Abstract:
:As multi-individual population-scale data become available, more complex modeling strategies are needed to quantify genome-wide patterns of nucleotide usage and associated mechanisms of evolution. Recently, the multivariate neutral Moran model was proposed. However, it was shown insufficient to explain the distribution of alleles in great apes. Here, we propose a new model that includes allelic selection. Our theoretical results constitute the basis of a new Bayesian framework to estimate mutation rates and selection coefficients from population data. We apply the new framework to a great ape dataset, where we found patterns of allelic selection that match those of genome-wide GC-biased gene conversion (gBGC). In particular, we show that great apes have patterns of allelic selection that vary in intensity-a feature that we correlated with great apes' distinct demographies. We also demonstrate that the AT/GC toggling effect decreases the probability of a substitution, promoting more polymorphisms in the base composition of great ape genomes. We further assess the impact of GC-bias in molecular analysis, and find that mutation rates and genetic distances are estimated under bias when gBGC is not properly accounted for. Our results contribute to the discussion on the tempo and mode of gBGC evolution, while stressing the need for gBGC-aware models in population genetics and phylogenetics.
journal_name
Geneticsjournal_title
Geneticsauthors
Borges R,Szöllősi GJ,Kosiol Cdoi
10.1534/genetics.119.302074subject
Has Abstractpub_date
2019-08-01 00:00:00pages
1321-1336issue
4eissn
0016-6731issn
1943-2631pii
genetics.119.302074journal_volume
212pub_type
杂志文章相关文献
GENETICS文献大全abstract::We describe 83 recessive autosomal male-sterile mutations, generated by single P element mutagenesis in Drosophila melanogaster. Each mutation has been localized to a lettered subdivision of the polytene map. Reversion analyses, as well as complementation tests using available chromosomal deficiencies, indicate that t...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1993-10-01 00:00:00
abstract::Chromatin organization and structure are crucial for transcriptional regulation, DNA replication, and damage repair. Although initially characterized in remodeling cell wall glucans, the β-1,3-glucanosyltransferase Gas1 was recently discovered to regulate transcriptional silencing in a manner separable from its activi...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.113.158824
更新日期:2014-04-01 00:00:00
abstract::The contribution of mismatch repair to genetic recombination in T4 phage has been evaluated by three independent approaches: (1) testing for non-additivity of recombinant frequencies; (2) measurements of double exchange frequencies in three-factor crosses: (3) comparisons of recombination abilities of mutations occupy...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1982-12-01 00:00:00
abstract::The evolutionary process leading to the fixation of newly duplicated genes is not well understood. It was recently proposed that the fixation of duplicate genes is frequently driven by positive selection for increased gene dosage (i.e., the gene dosage hypothesis), because haploinsufficient genes were reported to have...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.108.090936
更新日期:2008-08-01 00:00:00
abstract::In Saccharomyces cerevisiae, genes located at the telomeres and the HM loci are subject to transcriptional silencing. Here, we report results of screening a Gal4 DNA-binding domain hybrid library for proteins that cause silencing when targeted to a silencer-defective HMR locus. ...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.166.1.631
更新日期:2004-01-01 00:00:00
abstract::Remarkably complex patterns of aneuploidy have been observed in the genomes of many eukaryotic cell types, ranging from brewing yeasts to tumor cells. Such aberrant karyotypes are generally thought to take shape progressively over many generations, but evidence also suggests that genomes may undergo faster modes of ev...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.120.303536
更新日期:2020-09-01 00:00:00
abstract::Heritable silencing effects are gene suppression phenomena that can persist for generations after induction. In the majority of RNAi experiments conducted in Caenorhabditis elegans, the silencing response results in a hypomorphic phenotype where the effects recede after the F1 generation. F2 and subsequent generations...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.108.089433
更新日期:2008-11-01 00:00:00
abstract::The spatial distributions of genetic variation under selection-mutation equilibrium within populations that have limited dispersal are investigated. The results show that directional selection with moderate strength rapidly reduces the amount of genetic structure and spatial autocorrelations far below that predicted f...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1990-03-01 00:00:00
abstract::We derive a formula for the distribution of the length T of the recombination interval containing a target gene and using N gametes in a region where R kilobases correspond to 1 cM. The formula can be used to calculate the number of meiotic events required to narrow a target gene down to a specific interval size and h...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2002-01-01 00:00:00
abstract::We describe here a new variant of transposon Tn10 especially adapted for transposon analysis of cloned yeast genes; it can equally well be used for analysis of prokaryotic genes. We have applied this element to analysis of the LEU2, RAD50, and CDC48 genes of Saccharomyces cerevisiae. This transposon, nicknamed mini-Tn...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1987-06-01 00:00:00
abstract::Notch signaling pathways can be regulated through a variety of cellular mechanisms, and genetically compromised systems provide useful platforms from which to search for the responsible modulators. The Caenorhabditis elegans gene aph-1 encodes a component of γ-secretase, which is essential for Notch signaling events t...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.111.136804
更新日期:2012-03-01 00:00:00
abstract::The island model with stochastically variable migration rate and immigrant gene frequency is investigated. It is supposed that the migration rate and the immigrant gene frequency are independent of each other in each generation, and each of them is independently and identically distributed in every generation. The tre...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1979-01-01 00:00:00
abstract::Persistence time of a mutant allele, the expected number of generations before its elimination from the population, can be estimated as the ratio of the number of segregating mutations per individual over the mutation rate per generation. We screened two natural populations of Drosophila melanogaster for mutations cau...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.105.046094
更新日期:2005-12-01 00:00:00
abstract::Genetic divergence in the form of the mandible is examined in ten inbred strains of mice. Several univariate and multivariate genetic distance estimates are given for the morphological data and these estimates are compared to measures of genealogical and molecular divergence. Highly significant divergence occurs among...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1988-09-01 00:00:00
abstract::An analysis of mortality is undertaken in two breeds of pigs: Danish Landrace and Yorkshire. Zero-inflated and standard versions of hierarchical Poisson, binomial, and negative binomial Bayesian models were fitted using Markov chain Monte Carlo (MCMC). The objectives of the study were to investigate whether there is s...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.109.110759
更新日期:2010-01-01 00:00:00
abstract::We found that heterozygous mutant alleles of E(Pc) and esc increased homologous recombination from an allelic template in somatic cells in a P-element-induced double-strand break repair assay. Flies heterozygous for mutant alleles of these genes showed increased genome stability and decreased levels of apoptosis in im...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.105.042473
更新日期:2006-04-01 00:00:00
abstract::The genetic effects of one generation of spermatogonial X-irradiation in rats, by a single dose of 600r in one experiment and by a fractionated dose of 450r in another, were measured in three generations of their descendants. Estimates of dominant lethal mutation rates--(2 to 3) X 10-4/gamete/r--from litter size diffe...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1977-02-01 00:00:00
abstract::One of the key factors contributing to the success of a quantitative trait locus (QTL) mapping experiment is the precision with which QTL positions can be estimated. We show, using simulations, that QTL mapping precision for an experimental cross can be increased by the use of a genotypically selected sample of indivi...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.104.033746
更新日期:2005-05-01 00:00:00
abstract::Host mutations in Escherichia coli K12 selected for the temperature-sensitive replication of the bacterial plasmid colicinogenic factor E(1) (ColE(1)) exhibit a pleiotropic effect with respect to the effect of the mutation on other extra-chromosomal elements. The mutations also vary with respect to the time of incubat...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1973-05-01 00:00:00
abstract::Plant endo-beta-1,3-glucanases (EGases) degrade the cell wall polysaccharides of attacking pathogens and release elicitors of additional plant defenses. Isozymes EGaseA and EGaseB of soybean differ in susceptibility to a glucanase inhibitor protein (GIP1) produced by Phytophthora sojae, a major soybean pathogen. EGase...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.103.025098
更新日期:2005-02-01 00:00:00
abstract::Two-dimensional paper chromatography was performed on methanol extracts of leaves of hexaploid bread wheat, Triticum aestivum L. em. Thell. cultivar Chinese Spring, and of the available nullisomic-tetrasomic compensating lines, the tetrasomic lines and the ditelocentric lines. The chromatograms had 27 spots identified...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1983-02-01 00:00:00
abstract::Vegetative incompatibility in fungi has long been known to reduce the transmission of viruses between individuals, but the barrier to transmission is incomplete. In replicated laboratory assays, we showed conclusively that the transmission of viruses between individuals of the chestnut blight fungus Cryphonectria para...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2001-09-01 00:00:00
abstract::Molecular heterogeneity in human breast cancer has challenged diagnosis, prognosis, and clinical treatment. It is well known that molecular subtypes of breast tumors are associated with significant differences in prognosis and survival. Assuming that the differences are attributed to subtype-specific pathways, we then...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.115.180125
更新日期:2015-12-01 00:00:00
abstract::The Drosophila melanogaster Chd3 gene encodes a member of the CHD group of SNF2/RAD54 ATPases. CHD proteins are conserved from yeast to man and many are subunits of chromatin-remodeling complexes that facilitate transcription. Drosophila CHD3 proteins are not found in protein complexes, but as monomers that remodel ch...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.110.115121
更新日期:2010-07-01 00:00:00
abstract::Intron sizes show an asymmetrical distribution in a number of organisms, with a large number of "short" introns clustered around a minimal intron length and a much broader distribution of longer introns. In Drosophila melanogaster, the short intron class is centered around 61 bp. The narrow length distribution suggest...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2003-12-01 00:00:00
abstract::Previously we have shown that the nucleolus organizer region (NOR) of Neurospora crassa changes size frequently during the premeiotic portion of the sexual phase. Here, we have investigated whether these changes in size originate only in specific regions of the NOR, or are distributed throughout the NOR. In two specia...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1990-10-01 00:00:00
abstract::Many genes that affect axon pathfinding and cell migration have been identified. Mechanisms by which these genes and the molecules they encode interact with one another in pathways and networks to control developmental events are unclear. Rac GTPases, the cytoskeletal signaling molecule Enabled, and NIK kinase have al...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.105.046359
更新日期:2006-02-01 00:00:00
abstract::When a polygenic character is exposed to natural selection in which the curve giving fitness as a function of phenotype is a mixture of two Gaussian (normal) curves, the population may respond either by evolving to a specialized phenotype near one of the two optimum phenotypes, or by evolving to a generalized phenotyp...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1979-11-01 00:00:00
abstract::During meiosis, the stable pairing of the homologous chromosomes is mediated by the assembly of the synaptonemal complex (SC). Its tripartite structure is well conserved in Metazoa and consists of two lateral elements (LEs) and a central region (CR) that in turn is formed by several transverse filaments (TFs) and a ce...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.113.156679
更新日期:2013-11-01 00:00:00
abstract::We developed stochastic population genetic theory for mitochondrial and chloroplast genes, using an infinite alleles model appropriate for molecular genetic data. We considered the effects of mutation, random drift, and migration in a finite island model on selectively neutral alleles. Recurrence equations were obtain...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1989-03-01 00:00:00