New Horizons in Evolution

New Horizons in Evolution
Copyright
Contents
List of contributors
Foreword
1 How should we think about evolution in the age of genomics?
	Background: tribute to a unique evolutionary biologist
	Basic principles of evolutionary change necessary to encompass Eibi’s work
	Cell fusions produced foundational evolutionary innovations
	Microbiomes and holobionts
	Interspecific hybridization
	Protein evolution
		Proteins as systems
		Coding sequences in pieces
	Horizontal DNA transfers
	The virosphere as an evolutionary R&D sector (online link 20)
	Extracellular vesicles—stress responses and crossing the Weismann Barrier in animals
	Evolutionary changes in genome composition
	Evolutionary thinking in the years to come
	List of abbreviations used
	References
	Declarations
2 Experience and the genome: the role of epigenetics
	Introduction
	DNA methylation conferring cell type identity on DNA
	DNA methylation and gene function
	Mechanisms of silencing of expression by DNA methylation
	Epigenetic programming by exposure and experience
	Epigenetic programming by maternal care
	Epigenetic programming by maternal behavior is reversible
	Early life adversity triggers epigenetic reprogramming
	Alterations in DNA methylation and chromatin modification in response to early life stress are broad and affect multiple ge...
	The response to early life social environment is evolutionary conserved
	The response to early life adversity is system wide
	Early life adversity affects dynamic developmental trajectories of DNA methylation
	Quebec Ice storm of 1998: a quasiexperimental design for studying early life adversity in humans
	How can early life stress produce a system-wide epigenetic response that lasts into adulthood?
	Summary and prospective: DNA methylation mediating life-long adaptation to early life signals
	Author contributions
	Funding
	References
3 Conflict-driven evolution*
	Introduction
	Competing interactions and frustration drive biological evolution
	Evolutionary entanglement between hosts and parasites as a key factor of evolution
	Competing interactions drive major innovations and transitions in evolution
	Cancer, aging, and death
	Frustration as the major cause of complexity in nature and specifics of biology
	Conclusions
	Declarations
		Ethical approval and consent to participate
		Consent for publication
		Availability of supporting data
		Competing interests
		Author contributions
		Funding
	References
4 Evolutionary perspectives on cancer and aging
	Introduction
	Background supporting data
	Origins of somatic genetic variation
	Mechanisms of somatic selection in adult tissue stem cells
	Quantitative model
	Discussion
	Conflict of interest
	Author contributions
	Acknowledgments
	References
5 Evolutionary medicine—Apolipoprotein L1 in human health and disease
	Introduction
	A glimpse into the Trypanosoma—APOL1 arms race, explaining the high frequencies of APOL1 renal risk variants
	The mode of inheritance paradox
	References
6 Network analyses of the impact of visual habitat structure on behavior, demography, genetic diversity, and gene flow in a...
	Introduction
	Methods
		Study system
		Behavioral methods
		Quantification of bedrock distribution
		Predicting population size from glade area and local bedrock clustering
		Measuring and testing dispersal
			Null model/homogenous
			Local habitat model
			Null model/flat
			Slope resistant model
		Genetic sampling and analyses
	Results
		Observed variation in bedrock distribution
		Impact of bedrock clustering on social structure
		Relationship between population size with area and residual correlation length
		Dispersal
		Relationship between bedrock distribution and within-glade genetic variation
		Association between genetic distance and the predicted resistance distances
	Discussion
	Conclusions
	Author contributions
	Acknowledgments
	Ethics approval
	Availability of data and materials
	References
7 Sensory perception of mole-rats and mole rats: assessment of a complex natural global evolutionary “experiment”
	Background
	Eye and vision: adaptation, neutral evolution, or side effect or …?
		Ecology: what is the optic environment of subterranean rodents like?
		Morphology: what does it look like?
		Physiology: what is its capacity?
		Evolution: what is it for?
			Photoperiod sensation?
			Seeing the light at the end of the tunnel?
			Short-wavelength-sensitivity as a byproduct of adaptation to low metabolism?
	Ear and hearing: degeneration or adaptation?
		Ecology: what is the acoustic environment of subterranean rodents like?
		Morphology: what does it look like?
		Physiology: what is its capacity?
		Evolution: what is it for?
	Magnetoreception underground: new possibilities for an old sense!
		How do we know?
			Digging straight burrows
			Nest-building preferences in rodents
			Magnetic novel object assay
			Orientation in a maze
		Morphology and physiology: what it looks like and how does it function?
		Ecology and evolution: what is it for?
	Declarations
	Acknowledgments
	References
8 Evolutionary agriculture domestication of wild emmer wheat
	Introduction
	Evolutionary domestication of Triticum dicoccides
		Triticum dicoccoides is of great importance in wheat domestication and breeding
		Triticum dicoccides has played a central role in wheat evolutionary domestication
		Where was Triticum dicoccides domesticated?
		How fast is the domestication process of Triticum dicoccides?
		Wheat traits subjected to domestication selection
			Brittle rachis
			Glume tenacity
			Free-threshing
			Seed size
			Developmental timing
			Grain yield
			Other quantitative traits modified through domestication
		Domestication syndrome factors
	Gene discovery in Triticum dicoccoides
		Gene loci for quantitatively inherited agronomic traits
			Grain yield
			Seed size
			Flowering time
			Plant height
			Spike number
			Spike compactness
			Spike weight
			Kernel number
		Genes for disease resistance
			Genes for rust resistance
			Genes for powdery mildew resistance
			Genes for Fusarium head blight resistance
		Genes for grain protein content and flour quality
		Genes for micronutrient mineral content
		Genes for tolerance to abiotic stresses
	Breeding application of Triticum dicoccoides germplasm in China
	Concluding remarks and future perspectives
	Conflict of interest
	Acknowledgments
	References
9 Evolutionary Modeling of Protein Families by Chromosomal Translocation Events
	Introduction
	Materials and methods
	Data resources
		Orthologous protein annotation
	Protein domain detection
	EvoProDomDB
	Results
		The EvoProDom model
	Mapping of genes to proteins and alternative splicing
	Protein domain content
	DA as a basic unit in EvoProDom
	Evolutionary mechanism in EvoProDom
		Implementation of domain architecture
		Definition: domain architecture (DA)
		Definition: active domains and unique active domains
		Translocation and indel events of a mobile domain
		Duplication of domains
	Translocation domains are enriched in chimeric transcripts
	Discussion
	Conflict of interest
	Author contributions
	Acknowledgments
	Abbreviations
	References
10 Evolution Canyons model: biodiversity, adaptation, and incipient sympatric ecological speciation across life: a revisit
	The Evolution Canyon model
	Evolution Plateau
	Evolution Slope
	Microclimatic interslope divergence underlying biodiversity contrasts in EC
		Biodiversity evolution
	Yeast pioneering discovery in micro- and macroscales in Israel
	Continental biome interslope divergence at a microsite EC I, Mount Carmel
	Adaptation to environmental stresses
	Cyanobacteria evolution at Evolution Canyon I
	Origin and evolution of circadian clock genes in prokaryotes
		Genetic polymorphism of cyanobacteria under permanent natural stress: a lesson from the Evolution Canyons
		Evolution of wild barley: adaptation, sympatric ecological speciation, and domestication at EC I
		Genomic adaptation to drought in wild barley caused by edaphic natural selection at Evolution Slope (Tabigha), AS, and micr...
		Evolution of tetraploid wild emmer wheat, Triticum dicoccoides: adaptive evolution and sympatric speciation at EC I, Mount ...
		Natural selection of allozyme polymorphisms: a microgeographical differentiation by edaphic, topographical, and temporal fa...
		Evolution of wild emmer wheat avenin-like proteins at Evolution Slope (Tabigha)
		Adaptive evolution and sympatric speciation of the crucifer Ricotia lunaria at EC I
		Evolution of fruit flies (Drosophilidae) in fitness, and incipient sympatric speciation at Evolution Canyon I, Mount Carmel
		Rodent genotypic and phenotypic interslope divergence at EC I
	Evolution caused by environmental stress
		Fungal soil mutation, crossing over, and gene conversion in soil fungus Sordaria fimicola
		Adaptive mutations in RNA-based regulatory mechanisms: computational and experimental investigations in soil bacteria at Ev...
		Retrotransposon BARE-1 evolution in wild barley, Hordeum spontaneum, at EC I
		Genome size is higher on the hot and dry more stressful tropical AS-SFS at EC I
	Repeatome evolution in Drosophila melanogaster
	Developmental instability of vascular plants in contrasting microclimates at EC
		Fluctuating helical asymmetry and morphology of snails (Gastropoda) in divergent microhabitats at Evolution Canyon I and II
		Parallel biodiversity evolution of plants and animals at EC I
		Xeric versus mesic patterns in woody plants at EC I
		Adaptation and incipient sympatric speciation of soil bacterium Bacillus simplex under microclimatic contrast at Evolution ...
		Microclimatic adaptive biodiversity interslope evolution of soil fungi across the four Evolution Canyons in Israel
	Soil fungi in four Israeli Evolution Canyons
	Solar radiation effects on adaptive melanin levels
		Molecular-genetic biodiversity in a natural population of the yeast Saccharomyces cerevisiae from “Evolution Canyon”: micro...
		Adaptive response of DNA-damaging agents in natural populations of yeast, Saccharomyces cerevisiae from “Evolution Canyon” I
		Oxidative stress responses in yeast strains, Saccharomyces cerevisiae, from “Evolution Canyon”
		Continental biome interslope divergence across life at EC I
		Adaptive evolution and incipient sympatric speciation of spiny mouse, Acomys cahirinus, at Evolution Canyon I
			Mitochondrial DNA
	Transcriptome analysis
		Evolution Canyon: a potential microscale monitor of global warming across life
		Host–parasite interaction: Natural selection causes adaptive genetic disease resistance in wild emmer wheat against powdery...
		Evolution in action: adaptation and incipient sympatric speciation with gene flow across life at “Evolution Canyon,” Israel
		Evolution Plateau: edaphic divergent microsite of incipient sympatric speciation in blind mole rat, and wild barley
			Blind mole rats, S. galili: possible incipient SS unfolded by mitochondrial DNA
			Blind mole rats, S. galili: incipient sympatric speciation unfolded by genomic analysis
			Blind mole rats S. galili, incipient SS by transcriptome analysis
			Adaptive methylation regulation of p53 pathway in SS of blind mole rats, S. galili
	Conclusions and prospects
		The genomic revolution, ecological stress, and the origin of species
		What next?
	Acknowledgments
	References
Index