title: Genetic identities and local inbreeding in pure diploid clones with homoplasic markers: SNPs may be misleading.
abstract: Expected values for observed heterozygosity, genetic diversity, and inbreeding of individuals relative to inbreeding of the population (F(IS)) are derived in the case of one locus displaying homoplasy with K possible allelic states (KAM model) in a clonal diploid population. Heterozygosity (H(O)) and genetic diversity (H(S)) are substantially affected by homoplasy as long as the number of alleles K ⩽ 10, while F(IS) remains weakly affected in any case. Simulations suggest that in big populations, or in case of maximum homoplasy (K = 2), expected values can appear far from the observed ones because equilibrium takes too many generations to be reached at homoplasic markers in clonally propagating populations. This raises some concern on the use of SNPs, at least in clonal populations.
authors.affiliation: IRD (INTERTRYP), UMR 177 IRD-CIRAD, Centre International de Recherche-Développement sur l'Elevage en zone Subhumide (CIRDES), 01 BP 454 Bobo-Dioulasso 01, Burkina Faso; IRD (INTERTRYP), UMR177 IRD-CIRAD, TA A-17/G, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France. Electronic address: thierry.demeeus@ird.fr.
authors.forename: Thierry
authors.initials: T
authors.lastname: De Meeûs
mesh_terms: D000465:Algorithms; D004171:Diploidy; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D006579:Heterozygote; D007178:Inbreeding; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide
chemical_list: D005819:Genetic Markers
keywords: Equilibrium; Genetic diversity; Heterozygosity; Homoplasy; Population genetics