Urban Evolutionary Biology

Cover
Urban Evolutionary Biology
Copyright
Dedication
Foreword
	References
Contents
List of Contributors
Chapter 1: Introduction
	1.1 Urban evolutionary biology
	1.2 Societal impact of urban evolutionary biology
		1.2.1 Education and outreach
		1.2.2 Sustainable cities
	1.3 Overview of chapters
	1.4 Challenges and emerging topics
		1.4.1 Challenges
		1.4.2 Are urban environments genetic sources or sinks?
		1.4.3 What are the sources of urban adaptation?
		1.4.4 Urbanization and mutation rates
		1.4.5 Domesticated species as case studies of microevolution
		1.4.6 The gut microbiome
	1.5 Conclusions
	Acknowledgements
	References
Chapter 2: How to Quantify Urbanization When Testing for Urban Evolution?
	2.1 Introduction
	2.2 Frameworks for describing and quantifying urbanization
		2.2.1 Classic urban ecology frameworks
		2.2.2 Time as a missing axis in the study of the evolutionary consequences of urbanization
		2.2.3 Parallel urban evolution framework: replicated insight into urban-driven evolutionary processes
	2.3 Quantifying axes of variation in the urban environment
		2.3.1 Urban metrics
		2.3.2 Univariate versus multivariate approaches
		2.3.3 How is urbanization quantified in published studies of urban evolution?
	2.4 Study design and statistical approaches for urban evolutionary biology
		2.4.1 Model selection and variable fitting
		2.4.2 Controlling for spatial autocorrelation
		2.4.3 The problem of scale
	2.5 Conclusions and outlook
	Acknowledgements
	References
Supplementary Information–Chapter 2
	Quantification of environmental variation in a heterogeneous urban landscape
		Variables collected on the ground
			1. Human presence
			2. Temperature (in C°)
			3. Sound pollution (in Db C)
		Variables collected using a GIS approach
			4. Distance to closest roads
			5. Distance to closest paths
		Variables collected with remote sensing (digital photography, satellite sensors)
			6. Light pollutionA map of light pollution
			7. Tree cover
			8. Imperviousness
			9. NDVI
		References
Chapter 3: Urban Environments as a Framework
to Study Parallel Evolution
	3.1 Introduction
	3.2 How often do species show parallel responses to urbanization?
	3.3 What agents drive parallel evolution across cities?
		3.3.1 Urban heat islands
		3.3.2 Pollution
		3.3.3 Habitat fragmentation
	3.4 Why does parallelism not occur?
		3.4.1 Environmental variation
		3.4.2 Gene flow
		3.4.3 Genetic drift
		3.4.4 Genetic architecture of adaptations
	3.5 Recommendations for future studies
	3.6 Conclusions
	Acknowledgements
	References
Chapter 4: Landscape Genetic Approaches to Understanding Movement and Gene Flow in Cities
	4.1 Introduction
	4.2 Analytical approaches for investigating movement and gene flow in urban areas
		4.2.1 Choice of molecular markers in urban evolution studies
		4.2.2 Advances in spatial population genomic sand landscape genetics for testing gene flow hypotheses in urban environments
		4.2.3 Analytical challenges to landscapegenetic analyses in cities
		4.2.4 Landscape genomics approaches to identifying genes under selection in urban environments
	4.3 Empirical studies of urban gene flow, drift, and landscape genetics
		4.3.1 Gene flow, drift, and landscape genetics within cities
		4.3.2 Gene flow and drift between urban and rural habitats
		4.3.3 Landscape genomics to identify local adaptation to urbanized environments
	4.4 Future directions
	4.5 Conclusions
	Acknowledgements
	References
Chapter 5: Adaptation Genomics in
Urban Environments
	5.1 Introduction
	5.2 Evolutionary significance of trait variation in an urban context: evidence for genetic adaptation
		5.2.1 Providing quantitative genetic empirical measures of urban-specific selection
		5.2.2 Testing for plastic versus genetic basis of adaptation
	5.3 Pinpointing genes implicated in adaptation to urban environments
		5.3.1 Pioneering use of low-resolution anonymous markers in urban evolution
		5.3.2 Candidate genes
		5.3.3 Urban evolution entering the genomic era: methods used so far
		5.3.4 Genome-wide sequencing pinpointing oligogenic adaptations in urban environments
		5.3.5 Polygenic adaptation in urban environments
		5.3.6 Further use of genomics in the field of urban evolution: methodological and taxonomic perspectives
	5.4 Epigenetics and the city
	5.5 Conclusions and summary of the perspectives
	Acknowledgements
	References
Chapter 6: Evolutionary Consequences
of the Urban Heat Island
	6.1 Introduction
	6.2 Evolution in response to urban temperature rise
	6.3 Morphology
	6.4 Physiology
	6.5 Life history
	6.6 Fitness
	6.7 Synthesis: vote-counting meta-analysis
	6.8 Future directions: beyond standard evolutionary biology in a warmer environment
	Acknowledgements
	References
Chapter 7: The Evolutionary Ecology of
Mutualisms in Urban Landscapes
	7.1 Introduction
	7.2 A mechanistic perspective on the evolutionary ecology of urban mutualisms
		7.2.1 Shifts from mutualism to antagonism
		7.2.2 Changes in trait–fitness relationships
		7.2.3 Partner switching
		7.2.4 Changes in partner behaviour
		7.2.5 Partner loss
	7.3 Transportation mutualisms
		7.3.1 Pollination mutualisms
		7.3.2 Seed dispersal mutualisms
	7.4 Protection mutualisms
	7.5 Nutritional mutualisms
	7.6 Future directions
		7.6.1 Do mutualisms respond differently (ecologically and evolutionarily) to urbanization than do other species interactions?
		7.6.2 What forms of mutualism will be most affected evolutionarily by urbanization?
		7.6.3 Is urbanization a unique evolutionary threat for mutualisms?
	Acknowledgements
	References
Chapter 8: Sidewalk Plants as a Model for
Studying Adaptation to Urban
Environments
	8.1 Introduction
	8.2 The sidewalk plants model
		8.2.1 Taking advantage of the urban geometry
		8.2.2 Crepis sancta along the rural–urban gradient
	8.3 Natural selection on dispersal traits in response to urban fragmentation
		8.3.1 Is dispersal costly in urban patches?
		8.3.2 Shift of the seed dispersal ratio
		8.3.3 An evolutionary scenario for reduced dispersal in urban patches
	8.4 Natural selection on physiological traits in the urban environment
		8.4.1 Plant physiological traits related to the urban heat island
		8.4.2 Are selection gradients in urban patches consistent with physiological traits?
	8.5 Contemporary evolution: what can we learn from urban systems?
		8.5.1 Compelling evidence for rapid evolution in an urban environment
		8.5.2 Adaptation to global change
		8.5.3 Modes and tempo of evolutionary processes
	8.6 Conclusions
	Acknowledgements
	References
Chapter 9: Adaptive Evolution of Plant Life
History in Urban Environments
	9.1 Introduction
	9.2 Potential effects of urban environments on plant life-history adaptation
	9.3 Life-history syndromes and tradeoffs
	9.4 Empirical approaches to studying urban evolution
	9.5 Empirical evidence
	9.6 Non-adaptive evolution
	9.7 Opportunities for the future
	9.8 Conclusions
	Acknowledgements
	References
Chapter 10: Urbanization and Evolution
in Aquatic Environments
	10.1 Introduction
	10.2 Biotic interactions
		10.2.1 Predation
		10.2.2 Competition
		10.2.3 Diet
	10.3 Physical environment
		10.3.1 Habitat fragmentation
		10.3.2 Urban stream flow
	10.4 Temperature
		10.4.1 Phenology
		10.4.2 Morphology
		10.4.3 Body size and pace-of-life
		10.4.4 Sex determination
	10.5 Pollution
		10.5.1 Metals and other inorganic pollutants
		10.5.2 Synthetic organic compounds, endocrine disruptors, and antibiotics
		10.5.3 Light pollution
		10.5.4 Anthropogenic sound
		10.5.5 Nutrients and suspended particles
	10.6 Conclusions
	References
Chapter 11: Evolutionary Dynamics of
Metacommunities in Urbanized
Landscapes
	11.1 Introduction
	11.2 The urban evolving metacommunity framework
		11.2.1 Metacommunity ecology and landscape genetics
		11.2.2 Evolving metacommunities in urbanized landscapes
	11.3 Urban evolving metacommunities: a hypothetical example
	11.4 Approaches to study evolving metacommunities across urbanization gradients
		11.4.1 Community trait change: eco-evolutionary partitioning metrics
		11.4.2 The dynamics of community change: common gardening experiments
	11.5 Eco-evolutionary feedbacks of urban evolution on ecosystem features
	11.6 Future directions
		11.6.1 Multispecies approach
		11.6.2 Urban niches
		11.6.3 Reconstructing urban evolution and its consequences: resurrection ecology and historical data
		11.6.4 Forward-looking empirical work on urban evolving metacommunities
	Acknowledgements
	References
Chapter 12: Terrestrial Locomotor Evolution in
Urban Environments
	12.1 Introduction
	12.2 Spatial organization of habitats
		12.2.1 Behaviourally mediated habitat use
		12.2.2 Mechanisms of locomotion in urban habitats
		12.2.3 Shifts in locomotion drive morphological change
	12.3 Substrate properties
		12.3.1 Climbing behaviour on urban substrates
		12.3.2 Mechanisms of climbing in the urban habitat
		12.3.3 Morphological changes associated with climbing urban substrates
	12.4 Conclusions
		12.4.1 Future directions
	Acknowledgements
	References
Chapter 13: Urban Evolutionary Physiology
	13.1 Why physiology?
	13.2 Challenges of studying evolution of plastic physiological traits
	13.3 Urban stressors or stimulators
	13.4 Urban habitats and detoxification of xenobiotics
		13.4.1 Urban pollution
		13.4.2 Air pollution and its consequences: a case study of birds
	13.5 Urban habitats and the endocrine regulation of reproduction
		13.5.1 Night light pollution and reproductive endocrinology
		13.5.2 Food availability/quality and reproductive endocrinology
	13.6 Urban habitats and endocrine responses to challenges
		13.6.1 Altered food availability and the HPA axis
		13.6.2 Human activity and the HPA axis
	13.7 Urban habitats and metabolic responses
		13.7.1 Food quality and metabolic responses
	13.8 Unanswered questions and concluding remarks
	Acknowledgements
	References
Chapter 14: Urban Sexual Selection
	14.1 Introduction
	14.2 Sexual selection and fitness in urban environments
	14.3 Changes in sexual selection pressures
	14.4 Responses of signal senders to urban changes
	14.5 Responses of signal receivers to urban environmental changes
	14.6 Consequences for mating and reproductive strategies
	14.7 Evidence for evolutionary changes
	14.8 Potential role for speciation
	14.9 Conclusions and future directions
	Acknowledgements
	References
Chapter 15: Cognition and Adaptation to Urban
Environments
	15.1 Introduction
	15.2 Cognition and phenotype–environment mismatch
	15.3 Is cognition facilitating or inhibiting adaptive evolution in urban environments?
	15.4 Evolution of cognition in urban
environments
	15.5 Future studies to investigate the role of cognition in urban evolution
	15.6 Conclusions
	Acknowledgements
	References
Chapter 16: Selection on Humans in Cities
	16.1 Introduction
	16.2 Signals from the past
		16.2.1 Old times, old friends, and selection at the dawn of urbanization
		16.2.2 How fast did traits respond genetically to past environmental changes?
	16.3 The transition to modernity
		16.3.1 Antagonistic pleiotropy across the transition to modernity
		16.3.2 When modernity chases our old friends away
		16.3.3 Opportunity for natural selection across the demographic transition
	16.4 Urban selection
		16.4.1 Opportunity for selection in cities
		16.4.2 Urban agents of selection: stressors
		16.4.3 Urban agents of selection: sociocultural factors
		16.4.4 Scale of urban selection
		16.4.5 Urban disease genetics
	16.5 Wrapping up: eco-evolutionary dynamics in the city
		16.5.1 Eco-evolutionary dynamics of health
		16.5.2 Implications for optimality models
	16.6 Conclusions
		16.6.1 Challenges for future research
		16.6.2 Transhumanism: the rise of a new selective forceWe close this chapter
	Acknowledgements
	References
List of Glossary Terms Definition
Index