DArTseq-generated SNPs revealed low genetic diversity and genetic erosion along life stages in fragmented populations of Afrocarpus gracilior (Pilg.) C.N.Page in southern Ethiopia

Forest fragmentation can have severe genetic impacts that threaten the long-term viability of tree species, though susceptibility varies by species. This study investigates the genetic effects of fragmentation on Afrocarpus gracilior populations in traditional agroforestry systems and relict forest patches. We used single nucleotide polymorphism (SNP) markers generated by the DArTseq platform to assess genetic diversity and population structure in both adult and progeny cohorts. Our findings indicate overall low genetic diversity (H_E < 0.1) across all A. gracilior populations studied, with progeny cohorts showing even lower diversity than adults. Progeny from isolated or few mother trees exhibited the lowest genetic diversity, suggesting heightened genetic drift and inbreeding. Genetic differentiation between populations ranged from little (F_ST < 0.05) to moderate (0.05 < F_ST < 0.15), with progeny cohorts from smaller populations showing relatively higher differentiation and significant index of association scores. A Mantel test found no significant correlation between genetic and geographic distances. Analysis of molecular variance indicated that most genetic variation occurred within populations (57–61 %), rather than between populations (1.07–4.93 %) or individuals (about 38 %). Clustering analysis using the discriminant analysis of principal components (DAPC) method, classified the genotypes into five groups, whereas phylogenetic analysis identified three major clusters with further subgrouping. Overall, the study highlights low genetic diversity in A. gracilior populations, with significant inbreeding and genetic drift in progeny from small, isolated populations. These results are crucial for informing conservation, restoration, and genetic rescue efforts for the species.