Brown rats (Rattus norvegicus) thrive in urban environments by navigating the anthro-12 pocentric environment and taking advantage of human resources and by-products. From 13 the human perspective, rats are a chronic problem that causes billions of dollars in damage 14 to agriculture, health and infrastructure. Did genetic adaptation play a role in the spread 15 of rats in cities? To approach this question, we collected whole-genome samples from 29 16 brown rats from New York City (NYC) and scanned for genetic signatures of adaptation. 17 We applied multiple methods, testing for (i) high-frequency, extended haplotypes that could 18 indicate selective sweeps and (ii) loci of extreme genetic divergence between the NYC sample 19 and a sample from the presumed ancestral range of brown rats in rural north east China. We 20 found candidate selective sweeps near or inside genes associated with metabolism, diet, organ 21 morphogenesis and locomotory behavior. The divergence between NYC and rural Chinese 22 rats at putative sweep loci suggests that many sweeps began after the split from the ancestral 23 population. Together, our results suggest several hypotheses for a genetic component behind 24 the adaptation of rats in response to human activity. 25 2 Background 26Urbanization has dramatic ecological and evolutionary consequences for wildlife [1, 2]. The 27 most commonly examined evolutionary responses to urbanization are changes in gene flow 28 and in the intensity of genetic drift [3, 4, 5, 6]. A small but growing number of stud-29 ies have also examined adaptive evolution in urban environments, including morphological 30 adaptations to urban infrastructure [7, 8], adaptive life history changes, thermal tolerance 31 to warming cities [9, 10], and behavioral changes [11]. The recent adoption of genomic scans 32 to identify loci under positive selection is a promising avenue for the discovery of adaptive 33 phenotypes in cities [12, 13].
34Commensal rodents-particularly house mice (Mus musculus), black rats (Rattus rattus), 35 and brown rats (Rattus norvegicus) are the most widespread urban mammals besides humans 36 and a notorious threat to urban quality of life [14, 15]. Recent analyses have revealed some 37 of the relationships between invasive urban rodent populations that spread around the world 38 with humans [16, 17, 18, 19] and the influence of heterogeneous urban environments on 39 gene flow [20, 21]. Much less is known about the role of natural selection in the success of 40 commensal rodents in cities.
41Brown rats have considerably less genetic diversity compared to house mice, possibly due 42 to a population bottleneck ∼20,000 years ago [22]. Taken at face value, this may suggest 43 a relatively small role for selection in their evolution compared to genetic drift. However, 44 brown rats have experienced major range expansions more recently, presumably due to their 45 association with agrarian, and later urban, human societies [19]. It is likely that selection 46 influenced a number of trai...