A Spatial Structure of Key Tree Species Metrodorea nigra St. Hill. (Rutaceae) Is Associated with Historical Disturbance and Isolation in Southeastern Brazil

The semi-deciduous Brazilian Atlantic Forest has faced intense fragmentation, impacting Metrodorea nigra St. Hill., a fly-pollinated and autochorous tree. We investigated population structure, inbreeding, and spatial genetic structure (SGS) across adult (Adu) and juvenile (Juv) generations in three fragmented populations of M. nigra in Ribeir&atilde:o Preto, S&atilde:o Paulo, Brazil. We tested whether the magnitude of these effects could result from its mating system, seed dispersal, anthropogenic disturbances, matrix, and fragment size. Populations affected by selective logging, fire, and trail openings include M13-Rib (84 ha) and FAC-Crav (8 ha), both surrounded by sugar cane and BSQ-Rib (3 ha) in an urban matrix. We evaluated phenological events and germination rates in the BSQ-Rib fragment. We sampled leaves and amplified their DNA using ISSR (UBC 1, 2, 820, 834, 851, 858, 860, 886) and SSR (Mtn 1, 3, 13, 16, 19, 87, 95) molecular markers. Fst, PCoA, and AMOVA values suggest a lack of generational isolation, with most variance within generations. Inbreeding values were significant in all populations (Fis and Fit, p = 0.001), probably intensified by natural seed dispersal and pollinator behavior favoring geitonogamy. However, fragmentation, anthropogenic disturbances, and the surrounding matrix influenced SGS. The urban BSQ-Rib fragment recorded the highest SGS values (26 m Juv, 24 m Adu [ISSR]: 7 m Juv, 9 m Adu [SSR]), which may result in low fruit and seed production and germination rates. Despite being the largest fragment, M13-Rib shows SGS in the first distance class (19 m Juv, 24 m Adu [ISSR]: 0 m Juv, and 10 m Adu [SSR]), possibly due to selective logging and fire. FAC-Crav, a more conserved fragment, showed no SGS in adults but punctual SGS in juveniles (27 m [ISSR] and 8 m [SSR]), pointing to it as a promising source for seed collections for reforestation purposes. In summary, inbreeding in M. nigra, influenced by pollinator behavior and seed dispersal, along with fragmentation, anthropogenic disturbances, and the surrounding matrix, are critical in shaping SGS. These factors potentially impact the reproductive success of M. nigra and their long-term survival in the face of climate change.