Population genomics of the endangered Peruvian algarrobo (Neltuma pallida) reveals low genetic diversity and a recent bottleneck in a protected dry-forest population

The Pomac Forest Historic Sanctuary (SHBP), a protected area on the northern coast of Peru, conserves biodiversity representative of Equatorial dry forests. SHBP is mainly composed of algarrobo ( Neltuma pallida ), a species adapted to the variable climate conditions and known for its multiple ecological functions and ecosystem services. Algarrobos face an unprecedented population decline despite their remarkable natural adaptation, worsened by their ongoing habitat degradation and overexploitation. In this study, we aim to characterize the genomic diversity of the protected forest in the SHBP to establish a baseline for future monitoring and research. Results show that the algarrobo population in the SHBP is unstructured, has low inbreeding indices, an average autosomal heterozygosity of 0.19%, and a per-site nucleotide diversity of 0.0023. Patterns of low genetic diversity are associated with a recent bottleneck decline starting around four generations ago. Potentially deleterious variants with varying effects, possibly playing a role in population adaptability were predicted. In conclusion, our results provide reference genetic indices for future monitoring of algarrobo in its native range and raises questions about the impact of recent habitat degradation on its genome.