Spatial epidemiological patterns suggest mechanisms of land-sea transmission for Sarcocystis neurona in a coastal marine mammal.

Sarcocystis neurona was recognised as an important cause of mortality in southern sea otters (Enhydra lutris nereis) after an outbreak in April 2004 and has since been detected in many marine mammal species in the Northeast Pacific Ocean. Risk of S. neurona exposure in sea otters is associated with consumption of clams and soft-sediment prey and is temporally associated with runoff events. We examined the spatial distribution of S. neurona exposure risk based on serum antibody testing and assessed risk factors for exposure in animals from California, Washington, British Columbia and Alaska. Significant spatial clustering of seropositive animals was observed in California and Washington, compared with British Columbia and Alaska. Adult males were at greatest risk for exposure to S. neurona, and there were strong associations with terrestrial features (wetlands, cropland, high human housing-unit density). In California, habitats containing soft sediment exhibited greater risk than hard substrate or kelp beds. Consuming a diet rich in clams was also associated with increased exposure risk. These findings suggest a transmission pathway analogous to that described for Toxoplasma gondii, with infectious stages traveling in freshwater runoff and being concentrated in particular locations by marine habitat features, ocean physical processes, and invertebrate bioconcentration

Effects of wildfire on sea otter ( Enhydra lutris ) gene transcript profiles

Wildfires have been shown to impact terrestrial species over a range of temporal scales. Little is known, however, about the more subtle toxicological effects of wildfires, particularly in downstream marine or downwind locations from the wildfire perimeter. These down‐current effects may be just as substantial as those effects within the perimeter. We used gene transcription technology, a sensitive indicator of immunological perturbation, to study the effects of the 2008 Basin Complex Fire on the California coast on a sentinel marine species, the sea otter ( Enhydra lutris ). We captured sea otters in 2008 (3 mo after the Basin Complex Fire was controlled) and 2009 (15 mo after the Basin Complex Fire was controlled) in the adjacent nearshore environment near Big Sur, California. Gene responses were distinctly different between Big Sur temporal groups, signifying detoxification of PAH s, possible associated response to potential malignant transformation, and suppression of immune function as the primary responses of sea otters to fire in 2008 compared to those captured in 2009. In general, gene transcription patterns in the 2008 sea otters were indicative of molecular reactions to organic exposure, malignant transformation, and decreased ability to respond to pathogens that seemed to consistent with short‐term hydrocarbon exposure.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/109779/1/mms12151.pd

Tools for quantifying isotopic niche space and dietary variation at the individual and population level

Ecologists are increasingly using stable isotope analysis to inform questions about variation in resource and habitat use from the individual to community level. In this study we investigate data sets from 2 California sea otter (Enhydra lutris nereis) populations to illustrate the advantages and potential pitfalls of applying various statistical and quantitative approaches to isotopic data. We have subdivided these tools, or metrics, into 3 categories: IsoSpace metrics, stable isotope mixing models, and DietSpace metrics. IsoSpace metrics are used to quantify the spatial attributes of isotopic data that are typically presented in bivariate (e.g., d 13 C versus d 15 N) 2-dimensional space. We review IsoSpace metrics currently in use and present a technique by which uncertainty can be included to calculate the convex hull area of consumers or prey, or both. We then apply a Bayesian-based mixing model to quantify the proportion of potential dietary sources to the diet of each sea otter population and compare this to observational foraging data. Finally, we assess individual dietary specialization by comparing a previously published technique, variance components analysis, to 2 novel DietSpace metrics that are based on mixing model output. As the use of stable isotope analysis in ecology continues to grow, the field will need a set of quantitative tools for assessing isotopic variance at the individual to community level. Along with recent advances in Bayesian-based mixing models, we hope that the IsoSpace and DietSpace metrics described here will provide another set of interpretive tools for ecologists

North to south: ecosystem features determine seagrass community response to sea otter foraging

We compared sea otter recovery in California (CA) and British Columbia (BC) to determine how key ecosystem properties shape top-down effects in seagrass communities. Potential ecosystem drivers of sea otter foraging in CA and BC seagrass beds that we examined include the role of coastline complexity and environmental stress on sea otter effects. In BC, we found greater species richness across seagrass trophic assemblages. Furthermore, Cancer spp. crabs, an important link in the seagrass trophic cascade observed in CA, was less common. Additionally, the more recent reintroduction of sea otters, more complex coastline, and reduced environmental stress in BC seagrass habitats supported the hypothesis that sea otter foraging pressure is currently reduced in more northern latitudes. In order to manage the ecosystem features that lead to regional differences in top predator effects in seagrass communities, we review our findings, their spatial and temporal constraints, and present a social-ecological framework for future re- search

Carbon on the Northwest European Shelf: Contemporary Budget and Future Influences

A carbon budget for the northwest European continental shelf seas (NWES) was synthesized using available estimates for coastal, pelagic and benthic carbon stocks and flows. Key uncertainties were identified and the effect of future impacts on the carbon budget were assessed. The water of the shelf seas contains between 210 and 230 Tmol of carbon and absorbs between 1.3 and 3.3 Tmol from the atmosphere annually. Off-shelf transport and burial in the sediments account for 60–100 and 0–40% of carbon outputs from the NWES, respectively. Both of these fluxes remain poorly constrained by observations and resolving their magnitudes and relative importance is a key research priority. Pelagic and benthic carbon stocks are dominated by inorganic carbon. Shelf sediments contain the largest stock of carbon, with between 520 and 1600 Tmol stored in the top 0.1 m of the sea bed. Coastal habitats such as salt marshes and mud flats contain large amounts of carbon per unit area but their total carbon stocks are small compared to pelagic and benthic stocks due to their smaller spatial extent. The large pelagic stock of carbon will continue to increase due to the rising concentration of atmospheric CO2, with associated pH decrease. Pelagic carbon stocks and flows are also likely to be significantly affected by increasing acidity and temperature, and circulation changes but the net impact is uncertain. Benthic carbon stocks will be affected by increasing temperature and acidity, and decreasing oxygen concentrations, although the net impact of these interrelated changes on carbon stocks is uncertain and a major knowledge gap. The impact of bottom trawling on benthic carbon stocks is unique amongst the impacts we consider in that it is widespread and also directly manageable, although its net effect on the carbon budget is uncertain. Coastal habitats are vulnerable to sea level rise and are strongly impacted by management decisions. Local, national and regional actions have the potential to protect or enhance carbon storage, but ultimately global governance, via controls on emissions, has the greatest potential to influence the long-term fate of carbon stocks in the northwestern European continental shelf

Structure and mechanism of diet specialisation: testing models of individual variation in resource use with sea otters

Studies of consumer-resource interactions suggest that individual diet specialisation is empirically widespread and theoretically important to the organisation and dynamics of populations and communities. We used weighted networks to analyze the resource use by sea otters, testing three alternative models for how individual diet specialisation may arise. As expected, individual specialisation was absent when otter density was low, but increased at high-otter density. A high-density emergence of nested resource-use networks was consistent with the model assuming individuals share preference ranks. However, a density-dependent emergence of a non-nested modular network for core resources was more consistent with the competitive refuge model. Individuals from different diet modules showed predictable variation in rank-order prey preferences and handling times of core resources, further supporting the competitive refuge model. Our findings support a hierarchical organisation of diet specialisation and suggest individual use of core and marginal resources may be driven by different selective pressures.Keywords: Sea otter, Bipartite networks, Nestedness, Modularity, Prey preference, Diet specialisatio

The Morphology of Galaxies in the Baryon Oscillation Spectroscopic Survey

We study the morphology of luminous and massive galaxies at 0.3<z<0.7 targeted in the Baryon Oscillation Spectroscopic Survey (BOSS) using publicly available Hubble Space Telescope imaging from COSMOS. Our sample (240 objects) provides a unique opportunity to check the visual morphology of these galaxies which were targeted based solely on stellar population modelling. We find that the majority (74+/-6%) possess an early-type morphology (elliptical or S0), while the remainder have a late-type morphology. This is as expected from the goals of the BOSS target selection which aimed to predominantly select slowly evolving galaxies, for use as cosmological probes, while still obtaining a fair fraction of actively star forming galaxies for galaxy evolution studies. We show that a colour cut of (g-i)>2.35 selects a sub-sample of BOSS galaxies with 90% early-type morphology - more comparable to the earlier Luminous Red Galaxy (LRG) samples of SDSS-I/II. The remaining 10% of galaxies above this cut have a late-type morphology and may be analogous to the "passive spirals" found at lower redshift. We find that 23+/-4% of the early-type galaxies are unresolved multiple systems in the SDSS imaging. We estimate that at least 50% of these are real associations (not projection effects) and may represent a significant "dry merger" fraction. We study the SDSS pipeline sizes of BOSS galaxies which we find to be systematically larger (by 40%) than those measured from HST images, and provide a statistical correction for the difference. These details of the BOSS galaxies will help users of the data fine-tune their selection criteria, dependent on their science applications. For example, the main goal of BOSS is to measure the cosmic distance scale and expansion rate of the Universe to percent-level precision - a point where systematic effects due to the details of target selection may become important.Comment: 18 pages, 11 figures; v2 as accepted by MNRA

New DArT markers for oat provide enhanced map coverage and global germplasm characterization

BACKGROUND: Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT). RESULTS: Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' × 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure. CONCLUSION: These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity

High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat

We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.publishersversionPeer reviewe