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45 results for “genotypic adaptation”
Data from: The magnitude of local adaptation under genotype-dependent dispersal
Dispersal moves individuals from patches where their immediate ancestors were successful to sites where their genotypes are untested. As a result, dispersal generally reduces fitness, a phenomenon known as "migration load." The strength of migration load depends on the pattern of dispersal and can be dramatically lessened or reversed when individuals move preferentially toward patches conferring higher fitness. Evolutionary ecologists have long modeled nonrandom dispersal, focusing primarily on its effects on population density over space, the maintenance of genetic variation, and reproductive isolation. Here, we build upon previous work by calculating how the extent of local adaptation and the migration load are affected when individuals differ in their dispersal rate in a genotype-dependent manner that alters their match to their environment. Examining a one-locus, two-patch model, we show that local adaptation occurs through a combination of natural selection and adaptive dispersal. For a substantial portion of parameter space, adaptive dispersal can be the predominant force generating local adaptation. Furthermore, genetic load may be largely averted with adaptive dispersal whenever individuals move before selective deaths occur. Thus, to understand the mechanisms driving local adaptation, biologists must account for the extent and nature of nonrandom, genotype-dependent dispersal, and the potential for adaptation via spatial sorting of genotypes.
Local adaptation to hosts and parasitoids shape Hamiltonella defensa genotypes across aphid species - Datasets and scripts
<p>Datasets and scripts from "Local adaptation to hosts and parasitoids shape <em>Hamiltonella defensa</em> genotypes across aphid species"</p>
Individually Adapted Therapy Duration for the Treatment of Chronic Hepatitis C Genotype 1 Infection
ClinicalTrials.gov study NCT00351403. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: The role of immigration and local adaptation on fine-scale genotypic and phenotypic population divergence in a less mobile passerine
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Data from: The magnitude of local adaptation under genotype-dependent dispersal
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Data from: Genotypic diversity in root-endophytic fungi reflects efficient dispersal and environmental adaptation
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Data from: Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide SNP genotyping
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Data from: Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing
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Data from: A phenotype-genotype codon model for detecting adaptive evolution
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Individual genotypes of 1 416 brook trout genotyped at 14 779 high-quality SNPs for studying local adaptation and maladaptation in small populations
<p><span><span><span><span><span><span><span><span><span><span><span>Investigating the relative importance of neutral <i>versus</i> selective processes governing the accumulation of genetic variants is a key goal in both evolutionary and conservation biology. This is particularly true in the context of small populations, where genetic drift can counteract the effect of selection. Using Brook Charr (<i>Salvelinus fontinalis</i>) from Québec, Canada as a case study, we investigated the importance of demographic <i>versus</i> selective processes governing the accumulation of both adaptive and maladaptive mutations in closed <i>versus</i> open and connected populations to assess gene flow effect. This was achieved by using 14 779 high-quality filtered SNPs genotyped among 1 416 fish representing 50 populations from three life history types: lacustrine (closed populations), riverine and anadromous (connected populations). Using the Provean algorithm, we observed a considerable accumulation of putative deleterious mutations across populations. The absence of correlation between the occurrence of putatively beneficial or deleterious mutations and local recombination rate supports the hypothesis that genetic drift might be the main driver of the accumulation of such variants. However, despite a lower genetic diversity observed in lacustrine than in riverine or anadromous populations, lacustrine populations do not exhibit more deleterious mutations than the two other history types, suggesting that the negative effect of genetic drift in lacustrine populations may be mitigated by that of relaxed purifying selection. Moreover, we also identified genomic regions associated with anadromy, as well as an overrepresentation of transposable elements associated with variation in environmental variables, thus supporting the importance of transposable elements in adaptation. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Evolutionary rescue and local adaptation under different rates of temperature increase: a combined analysis of changes in phenotype expression and genotype frequency in Paramecium microcosms
Evolutionary Rescue (ER) occurs when populations, which have declined due to rapid environmental change, recover through genetic adaptation. The success of this process and the evolutionary trajectory of the population strongly depend on the rate of environmental change. Here we investigated how different rates of temperature increase (from 23°C to 32°C) affect population persistence and evolutionary change in experimental microcosms of the protozoan Paramecium caudatum. Consistent with theory on ER, we found that those populations experiencing the slowest rate of temperature increase were the least likely to become extinct and tended to be the best adapted to the new temperature environment. All high-temperature populations were more tolerant to severe heat stress (35°C, 37°C), indicating a common mechanism of heat protection. High-temperature populations also had superior growth rates at optimum temperatures, leading to the absence of a pattern of local adaptation to control (23°C) and high-temperature (32°C) environments. However, high-temperature populations had reduced growth at low temperatures (5-9°C), causing a shift in the temperature niche. In part, the observed evolutionary change can be explained by selection from standing variation. Using mitochondrial markers, we found complete divergence between control and high-temperature populations in the frequencies of six initial founder genotypes. Our results confirm basic predictions of ER and illustrate how adaptation to an extreme local environment can produce positive as well as negative correlated responses to selection over the entire range of the ecological niche.
Data from: Inferring the potentially complex genetic architectures of adaptation, sexual dimorphism, and genotype by environment interactions by partitioning of mean phenotypes.
Genetic architecture fundamentally affects the way that traits evolve. However, the mapping of genotype to phenotype includes complex interactions with the environment or even the sex of an organism that can modulate the expressed phenotype. Line cross analysis is a powerful quantitative genetics method to infer genetic architecture by analyzing the mean phenotype value of two diverged strains and a series of subsequent crosses and backcrosses. However, it has been difficult to account for complex interactions with the environment or sex within this framework. We have developed extensions to line cross analysis that allow for gene by environment and gene by sex interactions. Using extensive simulations studies and reanalysis of empirical data, we show that our approach can account for both unintended environmental variation when crosses cannot be reared in a common garden and can be used to test for the presence of gene by environment or gene by sex interactions. In analyses that fail to account for environmental variation between crosses we find that line cross analysis has low power and high false positive rates. However, we illustrate that accounting for environmental variation allows for the inference of adaptive divergence, and that accounting for sex differences in phenotypes allows practitioners to infer the genetic architecture of sexual dimorphism.
Fig. 3 in Host-adapted Cryptosporidium and Enterocytozoon bieneusi genotypes in straw-colored fruit bats in Nigeria
Fig. 3. Phylogeny of Cryptosporidium genotypes in bats based on Bayesian inference of sequences of the small subunit rRNA gene. The posterior probability values are indicated on the branches. Red ones are Cryptosporidium genotypes identified in straw-colored fruit bats in the present study, while blue ones are known Cryptosporidium genotypes previously reported in bats. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)
PERVASIVE ADAPTATION OF HEPATITIS C VIRUS TO INTERFERON LAMBDA POLYMORPHISM ACROSS MULTIPLE GENOTYPES
<p>Genetic polymorphism in the interferon lambda (IFN-λ) region is associated with spontaneous clearance of hepatitis C virus (HCV) infection and with response to interferon-based antiviral treatment. Here, we evaluate the associations between IFN-λ polymorphism and HCV variation by performing a genome-to-genome analysis in 8,729 patients from diverse ancestral backgrounds infected with various HCV genotypes. We searched for associations between human rs12979860 genotype, a tag for IFN-λ haplotypes, and amino acid variants in the NS3, NS4A, NS5A and NS5B proteins of HCV. We report multiple associations between host and pathogen variants in the full cohort as well as in subgroups defined by viral genotype and human ancestry. We also assess the combined impact of human and HCV variation on pre-treatment viral load. By demonstrating that IFN-λ genetic variation leaves a large footprint in the viral genome, this study provides strong evidence of pervasive viral adaptation to host innate immune pressure during chronic HCV infection.</p>
Data from: Evolutionary rescue and local adaptation under different rates of temperature increase: a combined analysis of changes in phenotype expression and genotype frequency in Paramecium microcosms
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Data from: Inferring the potentially complex genetic architectures of adaptation, sexual dimorphism, and genotype by environment interactions by partitioning of mean phenotypes.
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Data from: Genotype-by-environment interactions due to antibiotic resistance and adaptation in Escherichia coli
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Individual genotypes of 1 416 brook trout genotyped at 14 779 high-quality SNPs for studying local adaptation and maladaptation in small populations
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Data from: Different DMRT3 genotypes are best adapted for harness racing and riding in Finnhorses
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Phenotype data, genotype input files, and scripts related to adaptation in wild house mice from Western North America
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
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.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.