GSED 3.0 (January 2015)

Copyright © 1985-2015 Elizabeth M. Gillet. Email egillet@gwdg.de URL http://www.uni-goettingen.de/forstgenetik/gsed

GSED ("Genetic Structures from Electrophoresis Data") calculates measures of genetic variation within and among populations for the purpose of characterizing genetic structures in population genetic investigations. Calculations are based on the single- or multilocus frequency distributions of the states of one or more genetic traits in the populations. GSED implements a conceptually and mathematically unified system of data analysis developed at the Department of Forest Genetics and Forest Tree Breeding of the University of Göttingen.

New features:

menu-driven choice of options
extended tabular output file importable into spreadsheets
graphical representations of subpopulation differentiation "snails" in Windows Metafile and Postscript formats

GSED characterizes genetic structures in population genetic investigations for genetic traits of the following types:

GENETIC TRAITS:

Codominant DNA markers, such as microsatellites (SSR)
Isoenzyme markers, including null alleles
Any codominantly expressed gene marker in diploid individuals or tissue
Any gene marker in haploid individuals, tissue, or organelles, such as chloroplast or mitochondrial cytotypes

FREQUENCY DISTRIBUTIONS:

Single-locus distributions:

Allele frequencies among haploid maternal gametic contributions
Allele frequencies among haploid paternal gametic contributions
Allele frequencies at diploid loci
Diploid genotype frequencies

Multilocus distributions for arbitrary multilocus combinations:

Haplotype frequencies among maternal contributions
Haplotype frequencies among paternal contributions
Haplotype frequencies
Genotype frequencies.

MEASURES OF GENETIC VARIATION:

Threshold frequency α for samples of the given size, such that the probability of detecting all types of frequency ≥α is at least 95% [4].
Measures of variation within populations:

Diversity v₂ [3,8]
Total population differentiation δ_T [8,9]
Evenness e [10]

Measures of variation among populations:

Genetic distance d₀ [1,2,3,5]
Subpopulation differentiation D_j and δ [6,7,9,11]
χ² and G-tests of homogeneity

Analysis of genotypic structure:

Heterozygosity (observed proportion of heterozygosity H_o [12]
Conditional heterozygosity H_c of single-locus genotypes [3,12]
Degree of heterozygosity of multilocus genotypes) [3]
Test of Hardy-Weinberg structure at single loci
Test of product structure at single loci (ordered genotypes only)

Analysis of the gene pool across loci:

Within populations: Gene pool diversity v [8]; Hypothetical gametic diversity v_gam [3]; Total population differentiation δ_T of the gene pool [8])
Among populations: Genetic distance d₀ between gene pools [7]; Differentiation δ of subdivided gene pools [7])

PROGRAM NOTES:

GSED is compiled using the GNU Fortran95 compiler for Win32 and Linux (SuSE 11.0).

Plots and widgets are constructed using routines of the scientific data plotting software DISLIN Copyright © 2009 Helmut Michels http://www.dislin.de

Send comments, suggestions, and bug reports to Email egillet@gwdg.de

DOWNLOAD GSED:

Download GSED 3.0 program package, including executable, example input, and GSED 3.0 User's Manual

Current version:

REFERENCES:

[1] Gregorius H.-R. 1974. Genetischer Abstand zwischen Populationen. I. Zur Konzeption der genetischen Abstandsmessung. Silvae Genetica 23, 22-27. http://www.bfafh.de/inst2/sg-pdf/23_1-3_22.pdf

[2] Gregorius H.-R. 1974. On the concept of genetic distance between populations based on gene frequencies. Proc. Joint IUFRO Meeting, S02.04.1-3, Stockholm, Session I, 17-26.

[3] Gregorius H.-R. 1978. The concept of genetic diversity and its formal relationship to heterozygosity and genetic distance. Mathematical Biosciences 41, 253-271. http://dx.doi.org/10.1016/0025-5564(78)90040-8

[4] Gregorius H.-R. 1980. The probability of losing an allele when diploid genotypes are sampled. Biometrics 36, 643-652.

[5] Gregorius H.-R. 1984. A unique genetic distance. Biometrical Journal 26, 13-18. http://dx.doi.org/10.1002/bimj.4710260103

[6] Gregorius H.-R. 1984. Measurement of genetic differentiation in plant populations. Pp. 276-285 in: Gregorius, H.-R. (ed.). Population Genetics in Forestry. Springer-Verlag, Berlin, Heidelberg, New York, Tokyo.

[7] Gregorius H.-R., Roberds J.H. 1986. Measurement of genetical differentiation among subpopulations. Theoretical and Applied Genetics 71, 826-834. http://dx.doi.org/10.1007/BF00276425

[8] Gregorius H.-R. 1987. The relationship between the concepts of genetic diversity and differentiation. Theoretical and Applied Genetics 74, 397-401. http://dx.doi.org/10.1007/BF00274724

[9] Gregorius H.-R. 1988. The meaning of genetic variation within and between subpopulations. Theoretical and Applied Genetics 76, 947-951. http://dx.doi.org/10.1007/BF00273686

[10] Gregorius H.-R. 1990. A diversity-independent measure of evenness. American Naturalist 136, 701-711.

[11] Gregorius H-R. 1996. Differentiation between populations and its measurement. Acta Biotheoretica 44, 23-36. http://dx.doi.org/10.1007/BF00046433

[12] Gregorius H.-R., Krauhausen J., and Müller-Starck G. 1986. Spatial and temporal genetic differentiation among the seed in a stand of Fagus sylvatica L. Heredity 57, 255-262.http://dx.doi.org/10.1038/hdy.1986.116

GSED is free software: you can redistribute it under the terms of the GNU General Public License (GPL) v.3, as published by the Free Software Foundation. GSED is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of merchantability or fitness for a particular purpose. Reassembling is not permitted. See the GNU General Public License, a copy of which is contained in the file COPYING included in the download file, or see http://www.gnu.org/licenses/.

GSED implements the scientific data plotting software DISLIN Copyright ©2009 Helmut Michels http://www.dislin.de.