New Horizons in Evolution

Description

New Horizons in Evolution is a compendium of the latest research, analyses, and theories of evolutionary biology. Chapters are collected from the international symposium held by the Board of Governors of the University of Haifa to honor Dr. Eviatar Nevo, founder and director of the Institute of Evolution. This book includes material written by top global scientists. Such detailed summaries and recent advances include topics like genomics, epigenetics, evolutionary theory, and the evolution of cancer. This book analyzes evolutionary biology of animals, such as lizards and subterranean mammals. It also discusses agricultural evolution, specifically the vital wheat crop in various climates and locations. Each chapter contributes the most up-to-date knowledge of evolution’s role in speciation, adaptation, and regulation. New Horizons in Evolution is a valuable resource for researchers involved in evolution, evolutionary biology, and evolutionary theory. Advanced undergraduate and graduate students in evolutionary biology courses will also find this useful due to the high expertise level and latest knowledge available through this resource. 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