Browse
Submit Data
Databases
API
Help

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes.

ABSTRACT: We present an expanded data set of 50 unlinked autosomal noncoding regions, resequenced in samples of Hausa from Cameroon, Italians, and Chinese. We use these data to make inferences about human demographic history by using a technique that combines multiple aspects of genetic data, including levels of polymorphism, the allele frequency spectrum, and linkage disequilibrium. We explore an extensive range of demographic parameters and demonstrate that our method of combining multiple aspects of the data results in a significant reduction of the compatible parameter space. In agreement with previous reports, we find that the Hausa data are compatible with demographic equilibrium as well as a set of recent population expansion models. In contrast to the Hausa, when multiple aspects of the data are considered jointly, the non-Africans depart from an equilibrium model of constant population size and are compatible with a range of simple bottleneck models, including a 50-90% reduction in effective population size occurring some time after the appearance of modern humans in Africa 160,000-120,000 years ago.

SUBMITTER: Voight BF

PROVIDER: S-EPMC1311907 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Experimental river delta size set by multiple floods and backwater hydrodynamics.

Project description:River deltas worldwide are currently under threat of drowning and destruction by sea-level rise, subsidence, and oceanic storms, highlighting the need to quantify their growth processes. Deltas are built through construction of sediment lobes, and emerging theories suggest that the size of delta lobes scales with backwater hydrodynamics, but these ideas are difficult to test on natural deltas that evolve slowly. We show results of the first laboratory delta built through successive deposition of lobes that maintain a constant size. We show that the characteristic size of delta lobes emerges because of a preferential avulsion node-the location where the river course periodically and abruptly shifts-that remains fixed spatially relative to the prograding shoreline. The preferential avulsion node in our experiments is a consequence of multiple river floods and Froude-subcritical flows that produce persistent nonuniform flows and a peak in net channel deposition within the backwater zone of the coastal river. In contrast, experimental deltas without multiple floods produce flows with uniform velocities and delta lobes that lack a characteristic size. Results have broad applications to sustainable management of deltas and for decoding their stratigraphic record on Earth and Mars.

| S-EPMC4928958 | biostudies-literature

Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation in Drosophila melanogaster.

Project description:Complete genome resequencing of populations holds great promise in deconstructing complex polygenic traits to elucidate molecular and developmental mechanisms of adaptation. Egg size is a classic adaptive trait in insects, birds, and other taxa, but its highly polygenic architecture has prevented high-resolution genetic analysis. We used replicated experimental evolution in Drosophila melanogaster and whole-genome sequencing to identify consistent signatures of polygenic egg-size adaptation. A generalized linear-mixed model revealed reproducible allele frequency differences between replicated experimental populations selected for large and small egg volumes at approximately 4,000 single nucleotide polymorphisms (SNPs). Several hundred distinct genomic regions contain clusters of these SNPs and have lower heterozygosity than the genomic background, consistent with selection acting on polymorphisms in these regions. These SNPs are also enriched among genes expressed in Drosophila ovaries and many of these genes have well-defined functions in Drosophila oogenesis. Additional genes regulating egg development, growth, and cell size show evidence of directional selection as genes regulating these biological processes are enriched for highly differentiated SNPs. Genetic crosses performed with a subset of candidate genes demonstrated that these genes influence egg size, at least in the large genetic background. These findings confirm the highly polygenic architecture of this adaptive trait, and suggest the involvement of many novel candidate genes in regulating egg size.

| S-EPMC4576704 | biostudies-literature

The components of xRNA: synthesis and fluorescence of a full genetic set of size-expanded ribonucleosides.

Project description:The synthesis and properties of a full set of four benzo-expanded ribonucleosides (xRNA), analogous to A, G, C, and U RNA monomers, are described. The nucleosides are efficient fluorophores with emission maxima of 369-411 nm. The compounds are expected to be useful as RNA pathway probes and as components of an unnatural ribopolymer.

| S-EPMC3039074 | biostudies-literature

Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster.

Project description:Body size is a classic quantitative trait with evolutionarily significant variation within many species. Locating the alleles responsible for this variation would help understand the maintenance of variation in body size in particular, as well as quantitative traits in general. However, successful genome-wide association of genotype and phenotype may require very large sample sizes if alleles have low population frequencies or modest effects. As a complementary approach, we propose that population-based resequencing of experimentally evolved populations allows for considerable power to map functional variation. Here, we use this technique to investigate the genetic basis of natural variation in body size in Drosophila melanogaster. Significant differentiation of hundreds of loci in replicate selection populations supports the hypothesis that the genetic basis of body size variation is very polygenic in D. melanogaster. Significantly differentiated variants are limited to single genes at some loci, allowing precise hypotheses to be formed regarding causal polymorphisms, while other significant regions are large and contain many genes. By using significantly associated polymorphisms as a priori candidates in follow-up studies, these data are expected to provide considerable power to determine the genetic basis of natural variation in body size.

| S-EPMC3060078 | biostudies-literature

Cannings models, population size changes and multiple-merger coalescents.

Project description:Multiple-merger coalescents, e.g. [Formula: see text]-n-coalescents, have been proposed as models of the genealogy of n sampled individuals for a range of populations whose genealogical structures are not captured well by Kingman's n-coalescent. [Formula: see text]-n-coalescents can be seen as the limit process of the discrete genealogies of Cannings models with fixed population size, when time is rescaled and population size [Formula: see text]. As established for Kingman's n-coalescent, moderate population size fluctuations in the discrete population model should be reflected by a time-change of the limit coalescent. For [Formula: see text]-n-coalescents, this has been explicitly shown for only a limited subclass of [Formula: see text]-n-coalescents and exponentially growing populations. This article gives a more general construction of time-changed [Formula: see text]-n-coalescents as limits of specific Cannings models with rather arbitrary time changes.

| S-EPMC7052052 | biostudies-literature

Infants use relative numerical group size to infer social dominance.

Project description:Detecting dominance relationships, within and across species, provides a clear fitness advantage because this ability helps individuals assess their potential risk of injury before engaging in a competition. Previous research has demonstrated that 10- to 13-mo-old infants can represent the dominance relationship between two agents in terms of their physical size (larger agent = more dominant), whereas younger infants fail to do so. It is unclear whether infants younger than 10 mo fail to represent dominance relationships in general, or whether they lack sensitivity to physical size as a cue to dominance. Two studies explored whether infants, like many species across the animal kingdom, use numerical group size to assess dominance relationships and whether this capacity emerges before their sensitivity to physical size. A third study ruled out an alternative explanation for our findings. Across these studies, we report that infants 6-12 mo of age use numerical group size to infer dominance relationships. Specifically, preverbal infants expect an agent from a numerically larger group to win in a right-of-way competition against an agent from a numerically smaller group. In addition, this is, to our knowledge, the first study to demonstrate that infants 6-9 mo of age are capable of understanding social dominance relations. These results demonstrate that infants' understanding of social dominance relations may be based on evolutionarily relevant cues and reveal infants' early sensitivity to an important adaptive function of social groups.

| S-EPMC4780600 | biostudies-literature

Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations.

Project description:Next-generation sequencing (NGS) technologies enable new insights into the diversity of virus populations within their hosts. Diversity estimation is currently restricted to single-nucleotide variants or to local fragments of no more than a few hundred nucleotides defined by the length of sequence reads. To study complex heterogeneous virus populations comprehensively, novel methods are required that allow for complete reconstruction of the individual viral haplotypes. Here, we show that assembly of whole viral genomes of ∼8600 nucleotides length is feasible from mixtures of heterogeneous HIV-1 strains derived from defined combinations of cloned virus strains and from clinical samples of an HIV-1 superinfected individual. Haplotype reconstruction was achieved using optimized experimental protocols and computational methods for amplification, sequencing and assembly. We comparatively assessed the performance of the three NGS platforms 454 Life Sciences/Roche, Illumina and Pacific Biosciences for this task. Our results prove and delineate the feasibility of NGS-based full-length viral haplotype reconstruction and provide new tools for studying evolution and pathogenesis of viruses.

| S-EPMC4132706 | biostudies-literature

Association Between Variation in Red Cell Size and Multiple Aging-Related Outcomes.

Project description:BackgroundWe tested whether greater variation in red blood cell size, measured by red cell distribution width (RDW), may predict aging-related degenerative conditions and therefore, serve as a marker of biological aging.MethodsThree thousand six hundred and thirty-five community-dwelling older men were enrolled in the prospective Osteoporotic Fractures in Men Study. RDW was categorized into 4 groups (≤13.0%, 13.1%-14.0%, 14.1%-15.0%, and ≥15.1%). Functional limitations, frailty, strength, physical performance, and cognitive function were measured at baseline and 7.4 years later. Falls were recorded in the year after baseline; hospitalizations were obtained for 2 years after baseline. Mortality was assessed during a mean of 8.3 years of follow-up.ResultsParticipants with greater variability in red cell size were weaker, walked more slowly, and had a worse cognitive function. They were more likely to have functional limitations (35.2% in the highest RDW category vs 16.0% in the lowest, p < .001) and frailty (30.3% vs 11.3%, p < .001). Those with greater variability in red cell size were more likely to develop new functional limitations and to become frail. The risk of having 2 or more falls was also greater (highest 19.2% vs lowest 10.3%, p < .001). The risk of hospitalization was higher in those with the highest variability (odds ratio [95% confidence interval], 1.8 [1.3-2.5]) compared with the lowest. Variability in red cell size was related to total and cause-specific mortality.ConclusionGreater variability in red cell size is associated with diverse aging-related outcomes, suggesting that it may have potential value as a marker for biological aging.

| S-EPMC8202142 | biostudies-literature

Cancer Bioinformatic Methods to Infer Meaningful Data From Small-Size Cohorts.

Project description:Whole-genome analyses have uncovered that most cancer-relevant genes cluster into 12 signaling pathways. Knowledge of the signaling pathways and associated gene signatures not only allows us to understand the mechanisms of oncogenesis inherent to specific cancers but also provides us with drug targets, molecular diagnostic and prognosis factors, as well as biomarkers for patient risk stratification and treatment. Publicly available genomic data sets constitute a wealth of gene mining opportunities for hypothesis generation and testing. However, the increasingly recognized genetic and epigenetic inter- and intratumor heterogeneity, combined with the preponderance of small-size cohorts, hamper reliable analysis and discovery. Here, we review two methods that are used to infer meaningful biological events from small-size data sets and discuss some of their applications and limitations.

| S-EPMC4631160 | biostudies-literature

Deep-Learning-Based Neural Tissue Segmentation of MRI in Multiple Sclerosis: Effect of Training Set Size.

Project description:BackgroundThe dependence of deep-learning (DL)-based segmentation accuracy of brain MRI on the training size is not known.PurposeTo determine the required training size for a desired accuracy in brain MRI segmentation in multiple sclerosis (MS) using DL.Study typeRetrospective analysis of MRI data acquired as part of a multicenter clinical trial.Study populationIn all, 1008 patients with clinically definite MS.Field strength/sequenceMRIs were acquired at 1.5T and 3T scanners manufactured by GE, Philips, and Siemens with dual turbo spin echo, FLAIR, and T1 -weighted turbo spin echo sequences.AssessmentSegmentation results using an automated analysis pipeline and validated by two neuroimaging experts served as the ground truth. A DL model, based on a fully convolutional neural network, was trained separately using 16 different training sizes. The segmentation accuracy as a function of the training size was determined. These data were fitted to the learning curve for estimating the required training size for desired accuracy.Statistical testsThe performance of the network was evaluated by calculating the Dice similarity coefficient (DSC), and lesion true-positive and false-positive rates.ResultsThe DSC for lesions showed much stronger dependency on the sample size than gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF). When the training size was increased from 10 to 800 the DSC values varied from 0.00 to 0.86 ± 0.016 for T2 lesions, 0.87 ± 009 to 0.94 ± 0.004 for GM, 0.86 ± 0.08 to 0.94 ± 0.005 for WM, and 0.91 ± 0.009 to 0.96 ± 0.003 for CSF.Data conclusionExcellent segmentation was achieved with a training size as small as 10 image volumes for GM, WM, and CSF. In contrast, a training size of at least 50 image volumes was necessary for adequate lesion segmentation.Level of evidence1 Technical Efficacy Stage: 1 J. Magn. Reson. Imaging 2020;51:1487-1496.

| S-EPMC7165037 | 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