important sea scallop, Placopecten magellanicus, to evaluate the correlations between oceanographic variation and a previously identified latitudinal genomic cline. Sea scallops span a broad latitudinal area (>10 degrees), and we hypothesized that climatic variation significantly drives clinal trends in allele frequency. Using a large environmental dataset, including temperature, salinity, chlorophyll a, and nutrient concentrations, we identified a suite of SNPs (285-621, depending on analysis and environmental dataset) potentially under selection through correlations with environmental variation. Principal components analysis of different outlier SNPs and environmental datasets revealed similar northern and southern clusters, with significant associations between the first axes of each (R2adj = .66-.79). Multivariate redundancy analysis of outlier SNPs and the environmental principal components indicated that environmental factors explained more than 32% of the variance. Similarly, multiple linear regressions and random-forest analysis identified winter average and minimum ocean temperatures as significant parameters in the link between genetic and environmental variation. This work indicates that oceanographic variation is associated with the observed genomic cline in this species and that seasonal periods of extreme cold may restrict gene flow along a latitudinal gradient in this marine benthic bivalve. Incorporating this finding into management may improve accuracy of management strategies and future predictions.
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Abstract
Marine animals with complex life cycles may move passively or actively for fertilization, dispersal, predator avoidance, resource acquisition, and migration, and over scales from micrometers to thousands of kilometers. This diversity has catalyzed idiosyncratic and unfocused research, creating unsound paradigms regarding the role of movement in ecology and evolution. The emerging movement ecology paradigm offers a framework to consolidate movement research independent of taxon, life-history stage, scale, or discipline. This review applies the framework to movement among life-history stages in marine animals with complex life cycles to consolidate marine movement research and offer insights for scientists working in aquatic and terrestrial realms. Irrespective of data collection or simulation strategy, breaking each life-history stage down into the fundamental units of movement allows each unit to be studied independently or interactively with other units. Understanding these underlying mechanisms of movement within each life-history stage can then be used to construct lifetime movement paths. These paths can allow further investigation of the relative contributions and interdependencies of steps and phases across a lifetime and how these paths influence larger research topics, such as population-level movements.
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Global Carbon Cycling on a Heterogeneous Seafloor. Trends Ecol Evol 2017; 33:96-105. [PMID: 29248328 DOI: 10.1016/j.tree.2017.11.004] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/25/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
Abstract
Diverse biological communities mediate the transformation, transport, and storage of elements fundamental to life on Earth, including carbon, nitrogen, and oxygen. However, global biogeochemical model outcomes can vary by orders of magnitude, compromising capacity to project realistic ecosystem responses to planetary changes, including ocean productivity and climate. Here, we compare global carbon turnover rates estimated using models grounded in biological versus geochemical theory and argue that the turnover estimates based on each perspective yield divergent outcomes. Importantly, empirical studies that include sedimentary biological activity vary less than those that ignore it. Improving the relevance of model projections and reducing uncertainty associated with the anticipated consequences of global change requires reconciliation of these perspectives, enabling better societal decisions on mitigation and adaptation.
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Identifying patterns of dispersal, connectivity and selection in the sea scallop, Placopecten magellanicus, using RADseq-derived SNPs. Evol Appl 2017; 10:102-117. [PMID: 28035239 PMCID: PMC5192885 DOI: 10.1111/eva.12432] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 08/23/2016] [Indexed: 12/29/2022] Open
Abstract
Understanding patterns of dispersal and connectivity among marine populations can directly inform fisheries conservation and management. Advances in high-throughput sequencing offer new opportunities for estimating marine connectivity. We used restriction-site-associated DNA sequencing to examine dispersal and realized connectivity in the sea scallop Placopecten magellanicus, an economically important marine bivalve. Based on 245 individuals sampled rangewide at 12 locations from Newfoundland to the Mid-Atlantic Bight, we identified and genotyped 7163 single nucleotide polymorphisms; 112 (1.6%) were identified as outliers potentially under directional selection. Bayesian clustering revealed a discontinuity between northern and southern samples, and latitudinal clines in allele frequencies were observed in 42.9% of the outlier loci and in 24.6% of neutral loci. Dispersal estimates derived using these clines and estimates of linkage disequilibrium imply limited dispersal; 373.1 ± 407.0 km (mean ± SD) for outlier loci and 641.0 ± 544.6 km (mean ± SD) for neutral loci. Our analysis suggests restricted dispersal compared to the species range (>2000 km) and that dispersal and effective connectivity differ. These observations support the hypothesis that limited effective dispersal structures scallop populations along eastern North America. These findings can help refine the appropriate scale of management and conservation in this commercially valuable species.
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Abstract
The 70 % of Earth's surface covered by oceans supports significant biological diversity and immense untapped potential for marine bioproducts. The recently completed international Census of Marine Life (2000-2010) invested heavily in evaluating the diversity, abundance, and distribution of life in the ocean but concluded that at least 50 % and potentially > 90 % of marine species remain undescribed by science. Despite this potential, and numerous successes spanning pharmaceuticals, nutraceuticals, anti-foulants and adhesives, biofuels, biocatalysts (enzymes), and cosmetics, several impediments have slowed marine bioproduct development. First, the sheer size of the ocean constrains comprehensive exploration. Second, marine taxonomists and ecologists generally do not focus on the most promising groups for bioproduct development. Third, the geographic mismatch between (often remote) biodiversity hotspots and science capacity limit discovery. Despite these challenges, new ocean sampling tools (digital imaging, remote vehicles, genetic approaches, in situ samplers), many developed or improved during the Census of Marine Life, should enhance future marine biodiversity and thus marine bioproduct discovery.
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Factors regulating early life history dispersal of Atlantic cod (Gadus morhua) from coastal Newfoundland. PLoS One 2013; 8:e75889. [PMID: 24058707 PMCID: PMC3776752 DOI: 10.1371/journal.pone.0075889] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 08/19/2013] [Indexed: 11/18/2022] Open
Abstract
To understand coastal dispersal dynamics of Atlantic cod (Gadus morhua), we examined spatiotemporal egg and larval abundance patterns in coastal Newfoundland. In recent decades, Smith Sound, Trinity Bay has supported the largest known overwintering spawning aggregation of Atlantic cod in the region. We estimated spawning and dispersal characteristics for the Smith Sound-Trinity Bay system by fitting ichthyoplankton abundance data to environmentally-driven, simplified box models. Results show protracted spawning, with sharply increased egg production in early July, and limited dispersal from the Sound. The model for the entire spawning season indicates egg export from Smith Sound is 13%•day−1 with a net mortality of 27%•day–1. Eggs and larvae are consistently found in western Trinity Bay with little advection from the system. These patterns mirror particle tracking models that suggest residence times of 10–20 days, and circulation models indicating local gyres in Trinity Bay that act in concert with upwelling dynamics to retain eggs and larvae. Our results are among the first quantitative dispersal estimates from Smith Sound, linking this spawning stock to the adjacent coastal waters. These results illustrate the biophysical interplay regulating dispersal and connectivity originating from inshore spawning of coastal northwest Atlantic.
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Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish. Evol Appl 2013; 6:450-61. [PMID: 23745137 PMCID: PMC3673473 DOI: 10.1111/eva.12026] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 09/28/2012] [Indexed: 12/17/2022] Open
Abstract
As populations diverge, genomic regions associated with adaptation display elevated differentiation. These genomic islands of adaptive divergence can inform conservation efforts in exploited species, by refining the delineation of management units, and providing genomic tools for more precise and effective population monitoring and the successful assignment of individuals and products. We explored heterogeneity in genomic divergence and its impact on the resolution of spatial population structure in exploited populations of Atlantic cod, Gadus morhua, using genome wide expressed sequence derived single nucleotide polymorphisms in 466 individuals sampled across the range. Outlier tests identified elevated divergence at 5.2% of SNPs, consistent with directional selection in one-third of linkage groups. Genomic regions of elevated divergence ranged in size from a single position to several cM. Structuring at neutral loci was associated with geographic features, whereas outlier SNPs revealed genetic discontinuities in both the eastern and western Atlantic. This fine-scale geographic differentiation enhanced assignment to region of origin, and through the identification of adaptive diversity, fundamentally changes how these populations should be conserved. This work demonstrates the utility of genome scans for adaptive divergence in the delineation of stock structure, the traceability of individuals and products, and ultimately a role for population genomics in fisheries conservation.
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Dispersal patterns, active behaviour, and flow environment during early life history of coastal cold water fishes. PLoS One 2012; 7:e46266. [PMID: 23029455 PMCID: PMC3460877 DOI: 10.1371/journal.pone.0046266] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 08/31/2012] [Indexed: 11/19/2022] Open
Abstract
During the pelagic larval phase, fish dispersal may be influenced passively by surface currents or actively determined by swimming behaviour. In situ observations of larval swimming are few given the constraints of field sampling. Active behaviour is therefore often inferred from spatial patterns in the field, laboratory studies, or hydrodynamic theory, but rarely are these approaches considered in concert. Ichthyoplankton survey data collected during 2004 and 2006 from coastal Newfoundland show that changes in spatial heterogeneity for multiple species do not conform to predictions based on passive transport. We evaluated the interaction of individual larvae with their environment by calculating Reynolds number as a function of ontogeny. Typically, larvae hatch into a viscous environment in which swimming is inefficient, and later grow into more efficient intermediate and inertial swimming environments. Swimming is therefore closely related to length, not only because of swimming capacity but also in how larvae experience viscosity. Six of eight species sampled demonstrated consistent changes in spatial patchiness and concomitant increases in spatial heterogeneity as they transitioned into more favourable hydrodynamic swimming environments, suggesting an active behavioural element to dispersal. We propose the tandem assessment of spatial heterogeneity and hydrodynamic environment as a potential approach to understand and predict the onset of ecologically significant swimming behaviour of larval fishes in the field.
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Exploring the role of environmental variables in shaping patterns of seabed biodiversity composition in regional-scale ecosystems. J Appl Ecol 2012; 49:670-679. [PMID: 22879681 PMCID: PMC3412211 DOI: 10.1111/j.1365-2664.2012.02148.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 04/03/2012] [Indexed: 11/29/2022]
Abstract
1. Environmental variables are often used as indirect surrogates for mapping biodiversity because species survey data are scant at regional scales, especially in the marine realm. However, environmental variables are measured on arbitrary scales unlikely to have simple, direct relationships with biological patterns. Instead, biodiversity may respond nonlinearly and to interactions between environmental variables. 2. To investigate the role of the environment in driving patterns of biodiversity composition in large marine regions, we collated multiple biological survey and environmental data sets from tropical NE Australia, the deep Gulf of Mexico and the temperate Gulf of Maine. We then quantified the shape and magnitude of multispecies responses along >30 environmental gradients and the extent to which these variables predicted regional distributions. To do this, we applied a new statistical approach, Gradient Forest, an extension of Random Forest, capable of modelling nonlinear and threshold responses. 3. The regional‐scale environmental variables predicted an average of 13–35% (up to 50–85% for individual species) of the variation in species abundance distributions. Important predictors differed among regions and biota and included depth, salinity, temperature, sediment composition and current stress. The shapes of responses along gradients also differed and were nonlinear, often with thresholds indicative of step changes in composition. These differing regional responses were partly due to differing environmental indicators of bioregional boundaries and, given the results to date, may indicate limited scope for extrapolating bio‐physical relationships beyond the region of source data sets. 4.
Synthesis and applications. Gradient Forest offers a new capability for exploring relationships between biodiversity and environmental gradients, generating new information on multispecies responses at a detail not available previously. Importantly, given the scarcity of data, Gradient Forest enables the combined use of information from disparate data sets. The gradient response curves provide biologically informed transformations of environmental layers to predict and map expected patterns of biodiversity composition that represent sampled composition better than uninformed variables. The approach can be applied to support marine spatial planning and management and has similar applicability in terrestrial realms. Gradient Forest offers a new capability for exploring relationships between biodiversity and environmental gradients, generating new information on multispecies responses at a detail not available previously. Importantly, given the scarcity of data, Gradient Forest enables the combined use of information from disparate data sets. The gradient response curves provide biologically informed transformations of environmental layers to predict and map expected patterns of biodiversity composition that represent sampled composition better than uninformed variables. The approach can be applied to support marine spatial planning and management and has similar applicability in terrestrial realms.
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Evaluating SNP ascertainment bias and its impact on population assignment in Atlantic cod, Gadus morhua. Mol Ecol Resour 2011; 11 Suppl 1:218-25. [PMID: 21429176 DOI: 10.1111/j.1755-0998.2010.02949.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The increasing use of single nucleotide polymorphisms (SNPs) in studies of nonmodel organisms accentuates the need to evaluate the influence of ascertainment bias on accurate ecological or evolutionary inference. Using a panel of 1641 expressed sequence tag-derived SNPs developed for northwest Atlantic cod (Gadus morhua), we examined the influence of ascertainment bias and its potential impact on assignment of individuals to populations ranging widely in origin. We hypothesized that reductions in assignment success would be associated with lower diversity in geographical regions outside the location of ascertainment. Individuals were genotyped from 13 locations spanning much of the contemporary range of Atlantic cod. Diversity, measured as average sample heterozygosity and number of polymorphic loci, declined (c. 30%) from the western (H(e) = 0.36) to eastern (H(e) = 0.25) Atlantic, consistent with a signal of ascertainment bias. Assignment success was examined separately for pools of loci representing differing degrees of reductions in diversity. SNPs displaying the largest declines in diversity produced the most accurate assignment in the ascertainment region (c. 83%) and the lowest levels of correct assignment outside the ascertainment region (c. 31%). Interestingly, several isolated locations showed no effect of assignment bias and consistently displayed 100% correct assignment. Contrary to expectations, estimates of accurate assignment range-wide using all loci displayed remarkable similarity despite reductions in diversity. Our results support the use of large SNP panels in assignment studies of high geneflow marine species. However, our evidence of significant reductions in assignment success using some pools of loci suggests that ascertainment bias may influence assignment results and should be evaluated in large-scale assignment studies.
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Abstract
Evaluating and understanding biodiversity in marine ecosystems are both necessary and challenging for conservation. This paper compiles and summarizes current knowledge of the diversity of marine taxa in Canada's three oceans while recognizing that this compilation is incomplete and will change in the future. That Canada has the longest coastline in the world and incorporates distinctly different biogeographic provinces and ecoregions (e.g., temperate through ice-covered areas) constrains this analysis. The taxonomic groups presented here include microbes, phytoplankton, macroalgae, zooplankton, benthic infauna, fishes, and marine mammals. The minimum number of species or taxa compiled here is 15,988 for the three Canadian oceans. However, this number clearly underestimates in several ways the total number of taxa present. First, there are significant gaps in the published literature. Second, the diversity of many habitats has not been compiled for all taxonomic groups (e.g., intertidal rocky shores, deep sea), and data compilations are based on short-term, directed research programs or longer-term monitoring activities with limited spatial resolution. Third, the biodiversity of large organisms is well known, but this is not true of smaller organisms. Finally, the greatest constraint on this summary is the willingness and capacity of those who collected the data to make it available to those interested in biodiversity meta-analyses. Confirmation of identities and intercomparison of studies are also constrained by the disturbing rate of decline in the number of taxonomists and systematists specializing on marine taxa in Canada. This decline is mostly the result of retirements of current specialists and to a lack of training and employment opportunities for new ones. Considering the difficulties encountered in compiling an overview of biogeographic data and the diversity of species or taxa in Canada's three oceans, this synthesis is intended to serve as a biodiversity baseline for a new program on marine biodiversity, the Canadian Healthy Ocean Network. A major effort needs to be undertaken to establish a complete baseline of Canadian marine biodiversity of all taxonomic groups, especially if we are to understand and conserve this part of Canada's natural heritage.
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Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature. Proc Biol Sci 2010; 277:3725-34. [PMID: 20591865 DOI: 10.1098/rspb.2010.0985] [Citation(s) in RCA: 185] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite the enormous economic and ecological importance of marine organisms, the spatial scales of adaptation and biocomplexity remain largely unknown. Yet, the preservation of local stocks that possess adaptive diversity is critical to the long-term maintenance of productive stable fisheries and ecosystems. Here, we document genomic evidence of range-wide adaptive differentiation in a broadcast spawning marine fish, Atlantic cod (Gadus morhua), using a genome survey of single nucleotide polymorphisms. Of 1641 gene-associated polymorphisms examined, 70 (4.2%) tested positive for signatures of selection using a Bayesian approach. We identify a subset of these loci (n=40) for which allele frequencies show parallel temperature-associated clines (p<0.001, r2=0.89) in the eastern and western north Atlantic. Temperature associations were robust to the statistical removal of geographic distance or latitude effects, and contrasted 'neutral' loci, which displayed no temperature association. Allele frequencies at temperature-associated loci were significantly correlated, spanned three linkage groups and several were successfully annotated supporting the involvement of multiple independent genes. Our results are consistent with the evolution and/or selective sweep of multiple genes in response to ocean temperature, and support the possibility of a new conservation paradigm for non-model marine organisms based on genomic approaches to resolving functional and adaptive diversity.
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Structural and functional connectivity of marine fishes within a semi-enclosed Newfoundland fjord. JOURNAL OF FISH BIOLOGY 2009; 75:1393-1409. [PMID: 20738621 DOI: 10.1111/j.1095-8649.2009.02391.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The interplay between structural connectivity (i.e. habitat continuity) and functional connectivity (i.e. dispersal probability) in marine fishes was examined in a coastal fjord (Holyrood Pond, Newfoundland, Canada) that is completely isolated from the North Atlantic Ocean for most of the year. Genetic differentiation was described in three species (rainbow smelt Osmerus mordax, white hake Urophycis tenuis and Atlantic cod Gadus morhua) with contrasting life histories using seven to 10 microsatellite loci and a protein-coding locus, PanI (G. morhua). Analysis of microsatellite differentiation indicated clear genetic differences between the fjord and coastal regions; however, the magnitude of difference was no more elevated than adjacent bays and was not enhanced by the fjord's isolation. Osmerus mordax was characterized by the highest structure overall with moderate differentiation between the fjord and St Mary's Bay (F(ST)c.0.047). In contrast, U. tenuis and G. morhua displayed weak differentiation (F(ST) < 0.01). Nonetheless, these populations did demonstrate high rates (< 75%) of Bayesian self-assignment. Furthermore, elevated differentiation was observed at the PanI locus in G. morhua between the fjord and other coastal locations. Interestingly, locus-specific genetic differentiation and expected heterozygosity were negatively associated in O. mordax, in contrast to the positive associations observed in U. tenuis and G. morhua. Gene flow in these species is apparently unencumbered by limited structural connectivity, yet the observed differentiation suggests that population structuring exists over small scales despite high dispersal potential.
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Global patterns in marine dispersal estimates: the influence of geography, taxonomic category and life history. Proc Biol Sci 2008; 275:1803-9. [PMID: 18445556 DOI: 10.1098/rspb.2008.0216] [Citation(s) in RCA: 213] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We examine estimates of dispersal in a broad range of marine species through an analysis of published values, and evaluate how well these values represent global patterns through a comparison with correlates of dispersal. Our analysis indicates a historical focus in dispersal studies on low-dispersal/low-latitude species, and we hypothesize that these studies are not generally applicable and representative of global patterns. Large-scale patterns in dispersal were examined using a database of correlates of dispersal such as planktonic larval duration (PLD, 318 species) and genetic differentiation (FST, 246 species). We observed significant differences in FST (p<0.001) and PLD (p<0.001) between taxonomic groups (e.g. fishes, cnidarians, etc.). Within marine fishes (more than 50% of datasets), the prevalence of demersal eggs was negatively associated with PLD (R2=0.80, p<0.001) and positively associated with genetic structure (R2=0.74, p<0.001). Furthermore, dispersal within marine fishes (i.e. PLD and FST) increased with latitude, adult body size and water depth. Of these variables, multiple regression identified latitude and body size as persistent predictors across taxonomic levels. These global patterns of dispersal represent a first step towards understanding and predicting species-level and regional differences in dispersal, and will be improved as more comprehensive data become available.
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Predation regulation of sedimentary faunal structure: potential effects of a fishery-induced switch in predators in a Newfoundland sub-Arctic fjord. Oecologia 2005; 144:125-36. [PMID: 15791429 DOI: 10.1007/s00442-005-0017-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Accepted: 01/19/2005] [Indexed: 12/01/2022]
Abstract
The collapse of the cod fishery in Newfoundland has coincided with marked increases in abundances of snow crab, pandalid shrimp, and other crustaceans that prey on sedimentary infauna. A 3-year sampling program in Bonne Bay, Newfoundland indicates differences in composition and number of these predators in the two main arms of the fjord that coincide with strong differences in benthic community structure. To test whether predation pressure contributes to the observed patterns in sedimentary fauna, exclusion field experiments with full and partial cages were deployed in both arms at 30-m depth and sampled along with ambient sediments at 0-, 4-, and 8-week periods. Predation significantly influenced species composition, abundance and, in some cases, diversity. The most striking changes included increases in the polychaetes Phöloe tecta and Ophelina cylindricaudata in exclusions relative to controls, and concurrent declines in the polychaete Paradoneis lyra and the cumacean Lamphros fuscata. In laboratory experiments, fresh non-disturbed sediment cores from each experimental area were either protected or exposed to snow crab, the most abundant predator in the bay. A snow crab inclusion experiment was also carried out in the field, using cages similar to those used for exclusions. Despite differences in sedimentary faunas in the two arms, both types of experiments detected a predator effect that was very similar to that documented in exclusion experiments. Thus, despite differences in the scales associated with each type of manipulation, our results suggest that crab predation is a significant structuring force in Newfoundland sedimentary communities. Given the historical changes that have occurred in predator composition as a result of cod over-fishing, we hypothesize that broad-scale community changes may be taking place in North Atlantic benthic ecosystems.
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Polychaete assemblages of a sub-arctic Newfoundland fjord: habitat, distribution, and identification. Polar Biol 2005. [DOI: 10.1007/s00300-005-0719-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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