Showing papers by "National Marine Fisheries Service published in 2018"

Recreational sea fishing in Europe in a global context-Participation rates, fishing effort, expenditure, and implications for monitoring and assessment

Abstract: Marine recreational fishing (MRF) is a high-participation activity with large economic value and social benefits globally, and it impacts on some fish stocks. Although reporting MRF catches is a European Union legislative requirement, estimates are only available for some countries. Here, data on numbers of fishers, participation rates, days fished, expenditures, and catches of two widely targeted species were synthesized to provide European estimates of MRF and placed in the global context. Uncertainty assessment was not possible due to incomplete knowledge of error distributions; instead, a semi-quantitative bias assessment was made. There were an estimated 8.7 million European recreational sea fishers corresponding to a participation rate of 1.6%. An estimated 77.6 million days were fished, and expenditure was €5.9 billion annually. There were higher participation, numbers of fishers, days fished and expenditure in the Atlantic than the Mediterranean, but the Mediterranean estimates were generally less robust. Comparisons with other regions showed that European MRF participation rates and expenditure were in the mid-range, with higher participation in Oceania and the United States, higher expenditure in the United States, and lower participation and expenditure in South America and Africa. For both northern European sea bass (Dicentrarchus labrax, Moronidae) and western Baltic cod (Gadus morhua, Gadidae) stocks, MRF represented 27% of the total removals. This study highlights the importance of MRF and the need for bespoke, regular and statistically sound data collection to underpin European fisheries management. Solutions are proposed for future MRF data collection in Europe and other regions to support sustainable fisheries management.

Projected sea surface temperatures over the 21st century: Changes in the mean, variability and extremes for large marine ecosystem regions of Northern Oceans

Abstract: Global climate models were used to assess changes in the mean, variability and extreme sea surface temperatures (SSTs) in northern oceans with a focus on large marine ecosystems (LMEs) adjacent to North America, Europe, and the Arctic Ocean. Results were obtained from 26 models in the Community Model Intercomparison Project Phase 5 (CMIP5) archive and 30 simulations from the National Center for Atmospheric Research Large Ensemble Community Project (CESM-LENS). All of the simulations used the observed greenhouse gas concentrations for 1976–2005 and the RCP8.5 “business as usual” scenario for greenhouse gases through the remainder of the 21st century. In general, differences between models are substantially larger than among the simulations in the CESM-LENS, indicating that the SST changes are more strongly affected by model formulation than internal climate variability. The annual SST trends over 1976–2099 in the 18 LMEs examined here are all positive ranging from 0.05 to 0.5 ° C decade–1. SST changes by the end of the 21st century are primarily due to a positive shift in the mean with only modest changes in the variability in most LMEs, resulting in a substantial increase in warm extremes and decrease in cold extremes. The shift in the mean is so large that in many regions SSTs during 2070–2099 will always be warmer than the warmest year during 1976–2005. The SST trends are generally stronger in summer than in winter, as greenhouse gas heating is integrated over a much shallower climatological mixed layer depth in summer than in winter, which amplifies the seasonal cycle of SST over the 21st century. In the Arctic, the mean SST and its variability increases substantially during summer, when it is ice free, but not during winter when a thin layer of ice reforms and SSTs remain near the freezing point.

Massive Mortality of a Planktivorous Seabird in Response to a Marine Heatwave

Abstract: Climate change has exacerbated the occurrence of large-scale sea-surface temperature anomalies, or marine heatwaves (MHW) - extreme phenomena often associated with mass mortality events of marine organisms. Using a combination of citizen science and federal datasets, we investigated the causal mechanisms of the 2014/15 die-off of Cassin's Auklets (Ptychoramphus aleuticus), a small zooplanktivorous seabird, during the NE Pacific MHW of 2013-2015. Carcass deposition followed an effective reduction in the energy content of mesozooplankton, coincident with the loss of cold-water foraging habitat caused by the intrusion of the NE Pacific MHW into the nearshore environment. Models examining interannual variability in effort-controlled carcass abundance (2001-2014) identified the biomass of lipid-poor zooplankton as the dominant predictor of increased carcass abundance. In 2014, Cassin's Auklets dispersing from colonies in British Columbia likely congregated into a nearshore band of cooler upwelled water, and ultimately died from starvation following the shift in zooplankton composition associated with onshore transport of the NE Pacific MHW. For Cassin's Auklets, already in decline due to ocean warming, large-scale and persistent MHWs might represent a global population precipice.

A guide to Bayesian model checking for ecologists

Abstract: Checking that models adequately represent data is an essential component of applied statistical inference. Ecologists increasingly use hierarchical Bayesian statistical models in their research. The appeal of this modeling paradigm is undeniable, as researchers can build and fit models that embody complex ecological processes while simultaneously controlling observation error. However, ecologists tend to be less focused on checking model assumptions and assessing potential lack-of-fit when applying Bayesian methods than when applying more traditional modes of inference such as maximum likelihood. There are also multiple ways of assessing the fit of Bayesian models, each of which has strengths and weaknesses. For instance, Bayesian p-values are relatively easy to compute, but are well known to be conservative, producing p-values biased toward 0.5. Alternatively, lesser known approaches to model checking, such as prior predictive checks, cross-validation probability integral transforms, and pivot discrepancy measures may produce more accurate characterizations of goodness-of-fit but are not as well known to ecologists. In addition, a suite of visual and targeted diagnostics can be used to examine violations of different model assumptions and lack-of-fit at different levels of the modeling hierarchy, and to check for residual temporal or spatial autocorrelation. In this review, we synthesize existing literature to guide ecologists through the many available options for Bayesian model checking. We illustrate methods and procedures with several ecological case studies, including i) analysis of simulated spatio-temporal count data, (ii) N-mixture models for estimating abundance and detection probability of sea otters from an aircraft, and (iii) hidden Markov modeling to describe attendance patterns of California sea lion mothers on a rookery. We find that commonly used procedures based on posterior predictive p-values detect extreme model inadequacy, but often do not detect more subtle cases of lack of fit. Tests based on cross-validation and pivot discrepancy measures (including the ``sampled predictive p-value'') appear to be better suited to model checking and to have better overall statistical performance. We conclude that model checking is an essential component of scientific discovery and learning that should accompany most Bayesian analyses presented in the literature.

Managing consequences of climate-driven species redistribution requires integration of ecology, conservation and social science

Abstract: Climate change is driving a pervasive global redistribution of the planet's species Species redistribution poses new questions for the study of ecosystems, conservation science and human societies that require a coordinated and integrated approach Here we review recent progress, key gaps and strategic directions in this nascent research area, emphasising emerging themes in species redistribution biology, the importance of understanding underlying drivers and the need to anticipate novel outcomes of changes in species ranges We highlight that species redistribution has manifest implications across multiple temporal and spatial scales and from genes to ecosystems Understanding range shifts from ecological, physiological, genetic and biogeographical perspectives is essential for informing changing paradigms in conservation science and for designing conservation strategies that incorporate changing population connectivity and advance adaptation to climate change Species redistributions present challenges for human well-being, environmental management and sustainable development By synthesising recent approaches, theories and tools, our review establishes an interdisciplinary foundation for the development of future research on species redistribution Specifically, we demonstrate how ecological, conservation and social research on species redistribution can best be achieved by working across disciplinary boundaries to develop and implement solutions to climate change challenges Future studies should therefore integrate existing and complementary scientific frameworks while incorporating social science and human-centred approaches Finally, we emphasise that the best science will not be useful unless more scientists engage with managers, policy makers and the public to develop responsible and socially acceptable options for the global challenges arising from species redistributions

momentuHMM: R package for generalized hidden Markov models of animal movement

Abstract: 1. Discrete‐time hidden Markov models (HMMs) have become an immensely popular tool for inferring latent animal behaviours from telemetry data. While movement HMMs typically rely solely on location data (e.g. step length and turning angle), auxiliary biotelemetry and environmental data are powerful and readily‐available resources for incorporating much more ecological and behavioural realism. However, complex movement or observation process models often necessitate custom and computationally demanding HMM model‐fitting techniques that are impractical for most practitioners, and there is a paucity of generalized user‐friendly software available for implementing multivariate HMMs of animal movement. 2. Here, we introduce an open‐source R package, momentuHMM, that addresses many of the deficiencies in existing HMM software. Features include: (1) data pre‐processing and visualization; (2) user‐specified probability distributions for an unlimited number of data streams and latent behaviour states; (3) biased and correlated random walk movement models, including dynamic “activity centres” associated with attractive or repulsive forces; (4) user‐specified design matrices and constraints for covariate modelling of parameters using formulas familiar to most R users; (5) multiple imputation methods that account for measurement error and temporally irregular or missing data; (6) seamless integration of spatio‐temporal covariate raster data; (7) cosinor and spline models for cyclical and other complicated patterns; (8) model checking and selection; and (9) simulation. 3. After providing an overview of the main features of the package, we demonstrate some of the capabilities of momentuHMM using real‐world examples. These include models for cyclical movement patterns of African elephants, foraging trips of northern fur seals, loggerhead turtle movements relative to ocean surface currents, and grey seal movements among three activity centres. 4. momentuHMM considerably extends the capabilities of existing HMM software while accounting for common challenges associated with telemetry data. It therefore facilitates more realistic hypothesis‐driven animal movement analyses that have hitherto been largely inaccessible to non‐statisticians. While motivated by telemetry data, the package can be used for analysing any type of data that is amenable to HMMs. Practitioners interested in additional features are encouraged to contact the authors.

Response of benthic fauna to experimental bottom fishing: A global meta‐analysis

Abstract: Bottom‐contact fishing gears are globally the most widespread anthropogenic sources of direct disturbance to the seabed and associated biota. Managing these fishing disturbances requires quantification of gear impacts on biota and the rate of recovery following disturbance. We undertook a systematic review and meta‐analysis of 122 experiments on the effects‐of‐bottom fishing to quantify the removal of benthos in the path of the fishing gear and to estimate rates of recovery following disturbance. A gear pass reduced benthic invertebrate abundance by 26% and species richness by 19%. The effect was strongly gear‐specific, with gears that penetrate deeper into the sediment having a significantly larger impact than those that penetrate less. Sediment composition (% mud and presence of biogenic habitat) and the history of fishing disturbance prior to an experimental fishing event were also important predictors of depletion, with communities in areas that were not previously fished, predominantly muddy or biogenic habitats being more strongly affected by fishing. Sessile and low mobility biota with longer life‐spans such as sponges, soft corals and bivalves took much longer to recover after fishing (>3 year) than mobile biota with shorter life‐spans such as polychaetes and malacostracans (<1 year). This meta‐analysis provides insights into the dynamics of recovery. Our estimates of depletion along with estimates of recovery rates and large‐scale, high‐resolution maps of fishing frequency and habitat will support more rigorous assessment of the environmental impacts of bottom‐contact gears, thus supporting better informed choices in trade‐offs between environmental impacts and fish production.

Microhaplotypes provide increased power from short‐read DNA sequences for relationship inference

Abstract: The accelerating rate at which DNA sequence data are now generated by high-throughput sequencing instruments provides both opportunities and challenges for population genetic and ecological investigations of animals and plants. We show here how the common practice of calling genotypes from a single SNP per sequenced region ignores substantial additional information in the phased short-read sequences that are provided by these sequencing instruments. We target sequenced regions with multiple SNPs in kelp rockfish (Sebastes atrovirens) to determine "microhaplotypes" and then call these microhaplotypes as alleles at each locus. We then demonstrate how these multi-allelic marker data from such loci dramatically increase power for relationship inference. The microhaplotype approach decreases false-positive rates by several orders of magnitude, relative to calling bi-allelic SNPs, for two challenging analytical procedures, full-sibling and single parent-offspring pair identification. We also show how the identification of half-sibling pairs requires so much data that physical linkage becomes a consideration, and that most published studies that attempt to do so are dramatically underpowered. The advent of phased short-read DNA sequence data, in conjunction with emerging analytical tools for their analysis, promises to improve efficiency by reducing the number of loci necessary for a particular level of statistical confidence, thereby lowering the cost of data collection and reducing the degree of physical linkage amongst markers used for relationship estimation. Such advances will facilitate collaborative research and management for migratory and other widespread species.

Attraction and repulsion of mobile wild organisms to finfish and shellfish aquaculture: a review

Abstract: Knowledge of aquaculture–environment interactions is essential for the development of a sustainable aquaculture industry and efficient marine spatial planning. The effects of fish and shellfish farming on sessile wild populations, particularly infauna, have been studied intensively. Mobile fauna, including crustaceans, fish, birds and marine mammals, also interact with aquaculture operations, but the interactions are more complex and these animals may be attracted to (attraction) or show an aversion to (repulsion) farm operations with various degrees of effects. This review outlines the main mechanisms and effects of attraction and repulsion of wild animals to/from marine finfish cage and bivalve aquaculture, with a focus on effects on fisheries-related species. Effects considered in this review include those related to the provision of physical structure (farm infrastructure acting as fish aggregating devices (FADs) or artificial reefs (ARs), the provision of food (e.g. farmed animals, waste feed and faeces, fouling organisms associated with farm structures) and some farm activities (e.g. boating, cleaning). The reviews show that the distribution of mobile organisms associated with farming structures varies over various spatial (vertical and horizontal) and temporal scales (season, feeding time, day/night period). Attraction/repulsion mechanisms have a variety of direct and indirect effects on wild organisms at the level of individuals and populations and may have implication for the management of fisheries species and the ecosystem in the context of marine spatial planning. This review revealed considerable uncertainties regarding the long-term and ecosystem-wide consequences of these interactions. The use of modelling may help better understand consequences, but long-term studies are necessary to better elucidate effects.

Phenological and distributional shifts in ichthyoplankton associated with recent warming in the northeast Pacific Ocean

Abstract: Understanding changes in the migratory and reproductive phenology of fish stocks in relation to climate change is critical for accurate ecosystem-based fisheries management. Relocation and changes in timing of reproduction can have dramatic effects upon the success of fish populations and throughout the food web. During anomalously warm conditions (1-4°C above normal) in the northeast Pacific Ocean during 2015-2016, we documented shifts in timing and spawning location of several pelagic fish stocks based on larval fish samples. Total larval concentrations in the northern California Current (NCC) during winter (January-March) 2015 and 2016 were the highest observed since annual collections first occurred in 1998, primarily due to increased abundances of Engraulis mordax (northern anchovy) and Sardinops sagax (Pacific sardine) larvae, which are normally summer spawning species in this region. Sardinops sagax and Merluccius productus (Pacific hake) exhibited an unprecedented early and northward spawning expansion during 2015-16. In addition, spawning duration was greatly increased for E. mordax, as the presence of larvae was observed throughout the majority of 2015-16, indicating prolonged and nearly continuous spawning of adults throughout the warm period. Larvae from all three of these species have never before been collected in the NCC as early in the year. In addition, other southern species were collected in the NCC during this period. This suggests that the spawning phenology and distribution of several ecologically and commercially important fish species dramatically and rapidly changed in response to the warming conditions occurring in 2014-2016, and could be an indication of future conditions under projected climate change. Changes in spawning timing and poleward migration of fish populations due to warmer ocean conditions or global climate change will negatively impact areas that were historically dependent on these fish, and change the food web structure of the areas that the fish move into with unforeseen consequences.

A global perspective on the trophic geography of sharks

Abstract: Sharks are a diverse group of mobile predators that forage across varied spatial scales and have the potential to influence food web dynamics. The ecological consequences of recent declines in shark biomass may extend across broader geographic ranges if shark taxa display common behavioural traits. By tracking the original site of photosynthetic fixation of carbon atoms that were ultimately assimilated into muscle tissues of 5,394 sharks from 114 species, we identify globally consistent biogeographic traits in trophic interactions between sharks found in different habitats. We show that populations of shelf-dwelling sharks derive a substantial proportion of their carbon from regional pelagic sources, but contain individuals that forage within additional isotopically diverse local food webs, such as those supported by terrestrial plant sources, benthic production and macrophytes. In contrast, oceanic sharks seem to use carbon derived from between 30° and 50° of latitude. Global-scale compilations of stable isotope data combined with biogeochemical modelling generate hypotheses regarding animal behaviours that can be tested with other methodological approaches.

Water, water everywhere: environmental DNA can unlock population structure in elusive marine species

Abstract: Determining management units for natural populations is critical for effective conservation and management. However, collecting the requisite tissue samples for population genetic analyses remains ...

Recent advances in conservation and population genomics data analysis

Abstract: New computational methods and next‐generation sequencing (NGS) approaches have enabled the use of thousands or hundreds of thousands of genetic markers to address previously intractable questions. The methods and massive marker sets present both new data analysis challenges and opportunities to visualize, understand, and apply population and conservation genomic data in novel ways. The large scale and complexity of NGS data also increases the expertise and effort required to thoroughly and thoughtfully analyze and interpret data. To aid in this endeavor, a recent workshop entitled “Population Genomic Data Analysis,” also known as “ConGen 2017,” was held at the University of Montana. The ConGen workshop brought 15 instructors together with knowledge in a wide range of topics including NGS data filtering, genome assembly, genomic monitoring of effective population size, migration modeling, detecting adaptive genomic variation, genomewide association analysis, inbreeding depression, and landscape genomics. Here, we summarize the major themes of the workshop and the important take‐home points that were offered to students throughout. We emphasize increasing participation by women in population and conservation genomics as a vital step for the advancement of science. Some important themes that emerged during the workshop included the need for data visualization and its importance in finding problematic data, the effects of data filtering choices on downstream population genomic analyses, the increasing availability of whole‐genome sequencing, and the new challenges it presents. Our goal here is to help motivate and educate a worldwide audience to improve population genomic data analysis and interpretation, and thereby advance the contribution of genomics to molecular ecology, evolutionary biology, and especially to the conservation of biodiversity.

Accounting for variable recruitment and fishing mortality in length-based stock assessments for data-limited fisheries

Abstract: In fisheries with limited capacity for monitoring, it is often easier to collect length measurements from fishery catch than quantify total catch. Conventional stock assessment tools that rely on l...

Ecological genomics predicts climate vulnerability in an endangered southwestern songbird.

Abstract: Few regions have been more severely impacted by climate change in the USA than the Desert Southwest. Here, we use ecological genomics to assess the potential for adaptation to rising global temperatures in a widespread songbird, the willow flycatcher (Empidonax traillii), and find the endangered desert southwestern subspecies (E. t. extimus) most vulnerable to future climate change. Highly significant correlations between present abundance and estimates of genomic vulnerability - the mismatch between current and predicted future genotype-environment relationships - indicate small, fragmented populations of the southwestern willow flycatcher will have to adapt most to keep pace with climate change. Links between climate-associated genotypes and genes important to thermal tolerance in birds provide a potential mechanism for adaptation to temperature extremes. Our results demonstrate that the incorporation of genotype-environment relationships into landscape-scale models of climate vulnerability can facilitate more precise predictions of climate impacts and help guide conservation in threatened and endangered groups.

Longitudinal thermal heterogeneity in rivers and refugia for coldwater species: effects of scale and climate change

Abstract: Climate-change driven increases in water temperature pose challenges for aquatic organisms. Predictions of impacts typically do not account for fine-grained spatiotemporal thermal patterns in rivers. Patches of cooler water could serve as refuges for anadromous species like salmon that migrate during summer. We used high-resolution remotely sensed water temperature data to characterize summer thermal heterogeneity patterns for 11,308 km of 2nd- to 7th-order rivers throughout the Pacific Northwest and northern California (USA). We evaluated (1) water temperature patterns at different spatial resolutions, (2) the frequency, size, and spacing of cool thermal patches suitable for Pacific salmon (i.e., contiguous stretches ≥0.25 km, ≤15°C and ≥2°C cooler than adjacent water), and (3) potential influences of climate change on availability of cool patches. Thermal heterogeneity was nonlinearly related to the spatial resolution of water temperature data, and heterogeneity at fine resolution ( 2.7 and 5.7 and <49.4 km. Thermal heterogeneity varied among rivers, some of which had long uninterrupted stretches of warm water ≥20°C, and others had many smaller cool patches. Our models predicted little change in future thermal heterogeneity among rivers, but within-river patterns sometimes changed markedly compared to contemporary patterns. These results can inform long-term monitoring programs as well as near-term climate-adaptation strategies.

Forcing of Multiyear Extreme Ocean Temperatures that Impacted California Current Living Marine Resources in 2016

Abstract: Introduction. Recent record high sea surface temperature anomalies (SSTa) in the California Current Large Marine Ecosystem (CCLME; Fig. 6.1a) produced dramatic impacts on marine life (Cavole et al. 2016; Peterson et al. 2016; Welch 2016). While effects on many species and fisheries may have been short-lived, salmon fisheries, for example, were heavily impacted in 2016 due to multiyear persistence of unfavorable conditions. Negative impacts on CCLME salmon fisheries are likely to persist until at least 2019, as poor stream and 2014–16 ocean conditions directly influence the 2016–19 Chinook salmon abundance. U.S. West Coast Chinook salmon catches in 2016 were approximately 52% of the average catch since 2006, quotas for Chinook salmon fisheries were not met, and spawning escapements to the Klamath and Sacramento River basins were very low (PFMC 2017a). For 2017, the Klamath River Chinook salmon abundance forecast is the lowest on record, and salmon fishing has been sharply restricted from southern Oregon to southern California (PFMC 2017b). Our analysis focuses on the climatic drivers of the 2014–16 CCLME warm period and its extremity in the context of the past century. This study is motivated by an important question from a fisheries management perspective: to what extent were the 2014–16 extremes due to natural variability versus anthropogenic climate change?

Genomics and conservation units: The genetic basis of adult migration timing in Pacific salmonids

Abstract: It is now routinely possible to generate genomics-scale datasets for nonmodel species; however, many questions remain about how best to use these data for conservation and management. Some recent genomics studies of anadromous Pacific salmonids have reported a strong association between alleles at one or a very few genes and a key life history trait (adult migration timing) that has played an important role in defining conservation units. Publication of these results has already spurred a legal challenge to the existing framework for managing these species, which was developed under the paradigm that most phenotypic traits are controlled by many genes of small effect, and that parallel evolution of life history traits is common. But what if a key life history trait can only be expressed if a specific allele is present? Does the current framework need to be modified to account for the new genomics results, as some now propose? Although this real-world example focuses on Pacific salmonids, the issues regarding how genomics can inform us about the genetic basis of phenotypic traits, and what that means for applied conservation, are much more general. In this perspective, we consider these issues and outline a general process that can be used to help generate the types of additional information that would be needed to make informed decisions about the adequacy of existing conservation and management frameworks.

Ocean Futures Under Ocean Acidification, Marine Protection, and Changing Fishing Pressures Explored Using a Worldwide Suite of Ecosystem Models

Abstract: Ecosystem-based management (EBM) of the ocean considers all impacts on and uses of marine and coastal systems. In recent years, there has been a heightened interest in EBM tools that allow testing of alternative management options and help identify tradeoffs among human uses. End-to-end ecosystem modelling frameworks that consider a wide range of management options are a means to provide integrated solutions to the complex ocean management problems encountered in EBM. Here, we leverage the global advances in ecosystem modelling to explore common opportunities and challenges for ecosystem-based management, including changes in ocean acidification, spatial management, and fishing pressure across eight Atlantis (atlantis.cmar.csiro.au) end-to-end ecosystem models. These models represent marine ecosystems from the tropics to the arctic, varying in size, ecology, and management regimes, using a three-dimensional, spatially-explicit structure parametrized for each system. Results suggest stronger impacts from ocean acidification and marine protected areas than from altering fishing pressure, both in terms of guild-level (i.e., aggregations of similar species or groups) biomass and in terms of indicators of ecological and fishery structure. Effects of ocean acidification were typically negative (reducing biomass), while MPAs led to both 'winners' and 'losers' at the level of particular species (or functional groups). Changing fishing pressure (doubling or halving) had smaller effects on the species guilds or ecosystem indicators than either OA or MPAs. Compensatory effects within guilds led to weaker average effects at the guild level than the species or group level. The impacts and tradeoffs implied by these future scenarios are highly relevant as ocean governance shifts focus from single-sector objectives (e.g., sustainable levels of individual fished stocks) to taking into account competing industrial sectors' objectives (e.g., simultaneous spatial management of energy, shipping, and fishing) while at the same time grappling with compounded impacts of global climate change (e.g., ocean acidification and warming).

Making the Otolith Magnesium Chemical Calendar-Clock Tick: Plausible Mechanism and Empirical Evidence

Abstract: The incorporation of a number of readily measured trace elements into otoliths is considered to be under some sort of physiological control, but rarely are explicit mechanisms proposed. Studies of ...

Characterization of Genetic and Epigenetic Variation in Sperm and Red Blood Cells from Adult Hatchery and Natural-Origin Steelhead, Oncorhynchus mykiss.

Abstract: While the goal of most conservation hatchery programs is to produce fish that are genetically and phenotypically indistinguishable from the wild stocks they aim to restore, there is considerable evidence that salmon and steelhead reared in hatcheries differ from wild fish in phenotypic traits related to fitness. Some evidence suggests that these phenotypic differences have a genetic basis (e.g., domestication selection) but another likely mechanism that remains largely unexplored is that differences between hatchery and wild populations arise as a result of environmentally-induced heritable epigenetic change. As a first step toward understanding the potential contribution of these two possible mechanisms, we describe genetic and epigenetic variation in hatchery and natural-origin adult steelhead, Oncorhynchus mykiss, from the Methow River, WA. Our main objectives were to determine if hatchery and natural-origin fish could be distinguished genetically and whether differences in epigenetic programming (DNA methylation) in somatic and germ cells could be detected between the two groups. Genetic analysis of 72 fish using 936 SNPs generated by Restriction Site Associated DNA Sequencing (RAD-Seq) did not reveal differentiation between hatchery and natural-origin fish at a population level. We performed Reduced Representation Bisulfite Sequencing (RRBS) on a subset of 10 hatchery and 10 natural-origin fish and report the first genome-wide characterization of somatic (red blood cells (RBCs)) and germ line (sperm) derived DNA methylomes in a salmonid, from which we identified considerable tissue-specific methylation. We identified 85 differentially methylated regions (DMRs) in RBCs and 108 DMRs in sperm of steelhead reared for their first year in a hatchery environment compared to those reared in the wild. This work provides support that epigenetic mechanisms may serve as a link between hatchery rearing and adult phenotype in steelhead; furthermore, DMRs identified in germ cells (sperm) highlight the potential for these changes to be passed on to future generations.

Correction: Popular interest in vertebrates does not reflect extinction risk and is associated with bias in conservation investment.

Abstract: The interrelationship between public interest in endangered species and the attention they receive from the conservation community is the 'flywheel' driving much effort to abate global extinction rates. Yet big international conservation non-governmental organisations have typically focused on the plight of a handful of appealing endangered species, while the public remains largely unaware of the majority. We quantified the existence of bias in popular interest towards species, by analysing global internet search interest in 36,873 vertebrate taxa. Web search interest was higher for mammals and birds at greater risk of extinction, but this was not so for fish, reptiles and amphibians. Our analysis reveals a global bias in popular interest towards vertebrates that is undermining incentives to invest financial capital in thousands of species threatened with extinction. Raising the popular profile of these lesser known endangered and critically endangered species will generate clearer political and financial incentives for their protection.

Three problems with the conventional delta-model for biomass sampling data, and a computationally efficient alternative

Abstract: Ecologists often analyse biomass sampling data that result in many zeros, where remaining samples can take any positive real number. Samples are often analysed using a “delta-model” that combines t...

Age and growth of sharks: do vertebral band pairs record age?

Abstract: Inaccurate age estimates can have severe consequences in the management of elasmobranchs. Numerous studies in shark age validation have demonstrated a disconnect between band pair counts and age, resulting in age underestimation, particularly in older individuals. To investigate the relationship between band pairs, vertebral shape and growth, we quantified intracolumn differences in centrum morphology (size and structure) and band pair counts in seven shark species: Squatina dumeril, Carcharodon carcharias, Lamna nasus, Isurus oxyrinchus, Alopias vulpinus, Prionace glauca and Carcharhinus obscurus. In all species examined, band pair deposition was closely related to body girth and the structural properties of the cartilaginous skeleton, relative to maximum size, and body type. These results have strong implications for accurately assessing age for fisheries management of these species.