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

Year: 2026

Type: article

Abstract: 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.

Source: Communications Biology

DOI: 10.1038/s42003-026-11187-8

Institutions: Instituto Nacional de Pesquisas da Amazônia, University of Salford, Universidade do Porto, Centro de Investigação em Biodiversidade e Recursos Genéticos, Brazilian Institute of Environment and Renewable Natural Resources, Universidade Federal do Amazonas, Barcelona Biomedical Research Park, Institut de Biologia Evolutiva, Centre for Genomic Regulation, Universidade Federal de Viçosa, University of Southern California, Naturalis Biodiversity Center, Illumina (United States), Hellenic Agricultural Organization - DIMITRA, Trinity University, Institució Catalana de Recerca i Estudis Avançats, Universitat Autònoma de Barcelona, Centro Nacional de Análisis Genómico, Institut Català de Paleontologia Miquel Crusafont, University of Calgary, Alberta Children's Hospital Research Institute, Washington University in St. Louis, Baylor College of Medicine, German Primate Center, Universidade Federal de Mato Grosso, Université Libre de Bruxelles, Instituto de Desenvolvimento Sustentável Mamirauá, New York University, Instituto Venezolano de Investigaciones Científicas, Bavarian State Collection of Zoology, Bavarian Natural History Collections, Ludwig-Maximilians-Universität München, Universidad Peruana Cayetano Heredia, Instituto de Medicina Tropical Alexander von Humboldt

Language: English

Topic: Genetic diversity and population structure

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Life on land

Open Access status: gold

Estimated APC paid: $4,190

Funders: National Geographic Society, Biodiversa+, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior, Conselho Nacional de Desenvolvimento Científico e Tecnológico, Fundação de Amparo à Pesquisa do Estado do Amazonas, Natural Environment Research Council, Fundação para a Ciência e a Tecnologia, Instituto Chico Mendes de Conservação da Biodiversidade

Awards: "Rise of the continent of the monkeys": an integrated genomic and fossil-based analysis of the adaptive radiation of New World primates, G1491336172, G2388152877, G2784589470, G4695082056, G5301814382, G6351871808, G6380996688, G6542968666, G7602796638, G8101102391, G8412322501

OpenAlex ID: W7213600814