Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Detecting sex-linked genes using genotyped individuals sampled in natural populations.

ABSTRACT: We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. It allows statistical testing for the presence or absence of sex chromosomes, and detection of sex-linked genes based on the posterior probabilities in the model. Furthermore, for gametologous sequences, the haplotype and level of nucleotide polymorphism of each copy can be inferred, as well as the divergence between them. We test the method using simulated data, as well as data from both a relatively recent and an old sex chromosome system (the plant Silene latifolia and humans) and show that, for most cases, robust predictions are obtained with 5 to 10 individuals per sex.

SUBMITTER: Kafer J

PROVIDER: S-EPMC8225351 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Detecting sex-linked genes using genotyped individuals sampled in natural populations.

Käfer Jos J Lartillot Nicolas N Marais Gabriel A B GAB Picard Franck F

Genetics 20210601 2

We propose a method, SDpop, able to infer sex-linkage caused by recombination suppression typical of sex chromosomes. The method is based on the modeling of the allele and genotype frequencies of individuals of known sex in natural populations. It is implemented in a hierarchical probabilistic framework, accounting for different sources of error. It allows statistical testing for the presence or absence of sex chromosomes, and detection of sex-linked genes based on the posterior probabilities in ...[more]

PMID: 33764439

Similar Datasets

Detecting QTL in natural populations

Project description:Whole genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations

| PRJEB11502 | ENA

Using GWAS summary data to impute traits for genotyped individuals.

Project description:Genome-wide association study (GWAS) summary data have become extremely useful in daily routine data analysis, largely facilitating new methods development and new applications. However, a severe limitation with the current use of GWAS summary data is its exclusive restriction to only linear single nucleotide polymorphism (SNP)-trait association analyses. To further expand the use of GWAS summary data, along with a large sample of individual-level genotypes, we propose a nonparametric method for large-scale imputation of the genetic component of the trait for the given genotypes. The imputed individual-level trait values, along with the individual-level genotypes, make it possible to conduct any analysis as with individual-level GWAS data, including nonlinear SNP-trait associations and predictions. We use the UK Biobank data to highlight the usefulness and effectiveness of the proposed method in three applications that currently cannot be done with only GWAS summary data (for SNP-trait associations): marginal SNP-trait association analysis under non-additive genetic models, detection of SNP-SNP interactions, and genetic prediction of a trait using a nonlinear model of SNPs.

| S-EPMC10173780 | biostudies-literature

Detecting Activated Cell Populations Using Single-Cell RNA-Seq

Project description:Single-cell RNA sequencing of mouse amygdala using Drop-Seq

2017-10-11 | GSE103976 | GEO

Expectation-maximization algorithm for determining natural selection of Y-linked genes through two-sex branching processes.

Project description:A two-dimensional bisexual branching process has recently been presented for the analysis of the generation-to-generation evolution of the number of carriers of a Y-linked gene. In this model, preference of females for males with a specific genetic characteristic is assumed to be determined by an allele of the gene. It has been shown that the behavior of this kind of Y-linked gene is strongly related to the reproduction law of each genotype. In practice, the corresponding offspring distributions are usually unknown, and it is necessary to develop their estimation theory in order to determine the natural selection of the gene. Here we deal with the estimation problem for the offspring distribution of each genotype of a Y-linked gene when the only observable data are each generation's total numbers of males of each genotype and of females. We set out the problem in a non parametric framework and obtain the maximum likelihood estimators of the offspring distributions using an expectation-maximization algorithm. From these estimators, we also derive the estimators for the reproduction mean of each genotype and forecast the distribution of the future population sizes. Finally, we check the accuracy of the algorithm by means of a simulation study.

| S-EPMC3440006 | biostudies-literature

Hierarchical organization of spontaneous co-fluctuations in densely sampled individuals using fMRI.

Project description:Edge time series decompose functional connectivity into its framewise contributions. Previous studies have focused on characterizing the properties of high-amplitude frames (time points when the global co-fluctuation amplitude takes on its largest value), including their cluster structure. Less is known about middle- and low-amplitude co-fluctuations (peaks in co-fluctuation time series but of lower amplitude). Here, we directly address those questions, using data from two dense-sampling studies: the MyConnectome project and Midnight Scan Club. We develop a hierarchical clustering algorithm to group peak co-fluctuations of all magnitudes into nested and multiscale clusters based on their pairwise concordance. At a coarse scale, we find evidence of three large clusters that, collectively, engage virtually all canonical brain systems. At finer scales, however, each cluster is dissolved, giving way to increasingly refined patterns of co-fluctuations involving specific sets of brain systems. We also find an increase in global co-fluctuation magnitude with hierarchical scale. Finally, we comment on the amount of data needed to estimate co-fluctuation pattern clusters and implications for brain-behavior studies. Collectively, the findings reported here fill several gaps in current knowledge concerning the heterogeneity and richness of co-fluctuation patterns as estimated with edge time series while providing some practical guidance for future studies.

| S-EPMC10473297 | biostudies-literature

Dynamics of a sex-linked deleterious mutation in populations subject to sex reversal.

Project description:The heterogametic sex chromosomes (i.e. mammalian Y and avian W) do not usually recombine with the homogametic sex chromosomes which is known to lead into rapid degeneration of Y and W due to accumulation of deleterious mutations. On the other hand, some 96% of amphibian species have homomorphic, i.e. non-degenerate Y chromosomes. Nicolas Perrin's fountain-of-youth hypothesis states that this is a result of recombination between X and Y chromosomes in sex-reversed individuals. In this study, I model the consequences of such recombination for the dynamics of a deleterious mutation occurring in Y chromosomes. As expected, even relatively low levels of sex reversal help to purge deleterious mutations. However, the population-dynamic consequences of this depend on the type of selection that operates on the population undergoing sex reversal. Under fecundity selection, sex reversal can be beneficial for some parameter values, whereas under survival selection, it seems to be always harmful.

| S-EPMC3189978 | biostudies-literature

Nutrition knowledge, food choices and diet quality of genotyped and non-genotyped individuals during the COVID-19 pandemic.

Project description:Background: Severe obesity (body mass index ≥ 40 kg/m2) and non-communicable diseases, both influenced by diet, have been associated with COVID-19. Genotype-based personalised nutrition advice may improve nutrition knowledge and enhance behaviour change towards better diet quality compared with conventional recommendations. Aim: To investigate the nutrition knowledge, food choices and diet quality in genotyped and non-genotyped individuals during the COVID-19 pandemic. Methods: One hundred and twenty-three healthy UK adults were recruited using convenience sampling through social networks. The online questionnaire consisted of the General Nutrition Knowledge Questionnaire, the Food Choices Questionnaire, and the EPIC-Norfolk Food Frequency Questionnaire (FFQ). FFQ was used to calculate participant diet quality with the Diet Quality Index-International and socio-demographic and anthropometric data. Results: Median general nutrition knowledge, diet variety and diet balance scores were higher in genotyped compared with non-genotyped individuals (71.0 ± 11.0 vs. 61.0 ± 15.0, p = <.001, 18.00 ± 5.00 vs. 15.00 ± 5.00, p = .007 and 2.00 ± 4.00 vs. 0.00 ± 2.00, p = .025, respectively). Pooled sample multiple regression showed that health motive positively influenced while familiarity motive negatively influenced diet quality index scores (β = .428, t = 4.822, p = <.001 and β = -.356, t = -4.021, p = .001, respectively). Conclusions: Nutrition knowledge and diet quality indices of balance and variety were higher among genotyped compared with non-genotyped individuals; overall diet quality was similar between groups. This may be due to pandemic-specific factors, such as altered motives of food choice and availability.

| S-EPMC9716056 | biostudies-literature

Sex differences in ageing in natural populations of vertebrates.

Project description:In many long-lived vertebrates (including humans), adult males have shorter lifespans than adult females, partly as a result of higher annual rates of mortality in males and partly owing to sex differences in the rate of ageing. A probable explanation of the evolution of sex differences in ageing is that, in polygynous species, intense intrasexual competition between males restricts the number of seasons for which individual males are able to breed successfully, weakening selection pressures favouring adult longevity in males relative to females. If this is the case, sex differences in adult longevity and in the onset and rate of senescence should be greater in polygynous species than in monogamous ones and their magnitude should be related to the duration of effective breeding males compared with females. Here, we use data from longitudinal studies of vertebrates to show that reduced longevity in adult males (relative to females) is commonly associated with a more rapid decline in male than female survival with increasing age and is largely confined to polygynous species. The magnitude of sex differences in adult longevity in different species is consistently related to the magnitude of sex differences in the duration of effective breeding, calculated across surviving adults. Our results are consistent with the suggestion that sex differences in senescence in polygynous species are a consequence of weaker selection for longevity in males than females.

| S-EPMC2293943 | biostudies-literature

Sex-dependent and sex-independent regulatory systems of size variation in natural populations.

Project description:Size of organs/organisms is a polygenic trait. Many of the growth-regulatory genes constitute conserved growth signaling pathways. However, how these multiple genes are orchestrated at the systems level to attain the natural variation in size including sexual size dimorphism is mostly unknown. Here we take a multi-layered systems omics approach to study size variation in the Drosophila wing. We show that expression levels of many critical growth regulators such as Wnt and TGFβ pathway components significantly differ between sexes but not between lines exhibiting size differences within each sex, suggesting a primary role of these regulators in sexual size dimorphism. Only a few growth genes including a receptor of steroid hormone ecdysone exhibit association with between-line size differences. In contrast, we find that between-line size variation is largely regulated by genes with a diverse range of cellular functions, most of which have never been implicated in growth. In addition, we show that expression quantitative trait loci (eQTLs) linked to these novel growth regulators accurately predict population-wide, between-line wing size variation. In summary, our study unveils differential gene regulatory systems that control wing size variation between and within sexes.

| S-EPMC6878047 | biostudies-literature

dQTG.seq: A comprehensive R tool for detecting all types of QTLs using extreme phenotype individuals in bi-parental segregation populations.

Project description:Although methodologies and software packages for bulked segregant analysis (BSA) are well established, it is difficult to detect extremely over-dominant and small-effect genes for quantitative traits in F2 population. To address this issue, we proposed a combinatorial strategy to identify all types of quantitative trait loci (QTLs) using extreme phenotype individuals in F2. To popularize this strategy, we developed an R software package dQTG.seq v1.0.1. It has some features not found in other BSA software packages: 1) new (dQTG-seq1 and dQTG-seq2) and existing (G', deltaSNP, Euclidean distance (ED), and SmoothLOD) methods are available to identify all types of QTLs in bi-parental segregation populations, one data file with two BSA and three QTL-mapping data formats was inputted, and two *.csv files and one figure were outputted; 2) main smoothing methods (AIC, Window size, and Block) have been incorporated into each of the above-mentioned methods; 3) the threshold value of LOD score for significant QTLs is determined by permutation experiments. To save running time, vroom function was used to read the dataset, and parallel operation was used to estimate parameters. In real data analyses, users should select a suitable initial value of window size, depending on the species, and appropriate smoothing methods to obtain the best result. dQTG-seq2 detects more known loci and genes for rice grain number per panicle than composite interval mapping (CIM) and inclusive CIM, especially extremely over-dominant and small-effect genes. A handbook for our software package (https://cran.r-project.org/web/packages/dQTG.seq/index.html) has been provided in the supplemental materials for the users' convenience.

| S-EPMC9120062 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data