Integrating Population Genomics and Historical Occurrence Data to Assess the Impact of Land‐Use Changes on <i>Centris</i> Oil Bees in the Brazilian Cerrado

Habitat loss and fragmentation (HLF) are among the major drivers of bee decline, yet closely related species often show contrasting responses depending on their ecological and demographic traits. The Brazilian Cerrado biodiversity hotspot experiences among the world's highest rates of HLF. Here we combined whole-genome sequencing and six decades of museum occurrence records to assess the population genomic diversity, demographic history, temporal trends and seasonal activity of two ecologically similar oil-collecting bees, Centris aenea and Centris fuscata, in the Brazilian Cerrado-a global biodiversity hotspot under intense anthropogenic pressure. Despite the occurrence in a fragmented landscape, our results revealed a high nucleotide diversity and weak population structure for both species. However, whereas C. aenea exhibited higher diversity, no inbreeding and negligible population genetic differentiation, C. fuscata displayed numerous runs of homozygosity and moderate differentiation between some populations. Demographic reconstructions revealed that both species underwent historical declines, likely linked to Holocene climatic transitions, but recent trajectories diverged: C. aenea maintained a stable effective population size, whereas C. fuscata showed strong fluctuations and a recent decline. Museum records corroborated these patterns, indicating a decline in C. fuscata but not in C. aenea. Our findings highlight how subtle differences in a species' ecology can drive divergent responses to HLF. While conserving natural vegetation is critical for both species, C. fuscata may require targeted monitoring and management to safeguard its long-term persistence in the increasingly threatened Cerrado biome.