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

Abstract

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.

Human Population Density Influences Genetic Diversity of Two Rattus Species Worldwide: A Macrogenetic Approach

“…The history of Rattus colonization in the world is the history of human migrations; consequently, the origin of commensalism in these rodents inevitably reflects the history of human settlement and associated anthropogenic factors. Although further studies are needed, the more recent dispersal of R. norvegicus from its center of origin in Siberia to Europe in the 16th century [40] may be one of the reasons for the lower average value of genetic diversity found in our metadata, compared to the dispersal of R. rattus, which is linked to the beginning of Indian civilization (approximately 5000 years BC) and subsequent dispersal dynamics, mainly by maritime routes [35]. Other evidence supporting this behavior of a higher average value of genetic diversity in R. rattus than in R. norvegicus was found in two studies with a comparative phylogeography approach to that reported in our study.…”

“…rattus and R. norvegicus are arguably the most successful invasive species on the planet, and human migrations have had a major influence on the spread and dispersal of invasive species populations within and between urban areas through processes such as genetic drift and gene flow [33,34]. Human movements and transportation networks can facilitate the dispersal of rats across urban environments, which can increase gene flow between populations and impact the genetic diversity of populations at different scales [31,[35][36][37]. For example, while [19], using SNPs, found divergent genomic signals in R. norvegicus in New York City at a scale of less than 600 m between colonies, Ref.…”

“…Although we identified several studies in regions other than developed countries and with tropical or subtropical distribution, e.g., Nigeria [31], Benin [42], Senegal [36], Gabon [30]; Brazil [6,21], India [35,43], Madagascar [29] and Ecuador [44], further sampling and genetic diversity analysis efforts are needed in the regions of Asia, Africa and Central and South America, given the specific projections of population expansion expected in the near future in these areas and to the socioeconomic, political, climatic and urban development characteristics, which may be very different from those of temperate zones, where the largest number of studies on landscape genetics of invasive rodent species to date have been carried out.…”

“…The following supporting information can be downloaded at: https: //www.mdpi.com/article/10.3390/genes14071442/s1, Table S1: Systematic review-final studies included [6,[19][20][21][28][29][30][31][35][36][37][38][39][41][42][43][44][48][49][50][51][52][53][54][55][56][57][58][59][60][61][62][63][64][65].…”