Abstract：
:Selective sweeps are typically associated with a local reduction of genetic diversity around the adaptive site. However, selective sweeps can also quickly carry neutral mutations to observable population frequencies if they arise early in a sweep and hitchhike with the adaptive allele. We show that the interplay between mutation and exponential amplification through hitchhiking results in a characteristic frequency spectrum of the resulting novel haplotype variation that depends only on the ratio of the mutation rate and the selection coefficient of the sweep. On the basis of this result, we develop an estimator for the selection coefficient driving a sweep. Since this estimator utilizes the novel variation arising from mutations during a sweep, it does not rely on preexisting variation and can also be applied to loci that lack recombination. Compared with standard approaches that infer selection coefficients from the size of dips in genetic diversity around the adaptive site, our estimator requires much shorter sequences but sampled at high population depth to capture low-frequency variants; given such data, it consistently outperforms standard approaches. We investigate analytically and numerically how the accuracy of our estimator is affected by the decay of the sweep pattern over time as a consequence of random genetic drift and discuss potential effects of recombination, soft sweeps, and demography. As an example for its use, we apply our estimator to deep sequencing data from human immunodeficiency virus populations.
journal_name
Geneticsjournal_title
Geneticsauthors
Messer PW,Neher RAdoi
10.1534/genetics.112.138461subject
Has Abstractpub_date
2012-06-01 00:00:00pages
593-605issue
2eissn
0016-6731issn
1943-2631pii
genetics.112.138461journal_volume
191pub_type
杂志文章相关文献
GENETICS文献大全abstract：:The Notch receptor is the central element in a cell signaling mechanism controlling a broad spectrum of cell fate choices. Genetic modifier screens in Drosophila and subsequent molecular studies have identified several Notch pathway components, but the biochemical nature of signaling is still elusive. Here, we report ...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1998-09-01 00:00:00
abstract：:Mutagenic DNA repair (MDR) employs low-fidelity DNA polymerases capable of replicating past DNA lesions resulting from exposure to high-energy ultraviolet radiation (UVR). MDR confers UVR tolerance and activation initiates a transient mutator phenotype that may provide opportunities for adaptation. To investigate the ...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.108.096131
更新日期：2009-01-01 00:00:00
abstract：:An extending axon growth cone is subjected to attractant and repellent cues. It is not clear how these growth cones discriminate the two opposing forces and select their projection paths. Here, we report that in the Drosophila nerve cord the growth cones of longitudinal tracts are subjected to attraction by the Netrin...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.104.036863
更新日期：2005-05-01 00:00:00
abstract：:The RAD54 gene, which encodes a protein in the SWI2/SNF2 family, plays an important role in recombination and DNA repair in Saccharomyces cerevisiae. The yeast genome project revealed a homologue of RAD54, RDH54/TID1. Properties of the rdh54/tid1 mutant and the rad54 rdh54/tid1 double mutant are shown for mitosis and ...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1997-12-01 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：:PGM plays a central role in the glycolytic pathway at the branch point leading to glycogen metabolism and is highly polymorphic in allozyme studies of many species. We have characterized the nucleotide diversity across the Pgm gene in Drosophila melanogaster and D. simulans to investigate the role that protein polymor...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2000-12-01 00:00:00
abstract：:In this article, we utilize stochastic search variable selection methodology to develop a Bayesian method for identifying multiple quantitative trait loci (QTL) for complex traits in experimental designs. The proposed procedure entails embedding multiple regression in a hierarchical normal mixture model, where latent ...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2003-07-01 00:00:00
abstract：:Individual inbreeding and historical demography can be estimated by analyzing runs of homozygosity (ROH), which are indicative of chromosomal segments of identity by descent (IBD). Such analyses have so far been rare in natural populations due to limited genomic resources. We analyzed ROH in whole genome sequences fro...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.116.198861
更新日期：2017-03-01 00:00:00
abstract：:Precocious entry into S phase due to overproduction of G1 regulators can cause genomic instability. The mechanisms of this phenomenon are largely unknown. We explored the consequences of precocious S phase in yeast by overproducing a deregulated form of Swi4 (Swi4-t). Swi4 is a late G1-specific transcriptional activat...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2002-01-01 00:00:00
abstract：:Previous models suggested that regulation of telomere length in Saccharomyces cerevisiae by Tel1(ATM) and Mec1(ATR) would parallel the established pathways regulating the DNA damage response. Here, we provide evidence that telomere length regulation differs from the DNA damage response in both the Tel1 and Mec1 pathwa...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.119.302713
更新日期：2019-12-01 00:00:00
abstract：:Paramutation generates heritable changes affecting regulation of specific alleles found at several Zea mays (maize) loci that encode transcriptional regulators of anthocyanin biosynthetic genes. Although the direction and extent of paramutation is influenced by poorly understood allelic interactions occurring in diplo...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.105.045260
更新日期：2005-10-01 00:00:00
abstract：:Age-specific effects of spontaneous mutations on mortality rates in Drosophila are inferred from three large demographic experiments. Data were collected from inbred lines that were allowed to accumulate spontaneous mutations for 10, 19, and 47 generations. Estimates of age-specific mutational variance for mortality w...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1999-10-01 00:00:00
abstract：:A locus is described in Drosophila melanogaster that modifies the expression of the white eye color gene. This trans-acting modifier reduces the expression of the white gene in the eye, but elevates the expression in other adult tissues. Because of the eye phenotype in which the expression of white is lessened but not...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1994-08-01 00:00:00
abstract：:The small heat-shock proteins have undergone a tremendous diversification in plants; whereas only a single small heat-shock protein is found in fungi and many animals, over 20 different small heat-shock proteins are found in higher plants. The small heat-shock proteins in plants have diversified in both sequence and c...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1995-10-01 00:00:00
abstract：:Sex differences occur in most species and affect a variety of biological traits including morphology, behavior, and life history. The nematode Caenorhabditis elegans exists as a population of self-fertile hermaphrodites with occasional males, which differ anatomically and behaviorally from hermaphrodites. Here we show...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.106.056093
更新日期：2006-06-01 00:00:00
abstract：:As part of our investigation of disease resistance in lettuce, we generated mutants that have lost resistance to Bremia lactucae, the casual fungus of downy mildew. Using a rapid and reliable screen, we identified 16 distinct mutants of Latuca sativa that have lost activity of one of four different downy mildew resist...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1994-07-01 00:00:00
abstract：:We present a two-part system for conditional FLP-out of FRT-flanked sequences in Caenorhabditis elegans to control gene activity in a spatially and/or temporally regulated manner. Using reporters, we assess the system for efficacy and demonstrate its use as a cell lineage marking tool. In addition, we construct and te...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.108.090274
更新日期：2008-09-01 00:00:00
abstract：:Mutation of a CCG sequence in the 5'-untranslated region of the mitochondrially encoded cytochrome b mRNA in Saccharomyces cerevisiae results in destabilization of the message and respiratory deficiency of the mutant strain. This phenotype mimics that of a mutation in the nuclear CBP1 gene. Here it is shown that overe...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.104.036467
更新日期：2005-11-01 00:00:00
abstract：:In mismatch repair (MMR), members of the MLH gene family have been proposed to act as key molecular matchmakers to coordinate mismatch recognition with downstream repair functions that result in mispair excision. Two members of this gene family, MLH1 and MLH3, have also been implicated in meiotic crossing over. These ...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2002-03-01 00:00:00
abstract：:A model of the evolution of a transposable element family in a Mendelian host population is proposed that incorporates heritable phenotypic mutations in the elements. The temporal behavior of the numbers of mutant and wild-type elements is studied, and the expected extinction time of the transposable element family is...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1985-02-01 00:00:00
abstract：:Aggression is a complex social behavior that is widespread in nature. To date, only a limited number of genes that affect aggression have been identified, in large part because the complexity of the phenotype makes screening difficult and time-consuming regardless of the species that is studied. We discovered that agg...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.117.300292
更新日期：2018-01-01 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：:At pH 6.8, a substantial fraction of recombinant colonies obtained from conjugation with an HfrH donor contained multiple recombinant classes in a single colony (polygenotype colony). In contrast, when the conjugation was performed at pH 7.6, the number of polygenotypic colonies was drastically reduced, and the recomb...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1975-07-01 00:00:00
abstract：:Oligosyndactylism (Os) is a radiation-induced mutation on mouse chromosome 8 associated with early postimplantation lethality in homozygotes and abnormal development of the limbs and kidneys in heterozygotes. The recessive lethal effect of Os is due to a mitotic block of the embryonic cells that becomes apparent at th...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1996-12-01 00:00:00
abstract：:Alteration of the subcellular distribution of Mod5p-I, a tRNA modification enzyme, member of the sorting isozyme family, affects tRNA-mediated nonsense suppression. Altered suppression efficiency was used to identify MDP genes, which, when mutant, change the mitochondrial/cytosolic distribution of Mod5p-I,KR6. MDP2 is...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1997-03-01 00:00:00
abstract：:The nuclear aod-1 gene of Neurospora crassa encodes the alternative oxidase and is induced when the standard cytochrome-mediated respiratory chain of mitochondria is inhibited. To study elements of the pathway responsible for alternative oxidase induction, we generated a series of mutations in the region upstream from...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.106.068635
更新日期：2007-04-01 00:00:00
abstract：:DNA topoisomerases, enzymes that alter the superhelicity of DNA, have been implicated in such critical cellular functions as transcription, DNA replication, and recombination. In the yeast Saccharomyces cerevisiae, a null mutation in the gene encoding topoisomerase I (TOP1) causes elevated levels of mitotic recombinat...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1993-04-01 00:00:00
abstract：:The essential neurotransmitter acetylcholine functions throughout the animal kingdom. In Caenorhabditis elegans, the acetylcholine biosynthetic enzyme [choline acetyltransferase (ChAT)] and vesicular transporter [vesicular acetylcholine transporter (VAChT)] are encoded by the cha-1 and unc-17 genes, respectively. Thes...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.114.173765
更新日期：2015-03-01 00:00:00
abstract：:Many data sets one could use for population genetics contain artifactual sites, i.e., sequencing errors. Here, we first explore the impact of such errors on several common summary statistics, assuming that sequencing errors are mostly singletons. We thus show that in the presence of those errors, estimators of can be ...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.107.082198
更新日期：2008-07-01 00:00:00
abstract：:Five bivariate distributions of wing dimensions of Drosophila melanogaster were measured, in flies 1) subjected to four defined environmental regimes during development, 2) taken directly from nature in seven U.S. states, 3) selected in ten populations for change in wing form, and 4) sampled from 21 long inbred wild-t...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1990-12-01 00:00:00
