Range-wide evolutionary relationships and historical demography of brown bears (Ursus arctos) revealed by whole-genome sequencing of isolated central Asian populations.

Phylogeographic studies uncover hidden pathways of divergence and inform conservation. Brown bears (Ursus arctos) have one of the broadest distributions of all land mammals, ranging from Eurasia to North America, and are an important model for evolutionary studies. Although several whole genomes were available for individuals from North America, Europe and Asia, limited whole-genome data were available from Central Asia, including the highly imperilled brown bears in the Gobi Desert. To fill this knowledge gap, we sequenced whole genomes from nine Asian brown bears from the Gobi Desert of Mongolia, Northern Mongolia and the Himalayas of Pakistan. We combined these data with published brown bear sequences from Europe, Asia and North America, as well as other bear species. Our goals were to determine the evolutionary relationships among brown bear populations worldwide, their genetic diversity and their historical demography. Our analyses revealed five major lineages of brown bears based on a filtered set of 684,081 single nucleotide polymorphisms. We found distinct evolutionary lineages of brown bears in the Gobi, Himalayas, northern Mongolia, Europe and North America. The lowest level of genetic diversity and the highest level of inbreeding were found in Pakistan, the Gobi Desert and Central Italy. Furthermore, the effective population size (Ne ) for all brown bears decreased over the last 70,000 years. Our results confirm the genetic distinctiveness and ancient lineage of brown bear subspecies in the Gobi Desert of Mongolia and the Himalayas of Pakistan and highlight their importance for conservation.

Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout.

Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low-coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids (GREB1L, ROCK1, SIX6). Genotype-environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high-elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high-elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change.

The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern.

Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels (Urocitellus brunneus-NIDGS, and U. endemicus-SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with restriction site-associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both the inter- and intraspecific level, and identified putatively adaptive SNPs using population structure outlier detection and genotype-environment association (GEA) analyses. At the interspecific level, we detected a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation putatively linked to torpor patterns. At the intraspecific level, we found evidence of both neutral and adaptive differentiation. For NIDGS, elevation appears to be the main driver of adaptive differentiation, while neutral variation patterns match and expand information on the low connectivity between some populations identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected natural geographical barriers, while adaptive variation reflected differences in land cover and temperature, as well as elevation. These results clearly highlight the roles of neutral and adaptive processes for understanding the complexity of the processes leading to species and population differentiation, which can have important conservation implications in susceptible and threatened species.

Detection criteria and post-field sample processing influence results and cost efficiency of occupancy-based monitoring.

Optimization of occupancy-based monitoring has focused on balancing the number of sites and surveys to minimize field efforts and costs. When survey techniques require post-field processing of samples to confirm species detections, there may be opportunities to further improve efficiency. We used scat-based noninvasive genetic sampling for kit foxes (Vulpes macrotis) in Utah, USA, as a model system to assess post-field data processing strategies, evaluate the impacts of these strategies on estimates of occupancy and associations between parameters and predictors, and identify the most cost-effective approach. We identified scats with three criteria that varied in costs and reliability: (1) field-based identification (expert opinion), (2) statistical-based morphological identification, and (3) genetic-based identification (mitochondrial DNA). We also considered four novel post-field sample processing strategies that integrated statistical and genetic identifications to reduce costly genetic procedures, including (4) a combined statistical-genetic identification, (5) a genetic removal design, (6) a within-survey conditional-replicate design, and (7) a single-genetic-replicate with false-positive modeling design. We considered results based on genetic identification as the best approximation of truth and used this to evaluate the performance of alternatives. Field-based and statistical-based criteria prone to misidentification produced estimates of occupancy that were biased high (˜1.8 and 2.1 times higher than estimates without misidentifications, respectively). These criteria failed to recover associations between parameters and predictors consistent with genetic identification. The genetic removal design performed poorly, with limited detections leading to estimates that were biased high with poor precision and patterns inconsistent with genetic identification. Both statistical-genetic identification and the conditional-replicate design produced occupancy estimates comparable to genetic identification, while recovering the same model structure and associations at cost reductions of 67% and 74%, respectively. The false-positive design had the lowest cost (88% reduction) and recovered patterns consistent with genetic identification but had occupancy estimates that were ˜32% lower than estimated occupancy based on genetic identification. Our results demonstrate that careful consideration of detection criteria and post-field data processing can reduce costs without significantly altering resulting inferences. Combined with earlier guidance on sampling designs for occupancy modeling, these findings can aid managers in optimizing occupancy-based monitoring.

Does harvest affect genetic diversity in grey wolves?

Harvest can affect vital rates such as reproduction and survival, but also genetic measures of individual and population health. Grey wolves (Canis lupus) live and breed in groups, and effective population size is a small fraction of total abundance. As a result, genetic diversity of wolves may be particularly sensitive to harvest. We evaluated how harvest affected genetic diversity and relatedness in wolves. We hypothesized that harvest would (a) reduce relatedness of individuals within groups in a subpopulation but increase relatedness of individuals between groups due to increased local immigration, (b) increase individual heterozygosity and average allelic richness across groups in subpopulations and (c) add new alleles to a subpopulation and decrease the number of private alleles in subpopulations due to an increase in breeding opportunities for unrelated individuals. We found harvest had no effect on observed heterozygosity of individuals or allelic richness at loci within subpopulations but was associated with a small, biologically insignificant effect on within-group relatedness values in grey wolves. Harvest was, however, positively associated with increased relatedness of individuals between groups and a net gain (+16) of alleles into groups in subpopulations monitored since harvest began, although the number of private alleles in subpopulations overall declined. Harvest likely created opportunities for wolves to immigrate into nearby groups and breed, thereby making groups in subpopulations more related over time. Harvest appears to affect genetic diversity in wolves at the group and population levels, but its effects are less apparent at the individual level given the population sizes we studied.

Natural re-colonization and admixture of wolves (Canis lupus) in the US Pacific Northwest: challenges for the protection and management of rare and endangered taxa.

Admixture resulting from natural dispersal processes can potentially generate novel phenotypic variation that may facilitate persistence in changing environments or result in the loss of population-specific adaptations. Yet, under the US Endangered Species Act, policy is limited for management of individuals whose ancestry includes a protected taxon; therefore, they are generally not protected under the Act. This issue is exemplified by the recently re-established grey wolves of the Pacific Northwest states of Washington and Oregon, USA. This population was likely founded by two phenotypically and genetically distinct wolf ecotypes: Northern Rocky Mountain (NRM) forest and coastal rainforest. The latter is considered potentially threatened in southeast Alaska and thus the source of migrants may affect plans for their protection. To assess the genetic source of the re-established population, we sequenced a ~ 300 bp portion of the mitochondrial control region and ~ 5 Mbp of the nuclear genome. Genetic analysis revealed that the Washington wolves share ancestry with both wolf ecotypes, whereas the Oregon population shares ancestry with NRM forest wolves only. Using ecological niche modelling, we found that the Pacific Northwest states contain environments suitable for each ecotype, with wolf packs established in both environmental types. Continued migration from coastal rainforest and NRM forest source populations may increase the genetic diversity of the Pacific Northwest population. However, this admixed population challenges traditional management regimes given that admixture occurs between an adaptively distinct ecotype and a more abundant reintroduced interior form. Our results emphasize the need for a more precise US policy to address the general problem of admixture in the management of endangered species, subspecies, and distinct population segments.

Spatiotemporal heterogeneity in prey abundance and vulnerability shapes the foraging tactics of an omnivore.

Prey abundance and prey vulnerability vary across space and time, but we know little about how they mediate predator-prey interactions and predator foraging tactics. To evaluate the interplay between prey abundance, prey vulnerability and predator space use, we examined patterns of black bear (Ursus americanus) predation of caribou (Rangifer tarandus) neonates in Newfoundland, Canada using data from 317 collared individuals (9 bears, 34 adult female caribou, 274 caribou calves). During the caribou calving season, we predicted that landscape features would influence calf vulnerability to bear predation, and that bears would actively hunt calves by selecting areas associated with increased calf vulnerability. Further, we hypothesized that bears would dynamically adjust their foraging tactics in response to spatiotemporal changes in calf abundance and vulnerability (collectively, calf availability). Accordingly, we expected bears to actively hunt calves when they were most abundant and vulnerable, but switch to foraging on other resources as calf availability declined. As predicted, landscape heterogeneity influenced risk of mortality, and bears displayed the strongest selection for areas where they were most likely to kill calves, which suggested they were actively hunting caribou. Initially, the per-capita rate at which bears killed calves followed a type-I functional response, but as the calving season progressed and calf vulnerability declined, kill rates dissociated from calf abundance. In support of our hypothesis, bears adjusted their foraging tactics when they were less efficient at catching calves, highlighting the influence that predation phenology may have on predator space use. Contrary to our expectations, however, bears appeared to continue to hunt caribou as calf availability declined, but switched from a tactic of selecting areas of increased calf vulnerability to a tactic that maximized encounter rates with calves. Our results reveal that generalist predators can dynamically adjust their foraging tactics over short time-scales in response to changing prey abundance and vulnerability. Further, they demonstrate the utility of integrating temporal dynamics of prey availability into investigations of predator-prey interactions, and move towards a mechanistic understanding of the dynamic foraging tactics of a large omnivore.

Age-specific infectious period shapes dynamics of pneumonia in bighorn sheep.

Superspreading, the phenomenon where a small proportion of individuals contribute disproportionately to new infections, has profound effects on disease dynamics. Superspreading can arise through variation in contacts, infectiousness or infectious periods. The latter has received little attention, yet it drives the dynamics of many diseases of critical public health, livestock health and conservation concern. Here, we present rare evidence of variation in infectious periods underlying a superspreading phenomenon in a free-ranging wildlife system. We detected persistent infections of Mycoplasma ovipneumoniae, the primary causative agent of pneumonia in bighorn sheep (Ovis canadensis), in a small number of older individuals that were homozygous at an immunologically relevant genetic locus. Interactions among age-structure, genetic composition and infectious periods may drive feedbacks in disease dynamics that determine the magnitude of population response to infection. Accordingly, variation in initial conditions may explain divergent population responses to infection that range from recovery to catastrophic decline and extirpation.

Harvest and group effects on pup survival in a cooperative breeder.

Recruitment in cooperative breeders can be negatively affected by changes in group size and composition. The majority of cooperative breeding studies have not evaluated human harvest; therefore, the effects of recurring annual harvest and group characteristics on survival of young are poorly understood. We evaluated how harvest and groups affect pup survival using genetic sampling and pedigrees for grey wolves in North America. We hypothesized that harvest reduces pup survival because of (i) reduced group size, (ii) increased breeder turnover and/or (iii) reduced number of female helpers. Alternatively, harvest may increase pup survival possibly due to increased per capita food availability or it could be compensatory with other forms of mortality. Harvest appeared to be additive because it reduced both pup survival and group size. In addition to harvest, turnover of breeding males and the presence of older, non-breeding males also reduced pup survival. Large groups and breeder stability increased pup survival when there was harvest, however. Inferences about the effect of harvest on recruitment require knowledge of harvest rate of young as well as the indirect effects associated with changes in group size and composition, as we show. The number of young harvested is a poor measure of the effect of harvest on recruitment in cooperative breeders.

Comparative landscape genetics of two frugivorous bats in a biological corridor undergoing agricultural intensification.

Agricultural intensification in tropical landscapes poses a new threat to the ability of biological corridors to maintain functional connectivity for native species. We use a landscape genetics approach to evaluate impacts of expanding pineapple plantations on two widespread and abundant frugivorous bats in a biological corridor in Costa Rica. We hypothesize that the larger, more mobile Artibeus jamaicensis will be less impacted by pineapple than the smaller Carollia castanea. In 2012 and 2013, we sampled 735 bats in 26 remnant forest patches surrounded by different proportions of forest, pasture, crops and pineapple. We used 10 microsatellite loci for A. jamaicensis and 16 microsatellite loci for C. castanea to estimate genetic diversity and gene flow. Canonical correspondence analyses indicate that land cover type surrounding patches has no impact on genetic diversity of A. jamaicensis. However, for C. castanea, both percentage forest and pineapple surrounding patches explained a significant proportion of the variation in genetic diversity. Least-cost transect analyses (LCTA) and pairwise G″st suggest that for A. jamaicensis, pineapple is more permeable to gene flow than expected, while as expected, forest is the most permeable land cover for gene flow of C. castanea. For both species, LCTA indicate that development may play a role in inhibiting gene flow. The current study answers the call for landscape genetic research focused on tropical and agricultural landscapes, highlights the value of comparative landscape genetics in biological corridor design and management and is one of the few studies of biological corridors in any ecosystem to implement a genetic approach to test corridor efficacy.

Effects of breeder turnover and harvest on group composition and recruitment in a social carnivore.

Breeder turnover can influence population growth in social carnivores through changes to group size, composition and recruitment. Studies that possess detailed group composition data that can provide insights about the effects of breeder turnover on groups have generally been conducted on species that are not subject to recurrent annual human harvest. We wanted to know how breeder turnover affects group composition and how harvest, in turn, affects breeder turnover in cooperatively breeding grey wolves (Canis lupus Linnaeus 1758). We used noninvasive genetic sampling at wolf rendezvous sites to construct pedigrees and estimate recruitment in groups of wolves before and after harvest in Idaho, USA. Turnover of breeding females increased polygamy and potential recruits per group by providing breeding opportunities for subordinates although resultant group size was unaffected 1 year after the turnover. Breeder turnover had no effect on the number of nonbreeding helpers per group. After breeding male turnover, fewer female pups were recruited in the new males' litters. Harvest had no effect on the frequency of breeder turnover. We found that breeder turnover led to shifts in the reproductive hierarchies within groups and the resulting changes to group composition were quite variable and depended on the sex of the breeder lost. We hypothesize that nonbreeding females direct help away from non-kin female pups to preserve future breeding opportunities for themselves. Breeder turnover had marked effects on the breeding opportunities of subordinates and the number and sex ratios of subsequent litters of pups. Seemingly subtle changes to groups, such as the loss of one individual, can greatly affect group composition, genetic content, and short-term population growth when the individual lost is a breeder.

Examining spatial patterns of selection and use for an altered predator guild.

Anthropogenic disturbances have altered species' distributions potentially impacting interspecific interactions. Interference competition is when one species denies a competing species access to a resource. One mechanism of interference competition is aggression, which can result in altered space-use of a subordinate species due to the threat of harm, otherwise known as a 'landscape of fear'. Alternatively, subordinates might outcompete dominant species in resource-poor environments via a superior ability to extract resources. Our goal was to evaluate spatial predictions of the 'landscape of fear' hypothesis for a carnivore guild in Newfoundland, Canada, where coyotes recently immigrated. Native Newfoundland carnivores include red foxes, Canada lynx, and black bears. We predicted foxes and lynx would avoid coyotes because of their larger size and similar dietary niches. We used scat-detecting dogs and genetic techniques to locate and identify predator scats. We then built resource selection functions and tested for avoidance by incorporating predicted values of selection for the alternative species into the best supported models of each species. We found multiple negative relationships, but notably did not find avoidance by foxes of areas selected by coyotes. While we did find that lynx avoided coyotes, we also found a reciprocal relationship. The observed patterns suggest spatial partitioning and not coyote avoidance, although avoidance could still be occurring at different spatial or temporal scales. Furthermore, Newfoundland's harsh climate and poor soils may swing the pendulum of interspecific interactions from interference competition to exploitative competition, where subordinates outcompete dominant competitors through a superior ability to extract resources.

Panmixia and Limited Interspecific Introgression in Coyotes (Canis latrans) from West Virginia and Virginia, USA.

The expansion of coyotes (Canis latrans) into the eastern United States has had major consequences for ecological communities and wildlife managers. Despite this, there has been little investigation of the genetics of coyotes across much of this region, especially outside of the northeast. Understanding patterns of genetic structure and interspecific introgression would provide insights into the colonization history of the species, its response to the modern environment, and interactions with other canids. We examined the genetic characteristics of 121 coyotes from the mid-Atlantic states of West Virginia and Virginia by genotyping 17 polymorphic nuclear DNA microsatellite loci. These genotypes were compared with those from other canid populations to evaluate the extent of genetic introgression. We conducted spatial clustering analyses and spatial autocorrelation to assess genetic structure among sampled coyotes. Coyotes across the 2 states had high genetic diversity, and we found no evidence of genetic structure. Six to sixteen percent of individuals displayed some evidence of genetic introgression from other species depending on the method and criteria used, but the population possessed predominantly coyote ancestry. Our findings suggested introgression from other canid populations has played less of a role in shaping the genetic character of coyotes in these states compared with populations closer to the Canadian border. Coyotes appear to display a panmictic population structure despite high habitat heterogeneity and heavy human influence in the spatial environment, underscoring the adaptability of the species.

Consequences for conservation: population density and genetic effects on reproduction of an endangered lagomorph.

Understanding reproduction and mating systems is important for managers tasked with conserving vulnerable species. Genetic tools allow biologists to investigate reproduction and mating systems with high resolution and are particularly useful for species that are otherwise difficult to study in their natural environments. We conducted parentage analyses using 19 nuclear DNA microsatellite loci to assess the influence of population density, genetic diversity, and ancestry on reproduction, and to examine the mating system of pygmy rabbits (Brachylagus idahoensis) bred in large naturalized enclosures for the reintroduction and recovery of the endangered distinct population in central Washington, USA. Reproductive output for females and males decreased as population density and individual homozygosity increased. We identified an interaction indicating that male reproductive output decreased as genetic diversity declined at high population densities, but there was no effect at low densities. Males with high amounts (> 50%) of Washington ancestry had higher reproductive output than the other ancestry groups, while reproductive output was decreased for males with high northern Utah/Wyoming ancestry and females with high Oregon/Nevada ancestry. Females and males bred with an average of 3.8 and 3.6 mates per year, respectively, and we found no evidence of positive or negative assortative mating with regards to ancestry. Multiple paternity was confirmed in 81% of litters, and we report the first documented cases of juvenile breeding by pygmy rabbits. This study demonstrates how variation in population density, genetic diversity, and ancestry impact fitness for an endangered species being bred for conservation. Our results advance understanding of basic life history characteristics for a cryptic species that is difficult to study in the wild and provide lessons for managing populations of vulnerable species in captive and free-ranging populations.

Estimating Sonoran pronghorn abundance and survival with fecal DNA and capture-recapture methods.

Population abundance estimates are important for management but can be challenging to determine in low-density, wide-ranging, and endangered species, such as Sonoran pronghorn (Antilocapra americana sonoriensis). The Sonoran pronghorn population has been increasing; however, population estimates are currently derived from a biennial aerial count that does not provide survival or recruitment estimates. We identified individuals through noninvasively collected fecal DNA and used robust-design capture-recapture to estimate abundance and survival for Sonoran pronghorn in the United States from 2013 to 2014. In 2014 we generated separate population estimates for pronghorn gathered near 13 different artificial water holes and for pronghorn not near water holes. The population using artificial water holes had 116 (95% CI 102-131) and 121 individuals (95% CI 112-132) in 2013 and 2014, respectively. For all locations, we estimated there were 144 individuals (95% CI 132-157). Adults had higher annual survival probabilities (0.83, 95% CI 0.69-0.92) than fawns (0.41, 95% CI 0.21-0.65). Our use of targeted noninvasive genetic sampling and capture-recapture with Sonoran pronghorn fecal DNA was an effective method for monitoring a large proportion of the population. Our results provided the first survival estimates for this population in over 2 decades and precise estimates of the population using artificial water holes. Our method could be used for targeted sampling of broadly distributed species in other systems, such as in African savanna ecosystems, where many species congregate at watering sites.

Evidence for Bombus occidentalis (Hymenoptera: Apidae) Populations in the Olympic Peninsula, the Palouse Prairie, and Forests of Northern Idaho.

Since the mid-1990s, Bombus occidentalis (Green) has declined from being one of the most common to one of the rarest bumble bee species in the Pacific Northwest of the United States. Although its conservation status is unresolved, a petition to list this species as endangered or threatened was recently submitted to the U.S. Fish and Wildlife Service. To shed light on the conservation situation and inform the U.S. Fish and Wildlife Service decision, we report on the detection and abundance of B. occidentalis following bumble bee collection between 2012 and 2014 across the Pacific Northwest. Collection occurred from the San Juan Islands and Olympic peninsula east to northern Idaho and northeastern Oregon, excluding the arid region in central Washington. B. occidentalis was observed at 23 collection sites out of a total of 234. With the exception of three sites on the Olympic peninsula, all of these were in the southeastern portion of the collection range.

Genetic Structure across Broad Spatial and Temporal Scales: Rocky Mountain Tailed Frogs (Ascaphus montanus; Anura: Ascaphidae) in the Inland Temperate Rainforest.

Contemporary and historical processes interact to structure genetic variation, however discerning between these can be difficult. Here, we analyze range-wide variation at 13 microsatellite loci in 2098 Rocky Mountain tailed frogs, Ascaphus montanus, collected from 117 streams across the species distribution in the Inland Northwest (INW) and interpret that variation in light of historical phylogeography, contemporary landscape genetics, and the reconstructed paleodistribution of the species. Further, we project species distribution models (SDMs) to predict future changes in the range as a function of changing climate. Genetic structure has a strong spatial signature that is precisely congruent with a deep (~1.8 MY) phylogeographic split in mtDNA when we partition populations into 2 clusters (K = 2), and is congruent with refugia areas inferred from our paleorange reconstructions. There is a hierarchical pattern of geographic structure as we permit additional clusters, with populations clustering following mountain ranges. Nevertheless, genetic diversity is the highest in populations at the center of the range and is attenuated in populations closer to the range edges. Similarly, geographic distance is the single best predictor of pairwise genetic differentiation, but connectivity also is an important predictor. At intermediate and local geographic scales, deviations from isolation-by-distance are more apparent, at least in the northern portion of the distribution. These results indicate that both historical and landscape factors are contributing to the genetic structure and diversity of tailed frogs in the Inland Northwest.

Inbreeding and inbreeding depression in endangered red wolves (Canis rufus).

In natural populations, the expression and severity of inbreeding depression can vary widely across taxa. Describing processes that influence the extent of inbreeding and inbreeding depression aid in our understanding of the evolutionary history of mating systems such as cooperative breeding and nonrandom mate selection. Such findings also help shape wildlife conservation theory because inbreeding depression reduces the viability of small populations. We evaluated the extent of inbreeding and inbreeding depression in a small, re-introduced population of red wolves (Canis rufus) in North Carolina. Since red wolves were first re-introduced in 1987, pedigree inbreeding coefficients (f) increased considerably and almost every wild born wolf was inbred (average f = 0.154 and max f = 0.383). The large inbreeding coefficients were due to both background relatedness associated with few founders and numerous close relative matings. Inbreeding depression was most evident for adult body size and generally absent for direct fitness measures such as reproductive success and survival; no lethal equivalents (LE = 0.00) were detected in juvenile survival. The lack of strong inbreeding depression in direct measures of fitness could be due to a founder effect or because there were no outbred individuals for comparison. Our results highlight the variable expression of inbreeding depression across traits and the need to measure a number of different traits when evaluating inbreeding depression in a wild population.

Resource pulses shape seasonal and individual variation in the diet of an omnivorous carnivore.

Resource pulses are ecologically important phenomenon that occur in most ecosystems globally. Following optimal foraging theory, many consumers switch to pulsatile foods when available, examples of which include fruit mast and vulnerable young prey. Yet how the availability of resource pulses shapes the ecology of predators is still an emerging area of research; and how much individual variation there is in response to pulses is not well understood. We hypothesized that resource pulses would lead to dietary convergence in our population, which we tested by tracking both population-level and individual coyote diets for 3 years in South Carolina, USA. We (1) described seasonal dietary shifts in relation to resource pulses; (2) compared male and female diets across seasons; and (3) tested this dietary convergence hypothesis by quantifying individual dietary variation both across and within periods when resource pulses were available. We found that pulses of white-tailed deer fawns and blackberries composed over half of coyote diet in summer, and persimmon fruits were an important component in fall. Male and female coyotes generally had similar diets, but males consumed more deer in fall, perhaps driven by scavenging more. We found support for our dietary convergence hypothesis, where individuals had more similar diets during resource pulses compared to a non-pulse period. We also found that this convergence happened before peak availability, suggesting a non-symmetric response to pulse availability. We show that nearly all coyotes eat fawns, suggesting that targeted efforts to remove "fawn killers" would be in vain. Instead, given how quickly coyotes collectively converge on resource pulses, our findings show that resource pulses could potentially be used by managers to alter the behavior of apex predators. More broadly, we open a new line of inquiry into how variation in individual foraging decisions scales up to shape the effects of resource pulses on ecological communities.