Groundwater Ecology And Evolution

Front Cover
GROUNDWATER ECOLOGY AND EVOLUTION
GROUNDWATER ECOLOGY AND EVOLUTION
Copyright
Contents
List of contributors
Preface
Groundwater ecology and evolution: an introduction
	Rocks, water, and life
	Research history in groundwater ecology and evolution
	Groundwater research in the Anthropocene
	Objective of the book
	Audience
	Structure and content of the book
	Acknowledgments
	References
1 - Setting the scene: groundwater as ecosystems
	1 - Hydrodynamics and geomorphology of groundwater environments
		Introduction
		The aquifer concept
			Drivers of groundwater flow
			Aquifer hydrodynamics
				Porosity
				Permeability and hydraulic conductivity
			Geologic types of aquifers
		Links to surface hydrology
		Aquifer function
			Flow and transport in aquifers
			Groundwater age
			Modeling aquifers
		The chemical composition of groundwater
			Origin of chemical compounds in surface waters
			Water–rock interactions within aquifers
			Major water quality types
			Reduced environments
		Chemical and nutrient fluxes in aquifers
			Biogeochemical reactions
			Oxygen in groundwater
			Nitrogen and emerging contaminants in groundwater
		Conclusion
		Acknowledgments
		References
	2 - Classifying groundwater ecosystems
		Introduction
		Classification systems
		Global scale
		Continental scale
		Landscape scale
		Habitat/local scale
			Compact aquifers
			Unconsolidated sediment aquifers
			Fractured aquifers
			Karst aquifers
			Ecotonal groundwater habitats
		Conclusions
			Glossary
		Acknowledgments
		References
	3 - Physical and biogeochemical processes of hyporheic exchange in alluvial rivers
		Introduction
		The hyporheic zone
		Predicting hyporheic exchange
			Bedform scale
			Reach and landscape scales
		The role of hyporheic flow on water quality
		Conclusion
		Acknowledgments
		References
	4 - Ecological and evolutionary jargon in subterranean biology
		Introduction
		Ecological classifications
			Schiødte's classification and two possible explanations
			Modern ecological classifications
			Critique and alternative classifications
		Colonization and speciation
			Climatic Relict and Adaptive Shift hypotheses and their historical background
			Critique of CRH and ASH
			Alternative terminology: swinging the pendulum from geography to processes generating reproductive isolation
			Should we retire the CRH and ASH as formal categories?
		Morphological modification for subterranean life
			Troglomorphy and the nature of selection
			Case studies of troglomorphy
			Critique and alternative classifications
		Overall recommendations
		Glossaries
			Aim and scope of two glossaries
		Eco-Evo Glossary
		Retired Speleobiological Glossary
		Acknowledgments
		References
2 - Drivers and patterns of groundwater biodiversity
	5 - Groundwater biodiversity and constraints to biological distribution
		Introduction
		An overview of groundwater biodiversity
			Viruses
			Prokaryotes: Archaea and Bacteria
			Microeukaryotes
			Metazoans
		Physical constraints to biological distribution
			Size of voids and their interconnectedness
			Hydrological connection to the surface environment
			Temperature
		Chemical constraints to biological distribution
			Groundwater chemistry
			Oxygen content and organic matter
		Species interactions
			Species interactions in surface water—groundwater ecotones
			Species interactions in groundwater
		The effect of the past: paleogeographic events and historical climates
		Conclusion
		Acknowledgments
		References
	6 - Patterns and determinants of richness and composition of the groundwater fauna
		Introduction
		Patterns of species richness
			Defining local and regional species richness
			Local species richness patterns
			Regional species richness patterns
				Europe
				North America
				South America
			Global pattern of species richness
		Patterns of species composition
			Variation in species composition among localities within a region
			Variation in species composition among regions
		Toward a multifaceted approach to groundwater biodiversity patterns
		Acknowledgments
		References
	7 - Phylogenies reveal speciation dynamics: case studies from groundwater
		Introduction
		Single colonization versus multiple colonizations from surface ancestors
		Speciation from subterranean ancestors
		Speciation from subterranean ancestors: likely mechanisms
		Drivers of subterranean diversity: the role of paleoclimatic and paleogeological events
			Tethys Ocean, plate tectonics and marine regression-transgression cycles
			Climatic oscillations
			New karst areas
		Synthesis and future prospects
		Acknowledgments
		References
	8 - Dispersal and geographic range size in groundwater
		Introduction
		Evolution of dispersal
			Extrinsic factors
				Environmental heterogeneity in space and time
				Environmental cues to disperse
				The dispersal-ecological specialization trade-off
				Interspecific interactions
			Intrinsic factors
				Body size
				Reproductive strategies
				Inbreeding
				Intraspecific interactions
		Range size
		Groundwater landscape connectivity modulates dispersal
		Conclusion
		Acknowledgments
		References
3 - Roles of organisms in groundwater
	9 - Microbial diversity and processes in groundwater
		Introduction
		Ecological processes determining microbial community diversity and composition
			Importance of environmental conditions, dispersal, and species interactions
			Differences between planktonic and surface-attached microbial communities
			Implications of assembly processes for community functioning and knowledge gaps
		Microbial communities and biogeochemical cycles
			The role of microbial networks in the cycling of DOM, nitrogen, and other elements
			Chemolithoautotrophy in groundwater
			Toward predictive models of microbial communities and biogeochemical fluxes
		Microbial attenuation of groundwater contaminants and bottlenecks
			Petroleum hydrocarbons
			Chlorinated organic compounds
			Toxic metals and metalloids
			Emerging organic contaminants and micropollutants
		Resistance and resilience of groundwater microbial communities to perturbations
		Outlook
		Acknowledgments
		References
	10 - Groundwater food webs
		Introduction
		Basal energy dynamics in groundwater food webs
			Detrital food webs
				Transport
				Transfer to higher trophic levels
			Chemolithoautotrophic food webs
		The role of habitat in groundwater food web dynamics
			Network structure
			Surface-subsurface connectivity
		The role of food web processes in groundwater community dynamics
		Trophic niche diversification in groundwater ecosystems
		Future directions
			Unpacking the microbial compartment of groundwater food webs
			Clarifying and quantifying food web structure
				Natural abundances of stable isotopes and mixing models
				Radiocarbon (14C) natural abundance
				Artificially enriched tracer compounds
				Compound specific methods
					Acknowledgments
		References
	11 - Role of invertebrates in groundwater ecosystem processes and services
		Introduction
		Trophic actions of invertebrates
			Karst systems
			Alluvial systems
		Ecosystem engineering activities by invertebrates
			Karst systems
			Alluvial systems
		Conceptual model of the role of invertebrates on ecosystem processes and consequences for ecosystem services
		Environmental impacts on surface water–groundwater interfaces and consequences for the provision of ecosystem services by i ...
		Suggestions for future research directions
		Acknowledgments
		References
4 - Principles of evolution in groundwater
	12 - Voices from the underground: animal models for the study of trait evolution during groundwater colonization an ...
		Introduction
		Brief historical timeline
		Groundwater model systems
		Troglomorphic traits
			Reductive traits
			Constructive traits
			Other traits
		Timeline of troglomorphic trait evolution
		Evolutionary developmental biology of groundwater organisms
			Loosing eyes
			The many ways to lose eyes during development
			Exchanging eyes for other senses during development
		Evolutionary genomics of groundwater organisms
			Coding mutations
			Regulatory changes
		Conclusions
		Acknowledgments
		References
	13 - The olm (Proteus anguinus), a flagship groundwater species
		Introduction
		The historical rise to fame
		Systematics and evolution
		Molecular ecology and conservation genetics
		Morphology and sensory systems of a groundwater top predator
		Reproductive peculiarities
		The overlooked part of groundwater ecology: symbioses, pathogens and parasites
		Conservation
		Conclusive remarks on flagship species in groundwater
		Acknowledgments
		References
	14 - The Asellus aquaticus species complex: an invertebrate model in subterranean evolution
		Introduction
		Phylogeography and population structure
			A widespread surface species with local subterranean populations budding off
			Subterranean populations
		Phenotypic evolution of subterranean populations
			Morphology
			Behavior
			Physiology
			Life history
		Raising and breeding in the laboratory
		Genetic basis of subterranean-related traits
		Evolutionary development (evo-devo)
		Comparative transcriptomics
		Conclusions and prospect
		Acknowledgments
		References
	15 - Developmental and genetic basis of troglomorphic traits in the teleost fish Astyanax mexicanus
		The history of genetic and genomic studies of troglomorphy in Astyanax
			Classical genetic studies
			Candidate gene studies
			QTL mapping
			Transcriptomics
			Genomics
		Developmental basis of troglomorphy in Astyanax
			Developmental basis of eye regression
			Developmental basis of constructive traits
			Developmental constraints for cavefish evolution
			Embryonic origins of cavefish evolution
		Conclusions
		Acknowledgments
		References
	16 - Ecological and evolutionary perspectives on groundwater colonization by the amphipod crustacean Gammarus minus
		Introduction
		Ecological setting and morphological variation
		Upstream colonization of subterranean waters by Gammarus minus
		Impetus for colonizing cave streams
			Size-selective predation, sexual selection and cave colonization
		Multiple independent colonization of cave streams
			Allozyme variation
			COI and ITS sequences
		Evolutionary perspectives
			Eye development gene expression
			Opsins show No loss of functional constraints in cave populations
			Changes in gene expression associated with adaptation to the cave habitat
				Evidence for positive selection
				Photolyase
		Melanin pigment loss and innate immunity
		Future directions
		Acknowledgments
		References
	17 - Evolutionary genomics and transcriptomics in groundwater animals
		Introduction
		Evolution of genes and genome architecture
			Cavefish genomics and gene decay
			Isopods genomics
				Genome size evolution
				Molecular evolution rate in subterranean habitats
				Life history traits
				Environmental radiation
				Elemental composition of genomes, transcriptomes and proteomes in subterranean habitats
		Evolution of gene expression in groundwater
			Cavefish transcriptomics
			Arthropod transcriptomics
		Conclusion
		Acknowledgments
		References
5 - Biological traits in groundwater
	18 - Dissolving morphological and behavioral traits of groundwater animals into a functional phenotype
		Introduction
		Habitat template
		Morphological-behavioral functional phenotype
			Sensory input
				Morphology
				Behavior and its interaction with morphology
				Beyond the darkness
			Locomotion
			Feeding
				Energy-saving mechanisms
				Differentiation with respect to type of food
			Reproduction
			Habitat choice and adaptation to specific habitats
			Antipredation mechanisms
		Synthesis and perspectives
		Acknowledgments
		References
	19 - Life histories in groundwater organisms
		Introduction
		A brief overview of life history evolution, life history traits, and life table variables
		The current conceptual model of life history evolution in groundwater species
		Support for the current conceptual model of life history evolution in groundwater species
			Expanding the conceptual model of life history evolution in groundwater species
			The environment and life history plasticity
			Trade-offs among life history, morphological, and physiological traits
			Life history evolution and population demography
			Linking life history traits to molecular evolution
		Conclusions
		Acknowledgments
		References
	20 - Physiological tolerance and ecotoxicological constraints of groundwater fauna
		Introduction
		Physiological tolerance of groundwater invertebrates to changing thermal conditions
			Tolerance to cold
			Tolerance to heat
			Insights and future perspectives for global warming scenarios
		Physiological tolerance of groundwater organisms to chemical stress
			Pattern of tolerance to chemicals
			Pattern of environmental risk
			Insights and future perspectives
		Physiological tolerance of groundwater organisms to light, food and oxygen variations: indications for ecotoxicological pro ...
			Tolerance to light
			Tolerance to oxygen depletion
			Tolerance to starvation
			Insights and future perspectives
		Conclusions
		Acknowledgments
		References
6 - Biodiversity and ecosystem management in groundwater
	21 - Global groundwater in the Anthropocene
		Introduction
		Groundwater availability and distribution
			Global distribution
			Interactions
			Climate
			Sustainable groundwater use and management
		Frameworks for sustainable use of groundwater in the Anthropocene
			Groundwater and its link to the United Nations Sustainable Development Goals
			Planetary boundary of freshwater use
		Anthropogenic threats to groundwater
			Depletion
			Seawater intrusion
			Global groundwater quality
		Outlook
			Glossary
		Acknowledgments
		References
	22 - Assessing groundwater ecosystem health, status, and services
		Introduction
		Assessing ecosystem health and condition
			Current approaches in surface and groundwaters
		Indicators of ecosystem health and condition
			Organizational indicators for assessing health
			Functional indicators for assessing health
			Stress indicators for assessing health
		Defining the reference condition for groundwater ecosystems
		Combining indicators into summary indices
		Predicting ecosystem health and condition
		Future directions
		Acknowledgments
		References
	23 - Recent concepts and approaches for conserving groundwater biodiversity
		Introduction
		Past concepts and approaches in groundwater biodiversity conservation
			Past concepts of groundwater biodiversity
			Past approaches to groundwater conservation
			Initial impediments to groundwater conservation
		Recent concepts and approaches in groundwater biodiversity conservation
			Introduction
			Environmental DNA and metabarcoding
			Vulnerability mapping
			Conserving hotspots of groundwater biodiversity and endemism
			Conservation biogeography of subterranean species
			Systematic conservation planning approaches
		Conclusion and future directions
		Acknowledgments
		References
	24 - Legal frameworks for the conservation and sustainable management of groundwater ecosystems
		Introduction
		Conservation of groundwater ecosystems and species at risk
		Why study, assess, and protect groundwater ecosystems?
		Legal frameworks related to groundwater ecosystems
			International and national conventions for the protection of groundwater ecosystems
			Legislation focused on the protection of endangered species
			Groundwater ecosystem protection by water laws
				Groundwater laws in Europe
				Groundwater laws in the United States
				Groundwater laws in Central and South America
				Groundwater laws in Australia
				Further international and national groundwater laws
		Current challenges and the future of groundwater conservation
		Acknowledgments
		References
	The ecological and evolutionary unity and diversity of groundwater ecosystems—conclusions and perspective
		Pattern detection and description
		Groundwater systems as ecological laboratories
		Groundwater systems as evolutionary laboratories
		Groundwater ecosystems' supporting services
		Epilogue
			Acknowledgments
		References
Index
	A
	B
	C
	D
	E
	F
	G
	H
	I
	J
	K
	L
	M
	N
	O
	P
	Q
	R
	S
	T
	U
	V
	W
	Y
	Z
Back Cover