Genetic variation within and relationships among populations of Asian goats (Capra bircus)

Genetic variation at 59 protein coding loci (16 polymorphic) and 25 microsa tellite loci was analysed for 11 indigenous south-east Asian goat populatio ns, and the Australian feral population, to determine the magnitude of gene tic differentiation and the genetic relationships among the populations. Si gnificant deviations from Hardy-Weinberg equilibrium were detected in one o r more populations for eight of the nine protein loci with codominant allel es, and for microsatellites for all except the two Sri Lankan populations a nd for all but four loci. For both marker types, average inbreeding coeffic ients (F-IS) were exceptionally high. Heterogeneity of deviations from Hard y-Weinberg equilibrium for the microsatellites showed no differences for am ong loci within populations as compared with among populations within loci. For protein loci, however, the former was higher, indicating selection aff ecting allele frequencies at some loci. The variance among protein loci was significantly higher than among microsatellite loci, further indicating se lection at some protein loci. There was significant differentiation among p opulations for both protein and microsatellite loci, most likely reflecting the geography of south-east Asia, and the presumed spread of goats through out the region. Phylogenies derived from pair-wise genetic distance estimat es show some similar clustering for the microsatellite and protein based tr ees, but bootstrap support was generally low for both. A phylogeny based on the combined set of 38 protein and microsatellite loci showed better consi stency with geography and higher bootstrap values. The genetic distance phy logeny and the Weitzman diversity tree derived from microsatellite data sho wed some identical clusters, and both identified the Ujung Pandang and Aust ralia populations as contributing most to overall genetic diversity.