Carles Vilà

Rescue of a severely bottlenecked wolf (Canis lupus) population by a single immigrant.

The fragmentation of populations is an increasingly important problem in the conservation of endangered species. Under these conditions, rare migration events may have important effects for the rescue of small and inbred populations. However, the relevance of such migration events to genetically depauperate natural populations is not supported by empirical data. We show here that the genetic diversity of the severely bottlenecked and geographically isolated Scandinavian population of grey wolves (Canis lupus), founded by only two individuals, was recovered by the arrival of a single immigrant. Before the arrival of this immigrant, for several generations the population comprised only a single breeding pack, necessarily involving matings between close relatives and resulting in a subsequent decline in individual heterozygosity. With the arrival of just a single immigrant, there is evidence of increased heterozygosity, significant outbreeding (inbreeding avoidance), a rapid spread of new alleles and exponential population growth. Our results imply that even rare interpopulation migration can lead to the rescue and recovery of isolated and endangered natural populations.

Mitochondrial DNA phylogeography and population history of the grey wolf Canis lupus

The grey wolf (Canis lupus) and coyote (C. latrans) are highly mobile carnivores that disperse over great distances in search of territories and mates. Previous genetic studies have shown little geographical structure in either species. However, population genetic structure is also influenced by past isolation events and population fluctuations during glacial periods. In this study, control region sequence data from a worldwide sample of grey wolves and a more limited sample of coyotes were analysed. The results suggest that fluctuating population sizes during the late Pleistocene have left a genetic signature on levels of variation in both species. Genealogical measures of nucleotide diversity suggest that historical population sizes were much larger in both species and grey wolves were more numerous than coyotes. Currently, about 300 000 wolves and 7 million coyotes exist. In grey wolves, genetic diversity is greater than that predicted from census population size, reflecting recent historical population declines. By contrast, nucleotide diversity in coyotes is smaller than that predicted by census population size, reflecting a recent population expansion following the extirpation of wolves from much of North America. Both species show little partitioning of haplotypes on continental or regional scales. However, a statistical parsimony analysis indicates local genetic structure that suggests recent restricted gene flow.

Genome Sequencing Highlights the Dynamic Early History of Dogs

To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history, we generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow. In dogs, the domestication bottleneck involved at least a 16-fold reduction in population size, a much more severe bottleneck than estimated previously. A sharp bottleneck in wolves occurred soon after their divergence from dogs, implying that the pool of diversity from which dogs arose was substantially larger than represented by modern wolf populations. We narrow the plausible range for the date of initial dog domestication to an interval spanning 11–16 thousand years ago, predating the rise of agriculture. In light of this finding, we expand upon previous work regarding the increase in copy number of the amylase gene (AMY2B) in dogs, which is believed to have aided digestion of starch in agricultural refuse. We find standing variation for amylase copy number variation in wolves and little or no copy number increase in the Dingo and Husky lineages. In conjunction with the estimated timing of dog origins, these results provide additional support to archaeological finds, suggesting the earliest dogs arose alongside hunter-gathers rather than agriculturists. Regarding the geographic origin of dogs, we find that, surprisingly, none of the extant wolf lineages from putative domestication centers is more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary.

Ebola Outbreak Killed 5000 Gorillas

Over the past decade, the Zaire strain of Ebola virus (ZEBOV) has repeatedly emerged in Gabon and Congo. Each human outbreak has been accompanied by reports of gorilla and chimpanzee carcasses in neighboring forests, but both the extent of ape mortality and the causal role of ZEBOV have been hotly debated. Here, we present data suggesting that in 2002 and 2003 ZEBOV killed about 5000 gorillas in our study area. The lag between neighboring gorilla groups in mortality onset was close to the ZEBOV disease cycle length, evidence that group-to-group transmission has amplified gorilla die-offs.

Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping.

The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds using a newly developed high-density genotyping array consisting of >170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary between breeds, and we identify novel associations with both morphological and behavioral traits. We next scan the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. This study provides a catalogue of genomic regions showing extreme reduction in genetic variation or population differentiation in dogs, including many linked to phenotypic variation. The many blocks of reduced haplotype diversity observed across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease.

Rethinking dog domestication by integrating genetics, archeology, and biogeography

The dog was the first domesticated animal but it remains uncertain when the domestication process began and whether it occurred just once or multiple times across the Northern Hemisphere. To ascertain the value of modern genetic data to elucidate the origins of dog domestication, we analyzed 49,024 autosomal SNPs in 1,375 dogs (representing 35 breeds) and 19 wolves. After combining our data with previously published data, we contrasted the genetic signatures of 121 breeds with a worldwide archeological assessment of the earliest dog remains. Correlating the earliest archeological dogs with the geographic locations of 14 so-called “ancient” breeds (defined by their genetic differentiation) resulted in a counterintuitive pattern. First, none of the ancient breeds derive from regions where the oldest archeological remains have been found. Second, three of the ancient breeds (Basenjis, Dingoes, and New Guinea Singing Dogs) come from regions outside the natural range of Canis lupus (the dog’s wild ancestor) and where dogs were introduced more than 10,000 y after domestication. These results demonstrate that the unifying characteristic among all genetically distinct so-called ancient breeds is a lack of recent admixture with other breeds likely facilitated by geographic and cultural isolation. Furthermore, these genetically distinct ancient breeds only appear so because of their relative isolation, suggesting that studies of modern breeds have yet to shed light on dog origins. We conclude by assessing the limitations of past studies and how next-generation sequencing of modern and ancient individuals may unravel the history of dog domestication.

Differentiation of tundra/taiga and boreal coniferous forest wolves: genetics, coat colour and association with migratory caribou

The grey wolf has one of the largest historic distributions of any terrestrial mammal and can disperse over great distances across imposing topographic barriers. As a result, geographical distance and physical obstacles to dispersal may not be consequential factors in the evolutionary divergence of wolf populations. However, recent studies suggest ecological features can constrain gene flow. We tested whether wolf–prey associations in uninterrupted tundra and forested regions of Canada explained differences in migratory behaviour, genetics, and coat colour of wolves. Satellite‐telemetry data demonstrated that tundra wolves (n = 19) migrate annually with caribou (n = 19) from denning areas in the tundra to wintering areas south of the treeline. In contrast, nearby boreal coniferous forest wolves are territorial and associated year round with resident prey. Spatially explicit analysis of 14 autosomal microsatellite loci (n = 404 individuals) found two genetic clusters corresponding to tundra vs. boreal coniferous forest wolves. A sex bias in gene flow was inferred based on higher levels of mtDNA divergence (FST = 0.282, 0.028 and 0.033; P < 0.0001 for mitochondrial, nuclear autosomal and Y‐chromosome markers, respectively). Phenotypic differentiation was substantial as 93% of wolves from tundra populations exhibited light colouration whereas only 38% of boreal coniferous forest wolves did (χ2 = 64.52, P < 0.0001). The sharp boundary representing this discontinuity was the southern limit of the caribou migration. These findings show that substantial genetic and phenotypic differentiation in highly mobile mammals can be caused by prey–habitat specialization rather than distance or topographic barriers. The presence of a distinct wolf ecotype in the tundra of North America highlights the need to preserve migratory populations.

Megafaunal Extinctions and the Disappearance of a Specialized Wolf Ecomorph

The gray wolf (Canis lupus) is one of the few large predators to survive the Late Pleistocene megafaunal extinctions [1]. Nevertheless, wolves disappeared from northern North America in the Late Pleistocene, suggesting they were affected by factors that eliminated other species. Using skeletal material collected from Pleistocene permafrost deposits of eastern Beringia, we present a comprehensive analysis of an extinct vertebrate by exploring genetic (mtDNA), morphologic, and isotopic (delta(13)C, delta(15)N) data to reveal the evolutionary relationships, as well as diet and feeding behavior, of ancient wolves. Remarkably, the Late Pleistocene wolves are genetically unique and morphologically distinct. None of the 16 mtDNA haplotypes recovered from a sample of 20 Pleistocene eastern-Beringian wolves was shared with any modern wolf, and instead they appear most closely related to Late Pleistocene wolves of Eurasia. Moreover, skull shape, tooth wear, and isotopic data suggest that eastern-Beringian wolves were specialized hunters and scavengers of extinct megafauna. Thus, a previously unrecognized, uniquely adapted, and genetically distinct wolf ecomorph suffered extinction in the Late Pleistocene, along with other megafauna. Consequently, the survival of the species in North America depended on the presence of more generalized forms elsewhere.

Legacy lost: genetic variability and population size of extirpated US grey wolves ( Canis lupus )

By the mid 20th century, the grey wolf (Canis lupus) was exterminated from most of the conterminous United States (cUS) and Mexico. However, because wolves disperse over long distances, extant populations in Canada and Alaska might have retained a substantial proportion of the genetic diversity once found in the cUS. We analysed mitochondrial DNA sequences of 34 pre‐extermination wolves and found that they had more than twice the diversity of their modern conspecifics, implying a historic population size of several hundred thousand wolves in the western cUS and Mexico. Further, two‐thirds of the haplotypes found in the historic sample are unique. Sequences from Mexican grey wolves (C. l. baileyi) and some historic grey wolves defined a unique southern clade supporting a much wider geographical mandate for the reintroduction of Mexican wolves than currently planned. Our results highlight the genetic consequences of population extinction within Ice Age refugia and imply that restoration goals for grey wolves in the western cUS include far less area and target vastly lower population sizes than existed historically.

Combined use of maternal, paternal and bi-parental genetic markers for the identification of wolf–dog hybrids

The identification of hybrids is often a subject of primary concern for the development of conservation and management strategies, but can be difficult when the hybridizing species are closely related and do not possess diagnostic genetic markers. However, the combined use of mitochondrial DNA (mtDNA), autosomal and Y chromosome genetic markers may allow the identification of hybrids and of the direction of hybridization. We used these three types of markers to genetically characterize one possible wolf–dog hybrid in the endangered Scandinavian wolf population. We first characterized the variability of mtDNA and Y chromosome markers in Scandinavian wolves as well as in neighboring wolf populations and in dogs. While the mtDNA data suggested that the target sample could correspond to a wolf, its Y chromosome type had not been observed before in Scandinavian wolves. We compared the genotype of the target sample at 18 autosomal microsatellite markers with those expected in pure specimens and in hybrids using assignment tests. The combined results led to the conclusion that the animal was a hybrid between a Scandinavian female wolf and a male dog. This finding confirms that inter-specific hybridization between wolves and dogs can occur in natural wolf populations. A possible correlation between hybridization and wolf population density and disturbance deserves further research.