Background:The largest terrestrial species in the order Carnivora are wide-ranging and rare because of their positions at the top of food webs. They are some of the world's most admired mammals and, ironically, some of the most imperiled. Most have experienced substantial population declines and range contractions throughout the world during the past two centuries. Because of the high metabolic demands that come with endothermy and large body size, these carnivores often require large prey and expansive habitats. These food requirements and wide-ranging behavior often bring them into confl ict with humans and livestock. This, in addition to human intolerance, renders them vulnerable to extinction. Large carnivores face enormous threats that have caused massive declines in their populations and geographic ranges, including habitat loss and degradation, persecution, utilization, and depletion of prey. We highlight how these threats can affect the conservation status and ecological roles of this planet's 31 largest carnivores.

The 22,000-year-old cave painting of an Atlantic salmon (Salmo salar) near the Vézère River in France is a reminder of our fascination with, and dependence on, Atlantic salmon throughout human history. Atlantic salmon belongs to the salmonid lineage which comprises 11 genera, with at least 70 species that exhibit a wide range of ecological adaptations and use a variety of marine and freshwater life history strategies 1 . Salmonids hold important positions as socially iconic species and economic resources within aquaculture, wild fisheries and recreational sport fisheries. Moreover, they serve as key indicator species of the health of North Atlantic and Pacific coastal and river ecosystems.All teleosts share at least three rounds of whole-genome duplication (WGD), 1R and 2R before the divergence of lamprey from the jawed vertebrates 2 , and a third teleost-specific WGD (Ts3R) at the base of the teleosts ~320 million years ago (Mya) [3][4][5] . Very little is known about the mechanisms of genomic and chromosomal reorganization after WGD in vertebrates because the 1R, 2R and Ts3R occurred so long ago that few clear signatures of post-WGD reorganization events remain. In contrast, a fourth WGD (the Ss4R salmonid-specific autotetraploidization event) occurred in the common ancestor of salmonids ~80 Mya after their divergence from Esociformes ~125 Mya 6-8 (Fig. 1), and the continued presence of multivalent pairing at meiosis and evidence of tetrasomic inheritance in salmonid species suggests that diploidy is not yet fully re-established 6,9,10 . Salmonids thus appear to provide an unprecedented opportunity for studying vertebrate genome evolution after an autotetraploid WGD 11,12 over a time period that is long enough to reveal long-term evolutionary patterns, but short enough to give a high-resolution picture of the process. In addition, they provide an excellent setting for contextualizing genome evolution with a dramatic post-WGD species radiation and intricate adaptations to a whole range of life history regimes.Here we present a high-quality reference genome assembly of the Atlantic salmon, and use it to describe major patterns characterizing the post-Ss4R salmonid genome evolution over the past 80 million years (Myr). Our results challenge the recent claim that rediploidization in salmonids has been a gradual process unlinked to significant genome rearrangements 13 . They also challenge current views about the relative importance of sub-and neofunctionalization in vertebrate genomes (reviewed in ref. 14), and the importance of dosage balance as a gene duplicate retention mechanism 15 . Genome characterizationThe Atlantic salmon reference genome assembly (GenBank: GCA_000233375.4) adds up to 2.97 gigabases (Gb) with aThe whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high...

A trophic cascade recently has been reported among wolves, elk, and aspen on the northern winter range of Yellowstone National Park, Wyoming, USA, but the mechanisms of indirect interactions within this food chain have yet to be established. We investigated whether the observed trophic cascade might have a behavioral basis by exploring environmental factors influencing the movements of 13 female elk equipped with GPS radio collars. We developed a simple statistical approach that can unveil the concurrent influence of several environmental features on animal movements. Paths of elk traveling on their winter range were broken down into steps, which correspond to the straight-line segment between successive locations at 5-hour intervals. Each observed step was paired with 200 random steps having the same starting point, but differing in length and/or direction. Comparisons between the characteristics of observed and random steps using conditional logistic regression were used to model environmental features influencing movement patterns. We found that elk movements were influenced by multiple factors, such as the distance from roads, the presence of a steep slope along the step, and the cover type in which they ended. The influence of cover type on elk movements depended on the spatial distribution of wolves across the northern winter range of the park. In low wolf-use areas, the relative preference for end point locations of steps followed: aspen stands Ͼ open areas Ͼ conifer forests. As the risks of wolf encounter increased, the preference of elk for aspen stands gradually decreased, and selection became strongest for steps ending in conifer forests in high wolf-use areas. Our study clarifies the behavioral mechanisms involved in the trophic cascade of Yellowstone's wolf-elk-aspen system: elk respond to wolves on their winter range by a shift in habitat selection, which leads to local reductions in the use of aspen by elk.

Morphological diversity within closely related species is an essential aspect of evolution and adaptation. Mutations in the Melanocortin 1 receptor (Mc1r) gene contribute to pigmentary diversity in natural populations of fish, birds, and many mammals. However, melanism in the gray wolf, Canis lupus, is caused by a different melanocortin pathway component, the K locus, that encodes a beta-defensin protein that acts as an alternative ligand for Mc1r. We show that the melanistic K locus mutation in North American wolves derives from past hybridization with domestic dogs, has risen to high frequency in forested habitats, and exhibits a molecular signature of positive selection. The same mutation also causes melanism in the coyote, Canis latrans, and in Italian gray wolves, and hence our results demonstrate how traits selected in domesticated species can influence the morphological diversity of their wild relatives.

Because some native ungulates have lived without top predators for generations, it has been uncertain whether runaway predation would occur when predators are newly restored to these systems. We show that landscape features and vegetation, which influence predator detection and capture of prey, shape large-scale patterns of predation in a newly restored predator-prey system. We analysed the spatial distribution of wolf (Canis lupus) predation on elk (Cervus elaphus) on the Northern Range of Yellowstone National Park over 10 consecutive winters. The influence of wolf distribution on kill sites diminished over the course of this study, a result that was likely caused by territorial constraints on wolf distribution. In contrast, landscape factors strongly influenced kill sites, creating distinct hunting grounds and prey refugia. Elk in this newly restored predator-prey system should be able to mediate their risk of predation by movement and habitat selection across a heterogeneous risk landscape.

Determining population sizes can be difficult, but is essential for conservation. By counting distinct microsatellite genotypes, DNA from noninvasive samples (hair, faeces) allows estimation of population size. Problems arise because genotypes from noninvasive samples are error-prone, but genotyping errors can be reduced by multiple polymerase chain reaction (PCR). For faecal genotypes from wolves in Yellowstone National Park, error rates varied substantially among samples, often above the 'worst-case threshold' suggested by simulation. Consequently, a substantial proportion of multilocus genotypes held one or more errors, despite multiple PCR. These genotyping errors created several genotypes per individual and caused overestimation (up to 5.5-fold) of population size. We propose a 'matching approach' to eliminate this overestimation bias.

Quaking aspen (Populus tremuloides) biomass has declined in Yellowstone National Park (YNP) in the past century. We installed permanent belt transects (plots) for long-term monitoring of aspen stands both within and outside of established wolf pack territories on YNP's northern range to determine if reintroduced wolves are influencing elk browsing patterns and aspen regeneration through a trophic cascades interaction. Wolves may have an indirect effect on aspen regeneration by altering elk movements, browsing patterns, and foraging behavior (predation risk effects). Elk pellet groups, aspen sucker heights, and the percentage of browsed suckers were the variables used to measure differences in aspen stands in high and low wolf-use areas of the northern range. The aspen stands in the high wolf-use areas had significantly lower counts of elk pellet groups in the mesic upland steppe and the combined mesic upland steppe and riparian/wet meadow habitat types. Based on our pellet group results, it appears that elk foraging behaviors may have been altered by the increased risk of predation due to the reintroduction of the wolf. In the riparian/ wet meadow habitat type, mean aspen sucker heights were significantly higher in the high wolf-use areas than in the low wolf-use areas. The percentage of browsed suckers in high and low wolf-use areas showed no significant differences in any of the habitat types. Considering the high browsing pressure in YNP aspen stands, it is uncertain whether the taller aspen suckers measured in the high wolf-use areas will eventually join the aspen overstory. These permanent plots represent a valuable baseline data set to assess any current and future aspen regeneration responses to the reintroduction of wolves in YNP. #

Summary1. The reintroduction of grey wolves Canis lupus (L.) to Yellowstone National Park provides a natural experiment in which to study the effects of a keystone predator on ecosystem function. 2. Grey wolves often provision scavengers with carrion by partially consuming their prey. 3. In order to examine how grey wolf foraging behaviour influences the availability of carrion to scavengers, we observed consumption of 57 wolf-killed elk Cervus elaphus (L.) and determined the percentage of edible biomass eaten by wolves from each carcass. 4. We found that the percentage of a carcass consumed by wolves increases as snow depth decreases and the ratio of wolf pack size to prey size and distance to the road increases. In addition, wolf packs of intermediate size provide the most carrion to scavengers. 5. Applying linear regression models to the years prior to reintroduction, we calculate carrion biomass availability had wolves been present, and contrast this to a previously published index of carrion availability. Our results demonstrate that wolves increase the time period over which carrion is available, and change the variability in scavenge from a late winter pulse dependent primarily on abiotic environmental conditions to one that is relatively constant across the winter and primarily dependent on wolf demographics. Wolves also decrease the year-to-year and month-to-month variation in carrion availability. 6. By transferring the availability of carrion from the highly productive late winter, to the less productive early winter and from highly productive years to less productive ones, wolves provide a temporal subsidy to scavengers.