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44 results for “genotypic selection”
SNP genotypes for 524 wild mice and selected laboratory strains
<p>SNP genotypes from the Mouse Universal Genotyping Array for 524 wild mice and 12 selected laboratory strains. Data are provided in PLINK binary format (*.bed/*.bim/*.fam files) with an accompanying sample manifest (comma-separated text.)</p>
Detecting frequency-dependent selection through the effects of genotype similarity on fitness components
<p>Frequency-dependent selection (FDS) is an evolutionary regime that can maintain or reduce polymorphisms. Despite the increasing availability of polymorphism data, few effective methods are available for estimating the gradient of FDS from the observed fitness components. We modeled the effects of genotype similarity on individual fitness to develop a selection gradient analysis of FDS. This modeling enabled us to estimate FDS by regressing fitness components on the genotype similarity among individuals. We detected known negative FDS on the visible polymorphism in a wild <em>Arabidopsis</em> and damselfly by applying this analysis to single-locus data. Further, we simulated genome-wide polymorphisms and fitness components to modify the single-locus analysis as a genome-wide association study (GWAS). The simulation showed that negative or positive FDS could be distinguished through the estimated effects of genotype similarity on simulated fitness. Moreover, we conducted the GWAS of the reproductive branch number in <em>Arabidopsis thaliana</em> and found that negative FDS was enriched among the top-associated polymorphisms of FDS. These results showed the potential applicability of the proposed method for FDS on both visible polymorphism and genome-wide polymorphisms. Overall, our study provides an effective method for selection gradient analysis to understand the maintenance or loss of polymorphism.</p>
Data for: Selective elimination of enterovirus genotypes by activated sludge and chlorination
<p>Raw data underlying the journal article "Selective elimination of enterovirus genotypes by activated sludge and chlorination" by Larivé et al., <em>Environmental Science: Water Research and Technology</em>, 2023 (doi: 10.1039/d3ew00050h)</p> <p>One CSV file for each of Figures 2-6 of the main manuscript $</p> <p>One CSV file for each of Figures S5, S6 and S7 of the Supplementary information. The data for Figures S2, S3 and S4 are summarized in a single CSV file.</p>
Detecting frequency-dependent selection through the effects of genotype similarity on fitness components
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Single-arm Trial of BIBW 2992 (Afatinib) in Demographically and Genotypically Selected NSCLC Patients
ClinicalTrials.gov study NCT00730925. IPD Sharing: Not stated. Countries: 2. Publications: 1.
SNP genotype and hyperspectral reflectance data from: Ensembles of genomic and hyperspectral imaging-based prediction enable selection for reduced deoxynivalenol content in wheat grains
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Data from: Supplementary stocking selects for domesticated genotypes
Stocking of hatchery produced fish is common practise to mitigate declines in natural populations and may have unwanted genetic consequences. Here we describe a novel phenomenon arising where broodstock used for stocking may be introgressed with farmed individuals. We test how stocking affects introgression in a wild population of Atlantic salmon (Salmo salar) by quantifying how the number of adult offspring recaptured in a stocked river depend on parental introgression. We found that hatchery conditions favour farmed genotypes such that introgressed broodstock produce up to four times the number of adult offspring compared to non-introgressed broodstock, leading to increased introgression in the recipient spawning population. Our results provide the first empirical evidence that stocking can unintentionally favour introgressed individuals and through selection for domesticated genotypes compromise the fitness of stocked wild populations.
Negative frequency-dependent selection maintains coexisting genotypes during fluctuating selection
Natural environments are rarely static; rather selection can fluctuate on time scales ranging from hours to centuries. However, it is unclear how adaptation to fluctuating environments differs from adaptation to constant environments at the genetic level. For bacteria, one key axis of environmental variation is selection for planktonic or biofilm modes of growth. We conducted an evolution experiment with <i>Burkholderia cenocepacia</i>, comparing the evolutionary dynamics of populations evolving under constant selection for either biofilm formation or planktonic growth with populations in which selection fluctuated between the two environments on a weekly basis. Populations evolved in the fluctuating environment shared many of the same genetic targets of selection as those evolved in constant biofilm selection, but were genetically distinct from the constant planktonic populations. In the fluctuating environment, mutations in the biofilm-regulating genes wspA and rpfR rose to high frequency in all replicate populations. A mutation in wspA first rose rapidly and nearly fixed during the initial biofilm phase but was subsequently displaced by a collection of rpfR mutants upon the shift to the planktonic phase. The wspA and rpfR genotypes coexisted via negative frequency-dependent selection around an equilibrium frequency that shifted between the environments. The maintenance of coexisting genotypes in the fluctuating environment was unexpected. Under temporally fluctuating environments coexistence of two genotypes is only predicted under a narrow range of conditions, but the frequency-dependent interactions we observed provide a mechanism that can increase the likelihood of coexistence in fluctuating environments.
Data from: SNP genotyping identifies new signatures of selection in a deep sample of West African P. falciparum malaria parasites
We used a high density SNP array to genotype 75 P. falciparum isolates recently collected from Senegal and The Gambia in order to search for signals of selection in this malaria endemic region. We found little geographic or temporal stratification of the genetic diversity among the sampled parasites. Through application of the iHS and REHH haplotype-based tests for positive selection, we found evidence of recent selective sweeps at a known drug resistance locus, at several known antigenic loci, and at several genomic regions not previously identified as sites of recent selection. We discuss the value of deep population-specific genomic analyses for identifying selection signals within sampled endemic populations of parasites, which may correspond to local selection pressures such as distinctive therapeutic regimes or mosquito vectors.
Data from: Evidence for selection-by-environment but not genotype-by-environment interactions for fitness-related traits in a wild mammal population
How do environmental conditions influence selection and genetic variation in wild populations? There is widespread evidence for selection-by-environment interactions (S*E), but we reviewed studies of natural populations estimating the extent of genotype-by-environment interactions (G*E) in response to natural variation in environmental conditions, and found that evidence for G*E appears to be rare within single populations in the wild. Studies estimating the simultaneous impact of environmental variation on both selection and genetic variation are especially scarce. Here, we used 24 years of data collected from a wild Soay sheep population to quantify how an important environmental variable, population density, impacts upon (1) selection through annual contribution to fitness and (2) expression of genetic variation, in six morphological and life-history traits: body weight; hind leg length; parasite burden; horn length; horn growth; and testicular circumference. Our results supported the existence of S*E: selection was stronger in years of higher population density in all traits apart from horn growth, with directional selection being stronger under more adverse conditions. Quantitative genetic models revealed significant additive genetic variance for body weight, leg length, parasite burden, horn length and testes size, but not for horn growth or our measure of annual fitness. However, random regression models found variation between individuals in their responses to the environment in only three traits, and did not support the presence of G*E for any trait. Our analyses of St Kilda Soay sheep data thus concurs with our cross-study review that, while natural environmental variation within a population can profoundly alter the strength of selection on phenotypic traits, there is less evidence for its effect on the expression of genetic variance in the wild.
Data from: Reconstructing paternal genotypes to infer patterns of sperm storage and sexual selection in the hawksbill turtle
Postcopulatory sperm storage can serve a range of functions, including ensuring fertility, allowing delayed fertilization and facilitating sexual selection. Sperm storage is likely to be particularly important in wide-ranging animals with low population densities, but its prevalence and importance in such taxa, and its role in promoting sexual selection, are poorly known. Here, we use a powerful microsatellite array and paternal genotype reconstruction to assess the prevalence of sperm storage and test sexual selection hypotheses of genetic biases to paternity in one such species, the critically endangered hawksbill turtle, Eretmochelys imbricata. In the majority of females (90.7%, N = 43), all offspring were sired by a single male. In the few cases of multiple paternity (9.3%), two males fertilized each female. Importantly, the identity and proportional fertilization success of males were consistent across all sequential nests laid by individual females over the breeding season (up to five nests over 75 days). No males were identified as having fertilized more than one female, suggesting that a large number of males are available to females. No evidence for biases to paternity based on heterozygosity or relatedness was found. These results indicate that female hawksbill turtles are predominantly monogamous within a season, store sperm for the duration of the nesting season and do not re-mate between nests. Furthermore, females do not appear to be using sperm storage to facilitate sexual selection. Consequently, the primary value of storing sperm in marine turtles may be to uncouple mating and fertilization in time and avoid costly re-mating.
Data from: Genotype by sequencing identifies natural selection as a driver of intraspecific divergence in Atlantic populations of the high dispersal marine invertebrate, Macoma petalum
Mitochondrial DNA analyses indicate that the Bay of Fundy population of the intertidal tellinid bivalve Macoma petalum is genetically divergent from coastal populations in the Gulf of Maine and Nova Scotia. To further examine the evolutionary forces driving this genetic break, we performed double digest genotype by sequencing (GBS) to survey the nuclear genome for evidence of both neutral and selective processes shaping this pattern. The resulting reads were mapped to a partial transcriptome of its sister species, M. balthica, to identify single nucleotide polymorphisms (SNPs) in protein-coding genes. Population assignment tests, principle components analyses, analysis of molecular variance, and outlier tests all support differentiation between the Bay of Fundy genotype and the genotypes of the Gulf of Maine, Gulf of St. Lawrence, and Nova Scotia. Although both neutral and non-neutral patterns of genetic subdivision were significant, genetic structure among the regions was nearly 20 times higher for loci putatively under selection, suggesting a strong role for natural selection as a driver of genetic diversity in this species. Genetic differences were the greatest between the Bay of Fundy and all other population samples, and some outlier proteins were involved in immunity-related processes. Our results suggest that in combination with limited gene flow across the mouth of the Bay of Fundy, local adaptation is an important driver of intraspecific genetic variation in this marine species with high dispersal potential.
Western redcedar single nucleotide polymorphism (SNP) genotyping data for genomic selection and population genetics
<p>Western redcedar (<em>Thuja plicata</em>) Single Nucleotide Polymorphism (SNP) data in Variant Call Format (VCF) for genomic selection training and target populations, genomic selection parents, and self-fertilized (selfing) lines, comprising 4,833 trees.</p> <p>Targeted sequencing-based genotyping was done by Capture-Seq methodology at Rapid Genomics (Neves est al. 2013). A set of 57,000 probes as designed for initial marker discovery, from which a panel of 20,858 probes was selected for genotyping. A set of transcriptomes (Shalev et al. 2018) (PRJNA704616) was aligned to the reference genome to identify SNPs. Candidate probes (120 nt) were initially designed in silico and 57,000 selected by removing candidates with poor base composition for hybridization (GC content <0.2 and >0.6, high G content >0.2 and long homopolymers >7), followed by removing probes aligning to more than one position on the reference genome (≥90% identity and length). The 57,000 probes represent 14,517 scaffolds (average 3.9 probes/scaffold), with 37,275 targeting at least one SNP and 19,725 mapping to intergenic regions not containing pre-identified SNPs. A set of 128 individuals were selected to validate the 57,000 probe panel and associated polymorphisms. Genomic DNA (0.5 ug) was fragmented (mean size 300 bp), followed by repair of ends, phosphorylation, adenylation, ligation of Illumina compatible adapters containing 8bp indexes and 5’ T-overhang, and 10 cycles PCR amplification with universal primers to produce sequencing-ready libraries. Libraries were quantified using PicoGreen. Libraries from 16 samples were pooled, hybridized to the 120 nt RNA probes following Agilent’s SureSelect Target Enrichment System (Agilent Technologies) and sequenced on an Illumina HiSeq X machine with paired-end 150bp cycle for an average sequencing depth per sample of 15X. Sequence data were aligned to the reference genome with BWA-MEM (http://arxiv.org/abs/1303.3997) and sets of four samples were combined to increase sequencing depth for identifying markers. Putative SNPs were identified using Freebayes (http://arxiv.org/abs/1207.3907) in 150bp on either side of the 57,000 probes and filtered probes that had more than 17 SNPs per 420 bp target region (150bp + 120bp + 150bp). The sequencing depth of the probes was used to select the final set of 20,885 probes, removing probes on both sides of the distribution (low and high sequencing depth), for Capture-Seq on the remainder of the samples.</p>
Genomic Selection Paves Way for the Identification of Rust Disease Resistant Genotypes in Bread Wheat (Triticum aestivum).
<p><span>In the last two decades, genomic prediction (GP) or Genomic Selection (GS) methods have been widely adopted in various plant and animal breeding programs globally. GP/GS is a promising method that employs genomic markers to calculate genomic-estimated breeding values (GEBVs) to select best individuals. To evaluate the performance of different genomic selection (GS) models, we examined six different models namely, ridge regression (RR), least absolute shrinkage and selection operator (LASSO), genomic best linear unbiased prediction (GBLUP), elastic net (EN), reproducing kernel Hilbert spacing (RKHS), and random forest (RF) models, for seedling and adult plant resistance to leaf, stem and stripe rust of wheat using a panel of 347 wheat germplasm accessions. The GBLUP and RF models performed noticeably better than the other GS models, with mean predictive abilities of 0.5 and 0.4 for seedling resistance and 0.4 and 0.3 for adult plant resistance (APR) for leaf and stem rust, respectively. Unfortunately, except for a few environments, the performance of GP models in the current study is quite low for stripe rust for both seedling and APR. The outcomes of this study revealed the capability of GP to be applied for breeding initiatives aimed at developing wheat varieties resistant to rust diseases. </span><span>Moreover, based on favorable allele analysis we also identified a total of 2 lines (CRP-165/42, HGP1-470) that showed resistance to most of the pathotypes at seedling and adult plant stage to all three rusts.<strong><span> </span></strong>These lines can serve as valuable resources for future breeding programs focused on rust resistance.</span></p> <p><strong><span>Keywords: </span></strong><span>GS;</span><strong><span> </span></strong><span>GEBVs; leaf rust; stem rust; stripe rust; seedling resistance; APR</span></p>
FIG. 3. Conchological diOEerentiation among the homozygous genotypes Aat 1 in Selection and habitat-speci®c allozyme variation in the self-fertilizing land snail Cochlicopa lubrica (O. F. MuÈller)
FIG. 3. Conchological diOEerentiation among the homozygous genotypes Aat 1`20 ' and Aat 1`80' of Cochlicopa lubrica. The two groups are very similar with respect to the four shell dimensions. Discriminant scores are extracted with`shell height',`shell diameter',`diameter of the last whorl' and`diameter of the penultimate shell whorl'. Data of 316 shells are incorporated.
Data for: Genotypes selected for early and late avian lay date differ in their phenotype, but not fitness, in the wild
<p><span>Global warming has shifted phenological traits in many species, but whether species are able to track further increasing temperatures depends on the fitness consequences of additional shifts in phenological traits. To test this, we conducted a genomic selection experiment on wild great tits from the Hoge Veluwe study population (The Netherlands) to obtain great tits (<em>Parus</em> <em>major</em>) with genotypes for extremely early and late egg lay dates and measured phenology and fitness of selected great tit females under wild conditions.</span></p> <p><span>Females with early genotypes advanced lay dates relative to females with late genotypes, but not relative to non-selected females. Females with early and late genotypes did not differ in the number of fledglings produced, in line with the weak effect of lay date on the number of fledglings produced by non-selected females in the years of the experiment. Our study is the first application of genomic selection in the wild and led to an asymmetric phenotypic response that indicates the presence of constraints toward early, but not late, lay dates.</span></p>
CYP2C19 Genotype-Guided P2Y12 Receptor Inhibitor Selection After Complex Percutaneous Coronary Intervention
ClinicalTrials.gov study NCT06283888. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Prospective Treatment Efficacy in IPF Using Genotype for Nac Selection (PRECISIONS) Trial
ClinicalTrials.gov study NCT04300920. IPD Sharing: YES. Countries: 1. Publications: 1.
Genotype Guided Versus Conventional Approach in Selection of Oral P2Y12 Receptor Blocker in Chinese Patients Suffering From Acute Coronary Syndrome
ClinicalTrials.gov study NCT01994941. IPD Sharing: Not stated. Countries: 1. Publications: 9.
Data from: Genotype x environment interaction obscures genetic sources of variation in seed size in Dithyrea californica but provides the opportunity for selection on phenotypic plasticity
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