Wolves and dogs are giving up their genetic secrets from 100,000 years of fossils, as researchers sequence ancient genomes to watch evolution happen in real time. Ancient DNA has transformed understanding of human history, but its power to reveal how evolution works across long timescales remains largely untapped. This project turns the grey wolf and its domesticated descendant, the dog, into a model system for evolutionary genomics. With a fossil record spanning 30,000 generations—far deeper than human remains allow—the team will track genetic changes across three phases: Ice Age wolf evolution over 100,000 years, the precise origins of dog domestication from two wolf ancestors, and how dogs adapted alongside human societies over the past 10,000 years. This is fundamental science with no immediate practical application. It asks how natural selection operates across millennia—whether evolution proceeds through single mutations sweeping through populations, or through more complex processes. The work could eventually inform understanding of zoonotic disease transmission by identifying ancient pathogen DNA preserved in dog remains. More broadly, it establishes a new temporal view of genome evolution, directly observed rather than inferred from modern DNA alone. Similar fundamental paleogenomic research has already reshaped medicine, conservation biology, and our understanding of inherited disease risk.
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Ancient genomics has provided abundant information about human genetic history, but has not fulfilled its promise to provide insights into a wider range of evolutionary processes. I propose to develop the dog and its wild ancestor the grey wolf as a model system for evolutionary genomics, leveraging a fossil record of 30,000 generations readily accessible with ancient DNA together with emerging functional genomic information. Canine evolution comprises multiple key evolutionary phenomena, and this project will specifically reconstruct evolution in three phases: 1) Ice age wolf evolution. How do evolutionary genomic processes appear with temporal genome transects over 100,000 years? How important are single mutations and single sweeps in evolution? How did wolves evolve during dynamic climate changes? We will establish grey wolves as the primary model system of evolutionary paleogenomics over the last Ice Age, reconstructing its genetic history, documenting the prevalence of selective sweeps, and specific loci targeted by natural selection. 2) Early dog domestication. When, where, and how did dogs originate? We have shown that dogs have two wolf ancestors, but the exact origins remain unknown. This project will locate the human societies where the canine-human bond formed, and reconstruct selection during the domestication process to understand the underpinnings of phenotypic differences between dogs and wolves. 3) Holocene dog. How did dogs evolve and adapt to changing human societies? We will reconstruct the genetic history of dogs, and ask how linked it was to that of humans. Using ancient genomes, we will infer which parts of the dog genome were targeted by natural selection in the past 10,000 years. Finally, the project will search for ancient pathogen DNA, which could shed new light on zoonotic transmission processes. Together, the project will provide a new temporal view of genome evolution, traced directly across 100,000 years.
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