Abstract:
:We explore the effects of demography and linkage on a maximum-likelihood (ML) method for estimating selection and mutation parameters in a reversible mutation model. This method assumes free recombination between sites and a randomly mating population of constant size and uses information from both polymorphic and monomorphic sites in the sample. Two likelihood-ratio test statistics were constructed under this ML framework: LRTγ for detecting selection and LRTκ for detecting mutational bias. By carrying out extensive simulations, we obtain the following results. When mutations are neutral and population size is constant, LRTγ and LRTκ follow a chi-square distribution with 1 d.f. regardless of the level of linkage, as long as the mutation rate is not very high. In addition, LRTγ and LRTκ are relatively insensitive to demographic effects and selection at linked sites. We find that the ML estimators of the selection and mutation parameters are usually approximately unbiased and that LRTκ usually has good power to detect mutational bias. Finally, with a recombination rate that is typical for Drosophila, LRTγ has good power to detect weak selection acting on synonymous sites. These results suggest that the method should be useful under many different circumstances.
journal_name
Geneticsjournal_title
Geneticsauthors
Zeng K,Charlesworth Bdoi
10.1534/genetics.110.122150subject
Has Abstractpub_date
2010-12-01 00:00:00pages
1411-24issue
4eissn
0016-6731issn
1943-2631pii
genetics.110.122150journal_volume
186pub_type
杂志文章相关文献
GENETICS文献大全abstract::Hydroxyurea (HU) has been used for the treatment of multiple diseases, such as cancer. The therapeutic effect is generally believed to be due to the suppression of ribonucleotide reductase (RNR), which slows DNA polymerase movement at replication forks and induces an S phase cell cycle arrest in proliferating cells. A...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.116.191536
更新日期:2016-11-01 00:00:00
abstract::In lytic cycle crosses with Red-Gam-lambda phage, particles were examined that had undergone an Int-mediated exchange. It was assumed that this exchange dimerized the circular lambda, making it packageable. Among these Int-mediated recombinants, particles were identified that had, in addition, enjoyed a close double e...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1984-12-01 00:00:00
abstract::The challenges of breeding autotetraploid potato (Solanum tuberosum) have motivated the development of alternative breeding strategies. A common approach is to obtain uniparental dihaploids from a tetraploid of interest through pollination with S. tuberosum Andigenum Group (formerly S. phureja) cultivars. The mechanis...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.119.302843
更新日期:2020-02-01 00:00:00
abstract::To understand long terminal repeat (LTR)-retrotransposon copy number dynamics, Ty1 elements were reintroduced into a "Ty-less" Saccharomyces strain where elements had been lost by LTR-LTR recombination. Repopulated strains exhibited alterations in chromosome size that were associated with Ty1 insertions, but did not b...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.104.037317
更新日期:2005-04-01 00:00:00
abstract::Previous work showed that C. elegans gon-14 is required for gonadogenesis. Here we report that gon-14 encodes a protein with similarity to LIN-15B, a class B synMuv protein. An extensive region of GON-14 contains blocks of sequence similarity to transposases of the hAT superfamily, but key residues are not conserved, ...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.105.048751
更新日期:2006-02-01 00:00:00
abstract::The type and frequency of simple sequence repeats (SSRs) in plant genomes was investigated using the expanding quantity of DNA sequence data deposited in public databases. In Arabidopsis, 306 genomic DNA sequences longer than 10 kb and 36,199 EST sequences were searched for all possible mono- to pentanucleotide repeat...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2000-10-01 00:00:00
abstract::Conditional lethal mutant systems developed in T-even bacteriophages T2, T4 and T6 have been used to study the partial exclusion which characterizes mixed infections of these phages. In bacteria mixedly infected with T2 and T4, the dominant phage (T4) acts against localized exclusion sensitivity determinants in the ge...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1974-12-01 00:00:00
abstract::Considering a random mating population of finite size, the variance of the number of loci having a given gene frequency was derived under the assumption of a steady flux of mutations. The variance of average heterozygosity among populations was also derived under the same assumption. It was shown that these variances ...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1973-02-01 00:00:00
abstract::Ataxia telangiectasia mutated (ATM) is a phosphatidyl-3-kinase-related protein kinase that functions as a central regulator of the DNA damage response in eukaryotic cells. In humans, mutations in ATM cause the devastating neurodegenerative disease ataxia telangiectasia. Previously, we characterized the homolog of ATM ...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.107.080879
更新日期:2008-02-01 00:00:00
abstract::RNAs are localized by microtubule-based pathways to both the anterior and posterior poles of the developing Drosophila oocyte. We describe a new gene, wispy, required for localization of mRNAs to both poles of the egg. Embryos from wispy mothers arrest development after abnormal oocyte meiosis and failure of pronuclei...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2000-04-01 00:00:00
abstract::RNA transcribed from the Saccharomyces cerevisiae retrotransposon Ty1 accumulates to a high level in mitotically growing haploid cells, yet transposition occurs at very low frequencies. The product of reverse transcription is a linear double-stranded DNA molecule that reenters the genome by either Ty1-integrase-mediat...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2000-02-01 00:00:00
abstract::Reproductive isolation that initiates speciation is likely caused by incompatibility among multiple loci in organisms belonging to genetically diverging populations. Laboratory C57BL/6J mice, which predominantly originated from Mus musculus domesticus, and a MSM/Ms strain derived from Japanese wild mice (M. m. molossi...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.106.062976
更新日期:2007-01-01 00:00:00
abstract::A specific host-pathogen interaction exists between Caenorhabditis elegans and the gram-positive bacterium Microbacterium nematophilum. This bacterium is able to colonize the rectum of susceptible worms and induces a defensive tail-swelling response in the host. Previous mutant screens have identified multiple loci th...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.106.060087
更新日期:2007-02-01 00:00:00
abstract::Retroviruses and their relatives, the long terminal repeat (LTR) retrotransposons, carry out complex life cycles within the cells of their hosts. We have exploited a collection of gene deletion mutants developed by the Saccharomyces Genome Deletion Project to perform a functional genomics screen for host factors that ...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2003-07-01 00:00:00
abstract::We tested the hypothesis that the time course of the evolution of antifungal drug resistance depends on the ploidy of the fungus. The experiments were designed to measure the initial response to the selection imposed by the antifungal drug fluconazole up to and including the fixation of the first resistance mutation i...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.104.033266
更新日期:2004-12-01 00:00:00
abstract::Trans-species polymorphism, meaning the presence of alleles in different species that are more similar to each other than they are to alleles in the same species, has been found at loci associated with vegetative incompatibility in filamentous fungi. If individuals differ at one or more of these loci (termed het for h...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2002-06-01 00:00:00
abstract::Accounting for gene-environment (G×E) interactions in complex trait association studies can facilitate our understanding of genetic heterogeneity under different environmental exposures, improve the ability to discover susceptible genes that exhibit little marginal effect, provide insight into the biological mechanism...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.114.171686
更新日期:2015-03-01 00:00:00
abstract::Genes expressed in testes are critical to male reproductive success, affecting spermatogenesis, sperm competition, and sperm-egg interaction. Comparing the evolution of testis proteins at different taxonomic levels can reveal which genes and functional classes are targets of natural and sexual selection and whether th...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.107.085902
更新日期:2008-08-01 00:00:00
abstract::The St. Thomas Hospital (STH) rabbit has been previously shown to have a Mendelian form of hypertriglyceridemia, accompanied by accelerated atherosclerosis, and these animals may serve as a useful model for human dyslipoproteinemia syndromes. Here we describe the establishment of a new colony of these STH animals, and...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1992-12-01 00:00:00
abstract::A genetic map for the model legume Lotus japonicus has been developed. The F(2) mapping population was established from an interspecific cross between L. japonicus and L. filicaulis. A high level of DNA polymorphism between these parents was the source of markers for linkage analysis and the map is based on a framewor...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2002-08-01 00:00:00
abstract::Individuals within a species vary in their responses to a wide range of stimuli, partly as a result of differences in their genetic makeup. Relatively little is known about the genetic and neuronal mechanisms contributing to diversity of behavior in natural populations. By studying intraspecies variation in innate avo...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.115.178491
更新日期:2015-08-01 00:00:00
abstract::We constructed a genetic linkage map of Gibberella zeae (Fusarium graminearum) by crossing complementary nitrate-nonutilizing (nit) mutants of G. zeae strains R-5470 (from Japan) and Z-3639 (from Kansas). We selected 99 nitrate-utilizing (recombinant) progeny and analyzed them for amplified fragment length polymorphis...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2002-04-01 00:00:00
abstract::By screening for suppressors of hypomorphic mutations of let-23, a receptor tyrosine kinase necessary for vulval induction in Caenorhabditis elegans, we recovered > or = 12 mutations defining the sli-1 (suppressor of lineage defect) locus. sli-1 mutations suppress four of five phenotypes associated with hypomorphic al...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1995-04-01 00:00:00
abstract::In Arabidopsis thaliana, DICER-LIKE 1 and DICER-LIKE 3 are involved in the generation of small RNAs. Double mutants between dicer-like 1 and dicer-like 3 exhibit a delay in flowering that is caused by increased expression of the floral repressor FLOWERING LOCUS C. This delayed-flowering phenotype is similar to that of...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.107.070649
更新日期:2007-06-01 00:00:00
abstract::As hamster scrapie cannot infect mice, due to sequence differences in their PrP proteins, we find "species barriers" to transmission of the [URE3] prion in Saccharomyces cerevisiae among Ure2 proteins of S. cerevisiae, paradoxus, bayanus, cariocanus, and mikatae on the basis of differences among their Ure2p prion doma...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.108.099929
更新日期:2009-03-01 00:00:00
abstract::In multicellular organisms, genetic programs guide cells to adopt cell fates as tissues are formed during development, maintained in adults, and repaired after injury. Here we explore how a small molecule in the environment can switch a genetic program from one fate to another. Wild-type Caenorhabditis elegans XX adul...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.114.169409
更新日期:2014-10-01 00:00:00
abstract::Associative overdominance, the fitness difference between heterozygotes and homozygotes at a neutral locus, is classically described using two categories of models: linkage disequilibrium in small populations or identity disequilibrium in infinite, partially selfing populations. In both cases, only equilibrium situati...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2000-08-01 00:00:00
abstract::A study of spontaneous mutation in Arabidopsis thaliana was initiated from a single inbred Columbia founder; 120 lines were established and advanced 17 generations by single-seed descent. Here, we report an assay of reproductive traits in a random set of 40 lines from generations 8 and 17, grown together at the same t...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2000-05-01 00:00:00
abstract::Adherence, an important virulence factor, is mediated by the EPA (Epithelial Adhesin) genes in the opportunistic pathogen Candida glabrata Expression of adhesin-encoding genes requires tight regulation to respond to harsh environmental conditions within the host. The majority of EPA genes are localized in subtelomeric...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.118.301202
更新日期:2018-09-01 00:00:00
abstract::The mutation rates of specific loci and chromosome regions were estimated for two types of dysgenic hybrid males. These came from crosses between P or Q males and M females in the P-M system of hybrid dysgenesis. The M X P hybrids were the more mutable for each of the loci and chromosome regions tested. The Beadex loc...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1984-01-01 00:00:00