DEMEtics (version 0.8-7)

DEMEtics-package: 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.

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

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