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21 results for “standing genetic variation”
Data from: Experimental evidence of rapid heritable adaptation in the absence of initial standing genetic variation
<p>The success of genetically depauperate populations in the face of environmental change is contrary to the expectation that high genetic diversity is required for rapid adaptation. Alternative pathways such as environmentally induced genetic modifications and non-genetic heritable phenotypes have been proposed mechanisms for heritable adaptation within an ecologically relevant timeframe. However, experimental evidence is currently lacking to establish if, and to what extent, these sources of phenotypic variation can produce a response.<br> <br> To test if adaptation can rapidly occur in the absence of initial standing genetic variation and recombination in small populations, we (i) exposed replicate monoclonal populations of the microzooplankton <em>Brachionus calyciflorus</em> to a culturing regime that selected for phenotypic variants with elevated population growth with either high or low phosphorus food for a period of 55 days and (ii) examined population-level response in two fully factorial common garden experiments at day 15 and 35 of the exposure experiment.<br> <br> Within six generations, we observed heritable local adaptation to nutrient limitation. More specifically, populations with a history of exposure to P-limited food exhibited higher population growth rates under low P food conditions than populations with a high P exposure history. However, the capacity for such a response was found to vary among clones.<br> <br> Our study finds that although standing genetic variation is considered essential for rapid heritable adaptation, the rapid emergence of <em>de novo</em> genetic variation or alternative sources of phenotypic variation could aid in the establishment and persistence of low diversity populations.</p>
Data from: Parallel genetic evolution and speciation from standing variation
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Data from: Experimental evidence of rapid heritable adaptation in the absence of initial standing genetic variation
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Data from: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation
A species' genetic diversity bears the marks of evolutionary processes that have occurred throughout its history. However, robust detection of selection in wild populations is difficult and often impeded by lack of replicate tests. Here, we investigate selection in pink salmon (Oncorhynchus gorbuscha) using genome scans coupled with inference from a haploid-assisted linkage map. Pink salmon have a strict 2-year semelparous life history which has resulted in temporally isolated (allochronic) lineages that remain sympatric through sharing of spawning habitats in alternate years. The lineages differ in a range of adaptive traits, suggesting different genetic backgrounds. We used genotyping by sequencing of haploids to generate a high-density linkage map with 7035 loci and screened an existing panel of 8036 loci for signatures of selection. The linkage map enabled identification of novel genomic regions displaying signatures of parallel selection shared between lineages. Furthermore, 24 loci demonstrated divergent selection and differences in genetic diversity between lineages, suggesting that adaptation in the 2 lineages has arisen from different pools of standing genetic variation. Findings have implications for understanding asynchronous population abundances as well as predicting future ecosystem impacts from lineage-specific responses to climate change.
Data from: Climate-related adaptive genetic variation and population structure in natural stands of Norway spruce in the South-Eastern Alps
Forest trees dominate many Alpine landscapes that are currently exposed to changing climate. Norway spruce is one of the most important conifer species of the Italian Alps, and natural populations are found across steep environmental gradients with large differences in temperature and moisture availability. This study seeks to determine and quantify patterns of genetic diversity in natural populations toward understanding adaptive responses to changing climate. Across the Italian species range, 24 natural stands were sampled with a major focus on the Eastern Italian Alps. Sampled trees were genotyped for 384 selected single nucleotide polymorphisms (SNPs) from 285 genes. A wide array of potential candidate genes was tested for correlation with climatic parameters. To minimize false-positive association between genotype and climate, population structure was investigated. Pairwise F ST estimates between sampled populations ranged between 0.000 and 0.075, with the highest values involving the two disjoint populations, Valdieri, on the western Italian Alps, and Campolino, the most southern population on the Apennines. Despite considerable genetic admixture among populations, both Bayesian and multivariate approach identified four genetic clusters. Selection scans revealed five F ST outliers, and the environmental association analysis detected ten SNPs associated to one or more climatic variables. Overall, 13 potentially adaptive loci were identified, three of which have been reported in a previous study on the same species conducted on a broader geographical scale. In our study, precipitation, more than temperature, was often associated with genotype; therefore, it appears as the most important environmental variable associated with the high sensitivity of Norway spruce to soil water supply. These findings provide relevant information for understanding and quantifying climate change effects on this species and its ability to genetically adapt.
Data from: Standing genetic variation in host preference for mutualist microbial symbionts
Many models of mutualisms show that mutualisms are unstable if hosts lack mechanisms enabling preferential associations with mutualistic symbiotic partners over exploitative partners. Despite the theoretical importance of mutualism-stabilizing mechanisms, we have little empirical evidence to infer their evolutionary dynamics in response to exploitation by non-beneficial partners. Using a model mutualism—the interaction between legumes and nitrogen-fixing soil symbionts—we tested for quantitative genetic variation in plant responses to mutualistic and exploitative symbiotic rhizobia in controlled greenhouse conditions. We found significant broad-sense heritability in a legume host's preferential association with mutualistic over exploitative symbionts and selection to reduce frequency of associations with exploitative partners. We failed to detect evidence that selection will favour the loss of mutualism-stabilizing mechanisms in the absence of exploitation, as we found no evidence for a fitness cost to the host trait or indirect selection on genetically correlated traits. Our results show that genetic variation in the ability to preferentially reduce associations with an exploitative partner exists within mutualisms and is under selection, indicating that micro-evolutionary responses in mutualism-stabilizing traits in the face of rapidly evolving mutualistic and exploitative symbiotic bacteria can occur in natural host populations.
varCADD: large sets of standing genetic variation enable genome-wide pathogenicity prediction
<p>Data and trained models for the manuscript <em>varCADD: large sets of standing genetic variation enable genome-wide pathogenicity prediction.</em></p>
Additional Files for "Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass"
<p>This dataset contains additional supporting files referenced by the following publication:</p> <p>• Kersten S, Chang J, Huber CD, Voichek Y, Lanz C, Hagmaier T, Lang P, Lutz U, Hirschberg I, Lerchl J, Porri A, Van de Peer Y, Schmid K, Weigel D, Rabanal FA. <strong>Standing genetic variation fuels rapid evolution of herbicide resistance in blackgrass. </strong><em>Proc Natl Acad Sci USA</em>.</p> <p> </p> <p>Directory structure:</p> <ul> <li><strong>Haplotypes_ACCase</strong>: this directory contains the two haplotypes (fasta format) inferred by pbaa (https://github.com/PacificBiosciences/pbAA ) for each of the 1,046 individuals for which it was possible to analyse the ACCase locus. </li> </ul> <p> </p> <ul> <li><strong>Haplotypes_ALS</strong>: his directory contains the two haplotypes (fasta format) inferred by pbaa (https://github.com/PacificBiosciences/pbAA ) for each of the 842 individuals for which it was possible to analyse the ALS1 locus. </li> </ul> <p> </p> <ul> <li><strong>Reference_genome</strong>: this directory contains the Pacbio CLR+Hi-C based chromosome level assembly (fasta file) of an <em>Alopecurus myosuroides</em> individual from the German herbicide-sensitive population DE01087 (Appels Wilde Samen GmbH, Darmstadt). In addition, it includes annotation files (gff format) for transposable elements and protein-coding genes.</li> </ul> <p> </p> <ul> <li><strong>SNP_matrix</strong>: this directory contains the SNP matrix (vcf format) for the population study carried out with ddRAD-sequencing data.</li> </ul>
Data from: Contemporary ancestor? Adaptive divergence from standing genetic variation in Pacific marine threespine stickleback
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Data from: Predictable genome-wide sorting of standing genetic variation during parallel adaptation to basic versus acidic environments in stickleback fish
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Data from: Standing genetic variation in host preference for mutualist microbial symbionts
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Data from: Climate-related adaptive genetic variation and population structure in natural stands of Norway spruce in the South-Eastern Alps
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Data from: Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation
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Standing genetic variation in laboratory populations of insecticide-susceptible Phlebotomus papatasi and Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae) for the evolution of resistance
<p>Insecticides can exert strong selection on insect pest species, including those that vector diseases, and have led to rapid evolution of resistance. Despite such rapid evolution, relatively little is known about standing genetic variation for resistance in insecticide-susceptible populations of many species. To help fill this knowledge gap, we generated genotyping-by-sequencing data from insecticide-susceptible Phlebotomus papatasi and Lutzomyia longipalpis sand flies that survived or died from a sub-diagnostic exposure to either permethrin or malathion using a modified version of the Centers for Disease Control and Prevention bottle bioassay. Multi-locus genome-wide association mapping methods were used to quantify standing genetic variation for insecticide resistance in these populations and to identify specific alleles associated with insecticide survival. For each insecticide treatment, we estimated the proportion of the variation in survival explained by the genetic data (i.e. 'chip' heritability) and the number and contribution of individual loci with measurable effects. For all treatments, survival to an insecticide exposure was heritable with a polygenic architecture. Both P. papatasi and L. longipalpis had alleles for survival that resided within many genes throughout their genomes. The implications for resistance conferred by many alleles, as well as inferences made about the utility of laboratory insecticide resistance association studies compared to field observations, are discussed in the manuscript that accompanies this data.</p>
Data from: QTL and quantitative genetic analysis of beak morphology reveals patterns of standing genetic variation in an Estrildid finch
The intra- and interspecific diversity of avian beak morphologies is one of the most compelling examples for the power of natural selection acting on a morphological trait. The development and diversification of the beak has also become a textbook example for evolutionary developmental biology, and variation in expression levels of several genes is known to causally affect beak shape. However, until now no genomic polymorphisms have been identified that are related to beak morphology in birds. QTL mapping does reveal the location of causal polymorphisms, albeit with poor spatial resolution. Here we estimate heritability and genetic correlations for beak length, depth and width and perform a QTL linkage analysis for these traits based on 1,404 informative single nucleotide polymorphisms genotyped in a four generation pedigree of 992 captive zebra finches (Taeniopygia guttata). Beak size, relative to body size, was sexually dimorphic (larger in males). Heritability estimates ranged from 0.47 for beak length to 0.74 for beak width. QTL mapping revealed four to five regions of significant or suggestive genome-wide linkage for each of the three beak dimensions (nine different regions in total). Eight out of eleven genes known to influence beak morphology are located in these nine peak regions. Five QTL do not cover known candidates demonstrating that yet unknown genes or regulatory elements may influence beak morphology in the zebra finch.
Data from: Evidence for adaptation from standing genetic variation on an antimicrobial peptide gene in the mussel Mytilus edulis
Genome scans of population differentiation identify candidate loci for adaptation but provide little information on how selection has influenced the genetic structure of these loci. Following a genome scan, we investigated the nature of the selection responsible for the outlying differentiation observed between populations of the marine mussel Mytilus edulis at a leucine/arginine polymorphism (L31R) in the antimicrobial peptide MGD2. We analysed DNA sequence polymorphisms, allele frequencies and population differentiation of polymorphisms closely linked to L31R, and pairwise and third-order linkage disequilibria. An outlying level of population differentiation was observed at L31R only, while no departure from panmixia was observed at linked loci surrounding L31R, as in most of the genome. Selection therefore seems to affect L31R directly. Three hypotheses can explain the lack of differentiation in the chromosomal region close to L31R: (i) hitchhiking has occurred but migration and recombination subsequently erased the signal, (ii) selection was weak enough and recombination strong enough to limit the hitchhiking effect to a very small chromosomal region or (iii) selection acted on a pre-existing polymorphism (i.e. standing variation) at linkage equilibrium with its background. Linkage equilibrium was observed between L31R and linked polymorphisms in every population analysed, as expected under the three hypotheses. However, linkage disequilibrium was observed in some populations between pairs of loci located upstream and downstream to L31R, generating a complex pattern of third-order linkage disequilibria which is best explained by the hypothesis of selection on a pre-existing polymorphism. We hypothesise that selection could be either balanced, maintaining alleles at different frequencies depending on the pathogen community encountered locally by mussels, or intermittent, resulting in sporadic fluctuations in allele frequency.
Data from: Evolution without standing genetic variation: change in transgenerational plastic response under persistent predation pressure
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Data from: Slower environmental change hinders adaptation from standing genetic variation
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Standing genetic variation in laboratory populations of insecticide-susceptible Phlebotomus papatasi and Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae) for the evolution of resistance
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Data from: QTL and quantitative genetic analysis of beak morphology reveals patterns of standing genetic variation in an Estrildid finch
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