Highland forest’s environmental complexity drives landscape genomics and connectivity of the rodent Peromyscus melanotis

Context Deciphering how the complex environmental dynamics of highland temperate forests drive local patterns of genetic variation is key to understanding species diversity and distribution. Objectives Evaluate how the environmental complexity of La Malinche volcano influences patterns of genomic variation in Peromyscus melanotis , across two mountain slopes and global and regional geographic scales. Methods Using reduced representation genomic sequencing we estimated population genetic diversity, subdivisions and migration rates. Remote sensing data and drone image processing were used to characterize landscape variables. We evaluated their effect on connectivity, based on a landscape analyses framework, using resistance surfaces, circuit theory and omnidirectional connectivity. Results In our global analysis assessing multiple elevation levels on two mountain slopes, we identified three genetic clusters differentiating two elevation levels of the north mountain slope (ECLM; 3150 m, 3300 m) from the rest of sampled areas. Within the northeast mountain slope (CVM), we found reduced genetic variation, limited connectivity, fewer migrants and isolation in higher elevation populations. ECLM populations showed higher genetic diversity and lowest connectivity at intermediate levels. NDVI and tree height were the main factors promoting connectivity in CVM, while tree height and litter cover were most important in ECLM. Conclusions Our findings showed how the forest environmental complexity across different geographic scales drives dispersal, genomic structure and connectivity patterns in this rodent, where dirt roads and disturbed areas limit its connectivity, while exhibiting higher connectivity at the highest elevations where the forest is less disturbed. Notably, that our 3D variable of tree height was significant demonstrates the utility in incorporating 3D vegetation structure variables into landscape genetic analyses.