Genomic Analysis Reveals Subdivision of Black Rats (Rattus rattus) in India, Origin of the Worldwide Species Spread

• Published in: Genes
• Main Authors: Mumtaz Baig, Sameera Farah, Ashwin Atkulwar, Jeremy B. Searle
• Format: Text
• Language: English
• Published: Multidisciplinary Digital Publishing Institute 2022
• Subjects: commensalism; Indian subcontinent; Indus civilization; invasive; population genomics; Indian; Rattus rattus
• Online Access: https://doi.org/10.3390/genes13020267

In contrast to the detailed and globally extensive studies on the spread of the commensal black rat, Rattus rattus, there has been relatively little work on the phylogeography of the species within India, from where this spread originated. Taking a genomic approach, we typed 27 R. rattus samples from Peninsular India using the genotyping-by-sequencing (GBS) method. Filtering and alignment of the FASTQ files yielded 1499 genome-wide SNPs. Phylogenomic tree reconstruction revealed a distinct subdivision in the R. rattus population, manifested as two clusters corresponding to the east and west coasts of India. We also identified signals of admixture between these two subpopulations, separated by an Fst of 0.20. This striking genomic difference between the east and west coast populations mirrors what has previously been described with mitochondrial DNA sequencing. It is notable that the west coast population of R. rattus has been spread globally, reflecting the origins of commensalism of the species in Western India and the subsequent transport by humans worldwide.