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26 results for “Genetic conflict”
Solutions and Genetic algorithm dataset of the Scenarios used for the Validation of the Conflict Detection and Resolution Use Case (ARTIMATION )
<p>This dataset contains the <strong>solution </strong>of the scenarios used for one of the validation of the ARTIMATION project: Conflict Detection and Resolution (CD&R) use case (link).</p> <p>The solution are computed by a Genetic Algorithm developped by Nicolas Durand.<br> <br> Inside, one can find:</p> <p>-One archive, "GA_Scenario_Solution_Dataset.zip", containing 10 couple of files (so 20 files). Each couple of file "sol_X_1.csv" and "sols_X_1.csv" are reciprocally the solutino given by the Genetic Algorithm to scenario X, and all the candidate solution explroed by the GA while solving scenario X. This archive also contain other versions of the solutions made by the GA with other parameters.<br> <br> -One archive, "GA_Toy_Dataset.zip" , containing solution to random scenarios, used to develop the first interfaces.</p> <p>Those solutions are used to developp the heatmatrix and heatmaps of the project (link), and visualisations for the validation (link).</p>
Data from: Testing concordance and conflict in spatial replication of landscape genetics inferences
<p class="MsoNormal">The degree to which landscape genetics findings can be extrapolated to different areas of a species range is poorly understood. Here, we used a broadly distributed ectothermic lizard (<em>Sceloporus occidentalis</em>, Western Fence lizard) as a model species to evaluate the full role of topography, climate, vegetation, and roads on dispersal and genetic differentiation. We conducted landscape genetics analyses in five areas within the Sierra Nevada mountain range. Genetic distances calculated from thousands of ddRAD markers were used to optimize landscape resistance surfaces and infer the effects of landscape and topographic features. Across study areas, we found a great deal of consistency in the primary environmental gradients impacting genetic connectivity, along with some site-specific differences, and a range in the proportion genetic variance explained by environmental factors across study sites. High-elevation colder areas were consistently found to be barriers to gene flow, as were areas of high ruggedness and slope. High temperature seasonality and high precipitation during the winter wet season also presented a substantial barrier to gene flow in a majority of study areas. The effect of other landscape variables on genetic differentiation was more idiosyncratic and depended on specific attributes at each site. Across study areas, canyon valleys were always implicated as facilitators to dispersal and key features linking populations and maintaining genetic connectivity, though the relative importance varied in different areas. We emphasize that spatial data layers are complex and multidimensional, and careful consideration of spatial data correlation structure and robust analytic frameworks will be critical to our continued understanding of spatial genetics processes.</p>
The sacred deer conflict of management after a 1000-year history: Hunting in the name of conservation or loss of their genetic identity
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Data from: Testing concordance and conflict in spatial replication of landscape genetics inferences
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Data from: Intralocus tactical conflict: genetic correlations between fighters and sneakers of the dung beetle Onthophagus taurus
Males and females differ in their phenotypic optima for many traits, and since the majority of genes are expressed in both sexes, some alleles can be beneficial to one sex but harmful to the other (intralocus sexual conflict; ISC). ISC theory has recently been extended to intrasexual dimorphisms, where certain alleles may have opposite effects on the fitness of males of different morphs that employ alternative reproductive tactics (intralocus tactical conflict; ITC). Here we use a half-sib breeding design to investigate the genetic basis for ISC and ITC in the dung beetle Onthophagus taurus. We found positive heritabilities and intersexual genetic correlations for almost all traits investigated. Next, we calculated the intrasexual genetic correlation between males of different morphs for horn length, a sexually selected trait, and compared it to intrasexual correlations for naturally selected traits in both sexes. Intrasexual genetic correlations did not differ significantly between the sexes or between naturally and sexually selected traits, failing to support the hypothesis that horns present a reduction of intrasexual genetic correlations due to ITC. We discuss the implications for the idea of developmental reprogramming between male morphs, and emphasize the importance of genetic correlations as constraints for the evolution of dimorphisms.
Data from: Sexual conflict and interacting phenotypes: a quantitative genetic analysis of fecundity and copula duration in Drosophila melanogaster
Many reproductive traits that have evolved under sexual conflict may be influenced by both sexes. Investigation of the genetic architecture of such traits can yield important insight into their evolution, but this entails that the heritable component of variation is estimated for males and females – as an interacting phenotype. We address the lack of research in this area through an investigation of egg production and copula duration in the fruit fly, Drosophila melanogaster. Despite egg production rate being determined by both sexes, which may cause sexual conflict, an assessment of this trait as an interacting phenotype is lacking. It is currently unclear whether copula duration is determined by males and/or females. We found significant female, but not male, genetic variance for egg production rate which may indicate reduced potential for ongoing sexually antagonistic coevolution. In contrast, copula duration was determined by significant genetic variance in both sexes. We also identified genetic variation in egg retention among virgin females. Although previously identified in wild populations, it is unclear why this should be present in a laboratory stock. This study provides a novel insight into the shared genetic architecture of reproductive traits that are the subject of sexual conflict.
Data from: Population biology of establishment in New Zealand hedgehogs inferred from genetic and historical data: conflict or compromise?
The crucial steps in biological invasions, related to the shaping of genetic architecture and the current evolution of adaptations to a novel environment, usually occur in small populations during the phases of introduction and establishment. However, these processes are difficult to track in nature due to invasion lag, large geographic and temporal scales compared with human observation capabilities, the frequent depletion of genetic variance, admixture and other phenomena. In this study, we compared genetic and historical evidence related to the invasion of the West European hedgehog to New Zealand to infer details about the introduction and establishment. Historical information indicates that the species was initially established on the South Island. A molecular assay of populations from Great Britain and New Zealand using mitochondrial sequences and nuclear microsatellite loci was performed based on a set of analyses including approximate Bayesian computation, a powerful approach for disentangling complex population demographies. According to these analyses, the population of the North Island was most similar to that of the native area and showed greatest reduction in genetic variation caused by founder demography and/or drift. This evidence indicated the location of the establishment phase. The hypothesis was corroborated by data on climate and urbanization. We discuss the contrasting results obtained by the molecular and historical approaches in the light of their different explanatory power and the possible biases influencing the description of particular aspects of invasions, and we advocate the integration of the two types of approaches in invasion biology.
Genetic basis of cytonuclear conflicts in citrus hybridization, domestication, and diversification
<p>184.cp.variations.map.vcf.zip--the chloroplast variation map of 184 samples<br> 184.mt.variations.map.vcf.zip----the mitochondrial variation map of 184 samples<br> aligment1.fa-- the group of grapefruit, sweet orange and sour orange for mitochondrial heteroplasmy analysis<br> aligment2.fa-- the group of lemon for mitochondrial heteroplasmy analysis<br> coverage depth of 184 short reads samples.zip -- the coverage depth of BAMs in mitochondrial variation map in 184 samples<br> Fortunella hindsii mitochondrial genome.gb -- the conservation proteins annotation of kumquat reference mitochondrial genome<br> GWAS-118.samples.input.phenotype.for GWAS.txt -- the inputfiles for GWAS <br> GWAS-LD.linked.input.gwas.vcf.gz -- the LD linked variations for GWAS<br> LD.purning.nuclear.variation.map.vcf.gz -- LD purning nuclear variations for demography analysis<br> normalization.RNA-seqs.txt -- the nomarlization data of expression of mitochondrial genome<br> nuclear.variation.map.vcf.gz -- the nuclaer variation map<br> ORFs annotation based on Augustus.gtf -- the annotation gene structure using Augustus <br> pan-genome and aligned mitochondrial genomes.zip -- the pan-genome(.fa and .gfa) and aligned mitochondrial genomes<br> scaffold-assemblies.zip -- the scaffolds of mitochondrial genomes</p>
Data from: Population biology of establishment in New Zealand hedgehogs inferred from genetic and historical data: conflict or compromise?
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Data from: Intralocus tactical conflict: genetic correlations between fighters and sneakers of the dung beetle Onthophagus taurus
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Data from: Sexual conflict and interacting phenotypes: a quantitative genetic analysis of fecundity and copula duration in Drosophila melanogaster
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Data from: Indirect genetic effects and sexual conflicts: Partner genotype influences multiple morphological and behavioural reproductive traits in a flatworm
The expression of an individual's phenotypic traits can be influenced by genes expressed in its social partners. Theoretical models predict that such indirect genetic effects (IGEs) on reproductive traits should play an important role in determining the evolutionary outcome of sexual conflict. However, empirical tests of (i) whether reproductive IGEs exist, (ii) how they vary among genotypes, and (iii) whether they are uniform for different types of reproductive traits are largely lacking. We addressed this in a series of experiments in the simultaneously hermaphroditic flatworm Macrostomum lignano. We found strong evidence for IGEs on both morphological and behavioural reproductive traits. Partner genotype had a significant impact on the testis size of focal individuals—varying up to 2.4-fold—suggesting that IGEs could mediate sexual conflicts that target the male sex function. We also found that time to first copulation was affected by a genotype × genotype interaction between mating partners, and that partner genotype affected the propensity to copulate and perform the postcopulatory suck behaviour, which may mediate conflicts over the fate of received ejaculate components. These findings provide clear empirical evidence for IGEs on multiple behavioural and morphological reproductive traits, which suggests that the evolutionary dynamics of these traits could be altered by genes contained in the social environment.
Data from: Genetic conflict with a parasitic nematode disrupts the legume-rhizobia mutualism
Genetic variation for partner quality in mutualisms is an evolutionary paradox. One possible resolution to this puzzle is that there is a tradeoff between partner quality and other fitness-related traits. Here, we tested whether a susceptibility to parasitism is one such tradeoff in the mutualism between legumes and nitrogen-fixing bacteria (rhizobia). We performed two greenhouse experiments with the legume Medicago truncatula. In the first, we inoculated each plant with the rhizobia Ensifer meliloti and with one of 40 genotypes of the parasitic root-knot nematode Meloidogyne hapla. In the second experiment, we inoculated all plants with rhizobia and half of the plants with a genetically variable population of nematodes. Using the number of nematode galls as a proxy for infection severity, we found that plant genotypes differed in susceptibility to nematode infection, and nematode genotypes differed in infectivity. Second, we showed that there was a genetic correlation between the number of mutualistic structures formed by rhizobia (nodules) and the number of parasitic structures formed by nematodes (galls). Finally, we found that nematodes disrupt the rhizobia mutualism: nematode-infected plants formed fewer nodules and had less nodule biomass than uninfected plants. Our results demonstrate that there is genetic conflict between attracting rhizobia and repelling nematodes in Medicago. If genetic conflict with parasitism is a general feature of mutualism, it could account for the maintenance of genetic variation in partner quality and influence the evolutionary dynamics of positive species interactions.
Data from: Divergent selection on, but no genetic conflict over, female and male timing and rate of reproduction in a human population
The sexes often have different phenotypic optima for important life-history traits, and because of a largely shared genome this can lead to a conflict over trait expression. In mammals, the obligate costs of reproduction are higher for females, making reproductive timing and rate especially liable to conflict between the sexes. While studies from wild vertebrates support such sexual conflict, it remains unexplored in humans. We used a pedigreed human population from preindustrial Finland to estimate sexual conflict over age at first and last reproduction, reproductive lifespan and reproductive rate. We found that the phenotypic selection gradients differed between the sexes. We next established significant heritabilities in both sexes for all traits. All traits, except reproductive rate, showed strongly positive intersexual genetic correlations and were strongly genetically correlated with fitness in both sexes. Moreover, the genetic correlations with fitness were almost identical in men and women. For reproductive rate, the intersexual correlation and the correlation with fitness were weaker but again similar between the sexes. Thus, in this population, an apparent sexual conflict at the phenotypic level did not reflect an underlying genetic conflict over the studied reproductive traits. These findings emphasize the need for incorporating genetic perspectives into studies of human life-history evolution.
Genetic Counselors' Experiences of Moral Value Conflicts With Clients
ClinicalTrials.gov study NCT00360711. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Mixed evidence for the erosion of inter-tactical genetic correlations through intralocus tactical conflict
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Data from: Genetic conflict with a parasitic nematode disrupts the legume-rhizobia mutualism
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Data from: Divergent selection on, but no genetic conflict over, female and male timing and rate of reproduction in a human population
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Data from: The mammalian complement system as an epitome of host–pathogen genetic conflicts
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Data from: Indirect genetic effects and sexual conflicts: Partner genotype influences multiple morphological and behavioural reproductive traits in a flatworm
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