Population Genetics
Byers KA, Booker TR, Combs M, Himsworth CG, Munshi-South J, Patrick DM, Whitlock MC. 2020. Evolutionary Applications 14: 198-209.
Urban Norway rats (Rattus norvegicus) carry several pathogens transmissible to people. However, pathogen prevalence can vary across fine spatial scales (i.e., by city block). Using a population genomics approach, we sought to describe rat movement patterns across an urban landscape and to evaluate whether these patterns align with pathogen distributions. We genotyped 605 rats from a single neighborhood in Vancouver, Canada, and used 1,495 genome‐wide single nucleotide polymorphisms to identify parent–offspring and sibling relationships using pedigree analysis. We resolved 1,246 pairs of relatives, of which only 1% of pairs were captured in different city blocks. Relatives were primarily caught within 33 meters of each other leading to a highly leptokurtic distribution of dispersal distances. Using binomial generalized linear mixed models, we evaluated whether family relationships influenced rat pathogen status with the bacterial pathogens Leptospira interrogans, Bartonella tribocorum, and Clostridium difficile, and found that an individual's pathogen status was not predicted any better by including disease status of related rats. The spatial clustering of related rats and their pathogens lends support to the hypothesis that spatially restricted movement promotes the heterogeneous patterns of pathogen prevalence evidenced in this population. Our findings also highlight the utility of evolutionary tools to understand movement and rat‐associated health risks in urban landscapes.
Harnessing Population Genetics for Pest Management: Theory and Application for Urban Rats
Combs M, Byers K, Himsworth C, Munshi-South J. 2019. Human-Wildlife Interactions 13(2): 250-263.
Effective management of rodent pests requires an ecological understanding of how they move through their environment, and how those movements influence the invasion, persistence, or reinvasion of problematic colonies. Traditional methodologies used to describe rodent movement patterns, such as mark-recapture, are hindered by their time-consuming nature and limited geographic scope. As such, our understanding of how rodents interact with urban environments remains limited. Population genetic principles and tools have the capacity to greatly increase our understanding of rodent population dynamics, ecological relationships, and movements across space but this field is often unapproachable to non-scientist pest management professionals. In this paper we aim to promote collaborative and integrative rodent pest management by introducing relevant population genetic principles, providing examples of their applications in studies of urban brown rats, and proposing future initiatives that link scientific, private, and government entities. Using a densely-sampled brown rat population in the city of Vancouver, BC we show how genetic relationships among individual brown rats can be leveraged to understand the geographic distribution of genetic clusters (i.e., colonies), natural barriers to migration, and the spatial scale of dispersal. We describe how these results can be exploited by PMPs to directly inform the creation of management units and decrease the likelihood of rapid post-treatment reinvasion. Further, we discuss the difficulties inherent in population genetic studies and the potential for high-quality model sites to develop generalizable strategies. Overall, we hope to expand the toolbox of pest management professionals, foster collaboration, and move towards more informed and sustainable management strategies.
Combs M, Byers KA, Ghersi BM, Blum MJ, Caccone A, Costa F, Himsworth CG, Richardson JL, Munshi-South J. 2018. Proceedings of the Royal Society B Biological Sciences 285: 20180245.
Urbanization often substantially influences animal movement and gene flow. However, few studies to date have examined gene flow of the same species across multiple cities. In this study, we examine brown rats (Rattus norvegicus) to test hypotheses about the repeatability of neutral evolution across four cities: Salvador, Brazil; New Orleans, USA; Vancouver, Canada; and New York City, USA. At least 150 rats were sampled from each city and genotyped for a minimum of 15 000 genome-wide single nucleotide polymorphisms. Levels of genome-wide diversity were similar across cities, but varied across neighbourhoods within cities. All four populations exhibited high spatial autocorrelation at the shortest distance classes (less than 500 m) owing to limited dispersal. Coancestry and evolutionary clustering analyses identified genetic discontinuities within each city that coincided with a resource desert in New York City, major waterways in New Orleans, and roads in Salvador and Vancouver. Such replicated studies are crucial to assessing the generality of predictions from urban evolution, and have practical applications for pest management and public health. Future studies should include a range of global cities in different biomes, incorporate multiple species, and examine the impact of specific characteristics of the built environment and human socioeconomics on gene flow.
Global population divergence and admixture of the brown rat (Rattus norvegicus).
Puckett EE, Park J, Combs M, Blum MJ, Bryant JE, Caccone A, Costa F, Deinum E, Esther A, Himsworth CG, Keightley PD, Ko A, Lundkvist A, McElhinney LM, Morand S, Robbins J, Russell J, Strand TM, Suarez O, Yon L, Munshi-South J. 2016. Proceedings of the Royal Society B 283: 20161762.
Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade. We inferred the global phylogeography of brown rats using 32 k SNPs, and detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia. Three additional clusters arose from two independent eastward expansions: one expansion from Russia to the Aleutian Archipelago, and a second to western North America. Westward expansion resulted in the colonization of Europe from which subsequent rapid colonization of Africa, the Americas and Australasia occurred, and multiple evolutionary clusters were detected. An astonishing degree of fine-grained clustering between and within sampling sites underscored the extent to which urban heterogeneity shaped genetic structure of commensal rodents. Surprisingly, few individuals were recent migrants, suggesting that recruitment into established populations is limited. Understanding the global population structure of R. norvegicus offers novel perspectives on the forces driving the spread of zoonotic disease, and aids in development of rat eradication programmes.
