Recent improvements in genetic analysis and genotyping methods have resulted in a rapid expansion of the power of molecular markers to address ecological questions. Microsatellites have emerged as ...the most popular and versatile marker type for ecological applications. The rise of commercial services that can isolate microsatellites for new study species and genotype samples at reasonable prices presents ecologists with the unprecedented ability to employ genetic approaches without heavy investment in specialized equipment. Nevertheless, the lack of accessible, synthesized information on the practicalities and pitfalls of using genetic tools impedes ecologists' ability to make informed decisions on using molecular approaches and creates the risk that some will use microsatellites without understanding the steps needed to evaluate the quality of a genetic data set. The first goal of this synthesis is to provide an overview of the strengths and limitations of microsatellite markers and the risks, cost and time requirements of isolating and using microsatellites with the aid of commercial services. The second goal is to encourage the use and consistent reporting of thorough marker screening to ensure high quality data. To that end, we present a multistep screening process to evaluate candidate loci for inclusion in a genetic study that is broadly targeted to both novice and experienced geneticists alike.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Humans interact with the oceans in diverse and profound ways. The scope, magnitude, footprint and ultimate cumulative impacts of human activities can threaten ocean ecosystems and have changed over ...time, resulting in new challenges and threats to marine ecosystems. A fundamental gap in understanding how humanity is affecting the oceans is our limited knowledge about the pace of change in cumulative impact on ocean ecosystems from expanding human activities - and the patterns, locations and drivers of most significant change. To help address this, we combined high resolution, annual data on the intensity of 14 human stressors and their impact on 21 marine ecosystems over 11 years (2003-2013) to assess pace of change in cumulative impacts on global oceans, where and how much that pace differs across the ocean, and which stressors and their impacts contribute most to those changes. We found that most of the ocean (59%) is experiencing significantly increasing cumulative impact, in particular due to climate change but also from fishing, land-based pollution and shipping. Nearly all countries saw increases in cumulative impacts in their coastal waters, as did all ecosystems, with coral reefs, seagrasses and mangroves at most risk. Mitigation of stressors most contributing to increases in overall cumulative impacts is urgently needed to sustain healthy oceans.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Marine ecosystems are threatened by a suite of anthropogenic stressors. Mitigating multiple threats is a daunting task, particularly when funding constraints limit the number of threats that can be ...addressed. Threats are typically assessed and prioritized via expert opinion workshops that often leave no record of the rationale for decisions, making it difficult to update recommendations with new information. We devised a transparent, repeatable, and modifiable method for collecting expert opinion that describes and documents how threats affect marine ecosystems. Experts were asked to assess the functional impact, scale, and frequency of a threat to an ecosystem; the resistance and recovery time of an ecosystem to a threat; and the certainty of these estimates. To quantify impacts of 38 distinct anthropogenic threats on 23 marine ecosystems, we surveyed 135 experts from 19 different countries. Survey results showed that all ecosystems are threatened by at least nine threats and that nine ecosystems are threatened by >90% of existing threats. The greatest threats (highest impact scores) were increasing sea temperature, demersal destructive fishing, and point-source organic pollution. Rocky reef, coral reef, hard-shelf, mangrove, and offshore epipelagic ecosystems were identified as the most threatened. These general results, however, may be partly influenced by the specific expertise and geography of respondents, and should be interpreted with caution. This approach to threat analysis can identify the greatest threats (globally or locally), most widespread threats, most (or least) sensitive ecosystems, most (or least) threatened ecosystems, and other metrics of conservation value. Additionally, it can be easily modified, updated as new data become available, and scaled to local or regional settings, which would facilitate informed and transparent conservation priority setting.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NMLJ, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK
Historical exploitation of the Mediterranean Sea and the absence of rigorous baselines makes it difficult to evaluate the current health of the marine ecosystems and the efficacy of conservation ...actions at the ecosystem level. Here we establish the first current baseline and gradient of ecosystem structure of nearshore rocky reefs at the Mediterranean scale. We conducted underwater surveys in 14 marine protected areas and 18 open access sites across the Mediterranean, and across a 31-fold range of fish biomass (from 3.8 to 118 g m(-2)). Our data showed remarkable variation in the structure of rocky reef ecosystems. Multivariate analysis showed three alternative community states: (1) large fish biomass and reefs dominated by non-canopy algae, (2) lower fish biomass but abundant native algal canopies and suspension feeders, and (3) low fish biomass and extensive barrens, with areas covered by turf algae. Our results suggest that the healthiest shallow rocky reef ecosystems in the Mediterranean have both large fish and algal biomass. Protection level and primary production were the only variables significantly correlated to community biomass structure. Fish biomass was significantly larger in well-enforced no-take marine reserves, but there were no significant differences between multi-use marine protected areas (which allow some fishing) and open access areas at the regional scale. The gradients reported here represent a trajectory of degradation that can be used to assess the health of any similar habitat in the Mediterranean, and to evaluate the efficacy of marine protected areas.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Human pressures on the ocean are thought to be increasing globally, yet we know little about their patterns of cumulative change, which pressures are most responsible for change, and which places are ...experiencing the greatest increases. Managers and policymakers require such information to make strategic decisions and monitor progress towards management objectives. Here we calculate and map recent change over 5 years in cumulative impacts to marine ecosystems globally from fishing, climate change, and ocean- and land-based stressors. Nearly 66% of the ocean and 77% of national jurisdictions show increased human impact, driven mostly by climate change pressures. Five percent of the ocean is heavily impacted with increasing pressures, requiring management attention. Ten percent has very low impact with decreasing pressures. Our results provide large-scale guidance about where to prioritize management efforts and affirm the importance of addressing climate change to maintain and improve the condition of marine ecosystems.
Management and conservation can be greatly informed by considering explicitly how environmental factors influence population genetic structure. Using simulated larval dispersal estimates based on ...ocean current observations, we demonstrate how explicit consideration of frequency of exchange of larvae among sites via ocean advection can fundamentally change the interpretation of empirical population genetic structuring as compared with conventional spatial genetic analyses. Both frequency of larval exchange and empirical genetic difference were uncorrelated with Euclidean distance between sites. When transformed into relative oceanographic distances and integrated into a genetic isolation-by-distance framework, however, the frequency of larval exchange explained nearly 50 per cent of the variance in empirical genetic differences among sites over scales of tens of kilometres. Explanatory power was strongest when we considered effects of multiple generations of larval dispersal via intermediary locations on the long-term probability of exchange between sites. Our results uncover meaningful spatial patterning to population genetic structuring that corresponds with ocean circulation. This study advances our ability to interpret population structure from complex genetic data characteristic of high gene flow species, validates recent advances in oceanographic approaches for assessing larval dispersal and represents a novel approach to characterize population connectivity at small spatial scales germane to conservation and fisheries management.
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A decade of seascape genetics Selkoe, Kimberly A.; D’Aloia, Cassidy C.; Crandall, Eric D. ...
Marine ecology. Progress series (Halstenbek),
07/2016, Volume:
554
Journal Article
Peer reviewed
Seascape genetics, a term coined in 2006, is a fast growing area of population genetics that draws on ecology, oceanography and geography to address challenges in basic understanding of marine ...connectivity and applications to management. We provide an accessible overview of the latest developments in seascape genetics that merge exciting new ideas from the field of marine population connectivity with statistical and technical advances in population genetics. After summarizing the historical context leading to the emergence of seascape genetics, we detail questions and methodological approaches that are evolving the discipline, highlight applications to conservation and management, and conclude with a summary of the field’s transition to seascape genomics. From 100 seascape genetic studies, we assess trends in taxonomic and geographic coverage, sampling and statistical design, and dominant seascape drivers. Notably, temperature, oceanography and geography show equal prevalence of influence on spatial genetic patterns, and tests of over 20 other seascape factors suggest that a variety of forces impact connectivity at distinct spatio-temporal scales. A new level of rigor in statistical analysis is critical for disentangling multiple drivers and spurious effects. Coupled with GIS data and genomic scale sequencing methods, this rigor is taking seascape genetics beyond an initial focus on identifying correlations to hypothesis-driven insights into patterns and processes of population connectivity and adaptation. The latest studies are illuminating differences between demographic, functional and neutral genetic connectivity, and informing applications to marine reserve design, fisheries science and strategies to assess resilience to climate change and other anthropogenic impacts.
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What shapes variation in genetic structure within a community of codistributed species is a central but difficult question for the field of population genetics. With a focus on the isolated coral ...reef ecosystem of the Hawaiian Archipelago, we assessed how life history traits influence population genetic structure for 35 reef animals. Despite the archipelago's stepping stone configuration, isolation by distance was the least common type of genetic structure, detected in four species. Regional structuring (i.e. division of sites into genetically and spatially distinct regions) was most common, detected in 20 species and nearly in all endemics and habitat specialists. Seven species displayed chaotic (spatially unordered) structuring, and all were nonendemic generalist species. Chaotic structure also associated with relatively high global FST. Pelagic larval duration (PLD) was not a strong predictor of variation in population structure (R² = 0.22), but accounting for higher FST values of chaotic and invertebrate species, compared to regionally structured and fish species, doubled the power of PLD to explain variation in global FST (adjusted R² = 0.50). Multivariate correlation of eight species traits to six genetic traits highlighted dispersal ability, taxonomy (i.e. fish vs. invertebrate) and habitat specialization as strongest influences on genetics, but otherwise left much variation in genetic traits unexplained. Considering that the study design controlled for many sampling and geographical factors, the extreme interspecific variation in spatial genetic patterns observed for Hawaìi marine species may be generated by demographic variability due to species‐specific abundance and migration patterns and/or seascape and historical factors.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Global Map of Human Impact on Marine Ecosystems Halpern, Benjamin S; Walbridge, Shaun; Selkoe, Kimberly A ...
Science (American Association for the Advancement of Science),
02/2008, Volume:
319, Issue:
5865
Journal Article
Peer reviewed
The management and conservation of the world's oceans require synthesis of spatial data on the distribution and intensity of human activities and the overlap of their impacts on marine ecosystems. We ...developed an ecosystem-specific, multiscale spatial model to synthesize 17 global data sets of anthropogenic drivers of ecological change for 20 marine ecosystems. Our analysis indicates that no area is unaffected by human influence and that a large fraction (41%) is strongly affected by multiple drivers. However, large areas of relatively little human impact remain, particularly near the poles. The analytical process and resulting maps provide flexible tools for regional and global efforts to allocate conservation resources; to implement ecosystem-based management; and to inform marine spatial planning, education, and basic research.
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Marine species frequently show weak and/or complex genetic structuring that is commonly dismissed as ‘chaotic’ genetic patchiness and ecologically uninformative. Here, using three datasets that ...individually feature weak chaotic patchiness, we demonstrate that combining inferences across species and incorporating environmental data can greatly improve the predictive value of marine population genetics studies on small spatial scales. Significant correlations in genetic patterns of microsatellite markers among three species, kelp bass Paralabrax clathratus, Kellet’s whelk Kelletia kelletii and California spiny lobster Panulirus interruptus, in the Southern California Bight suggest that slight differences in diversity and pairwise differentiation across sampling sites are not simply noise or chaotic patchiness, but are ecologically meaningful. To test whether interspecies correlations potentially result from shared environmental drivers of genetic patterns, we assembled data on kelp bed size, sea surface temperature and estimates of site‐to‐site migration probability derived from a high resolution multi‐year ocean circulation model. These data served as predictor variables in linear models of genetic diversity and linear mixed models of genetic differentiation that were assessed with information–theoretic model selection. Kelp was the most informative predictor of genetics for all three species, but ocean circulation also played a minor role for kelp bass. The shared patterns suggest a single spatial marine management strategy may effectively protect genetic diversity of multiple species. This study demonstrates the power of environmental and ecological data to shed light on weak genetic patterns and highlights the need for future focus on a mechanistic understanding of the links between oceanography, ecology and genetic structure.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
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