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Phylogeography and zooarchaeology are largely separate disciplines, yet each interrogates relationships between humans and commensal species. Knowledge gained about human history from studies of four commensal rats (Rattus rattus, R. tanezumi, R. exulans, and R. norvegicus) is outlined, and open questions about their spread alongside humans are identified. Limitations of phylogeographic and zooarchaeological studies are highlighted, then how integration would increase understanding of species’ demographic histories and resultant inferences about human societies is discussed. How rat expansions have informed the understanding of human migration, urban settlements, trade networks, and intra- and interspecific competition is reviewed. Since each rat species is associated with different human societies, they identify unique ecological and historical/cultural conditions that influenced their expansion. Finally, priority research areas including nuclear genome based phylogeographies are identified using archaeological evidence to understand R. norvegicus expansion across China, multi-wave colonization of R. rattus across Europe, and competition between R. rattus and R. norvegicus.

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 (PMPs). In this commentary, 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 (Rattus norvegicus), and proposing future initiatives that link scientific, private, and government entities. We reinterpret results from a 2018 study of brown rats in Vancouver, British Columbia, Canada to show how genetic relationships among individual brown rats can be used to understand the geographic distribution of genetic clusters (i.e., colonies), natural barriers to migration, and the spatial scale of dispersal. While the 2018 study originally aimed to describe patterns of population genetic structure to understand the influence of urban landscapes on rats, here 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 PMPs, foster collaboration, and move toward more informed and sustainable management strategies.

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.

Supplemental Methods, Supplemental Figures S1-S13

This PowerPoint contains simple slides that I put together for a GSAS Futures workshop on CVs in the sciences. The workshop was held on 24 February 2015 at the Rose Hill campus. Note that the information applies only to CVs for applying to academic jobs. The presentation also included handouts of 3 exemplary CVs from recent hires or postdocs on the job market. We also looked at their associated websites, as well as online bios on Google Scholar and ORCID.

Slides from Ignite talk presented at ESA 2013 on 07 August 2013 in Minneapolis, MN in IGN 9: Urban Ecology - from Biophysics to Society ABSTRACT: Cities are comprised of “gray” and “green” spaces that may harbor non-overlapping species assemblages. This habitat partitioning occurs on microgeographic scales (e.g. opposite sides of a street), resulting in the spatial distribution of green species resembling a photographic negative of the gray species. The spatial genetic structure of gray and green populations should thus reflect contrasting landscape features (e.g. infrastructure / human socioeconomic variables vs. vegetation cover). Selection pressures will also differ between these habitat classes. I discuss the utility of this concept for explaining community structure and population genetics of rodents and invertebrates in NYC.

Slides from presentation at American Society of Mammalogists' 2013 conference in Philadelphia, PA on 15 June 2013: Thematic Session on Recent Advances in Mammalogy ABSTRACT Over 50% of humans now live in cities, and urbanization is 1 of the most important drivers of land transformationaround the world. Increasingly, humans are also a selective force driving rapid evolutionary change in other species. This presentation describes ongoing efforts to develop Peromyscus (white-footed mice) in New York City as a model for examining the evolutionary implications of urbanization. Our lab integrates complementary approaches fromlandscape ecology, urban ecology, and population genomics. Most recently, we have been using a landscape genomics approach to examine how urbanization structures both neutral and adaptive genetic variation. We have generated high-density, genome-wide SNP (single nucleotide polymorphism) genotypes using RAD-Seq from over 200 mice sampled from 25 populations along an urban-to-rural gradient spanning New York City to rural Connecticut.We are using outlier analyses to identify candidate genomic regions experiencing selection, and spatial approaches to identify SNPs exhibiting a strong frequency threshold along an urban-to-rural gradient. We are also examining environmental correlations between SNP frequencies and variables related to urbanization. Preliminary results indicate that spatial models based on relatively few high-contrast landscape variables (e.g., vegetation versus impervious urban surfaces) explain connectivity between urban-suburban-rural populations. Genomic regions containing coding sequences involved in metabolism, immunity, and reproduction exhibit statistical signatures ofselection in isolated urban populations of white-footed mice. Ongoing work examines variation in gene expression and environment-genotype correlations in urban versus rural populations.

As urbanization leads to repeated, marked environmental gradients in space, it provides an ideal ‘natural’ experiment to study how evolving metacommunities, in which evolutionary and community ecological processes interact in a landscape context, respond to anthropogenic disturbances. An integrated approach that combines community data with data on genetic responses of focal taxa to urbanization is still lacking, notwithstanding the likely importance of eco-evolutionary feedbacks on urban ecosystem functions and services. Such a joint analysis is most easily achieved by focusing on shifts in trait values and their interspecific (cf. community ecology) and intraspecific components. The latter involves both non-genetic and genetic responses, and should be quantified for all dominant, abundant, or ecologically important species in the (meta)community. This chapter introduces the evolving metacommunity framework and discusses the use of cities to study how this framework can contribute to our insight into population and community responses to anthropogenic change. It discusses how this framework can enhance our capacity to predict responses to contemporary and future urbanization as well as its possible consequences for ecosystem functioning. It predicts that evolutionary trait change contributes substantially to observed trait shifts at the community level. Conversely, genetic adaptation might often be constrained by rapid changes in species composition. It explores eco-evolutionary partitioning metrics that quantify the evolutionary and ecological contributions to responses to urbanization. Finally, it provides guidelines for experimental studies on urban evolving metacommunities, and suggests directions on research that will build towards a fully integrated evolving metacommunity framework addressing biological responses to urbanization.