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.

Note that in merging the NYC and 9 of the Chinese samples of Deinum et al. 2015, we have used the option --missing-to-ref in the vcf-merge command of vcftools.  Therefore, sites that were polymorphic in one sample but either monomorphic or of low quality in the other sample were imputed as the reference allele of the Rn5 reference.

The file nyc_and_china_ref_for_missing_fixedploidy.vcf.gz is in Variant Calling Format (VCF) in its zipped form. To unzip the file, use the bgzip command from the Samtools software package.  The file nyc_and_china_ref_for_missing_fixedploidy.vcf.gz.tbi is the corresponding tabix index file.