Y‐chromosome evidence supports asymmetric dog introgression into eastern coyotes

Hybridization has played an important role in the evolutionary history of Canis species in eastern North America. Genetic evidence of coyote–dog hybridization based on mitochondrial DNA (mtDNA) is lacking compared to that based on autosomal markers. This discordance suggests dog introgression into coyotes has potentially been male biased, but this hypothesis has not been formally tested. Therefore, we investigated biparentally, maternally, and paternally inherited genetic markers in a sample of coyotes and dogs from southeastern Ontario to assess potential asymmetric dog introgression into coyotes. Analysis of autosomal microsatellite genotypes revealed minimal historical and contemporary admixture between coyotes and dogs. We observed only mutually exclusive mtDNA haplotypes in coyotes and dogs, but we observed Y‐chromosome haplotypes (Y‐haplotypes) in both historical and contemporary coyotes that were also common in dogs. Species‐specific Zfy intron sequences of Y‐haplotypes shared between coyotes and dogs confirmed their homology and indicated a putative origin from dogs. We compared Y‐haplotypes observed in coyotes, wolves, and dogs profiled in multiple studies, and observed that the Y‐haplotypes shared between coyotes and dogs were either absent or rare in North American wolves, present in eastern coyotes, but absent in western coyotes. We suggest the eastern coyote has experienced asymmetric genetic introgression from dogs, resulting from predominantly historical hybridization with male dogs and subsequent backcrossing of hybrid offspring with coyotes. We discuss the temporal and spatial dynamics of coyote–dog hybridization and the conditions that may have facilitated the introgression of dog Y‐chromosomes into coyotes. Our findings clarify the evolutionary history of the eastern coyote.     

Underestimating the frequency,strength and cost of antipredator responses with data from GPS collars: an example with wolves and elk

Field studies that rely on fixes from GPS‐collared predators to identify encounters with prey will often underestimate the frequency and strength of antipredator responses. These underestimation biases have several mechanistic causes. (1) Step bias: The distance between successive GPS fixes can be large, and encounters that occur during these intervals go undetected. This bias will generally be strongest for cursorial hunters that can rapidly cover large distances (e.g., wolves and African wild dogs) and when the interval between GPS fixes is long relative to the duration of a hunt. Step bias is amplified as the path travelled between successive GPS fixes deviates from a straight line. (2) Scatter bias: Only a small fraction of the predators in a population typically carry GPS collars, and prey encounters with uncollared predators go undetected unless a collared group‐mate is present. This bias will generally be stronger for fission–fusion hunters (e.g., spotted hyenas, wolves, and lions) than for highly cohesive hunters (e.g., African wild dogs), particularly when their group sizes are large. Step bias and scatter bias both cause underestimation of the frequency of antipredator responses. (3) Strength bias: Observations of prey in the absence of GPS fix from a collared predator will generally include a mixture of cases in which predators were truly absent and cases in which predators were present but not detected, which causes underestimation of the strength of antipredator responses. We quantified these biases with data from wolves and African wild dogs and found that fixes from GPS collars at 3‐h intervals underestimated the frequency and strength of antipredator responses by a factor >10. We reexamined the results of a recent study of the nonconsumptive effects of wolves on elk in light of these results and confirmed that predation risk has strong effects on elk dynamics by reducing the pregnancy rate.     

The evolutionary history of grey wolf Y chromosomes

Analyses of Y chromosome haplotypes uniquely provide a paternal picture of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA (mtDNA). Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf (Canis lupis) Y chromosome, probably representing most of the male‐specific, nonampliconic sequence from the euchromatic part of the chromosome. We characterized this sequence and then identified ≈1,500 Y‐linked single nucleotide polymorphisms in a sample of 145 resequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in 24 dogs and eight other canids. We found 53 Y chromosome haplotypes, of which 26 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated because individual haplotypes were never shared between geographically distant areas, and genetically similar haplotypes were only found within the same geographical region. The deepest split between grey wolf haplogroups was estimated to have occurred 125,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as most recent immigrant haplotypes were present in the neighbouring Finnish population, but not in sequenced wolves from elsewhere in the world, or in dogs.     

Genome‐wide analyses suggest parallel selection for universal traits may eclipse local environmental selection in a highly mobile carnivore

Ecological and environmental heterogeneity can produce genetic differentiation in highly mobile species. Accordingly, local adaptation may be expected across comparatively short distances in the presence of marked environmental gradients. Within the European continent, wolves (Canis lupus) exhibit distinct north–south population differentiation. We investigated more than 67‐K single nucleotide polymorphism (SNP) loci for signatures of local adaptation in 59 unrelated wolves from four previously identified population clusters (northcentral Europe n = 32, Carpathian Mountains n = 7, Dinaric‐Balkan n = 9, Ukrainian Steppe n = 11). Our analyses combined identification of outlier loci with findings from genome‐wide association study of individual genomic profiles and 12 environmental variables. We identified 353 candidate SNP loci. We examined the SNP position and neighboring megabase (1 Mb, one million bases) regions in the dog (C. lupus familiaris) genome for genes potentially under selection, including homologue genes in other vertebrates. These regions included functional genes for, for example, temperature regulation that may indicate local adaptation and genes controlling for functions universally important for wolves, including olfaction, hearing, vision, and cognitive functions. We also observed strong outliers not associated with any of the investigated variables, which could suggest selective pressures associated with other unmeasured environmental variables and/or demographic factors. These patterns are further supported by the examination of spatial distributions of the SNPs associated with universally important traits, which typically show marked differences in allele frequencies among population clusters. Accordingly, parallel selection for features important to all wolves may eclipse local environmental selection and implies long‐term separation among population clusters.     

Assessment of coyote–wolf–dog admixture using ancestry‐informative diagnostic SNPs

The evolutionary importance of hybridization as a source of new adaptive genetic variation is rapidly gaining recognition. Hybridization between coyotes and wolves may have introduced adaptive alleles into the coyote gene pool that facilitated an expansion in their geographic range and dietary niche. Furthermore, hybridization between coyotes and domestic dogs may facilitate adaptation to human‐dominated environments. We genotyped 63 ancestry‐informative single‐nucleotide polymorphisms in 427 canids to examine the prevalence, spatial distribution and the ecology of admixture in eastern coyotes. Using multivariate methods and Bayesian clustering analyses, we estimated the relative contributions of western coyotes, western and eastern wolves, and domestic dogs to the admixed ancestry of Ohio and eastern coyotes. We found that eastern coyotes form an extensive hybrid swarm, with all our samples having varying levels of admixture. Ohio coyotes, previously thought to be free of admixture, are also highly admixed with wolves and dogs. Coyotes in areas of high deer density are genetically more wolf‐like, suggesting that natural selection for wolf‐like traits may result in local adaptation at a fine geographic scale. Our results, in light of other previously published studies of admixture in Canis, revealed a pattern of sex‐biased hybridization, presumably generated by male wolves and dogs mating with female coyotes. This study is the most comprehensive genetic survey of admixture in eastern coyotes and demonstrates that the frequency and scope of hybridization can be quantified with relatively few ancestry‐informative markers.     

Viral gut metagenomics of sympatric wild and domestic canids,and monitoring of viruses: Insights from an endangered wolf population

Animal host–microbe interactions are a relevant concern for wildlife conservation, particularly regarding generalist pathogens, where domestic host species can play a role in the transmission of infectious agents, such as viruses, to wild animals. Knowledge on viral circulation in wild host species is still scarce and can be improved by the recent advent of modern molecular approaches. We aimed to characterize the fecal virome and identify viruses of potential conservation relevance of diarrheic free‐ranging wolves and sympatric domestic dogs from Central Portugal, where a small and threatened wolf population persists in a highly anthropogenically modified landscape. Using viral metagenomics, we screened diarrheic stools collected from wolves (n = 8), feral dogs (n = 4), and pet dogs (n = 6), all collected within wolf range. We detected novel highly divergent viruses as well as known viral pathogens with established effects on population dynamics, including canine distemper virus, a novel bocavirus, and canine minute virus. Furthermore, we performed a 4‐year survey for the six wolf packs comprising this endangered wolf population, screening 93 fecal samples from 36 genetically identified wolves for canine distemper virus and the novel bocavirus, previously identified using our metagenomics approach. Our novel approach using metagenomics for viral screening in noninvasive samples of wolves and dogs has profound implications on the knowledge of both virology and wildlife diseases, establishing a complementary tool to traditional screening methods for the conservation of threatened species.     

Using the dog genome to find single nucleotide polymorphisms in red foxes and other distantly related members of the Canidae

Single nucleotide polymorphisms (SNP) are the ideal marker for characterizing genomic variation but can be difficult to find in nonmodel species. We explored the usefulness of the dog genome for finding SNPs in distantly related nonmodel canids and evaluated so-ascertained SNPs. Using 40 primer pairs designed from randomly selected bacterial artificial chromosome clones from the dog genome, we successfully sequenced 80-88% of loci in a coyote (Canis latrans), grey fox (Urocyon cinereoargenteus), and red fox (Vulpes vulpes), which compared favourably to a 60% success rate for each species using 10 primer pairs conserved across mammals. Loci were minimally heterogeneous with respect to SNP density, which was similar, overall, in a discovery panel of nine red foxes to that previously reported for a panel of eight wolves (Canis lupus). Additionally, individual heterozygosity was similar across the three canids in this study. However, the proportion of SNP sites shared with the dog decreased with phylogenetic divergence, with no SNPs shared between red foxes and dogs. Density of interspecific SNPs increased approximately linearly with divergence time between species. Using red foxes from three populations, we estimated F(ST) based on each of 42 SNPs and 14 microsatellites and simulated null distributions conditioned on each marker type. Relative to SNPs, microsatellites systematically underestimated F(ST) and produced biased null distributions, indicating that SNPs are superior markers for these functions. By reconstituting the frequency spectrum of SNPs discovered in nine red foxes, we discovered an estimated 77-89% of all SNPs (within the region screened) present in North American red foxes. In sum, these findings indicate that information from the dog genome enables easy ascertainment of random and gene-linked SNPs throughout the Canidae and illustrate the value of SNPs in ecological and evolutionary genetics.     

Sympatric wolf and coyote populations of the western Great Lakes region are reproductively isolated

Interpretation of the genetic composition and taxonomic history of wolves in the western Great Lakes region (WGLR) of the United States has long been debated and has become more important to their conservation given the recent changes in their status under the Endangered Species Act. Currently, the two competing hypotheses on WGLR wolves are that they resulted from hybridization between (i) grey wolves (Canis lupus) and western coyotes (C. latrans) or (ii) between grey wolves and eastern wolves (C. lycaon). We performed a genetic analysis of sympatric wolves and coyotes from the region to assess the degree of reproductive isolation between them and to clarify the taxonomic status of WGLR wolves. Based on data from maternal, paternal and bi‐parental genetic markers, we demonstrate a clear genetic distinction between sympatric wolves and coyotes and conclude that they are reproductively isolated and that wolf–coyote hybridization in the WGLR is uncommon. The data reject the hypothesis that wolves in the WGLR derive from hybridization between grey wolves and western coyotes, and we conclude that the extant WGLR wolf population is derived from hybridization between grey wolves and eastern wolves. Grey‐eastern wolf hybrids (C. lupus × lycaon) comprise a substantial population that extends across Michigan, Wisconsin, Minnesota and western Ontario. These findings have important implications for the conservation and management of wolves in North America, specifically concerning the overestimation of grey wolf numbers in the United States and the need to address policies for hybrids.     

Size‐assortative choice and mate availability influences hybridization between red wolves (Canis rufus) and coyotes (Canis latrans)

Anthropogenic hybridization of historically isolated taxa has become a primary conservation challenge for many imperiled species. Indeed, hybridization between red wolves (Canis rufus) and coyotes (Canis latrans) poses a significant challenge to red wolf recovery. We considered seven hypotheses to assess factors influencing hybridization between red wolves and coyotes via pair‐bonding between the two species. Because long‐term monogamy and defense of all‐purpose territories are core characteristics of both species, mate choice has long‐term consequences. Therefore, red wolves may choose similar‐sized mates to acquire partners that behave similarly to themselves in the use of space and diet. We observed multiple factors influencing breeding pair formation by red wolves and found that most wolves paired with similar‐sized conspecifics and wolves that formed congeneric pairs with nonwolves (coyotes and hybrids) were mostly female wolves, the smaller of the two sexes. Additionally, we observed that lower red wolf abundance relative to nonwolves and the absence of helpers increased the probability that wolves consorted with nonwolves. However, successful pairings between red wolves and nonwolves were associated with wolves that maintained small home ranges. Behaviors associated with territoriality are energetically demanding and behaviors (e.g., aggressive interactions, foraging, and space use) involved in maintaining territories are influenced by body size. Consequently, we propose the hypothesis that size disparities between consorting red wolves and coyotes influence positive assortative mating and may represent a reproductive barrier between the two species. We offer that it may be possible to maintain wild populations of red wolves in the presence of coyotes if management strategies increase red wolf abundance on the landscape by mitigating key threats, such as human‐caused mortality and hybridization with coyotes. Increasing red wolf abundance would likely restore selection pressures that increase mean body and home‐range sizes of red wolves and decrease hybridization rates via reduced occurrence of congeneric pairs.     

Genomewide scan for adaptive differentiation along altitudinal gradient in the Andrew's toad Bufo andrewsi

Recent studies of humans, dogs and rodents have started to discover the genetic underpinnings of high altitude adaptations, yet amphibians have received little attention in this respect. To identify possible signatures of adaptation to altitude, we performed a genome scan of 15 557 single nucleotide polymorphisms (SNPs) obtained with restriction site‐associated DNA sequencing of pooled samples from 11 populations of Andrew's toad (Bufo andrewsi) from the edge of the Tibetan Plateau, spanning an altitudinal gradient from 1690 to 2768 m.a.s.l. We discovered significant geographic differentiation among all sites, with an average F_ST = 0.023 across all SNPs. Apart from clear patterns of isolation by distance, we discovered numerous outlier SNPs showing strong associations with variation in altitude (1394 SNPs), average annual temperature (1859 SNPs) or both (1051 SNPs). Levels and patterns of genetic differentiation in these SNPs were consistent with the hypothesis that they have been subject to directional selection and reflect adaptation to altitudinal variation among the study sites. Genes with footprints of selection were significantly enriched in binding and metabolic processes. Several genes potentially related to high altitude adaptation were identified, although the identity and functional significance of most genomic targets of selection remain unknown. In general, the results provide genomic support for results of earlier common garden and low coverage genetic studies that have uncovered substantial adaptive differentiation along altitudinal and latitudinal gradients in amphibians.     

A Comparison of the Sensory Development of Wolves (Canis lupus lupus) and Dogs (Canis lupus familiaris)

Little is known about the development of the sensory systems of wolves. The timing of sensory development in wolves is usually extrapolated from studies on dogs, since they are members of the same species. However, early developmental differences between these two subspecies have already been identified. For example, wolves tend to approach and investigate objects in their environment 2 wk before dogs. These changes in developmental timing may play an important role in the behavioral differences between adult wolves and dogs. The purpose of this study is to compare the development of the sensory systems in wolves and dogs. Responses of seven wolf pups and 43 dog pups to familiar and novel olfactory, auditory, and visual stimuli were tested weekly from 2–7 wk of age. Eleven wolf pups were also observed for orientation towards auditory and visual stimuli during 2‐h sessions, 5 d a week, from 2–8 wk of age. These observations were supplemented by the daily records of caretakers. The results suggest that wolves and dogs both develop olfaction by 2 wk, audition by 4 wk, and vision by 6 wk on average, despite the 2‐wk shift in their ability to explore. This means that when wolves begin to explore at 2 wk, they are blind and deaf, and must rely primarily on their sense of smell. Thus, there is a significant alteration of how these subspecies experience their environment during the critical period of socialization. These findings lead to an alternative explanation for the difference in dogs' and wolves' abilities to form interspecies social attachments, such as those with humans.     

Spatio-temporal co-occurrence of cougars (Felis concolor), wolves (Canis lupus) and their prey during winter: a comparison of two analytical methods

Aims To examine the spatio‐temporal co‐occurrence of cougars (Felis concolor), wolves (Canis lupus), and their prey during winter using monthly (November–March) species–environment relationship models. In addition, to contrast predictions across two methods: logistic regression and Geographic Information System (GIS) image correlation. Location The eastern front ranges of the Canadian Rocky Mountains (south‐central Alberta), approximately 100 km west of Calgary, including portions of Banff National Park and Kananaskis Country. Methods Snow‐tracking data were collected simultaneously for cougars, wolves, elk (Cervus elaphus), and deer (Odocoileus virginianus and O. hemionus) between November and March, 1997–2000. Track data were synthesized in a GIS. Logistic regression and Akaike's information criterion (AIC) were used to select optimal environmental relationship models for each species. We first examined co‐occurrence by iteratively using each species as a dependent variable (presence/absence) in a logistic regression analysis and using all other species track‐density estimates as independent variables. We built predictive surfaces in a GIS using the exponent form of the logistic regression models, and assessed model accuracy with a receiver operating characteristic curve. We then re‐examined co‐occurrence using pairwise correlations of species probability surfaces by month. The correlation results were compared with logistic regression results to illuminate mechanisms of co‐occurrence and to investigate predictive consistency across the two methods. Results Cougars showed a trend in distribution from higher elevation and less rugged terrain in December, to lower elevation and more rugged terrain in March. This trend differed from that for wolves, which showed a more stable affinity for low elevation and less rugged valley bottoms across all months. The logistic regression models indicated variable positive and negative associations of cougars with wolves by month, and changes in prey associations over time. Notably, there was a shift in co‐occurrence for both predators from elk to deer in March. We found high predictive accuracy for all probability surfaces, except for the month of January. Our image comparison showed that spatial co‐occurrence amongst all species increased over winter, except that wolves and cougars were negatively correlated in February. Combining the results of each approach we found that cougars and wolves converged spatially over winter at the landscape scale (i.e. the valley), while showing more discrete use of that space over time and by habitat attributes (e.g. forest cover, topographic complexity, and prey track density). Main conclusions In the Rocky Mountains, the spatial distributions of cougars and wolves converged into the valley floor as winter progressed. Cougars were distinct from wolves and prey in the intensity of this shift. We determined that a comparison of predictive surfaces alone fails to explain species co‐occurrence. The surfaces must be coupled with investigation of respective species–environment models to account for temporal changes in associations. We suggest that the two approaches represent different ecological scales: image comparison may be best for landscape‐ (valley) level analysis, while logistic regression is best for site‐level analysis. Ultimately, both approaches were critical to our analysis. Finally, the variability observed over time suggested that annual and seasonal models may obscure important ecological patterns and processes, especially for cougars.     

SNPs in ecological and conservation studies: a test in the Scandinavian wolf population

Single nucleotide polymorphisms (SNPs) have the potential to become the genetic marker of choice in studies of the ecology and conservation of natural populations because of their capacity to access variability across the genome. In this study, we provide one of the first demonstrations of SNP discovery in a wild population in order to address typical issues of importance in ecology and conservation in the recolonized Scandinavian and neighbouring Finnish wolf Canis lupus populations. Using end sequence from BAC (bacterial artificial chromosome) clones specific for dogs, we designed assays for 24 SNP loci, 20 sites of which had previously been shown to be polymorphic in domestic dogs and four sites were newly identified as polymorphic in wolves. Of the 24 assayed loci, 22 SNPs were found to be variable within the Scandinavian population and, importantly, these were able to distinguish individual wolves from one another (unbiased probability of identity of 4.33 x 10(-8)), providing equivalent results to that derived from 12 variable microsatellites genotyped in the same population. An assignment test shows differentiation between the Scandinavian and neighbouring Finnish wolf populations, although not all known immigrants are accurately identified. An exploration of the misclassification rates in the identification of relationships shows that neither 22 SNP nor 20 microsatellite loci are able to discriminate across single order relationships. Despite the remaining obstacle of SNP discovery in nonmodel organisms, the use of SNPs in ecological and conservation studies is encouraged by the advent of large scale screening methods. Furthermore, the ability to amplify extremely small fragments makes SNPs of particular use for population monitoring, where faecal and other noninvasive samples are routinely used.     

Transit time and digestibility of two experimental diets in the maned wolf (Chrysocyon brachyurus) and domestic dog (Canis lupus)

Recent research involving nutritional management of clinical disease secondary to cystinuria in captive maned wolves (Chrysocyon brachyurus) in the United States resulted in the production of a commercially manufactured maintenance diet and subsequently, a further modified experimental diet. These two diets differed only in their protein sources and sodium concentrations. The purpose of this study was to further investigate these diets by determining their digestibility and transit time in maned wolves, and also to compare these results to the digestibility and transit time of the diets in domestic dogs. The experiment consisted of two diets (maned wolf commercial maintenance diet and experimental diet) and two species (maned wolf and domestic dog [beagle]) arranged as a 2 × 2 factorial design. For the transit time study, titanium dioxide (TiO₂, 5 g/kg diet) was administered as a pulse dose and total collection of feces was carried out for 50 hr. There was no effect of diet or species on initial Ti recovery time (IRT), the amount of Ti recovered at IRT, or the time to reach 50% of Ti excretion in the feces. Maned wolves had lower total percent recovery (P<0.01) of Ti than dogs and shorter time to last recovery of Ti in the feces (P<0.05), however, marker excretion in the maned wolves may not have been complete. For the digestibility study, in which chromic oxide was used as a marker, fecal samples were collected on 2 consecutive days immediately after 12 days of being fed the diets and then analyzed for dry matter, energy, protein, and minerals. Crude protein, calcium, phosphorus, and zinc apparent digestibilities were unaffected by species or diet (P>0.05). Apparent digestibility of dry matter (P<0.05) and energy (P<0.01) were higher in the experimental diet and in the dogs. Both dogs and maned wolves fed the maintenance diet exhibited a greater apparent retention of copper, iron, and magnesium (P<0.01). Dogs had a higher apparent retention of magnesium and sodium than the maned wolves. Zoo Biol 0:1–13, 2006. © 2006 Wiley‐Liss, Inc.     

Heritability of interpack aggression in a wild pedigreed population of North American grey wolves

Aggression is a quantitative trait deeply entwined with individual fitness. Mapping the genomic architecture underlying such traits is complicated by complex inheritance patterns, social structure, pedigree information and gene pleiotropy. Here, we leveraged the pedigree of a reintroduced population of grey wolves (Canis lupus) in Yellowstone National Park, Wyoming, USA, to examine the heritability of and the genetic variation associated with aggression. Since their reintroduction, many ecological and behavioural aspects have been documented, providing unmatched records of aggressive behaviour across multiple generations of a wild population of wolves. Using a linear mixed model, a robust genetic relationship matrix, 12,288 single nucleotide polymorphisms (SNPs) and 111 wolves, we estimated the SNP‐based heritability of aggression to be 37% and an additional 14% of the phenotypic variation explained by shared environmental exposures. We identified 598 SNP genotypes from 425 grey wolves to resolve a consensus pedigree that was included in a heritability analysis of 141 individuals with SNP genotype, metadata and aggression data. The pedigree‐based heritability estimate for aggression is 14%, and an additional 16% of the phenotypic variation was explained by shared environmental exposures. We find strong effects of breeding status and relative pack size on aggression. Through an integrative approach, these results provide a framework for understanding the genetic architecture of a complex trait that influences individual fitness, with linkages to reproduction, in a social carnivore. Along with a few other studies, we show here the incredible utility of a pedigreed natural population for dissecting a complex, fitness‐related behavioural trait.     

Genomic variation at the tips of the adaptive radiation of Darwin's finches

Adaptive radiation unfolds as selection acts on the genetic variation underlying functional traits. The nature of this variation can be revealed by studying the tips of an ongoing adaptive radiation. We studied genomic variation at the tips of the Darwin's finch radiation; specifically focusing on polymorphism within, and variation among, three sympatric species of the genus Geospiza. Using restriction site‐associated DNA (RAD‐seq), we characterized 32 569 single‐nucleotide polymorphisms (SNPs), from which 11 outlier SNPs for beak and body size were uncovered by a genomewide association study (GWAS). Principal component analysis revealed that these 11 SNPs formed four statistically linked groups. Stepwise regression then revealed that the first PC score, which included 6 of the 11 top SNPs, explained over 80% of the variation in beak size, suggesting that selection on these traits influences multiple correlated loci. The two SNPs most strongly associated with beak size were near genes associated with beak morphology across deeper branches of the radiation: delta‐like 1 homologue (DLK1) and high‐mobility group AT‐hook 2 (HMGA2). Our results suggest that (i) key adaptive traits are associated with a small fraction of the genome (11 of 32 569 SNPs), (ii) SNPs linked to the candidate genes are dispersed throughout the genome (on several chromosomes), and (iii) micro‐ and macro‐evolutionary variation (roots and tips of the radiation) involve some shared and some unique genomic regions.     

Association of dopamine‐ and serotonin‐related genes with canine aggression

Human‐directed canine aggression was studied using 50 aggressive and 81 non‐aggressive dogs. We examined 62 single nucleotide polymorphisms (SNPs) occurring in or in the close vicinity of 16 neurotransmitter‐related genes. Allelic associations with aggression were identified for DRD1, HTR1D, HTR2C and SLC6A1. Risk or protective haplotypes for aggressive behaviour based on 2–5 SNPs were identified. The frequency of aggressive dogs varied significantly between the haplotypes within loci and the odds ratios of aggression in dogs with risk haplotypes compared with protective haplotypes varied from 4.4 (HTR2C) to 9.0 (SLC6A1). A risk haplotype across the neurotransmitter receptor gene HTR1D harboured a non‐synonymous SNP with a potential effect on protein function. We identified no haplotypes in complete association with the recorded phenotypes, supporting a complex inheritance of aggression.     

Fences can support restoration in human‐dominated ecosystems when rewilding with large predators

The use of fences in conservation can be controversial, as artificial barriers constrain natural behavior and ecological dynamics. However, in the case of large predators inhabiting protected areas within a hostile human‐dominated landscape, predators may remain at low densities if they face high mortality upon leaving the reserve. In turn, this may compromise the potential for density‐dependent effects such as top‐down regulation of prey species abundance. We simulate the hypothetical reintroduction of gray wolves (Canis lupus) to reserves in their former range (Scottish Highlands), with the objectives of identifying parameters that allow a viable wolf population and the potential for direct top‐down forcing of red deer (Cervus elaphus) densities. We examine the extent to which the number of dispersing wolves leaving the protected area influences whether these objectives are achieved. Our simulations confirm that source‐sink population dynamics can result in a self‐perpetuating wolf population, but one that never achieves densities needed for strong top‐down forcing. When wolf density is weakly controlled by intraspecific competition, strong top‐down forcing occurs when 20% of dispersing wolves or less leave the population. When 20–35% of dispersing wolves leave, the strength of top‐down forcing is highly variable. The wolf population remained viable when 35–60% of dispersing wolves left, but then did not exert strong top‐down forcing. Wolves were vulnerable to extinction at greater than 60% disperser loss. Despite their negative connotations, fences (including semi‐permeable ones) could increase the potential for interspecific density‐dependent processes in some cases, thereby facilitating trophic rewilding.     

Testing the myth: tolerant dogs and aggressive wolves

Cooperation is thought to be highly dependent on tolerance. For example, it has been suggested that dog–human cooperation has been enabled by selecting dogs for increased tolerance and reduced aggression during the course of domestication (‘emotional reactivity hypothesis’). However, based on observations of social interactions among members of captive packs, a few dog–wolf comparisons found contradictory results. In this study, we compared intraspecies aggression and tolerance of dogs and wolves raised and kept under identical conditions by investigating their agonistic behaviours and cofeeding during pair-wise food competition tests, a situation that has been directly linked to cooperation. We found that in wolves, dominant and subordinate members of the dyads monopolized the food and showed agonistic behaviours to a similar extent, whereas in dogs these behaviours were privileges of the high-ranking individuals. The fact that subordinate dogs rarely challenged their higher-ranking partners suggests a steeper dominance hierarchy in dogs than in wolves. Finally, wolves as well as dogs showed only rare and weak aggression towards each other. Therefore, we suggest that wolves are sufficiently tolerant to enable wolf–wolf cooperation, which in turn might have been the basis for the evolution of dog–human cooperation (canine cooperation hypothesis).