Genetic Adaptation in New York City Rats

Brown rats (Rattus norvegicus) thrive in urban environments by navigating
the anthropocentric environment and taking advantage of human resources
and by-products.  From the human perspective, rats are a chronic
problem that causes billions of dollars in damage to agriculture, health
and infrastructure.  Did genetic adaptation play a role in the
spread of rats in cities?  To approach this question, we
collected whole-genome sequences from 29 brown rats from New York City
(NYC) and scanned for genetic signatures of adaptation.  We
tested for (i) high-frequency, extended haplotypes that could indicate
selective sweeps and (ii) loci of extreme genetic differentiation between
the NYC sample and a sample from the presumed ancestral range of brown
rats in northeast China.  We found candidate selective sweeps
near or inside genes associated with metabolism, diet, the nervous system
and locomotory behavior.  Patterns of differentiation between NYC
and Chinese rats at putative sweep loci suggests that many sweeps began
after the split from the ancestral population. Together, our results
suggest several hypotheses on adaptation in rats living in close proximity
to humans.