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The history of wolves, and their contribution to adaptation and phenotypic diversity in dogs

Periodic Reporting for period 1 - WhereWolf (The history of wolves, and their contribution to adaptation and phenotypic diversity in dogs)

Reporting period: 2016-09-01 to 2018-08-31

The gray wolf has been on the rebound in Europe and its re-emergence in northern Europe, including Denmark, demands that we better understand the species, to aid application of well informed conservation and management policies to these populations. In order to better understand the European wolves, we need to examine them in the context of wolves of the world, and further, other canids that they interact with. This action proposed to study the worldwide diversity of wolves, and examine their evolutionary relationships with related canids such as coyotes, red wolves, African golden wolves, golden jackals, Ethiopian wolves, dholes and African hunting dogs.
The main objectives of the project can be summarized into 3 major parts - 1. finding out the relationship between wolves from different parts of the world and their relationships to other canids, 2. figuring out if gene flow or mixing between the different canids has played a major role in their evolution, and finally 3. using modern and ancient genomes to understand when and where modern dogs were domesticated.
Understanding these relationships will allow us to implement appropriate and sensible conservation and management policies to the resurging wolf populations in Europe. As an outcome of this action, we have estimated the extent of gene flow among the different species of canids. Specifically, we find that gene flow is a major contributor to the evolutionary patterns that we see in these canids. This adds to an increasing body of evidence where gene flow is a common occurrence in natural populations, and is proposed to be a major driver of evolution. We find that multiple waves of mixing have affected the wolf population, both in Eurasia and North America. Finally, in possibly the most exciting finding, we hypothesise that the African golden wolf is a hybrid species, deriving ancestry from the Eurasian gray wolf and the Ethiopian wolf.
This project involved sequencing and analysing more than 100 canid genomes, including both modern samples, historical samples spanning the last 200 years and ancient samples, ranging from 15000 to 50000 years before present. An amalgamation of these data allowed us to answer elementary questions, such as how the various wolves in the world are related to each other, and how these wolves are related to other species in the genus.
To answer these questions, we constructed a phylogeny using randomly chosen regions of the genome, including man wolf populations, dog breeds, African, North American and Eurasian canids, such as dholes, golden jackals, and Ethiopian wolves. Since the phylogeny (relationships) between these canids are affected by gene flow/admixture between these canids, the amount of uncertainly in the phylogeny was summarized using methods used to examine the frequencies of various gene trees. Our investigations show that the gray wolves have been mixing with other canids, such as dogs, coyotes and golden jackals depending on the local canids that inhabit the same environment as the gray wolves. Specifically, the gray wolves from the Middle East have a substantial amount of mixing with golden jackals, and North American wolves share significant amounts of ancestry with coyotes. In terms of genetic contributions of the gray wolves to other canids, we hypothesize, based on the measures of genetic similarity, that the African golden wolf is a hybrid species, with genetic contributions from Eurasian gray wolves and Ethiopian wolves. Additionally, in terms admixture among other canid groups, we found evidence of gene flow from a as yet unknown canid into the ancestors of wolves and coyotes.
In North American wolves, we performed a study using 15 newly sequenced North American wolves and coyotes. We investigated the population structure among the different populations of North American wolves, and further estimated the amount of coyote admixture to the different wolf populations. Our results showed that the Polar wolf (which inhabits Greenland) is closely related to the Arctic wolves (inhabiting Ellesmere and Baffin Islands), and the Arctic/Polar wolf is a distinct population of North American wolves. We also find that extensive gene flow between coyotes and gray wolves wherever their ranges overlap. The taxonomically controversial red wolves and eastern timber wolves appear to be of hybrid origin, with varying combinations of gray wolves and coyotes.
To supplement the information obtained from the modern genomes, we sequenced 5 individuals of Pleistocene wolves, a wolf type that went extinct more than 10000 years ago. We also sequenced a single samples of a dog dating back to 10000 years ago - this dog, at the time of this report, is the oldest known dog to be whole genome sequenced. Based on the placement and shared genetic affinity between the ancient dog and the sled dogs, we surmised that the sled dogs form a basal lineage of dogs, which diverged from other dog lineages at least 10000 years ago. Further, the sled dogs have some genetic material from the Pleistocene wolves, and show signatures of selection related to adaptation to the arctic environment.
Our results have highlighted the role of gene flow in the evolution of canids. In particular, we have shown that the African golden wolf is potentially a hybrid species arising out of mixing between Eurasian gray wolves and Ehtiopian wolves. In terms of impacting future research, we have assembled a de novo wolf reference genome as part of this project, so that all future studies in canids can be performed without bias due to choice of reference genome. In addition to the reference genome, we have published the data from all our studies, which include the sequencing data from a large number of wolves and wolf-like canids. The availability of these resources should impact future studies of these charismatic group of animal significantly.
The improved understanding of the relationships and gene flow between these different canids will allow us to implement a knowledge-based conservation and management strategy for wolves in Europe and the rest of the world.
Summary of estimated mixture events among the canids of the genus Canis