The genetic diversitywas analyzed among spotted paca (Agouti paca) from three commercial flockslocated in Brazil. As the genome of this species is unknown, the RAPD-PCR techniquewas used. Ten primers generated sixty polymorphic bands. The among and withinpopulation genetic variability estimated by analysis of molecular variance (AMOVA)was 12.55 and 87.45%, respectively. The shortest Nei distance value was 11.76%among the Carangola (CG) and São Francisco do Glória (SF) populations.This value can be explained by the exchange of reproduction males and femalesbetween the two geographically close breeding sites. The analysis of principalcomponents showed well defined and structured groups aggregating animals accordingtheir population of origin, with some exceptions. Lower diversity was foundin the São Francisco population than in the Carangola and Castelo (CS)populations. This result suggested the variability is better conserved in breedingfarms with fifty or sixty animals (CG and CS) than in the breeding farm witha dozen animals (SF). The RADP-PCR technique proved to be informative for thequantification of among and within population genetic variability of the spottedpaca. The phenogram generated by UPGMA using the NTSYS-PC software from theNei Distance, grouped CG and SF on a single branch connected to the CS, with76 and 100% accuracy, respectively, to the bootstrap. This result was not onlyconsistent with the historical and geographical information on flocks, but alsoshows the need for periodic reproductive male replacement. Future studies shouldbe developed with co-dominant markers and include spotted paca from more distantplaces.
