Jason Munshi-South

AbstractUrban 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.

AbstractBrown rats (Rattus norvegicus) have commensally spread from northern China and Mongolia to become among the most invasive species on the planet. Understanding the proximate source(s) of invasion can inform biosecurity plans and eradication strategies for preventing or mitigating impacts to native biodiversity. The Haida Gwaii archipelago, located off the coast of British Columbia, Canada, is a significant nesting site for 1.5 million seabirds across 12 species, half of which are now threatened by brown rats. Local knowledge points to a European origin in the late 1800’s to early 1900’s, though the true source(s) and firm date(s) of invasion remain unknown. To fill these knowledge gaps, we analyzed genotypic data (16,598 SNPs) for 280 brown rats sampled throughout Haida Gwaii relative to a published global database of potential source populations. Principle component analysis and population assignment tests supported multiple potential invasion sources from Europe and North America. Likewise, demographic modelling best supported two invasions into the islands. The first invasion likely occurred in the early 1900’s into the south-central archipelago from Western Europe followed by a more recent invasion in the early 2000’s from Vancouver, British Columbia, into northern Haida Gwaii. The northern invasion of Haida Gwaii could also be indicative of contemporary gene flow between Haida Gwaii and the mainland, representing a significant biosecurity risk. Our results will inform management strategies for invasive rats in Haida Gwaii, and serve as a guide for studies in other isolated systems worldwide.

AbstractUrbanization 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; New York City, USA. At least 150 rats were sampled from each city and genotyped for a minimum of 15,000 genome-wide SNPs. Levels of genome-wide diversity were similar across cities, but varied across neighborhoods within cities. All four populations exhibited high spatial autocorrelation at the shortest distance classes (< 500 m) due 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.

Evidence is growing that human modification of landscapes has dramatically altered evolutionary processes. In urban population genetic studies, urbanization is typically predicted to act as a barrier that isolates populations of species, leading to increased genetic drift within populations and reduced gene flow between populations. However, urbanization may also facilitate dispersal among populations, leading to higher genetic diversity within and lower differentiation between urban populations. We reviewed the literature on non-adaptive urban evolution to evaluate the support for each of these urbanse urban fragmentation and facilitation models. In a review of the literature with supporting quantitative analyses of 167 published urban population genetics studies, we found a weak signature of reduced within-population genetic diversity, and no evidence of consistently increased between-population genetic differentiation associated with urbanization. In addition, we found that urban landscape features act as barriers or conduits to gene flow, depending on the species and city in question. Thus, we speculate that dispersal ability of species and environmental heterogeneity between cities contribute to the variation exhibited in our results. However, greater than 90% of published studies reviewed here showed an association of urbanization with genetic drift or gene flow, highlighting the strong impact of urbanization on non-adaptive evolution. It is clear that organism biology and city heterogeneity obscure patterns of genetic drift and gene flow in a quantitative analysis. Thus, we suggest that future research makes comparisons of multiple cities and nonurban habitats, and takes into consideration species’ natural history, environmental variation, spatial modelling, and marker selection.

Theory predicts that range expansion results in genetic diversity loss in colonizing populations. Rapid reduction of population size exacerbates negative effects of genetic drift, while sustained isolation decreases neutral variation. Amid this demographic change, natural selection can act to maintain functional diversity. Thus, characterizing neutral and functional variation is critical for disentangling the evolutionary forces that shape genetic variation in newly established populations. Coyotes (Canis latrans) provide an ideal study system for examining the genetic effects of urban colonization. Capable of thriving in environments ranging from natural to highly urbanized, this mobile carnivore recently established a breeding population in New York City (NYC), one of the most densely populated areas in the United States. In the present study, we characterized neutral and functionally linked genetic diversity on a regional scale, traversing NYC and its surrounding counties in the New York metropolitan area. We report decreased variation and significant genotypic differentiation in NYC coyotes following recent colonization of this super-urban environment. In accordance with our hypotheses, we observed evidence for a recent population bottleneck as coyotes entered NYC. Counter to our expectations, we found only minimal support for selection maintaining diversity at immune-linked loci. These findings suggest that stochastic processes, such as genetic drift, are more likely driving patterns of decreased variation in super-urban coyotes. This work not only improves our understanding of NYC’s newest inhabitants, but also contributes to the growing body of knowledge surrounding urban colonization ecology. It highlights the importance of examining both neutral and functional variation when assessing the roles of drift and selection in newly established populations. When combined with similar studies across diverse systems, these insights can aid wildlife management and green design to better facilitate gene flow and maintain healthy populations of wildlife in an increasingly urban world.

The lower Congo River (LCR) is a freshwater biodiversity hotspot in Africa characterized by some of the world's largest rapids. However, little is known about the evolutionary forces shaping this diversity, which include numerous endemic fishes. We investigated phylogeographic relationships in Teleogramma, a small clade of rheophilic cichlids, in the context of regional geography and hydrology. Previous studies have been unable to resolve phylogenetic relationships within Teleogramma due to lack of variation in nuclear genes and discrete morphological characters among putative species. To sample more broadly across the genome we analyzed double-digest restriction-associated sequencing (ddRAD) data from 53 individuals across all described species in the genus. We also assessed body shape and mitochondrial variation within and between taxa. Phylogenetic analyses reveal previously unrecognized lineages and instances of microallopatric divergence across as little as ~1.5 km. Species ranges appear to correspond to geographic regions broadly separated by major hydrological and topographic barriers, indicating these features are likely important drivers of diversification. Mitonuclear discordance indicates one or more introgressive hybridization events, but no clear evidence of admixture is present in nuclear genomes, suggesting these events were likely ancient. A survey of female fin patterns hints that previously undetected lineage-specific patterning may be acting to reinforce species cohesion. These analyses highlight the importance of hydrological complexity in generating diversity in certain freshwater systems, as well as the utility of ddRAD-Seq data in understanding diversification processes operating both below and above the species level.

Nexus file of 37 unique haplotypes identified from 324 bp of mitochondrial D-loop sequence from urban white-footed mice (Peromyscus leucopus). Partial D-loop sequence was obtained for 110 white-footed mice (Peromyscus leucopus) from 14 urban parks in New York City. The Nexus file also identifies the number of individuals with the same haplotype sequence. This file can be used in DnaSP or other software to recreate the mismatch distribution analyses, calculation of basic mtDNA diversity statistics, and tests of neutrality (Fu's Fs, Tajima's D) presented in the associated publication.