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