The First Sequenced Carnivore Genome Shows Complex Host-Endogenous Retrovirus Relationships

Host-retrovirus interactions influence the genomic landscape and have contributed substantially to mammalian genome evolution. To gain further insights, we analyzed a female boxer (Canis familiaris) genome for complexity and integration pattern of canine endogenous retroviruses (CfERV). Intriguingly, the first such in-depth analysis of a carnivore species identified 407 CfERV proviruses that represent only 0.15% of the dog genome. In comparison, the same detection criteria identified about six times more HERV proviruses in the human genome that has been estimated to contain a total of 8% retroviral DNA including solitary LTRs. These observed differences in man and dog are likely due to different mechanisms to purge, restrict and protect their genomes against retroviruses. A novel group of gammaretrovirus-like CfERV with high similarity to HERV-Fc1 was found to have potential for active retrotransposition and possibly lateral transmissions between dog and human as a result of close interactions during at least 10.000 years. The CfERV integration landscape showed a non-uniform intra- and inter-chromosomal distribution. Like in other species, different densities of ERVs were observed. Some chromosomal regions were essentially devoid of CfERVs whereas other regions had large numbers of integrations in agreement with distinct selective pressures at different loci. Most CfERVs were integrated in antisense orientation within 100 kb from annotated protein-coding genes. This integration pattern provides evidence for selection against CfERVs in sense orientation relative to chromosomal genes. In conclusion, this ERV analysis of the first carnivorous species supports the notion that different mammals interact distinctively with endogenous retroviruses and suggests that retroviral lateral transmissions between dog and human may have occurred

The FAIR Guiding Principles for scientific data management and stewardship

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community

Erythrocyte and Porcine Intestinal Glycosphingolipids Recognized by F4 Fimbriae of Enterotoxigenic Escherichia coli

Enterotoxigenic F4-fimbriated Escherichia coli is associated with diarrheal disease in neonatal and postweaning pigs. The F4 fimbriae mediate attachment of the bacteria to the pig intestinal epithelium, enabling an efficient delivery of diarrhea-inducing enterotoxins to the target epithelial cells. There are three variants of F4 fimbriae designated F4ab, F4ac and F4ad, respectively, having different antigenic and adhesive properties. In the present study, the binding of isolated F4ab, F4ac and F4ad fimbriae, and F4ab/ac/ad-fimbriated E. coli, to glycosphingolipids from erythrocytes and from porcine small intestinal epithelium was examined, in order to get a comprehensive view of the F4-binding glycosphingolipids involved in F4-mediated hemagglutination and adhesion to the epithelial cells of porcine intestine. Specific interactions between the F4ab, F4ac and F4ad fimbriae and both acid and non-acid glycosphingolipids were obtained, and after isolation of binding-active glycosphingolipids and characterization by mass spectrometry and proton NMR, distinct carbohydrate binding patterns were defined for each fimbrial subtype. Two novel glycosphingolipids were isolated from chicken erythrocytes, and characterized as GalNAcα3GalNAcß3Galß4Glcß1Cer and GalNAcα3GalNAcß3Galß4GlcNAcß3Galß4Glcß1Cer. These two compounds, and lactosylceramide (Galß4Glcß1Cer) with phytosphingosine and hydroxy fatty acid, were recognized by all three variants of F4 fimbriae. No binding of the F4ad fimbriae or F4ad-fimbriated E. coli to the porcine intestinal glycosphingolipids occurred. However, for F4ab and F4ac two distinct binding patterns were observed. The F4ac fimbriae and the F4ac-expressing E. coli selectively bound to galactosylceramide (Galß1Cer) with sphingosine and hydroxy 24:0 fatty acid, while the porcine intestinal glycosphingolipids recognized by F4ab fimbriae and the F4ab-fimbriated bacteria were characterized as galactosylceramide, sulfatide (SO3-3Galß1Cer), sulf-lactosylceramide (SO3-3Galß4Glcß1Cer), and globotriaosylceramide (Galα4Galß4Glcß1Cer) with phytosphingosine and hydroxy 24:0 fatty acid. Finally, the F4ad fimbriae and the F4ad-fimbriated E. coli, but not the F4ab or F4ac subtypes, bound to reference gangliotriaosylceramide (GalNAcß4Galß4Glcß1Cer), gangliotetraosylceramide (Galß3GalNAcß4Galß4Glcß1Cer), isoglobotriaosylceramide (Galα3Galß4Glcß1Cer), and neolactotetraosylceramide (Galß4GlcNAcß3Galß4Glcß1Cer)

Population Ecology of Sage-grouse in the Great Basin: Predictable Patterns in a Variable Environment

The greater sage-grouse (Centrocercus urophasianus; hereafter sage-grouse) is an iconic species endemic to the sagebrush (Artemesia spp.) ecosystems of western North America. Sage-grouse have experienced dramatic contemporary declines in distribution and abundance, coincident with human disturbance of sagebrush habitats. These declines have led to sage-grouse being listed as a candidate species for protection under the United States Endangered Species Act, and listing as an endangered species by the Committee on the Status of Endangered Wildlife in Canada. Increased legal protection, coupled with long-term interest in sage-grouse conservation, has prompted considerable interest in sage-grouse ecology and the response of populations to environmental variation across multiple spatial and temporal scales. My dissertation research focused on the population ecology of sage-grouse in Eureka County, NV, and is comprised of 4 main chapters. In chapter 2, I used robust design and Pradel capture-mark-recapture models to evaluate the influence of climatic processes and disturbance associated with post-wildfire exotic grass invasion on annual survival, per-capita recruitment, and population growth of breeding male sage-grouse in eastern Nevada, USA. Climatic processes, indexed by annual rainfall and maximum summertime temperatures, had a strong relationship with recruitment and adult survival, respectively. The range of variation in recruitment during the study was greater than the range of variation in survival, consistent with a life-history strategy that features lengthened lifespan to capitalize on periodically favorable reproductive conditions. Annual variation in precipitation variables (e.g., rainfall or snow depth) explained as much as 75% of the annual variance in population size during the study. These results are consistent with bottom-up regulation of sage-grouse populations, where abundance is determined in large part by climate-driven variation in resource availability. Exotic grasslands had a negative influence on recruitment that was interactive with annual rainfall; recruitment was low in areas with a substantial exotic grassland footprint even following years of favorable rainfall. I found males breeding at leks with substantial exotic grassland impacts had lower annual survival compared to males at leks surrounded by native sagebrush habitats. However, models containing an interaction between exotic grasslands and maximum summer temperature were not clearly superior to models that considered only additive effects of the two variables. In my 3rd chapter, I investigated tradeoffs associated with reproductive costs to survival for female greater sage-grouse in our study system, while also considering reproductive heterogeneity by examining covariance among current and future reproductive success. I analyzed survival and reproductive histories from 328 unique female sage-grouse captured between 2003 and 2011, and examined the effect of reproductive success on survival and future reproductive success. Female survival was variable within years, and this within-year variation was associated with distinct biologic seasons. Monthly survival was greatest during the winter (November - March; ΦW = 0.99 ± 0.001 SE), and summer (June - July; ΦS = 0.98 ± 0.01 SE), and lower during nesting (April - May; ΦN = 0.93 ± 0.02 SE) and fall (August - October; ΦF = 0.92 ± 0.02 SE). Successful reproduction was associated with reduced monthly survival during summer and fall. This effect was greatest during the fall, and females that successfully fledged chicks had lower annual survival (0.47 ± 0.05 SE) than females who were not successful (0.64 ± 0.04 SE). Annual survival did not vary across years, consistent with a slow-paced life history strategy in sage-grouse. In contrast, reproductive success varied widely, and was positively correlated with annual rainfall. I found evidence for heterogeneity among females with respect to reproductive success; compared with unsuccessful females, females that raised a brood successfully in year t were more than twice as likely to be successful in year t+1. In chapter 4, I used 8 years of banding data from male sage-grouse in eastern Nevada, and capture-mark-recapture analyses, to evaluate the effect of breeding propensity on annual and long-term trends derived from lek counts. I estimated the proportion of variance in annual lek count trends that corresponded with an independent estimate of λ, versus variance associated with breeding propensity. Annual male breeding propensity (the probability a male attends a lek at least once) during the study ranged from a low of 0.56 (± 0.22 SE) to a high of 0.87 (± 0.11 SE). Variance in annual lek count trends was associated with both realized λ (semipartial R2 = 0.57), and sampling error associated with breeding propensity (semipartial R2 = 0.40). I found substantial discrepancies between lek count and realized λ in 3 out of 7 intervals, whereas estimates of long-term λ were extremely similar between count-based and capture-mark-recapture methods (λ = 0.90 ± 0.05 SE and λ = 0.91 ± 0.05 SE, respectively). Male density during the previous year appeared to have the most substantial influence on breeding propensity, perhaps driven by density-dependent competition and availability of food resources. Lek counts are well-suited for deriving long-term estimates of sage-grouse population growth, whereas short-term estimates of λ should be viewed cautiously if breeding propensity is not directly incorporated. In my fifth chapter, I developed an alternative approach for classifying diet of pre-fledging sage-grouse using carbon (δ13C) and nitrogen (δ15N) stable isotopes in feather tissue. Sequential sampling of δ13C and δ15N from feather tissue that was synthesized throughout growth allowed me to distinguish between plant and invertebrate contributions to chick diet during the first 28 days post-hatch. Feathers became progressively depleted in δ15N throughout growth, and Bayesian mixing models confirmed that the proportional contribution of invertebrate nitrogen declined with chick age. I estimate that invertebrate contributions to the protein in chick diets decreased from 33% at 1 week of age, to 14% at 4 weeks of age, consistent with previous research that used traditional diet sampling methods. I found a quadratic relationship between diet composition and chick size at 28 days; chicks that consumed a mixed-diet during growth had larger tarsi and body mass than chicks that were more strictly herbivorous or insectivorous. These growth patterns were consistent with an optimal diet strategy, where supplemental nutrients provided by invertebrates decreased in importance as the digestive capacity of chicks increased and facilitated greater herbivory. In contrast to δ15N, δ13C produced anomalous results that we believe were the product of digestive development as chicks aged. My research has significant implications for sage-grouse persistence in a changing climate, and demonstrates that multiple aspects of sage-grouse ecology are tied to water balance in the sagebrush ecosystem. In climate change results in more frequent drought and/or increased spread of exotic grasslands, negative impacts to sage-grouse populations may be expected

How many leks does it take? Minimum samples sizes for measuring local-scale conservation outcomes in Greater Sage-Grouse

Monitoring population response to conservation actions, such as habitat management, is critical to evaluate conservation outcomes. Greater Sage-Grouse (Centrocercus urophasianus) has been the recipient of substantial recent conservation efforts in North America. Sage-Grouse are often surveyed using counts of males displaying on breeding leks, and these lek counts offer a practical method for monitoring Sage-Grouse population trends. Although substantial work has assessed the utility of lek count data for large-scale population monitoring, there has been comparably little effort focused on the use of lek counts to evaluate local-scale management. We used Greater Sage-Grouse lek count data from Oregon, USA, combined with simulation, to evaluate the sample sizes (number of leks, years of monitoring) required to detect a positive outcome of habitat management on population growth. We further assessed assumptions associated with male detection, and compared analyses that both did (N-mixture models) and did not (Poisson regression) account for detection probability. We found that when treatments produced a 5% increase in annual population growth, and leks were monitored for at least 10 years, lek counts produced unbiased and detectable estimates of treatment effects with as few as seven treatment and seven control leks. Using an unbalanced design with a greater number of control leks (n = 16) permitted inference from even fewer treatment leks (n = 4), however, we found no scenarios where use of more control leks permitted detection of smaller treatment effects or allowed shorter duration studies. We found that N-mixture models and Poisson regression of the maximum of three repeated counts produced equivalent results when detection probability was constant, but at the small sample sizes we evaluated, confounding between detection probability and habitat management compromised the accuracy of all analysis methods. Our results show that lek counts hold promise for efficient monitoring of local-scale conservation, but further work is needed to understand the mechanisms that affect male detection during lek surveys

Evaluating vegetation effects on animal demographics: the role of plant phenology and sampling bias

Plant phenological processes produce temporal variation in the height and cover of vegetation. Key aspects of animal life cycles, such as reproduction, often coincide with the growing season and therefore may inherently covary with plant growth. When evaluating the influence of vegetation variables on demographic rates, the decision about when to measure vegetation relative to the timing of demographic events is important to avoid confounding between the demographic rate of interest and vegetation covariates. Such confounding could bias estimated effect sizes or produce results that are entirely spurious. We investigated how the timing of vegetation sampling affected the modeled relationship between vegetation structure and nest survival of greater sage-grouse (Centrocercus urophasianus), using both simulated and observational data. We used the height of live grasses surrounding nests as an explanatory covariate, and analyzed its effect on daily nest survival. We compared results between models that included grass height measured at the time of nest fate (hatch or failure) with models where grass height was measured on a standardized date - that of predicted hatch date. Parameters linking grass height to nest survival based on measurements at nest fate produced more competitive models, but slope coefficients of grass height effects were biased high relative to truth in simulated scenarios. In contrast, measurements taken at predicted hatch date accurately predicted the influence of grass height on nest survival. Observational data produced similar results. Our results demonstrate the importance of properly considering confounding between demographic traits and plant phenology. Not doing so can produce results that are plausible, but ultimately inaccurate

Predicting landscape-scale habitat distribution for ruffed grouse bonasa umbellus using presence-only data

Ruffed grouse Bonasa umbellus populations in North America have declined as forests have matured and the extent of early successional forest habitat required by the species has diminished. When wildlife species decline because of habitat loss, determining where to focus habitat management efforts is difficult because both the wildlife population and the required habitat(s) are usually limited in distribution. We adopted a relatively new ecological modeling method, partitioned Mahalanobis D2, which allowed us to predict the distribution of potential ruffed grouse habitat across a landscape of management concern where high quality habitat was uncommon. We used presence data derived from radio-telemetry locations, and GIS habitat data from publicly available sources to create competing partitioned Mahalanobis D2 models. The competing models identified important habitat variables and predicted ruffed grouse habitat distribution at 1-ha and 25-ha scales in southwestern Rhode Island, USA. The 1- and 25-ha models produced comparable overall classification accuracy (83.1% and 81.4%, respectively) but differed substantially in the area of predicted habitat (4,475.5 ha and 10,133.8 ha, respectively). We selected the more conservative 1-ha model as the \u27best\u27 model, and expanded it to a larger landscape extent. Once expanded, the model predicted 11,463 ha (15.5% of total land area) of potential ruffed grouse habitat for a 735-km2 landscape in southwestern Rhode Island. This model identified those areas with varying proximities to the following features as likely to contain ruffed grouse habitat: early successional forests, river and stream corridors, mixed conifer forests, conifer forests, shrub wetlands and deciduous forests. Early successional forests were the most consistent component of habitat used by grouse, despite the fact that this habitat type was uncommon in our study area (\u3c 1% of total land area). Our model can be used to identify areas of existing ruffed grouse habitat for management focus. © 2009 Wildlife Biology, NKV