scholarly journals Evolution of polygenic traits under global vs local adaptation

Genetics ◽  
2022 ◽  
Vol 220 (1) ◽  
Author(s):  
Sam Yeaman
Keyword(s):  
Local Adaptation ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Population Genomics ◽  
Natural Populations ◽  
Evolutionary Process ◽  
Frequency Effect ◽  
Theoretical Predictions ◽  
Using Data ◽  
And Migration

Abstract Observations about the number, frequency, effect size, and genomic distribution of alleles associated with complex traits must be interpreted in light of evolutionary process. These characteristics, which constitute a trait’s genetic architecture, can dramatically affect evolutionary outcomes in applications from agriculture to medicine, and can provide a window into how evolution works. Here, I review theoretical predictions about the evolution of genetic architecture under spatially homogeneous, global adaptation as compared with spatially heterogeneous, local adaptation. Due to the tension between divergent selection and migration, local adaptation can favor “concentrated” genetic architectures that are enriched for alleles of larger effect, clustered in a smaller number of genomic regions, relative to expectations under global adaptation. However, the evolution of such architectures may be limited by many factors, including the genotypic redundancy of the trait, mutation rate, and temporal variability of environment. I review the circumstances in which predictions differ for global vs local adaptation and discuss where progress can be made in testing hypotheses using data from natural populations and lab experiments. As the field of comparative population genomics expands in scope, differences in architecture among traits and species will provide insights into how evolution works, and such differences must be interpreted in light of which kind of selection has been operating.

Complex Traits in Natural Populations

2020 ◽  
pp. 263-290
Author(s):  
Daniel L. Hartl
Keyword(s):  
Complex Traits ◽  
Population Genomics ◽  
Association Studies ◽  
Natural Populations ◽  
Complex Diseases ◽  
Stabilizing Selection ◽  
Phenotypic Evolution ◽  
Genetic Changes ◽  
Number Of Genes ◽  
Almost All

This chapter could as well be titled “Population Genomics,” although many aspects of population genomics are integrated throughout the other chapters. It includes estimates of mutational variance and standing variance, phenotypic evolution under directional selection as measured by the linear selection gradient, and phenotypic evolution under stabilizing selection. It explores the strengths and limitations of genome-wide association studies of quantitative trait loci (QTLs) and expression (eQTLs) to detect genetic influencing complex traits in natural populations and genetic risk factors for complex diseases such as heart disease or diabetes. The number of genes affecting complex traits is considered, as well as evidence bearing on the issue of whether complex diseases are primarily affected by a very large number of genes, almost all of small effect, and how this bears on direct-to-consumer and over-the-counter genetic testing. The population genomics of adaptation is considered, including drug resistance, domestication, and local selection versus gene flow. The chapter concludes with the population genomics of speciation as illustrated by reinforcement of mating barriers, the reproducibility of phenotypic and genetic changes, and the accumulation of genetic incompatibilities.

scholarly journals Abandoning the ship using sex, dispersal or dormancy: multiple escape routes from challenging conditions

2018 ◽  
Vol 373 (1757) ◽  
pp. 20170424 ◽  
Author(s):  
Nina Gerber ◽  
Hanna Kokko
Keyword(s):  
Sexual Reproduction ◽  
Local Adaptation ◽  
Natural Populations ◽  
Reproductive Mode ◽  
Bet Hedging ◽  
Local Conditions ◽  
Theoretical Predictions ◽  
Risk Spreading ◽  
Spatio Temporal ◽  
Shed Light

Natural populations often experience environments that vary across space and over time, leading to spatio-temporal variation of the fitness of a genotype. If local conditions are poor, organisms can disperse in space (physical movement) or time (dormancy, diapause). Facultatively sexual organisms can switch between asexual and sexual reproduction, and thus have a third option available to deal with maladaptedness: they can engage in sexual reproduction in unfavourable conditions (an ‘abandon-ship’ response). Sexual reproduction in facultatively sexual organisms is often coupled with dispersal and/or dormancy, while bet-hedging theory at first sight predicts sex, dispersal and dormancy to covary negatively, as they represent different escape mechanisms that could substitute for each other. Here we briefly review the observed links between sex, dormancy and dispersal, and model the expected covariation patterns of dispersal, dormancy and the reproductive mode in the context of local adaptation to spatio-temporally fluctuating environments. The correlations between sex, dormancy and dispersal evolve differently within species versus across species. Various risk-spreading strategies are not completely interchangeable, as each has dynamic consequences that can feed back into the profitability of others. Our results shed light on the discrepancy between previous theoretical predictions on covarying risk-spreading traits and help explain why sex often associates with other means of escaping unfavourable situations. This article is part of the theme issue ‘Linking local adaptation with the evolution of sex differences’.

scholarly journals Phenotypic plasticity in evolutionary rescue experiments

2013 ◽  
Vol 368 (1610) ◽  
pp. 20120089 ◽  
Author(s):  
Luis-Miguel Chevin ◽  
Romain Gallet ◽  
Richard Gomulkiewicz ◽  
Robert D. Holt ◽  
Simon Fellous
Keyword(s):  
Experimental Evolution ◽  
Natural Populations ◽  
Evolutionary Process ◽  
Genetic Evolution ◽  
Controlled Experiments ◽  
Stressful Environment ◽  
Evolutionary Rescue ◽  
Theoretical Predictions ◽  
In The Wild ◽  
Phenotypic Responses

Population persistence in a new and stressful environment can be influenced by the plastic phenotypic responses of individuals to this environment, and by the genetic evolution of plasticity itself. This process has recently been investigated theoretically, but testing the quantitative predictions in the wild is challenging because (i) there are usually not enough population replicates to deal with the stochasticity of the evolutionary process, (ii) environmental conditions are not controlled, and (iii) measuring selection and the inheritance of traits affecting fitness is difficult in natural populations. As an alternative, predictions from theory can be tested in the laboratory with controlled experiments. To illustrate the feasibility of this approach, we briefly review the literature on the experimental evolution of plasticity, and on evolutionary rescue in the laboratory, paying particular attention to differences and similarities between microbes and multicellular eukaryotes. We then highlight a set of questions that could be addressed using this framework, which would enable testing the robustness of theoretical predictions, and provide new insights into areas that have received little theoretical attention to date.

scholarly journals Highly pleiotropic variants of human traits are enriched in genomic regions with strong background selection

2021 ◽  
Author(s):  
Irene Novo ◽  
Eugenio López-Cortegano ◽  
Armando Caballero
Keyword(s):  
Complex Traits ◽  
Rare Variants ◽  
Purifying Selection ◽  
Frequency Effect ◽  
Background Selection ◽  
The Mean ◽  
Using Data ◽  
Genomic Regions ◽  
Human Complex ◽  
Gwas Catalog

AbstractRecent studies have shown the ubiquity of pleiotropy for variants affecting human complex traits. These studies also show that rare variants tend to be less pleiotropic than common ones, suggesting that purifying natural selection acts against highly pleiotropic variants of large effect. Here, we investigate the mean frequency, effect size and recombination rate associated with pleiotropic variants, and focus particularly on whether highly pleiotropic variants are enriched in regions with putative strong background selection. We evaluate variants for 41 human traits using data from the NHGRI-EBI GWAS Catalog, as well as data from other three studies. Our results show that variants involving a higher degree of pleiotropy tend to be more common, have larger mean effect sizes, and contribute more to heritability than variants with a lower degree of pleiotropy. This is consistent with the fact that variants of large effect and frequency are more likely detected by GWAS. Using data from four different studies, we also show that more pleiotropic variants are enriched in genome regions with stronger background selection than less pleiotropic variants, suggesting that highly pleiotropic variants are subjected to strong purifying selection. From the above results, we hypothesized that a number of highly pleiotropic variants of low effect/frequency may pass undetected by GWAS.

scholarly journals Highly pleiotropic variants of human traits are enriched in genomic regions with strong background selection

2021 ◽  
Author(s):  
Irene Novo ◽  
Eugenio López-Cortegano ◽  
Armando Caballero
Keyword(s):  
Complex Traits ◽  
Rare Variants ◽  
Effect Sizes ◽  
Frequency Effect ◽  
Background Selection ◽  
The Mean ◽  
Using Data ◽  
Genomic Regions ◽  
Human Complex ◽  
Gwas Catalog

Abstract Recent studies have shown the ubiquity of pleiotropy for variants affecting human complex traits. These studies also show that rare variants tend to be less pleiotropic than common ones, suggesting that purifying natural selection acts against highly pleiotropic variants of large effect. Here we investigate the mean frequency, effect size and recombination rate associated with pleiotropic variants, and focus particularly on whether highly pleiotropic variants are enriched in regions with putative strong background selection. We evaluate variants for 41 human traits using data from the NHGRI-EBI GWAS Catalog, as well as data from other three studies. Our results show that variants involving a higher degree of pleiotropy tend to be more common, have larger mean effect sizes, and contribute more to heritability than variants with a lower degree of pleiotropy. Using data from four different studies, we show that more pleiotropic variants are enriched in genome regions with stronger background selection than less pleiotropic variants. Thus, we conclude that even though highly pleiotropic variants found so far have larger average effect sizes and frequencies than less pleiotropic ones, they are likely to be subjected to stronger background selection.

scholarly journals Leveraging molecular QTL to understand the genetic architecture of diseases and complex traits

2017 ◽  
Author(s):  
Farhad Hormozdiari ◽  
Steven Gazal ◽  
Bryce van de Geijn ◽  
Hilary Finucane ◽  
Chelsea J.-T. Ju ◽  
...  
Keyword(s):  
Complex Traits ◽  
Genetic Architecture ◽  
Genetic Correlations ◽  
Complex Trait ◽  
Effect Sizes ◽  
Joint Analysis ◽  
Loss Of Function ◽  
Tissue Specific ◽  
Functional Annotations ◽  
Using Data

AbstractThere is increasing evidence that many GWAS risk loci are molecular QTL for gene ex-pression (eQTL), histone modification (hQTL), splicing (sQTL), and/or DNA methylation (meQTL). Here, we introduce a new set of functional annotations based on causal posterior prob-abilities (CPP) of fine-mapped molecular cis-QTL, using data from the GTEx and BLUEPRINT consortia. We show that these annotations are very strongly enriched for disease heritability across 41 independent diseases and complex traits (average N = 320K): 5.84x for GTEx eQTL, and 5.44x for eQTL, 4.27-4.28x for hQTL (H3K27ac and H3K4me1), 3.61x for sQTL and 2.81x for meQTL in BLUEPRINT (all P ≤ 1.39e-10), far higher than enrichments obtained using stan-dard functional annotations that include all significant molecular cis-QTL (1.17-1.80x). eQTL annotations that were obtained by meta-analyzing all 44 GTEx tissues generally performed best, but tissue-specific blood eQTL annotations produced stronger enrichments for autoimmune dis-eases and blood cell traits and tissue-specific brain eQTL annotations produced stronger enrich-ments for brain-related diseases and traits, despite high cis-genetic correlations of eQTL effect sizes across tissues. Notably, eQTL annotations restricted to loss-of-function intolerant genes from ExAC were even more strongly enriched for disease heritability (17.09x; vs. 5.84x for all genes; P = 4.90e-17 for difference). All molecular QTL except sQTL remained significantly enriched for disease heritability in a joint analysis conditioned on each other and on a broad set of functional annotations from previous studies, implying that each of these annotations is uniquely informative for disease and complex trait architectures.

scholarly journals Assortative Mating Biases Marker-based Heritability Estimators

2021 ◽  
Author(s):  
Richard Border ◽  
Sean O'Rourke ◽  
Teresa de Candia ◽  
Michael E Goddard ◽  
Peter M Visscher ◽  
...  
Keyword(s):  
Assortative Mating ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Molecular Genetic ◽  
Simulation Based ◽  
Theoretical Predictions ◽  
Causal Variants ◽  
The Uk ◽  
Moments Estimators ◽  
Biased Estimates

Many complex traits are subject to assortative mating (AM), with recent molecular genetic findings confirming longstanding theoretical predictions that AM alters genetic architecture by inducing long range dependence across causal variants. However, all marker-based heritability estimators assume mating is random. We provide mathematical and simulation-based evidence demonstrating that both method-of-moments estimators and likelihood-based estimators produce biased estimates in the presence of AM and that common approaches to account for population structure fail to mitigate this bias. Then, examining height and educational attainment in the UK Biobank, we demonstrate that these biases affect real world traits. Finally, we derive corrected heritability estimators for traits under equilibrium AM.

Migration and the Internet

2017 ◽  
Vol 14 (3) ◽  
pp. 331-342 ◽  
Author(s):  
Thomas John Cooke ◽  
Ian Shuttleworth
Keyword(s):  
United States ◽  
Information And Communication Technologies ◽  
Unobserved Heterogeneity ◽  
Panel Study ◽  
The United States ◽  
Negative Effect ◽  
Information And Communication ◽  
Using Data ◽  
And Migration ◽  
Dynamics Models

It is widely presumed that information and communication technologies, or ICTs, enable migration in several ways; primarily by reducing the costs of migration. However, a reconsideration of the relationship between ICTs and migration suggests that ICTs may just as well hinder migration; primarily by reducing the costs of not moving.  Using data from the US Panel Study of Income Dynamics, models that control for sources of observed and unobserved heterogeneity indicate a strong negative effect of ICT use on inter-state migration within the United States. These results help to explain the long-term decline in internal migration within the United States.

scholarly journals On the mod resc Model and the Evolution of Wolbachia Compatibility Types

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1415-1422 ◽  
Author(s):  
Sylvain Charlat ◽  
Claire Calmet ◽  
Hervé Merçot
Keyword(s):  
Cytoplasmic Incompatibility ◽  
Natural Populations ◽  
Evolutionary Process ◽  
Embryonic Mortality ◽  
Step Process ◽  
Zygote Development ◽  
Specific Manner

Abstract Cytoplasmic incompatibility (CI) is induced by the endocellular bacterium Wolbachia. It results in an embryonic mortality occurring when infected males mate with uninfected females. The mechanism involved is currently unknown, but the mod resc model allows interpretation of all observations made so far. It postulates the existence of two bacterial functions: modification (mod) and rescue (resc). The mod function acts in the males' germline, before Wolbachia are shed from maturing sperm. If sperm is affected by mod, zygote development will fail unless resc is expressed in the egg. Interestingly, CI is also observed in crosses between infected males and infected females when the two partners bear different Wolbachia strains, demonstrating that mod and resc interact in a specific manner: Two Wolbachia strains are compatible with each other only if they harbor the same compatibility type. Here we focus on the evolutionary process involved in the emergence of new compatibility types from ancestral ones. We argue that new compatibility types are likely to evolve under a wider range of conditions than previously thought, through a two-step process. First, new mod variants can arise by mutation and spread by drift. This is possible because mod is expressed in males and Wolbachia is transmitted by females. Second, once such a mod variant achieves a certain frequency, it can create the conditions for the deterministic invasion of a new resc variant, allowing the invasion of a new mod resc pair. Furthermore, we show that a stable polymorphism might be maintained in natural populations, allowing the long-term existence of “suicidal” Wolbachia strains.

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