Infectious and inflammatory diseases have repeatedly shown strong genetic associations within the major histocompatibility complex (MHC); however, the basis for these associations remains elusive. To define host genetic effects on the outcome of a chronic viral infection, we performed genome-wide association analysis in a multiethnic cohort of HIV-1 controllers and progressors, and we analyzed the effects of individual amino acids within the classical human leukocyte antigen (HLA) proteins. We identified >300 genome-wide significant single-nucleotide polymorphisms (SNPs) within the MHC and none elsewhere. Specific amino acids in the HLA-B peptide binding groove, as well as an independent HLA-C effect, explain the SNP associations and reconcile both protective and risk HLA alleles. These results implicate the nature of the HLA–viral peptide interaction as the major factor modulating durable control of HIV infection.

To develop effective management strategies for the recovery of threatened and endangered species, it is critical to identify those vital rates (survival and reproductive parameters) responsible for poor population performance and those whose increase will most efficiently change a population's trajectory. In actual application, however, approaches identifying key vital rates are often limited by inadequate demographic data, by unrealistic assumptions of asymptotic population dynamics, and of equal, infinitesimal changes in mean vital rates. We evaluated the consequences of these limitations in an analysis of vital rates most important in the dynamics of federally endangered Sierra Nevada bighorn sheep (Ovis canadensis sierrae). Based on data collected from 1980 to 2007, we estimated vital rates in three isolated populations, accounting for sampling error, variance, and covariance. We used analytical sensitivity analysis, life-stage simulation analysis, and a novel non-asymptotic simulation approach to (1) identify vital rates that should be targeted for subspecies recovery; (2) assess vital rate patterns of endangered bighorn sheep relative to other ungulate populations; (3) evaluate the performance of asymptotic vs. non-asymptotic models for meeting short-term management objectives; and (4) simulate management scenarios for boosting bighorn sheep population growth rates. We found wide spatial and temporal variation in bighorn sheep vital rates, causing rates to vary in their importance to different populations. As a result, Sierra Nevada bighorn sheep exhibited population-specific dynamics that did not follow theoretical expectations or those observed in other ungulates. Our study suggests that vital rate inferences from large, increasing, or healthy populations may not be applicable to those that are small, declining, or endangered. We also found that, while asymptotic approaches were generally applicable to bighorn sheep conservation planning; our non-asymptotic population models yielded unexpected results of importance to managers. Finally, extreme differences in the dynamics of individual bighorn sheep populations imply that effective management strategies for endangered species recovery may often need to be population-specific.

There is growing recognition that interdisciplinary approaches that account for both ecological and social processes are necessary to successfully address human-wildlife interactions. However, such approaches are hindered by challenges in aligning data types, communicating across disciplines, and applying social science information to conservation actions. To meet these challenges, we propose a conceptual model that adopts a social-ecological systems approach and integrates social and ecological theory to identify the multiple, nested levels of influence on both human and animal behavior. By accounting for a diverse array of influences and feedback mechanisms between social and ecological systems, this model fulfills a need for approaches that treat social and ecological processes with equal depth and facilitates a comprehensive understanding of the drivers of human and animal behaviors that perpetuate human-wildlife interactions. We apply this conceptual model to our work on human-black bear conflicts in Colorado, USA to demonstrate its utility. Using this example, we identify key lessons and offer guidance to researchers and conservation practitioners for applying integrated approaches to other human-wildlife systems.

Summary1. Well-informed management of harvested species requires understanding how changing ecological conditions affect demography and population dynamics, information that is lacking for many species. We have limited understanding of the relative influence of carnivores, harvest, weather and forage availability on elk Cervus elaphus demography, despite the ecological and economic importance of this species. We assessed adult female survival, a key vital rate for population dynamics, from 2746 radio-collared elk in 45 populations across western North America that experience wide variation in carnivore assemblage, harvest, weather and habitat conditions. 2. Proportional hazard analysis revealed that 'baseline' (i.e. not related to human factors) mortality was higher with very high winter precipitation, particularly in populations sympatric with wolves Canis lupus. Mortality may increase via nutritional stress and heightened vulnerability to predation in snowy winters. Baseline mortality was unrelated to puma Puma concolor presence, forest cover or summer forage productivity. 3. Cause-specific mortality analyses showed that wolves and all carnivore species combined had additive effects on baseline elk mortality, but only reduced survival by <2%. When human factors were included, 'total' adult mortality was solely related to harvest; the influence of native carnivores was compensatory. Annual total mortality rates were lowest in populations sympatric with both pumas and wolves because managers reduced female harvest in areas with abundant or diverse carnivores. ‡Present address: Natural Resources Canada, 506 Burnside Road W, Victoria, BC V8Z 1M5, Canada *Correspondence author. E-mail: jedediah.brodie@gmail.com †Authorship alphabetical after B. Johnson.© 2013 This article is a US Government work and is in the public domain in the USA. 2013, 50, 295-305 doi: 10.1111/1365-2664.12044 4. Mortality from native carnivores peaked in late winter and early spring, while harvest-induced mortality peaked in autumn. The strong peak in harvest-induced mortality during the autumn hunting season decreased as the number of native carnivore species increased. 5. Synthesis and applications. Elevated baseline adult female elk mortality from wolves in years with high winter precipitation could affect elk abundance as winters across the western US become drier and wolves recolonize portions of the region. In the absence of human harvest, wolves had additive, although limited, effects on mortality. However, human harvest, and its apparent use by managers to offset predation, primarily controls overall variation in adult female mortality. Altering harvest quotas is thus a strong tool for offsetting impacts of carnivore recolonization and shifting weather patterns on elk across western North America. Journal of Applied Ecology

a b s t r a c tAs landscapes across the globe experience increasing human development, it is critical to identify the behavioral responses of wildlife to this change given associated shifts in resource availability and risk from human activity. This is particularly important for large carnivores as their interactions with people are often a source of conflict, which can impede conservation efforts and require extensive management. To examine the adaptations of a large carnivore to benefits and risks associated with human development we investigated black bear behavior in three systems in the western United States. Our objectives were to (1) identify temporal patterns of selection for development within a year and across years based on natural food conditions, (2) compare spatial patterns of selection for development across systems, and (3) examine individual characteristics associated with increased selection for development. Using mixed effects resource selection models we found that bear selection for development was highly dynamic, varying as a function of changing environmental and physiological conditions. Bears increased their use of development in years when natural foods were scarce, throughout the summer-fall, as they aged, and as a function of gender, with males exhibiting greater use of development. While patterns were similar across systems, bears at sites with poorer quality habitat selected development more consistently than bears at sites with higher quality habitat. Black bears appear to use development largely for food subsidy, suggesting that conflicts with bears, and potentially other large carnivores, will increase when the physiological demand for resources outweighs risks associated with human activity.Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).