Genomic adaptation in domestic dogs

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.