scholarly journals Light-induced stress as a primary evolutionary driver of eye origins

2019 ◽  
Vol 59 (4) ◽  
pp. 739-750 ◽  
Author(s):  
Andrew J M Swafford ◽  
Todd H Oakley
Keyword(s):  
Natural Selection ◽  
Complex Traits ◽  
Light Stress ◽  
Building Blocks ◽  
Morphological Variations ◽  
Stress Prevention ◽  
Eye Evolution ◽  
Genetic Components ◽  
Induced Stress ◽  
Ultraviolet Damage

Abstract Eyes are quintessential complex traits and our understanding of their evolution guides models of trait evolution in general. A long-standing account of eye evolution argues natural selection favors morphological variations that allow increased functionality for sensing light. While certainly true in part, this focus on visual performance does not entirely explain why diffuse photosensitivity persists even after eyes evolve, or why eyes evolved many times, each time using similar building blocks. Here, we briefly review a vast literature indicating most genetic components of eyes historically responded to stress caused directly by light, including ultraviolet damage of DNA, oxidative stress, and production of aldehydes. We propose light-induced stress had a direct and prominent role in the evolution of eyes by bringing together genes to repair and prevent damage from light-stress, both before and during the evolution of eyes themselves. Stress-repair and stress-prevention genes were perhaps originally deployed as plastic responses to light and/or as beneficial mutations genetically driving expression where light was prominent. These stress-response genes sense, shield, and refract light but only as reactions to ongoing light stress. Once under regulatory-genetic control, they could be expressed before light stress appeared, evolve as a module, and be influenced by natural selection to increase functionality for sensing light, ultimately leading to complex eyes and behaviors. Recognizing the potentially prominent role of stress in eye evolution invites discussions of plasticity and assimilation and provides a hypothesis for why similar genes are repeatedly used in convergent eyes. Broadening the drivers of eye evolution encourages consideration of multi-faceted mechanisms of plasticity/assimilation and mutation/selection for complex novelties and innovations in general.

scholarly journals Light-Induced Stress as a Primary Evolutionary Driver of Eye Origins

2019 ◽  
Author(s):  
Andrew J. M. Swafford ◽  
Todd H. Oakley
Keyword(s):  
Natural Selection ◽  
Complex Traits ◽  
Light Stress ◽  
Building Blocks ◽  
Morphological Variations ◽  
Stress Prevention ◽  
Eye Evolution ◽  
Genetic Components ◽  
Induced Stress ◽  
Plastic Responses

Eyes are quintessential complex traits and our understanding of their evolution guides understanding of trait evolution in general. A long-standing account of eye evolution argues natural selection favors morphological variations that allow increased functionality for sensing light (Darwin 1859; v. Salvini-Plawen and Mayr 1977; Nilsson and Pelger 1994; Nilsson 2013). While certainly true in part, this focus on visual performance does not entirely explain why diffuse photosensitivity persists even after eyes evolve, or why eyes evolved many times, each time using similar building blocks. Here we briefly review a vast literature indicating most genetic components of eyes historically responded to stress caused directly by light, including UV damage of DNA, oxidative stress, and production of aldehydes. We propose light-induced stress had a direct and prominent role in the evolution of eyes by bringing together genes to repair and prevent damage from light-stress, both before and during the evolution of eyes themselves. Stress-repair and stress-prevention genes were perhaps originally deployed as plastic responses to light and/or as beneficial mutations genetically driving expression where light was prominent. These stress-response genes sense, shield, and refract light but only under UV exposure. Once under regulatory-genetic control, they could be expressed before UV stress appeared, evolve as a single unit, and be influenced by natural selection to increase functionality for sensing light, ultimately leading to complex eyes and behaviors. Recognizing the potentially prominent role of stress in eye evolution invites discussions of plasticity and assimilation and provides a hypothesis for why similar genes are repeatedly used in convergent eyes. Broadening the drivers of eye evolution encourages consideration of multi-faceted mechanisms of plasticity/assimilation and mutation/selection for complex novelties and innovations in general.

scholarly journals Light-Induced Stress as a Primary Evolutionary Driver of Eye Origins

2019 ◽  
Author(s):  
Andrew J. M. Swafford ◽  
Todd H. Oakley
Keyword(s):  
Natural Selection ◽  
Complex Traits ◽  
Light Stress ◽  
Building Blocks ◽  
Morphological Variations ◽  
Stress Prevention ◽  
Eye Evolution ◽  
Genetic Components ◽  
Induced Stress ◽  
Plastic Responses

Eyes are quintessential complex traits and our understanding of their evolution guides models of trait evolution in general. A long-standing account of eye evolution argues natural selection favors morphological variations that allow increased functionality for sensing light (Darwin 1859; v. Salvini-Plawen and Mayr 1977; Nilsson and Pelger 1994; Nilsson 2013). While certainly true in part, this focus on visual performance does not entirely explain why diffuse photosensitivity persists even after eyes evolve, or why eyes evolved many times, each time using similar building blocks. Here we briefly review a vast literature indicating most genetic components of eyes historically responded to stress caused directly by light, including UV damage of DNA, oxidative stress, and production of aldehydes. We propose light-induced stress had a direct and prominent role in the evolution of eyes by bringing together genes to repair and prevent damage from light-stress, both before and during the evolution of eyes themselves. Stress-repair and stress-prevention genes were perhaps originally deployed as plastic responses to light and/or as beneficial mutations genetically driving expression where light was prominent. These stress-response genes sense, shield, and refract light but only as reactions to ongoing light stress. Once under regulatory-genetic control, they could be expressed before light stress appeared, evolve as a module, and be influenced by natural selection to increase functionality for sensing light, ultimately leading to complex eyes and behaviors. Recognizing the potentially prominent role of stress in eye evolution invites discussions of plasticity and assimilation and provides a hypothesis for why similar genes are repeatedly used in convergent eyes. Broadening the drivers of eye evolution encourages consideration of multi-faceted mechanisms of plasticity/assimilation and mutation/selection for complex novelties and innovations in general.

Trends in temperate Australian grass breeding and selection

2003 ◽  
Vol 54 (3) ◽  
pp. 211 ◽  
Author(s):  
Rex Oram ◽  
Greg Lodge
Keyword(s):  
Natural Selection ◽  
Introduced Species ◽  
Complex Traits ◽  
Environmental Changes ◽  
Breeding Systems ◽  
Ecological Knowledge ◽  
Native Grasses ◽  
Species Diversification ◽  
Cultivar Development ◽  
Grass Breeding

Current trends in grass cultivar development are reviewed, with respect to the range of species involved, and the objectives and methodology within each species. Extrapolations and predictions are made about future directions and methodologies. It is assumed that selection will necessarily cater for the following environmental changes: (1) higher year-round temperatures, higher variability of rainfall incidence, and lower total winter and spring rainfall along the south of the continent; (2) higher nutrient and lime inputs as land utilisation intensifies; and (3) the grazing management requirements of the important pasture components will be increasingly defined and met in practice.The 'big four' species, perennial ryegrass, phalaris, cocksfoot and tall fescue, will continue to be the most widely sown species in temperate regions for many decades, with the latter 3 increasing most in area and genetic differentiation. However, species diversification will continue, especially with native grasses, legumes, and shrubs from fertile regions of Australia and exotics from little-explored parts of the world, such as South Africa, western North and South America, coastal Caucasus, and Iraq–Iran. By contrast, the recent high rate of species diversification in the tropics and subtropics will probably give way to a much lower rate of cultivar development by refinement and diversification within the established species. Domestication of native grasses will continue for amenity, recreational, land protection, and grazing purposes. As seed harvesting technologies and ecological knowledge improve, natural stands will become increasingly important as local sources of seed. It is suggested that many native grasses have been greatly changed by natural selection so as to withstand strong competition from introduced species under conditions of higher soil fertility and grazing pressure. Conversely, some introduced species are being selected consciously and naturally to persist in regions with irregular rainfall and less fertile soils. Therefore, the distinction between native and introduced grasses may be disappearing, and many populations of native species could now be as foreign to the habitats of pre-European settlement as are populations of introduced species that have been evolving here for 50–200 years. Methods used for genetic improvement will continue to be selection among both overseas accessions and the many native and introduced populations that have responded to natural selection in Australia. As well, there will be deliberate recurrent crossing and selection programs in both native and introduced species for specific purposes and environments. Increasingly, molecular biology methods will complement traditional ones, at first by the provision of DNA markers to assist the selection of complex traits, and for proving distinctness to obtain Plant Breeders' Rights for new cultivars. Later, genetic engineering will be used to manipulate nutritive value, resistance to fungal and viral diseases, and breeding systems, especially cytoplasmic male sterility and apomixis, to utilise heterosis in hybrid cultivars of grasses, particularly for dairying and intensive meat production.Areas where the practice and management of grass breeding and selection programs could be improved are highlighted throughout the review, and reiterated in a concluding statement. Most problems appear to stem from inadequate training in population ecology, population genetics, evolution, and quantitative inheritance.

scholarly journals Global genetic differentiation of complex traits shaped by natural selection in humans

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Jing Guo ◽  
Yang Wu ◽  
Zhihong Zhu ◽  
Zhili Zheng ◽  
Maciej Trzaskowski ◽  
...  
Keyword(s):  
Natural Selection ◽  
Genetic Differentiation ◽  
Complex Traits

scholarly journals Epistasis and natural selection shape the mutational architecture of complex traits

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Adam G. Jones ◽  
Reinhard Bürger ◽  
Stevan J. Arnold
Keyword(s):  
Natural Selection ◽  
Complex Traits

scholarly journals Ancestral contributions to contemporary European complex traits

2021 ◽  
Author(s):  
Davide Marnetto ◽  
Vasili Pankratov ◽  
Mayukh Mondal ◽  
Francesco Montinaro ◽  
Katri Pärna ◽  
...  
Keyword(s):  
Bronze Age ◽  
Complex Traits ◽  
Phenotypic Variability ◽  
Complex Trait ◽  
Blood Cholesterol ◽  
Hunter Gatherers ◽  
Genetic Components ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

The contemporary European genetic makeup formed in the last 8000 years as the combination of three main genetic components: the local Western Hunter-Gatherers, the incoming Neolithic Farmers from Anatolia and the Bronze Age component from the Pontic Steppes. When meeting into the post-Neolithic European environment, the genetic variants accumulated during their three distinct evolutionary histories mixed and came into contact with new environmental challenges. Here we investigate how this genetic legacy reflects on the complex trait landscape of contemporary European populations, using the Estonian Biobank as a case study. For the first time we directly connect the phenotypic information available from biobank samples with the genetic similarity to these ancestral groups, both at a genome-wide level and focusing on genomic regions associated with each of the 27 complex traits we investigated. We also found SNPs connected to pigmentation, cholesterol, sleep, diastolic blood pressure, and body mass index (BMI) to show signals of selection following the post Neolithic admixture events. We recapitulate existing knowledge about pigmentation traits, corroborate the connection between Steppe ancestry and height and highlight novel associations. Among others, we report the contribution of Hunter Gatherer ancestry towards high BMI and low blood cholesterol levels. Our results show that the ancient components that form the contemporary European genome were differentiated enough to contribute ancestry-specific signatures to the phenotypic variability displayed by contemporary individuals in at least 11 out of 27 of the complex traits investigated here.

scholarly journals Polygenic risk modeling with latent trait-related genetic components

2019 ◽  
Author(s):  
Matthew Aguirre ◽  
Yosuke Tanigawa ◽  
Guhan Ram Venkataraman ◽  
Rob Tibshirani ◽  
Trevor Hastie ◽  
...  
Keyword(s):  
Fat Mass ◽  
Genetic Risk ◽  
Complex Traits ◽  
Fat Free Mass ◽  
Risk Scores ◽  
Polygenic Risk Score ◽  
Genetic Associations ◽  
Polygenic Risk ◽  
Genetic Components ◽  
Mass Component

AbstractPolygenic risk models have led to significant advances in understanding complex diseases and their clinical presentation. While models like polygenic risk scores (PRS) can effectively predict outcomes, they do not generally account for disease subtypes or pathways which underlie within-trait diversity. Here, we introduce a latent factor model of genetic risk based on components from Decomposition of Genetic Associations (DeGAs), which we call the DeGAs polygenic risk score (dPRS). We compute DeGAs using genetic associations for 977 traits in the UK Biobank and find that dPRS performs comparably to standard PRS while offering greater interpretability. We show how to decompose an individual’s genetic risk for a trait across DeGAs components, highlighting specific results for body mass index (BMI), myocardial infarction (heart attack), and gout in 337,151 white British individuals, with replication in a further set of 25,486 non-British white individuals from the Biobank. We find that BMI polygenic risk factorizes into components relating to fat-free mass, fat mass, and overall health indicators like physical activity measures. Most individuals with high dPRS for BMI have strong contributions from both a fat mass component and a fat-free mass component, whereas a few ‘outlier’ individuals have strong contributions from only one of the two components. Overall, our method enables fine-scale interpretation of the drivers of genetic risk for complex traits.

scholarly journals Natural selections on both amino acid sequences and expression levels are determinants of ohnolog retention

2021 ◽  
Author(s):  
Lin Miao ◽  
Miaoxin Li
Keyword(s):  
Natural Selection ◽  
Amino Acid ◽  
Complex Traits ◽  
Evolutionary Biology ◽  
Amino Acid Sequences ◽  
Regulatory Sequences ◽  
Unified Framework ◽  
Retention Model ◽  
Coding Sequences ◽  
Expression Levels

AbstractThe mechanism of ohnolog retention is a subject of concern in evolutionary biology. Natural selections on coding sequences and gene dosages have been proposed to be determinants of ohnolog retention. However, the relationship between the two models is not widely accepted, and the role of regulatory sequences on ohnolog retention has long been neglected. In this study, based on a model of complex traits’ genetic architecture, we compared the natural selection’s strength on corresponding sequences between ohnologs and non-ohnologs by comparing complex traits’ heritability enrichments. We showed that complex traits’ regulatory sequences’ heritability enrichments (p = 1.1 × 10−5 in 5 kb flanking regions) and expression-mediated heritability enrichments (p = 2.1 × 10−5) of ohnologs were significantly higher than non-ohnologs. Then, we deduced that regulatory sequences of ohnologs were under substantial natural selection, which was also a determent of ohnolog retention. Meanwhile, we showed that in coding sequences, the complex traits’ heritability enrichments of ohnologs were significantly higher than of non-ohnologs (p = 9.9 × 10−5), supporting the ohnolog retention model of natural selection on coding sequences. We also showed that complex traits’ causal gene expression effect sizes of ohnologs were significantly larger than of non-ohnologs (p = 8.8 × 10−6), supporting the ohnolog retention model of natural selection on gene dosages. In conclusion, we provide the first unified framework to show that both amino acid sequences and expression levels of ohnologs are under substantial selection, which may end the long-standing debate on ohnolog retention models.

scholarly journals An Alternative Molecular View of Evolution: How DNA was Altered over Geological Time

Molecules ◽  
2020 ◽  
Vol 25 (21) ◽  
pp. 5081
Author(s):  
Fredric M. Menger
Keyword(s):  
Natural Selection ◽  
Complex Traits ◽  
Convergent Evolution ◽  
Common Ancestor ◽  
Cambrian Explosion ◽  
Natural Phenomena ◽  
Geological Time ◽  
Multiple Mutation ◽  
Total Lack ◽  
Physical Changes

Four natural phenomena are cited for their defiance of conventional neo-Darwinian analysis: human intelligence; cat domesticity; the Cambrian explosion; and convergent evolution. 1. Humans are now far more intelligent than needed in their hunting–gathering days >10,000 years ago. 2. Domestic cats evolved from wildcats via major genetic and physical changes, all occurring in less than 12,000 years. 3. The Cambrian explosion refers to the remarkable expansion of species that mystifies evolutionists, as there is a total lack of fossil evidence for precursors of this abundant new life. 4. Convergent evolution often involves formation of complex, multigene traits in two or more species that have no common ancestor. These four evolutionary riddles are discussed in terms of a proposed “preassembly” mechanism in which genes and gene precursors are collected silently and randomly over extensive time periods within huge non-coding sections of DNA. This is followed by epigenetic release of the genes, when the environment so allows, and by natural selection. In neo-Darwinism, macroevolution of complex traits involves multiple mutation/selections, with each of the resulting intermediates being more favorable to the species than the previous one. Preassembly, in contrast, invokes natural selection only after a partially or fully formed trait is already in place. Preassembly does not supplant neo-Darwinism but, instead, supplements neo-Darwinism in those important instances where the classical theory is wanting.

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