Landscape Genetic Approaches to Understanding Movement and Gene Flow in Cities

Cities are home to a continuum of species that range from those specially adapted to exploit urban habitats, to others passing through as transient dispersers. Urbanization often has a profound impact on the movement and gene flow of these species. Compared to natural landscapes, urban environments are complex matrices of roads, buildings, bare soil, slopes, green space, and subterranean infrastructure. Urban neighbourhoods also vary greatly in their socioeconomic and cultural characteristics. This heterogeneity can lead to complex movement patterns in wildlife that are difficult or impossible to characterize using direct tracking methods. Population genetic analyses provide powerful approaches to evaluate spatial patterns of genetic variation and even signatures of adaptive evolution across the genome. When analysed with landscape, environmental, and socioeconomic data, genetic approaches may also identify which features of urban habitats impede or facilitate gene flow. These landscape genetic approaches, when paired with high-resolution sampling and replicated studies across multiple cities, identify dynamic processes that underpin wildlife movement in cities. This chapter reviews the use of spatially explicit genetic approaches in understanding urban wildlife movement, and highlights the many insights gained from rodents in particular as models for urban landscape genetics.

Supplementary Information – Chapter 2

Environmental variation was quantified at nestboxes monitored as part of a prospectively long-term project on the ecology and evolution of great tits Parus major and blue tits Cyanistes caeruleus in Warsaw, Poland. Nine axes of environmental variation were investigated across 9 different urban sites, for a total of 565 specific locations (here: nestboxes). Data was collected on the ground, with the use of GIS and remote sensing using the following methodology:...

Urban Sexual Selection

Human-modified habitats can present both challenges and opportunities for wild animals. Changes in the environment caused by urbanization can affect who survives and reproduces in wild animal populations. Accordingly, we can expect that changes in sexual selection pressures may occur in response to urbanization. Changes in sexually selected traits like bird song and colouration have been one of the main thrusts of urban ecology in recent decades. However, studies to date have focused on describing changes in sexual phenotypes in response to urban environmental change, and knowledge about genetic/microevolutionary change is lacking. Also, while some signalling modalities have been well studied and linked to human activities (e.g., changes in auditory signals in response to anthropogenic noise), others have received comparatively less attention in this context (e.g., effects of air pollution on chemical signalling). In addition, the focus has been mainly on the signal sender, instead of the signal receiver, thereby missing an important side of sexual selection. This chapter reviews the evidence that sexual selection pressures and sexually selected traits have been impacted by urban environments, with attention to the potential for rapid adaptive and plastic shifts in traits of signallers and receivers. It explores the possibilities that urbanization causes evolutionary change and speciation in wild animal populations through sexual selection. Finally, it provides new ideas for future studies to explore these questions and especially the evolution of female preferences in urban environments.

Evolutionary Consequences of the Urban Heat Island

As humans continue to modify the climatic conditions organisms encounter, downstream effects on the phenotypes of organisms are likely to arise. In particular, the worldwide proliferation of human settlements rapidly generates pockets of localized warming across the landscape. These urban heat island effects are frequently intense, especially for moderate to larger sized cities, where urban centres can be several degrees Celsius warmer compared with nearby non-urban areas. Although organisms likely ameliorate the effects of warming through phenotypic plasticity, the evolution of thermally sensitive traits may be an important yet underappreciated means of survival. Recent work suggests the potential for contemporary evolutionary change in association with urban heat islands across a diverse suite of traits from morphology to physiological tolerance, growth rate, and metabolism. This chapter reviews and synthesizes this work. It first develops a comprehensive set of predictions for adaptive evolutionary changes in morphology, physiology, and life-history traits driven by urban heat islands. It then evaluates these predictions with regard to the burgeoning literature on urban evolution of thermally sensitive traits.

Urbanization and Evolution in Aquatic Environments

Human impacts on freshwater and marine ecosystems have long been of special concern due to water’s essential role in ecosystem functioning and human civilization. Urban development causes a large number of changes in all types of aquatic environments, from small ephemeral pools to rivers to great lakes to expansive coastal habitats. These changes can strongly influence evolution of life in the water by altering selection, gene flow, and genetic drift. Yet our understanding of the evolutionary consequences of urbanization on aquatic organisms is still in early stages. This chapter reviews the impacts of urbanization on aquatic taxa, examining the evolutionary consequences (known or likely) of four major types of urban-induced changes to ecosystems: biotic interactions, physical environment, temperature, and pollution. By drawing connections between literature on ecological and evolutionary impacts in aquatic urban environments, the chapter concludes that (1) several anthropogenic factors seem to commonly drive evolutionary and phenotypic change (organic-compound pollution, altered temperature, and hydrologic shifts), (2) predictability of evolutionary changes are often taxa specific, and may commonly depend on the focal ‘scale’ (e.g., whole-organism performance, morphology, or gene), and (3) there are a few key ‘frontier topics’ (altered biotic interactions, artificial light, sound pollution, and fragmentation) where additional research on phenotypic evolution would be particularly informative.

Adaptive Evolution of Plant Life History in Urban Environments

Many of the environmental factors that shape selection on plant life-history traits, including temperature, water availability, growing-season length, nutrient availability, and biotic community, differ between urban and rural environments, as well as within urban environments. Therefore, we might expect that plant life-history traits are of central importance to plant adaptation to urban environments. While the study of adaptive evolution of plant life-history traits in urban environments is in its early stages, those studies that have been conducted provide clear evidence for adaptive divergence between urban and rural plant populations in plant life-history traits related to phenology, fecundity, and dispersal. This chapter reviews the existing studies that provide a foundation for understanding the adaptation of plant life histories in urban environments, and also point to directions of potentially fruitful further research.

The Evolutionary Ecology of Mutualisms in Urban Landscapes

Mutualisms are critically important in maintaining the biodiversity and functioning of ecosystems. Mutualisms include a diverse array of interactions that result in reciprocal positive effects for both partners, including plant–pollinator, plant–seed disperser, and plant–rhizobia interactions. There is growing recognition that global environmental change can affect the ecological outcomes of mutualisms, but less attention has been paid to how urbanization in particular affects their evolution. This chapter builds from an ecological perspective and considers how urban landscapes may affect the evolutionary ecology of mutualism. It reviews the adaptive evolutionary processes that could affect mutualism in urban landscapes. It then surveys transportation, protection, and nutritional mutualisms to assess how urbanization may affect these mutualistic interactions in an evolutionary framework. The survey described in the chapter highlights a dearth of empirical and theoretical investigations on urban mutualisms from an evolutionary perspective despite potentially strong changes in selection pressures in urban areas. The chapter ends by outlining research directions to further the study of the evolutionary ecology of mutualisms in urban landscapes.

Adaptation Genomics in Urban Environments

The field of urban ecology has provided many fascinating examples of organisms that display novel biological features in urban environments compared to natural habitats. Quantitative genetics provides a framework that can be used to investigate whether this phenotypic differentiation between urban and natural habitats is adaptive and is the result of heritable changes in response to divergent selection. New generation sequencing tools offer unique opportunities to expand our understanding of the genes and genetic mechanisms implicated in evolution in urban environments. This chapter first reviews quantitative genetics studies investigating the mechanisms of evolution in the city. It then reviews pioneering genomic studies that have shed light on the genes and genetic mechanisms implicated in urban microevolution. The authors discuss how further use of cost-effective high-resolution genomic approaches may improve the comprehension of both genomic and epigenomic mechanisms implicated in such evolution. Finally, the chapter provides an overview of how the integrated use of quantitative genetics, field experiments, and genomics could expand our knowledge of the processes leading to urban evolution.

Selection on Humans in Cities

As shown throughout this book, urbanization moulds evolutionary processes in many biological systems. But what are its effects on the species that is itself the cause of this radical habitat modification? At least two major cultural transitions in history have involved urbanization: the transition to agriculture, and the continuing transition to modernity. Humans both endure and create the selective pressures associated with urbanization, a process of niche construction with complex evolutionary consequences. Urbanization modifies extrinsic mortality, nutrition, hygiene, demography, the toxicity of air, our microbiota, social interactions, and other factors known to shape selection on morphological, physiological, immunological, life-history, and behavioural traits. Today more than half of humanity lives in cities and is exposed to this new evolutionary context. This chapter presents the elements needed to understand the evolutionary potential of humans living in cities, focusing on traits affecting health. Urbanization can alter the expression of tradeoffs and the selection on traits in ways that change the prevalence of both infectious and non-communicable diseases. The chapter identifies several challenges for research. These include the difficulty of separating the effects of urbanization per se from those of modernization in general, and the need to better integrate eco-evolutionary feedbacks, culture, and learning into microevolutionary models to understand how urban life modifies selection on health. Finally, the chapter discusses why the application to humans of gene editing technologies, such as CRISPR-Cas9, is likely to interact with natural selection, an issue deserving closer attention from evolutionary biologists.

Urban Evolutionary Physiology

Organisms living in urban environments are exposed to many novel, sometimes beneficial, but most often challenging conditions. These conditions include increased exposure to chemical pollution, artificial light at night, noise, altered pathogen and predator communities, increased abundance of often poor quality food, increased temperature, and increased human presence and disturbances. Given the central role of a variety of physiological responses in coping with challenges such as these, the authors of the chapter expect that the range of physiological phenotypes expressed by individuals and species will dramatically influence their ability to persist in urban habitat and cope with urban challenges. They also expect that plasticity in components of these physiological systems will be an important target of selection imposed by the challenges confronting urban populations. The chapter takes a closer look at three fundamental physiological systems in animals that are central components of coping responses to environmental challenges, namely detoxification, and endocrine and metabolic systems.