Effect of fragmentation on the natural genetic diversity of Theobroma speciosum Willd. ex Spreng. populations.

Forest fragmentation reduces the effective size of natural populations, isolates individuals in the landscape, and, consequently, changes species' mating systems by increasing the degree of relatedness between individuals and inbreeding. Investigating the impact of habitat degradation on forest fragments helps to assess the genetic and ecological consequences of these changes, and allows the development of effective and sustainable conservation strategies to manage the genetic resources of species living in degraded landscapes. The aim of the present study was to assess the genetic diversity of fragmented Theobroma speciosum populations using microsatellite markers. Three urban forest fragments were selected in the municipality of Alta Floresta, Mato Grosso State, Brazil, namely C/E park, J park, and Zoo Botanical park. Seventy-five individuals (25 in each fragment) were sampled by collecting their leaves for genomic DNA extraction. Polymerase chain reaction amplifications were performed using nine polymorphic simple sequence repeat primers, which amplified 84 alleles. The mean expected heterozygosity was 0.970, and it was always higher than the observed heterozygosity. Analysis of molecular variance revealed that most variability occurred within populations (64%) rather than between them (36%). The Structure software and an unweighted pair group method with arithmetic mean dendrogram revealed three distinct groups, showing that individuals were allocated to their correct populations. Genotype number 3 from C/E park, number 45 from J park, and number 51 from Zoo Botanical park could be used as stock plants in breeding programs, because they were the most dissimilar within the populations studied. The high genetic diversity levels detected in all three populations studied emphasize the importance of protecting this species in its natural habitat.