scholarly journals Catch me if you can: Adaptation from standing genetic variation to a moving phenotypic optimum

2015 ◽  
Author(s):  
Sebastian Matuszewski ◽  
Joachim Hermisson ◽  
Michael Kopp
Keyword(s):  
Genetic Variation ◽  
De Novo ◽  
Darwinian Evolution ◽  
De Novo Mutations ◽  
Population Means ◽  
Standing Variation ◽  
Analytical Approximations ◽  
Formal Framework ◽  
Phenotype Space ◽  
Effect Size Distribution

Adaptation lies at the heart of Darwinian evolution. Accordingly, numerous studies have tried to provide a formal framework for the description of the adaptive process. Out of these, two complementary modelling approaches have emerged: While so-called adaptive-walk models consider adaptation from the successive fixation of de-novo mutations only, quantitative genetic models assume that adaptation proceeds exclusively from pre-existing standing genetic variation. The latter approach, however, has focused on short-term evolution of population means and variances rather than on the statistical properties of adaptive substitutions. Our aim is to combine these two approaches by describing the ecological and genetic factors that determine the genetic basis of adaptation from standing genetic variation in terms of the effect-size distribution of individual alleles. Specifically, we consider the evolution of a quantitative trait to a gradually changing environment. By means of analytical approximations, we derive the distribution of adaptive substitutions from standing genetic variation, that is, the distribution of the phenotypic effects of those alleles from the standing variation that become fixed during adaptation. Our results are checked against individual-based simulations. We find that, compared to adaptation from de-novo mutations, (i) adaptation from standing variation proceeds by the fixation of more alleles of small effect; (ii) populations that adapt from standing genetic variation can traverse larger distances in phenotype space and, thus, have a higher potential for adaptation if the rate of environmental change is fast rather than slow.

scholarly journals Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass

2021 ◽  
Author(s):  
Sonja Kersten ◽  
Jiyang Chang ◽  
Christian D Huber ◽  
Yoav Voichek ◽  
Christa Lanz ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Herbicide Resistance ◽  
Large Scale ◽  
De Novo ◽  
Bulked Segregant Analysis ◽  
Target Site ◽  
Temperate Climate ◽  
Minor Role ◽  
Standing Variation ◽  
Target Site Resistance

Repeated herbicide applications exert enormous selection on blackgrass (Alopecurus myosuroides), a major weed in cereal crops of the temperate climate zone including Europe. This inadvertent large-scale experiment gives us the opportunity to look into the underlying genetic mechanisms and evolutionary processes of rapid adaptation, which can occur both through mutations in the direct targets of herbicides and through changes in other, often metabolic, pathways, known as non-target-site resistance. How much either type of adaptation relies on de novo mutations versus pre-existing standing variation is important for developing strategies to manage herbicide resistance. We generated a chromosome-level reference genome for A. myosuroides for population genomic studies of herbicide resistance and genome-wide diversity across Europe in this species. Bulked-segregant analysis evidenced that non-target-site resistance has a complex genetic architecture. Through empirical data and simulations, we showed that, despite its simple genetics, target-site resistance mainly results from standing genetic variation, with only a minor role for de novo mutations.

scholarly journals Local ancestry analysis reveals genomic convergence in extremophile fishes

2019 ◽  
Vol 374 (1777) ◽  
pp. 20180240 ◽  
Author(s):  
Anthony P. Brown ◽  
Kerry L. McGowan ◽  
Enrique J. Schwarzkopf ◽  
Ryan Greenway ◽  
Lenin Arias Rodriguez ◽  
...  
Keyword(s):  
Candidate Genes ◽  
De Novo ◽  
Large Population ◽  
Significant Proportion ◽  
Nucleotide Polymorphisms ◽  
De Novo Mutations ◽  
Genetic Constraints ◽  
Standing Variation ◽  
Whole Genome Resequencing ◽  
Genomic Convergence

The molecular basis of convergent phenotypes is often unknown. However, convergence at a genomic level is predicted when there are large population sizes, gene flow among diverging lineages or strong genetic constraints. We used whole-genome resequencing to investigate genomic convergence in fishes ( Poecilia spp.) that have repeatedly colonized hydrogen sulfide (H 2 S)-rich environments in Mexico. We identified genomic similarities in both single nucleotide polymorphisms (SNPs) and structural variants (SVs) among independently derived sulfide spring populations, with approximately 1.2% of the genome being shared among sulfidic ecotypes. We compared these convergent genomic regions to candidate genes for H 2 S adaptation identified from transcriptomic analyses and found that a significant proportion of these candidate genes (8%) were also in regions where sulfidic individuals had similar SNPs, while only 1.7% were in regions where sulfidic individuals had similar SVs. Those candidate genes included genes involved in sulfide detoxification, the electron transport chain (the main toxicity target of H 2 S) and other processes putatively important for adaptation to sulfidic environments. Regional genomic similarity across independent populations exposed to the same source of selection is consistent with selection on standing variation or introgression of adaptive alleles across divergent lineages. However, combined with previous analyses, our data also support that adaptive changes in mitochondrially encoded subunits arose independently via selection on de novo mutations. Pressing questions remain on what conditions ultimately facilitate the independent rise of adaptive alleles at the same loci in separate populations, and thus, the degree to which evolution is repeatable or predictable. This article is part of the theme issue ‘Convergent evolution in the genomics era: new insights and directions'.

scholarly journals How does adaptation sweep through the genome? Insights from long-term selection experiments

2012 ◽  
Vol 279 (1749) ◽  
pp. 5029-5038 ◽  
Author(s):  
Molly K. Burke
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Population Biology ◽  
De Novo ◽  
Whole Genome ◽  
Beneficial Mutations ◽  
Adaptive Mutations ◽  
Laboratory Selection ◽  
Standing Variation ◽  
New Mutations

A major goal in evolutionary biology is to understand the origins and fates of adaptive mutations. Natural selection may act to increase the frequency of de novo beneficial mutations, or those already present in the population as standing genetic variation. These beneficial mutations may ultimately reach fixation in a population, or they may stop increasing in frequency once a particular phenotypic state has been achieved. It is not yet well understood how different features of population biology, and/or different environmental circumstances affect these adaptive processes. Experimental evolution is a promising technique for studying the dynamics of beneficial alleles, as populations evolving in the laboratory experience natural selection in a replicated, controlled manner. Whole-genome sequencing, regularly obtained over the course of sustained laboratory selection, could potentially reveal insights into the mutational dynamics that most likely occur in natural populations under similar circumstances. To date, only a few evolution experiments for which whole-genome data are available exist. This review describes results from these resequenced laboratory-selected populations, in systems with and without sexual recombination. In asexual systems, adaptation from new mutations can be studied, and results to date suggest that the complete, unimpeded fixation of these mutations is not always observed. In sexual systems, adaptation from standing genetic variation can be studied, and in the admittedly few examples we have, the complete fixation of standing variants is not always observed. To date, the relative frequency of adaptation from new mutations versus standing variation has not been tested using a single experimental system, but recent studies using Caenorhabditis elegans and Saccharomyces cerevisiae suggest that this a realistic future goal.

De-novo mutations and genetic variation in the SCN1A gene in Malaysian patients with generalized epilepsy with febrile seizures plus (GEFS+)

2012 ◽  
Vol 102 (3) ◽  
pp. 210-215
Author(s):  
Emmilia Husni Tan ◽  
Salmi Abdul Razak ◽  
Jafri Malin Abdullah ◽  
Abdul Aziz Mohamed Yusoff
Keyword(s):  
Genetic Variation ◽  
De Novo ◽  
Febrile Seizures ◽  
De Novo Mutations ◽  
Generalized Epilepsy ◽  
Febrile Seizures Plus ◽  
Scn1a Gene

scholarly journals Genetic Variation and De Novo Mutations in the Parthenogenetic Caucasian Rock Lizard Darevskia unisexualis

PLoS ONE ◽  
2008 ◽  
Vol 3 (7) ◽  
pp. e2730 ◽  
Author(s):  
Tatiana N. Badaeva ◽  
Daria N. Malysheva ◽  
Vitaly I. Korchagin ◽  
Alexei P. Ryskov
Keyword(s):  
Genetic Variation ◽  
De Novo ◽  
De Novo Mutations ◽  
Rock Lizard

scholarly journals Adaptive Changes in Hemoglobin Function in High-Altitude Tibetan Canids Were Derived via Gene Conversion and Introgression

2019 ◽  
Vol 36 (10) ◽  
pp. 2227-2237 ◽  
Author(s):  
Anthony V Signore ◽  
Ying-Zhong Yang ◽  
Quan-Yu Yang ◽  
Ga Qin ◽  
Hideaki Moriyama ◽  
...  
Keyword(s):  
High Altitude ◽  
Gene Conversion ◽  
De Novo ◽  
Globin Gene ◽  
Introgressive Hybridization ◽  
Lateral Transfer ◽  
Hypoxia Tolerance ◽  
De Novo Mutations ◽  
Standing Variation ◽  
Different Sources

Abstract A key question in evolutionary biology concerns the relative importance of different sources of adaptive genetic variation, such as de novo mutations, standing variation, and introgressive hybridization. A corollary question concerns how allelic variants derived from these different sources may influence the molecular basis of phenotypic adaptation. Here, we use a protein-engineering approach to examine the phenotypic effect of putatively adaptive hemoglobin (Hb) mutations in the high-altitude Tibetan wolf that were selectively introgressed into the Tibetan mastiff, a high-altitude dog breed that is renowned for its hypoxia tolerance. Experiments revealed that the introgressed coding variants confer an increased Hb–O2 affinity in conjunction with an enhanced Bohr effect. We also document that affinity-enhancing mutations in the β-globin gene of Tibetan wolf were originally derived via interparalog gene conversion from a tandemly linked β-globin pseudogene. Thus, affinity-enhancing mutations were introduced into the β-globin gene of Tibetan wolf via one form of intragenomic lateral transfer (ectopic gene conversion) and were subsequently introduced into the Tibetan mastiff genome via a second form of lateral transfer (introgression). Site-directed mutagenesis experiments revealed that the increased Hb–O2 affinity requires a specific two-site combination of amino acid replacements, suggesting that the molecular underpinnings of Hb adaptation in Tibetan mastiff (involving mutations that arose in a nonexpressed gene and which originally fixed in Tibetan wolf) may be qualitatively distinct from functionally similar changes in protein function that could have evolved via sequential fixation of de novo mutations during the breed’s relatively short duration of residency at high altitude.

scholarly journals De Novo Mutation and Rapid Protein (Co-)evolution during Meiotic Adaptation in Arabidopsis arenosa

2021 ◽  
Author(s):  
Magdalena Bohutínská ◽  
Vinzenz Handrick ◽  
Levi Yant ◽  
Roswitha Schmickl ◽  
Filip Kolář ◽  
...  
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
De Novo ◽  
Empirical Studies ◽  
De Novo Mutation ◽  
Rapid Adaptation ◽  
De Novo Mutations ◽  
Standing Variation ◽  
Arabidopsis Arenosa ◽  
Meiosis Genes

Abstract A sudden shift in environment or cellular context necessitates rapid adaptation. A dramatic example is genome duplication, which leads to polyploidy. In such situations, the waiting time for new mutations might be prohibitive; theoretical and empirical studies suggest that rapid adaptation will largely rely on standing variation already present in source populations. Here, we investigate the evolution of meiosis proteins in Arabidopsis arenosa, some of which were previously implicated in adaptation to polyploidy, and in a diploid, habitat. A striking and unexplained feature of prior results was the large number of amino acid changes in multiple interacting proteins, especially in the relatively young tetraploid. Here, we investigate whether selection on meiosis genes is found in other lineages, how the polyploid may have accumulated so many differences, and whether derived variants were selected from standing variation. We use a range-wide sample of 145 resequenced genomes of diploid and tetraploid A. arenosa, with new genome assemblies. We confirmed signals of positive selection in the polyploid and diploid lineages they were previously reported in and find additional meiosis genes with evidence of selection. We show that the polyploid lineage stands out both qualitatively and quantitatively. Compared with diploids, meiosis proteins in the polyploid have more amino acid changes and a higher proportion affecting more strongly conserved sites. We find evidence that in tetraploids, positive selection may have commonly acted on de novo mutations. Several tests provide hints that coevolution, and in some cases, multinucleotide mutations, might contribute to rapid accumulation of changes in meiotic proteins.

scholarly journals Different Sources of Allelic Variation Drove Repeated Color Pattern Divergence in Cichlid Fishes

2020 ◽  
Author(s):  
Sabine Urban ◽  
Alexander Nater ◽  
Axel Meyer ◽  
Claudius F Kratochwil
Keyword(s):  
Genetic Variation ◽  
De Novo ◽  
Allelic Variation ◽  
Lake Victoria ◽  
Cichlid Fish ◽  
Lake Malawi ◽  
Color Pattern ◽  
Species Flock ◽  
De Novo Mutations ◽  
Phenotypic Divergence

Abstract The adaptive radiations of East African cichlid fish in the Great Lakes Victoria, Malawi, and Tanganyika are well known for their diversity and repeatedly evolved phenotypes. Convergent evolution of melanic horizontal stripes has been linked to a single locus harboring the gene agouti-related peptide 2 (agrp2). However, where and when the causal variants underlying this trait evolved and how they drove phenotypic divergence remained unknown. To test the alternative hypotheses of standing genetic variation versus de novo mutations (independently originating in each radiation), we searched for shared signals of genomic divergence at the agrp2 locus. Although we discovered similar signatures of differentiation at the locus level, the haplotypes associated with stripe patterns are surprisingly different. In Lake Malawi, the highest associated alleles are located within and close to the 5′ untranslated region of agrp2 and likely evolved through recent de novo mutations. In the younger Lake Victoria radiation, stripes are associated with two intronic regions overlapping with a previously reported cis-regulatory interval. The origin of these segregating haplotypes predates the Lake Victoria radiation because they are also found in more basal riverine and Lake Kivu species. This suggests that both segregating haplotypes were present as standing genetic variation at the onset of the Lake Victoria adaptive radiation with its more than 500 species and drove phenotypic divergence within the species flock. Therefore, both new (Lake Malawi) and ancient (Lake Victoria) allelic variation at the same locus fueled rapid and convergent phenotypic evolution.

scholarly journals De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population

2020 ◽  
Vol 117 (5) ◽  
pp. 2560-2569 ◽  
Author(s):  
Michael D. Kessler ◽  
Douglas P. Loesch ◽  
James A. Perry ◽  
Nancy L. Heard-Costa ◽  
Daniel Taliun ◽  
...  
Keyword(s):  
Genetic Variation ◽  
De Novo ◽  
Whole Genome Sequencing Data ◽  
Human Populations ◽  
Founder Population ◽  
Sequencing Data ◽  
De Novo Mutations ◽  
Narrow Sense Heritability ◽  
High Coverage ◽  
Genome Wide

De novo mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole-genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) Program, we called 93,325 single-nucleotide DNMs across 1,465 trios from an array of diverse human populations, and used them to directly estimate and analyze DNM counts, rates, and spectra. We find a significant positive correlation between local recombination rate and local DNM rate, and that DNM rate explains a substantial portion (8.98 to 34.92%, depending on the model) of the genome-wide variation in population-level genetic variation from 41K unrelated TOPMed samples. Genome-wide heterozygosity does correlate with DNM rate, but only explains <1% of variation. While we are underpowered to see small differences, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, we did find significantly fewer DNMs in Amish individuals, even when compared with other Europeans, and even after accounting for parental age and sequencing center. Specifically, we found significant reductions in the number of C→A and T→C mutations in the Amish, which seem to underpin their overall reduction in DNMs. Finally, we calculated near-zero estimates of narrow sense heritability (h2), which suggest that variation in DNM rate is significantly shaped by nonadditive genetic effects and the environment.

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