tajima.test: Test of the Neutral Mutation Hypothesis

In pegas: Population and Evolutionary Genetics Analysis System

Description

This function tests the neutral mutation hypothesis with Tajima's D.

Usage

tajima.test(x)

Arguments

x	a set of DNA sequences (object of class "DNAbin").

Value

A list with three numeric values:

D	Tajima's D statistic.
Pval.normal	the p-value assuming that D follows a normal distribution with mean zero and variance one.
Pval.beta	the p-value assuming that D follows a beta distribution after rescaling on [0, 1] (Tajima, 1989).

Note

Alignment gaps in the sequences are ignored when calculating pairwise distances.

Author(s)

Emmanuel Paradis

References

Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 595–595.

Examples

require(ape)
data(woodmouse)
tajima.test(woodmouse)

Example output

Loading required package: ape
Loading required package: adegenet
Loading required package: ade4

   /// adegenet 2.0.1 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()



Attaching package: 'pegas'

The following object is masked from 'package:ade4':

    amova

The following object is masked from 'package:ape':

    mst

$D
[1] -1.365449

$Pval.normal
[1] 0.1721118

$Pval.beta
[1] 0.1747609

pegas documentation built on Dec. 16, 2021, 5:09 p.m.