Dogs’ genomes carry a detailed record of how humans reshaped a wolf into a companion animal, and this project will read that record by sequencing hundreds of dog and wolf genomes, including DNA from ancient bones. The research tackles three unsolved questions. First, no one knows exactly which genetic changes separate all dogs from all wolves. Second, dogs and humans independently evolved extra copies of the starch-digesting amylase gene after agriculture began, but the structure and timing of that expansion remain unclear. Third, Madagascar’s human population is a roughly equal mix of Southeast Asian and East African ancestry, yet no one has asked whether the island’s dogs show a similar dual heritage. Because this is fundamental science, it has no immediate practical application. But understanding how a species adapts to a human-dominated world—from diet to behaviour to disease resistance—can eventually inform breeding for health, reveal how genomes respond to rapid environmental change, and clarify the evolutionary rules that shape any species under strong artificial selection. Past work on dog genomics has already pinpointed genes behind skeletal disorders and cancer risk in purebreds; this project extends that logic to the deeper, pre-breed history of domestication itself.
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The dog was the first species to be domesticated by humans, and is the only animal that evolved alongside us through the major lifestyle changes of the last ~10,000 years, including the rise of agriculture. This project will use whole-genome sequencing technologies to ask: how have humans changed the genomes of dogs? 1. What makes a dog a dog? We still don't understand what the fundamental genetic changes that make dogs different from wolves are. The project will develop new approaches to tackle this question using the many whole genomes, including ancient ones, from dogs and wolves that are now available. 2. What is the structure and evolution of the dog amylase locus? Copy number expansions of amylase genes, involved in starch digestion, represent a remarkable example of convergent evolution between humans and dogs. The project will use recently published, high-quality long-read assemblies to dissect the structure and evolutionary history of this locus. 3. Does the genomic history of dogs on Madagascar mirror humans? Humans on Madagascar trace their genetic ancestry to Southeast Asia and south eastern Africa in about equal proportions. The project will sequence Madagascan dog genomes and compare their genetic history and diversity to that of humans. The student will receive broad training in genomics, bioinformatics, programming, population genetic theory and analyses of genetic ancestry and natural selection. This will also include training in human genomics, to perform cross-species comparisons between humans and dogs. The student will take part in journal clubs and departmental seminars, present their work at conferences and develop skills in critical thinking and science communication. The ideal candidate will have a background in a biological science (e.g. genetics, molecular biology, zoology, evolution) or a quantitative science (e.g. computer science, statistics, physics), and have strong interests in genomics, evolution and data analysis.
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