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The Journal of Heredity 2001:92(5)
© 2001 The American Genetic Association 92:447-448

Computer Note

SGS—Spatial Genetic Software: A Computer Program for Analysis of Spatial Genetic and Phenotypic Structures of Individuals and Populations

B. Degen, R. Petit, and A. Kremer

From SILVOLAB Guyane, INRA Station de Recherches Forestières, Campus agronomique, BP 709, 97387—Kourou cedex, France D.O.M. Guyane (French Guiana) (Degen), and INRA Station de Recherches Forestières, Laboratoire de Génétique des Arbres Forestiers, BP 45, F-33611 Gazinet cedex, France (Petit and Kremer).

Address correspondence to B. Degen at the address above or e-mail: degen.b{at}kourou.cirad.fr.

We have developed a program called Spatial Genetic Software (SGS), which provides a user-friendly Windows tool to analyze both local and broad scale genetic and phenotypic structure. It can deal with nearly any type of genetic data, codominant (allozyme, PCR-RFLP, microsatellite) or dominant (RAPD, AFLP) markers, or biparentally (nuclear) or uniparentally (cpDNA and mtDNA) inherited markers. Data based on any of these markers can be analyzed, either as individual genotypes within a single population (local scale) or as allele or haplotype frequencies from different populations (broad scale). We also include a simple approach to analysis of spatial structure for continuous quantitative traits. The program implements various parameters to analyze spatial genetic and phenotypic structure: Moran's index, Geary's index, number of alleles in common, and approaches using genetic distances and FST values. The statistical significance of all measures is verified by the use of a permutation test. The results are assessed by graphics that can be integrated, via the clipboard, to other Windows programs. The details of the computations are given in a table and can be stored as ASCII files.


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