Abstract:
:The distribution of fitness effects (DFE) of new mutations is of fundamental importance in evolutionary genetics. Recently, methods have been developed for inferring the DFE that use information from the allele frequency distributions of putatively neutral and selected nucleotide polymorphic variants in a population sample. Here, we extend an existing maximum-likelihood method that estimates the DFE under the assumption that mutational effects are unconditionally deleterious, by including a fraction of positively selected mutations. We allow one or more classes of positive selection coefficients in the model and estimate both the fraction of mutations that are advantageous and the strength of selection acting on them. We show by simulations that the method is capable of recovering the parameters of the DFE under a range of conditions. We apply the method to two data sets on multiple protein-coding genes from African populations of Drosophila melanogaster. We use a probabilistic reconstruction of the ancestral states of the polymorphic sites to distinguish between derived and ancestral states at polymorphic nucleotide sites. In both data sets, we see a significant improvement in the fit when a category of positively selected amino acid mutations is included, but no further improvement if additional categories are added. We estimate that between 1% and 2% of new nonsynonymous mutations in D. melanogaster are positively selected, with a scaled selection coefficient representing the product of the effective population size, N(e), and the strength of selection on heterozygous carriers of ∼2.5.
journal_name
Geneticsjournal_title
Geneticsauthors
Schneider A,Charlesworth B,Eyre-Walker A,Keightley PDdoi
10.1534/genetics.111.131730subject
Has Abstractpub_date
2011-12-01 00:00:00pages
1427-37issue
4eissn
0016-6731issn
1943-2631pii
genetics.111.131730journal_volume
189pub_type
杂志文章相关文献
GENETICS文献大全abstract::The results from a simulation model of selection, mutation and genetic drift in a geographically subdivided population are presented. The infinite-alleles mutation model of Kimura and Crow (1964) is asumed, and both advantageous and deleterious mutations are considered. It is shown that the average frequency of an all...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1981-10-01 00:00:00
abstract::Mutants of Paramecium caudatum with abnormal swimming behavior or responses to cations were obtained by mutagenesis with N-methyl-N'-nitro-N-nitrosoguanidine. Some of the mutants, like pawn in P. tetraurelia, cannot swim backward and are called CNR. Seven independently obtained CNR mutants belonged to three complement...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1979-03-01 00:00:00
abstract::The glp-1 gene product mediates cell-cell interactions required for cell fate specification during development in Caenorhabditis elegans. To identify genes that interact with glp-1, we screened for dominant suppressors of two temperature-sensitive glp-1 alleles and recovered 18 mutations that suppress both germline an...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1993-12-01 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::We have studied lethal mutations in the single calmodulin gene (Cam) of Drosophila to gain insight into the in vivo functions of this important calcium sensor. As a result of maternal calmodulin (CaM) in the mature egg, lethality is delayed until the postembryonic stages. Prior to death in the first larval instar, Cam...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2003-11-01 00:00:00
abstract::The transmission of transposed Ac elements in progeny derived by self-pollination of ten transformed tomato plants has been examined by Southern hybridization analysis. We show that six of these primary transformants have transmitted a transposed Ac to at least one progeny. One of the families was segregating for at l...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1989-09-01 00:00:00
abstract::Plant breeders make selection decisions based on multiple traits, such as yield, plant height, flowering time, and disease resistance. A commonly used approach in multi-trait genomic selection is index selection, which assigns weights to different traits relative to their economic importance. However, classical index ...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.120.303305
更新日期:2020-08-01 00:00:00
abstract::Thirteen of 14 temperature-sensitive mutants deficient in successive steps of mitotic chromosome transmission (cdc2, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17 and 20) from spindle pole body separation to a late stage of nuclear division exhibited a dramatic increase in the frequency of chromosome loss and/or mitotic recomb...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1985-07-01 00:00:00
abstract::While mitochondria are renowned for their role in energy production, they also perform several other integral functions within the cell. Thus, it is not surprising that mitochondrial dysfunction can negatively impact cell viability. Although mitochondria have received an increasing amount of attention in recent years,...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.110.117200
更新日期:2010-08-01 00:00:00
abstract::We show that major chromosomal rearrangements can occur upon T-DNA transformation of Arabidopsis thaliana. In the ACL4 line, two T-DNA insertion loci were found; one is a tandem T-DNA insert in a head-to-head orientation, and the other is a truncated insert with only the left part of the T-region. The four flanking DN...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1998-06-01 00:00:00
abstract::A major challenge in undergraduate life science curricula is the continual evaluation and development of courses that reflect the constantly shifting face of contemporary biological research. Synthetic biology offers an excellent framework within which students may participate in cutting-edge interdisciplinary researc...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.108.096784
更新日期:2009-01-01 00:00:00
abstract::The evolution of domesticated maize from its wild ancestor teosinte is a dramatic example of the effect of human selection on agricultural crops. Maize has one dominant axis of growth, whereas teosinte is highly branched. The axillary branches in maize are short and feminized whereas the axillary branches of teosinte ...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2002-12-01 00:00:00
abstract::Although the role of U1 small nuclear RNAs (snRNAs) in 5' splice site recognition is well established, suppressor U1 snRNAs active in intact multicellular animals have been lacking. Here we describe suppression of a 5' splice site mutation in the Drosophila melanogaster white gene (wDR18) by compensatory changes in U1...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1994-10-01 00:00:00
abstract::Three hundred and fifteen kilobases of DNA from the rosy-Ace region on chromosome 3R of D. melanogaster have previously been cloned and extensively characterized. We describe the isolation of nine new deficiency mutants that break within the 315-kb interval. The position of these breakpoints on the DNA map was determi...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1986-01-01 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::We propose a simple algorithm for estimating the number of nucleotide differences between a pair of RNA or DNA sequences through comparison of their RNAse A mismatch cleavage patterns. In the RNAse A mismatch cleavage technique two or more sample sequences are hybridized to the same RNA probe, the hybrids are partiall...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1996-12-01 00:00:00
abstract::The specification of floral organ identity in the higher dicots depends on the function of a limited set of homeotic genes, many of them members of the MADS-box gene family. Two such genes, APETALA3 (AP3) and PISTILLATA (PI), are required for petal and stamen identity in Arabidopsis; their orthologs in Antirrhinum exh...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1998-06-01 00:00:00
abstract::Evolution through natural selection suggests unnecessary genes are lost. We observed that the yeast Candida glabrata lost the gene encoding a phosphate-repressible acid phosphatase (PHO5) present in many yeasts including Saccharomyces cerevisiae. However, C. glabrata still had phosphate starvation-inducible phosphatas...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.110.120824
更新日期:2010-11-01 00:00:00
abstract::In this paper we study the process of allele frequency change in finite populations with overlapping generations with the purpose of evaluating the possibility of estimating the effective size from observations of temporal frequency shifts of selectively neutral alleles. Focusing on allele frequency changes between su...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1995-02-01 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::Most studies of mutation rates implicitly assume that they remain constant throughout development of the germline. However, researchers recently used a novel statistical framework to reveal that mutation rates differ dramatically during sperm development in Drosophila melanogaster. Here a general framework is describe...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.113.151571
更新日期:2013-08-01 00:00:00
abstract::We studied P element-induced recombination in germline mitotic cells by examining the structure of the recombinant chromosomes. We found that most recombinants retain a mobile P element at the site of the recombination, usually with either a deletion or a duplication immediately adjacent to the P end at which the cros...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1996-12-01 00:00:00
abstract::We have previously isolated mutants of Escherichia coli that replicate their DNA with increased fidelity. These mutants have a mutation in the dnaE gene, encoding the alpha subunit of DNA polymerase III. They were isolated in a mismatch-repair-defective mutL background, in which mutations can be considered to represen...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1994-10-01 00:00:00
abstract::Genetic screens in Drosophila melanogaster and other organisms have been pursued to filter the genome for genetic functions important for memory formation. Such screens have employed primarily chemical or transposon-mediated mutagenesis and have identified numerous mutants including classical memory mutants, dunce and...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.114.173575
更新日期:2015-04-01 00:00:00
abstract::The value of molecular markers and pedigree records, separately or in combination, to assist in the management of conserved populations has been tested. The general strategy for managing the population was to optimize contributions of parents to the next generation for minimizing the global weighted coancestry. Strate...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.104.037325
更新日期:2005-07-01 00:00:00
abstract::The purpose of this study was to characterize two mutator stocks of yeast which were induced and selected on the basis of high spontaneous reversion rates of the suppressible "ochre" nonsense allele lys1-1. In the mutator stock VA-3, a single mutation, designated mut1-1, is responsible for the increase in the reversio...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1976-08-01 00:00:00
abstract::The sequentially Markov coalescent is a simplified genealogical process that aims to capture the essential features of the full coalescent model with recombination, while being scalable in the number of loci. In this article, the sequentially Markov framework is applied to the conditional sampling distribution (CSD), ...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.110.125534
更新日期:2011-04-01 00:00:00
abstract::The impact of among-environment heteroscedasticity and genetic autocorrelation on the analysis of phenotypic plasticity is examined. Among-environment heteroscedasticity occurs when genotypic variances differ among environments. Genetic autocorrelation arises whenever the responses of a genotype to different environme...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1995-04-01 00:00:00
abstract::Sxl appears to head a regulatory gene hierarchy that controls Drosophila sexual dimorphism in response to the X chromosome/autosome balance. Only XXAA cells normally have Sxl(+) activity. It maintains both the female morphogenetic sequence and a level of X-linked dosage-compensated gene expression compatible with dipl...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1984-06-01 00:00:00
abstract::To understand the in vivo function of the unique and conserved carboxy-terminal repeat domain (CTD) of RNA polymerase II largest subunit (RpII215), we have studied RNA polymerase II biosynthesis, activity and genetic function in Drosophila RpII215 mutants that possessed all (C4), half (W81) or none (IIt) of the CTD re...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1995-06-01 00:00:00