DEMEtics-package: Evaluating the genetic differentiation between populations...

In DEMEtics: Evaluating the genetic differentiation between populations based on Gst and D values.

Description

This package allows to calculate the fixation index Gst (Nei, 1973) and the differentiation index D (Jost, 2008) pairwise between or averaged over several populations. P-values, stating the significance of differentiation, and 95 percent confidence intervals can be estimated using bootstrap resamplings. In the case that more than two populations are compared pairwise, the p-values are adjusted by bonferroni correction and in several other ways due to the multiple comparison from one data set.

Details

Package:	DEMEtics
Type:	Package
Version:	0.8-7
Date:	2013-12-02
Depends:	R (>= 2.8.0)
License:	GPL (>= 2)
Literature:	Gerlach G., Jueterbock A., Kraemer P., Deppermann J. and Harmand P. 2010
	Calculations of population differentiation based on Gst and D:
	forget Gst but not all of statistics!
	Molecular Ecology 19, p. 3845--3852.
	Goudet J., Raymond M., deMeeues T. and Rousset F. 1996
	Testing differentiation in diploid populations.
	Genetics 144, 4, p. 1933--1940.
	Jost, L. 2008
	Gst and its relatives do not measure differentiation.
	Molecular Ecology 17, 18, p. 4015--4026.
	Manly, B.F.J. 1997
	Randomization, bootstrap and Monte Carlo methods in biology
	Chapman & Hall.
	Nei, M. 1973
	Analysis of gene diversity in subdivided populations.
	Proceedings of the National Academy of Sciences of the United States of America
	70, 12, p. 3321--3323.
	Nei M., Chesser R. 1983
	Estimation of fixation indices and gene diversities.
	Annals of Human Genetics 47, 253--259.
	Wright, S.P. 1992
	Adjusted p-values for simultaneous inference.
	Biometrics 48, 1005--1013.
LazyLoad:	yes
Packaged:	2010-12-18 13:48:33 UTC; alexj
Built:	R 2.10.1; ; 2010-12-18 13:48:39 UTC; unix

Index:

D.Jost-and-Gst.Nei      Comparing Populations - Differentiation and
                        Fixation Indices
Example.transformed     Allelic Data of Three Populations For Three
                        Loci
Example.untransformed   Allelic Data of Three Populations for Three
                        Loci

Citation

To cite the package 'DEMEtics' in publications use:

Gerlach, G., Jueterbock, A., Kraemer, P., Deppermann, J. and Harmand, P. 2010
Calculations of population differentiation based on G(ST) and D: forget G(ST)
but not all of statistics! Molecular Ecology 19, 3845-3852

Author(s)

Alexander Jueterbock, Philipp Kraemer, Gabriele Gerlach and Jana Deppermann

Maintainer: Alexander Jueterbock <[e-mail]>

DEMEtics documentation built on May 1, 2019, 10:09 p.m.