scholarly journals The evolution of group differences in changing environments

PLoS Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
pp. e3001072
Author(s):  
Arbel Harpak ◽  
Molly Przeworski
Keyword(s):  
Environmental Effects ◽  
Complex Traits ◽  
Genetic Basis ◽  
Rapid Evolution ◽  
Group Differences ◽  
Stabilizing Selection ◽  
Trait Variation ◽  
Fitness Consequences ◽  
The Face ◽  
Selection For

The selection pressures that have shaped the evolution of complex traits in humans remain largely unknown, and in some contexts highly contentious, perhaps above all where they concern mean trait differences among groups. To date, the discussion has focused on whether such group differences have any genetic basis, and if so, whether they are without fitness consequences and arose via random genetic drift, or whether they were driven by selection for different trait optima in different environments. Here, we highlight a plausible alternative: that many complex traits evolve under stabilizing selection in the face of shifting environmental effects. Under this scenario, there will be rapid evolution at the loci that contribute to trait variation, even when the trait optimum remains the same. These considerations underscore the strong assumptions about environmental effects that are required in ascribing trait differences among groups to genetic differences.

Evidence of local adaptation and stabilizing selection on quantitative traits in populations of the multipurpose American species Acacia aroma (Fabaceae)

2019 ◽  
Vol 191 (1) ◽  
pp. 128-141 ◽  
Author(s):  
Carolina L Pometti ◽  
Cecilia F Bessega ◽  
Ana M Cialdella ◽  
Mauricio Ewens ◽  
Beatriz O Saidman ◽  
...  
Keyword(s):  
Quantitative Traits ◽  
Genetic Basis ◽  
Natural Populations ◽  
Tree Height ◽  
Phenotypic Traits ◽  
Stabilizing Selection ◽  
Trait Variation ◽  
Chaco Region ◽  
Neutral Genetic Variation ◽  
Selection For

Abstract Economically and ecologically important quantitative traits of Acacia aroma are related to life history and the size and shape of fruits and leaves. Substantial variation is observed for these traits in natural populations, suggesting a possible genetic basis that could be useful for selection programmes. Our objective was to detect signals of selection on 12 phenotypic traits in 170 individuals belonging to seven populations of A. aroma in the Chaco Region of Argentina. Phenotypic traits were compared with molecular markers assessed in the same populations. Here, we search for signatures of natural selection by comparing quantitative trait variation to neutral genetic variation through the PST–FST test. We further test for differences among populations for the 12 phenotypic traits, an association of phenotypic variation with environmental variables and geographical distance, and we compare the power of discrimination between the phenotypic and AFLP datasets. The PST–FST test suggested directional selection for tree height and stabilizing selection for the remaining traits. Analyses of variance showed significant differentiation for eight phenotypic traits. These results suggest selecting among provenances as a management strategy to improve tree height (which showed divergent selection), whereas significant genetic gain for the other traits might be obtained by selection within provenances.

scholarly journals Optimizing the power to identify the genetic basis of complex traits with Evolve and Resequence studies

2019 ◽  
Author(s):  
Christos Vlachos ◽  
Robert Kofler
Keyword(s):  
Complex Traits ◽  
Quantitative Traits ◽  
Genetic Basis ◽  
Optimal Selection ◽  
Selection Regime ◽  
Higher Power ◽  
Powerful Approach ◽  
Selection For ◽  
Generation Sequencing

AbstractEvolve and Resequence (E&R) studies are frequently used to dissect the genetic basis of quantitative traits. By subjecting a population to truncating selection for several generations and estimating the allele frequency differences between selected and non-selected populations using Next Generation Sequencing, the loci contributing to the selected trait may be identified. The role of different parameters, such as, the population size or the number of replicate populations have been examined in previous works. However, the influence of the selection regime, i.e. the strength of truncating selection during the experiment, remains little explored. Using whole genome, individual based forward simulations of E&R studies, we found that the power to identify the causative alleles may be maximized by gradually increasing the strength of truncating selection during the experiment. Notably, such an optimal selection regime comes at no or little additional cost in terms of sequencing effort and experimental time. Interestingly, we also found that a selection regime which optimizes the power to identify the causative loci is not necessarily identical to a regime that maximizes the phenotypic response. Finally, our simulations suggest that an E&R study with an optimized selection regime may have a higher power to identify the genetic basis of quantitative traits than a GWAS, highlighting that E&R is a powerful approach for finding the loci underlying complex traits.

scholarly journals Seeing spots: Measuring, quantifying heritability, and assessing fitness consequences of coat pattern traits in a wild population of giraffes (Giraffa camelopardalis)

2017 ◽  
Author(s):  
Derek E. Lee ◽  
Douglas R. Cavener ◽  
Monica L. Bond
Keyword(s):  
Coat Color ◽  
Adult Survival ◽  
Stabilizing Selection ◽  
Juvenile Survival ◽  
Spot Pattern ◽  
Trait Variation ◽  
Fitness Consequences ◽  
Coat Pattern ◽  
Study Population

ABSTRACTPolymorphic phenotypes of mammalian coat color have been important to the study of genetics and evolution, but little is known about the heritability and fitness consequences of variation in complex coat pattern traits in wild populations. Understanding the current evolution of coat patterns requires reliably measuring traits, quantifying heritability of the traits, and identifying the fitness consequences of specific phenotypes. Giraffe coat markings are highly variable and it has been hypothesized that variation in coat patterns most likely affects fitness by camouflaging neonates against predators. We quantified spot pattern traits of wild Masai giraffes using image analysis software, determined whether spot pattern traits were heritable, and assessed whether variation in heritable spot pattern traits was related to fitness as measured by juvenile survival. The methods we described comprise a framework for objective quantification of mammalian coat pattern traits based on photographic coat pattern data. We demonstrated that characteristics of giraffe coat spot shape are heritable. We did not find evidence for juvenile survival consequences of variation in spot traits, suggesting that spot traits are currently not under strong directional, disruptive, or stabilizing selection for neonate camouflage in our study population, but our sample size could not detect small differences in survival. Spot trait variation also may be more relevant to other components of fitness, such as adult survival or fecundity. We hope this case study will inspire further investigations of coat pattern traits.

scholarly journals Extinctions in marine plankton preceded by stabilizing selection

2019 ◽  
Author(s):  
Manuel F. G. Weinkauf ◽  
Fabian G. W. Bonitz ◽  
Rossana Martini ◽  
Michal Kučera
Keyword(s):  
Planktonic Foraminifera ◽  
Natural Populations ◽  
Marine Species ◽  
Stabilizing Selection ◽  
Marine Plankton ◽  
Trait Variation ◽  
Trait Divergence ◽  
Quaternary Climate ◽  
Geological Past ◽  
The Face

AbstractUnless they adapt, populations facing persistent stress are threatened by extinction. Theoretically, populations facing stress can react by either disruption, increasing trait variation, or stabilisation, decreasing trait variation. In the short term, the more economical response is stabilisation, because it quickly transfers a large part of the population closer to a new ecological optimum. However, canalisation is deleterious in the face of persistently increasing stress because it reduces variability and thus decreases the ability to react to further change in stress. Understanding how natural populations react to intensifying stress reaching terminal levels is key to assessing their resilience to environmental change such as that caused by global warming. Because extinctions are hard to predict, observational data on the adaptive reaction of populations facing extinction are rare. In this study, we make use of the glacial salinity rise in the Red Sea as a natural experiment allowing us to analyse the reaction of planktonic Foraminifera to stress escalation in the geological past. We analyse morphological trait state and variance in two species across a salinity rise leading to their local extinction. One species reacted by stabilisation in shape and size, detectable several thousand years prior to extinction. The second species reacted by trait divergence, but each of the two divergent populations remains stable or reacted by further stabilisation. These observations indicate that the default reaction of the studied Foraminifera is stabilisation and that stress escalation did not lead to the local emergence of adapted forms. Inability to breach the global adaptive threshold would explain why communities of Foraminifera, and many other groups of marine plankton, reacted to Quaternary climate change by faithfully tracking their zonally shifting environments. It also means that populations of marine species adapted to response by migration, when exposed to stress outside of the adaptive range, will be at risk of extinction.

scholarly journals Contextualizing genetic risk score for disease screening and rare variant discovery

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dan Zhou ◽  
Dongmei Yu ◽  
Jeremiah M. Scharf ◽  
Carol A. Mathews ◽  
Lauren McGrath ◽  
...  
Keyword(s):  
Complex Traits ◽  
Genetic Basis ◽  
Clinical Decision Making ◽  
Genetic Risk Score ◽  
Sufficient Conditions ◽  
Clinical Decision ◽  
Generative Models ◽  
Variant Discovery ◽  
Models Of Disease ◽  
The Uk

AbstractStudies of the genetic basis of complex traits have demonstrated a substantial role for common, small-effect variant polygenic burden (PB) as well as large-effect variants (LEV, primarily rare). We identify sufficient conditions in which GWAS-derived PB may be used for well-powered rare pathogenic variant discovery or as a sample prioritization tool for whole-genome or exome sequencing. Through extensive simulations of genetic architectures and generative models of disease liability with parameters informed by empirical data, we quantify the power to detect, among cases, a lower PB in LEV carriers than in non-carriers. Furthermore, we uncover clinically useful conditions wherein the risk derived from the PB is comparable to the LEV-derived risk. The resulting summary-statistics-based methodology (with publicly available software, PB-LEV-SCAN) makes predictions on PB-based LEV screening for 36 complex traits, which we confirm in several disease datasets with available LEV information in the UK Biobank, with important implications on clinical decision-making.

scholarly journals Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jose Miguel Soriano ◽  
Pasqualina Colasuonno ◽  
Ilaria Marcotuli ◽  
Agata Gadaleta
Keyword(s):  
Molecular Markers ◽  
Abiotic Stress ◽  
Durum Wheat ◽  
Candidate Genes ◽  
Biotic Stress ◽  
Qtl Analysis ◽  
Complex Traits ◽  
Genetic Basis ◽  
Agronomic Traits ◽  
Plant Performance

AbstractThe genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.

scholarly journals Epistasis for Three Grain Yield Components in Rice (Oryxa sativa L.)

Genetics ◽  
1997 ◽  
Vol 145 (2) ◽  
pp. 453-465 ◽  
Author(s):  
Zhikang Li ◽  
Shannon R M Pinson ◽  
William D Park ◽  
Andrew H Paterson ◽  
James W Stansel
Keyword(s):  
Grain Yield ◽  
Complex Traits ◽  
Yield Components ◽  
Genetic Basis ◽  
Kernel Weight ◽  
Progeny Testing ◽  
Grain Yield Components ◽  
Main Effects ◽  
Grain Number Per Panicle

The genetic basis for three grain yield components of rice, 1000 kernel weight (KW), grain number per panicle (GN), and grain weight per panicle (GWP), was investigated using restriction fragment length polymorphism markers and F4 progeny testing from a cross between rice subspecies japonica (cultivar Lemont from USA) and indica (cv. Teqing from China). Following identification of 19 QTL affecting these traits, we investigated the role of epistasis in genetic control of these phenotypes. Among 63 markers distributed throughout the genome that appeared to be involved in 79 highly significant (P < 0.001) interactions, most (46 or 73%) did not appear to have “main” effects on the relevant traits, but influenced the trait(s) predominantly through interactions. These results indicate that epistasis is an important genetic basis for complex traits such as yield components, especially traits of low heritability such as GN and GWP. The identification of epistatic loci is an important step toward resolution of discrepancies between quantitative trait loci mapping and classical genetic dogma, contributes to better understanding of the persistence of quantitative genetic variation in populations, and impels reconsideration of optimal mapping methodology and marker-assisted breeding strategies for improvement of complex traits.

scholarly journals Stabilizing selection on individual pattern elements of aposematic signals

2017 ◽  
Vol 284 (1861) ◽  
pp. 20170926 ◽  
Author(s):  
Anne E. Winters ◽  
Naomi F. Green ◽  
Nerida G. Wilson ◽  
Martin J. How ◽  
Mary J. Garson ◽  
...  
Keyword(s):  
Pattern Analysis ◽  
Marine Organism ◽  
Warning Signal ◽  
Colour Pattern ◽  
Stabilizing Selection ◽  
Warning Signals ◽  
Fish Predator ◽  
Selection For ◽  
Aposematic Signals ◽  
Behavioural Experiments

Warning signal variation is ubiquitous but paradoxical: low variability should aid recognition and learning by predators. However, spatial variability in the direction and strength of selection for individual elements of the warning signal may allow phenotypic variation for some components, but not others. Variation in selection may occur if predators only learn particular colour pattern components rather than the entire signal. Here, we used a nudibranch mollusc, Goniobranchus splendidus , which exhibits a conspicuous red spot/white body/yellow rim colour pattern, to test this hypothesis. We first demonstrated that secondary metabolites stored within the nudibranch were unpalatable to a marine organism. Using pattern analysis, we demonstrated that the yellow rim remained invariable within and between populations; however, red spots varied significantly in both colour and pattern. In behavioural experiments, a potential fish predator, Rhinecanthus aculeatus , used the presence of the yellow rims to recognize and avoid warning signals. Yellow rims remained stable in the presence of high genetic divergence among populations. We therefore suggest that how predators learn warning signals may cause stabilizing selection on individual colour pattern elements, and will thus have important implications on the evolution of warning signals.

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