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

Abstract

On a planet experiencing constant human population growth, it is necessary to explore the anthropogenic effects on the genetic diversity of species, and specifically invasive species. Using an analysis that integrates comparative phylogeography, urban landscape genetics, macrogenetics and a systematic review, we explore the worldwide genetic diversity of the human commensal and anthropogenic species Rattus rattus and Rattus norvegicus. Based on metadata obtained considering 35 selected studies related to observed heterozygosity, measured by nuclear molecular markers (microsatellites, Single Nucleotide Polymorphisms-SNPs-, restrictition site-associated DNA sequencing -RAD-Seq-), socioeconomic and mobility anthropogenic factors were used as predictors of genetic diversity of R. rattus and R. norvegicus, using the Gini index, principal component analysis and Random Forest Regression as analysis methodology. Population density was on average the best predictor of genetic diversity in the Rattus species analyzed, indicating that the species respond in a particular way to the characteristics present in urban environments because of a combination of life history characteristics and human-mediated migration and colonization processes. To create better management and control strategies for these rodents and their associated diseases, it is necessary to fill the existing information gap in urban landscape genetics studies with more metadata repositories, with emphasis on tropical and subtropical regions of the world.

Keywords: comparative phylogeography; invasive species; metadata; systematic review; urban landscape genetics.

Figure 1

PRISMA flow diagram of literature search and selection for articles included in the systematic review. The asterisk (*) was used to extend the Boolean search to include various word forms and endings (e.g., “phylogeography”, “phylogeographical”). Adapted from [18].

Figure 2

Map with the distribution of sampling points used in the 35 studies considered. Red dots: 141 records of Rattus rattus; blue dots: 234 records of R. norvegicus. Background: the deprivation index displayed as poverty proxy.

Figure 3

Map with the distribution of observed heterozygosity for Rattus rattus, considering the information of 35 studies analyzed. Blue dots: Sampling areas considered.

Figure 4

Map with the distribution of observed heterozygosity for Rattus norvegicus, considering the information of 35 studies analyzed. Blue dots: Sampling areas considered.

Figure 5

Random forest regression between observed vs. predicted heterozygosity values including regression lines, R² and p values per species. R. norvegicus (blue); R. rattus (red).

Figure 6

Principal component analysis of predictors of genetic diversity for R. rattus and R. norvegicus, considering the information of 35 studies analyzed. R. norvegicus island records (light blue). R. norvegicus mainland records (blue). R. rattus island records (red). R. rattus mainland records (light brown). The acronyms of the predictors are as described in Table 1.