Genome-wide analyses reveal recent diversification and hidden diversity in Amazonian howler monkeys, including two new species

Complex ecological and evolutionary patterns shaped the rich biodiversity of the Neotropics. Understanding how diversity emerges and is maintained is key to anticipating potential biotic responses to current anthropogenic changes. Howler monkeys ( Alouatta ) are one of the most successful radiations inhabiting this region. However, 11 of the 16 taxa currently recognised are classified as threatened by the IUCN Red List, and the genus faces increasing threats from deforestation, habitat fragmentation, and hunting. Here, we present a genomic-wide analysis covering 11 of the 13 recognised Alouatta species. Our results indicate that most of this genus’ diversity in Amazonia originated in the last million years, driven by major biogeographic and ecological factors, such as geographical barriers (e.g., Amazonian rivers, and the Andes), as well as by ecological gradients, including savanna-forest mosaics and ecotonal zones. Historical biogeographic reconstructions support a trans-Andean origin for Alouatta . Based on integrative taxonomy, including genomic and morphological evidence from numerous specimens, we formally identify groups and provide descriptions for two new species. Our findings underscore the power of genome-wide data to uncover hidden diversity and to inform conservation strategies, particularly in rapidly transforming tropical ecosystems where undescribed species may already be at risk.