When native meets exotic: Uncovering hybridization between Cuban and introduced mahogany using chloroplast and nuclear microsatellites

The introduction of closely related species can threaten the genetic integrity of endemic taxa through hybridization and introgression. In Cuba, Swietenia macrophylla was widely planted in the 1970s for its fast growth and high-value timber, raising concerns about its potential genetic impact on the native S. mahagoni and the emergence of hybrids. This study investigates the genetic consequences of introducing S. macrophylla to Cuba by analysing 357 individuals from five populations, including two naturally regenerated S. mahagoni populations, a pure S. macrophylla remnant, and two mixed stands containing both species and morphologically intermediate forms. The two predominant cpDNA haplotypes were shared across all five populations, whereas one mixed stand exhibited the highest diversity, with nine chloroplast DNA haplotypes—suggesting that its establishment involved seeds from multiple sources. cpDNA markers didn't reveal clear species-level differentiation. In contrast, nuclear microsatellites indicated moderate genetic differentiation (mean FST= 0.15±0.02) and substantial within-population variability, with expected heterozygosity (He) ranging from 0.46 to 0.85. At the same time, S. mahagoni showed a higher number of alleles (Na = 12.4–13.3) and expected heterozygosity (He = 0.73–0.78) than the remnant S. macrophylla population (Na = 5.75; He = 0.59), likely reflecting the smaller size of the existing S. macrophylla plantation in Cuba. Based on discriminant analysis of principal components and STRUCTURE results, the two parental species were clearly separated into distinct genetic clusters, while putative hybrid individuals were mainly concentrated in the two mixed stands. Leaf morphological and molecular classifications were highly concordant in parental populations (≈91%), confirming the phenotypic identifiability of S. mahagoni and S. macrophylla. The estimated proportion of hybrids varied: STRUCTURE (7.8–15.1%), whereas NewHybrids (36.1–39.2%). These findings provide a genetic framework for conservation-oriented management of native tree species, which is a tool for implementing long-term genetic monitoring and consolidating certified germplasm banks to safeguard the native Cuban mahogany.