Presentation on theme: "SPAGeDi a program for Spatial Pattern Analysis of Genetic Diversity"— Presentation transcript:
1 SPAGeDi a program for Spatial Pattern Analysis of Genetic Diversity by Olivier J. Hardy and Xavier VekemansGoal: characterise spatial genetic structure ofmapped individuals or populations usinggenotype data of any ploidy levelCompute: - inbreeding coef- pairwise relatedness/differentiation coef between indiv/pop averages / distance classes association with distance (regression with lin/log distance)( isolation by distance, neighbourhood size estimates)- actual variance of relatedness coef Ritland’s approach for marker based estimate of h2Tests: permutations (of genes, individuals, or spatial locations)- jackknife over loci ( SE for multilocus estimates)Option: restricted analysis within or among categories of ind/pop
2 Input data Input file with : format #’s (#ind, #categ, #spat coord, #loci, #digits/allele, ploidy)distance intervalsfor each ind :namecategory (facultative)spatial coordinatesgenotype at each locusAnalyses defined on keyboard while running the program :indiv vs pop levelstat to compute (+ within/among categ)tests, …
3 Statistics computed: "relatedness" coef at the individual level 2-genes coef :- "kinship" coef(Loiselle 1995; Ritland 1996)- "relationship" coef(Moran’s I; Lynch & Ritland 1999; Wang 2002)- kinship type coef based on allele size(Streiff et al. 1999)- ar distance measure(Rousset 2000)4-genes coef :- "fraternity" coef(Lynch & Ritland 1999; Wang 2002)also for dominant marker(Hardy 2003)
4 Estimates of the actual variance of pairwise kinship coef in natural populations
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