Bias and precision in QST estimates: problems and some solutions.

Abstract:

:Comparison of population differentiation in neutral marker genes and in genes coding quantitative traits by means of F(ST) and Q(ST) indexes has become commonplace practice. While the properties and estimation of F(ST) have been the subject of much interest, little is known about the precision and possible bias in Q(ST) estimates. Using both simulated and real data, we investigated the precision and bias in Q(ST) estimates and various methods of estimating the precision. We found that precision of Q(ST) estimates for typical data sets (i.e., with <20 populations) was poor. Of the methods for estimating the precision, a simulation method, a parametric bootstrap, and the Bayesian approach returned the most precise estimates of the confidence intervals.

journal_name

Genetics

journal_title

Genetics

authors

O'Hara RB,Merilä J

doi

10.1534/genetics.105.044545

keywords:

subject

Has Abstract

pub_date

2005-11-01 00:00:00

pages

1331-9

issue

3

eissn

0016-6731

issn

1943-2631

pii

genetics.105.044545

journal_volume

171

pub_type

杂志文章

相关文献

GENETICS文献大全
  • A genomewide RNA interference screen for modifiers of aggregates formation by mutant Huntingtin in Drosophila.

    abstract::Protein aggregates are a common pathological feature of most neurodegenerative diseases (NDs). Understanding their formation and regulation will help clarify their controversial roles in disease pathogenesis. To date, there have been few systematic studies of aggregates formation in Drosophila, a model organism that h...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.109.112516

    authors: Zhang S,Binari R,Zhou R,Perrimon N

    更新日期:2010-04-01 00:00:00

  • Genetic Variant Selection: Learning Across Traits and Sites.

    abstract::We consider resequencing studies of associated loci and the problem of prioritizing sequence variants for functional follow-up. Working within the multivariate linear regression framework helps us to account for the joint effects of multiple genes; and adopting a Bayesian approach leads to posterior probabilities that...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.115.184572

    authors: Stell L,Sabatti C

    更新日期:2016-02-01 00:00:00

  • The Schizosaccharomyces pombe rec16 gene product regulates multiple meiotic events.

    abstract::Previously isolated meiotic recombination (rec) mutants of Schizosaccharomyces pombe define 16 complementation groups. The rec genes cloned and sequenced to date reveal little amino acid sequence identity to other reported proteins. We examined the rec mutants for alterations in meiotic events other than recombination...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Li YF,Smith GR

    更新日期:1997-05-01 00:00:00

  • Genetic modifier screens in Drosophila demonstrate a role for Rho1 signaling in ecdysone-triggered imaginal disc morphogenesis.

    abstract::Drosophila adult leg development provides an ideal model system for characterizing the molecular mechanisms of hormone-triggered morphogenesis. A pulse of the steroid hormone ecdysone at the onset of metamorphosis triggers the rapid transformation of a flat leg imaginal disc into an immature adult leg, largely through...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Ward RE,Evans J,Thummel CS

    更新日期:2003-11-01 00:00:00

  • Linkage disequilibrium analysis of chromosomal inversion polymorphisms of Drosophila.

    abstract::The linkage disequilibrium pattern analysis is a method that allows one to detect present and past events of selection. We applied it to our data on the inversions of Drosophila mediopunctata and to published data of Drosophila subobscura, which are systems probably under complex modes of selection. The method gave me...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Peixoto AA,Klaczko LB

    更新日期:1991-11-01 00:00:00

  • Evidence for parallel processing of sensory information controlling dauer formation in Caenorhabditis elegans.

    abstract::Dauer formation in Caenorhabditis elegans is induced by chemosensation of high levels of a constitutively secreted pheromone. Seven genes defined by mutations that confer a dauer-formation constitutive phenotype (Daf-c) can be congruently divided into two groups by any of three criteria. Group 1 genes (daf-11 and daf-...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Thomas JH,Birnby DA,Vowels JJ

    更新日期:1993-08-01 00:00:00

  • Amplified fragment length polymorphism mapping of quantitative trait loci for malaria parasite susceptibility in the yellow fever mosquito Aedes aegypti.

    abstract::The yellow fever mosquito Aedes aegypti has been the subject of extensive genetic research due to its medical importance and the ease with which it can be manipulated in the laboratory. A molecular genetic linkage map was constructed using 148 amplified fragment length polymorphism (AFLP) and six single-strand conform...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.105.055178

    authors: Zhong D,Menge DM,Temu EA,Chen H,Yan G

    更新日期:2006-07-01 00:00:00

  • Higher-order septin assembly is driven by GTP-promoted conformational changes: evidence from unbiased mutational analysis in Saccharomyces cerevisiae.

    abstract::Septin proteins bind GTP and heterooligomerize into filaments with conserved functions across a wide range of eukaryotes. Most septins hydrolyze GTP, altering the oligomerization interfaces; yet mutations designed to abolish nucleotide binding or hydrolysis by yeast septins perturb function only at high temperatures. ...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.114.161182

    authors: Weems AD,Johnson CR,Argueso JL,McMurray MA

    更新日期:2014-03-01 00:00:00

  • DNA sequence-mediated, evolutionarily rapid redistribution of meiotic recombination hotspots.

    abstract::Hotspots regulate the position and frequency of Spo11 (Rec12)-initiated meiotic recombination, but paradoxically they are suicidal and are somehow resurrected elsewhere in the genome. After the DNA sequence-dependent activation of hotspots was discovered in fission yeast, nearly two decades elapsed before the key real...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.111.134130

    authors: Wahls WP,Davidson MK

    更新日期:2011-11-01 00:00:00

  • Components of selection in X chromosome lines of Drosophila melanogaster: sex ratio modification by meiotic drive and viability selection.

    abstract::Selection coefficients and segregation parameters have been estimated in 18 randomly chosen lines carrying wild X chromosomes on the cn bw genetic background. Each line was studied in replicated crosses of four types, with approximately 100 replications per line per cross. Crosses in which male X chromosomes differed ...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Curtsinger JW

    更新日期:1984-12-01 00:00:00

  • Response of two heat shock genes to selection for knockdown heat resistance in Drosophila melanogaster.

    abstract::To identify genes involved in stress resistance and heat hardening, replicate lines of Drosophila melanogaster were selected for increased resistance to knockdown by a 39 degrees heat stress. Two selective regimes were used, one with and one without prior hardening. Mean knockdown times were increased from approximate...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: McColl G,Hoffmann AA,McKechnie SW

    更新日期:1996-08-01 00:00:00

  • UGA suppressors in Saccharomyces cerevisiae: allelism, action spectra and map positions.

    abstract::Sixty independent UGA suppressors of Saccharomyces cerevisiae have been studied. They are dominant and are divided into 16 groups (loci) by recombination. Suppressors representing these loci are divided into two classes by action spectra; four in class 1 (a broad action spectrum) and 12 in class 2 (a narrow action spe...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Ono BI,Fujimoto R,Ohno Y,Maeda N,Tsuchiya Y,Usui T,Ishino-Arao Y

    更新日期:1988-01-01 00:00:00

  • Evolutionary strata in a small mating-type-specific region of the smut fungus Microbotryum violaceum.

    abstract::DNA sequence analysis and genetic mapping of loci from mating-type-specific chromosomes of the smut fungus Microbotryum violaceum demonstrated that the nonrecombining mating-type-specific region in this species comprises approximately 25% ( approximately 1 Mb) of the chromosome length. Divergence between homologous ma...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.109.103192

    authors: Votintseva AA,Filatov DA

    更新日期:2009-08-01 00:00:00

  • Concerted evolution of two novel protein families in Caenorhabditis species.

    abstract::Among a large number of homologous gene clusters in C. elegans, two gene families that appear to undergo concerted evolution were studied in detail. Both gene families are nematode specific and encode small secreted proteins of unknown function. For both families in three Caenorhabditis species, concerted groups of ge...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.105.052746

    authors: Thomas JH

    更新日期:2006-04-01 00:00:00

  • Quantitative trait loci (QTL) detection in multicross inbred designs: recovering QTL identical-by-descent status information from marker data.

    abstract::Mapping quantitative trait loci in plants is usually conducted using a population derived from a cross between two inbred lines. The power of such QTL detection and the parameter estimates depend largely on the choice of the two parental lines. Thus, the QTL detected in such populations represent only a small part of ...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.104.028993

    authors: Crepieux S,Lebreton C,Servin B,Charmet G

    更新日期:2004-11-01 00:00:00

  • Repair replication and photorepair of DNA in larvae of Drosophila melanogaster.

    abstract::Repair replication of DNA has been studied in first instar larvae of Drosophila melanogaster with isopycnic centrifugation techniques. Larvae were fed BUdR, FUdR, streptomycin, penicillin, and Fungazone for two to four hours prior to exposure to UV, X-rays, MMS, or EMS. Feeding was continued for four hours in the pres...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Boyd JB,Presley JM

    更新日期:1974-08-01 00:00:00

  • Extensive long-range and nonsyntenic linkage disequilibrium in livestock populations: deconstruction of a conundrum.

    abstract::Great interest was aroused by reports, based on microsatellite markers, of high levels of statistically significant long-range and nonsyntenic linkage disequilibrium (LD) in livestock. Simulation studies showed that this could result from population family structure. In contrast, recent SNP-based studies of livestock ...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.108.097402

    authors: Lipkin E,Straus K,Stein RT,Bagnato A,Schiavini F,Fontanesi L,Russo V,Medugorac I,Foerster M,Sölkner J,Dolezal M,Medrano JF,Friedmann A,Soller M

    更新日期:2009-02-01 00:00:00

  • Unique and Overlapping Functions of Formins Frl and DAAM During Ommatidial Rotation and Neuronal Development in Drosophila.

    abstract::The noncanonical Frizzled/planar cell polarity (PCP) pathway regulates establishment of polarity within the plane of an epithelium to generate diversity of cell fates, asymmetric, but highly aligned structures, or to orchestrate the directional migration of cells during convergent extension during vertebrate gastrulat...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.115.181438

    authors: Dollar G,Gombos R,Barnett AA,Sanchez Hernandez D,Maung SM,Mihály J,Jenny A

    更新日期:2016-03-01 00:00:00

  • The basic helix-loop-helix leucine zipper transcription factor Mitf is conserved in Drosophila and functions in eye development.

    abstract::The MITF protein is a member of the MYC family of basic helix-loop-helix leucine zipper (bHLH-Zip) transcription factors and is most closely related to the TFE3, TFEC, and TFEB proteins. In the mouse, MITF is required for the development of several different cell types, including the retinal pigment epithelial (RPE) c...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.167.1.233

    authors: Hallsson JH,Haflidadóttir BS,Stivers C,Odenwald W,Arnheiter H,Pignoni F,Steingrímsson E

    更新日期:2004-05-01 00:00:00

  • A Bayesian multilocus association method: allowing for higher-order interaction in association studies.

    abstract::For most common diseases with heritable components, not a single or a few single-nucleotide polymorphisms (SNPs) explain most of the variance for these disorders. Instead, much of the variance may be caused by interactions (epistasis) among multiple SNPs or interactions with environmental conditions. We present a new ...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.107.071696

    authors: Albrechtsen A,Castella S,Andersen G,Hansen T,Pedersen O,Nielsen R

    更新日期:2007-06-01 00:00:00

  • Excursions along the Interface between Disruptive and Stabilizing Selection.

    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:

    authors: Felsenstein J

    更新日期:1979-11-01 00:00:00

  • Management of subdivided populations in conservation programs: development of a novel dynamic system.

    abstract::Within the context of a conservation program the management of subdivided populations implies a compromise between the control of the global genetic diversity, the avoidance of high inbreeding levels, and, sometimes, the maintenance of a certain degree of differentiation between subpopulations. We present a dynamic an...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.107.083816

    authors: Fernández J,Toro MA,Caballero A

    更新日期:2008-05-01 00:00:00

  • Deep haplotype divergence and long-range linkage disequilibrium at xp21.1 provide evidence that humans descend from a structured ancestral population.

    abstract::Fossil evidence links human ancestry with populations that evolved from modern gracile morphology in Africa 130,000-160,000 years ago. Yet fossils alone do not provide clear answers to the question of whether the ancestors of all modern Homo sapiens comprised a single African population or an amalgamation of distinct ...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.105.041095

    authors: Garrigan D,Mobasher Z,Kingan SB,Wilder JA,Hammer MF

    更新日期:2005-08-01 00:00:00

  • Analysis of the inheritance, selection and evolution of growth trajectories.

    abstract::We present methods for estimating the parameters of inheritance and selection that appear in a quantitative genetic model for the evolution growth trajectories and other "infinite-dimensional" traits that we recently introduced. Two methods for estimating the additive genetic covariance function are developed, a "full...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Kirkpatrick M,Lofsvold D,Bulmer M

    更新日期:1990-04-01 00:00:00

  • Mu element-generated gene conversions in maize attenuate the dominant knotted phenotype.

    abstract::The knotted1 gene was first defined by dominant mutations that affect leaf morphology. The original allele, Kn1-O, results from a 17-kb tandem duplication. Mutator (Mu) insertions near the junction of the two repeats suppress the leaf phenotype to different degrees depending on the position of the insertion. The Mu in...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Mathern J,Hake S

    更新日期:1997-09-01 00:00:00

  • The use of microsatellite variation to infer population structure and demographic history in a natural model system.

    abstract::To assess the reliability of genetic markers it is important to compare inferences that are based on them to a priori expectations. In this article we present an analysis of microsatellite variation within and among populations of island foxes (Urocyon littoralis) on California's Channel Islands. We first show that mi...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Goldstein DB,Roemer GW,Smith DA,Reich DE,Bergman A,Wayne RK

    更新日期:1999-02-01 00:00:00

  • A genome-wide survey of reproductive barriers in an intraspecific hybrid.

    abstract::Genetic study of the reproductive barriers between related species plays an essential role in understanding the process of speciation. We developed a new method for mapping all possible factors causing deviations from expected Mendelian segregation ratios in F(2) progeny, which substantially contribute to reproductive...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Harushima Y,Nakagahra M,Yano M,Sasaki T,Kurata N

    更新日期:2001-10-01 00:00:00

  • The effects of demography and linkage on the estimation of selection and mutation parameters.

    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 mon...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.110.122150

    authors: Zeng K,Charlesworth B

    更新日期:2010-12-01 00:00:00

  • Single-gene detection and karyotyping using small-target fluorescence in situ hybridization on maize somatic chromosomes.

    abstract::Combined with a system for identifying each of the chromosomes in a genome, visualizing the location of individual genetic loci by fluorescence in situ hybridization (FISH) would aid in assembling physical and genetic maps. Previously, large genomic clones have been successfully used as FISH probes onto somatic chromo...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:10.1534/genetics.106.065573

    authors: Lamb JC,Danilova T,Bauer MJ,Meyer JM,Holland JJ,Jensen MD,Birchler JA

    更新日期:2007-03-01 00:00:00

  • Human diseases with genetically altered DNA repair processes.

    abstract::DNA repair of single-strand breaks (produced by ionizing radiation) and of base damage (produced by ultraviolet (UV) light) are two repair mechanisms that most mammalian cells possess. Genetic defects in these repair mechanisms are exemplified by cells from the human premature-aging disease, progeria, which fail to re...

    journal_title:Genetics

    pub_type: 杂志文章

    doi:

    authors: Cleaver JE,Bootsma D,Friedberg E

    更新日期:1975-06-01 00:00:00