Literature DB >> 14668409

Effect of misoriented sites on neutrality tests with outgroup.

Emmanuelle Baudry1, Frantz Depaulis.   

Abstract

Several neutrality tests use outgroups to infer the ancestral and derived states for polymorphism data. However, homoplasy can result in the incorrect inference of the derived variant. We show that empirically derived rates of misorientation strongly influence Fay and Wu's H-test, especially when the sample size is large.

Mesh：

Year:  2003        PMID： 14668409      PMCID： PMC1462824     

Source DB:  PubMed          Journal:  Genetics        ISSN： 0016-6731            Impact factor:   4.562


  19 in total

1.  DNA variation in the basic chitinase locus (ChiB) region of the wild plant Arabidopsis thaliana.

Authors:  A Kawabe; N T Miyashita
Journal:  Genetics       Date:  1999-11       Impact factor: 4.562

2.  Hitchhiking under positive Darwinian selection.

Authors:  J C Fay; C I Wu
Journal:  Genetics       Date:  2000-07       Impact factor: 4.562

3.  Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels.

Authors:  L Frisse; R R Hudson; A Bartoszewicz; J D Wall; J Donfack; A Di Rienzo
Journal:  Am J Hum Genet       Date:  2001-08-29       Impact factor: 11.025

4.  The signature of positive selection at randomly chosen loci.

Authors:  Molly Przeworski
Journal:  Genetics       Date:  2002-03       Impact factor: 4.562

5.  Estimate of the mutation rate per nucleotide in humans.

Authors:  M W Nachman; S L Crowell
Journal:  Genetics       Date:  2000-09       Impact factor: 4.562

6.  Nucleotide variation at the CHALCONE ISOMERASE locus in Arabidopsis thaliana.

Authors:  H Kuittinen; M Aguadé
Journal:  Genetics       Date:  2000-06       Impact factor: 4.562

7.  Reduced X-linked nucleotide polymorphism in Drosophila simulans.

Authors:  D J Begun; P Whitley
Journal:  Proc Natl Acad Sci U S A       Date:  2000-05-23       Impact factor: 11.205

8.  The amounts of nucleotide variation within and between allelic classes and the reconstruction of the common ancestral sequence in a population.

Authors:  H Innan; F Tajima
Journal:  Genetics       Date:  1997-11       Impact factor: 4.562

9.  Contrasting patterns of nucleotide polymorphism at the alcohol dehydrogenase locus in the outcrossing Arabidopsis lyrata and the selfing Arabidopsis thaliana.

Authors:  O Savolainen; C H Langley; B P Lazzaro; H Fr
Journal:  Mol Biol Evol       Date:  2000-04       Impact factor: 16.240

10.  A simple method for estimating the parameter of substitution rate variation among sites.

Authors:  X Gu; J Zhang
Journal:  Mol Biol Evol       Date:  1997-11       Impact factor: 16.240
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  28 in total

1.  Weak selection and recent mutational changes influence polymorphic synonymous mutations in humans.

Authors:  Josep M Comeron
Journal:  Proc Natl Acad Sci U S A       Date:  2006-04-21       Impact factor: 11.205

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

Authors:  Kai Zeng; Brian Charlesworth
Journal:  Genetics       Date:  2010-10-05       Impact factor: 4.562

3.  GC-biased segregation of noncoding polymorphisms in Drosophila.

Authors:  Nicolas Galtier; Eric Bazin; Nicolas Bierne
Journal:  Genetics       Date:  2005-09-12       Impact factor: 4.562

4.  Evaluation of the genomic extent of effects of fixed inversion differences on intraspecific variation and interspecific gene flow in Drosophila pseudoobscura and D. persimilis.

Authors:  Carlos A Machado; Tamara S Haselkorn; Mohamed A F Noor
Journal:  Genetics       Date:  2006-12-18       Impact factor: 4.562

5.  Frequency spectrum neutrality tests: one for all and all for one.

Authors:  Guillaume Achaz
Journal:  Genetics       Date:  2009-06-22       Impact factor: 4.562

6.  Transition Densities and Sample Frequency Spectra of Diffusion Processes with Selection and Variable Population Size.

Authors:  Daniel Živković; Matthias Steinrücken; Yun S Song; Wolfgang Stephan
Journal:  Genetics       Date:  2015-04-14       Impact factor: 4.562

7.  Triallelic Population Genomics for Inferring Correlated Fitness Effects of Same Site Nonsynonymous Mutations.

Authors:  Aaron P Ragsdale; Alec J Coffman; PingHsun Hsieh; Travis J Struck; Ryan N Gutenkunst
Journal:  Genetics       Date:  2016-03-30       Impact factor: 4.562

8.  Detecting Recent Positive Selection with a Single Locus Test Bipartitioning the Coalescent Tree.

Authors:  Zongfeng Yang; Junrui Li; Thomas Wiehe; Haipeng Li
Journal:  Genetics       Date:  2017-12-07       Impact factor: 4.562

9.  Investigation of the demographic and selective forces shaping the nucleotide diversity of genes involved in nod factor signaling in Medicago truncatula.

Authors:  Stéphane De Mita; Joëlle Ronfort; Heather I McKhann; Charles Poncet; Redouane El Malki; Thomas Bataillon
Journal:  Genetics       Date:  2007-12       Impact factor: 4.562

10.  Using classical population genetics tools with heterochroneous data: time matters!

Authors:  Frantz Depaulis; Ludovic Orlando; Catherine Hänni
Journal:  PLoS One       Date:  2009-05-14       Impact factor: 3.240
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