Spatial and temporal changes in agricultural landscapes and vegetation structure affect genomic diversity of a Neotropical understory shrub

Landscape changes due to intensive agriculture expansion affect plant community structure and ultimately genetic diversity. Plants may exhibit a time lag in their responses to ongoing landscape changes due to long life cycles, especially in areas where intensive farming practices were introduced only recently. We address the spatial and temporal effects of landscape changes and time lag response using a landscape genomics approach. Our work focuses on Palicourea prunifolia , a tropical forest understory specialist. We used data from 26,349 SNP loci to estimate genetic parameters and implemented coalescent analyses to estimate effective migration surfaces. We analyzed vegetation structure using ground LiDAR scans, then we extracted landscape metrics of composition and configuration from 1985 to 2022. Genomic diversity was higher in landscapes with lower forest cover and in remnants with a more open canopy. Inbreeding coefficients were higher in landscapes with higher agricultural cover and in remnants with more canopy closure. Migration was very low among all populations. Genomic differentiation between populations was high and best explained by prior landscape configuration, primarily proportion of pasture. We found no time lag in genetic diversity or inbreeding responses to landscape changes, but genetic differentiation has responded to past landscape changes. Our results point to a high degree of habitat loss and fragmentation, and to the high amounts of agroecosystems in the landscapes that have already been impacting populations of P. prunifolia. Restoration of forests, particularly methods aimed at increasing landscape connectivity should be a priority towards efforts to increase gene flow and genetic diversity and decrease differentiation among populations of P. prunifolia .