Conceptual and methodological advances in habitat-selection modeling: guidelines for ecology and evolution.

Habitat selection is a fundamental animal behavior that shapes a wide range of ecological processes, including animal movement, nutrient transfer, trophic dynamics and population distribution. Although habitat selection has been a focus of ecological studies for decades, technological, conceptual and methodological advances over the last 20 yr have led to a surge in studies addressing this process. Despite the substantial literature focused on quantifying the habitat-selection patterns of animals, there is a marked lack of guidance on best analytical practices. The conceptual foundations of the most commonly applied modeling frameworks can be confusing even to those well versed in their application. Furthermore, there has yet to be a synthesis of the advances made over the last 20 yr. Therefore, there is a need for both synthesis of the current state of knowledge on habitat selection, and guidance for those seeking to study this process. Here, we provide an approachable overview and synthesis of the literature on habitat-selection analyses (HSAs) conducted using selection functions, which are by far the most applied modeling framework for understanding the habitat-selection process. This review is purposefully non-technical and focused on understanding without heavy mathematical and statistical notation, which can confuse many practitioners. We offer an overview and history of HSAs, describing the tortuous conceptual path to our current understanding. Through this overview, we also aim to address the areas of greatest confusion in the literature. We synthesize the literature outlining the most exciting conceptual advances in the field of habitat-selection modeling, discussing the substantial ecological and evolutionary inference that can be made using contemporary techniques. We aim for this paper to provide clarity for those navigating the complex literature on HSAs while acting as a reference and best practices guide for practitioners.

Are VNTRs co-localizing with breast cancer-associated SNPs?

PURPOSE: Several common genetic variants (single-nucleotide polymorphisms, SNPs) have been shown to be associated with breast cancer (BC) risk in the general population, and to modify BC risk for BRCA1 and BRCA2 mutation carriers. Co-localization of variable number of tandem repeats (VNTRs) with these BC-associated SNPS has not been comprehensively studied. METHODS: Cross referencing of genome-wide VNTRs with the known BC genome-wide association studies (GWAS) SNPs significantly associated with increased risk for developing breast cancer was carried out. Analysis was based on the overlap between the VNTRs and 10-kb windows around these BC-susceptibility SNPs. RESULTS: Cross referencing of the 1.2 million TR with the 161 known BC-associated SNPs in the general population led to 690 matches. Of those, in 17 VNTRs, the SNP was within the VNTR. Analysis restricted to loci known to modify BC penetrance in BRCA1 (n = 31) and BRCA2 (n = 33) mutation carriers led to 139 and 170 co-localization matches, respectively. For these, none of the SNPs were within the VNTR. The distances between the SNPs and the VNTRs were not significantly different from what was expected to occur by chance alone (p = 0.61; p = 0.44; p = 0.25, respectively). CONCLUSION: There is no evidence that VNTRs co-localize with currently reported SNP tagged BC GWAS loci.

Sociodemographic factors modulate the spatial response of brown bears to vacancies created by hunting.

There is a growing recognition of the importance of indirect effects from hunting on wildlife populations, e.g. social and behavioural changes due to harvest, which occur after the initial offtake. Nonetheless, little is known about how the removal of members of a population influences the spatial configuration of the survivors. We studied how surviving brown bears (Ursus arctos) used former home ranges that had belonged to casualties of the annual bear hunting season in southcentral Sweden (2007-2015). We used resource selection functions to explore the effects of the casualty's and survivor's sex, age and their pairwise genetic relatedness, population density and hunting intensity on survivors' spatial responses to vacated home ranges. We tested the competitive release hypothesis, whereby survivors that increase their use of a killed bear's home range are presumed to have been released from intraspecific competition. We found strong support for this hypothesis, as survivors of the same sex as the casualty consistently increased their use of its vacant home range. Patterns were less pronounced or absent when the survivor and casualty were of opposite sex. Genetic relatedness between the survivor and the casualty emerged as the most important factor explaining increased use of vacated male home ranges by males, with a stronger response from survivors of lower relatedness. Relatedness was also important for females, but it did not influence use following removal; female survivors used home ranges of higher related female casualties more, both before and after death. Spatial responses by survivors were further influenced by bear age, population density and hunting intensity. We have shown that survivors exhibit a spatial response to vacated home ranges caused by hunting casualties, even in nonterritorial species such as the brown bear. This spatial reorganization can have unintended consequences for population dynamics and interfere with management goals. Altogether, our results underscore the need to better understand the short- and long-term indirect effects of hunting on animal social structure and their resulting distribution in space.

Hunting promotes sexual conflict in brown bears.

The removal of individuals through hunting can destabilize social structure, potentially affecting population dynamics. Although previous studies have shown that hunting can indirectly reduce juvenile survival through increased sexually selected infanticide (SSI), very little is known about the spatiotemporal effects of male hunting on juvenile survival. Using detailed individual monitoring of a hunted population of brown bears (Ursus arctos) in Sweden (1991-2011), we assessed the spatiotemporal effect of male removal on cub survival. We modelled cub survival before, during and after the mating season. We used three proxies to evaluate spatial and temporal variation in male turnover; distance and timing of the closest male killed and number of males that died around a female's home range centre. Male removal decreased cub survival only during the mating season, as expected in seasonal breeders with SSI. Cub survival increased with distance to the closest male killed within the previous 1·5 years, and it was lower when the closest male killed was removed 1·5 instead of 0·5 year earlier. We did not detect an effect of the number of males killed. Our results support the hypothesis that social restructuring due to hunting can reduce recruitment and suggest that the distribution of the male deaths might be more important than the overall number of males that die. As the removal of individuals through hunting is typically not homogenously distributed across the landscape, spatial heterogeneity in hunting pressure may cause source-sink dynamics, with lower recruitment in areas of high human-induced mortality.

SNP Set Association Testing for Survival Outcomes in the Presence of Intrafamilial Correlation.

In this work, we propose a single nucleotide polymorphism (SNP) set association test for censored phenotypes in the presence of a family-based design. The proposed test is valid for both common and rare variants. A proportional hazards Cox model is specified for the marginal distribution of the trait and the familial dependence is modeled via a Gaussian copula. Censored values are treated as partially missing data and a multiple imputation procedure is proposed in order to compute the test statistics. The P-value is then deduced analytically. The finite-sample empirical properties of the proposed method are evaluated and compared to existing competitors by simulations and its use is illustrated using a breast cancer data set from the Consortium of Investigators of Modifiers of BRCA1 and BRCA2.

Can hunting data be used to estimate unbiased population parameters? A case study on brown bears.

Quantifying temporal changes in harvested populations is critical for applied and fundamental research. Unbiased data are required to detect true changes in phenotypic distribution or population size. Because of the difficulty of collecting detailed individual data from wild populations, data from hunting records are often used. Hunting records, however, may not represent a random sample of a population. We aimed to detect and quantify potential bias in hunting records. We compared data from a long-term monitoring project with hunting records of brown bears (Ursus arctos) in Sweden and investigated temporal trends (1996-2013) in the ratio of yearlings to adult females, yearling mass and adult female mass. Data from hunting records underestimated the decline in yearling and adult female mass over time, most likely owing to the legal protection of family groups from hunting, but reflected changes in the ratio of yearlings to adult females more reliably. Although hunting data can be reliable to approximate population abundance in some circumstances, hunting data can represent a biased sample of a population and should be used with caution in management and conservation decisions.

Quantifying consistent individual differences in habitat selection.

Habitat selection is a fundamental behaviour that links individuals to the resources required for survival and reproduction. Although natural selection acts on an individual's phenotype, research on habitat selection often pools inter-individual patterns to provide inferences on the population scale. Here, we expanded a traditional approach of quantifying habitat selection at the individual level to explore the potential for consistent individual differences of habitat selection. We used random coefficients in resource selection functions (RSFs) and repeatability estimates to test for variability in habitat selection. We applied our method to a detailed dataset of GPS relocations of brown bears (Ursus arctos) taken over a period of 6 years, and assessed whether they displayed repeatable individual differences in habitat selection toward two habitat types: bogs and recent timber-harvest cut blocks. In our analyses, we controlled for the availability of habitat, i.e. the functional response in habitat selection. Repeatability estimates of habitat selection toward bogs and cut blocks were 0.304 and 0.420, respectively. Therefore, 30.4 and 42.0 % of the population-scale habitat selection variability for bogs and cut blocks, respectively, was due to differences among individuals, suggesting that consistent individual variation in habitat selection exists in brown bears. Using simulations, we posit that repeatability values of habitat selection are not related to the value and significance of ß estimates in RSFs. Although individual differences in habitat selection could be the results of non-exclusive factors, our results illustrate the evolutionary potential of habitat selection.

Behavioural strategies towards human disturbances explain individual performance in woodland caribou.

Behavioural strategies may have important fitness, ecological and evolutionary consequences. In woodland caribou, human disturbances are associated with higher predation risk. Between 2004 and 2011, we investigated if habitat selection strategies of female caribou towards disturbances influenced their calf's survival in managed boreal forest with varying intensities of human disturbances. Calf survival was 53% and 43% after 30 and 90 days following birth, respectively, and 52% of calves that died were killed by black bear. The probability that a female lose its calf to predation was not influenced by habitat composition of her annual home range, but decreased with an increase in proportion of open lichen woodland within her calving home range. At the local scale, females that did not lose their calf displayed stronger avoidance of high road density areas than females that lost their calf to predation. Further, females that lost their calf to predation and that had a low proportion of ≤5-year-old cutovers within their calving home range were mostly observed in areas where these young cutovers were locally absent. Also, females that lost their calf to predation and that had a high proportion of ≤5-year-old cutovers within their calving home range were mostly observed in areas with a high local density of ≤5-year-old cutovers. Our study demonstrates that we have to account for human-induced disturbances at both local and regional scales in order to further enhance effective caribou management plans. We demonstrate that disturbances not only impact spatial distribution of individuals, but also their reproductive success.

Selection of summer feeding sites and food resources by female migratory caribou (Rangifer tarandus) determined using camera collars.

Migratory caribou (Rangifer tarandus) is a socioeconomically and culturally key species for northern communities in the Arctic, and most of its populations are experiencing a sharp decline. Female migratory caribou depend on the availability of summer habitat resources to meet the needs associated with lactation and the accumulation of fat reserves to survive when resources are less abundant. Because of the large scales at which habitat and resource data are usually available, information on how female migratory caribou select habitat and resources at fine scales in the wild is lacking. To document selection of summer feeding sites, we equipped 60 female caribou with camera collars from 2016 to 2018. We collected a total of 65,150 10-sec videos between June 1st and September 1st for three years with contrasted spring phenology. We determined the selection at the feeding site scale (3rd scale of Johnson) and food item scale (4th scale of Johnson) using resource selection probability functions. Wetlands were highly selected as feeding sites in June and July while they were avoided in August. Shrublands were mostly selected in July and August. At the resources scale, lichen, birch, willow, and mushrooms were the most strongly selected resources. Our results provide precise and novel information on habitat selection at feeding sites and food resources selected by female caribou in the wild. This information will help understand foraging patterns and habitat selection behavior of female migratory caribou and will contribute to the management and conservation of its declining populations.

[Prevalence of gambling habits in Gaspésie and Îles-de-la-Madeleine in 2009]. / [Prévalence des habitudes de jeu en Gaspésie et aux Îles-de-la-Madeleine en 2009].

UNLABELLED: OBJECTIF : Estimer la prévalence des habitudes aux jeux de hasard et d'argent (JHA), du jeu à risque (JAR) et du jeu pathologique probable (JPP) dans la région de la Gaspésie et des Îles-de-la-Madeleine (GIM) (Québec). MÉTHODE : Un sondage téléphonique portant sur les habitudes de jeu a été réalisé auprès de 1014 adultes résidents de la région de la GIM. Les participants ont été sélectionnés aléatoirement. L'échelle Problem Gambling Severity Index de l'Indice canadien du jeu excessif a servi à l'évaluation du jeu pathologique. RÉSULTATS : Quatre-vingt-cinq pour cent des répondants rapportent avoir joué à un JHA au cours de l'année précédente. Les activités les plus populaires sont l'achat de billets de loterie, la participation à des tirages et collectes de fonds, le bingo, les cartes ou jeux de société en famille ou avec des amis pour de l'argent, la loterie vidéo et les jeux de casino. Les taux de prévalence du JAR et du JPP s'élèvent à 1,5 % et 0,8 % respectivement. La loterie vidéo s'avère le jeu le plus souvent identifié comme étant problématique, suivi des loteries instantanées et ordinaires (par exemple, Lotto 6/49). CONCLUSION: Les habitudes de jeu des Gaspésiens et des Madelinots sont similaires à celles observées chez l'ensemble des Québécois. La discussion soulève entre autres la question de la validité de l'évaluation de la présence d'un problème de jeu parmi les membres de l'entourage, et certaines perceptions à risque, dont celle qu'il est impossible de développer un problème aux loteries instantanées et au bingo.

Offspring mass variation in tree swallows: A case of bet-hedging?

The evolution of reproductive strategies is affected by the ability of organisms to deal with future environmental conditions. When environments are temporally unpredictable, however, it is difficult to anticipate optimal offspring phenotype. Diversification of offspring phenotypes, a strategy called diversified bet-hedging, may allow parents to maximize their fitness by reducing between-year variation in reproductive success. The link between diversification of offspring phenotypes and individual reproductive success, however, has rarely been documented empirically. We used an eight-year dataset (1215 broods, 870 females) on individually marked tree swallows (Tachycineta bicolor) to assess whether intra-brood mass variation was compatible with a diversified bet-hedging strategy. Intra-brood mass variation was weakly, but significantly repeatable within females, suggesting consistent individual differences. Greater intra-brood mass variation, however, was not associated with reduced between-year variation in reproductive success or increased female reproductive success. Moreover, contrary to diversified bet-hedging expectations, fledging success of large broods was greater when hatchlings had similar rather than variable masses. Our results suggest that intra-brood mass variation may not result from diversified bet-hedging, but rather from complex interactions between environmental, brood, and maternal characteristics.

Functional Analysis of Promoter Variants in Genes Involved in Sex Steroid Action, DNA Repair and Cell Cycle Control.

Genetic variants affecting the regulation of gene expression are among the main causes of human diversity. The potential importance of regulatory polymorphisms is underscored by results from Genome Wide Association Studies, which have already implicated such polymorphisms in the susceptibility to complex diseases such as breast cancer. In this study, we re-sequenced the promoter regions of 24 genes involved in pathways related to breast cancer including sex steroid action, DNA repair, and cell cycle control in 60 unrelated Caucasian individuals. We constructed haplotypes and assessed the functional impact of promoter variants using gene reporter assays and electrophoretic mobility shift assays. We identified putative functional variants within the promoter regions of estrogen receptor 1 (ESR1), ESR2, forkhead box A1 (FOXA1), ubiquitin interaction motif containing 1 (UIMC1) and cell division cycle 7 (CDC7). The functional polymorphism on CDC7, rs13447455, influences CDC7 transcriptional activity in an allele-specific manner and alters DNA⁻protein complex formation in breast cancer cell lines. Moreover, results from the Breast Cancer Association Consortium show a marginal association between rs13447455 and breast cancer risk (p=9.3x10-5), thus warranting further investigation. Furthermore, our study has helped provide methodological solutions to some technical difficulties that were encountered with gene reporter assays, particularly regarding inter-clone variability and statistical consistency.