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396 results for “genetic adaptation”
Data from: Insights into the genomics of clownfish adaptive radiation: genetic basis of the mutualism with sea anemones
<p>Genomic data of 9 clownfish (<em>Amphiprion akallopisos, A. bicinctus, A. melanopus, A. nigripes, A. ocellaris, A. preideraion, A. polymnus, A. sebae, Premnas biaculeatus</em>) species and 1 damselfish species (<em>Pomacentrus moluccensis</em>), presented in " Insights into the genomics of clownfish adaptive radiation: genetic basis of the mutualism with sea anemones".</p> <p>For each species, the following files are available:</p> <p><strong>Species_genome.fasta</strong>: Genome assembly of the species in fasta format. The genome was obtained using Illumina paired-end reads, following a reference-based method. For more information, please refer to the publication</p> <p><strong>Species_genome.Annotation.gff3</strong>: Structural genome annotation of the species, in gff3 format. Structural annotation was obtained with a combination of ab initio and RNAseq-data based approaches. Fina gene models were obtained with MAKER2. For more information, please refer to the publication</p> <p><strong>Species_genome.proteins.uniprot.fa</strong>: Predicted protein sequences from the genome assembly of the species, in fasta format. Each protein is annotated with the best blast hit with SwissProt database. For more information, please refer to the publication</p> <p><strong>Species_genome.transcripts.uniprot.fa</strong>: Predicted coding sequences (CDS) from the genome assembly of the species, in fasta format. Each CDS is annotated with the best blast hit with SwissProt database. For more information, please refer to the publication</p> <p>For <em>Amphiprion ocellaris</em> data, additional to the files presented above, we provided as well the secondary results of the genome assembly using a de novo strategy (Aocellaris_GenomeDeNovo.fasta), its structural annotation (Aocellaris_GenomeDeNovo.Annotation.gff3), and its predicted protein (Aocellaris_GenomeDeNovo.proteins.uniprot.fa) and CDS (Aocellaris_GenomeDeNovo.transcripts.uniprot.fa) sequences. For more information, please refer to the publication</p>
Data from: The genetic architecture of adaptations to high altitude in Ethiopia
<p>Data from </p> <p>Alkorta-Aranburu G, Beall CM, Witonsky DB, Gebremedhin A, Pritchard JK, Di Rienzo A. The genetic architecture of adaptations to high altitude in Ethiopia. PLoS Genet. 2012;8(12):e1003110. doi: 10.1371/journal.pgen.1003110. Epub 2012 Dec 6. PMID: 23236293; PMCID: PMC3516565.</p> <p>Phenotypic and raw methylation data measured at 27,578 CpG sites on Infinium HumanMethylation27 arrays for 66 Ethiopian samples. Initially, 17 HA and 17 LA Amhara and Oromo DNA samples were measured;, however, two LA Amhara sample data were discarded due to low data quality. </p>
The genetic architecture of temperature adaptation is shaped by population ancestry and not by selection regime
<p class="western"><span>Understanding the genetic architecture of temperature adaptation is key for characterizing and predicting the effect of climate change on natural populations. One particularly promising approach is Evolve and Resequence (E&R), which combines advantages of experimental evolution such as time series, replicate populations and controlled environmental conditions, with whole genome sequencing. </span></p> <p class="western"><span>The recent analysis of replicate populations from two different </span><span><i>Drosophila simulans</i></span><span> founder populations, which were adapting to the same novel hot environment, uncovered very different architectures - either many selection targets with large heterogeneity among replicates or fewer selection targets with a consistent response among replicates. </span></p> <p class="western"><span>Here, we exposed the founder population from Portugal to a cold temperature regime. Although almost no selection targets were shared between the hot and cold selection regime, the adaptive architecture was similar: we identified a moderate number of targets under strong selection (19 selection targets, mean selection coefficient = 0.072) and very parallel responses in the cold evolved replicates. This similarity across different environments indicates that the adaptive architecture depends more on the ancestry of the founder population than the specific selection regime. These observations will have broad implications for the correct interpretation of the genomic responses to a changing climate in natural populations.</span></p> <p class="western"> </p>
Evidence for genetic isolation and local adaptation in the field cricket Gryllus campestris
<p>Understanding how species can thrive in a range of environments is a central challenge for evolutionary ecology. There is strong evidence for local adaptation along large-scale ecological clines in insects. However, potential adaptation among neighbouring populations differing in their environment has been studied much less. We used RAD-sequencing to quantify genetic divergence and clustering of ten populations of the field cricket <i>Gryllus campestris </i>in the Cantabrian Mountains of northern Spain, and an outgroup on the coastal plain. Our populations were chosen to represent replicate high and low altitude habitats. We identified genetic clusters that include both high and low altitude populations indicating that the two habitat types do not hold ancestrally distinct lineages. Using common-garden rearing experiments to remove environmental effects, we found evidence for differences between high and low altitude populations in physiological and life-history traits. As predicted by the local adaptation hypothesis, crickets with parents from cooler (high altitude) populations recovered from periods of extreme cooling more rapidly than those with parents from warmer (low altitude) populations. Growth rates also differed between offspring from high and low altitude populations. However, contrary to our prediction that crickets from high altitudes would grow faster, the most striking difference was that at high temperatures, growth was fastest in individuals from low altitudes. Our findings reveal that populations a few tens of kilometres apart have independently evolved adaptations to their environment. This suggests that local adaptation in a range of traits may be commonplace even in mobile invertebrates at scales of a small fraction of species' distributions.</p>
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>
Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies
<p class="MsoNormal"><strong><u><span>Aim:</span></u></strong><span> Discerning when, where, and how processes of isolation lead to differing biogeography is especially complex for marine species with similar ecological niches and within the same geographic location. We assessed population genetics of congeneric and ecologically similar damselfishes within their overlapping distributions and across potential barriers to geneflow.</span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Taxon:</span></u></strong><span> <em>Dascyllus marginatus </em>(endemic) and <em>Dascyllus abudafur </em>(widespread)<em>.</em></span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Location:</span></u></strong><span> Coral reefs from the Red Sea, Djibouti, Yemen, Oman, and Madagascar. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Methods:</span></u></strong><span> We used RADseq derived SNPs to investigate key differences in population genetics between both species and discuss barriers shaping genetic differentiation (neutral vs. selective) and biogeography. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Results:</span></u></strong><strong><span> </span></strong><em><span>Dascyllus marginatus </span></em><span>inhabited the Red Sea, the coasts of Yemen (including Socotra), and the Gulf of Oman. <em>Dascyllus abudafur</em> species was present from the Red Sea to Madagascar but was absent from Yemen and Oman. Populations of <em>D. marginatus </em>had an order of magnitude higher genetic differentiation compared to <em>D. abudafur</em>, as well as several outlier loci (suggesting selective pressure), which were absent in <em>D. abudafur</em> despite equal sampling locations. In both species, specimens from the Red Sea and Djibouti formed one genetic cluster separated from all other locations. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Main conclusions:</span></u></strong><span> The stronger genetic structure at smaller geographic scale of the endemic species seems associated to faster adaptation to environmental differences; whereas the widespread species only experienced reduced geneflow and neutral differentiation at much larger geographic scales. Restrictive transitions (between the Gulf of Aqaba and the Red Sea or the Red Sea and the Gulf of Aden) did not affect the genetic architecture of either species, while the environmental shift within the Red Sea (at 22°N/20°N) affected the endemic but not the widespread species. Samples from continental Yemen revealed that a genetic break in the Gulf of Aden likely reflects historical colonization processes and not contemporary environmental regimes.</span></p>
The genetic basis of plumage coloration and elevation adaptation in a clade of recently diverged alpine and arctic songbirds
<p>Trait genetic architecture plays an important role in the probability that variation in that trait leads to divergence and speciation. In some cases, speciation may be driven by the generation of novel phenotypes through the recombination of genes associated with traits that are important for local adaptation or sexual selection. Here, we investigate the genetic basis of three plumage color traits, and one ecological trait, breeding elevation, in a recent avian radiation, the North American rosy-finches (<em>Leucosticte</em> spp.). We identify unique genomic regions associated with each trait and highlight 11 candidate genes. Among these are well-characterized melanogenesis genes, including Mitf and Tyrp1, and previously reported hypoxia-related genes including Egln1. Additionally, we use mitochondrial data to date the divergence of rosy-finch clades which appear to have diverged within the past 250 ky. Given the low levels of genome-wide differentiation among rosy-finch taxa, and evidence for extensive introgression in North America, plumage coloration and adaptation to high elevations have likely played large roles in generating the observed patterns of lineage divergence. The relative independence of these candidate regions across the genome suggests that recombination might have led to multiple phenotypes, and subsequent rosy-finch speciation, over short periods of time.</p>
Data from: Ecological genetics of local adaptation in Arabidopsis: an 8-year field experiment
<p>There is considerable evidence for local adaptation in nature, yet important questions remain regarding its genetic basis. How many loci are involved? What are their effect sizes? What is the relative importance of conditional neutrality vs. genetic trade-offs? Here we address these questions in the self-pollinating, annual plant <em>Arabidopsis thaliana</em>. We used 400 recombinant inbred lines (RIL) derived from two locally adapted populations in Italy and Sweden, grew the RILs and parents at the parental locations, and mapped quantitative trait loci (QTL) for mean fitness (fruits/seedling planted). We previously published results from the first three years of the study, and here add five additional years, providing a unique opportunity to assess how temporal variation in selection might affect QTL detection and classification. We found ten adaptive and one maladaptive QTL in Italy, and six adaptive and four maladaptive QTL in Sweden. The discovery of maladaptive QTL at both sites suggests that even locally adapted populations are not always at their genotypic optimum. Mean effect sizes for adaptive QTL, 0.97 and 0.55 fruits in Italy and Sweden respectively, were large relative to the mean fitness of the RILs (approximately 8 fruits/seedling planted at both sites). Both genetic trade-offs (four cases) and conditional neutrality (seven cases) contribute to local adaptation in this system. The eight-year dataset provided greater power to detect QTL and to estimate their locations compared to our previous three-year study, identifying one new genetic trade-off and reclassifying one QTL from genetic trade-off to conditionally neutral.</p>
Landscape genomics reveals genetic signals of environmental adaptation of African wild eggplant
<p><span>Crop wild relatives possess desirable traits that confer resilience to various environmental stresses. We applied landscape genomics, that associates environment with genomic variation to understand the genetic basis of their adaptation. <br></span></p> <p> </p> <p><span>In this study, we applied landscape genomics to examine the differences in allele frequency of 15,416 Single Nucleotide Polymorphisms (SNPs) among 153 accessions of wild eggplant relatives from Africa, the principal hotspot of these wild relatives. Further, we explored the correlation between the genetic variations and the bio-climatic and soil conditions at their collection sites.</span></p> <p> </p> <p><span><span>Our results showed that the environment has a greater impact on the genetic variation in the eggplant wild relative populations compared to the geographical distances between collection sites while controlling for population structure. These findings indicate the relevance of the environment in shaping genetic variation in eggplant relatives over time. We detected also candidate SNPs associated with ten environmental factors. Some of these SNPs signal genes involved in pathways that help with adaptation to environmental stresses such as drought, heat, cold, salinity, pests, and diseases. </span><br></span></p>
Soil composition, phenotypic and genetic data to: Adaptive differentiation on serpentine soil in diploid versus autotetraploid populations of Biscutella laevigata (Brassicaceae)
<p><span>Serpentine soils exhibit extreme properties (e.g. high magnesium content) influencing plant growth and survival and have been repeatedly documented to promote adaptive edaphic differentiation in plants. Individuals from four pairs of nearby diploid and autotetraploid populations of <em>Biscutella laevigata</em> sampled on serpentine vs non-serpentine soils in a factorial design are used to assess the genetic and phenotypic changes associated with edaphic origin and ploidy level. Individual samples from natural populations were subjected to soil elemental analysis and genotyping using restriction site-associated DNA sequences (RAD-seq) to link genetic variation with contrasting soils and ploidy levels. In diploids, genetic variation was consistent with demographic contraction and a pattern of isolation by environment with respect to the ratio of calcium / magnesium concentrations, whereas tetraploids presented evidence of expansion with limited edaphic differentiation. The genetic basis of tolerance and adaptation to serpentine was further assessed experimentally on seed-grown individuals from all populations subjected to high (serpentine-like) vs low (control) concentrations of magnesium in hydropony. Fitness-related phenotypic traits under experimental cultivation were consistent with adaptive differentiation among diploid ecotypes but not among the tetraploids that similarly grow in both habitats and consistently present higher investment in roots. Further work comparing experimentally resynthesized polyploids to natural diploids and polyploids has to tease the role of whole genome duplication apart from the impact of post-polyploidy evolution.</span></p>
Rapid and strong population genetic differentiation and genomic signatures of climatic adaptation in an invasive mealybug
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Data from: Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America
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The genetic architecture of repeated local adaptation to climate in distantly related plants
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Data from: Signs of local adaptation by genetic selection and isolation promoted by extreme temperature and salinity in the Mediterranean seagrass Posidonia oceanica
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Data from: Adaptive landscape genetics and malaria across divergent island bird populations
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Evidence that genetic drift not adaptation drives fast-Z and large-Z effects in Ficedula flycatchers
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Genetic differentiation and signatures of local adaptation revealed by RADseq for a highly-dispersive mud crab Scylla olivacea in the Sulu Sea
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The genetic basis of plumage coloration and elevation adaptation in a clade of recently diverged alpine and arctic songbirds
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Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies
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Genetic architecture and adaptation of flowering time among environments
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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