In this study, I examine the influence of urban canopy cover on gene flow between 15 white‐footed mouse (Peromyscus leucopus) populations in New York City parklands. Parks in the urban core are often ...highly fragmented, leading to rapid genetic differentiation of relatively nonvagile species. However, a diverse array of ‘green’ spaces may provide dispersal corridors through ‘grey’ urban infrastructure. I identify urban landscape features that promote genetic connectivity in an urban environment and compare the success of two different landscape connectivity approaches at explaining gene flow. Gene flow was associated with ‘effective distances’ between populations that were calculated based on per cent tree canopy cover using two different approaches: (i) isolation by effective distance (IED) that calculates the single best pathway to minimize passage through high‐resistance (i.e. low canopy cover) areas, and (ii) isolation by resistance (IBR), an implementation of circuit theory that identifies all low‐resistance paths through the landscape. IBR, but not IED, models were significantly associated with three measures of gene flow (Nm from FST, BayesAss+ and Migrate‐n) after factoring out the influence of isolation by distance using partial Mantel tests. Predicted corridors for gene flow between city parks were largely narrow, linear parklands or vegetated spaces that are not managed for wildlife, such as cemeteries and roadway medians. These results have implications for understanding the impacts of urbanization trends on native wildlife, as well as for urban reforestation efforts that aim to improve urban ecosystem processes.
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Urbanization may restrict, facilitate, or have no effect on gene flow, depending on the organism and extent of urbanization. In human commensals, with high dispersal ability, urbanization can ...facilitate gene flow by providing continuous suitable habitat across a wide range. Additionally, suburban or rural areas with lower human population density may act as a barrier to gene flow for these human commensals. Spatial population genetic approaches provide a means to understand genetic connectivity across geographically expansive areas that encompass multiple metropolitan areas. Here, we examined the spatial genetic patterns of feral pigeons (Columba livia) living in cities in the eastern United States. We focused our sampling on the Northeastern megacity, which is a region covering six large cities (Boston, Providence, New York City, Philadelphia, Baltimore, and Washington, DC). We performed ddRAD‐Seqon 473 samples, recovered 35,200 SNPs, and then used multiple evolutionary clustering analyses to investigate population structuring. These analyses revealed that pigeons formed two genetic clusters—a northern cluster containing samples from Boston and Providence and a southern cluster containing all other samples. This substructuring is possibly due to reduced urbanization across coastal Connecticut that separates Boston and Providence from New York and mid‐Atlantic cities. We found that pairs of pigeons within 25 km are highly related (Mantel r = 0.217, p = .001) and that beyond 50 km, pigeons are no more related than they would be at random. Our analysis detected higher‐than‐expected gene flow under an isolation by distance model within each city. We conclude that the extreme urbanization characteristic of the Northeastern megacity is likely facilitating gene flow in feral pigeons.
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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.
By combining phylogeography and zooarchaeology, the spatial distribution and temporal dynamics of within species lineages can be reconstructed. Both approaches should be used with four rat species (black, Asian house, Pacific, and brown) to understand the minimum dates of commensalism, urbanization dynamics, and connections among human societies.
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Gene flow and genetic drift in urban environments Miles, Lindsay S.; Rivkin, L. Ruth; Johnson, Marc T. J. ...
Molecular ecology,
September 2019, 2019-09-00, 20190901, Volume:
28, Issue:
18
Journal Article
Peer reviewed
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 nonadaptive urban evolution to evaluate the support for each of these 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 contributes to the variation exhibited in our results. However, >90% of published studies reviewed here showed an association of urbanization with genetic drift or gene flow, highlighting the strong impact of urbanization on nonadaptive evolution. It is clear that species 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.
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Our planet is an increasingly urbanized landscape, with over half of the human population residing in cities. Despite advances in urban ecology, we do not adequately understand how urbanization ...affects the evolution of organisms, nor how this evolution may affect ecosystems and human health. Here, we review evidence for the effects of urbanization on the evolution of microbes, plants, and animals that inhabit cities. Urbanization affects adaptive and nonadaptive evolutionary processes that shape the genetic diversity within and between populations. Rapid adaptation has facilitated the success of some native species in urban areas, but it has also allowed human pests and disease to spread more rapidly. The nascent field of urban evolution brings together efforts to understand evolution in response to environmental change while developing new hypotheses concerning adaptation to urban infrastructure and human socioeconomic activity. The next generation of research on urban evolution will provide critical insight into the importance of evolution for sustainable interactions between humans and our city environments.
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BFBNIB, NMLJ, NUK, ODKLJ, PNG, SAZU, UL, UM, UPUK
Urbanization significantly alters natural ecosystems and has accelerated globally. Urban wildlife populations are often highly fragmented by human infrastructure, and isolated populations may adapt ...in response to local urban pressures. However, relatively few studies have identified genomic signatures of adaptation in urban animals. We used a landscape genomic approach to examine signatures of selection in urban populations of white‐footed mice (Peromyscus leucopus) in New York City. We analysed 154,770 SNPs identified from transcriptome data from 48 P. leucopus individuals from three urban and three rural populations and used outlier tests to identify evidence of urban adaptation. We accounted for demography by simulating a neutral SNP data set under an inferred demographic history as a null model for outlier analysis. We also tested whether candidate genes were associated with environmental variables related to urbanization. In total, we detected 381 outlier loci and after stringent filtering, identified and annotated 19 candidate loci. Many of the candidate genes were involved in metabolic processes and have well‐established roles in metabolizing lipids and carbohydrates. Our results indicate that white‐footed mice in New York City are adapting at the biomolecular level to local selective pressures in urban habitats. Annotation of outlier loci suggests selection is acting on metabolic pathways in urban populations, likely related to novel diets in cities that differ from diets in less disturbed areas.
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Aim
Ecological limits on population sizes and the number of species a region can sustain are thought to simultaneously produce spatial patterns in population genetic diversity and species richness ...due to the effects of random drift operating in parallel across population and community levels. Here, we test the extent to which resource‐based environmental limits jointly determine these patterns of biodiversity in amphibians.
Location
North America.
Taxon
Amphibians.
Methods
We repurposed open, raw microsatellite data from 19 species sampled at 554 sites in North America and mapped nuclear genetic diversity at the continental scale. We then tested whether ecological limits defined by resource availability and environmental heterogeneity could simultaneously shape biogeographic patterns in genetic diversity and species richness with structural equation modelling.
Results
Spatial patterns of population genetic diversity run opposite patterns of species richness and genetic differentiation. However, while measures of resource availability and niche heterogeneity predict 89% of the variation in species richness, these landscape metrics were poor predictors of genetic diversity.
Main conclusions
Although heterogeneity appears to be an important driver of genetic and species biodiversity patterns in amphibians, variation in genetic diversity both within and across species makes it difficult to infer general processes producing spatial patterns of amphibian genetic diversity. This result differs from those found in endotherms and may be due to the considerable life history variation found across amphibians.
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Natural landscape heterogeneity and barriers resulting from urbanization can reduce genetic connectivity between populations. The evolutionary, demographic, and ecological effects of reduced ...connectivity may lead to population isolation and ultimately extinction. Alteration to the terrestrial and aquatic environment caused by urban influence can affect gene flow, specifically for stream salamanders who depend on both landscapes for survival and reproduction. To examine how urbanization affects a relatively common stream salamander species, we compared genetic connectivity of Eurycea bislineata (northern two‐lined salamander) populations within and between streams in an urban, suburban, and rural habitat around the New York City (NYC) metropolitan area. We report reduced genetic connectivity between streams within the urban landscape found to correspond with potential barriers to gene flow, that is, areas with more dense urbanization (roadways, industrial buildings, and residential housing). The suburban populations also exhibited areas of reduced connectivity correlated with areas of greater human land use and greater connectivity within a preserve protected from development. Connectivity was relatively high among neighboring rural streams, but a major roadway corresponded with genetic breaks even though the habitat contained more connected green space overall. Despite greater human disturbance across the landscape, urban and suburban salamander populations maintained comparable levels of genetic diversity to their rural counterparts. Yet small effective population size in the urban habitats yielded a high probability of loss of heterozygosity due to genetic drift in the future. In conclusion, urbanization impacted connectivity among stream salamander populations where its continual influence may eventually hinder population persistence for this native species in urban habitats.
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Human commensal species such as rodent pests are often widely distributed across cities and threaten both infrastructure and public health. Spatially explicit population genomic methods provide ...insights into movements for cryptic pests that drive evolutionary connectivity across multiple spatial scales. We examined spatial patterns of neutral genomewide variation in brown rats (Rattus norvegicus) across Manhattan, New York City (NYC), using 262 samples and 61,401 SNPs to understand (i) relatedness among nearby individuals and the extent of spatial genetic structure in a discrete urban landscape; (ii) the geographic origin of NYC rats, using a large, previously published data set of global rat genotypes; and (iii) heterogeneity in gene flow across the city, particularly deviations from isolation by distance. We found that rats separated by ≤200 m exhibit strong spatial autocorrelation (r = .3, p = .001) and the effects of localized genetic drift extend to a range of 1,400 m. Across Manhattan, rats exhibited a homogeneous population origin from rats that likely invaded from Great Britain. While traditional approaches identified a single evolutionary cluster with clinal structure across Manhattan, recently developed methods (e.g., fineSTRUCTURE, sPCA, EEMS) provided evidence of reduced dispersal across the island's less residential Midtown region resulting in fine‐scale genetic structuring (FST = 0.01) and two evolutionary clusters (Uptown and Downtown Manhattan). Thus, while some urban populations of human commensals may appear to be continuously distributed, landscape heterogeneity within cities can drive differences in habitat quality and dispersal, with implications for the spatial distribution of genomic variation, population management and the study of widely distributed pests.
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We investigated genetic diversity and structure of urban white-footed mouse, Peromyscus leucopus, populations in New York City (NYC) using variation at 18 microsatellite loci. White-footed mice are ...'urban adapters' that occur at higher population densities as habitat fragments are reduced in area but have a limited ability to disperse through urbanized areas. We hypothesized that this combination of traits has produced substantial genetic structure but minimal loss of genetic variation over the last century in NYC. Allelic diversity and heterozygosity in 14 NYC populations were high, and nearly all of our NYC study sites contained genetically distinct populations of white-footed mice as measured by pairwise FST, assignment tests, and Bayesian clustering analyses performed by Structure and baps. Analysis of molecular variance revealed that genetic differences between populations separated by a few kilometres are more significant than differences between prehistorically isolated landmasses (i.e. Bronx, Queens, and Manhattan). Allele size permutation tests and lack of isolation by distance indicated that mutation and migration are less important than drift as explanations for structure in urban, fragmented P. leucopus populations. Peromyscus often exhibit little genetic structure over even regional scales, prompting us to conclude that urbanization is a particularly potent driver of genetic differentiation compared to natural fragmentation.
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