scholarly journals Ecological Genetic Conflict: Genetic Architecture Can Shift the Balance between Local Adaptation and Plasticity

2019 ◽  
Vol 193 (1) ◽  
pp. 70-80 ◽  
Author(s):  
Olof Leimar ◽  
Sasha R. X. Dall ◽  
John M. McNamara ◽  
Bram Kuijper ◽  
Peter Hammerstein
Keyword(s):  
Local Adaptation ◽  
Genetic Architecture ◽  
Genetic Conflict

scholarly journals Ecological genetic conflict between specialism and plasticity through genomic islands of divergence

2018 ◽  
Author(s):  
Olof Leimar ◽  
Sasha R. X. Dall ◽  
John M. McNamara ◽  
Bram Kuijper ◽  
Peter Hammerstein
Keyword(s):  
Phenotypic Plasticity ◽  
Local Adaptation ◽  
Genetic Architecture ◽  
Genomic Island ◽  
Reaction Norm ◽  
Genomic Islands ◽  
Genetic Conflict ◽  
Heterogeneous Habitats ◽  
Developmental Responses ◽  
Insight Into

AbstractThere can be genetic conflict between genome elements differing in transmission patterns, and thus in evolutionary interests. We show here that the concept of genetic conflict provides new insight into local adaptation and phenotypic plasticity. Local adaptation to heterogeneous habitats sometimes occurs as tightly linked clusters of genes with among-habitat polymorphism, referred to as genomic islands of divergence, and our work sheds light on their evolution. Phenotypic plasticity can also influence the divergence between ecotypes, through developmental responses to habitat-specificcues. We show that clustered genes coding for ecological specialism and unlinked generalist genes coding for phenotypic plasticity differ in their evolutionary interest. This is an ecological genetic conflict, operating between habitat specialism and phenotypically plastic generalism. The phenomenon occurs both for single traits and for syndromes of co-adapted traits. Using individual-based simulations and numerical analysis, we investigate how among-habitat genetic polymorphism and phenotypic plasticity depend on genetic architecture. We show that for plasticity genes that are unlinked to a genomic island of divergence, the slope of a reaction norm will be steeper in comparison with the slope favored by plasticity genes that are tightly linked to genes for local adaptation.

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.

scholarly journals The relative strength of selection on modifiers of genetic architecture under migration load

2021 ◽  
Author(s):  
Stephen R Proulx ◽  
Henrique Teotonio
Keyword(s):  
Local Adaptation ◽  
Genetic Architecture ◽  
Absolute Magnitude ◽  
Relative Strength ◽  
Demographic Stochasticity ◽  
Recombination Rates ◽  
Relative Population ◽  
Population Sizes ◽  
The Mean ◽  
Selection For

Gene flow between populations adapting to differing local environmental conditions creates a "migration load" because individuals might disperse to habitats where their survival is low or because they might reproduce with locally maladapted individuals. The amount by which the mean relative population fitness is kept below one creates an opportunity for modifiers of the genetic architecture to spread due to selection. Prior work that separately considered modifiers changing dispersal or recombination rates, or altering dominance or epistasis, has typically focused on the direction of selection rather than its absolute magnitude. We here develop methods to determine the strength of selection on modifiers of the genetic architecture, including modifiers of the dispersal rate, after populations evolved local adaptation. We consider scenarios with up to five loci contributing to local adaptation and derive a matrix model for the deterministic spread of modifiers. We find that selection for modifiers of epistasis and dominance is stronger than selection for decreased recombination, and that selection for partial reductions in recombination are extremely weak, regardless of the number of loci contributing to local adaptation. The spread of modifiers for a reduction in dispersal depends on the number of loci, pre-existing epistasis and extent of migration load. We identify a novel effect, that modifiers of dominance are more strongly selected when they are unlinked to the locus that they modify. Overall, these results help explain population differentiation and reproductive isolation and provide a benchmark to compare selection on genetic architecture modifiers in finite population sizes and under demographic stochasticity.

scholarly journals Genetic architecture of dispersal and local adaptation drives accelerating range expansions

2021 ◽  
Author(s):  
Jhelam N. Deshpande ◽  
Emanuel A. Fronhofer
Keyword(s):  
Local Adaptation ◽  
Range Expansion ◽  
Genetic Architecture ◽  
Regulatory Networks ◽  
Large Scale ◽  
Contemporary Evolution ◽  
Evolutionary Changes ◽  
Simplifying Assumptions ◽  
Gene Regulatory ◽  
The Impact

AbstractContemporary evolution has the potential to significantly alter biotic responses to global change, including range expansion dynamics and biological invasions. However, predictive models often make highly simplifying assumptions about the genetic architecture underlying relevant traits. This can be problematic since genetic architecture defines evolvability, that is, evolutionary rates, and higher order evolutionary processes, which determine whether evolution will be able to keep up with environmental change or not. Therefore, we here study the impact of the genetic architecture of dispersal and local adaptation, two central traits of high relevance for range expansion dynamics, on the speed and variability of range expansions into an environmental gradient, such as temperature. In our theoretical model we assume that dispersal and local adaptation traits result from the products of two non-interacting gene-regulatory networks (GRNs). We compare our model to simpler quantitative genetics models and show that in the GRN model, range expansions are accelerated, faster and more variable. Increased variability implies that these evolutionary changes reduce predictability. We further find that acceleration in the GRN model is primarily driven by an increase in the rate of local adaptation to novel habitats which results from greater sensitivity to mutation (decreased robustness) and increased gene expression. Our results highlight how processes at microscopic scales, here, within genomes, can impact the predictions of large scale, macroscopic phenomena, such as range expansions, by modulating the rate of evolution.

scholarly journals Explorations of the polygenic genetic architecture of flowering time in the worldwide Arabidopsis thaliana population

2017 ◽  
Author(s):  
Yanjun Zan ◽  
Örjan Carlborg
Keyword(s):  
Arabidopsis Thaliana ◽  
Flowering Time ◽  
Local Adaptation ◽  
Time Variation ◽  
Native Species ◽  
Genetic Architecture ◽  
Complex Trait ◽  
Local Adaptations ◽  
Wide Range ◽  
Ecological Habitats

AbstractAs a locally adapted complex trait, flowering time in Arabidopsis thaliana has attracted much attention in genetics. Most studies have, however, focused on contributions by individual loci rather than the joint contributions by the large number of loci in the genetic architecture of flowering time to local and global adaptation. In an earlier study, we reported 46 loci associated with flowering time variation during growth at 10°C, 16°C or both in the 1,001-genomes collection of Arabidopsis thaliana accessions. Here, we explore how these loci together contribute to differences among genetically defined, and geographically divided, subpopulations across the native range of this species. Our approach was to define flowering time as a trait, and the measurements at 10 and 16 °C as two independent measurements of it. This facilitated explorations of the dynamics in the genetic architecture –which loci contribute and their effects– of flowering time across growth temperatures and their potential roles in local and global adaptation. The overall flowering time differences between populations could be explained by subtle changes in allele-frequencies and gradual changes in phenotype due to globally present alleles. More extreme local adaptations were on several occasions due to contributions by regional alleles with relatively large effects. About 2/3 of the 48 evaluated flowering time loci had similar effects on flowering time at 10°C and 16°C, while the remaining 1/3 had different effects in the two temperatures, suggesting an important contribution of gene by temperature interactions to this trait. There are also indications that co-evolution of functionally connected alleles in local populations has been important for local adaptation. Overall, this study provides deeper insights to the polygenic genetic basis of flowering time variation in Arabidopsis thaliana across a wide range of ecological habitats.Author SummaryMany genes can affect flowering time in Arabidopsis thaliana, but their contribution to natural flowering time variation in the worldwide population is largely unknown. We explored how 48 loci associated with flowering time, measured at 10°C and 16°C, or their difference, for the same wild collected 1,001-genomes Arabidopsis thaliana accessions together contribute to differences among the genetically defined and geographically divided subpopulations from the native species range. The overall flowering time differences among these subpopulations could be explained by the joint small effects of globally present alleles, suggesting an important contribution by polygenic adaptation for this trait. Most alleles with large effects on flowering were present only in some populations, facilitating more extreme local adaptations. Long-range LD was observed between genes in several biological pathways, indicating possible local adaptation via co-evolution of functionally connected polymorphisms. The genetic architecture of flowering time was also found to depend on the growth temperature. Most flowering time loci had similar effects on flowering time measured at 10°C and 16°C, but the effects of about 1/3 of them had effects that varied with temperature. Overall, new insights are provided to how the polygenic architecture of flowering time has facilitated its colonisation of a wide range of ecological habitats.

scholarly journals The genetic architecture of local adaptation and reproductive isolation in sympatry within theMimulus guttatusspecies complex

2016 ◽  
Vol 26 (1) ◽  
pp. 208-224 ◽  
Author(s):  
Kathleen G. Ferris ◽  
Laryssa L. Barnett ◽  
Benjamin K. Blackman ◽  
John H. Willis
Keyword(s):  
Reproductive Isolation ◽  
Local Adaptation ◽  
Genetic Architecture

scholarly journals Unique signals of clinal and seasonal allele frequency change at eQTLs in Drosophila melanogaster

2021 ◽  
Author(s):  
Yang Yu ◽  
Alan O. Bergland
Keyword(s):  
Drosophila Melanogaster ◽  
Allele Frequency ◽  
Local Adaptation ◽  
Genetic Architecture ◽  
Environmental Heterogeneity ◽  
Expression Profiles ◽  
Frequency Change ◽  
Seasonal Adaptation ◽  
Starvation Tolerance ◽  
Latitudinal Clines

Populations of short-lived organisms can respond to spatial and temporal environmental heterogeneity through local adaptation. Local adaptation can be reflected on both phenotypic and genetic levels, and it has been documented in many organisms. Although some complex fitness-related phenotypes have been shown to vary across latitudinal clines and seasons in similar ways in Drosophila melanogaster populations, we lack a general understanding of the genetic architecture of local adaptation across space and time. To address this problem, we examined patterns of allele frequency change across latitudinal clines and between seasons at previously reported expression quantitative trait loci (eQTLs). We divided eQTLs into groups by utilizing differential expression profiles of fly populations collected across a latitudinal cline or exposed to different environmental conditions. We also examined clinal and seasonal patterns of allele frequency change at eQTLs grouped by tissues. In general, we find that clinally varying polymorphisms are enriched for eQTLs, and that these eQTLs change in frequency in predictable ways across the cline and in response to starvation tolerance. The enrichment of eQTL among seasonally varying polymorphisms is more subtle, and the direction of allele frequency change at eQTL appears to be somewhat idiosyncratic. Taken together, we suggest that clinal adaptation at eQTLs is distinct than that of seasonal adaptation.

scholarly journals Not so local: the population genetics of convergent adaptation in maize and teosinte

2021 ◽  
Author(s):  
Silas Tittes ◽  
Anne Lorant ◽  
Sean McGinty ◽  
John F. Doebley ◽  
James B. Holland ◽  
...  
Keyword(s):  
Population Genetics ◽  
Zea Mays ◽  
Local Adaptation ◽  
Genetic Architecture ◽  
Wild Relative ◽  
Selective Sweeps ◽  
Sympatric Population ◽  
Geographic Scale ◽  
Standing Variation ◽  
Maize Populations

ABSTRACTWhat is the genetic architecture of local adaptation and what is the geographic scale that it operates over? We investigated patterns of local and convergent adaptation in five sympatric population pairs of traditionally cultivated maize and its wild relative teosinte (Zea mays subsp. parviglumis). We found that signatures of local adaptation based on the inference of adaptive fixations and selective sweeps are frequently exclusive to individual populations, more so in teosinte compared to maize. However, for both maize and teosinte, selective sweeps are frequently shared by several populations, and often between the subspecies. We were further able to infer that selective sweeps were shared among populations most often via migration, though sharing via standing variation was also common. Our analyses suggest that teosinte has been a continued source of beneficial alleles for maize, post domestication, and that maize populations have facilitated adaptation in teosinte by moving beneficial alleles across the landscape. Taken together, out results suggest local adaptation in maize and teosinte has an intermediate geographic scale, one that is larger than individual populations, but smaller than the species range.

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