The role of Cacao agroforests in the genetic conservation of Cariniana legalis, an emblematic species of the atlantic forest

Deforestation in the Atlantic Forest has reached critical levels, threatening multiple levels of biodiversity. In these deforested landscapes, conservation strategies could benefit from preserving agroforestry systems known as Cabruca, a traditional method of cultivating cocoa under a canopy of native trees. In this context, Cariniana legalis (Jequitibá-rosa), an endemic tree species of the Atlantic Forest listed as endangered, was selected to evaluate the role of cocoa agroforests (Cabrucas) and forest remnants in the genetic conservation of this species. The study assessed the genetic diversity, inbreeding levels, and genetic structure of five populations of C. legalis located in forest remnants protected by law and in Cabrucas in southern Bahia, Brazil. Using 11 microsatellite loci, 294 individuals were genotyped for adult and juvenile ontogenetic stages. Despite forest fragmentation, some populations, especially those located in Cabrucas, retained high levels of genetic diversity in both stages. In contrast, a protected area exhibited lower genetic diversity and elevated inbreeding levels (f > 0.43) in both adults and juveniles. Analyses of genetic differentiation (F_ST) and migration rate (Nm) indicated reduced historical gene flow in certain populations, while network analysis and Discriminant Analysis of Principal Components (DAPC) identified Cabrucas as central genetic hubs promoting connectivity across the landscape in both ontogenetic stages. Our results highlight the conservation value of cocoa agroforests for maintaining the genetic diversity and connectivity of this endangered tree species. We therefore recommend the inclusion of Cabrucas in integrated genetic conservation strategies for C. legalis in anthropogenically modified Atlantic Forest landscapes.