Genome-wide analyses reveal recent diversification and hidden diversity in Amazonian howler monkeys, including two new species
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.
Authors
- Thiago Borges Fernandes Semedo (ORCID: https://orcid.org/0000-0003-4379-5993)
- Javier Prado-Martinez (ORCID: https://orcid.org/0000-0001-5402-2721)
- Christian Roos (ORCID: https://orcid.org/0000-0003-0190-4266)
- Sebastián Cuadros-Espinoza (ORCID: https://orcid.org/0000-0002-6240-281X)
- Mark C. Gibson
- Ian Goodhead (ORCID: https://orcid.org/0000-0002-3110-9442)
- John Seyjagat
- Anneke H. van Heteren (ORCID: https://orcid.org/0000-0003-1018-7991)
- Izeni Pires Farias (ORCID: https://orcid.org/0000-0002-1416-4351)
- Russell A. Mittermeier (ORCID: https://orcid.org/0000-0002-8002-826X)
- CAMILA CHEREM RIBAS (ORCID: https://orcid.org/0000-0002-9088-4828)
- Fernando J. Vilchez-Delgado (ORCID: https://orcid.org/0000-0002-7407-1114)
- Pedro Bittencourt (ORCID: https://orcid.org/0000-0002-4074-3541)
- Chrysoula Gubili (ORCID: https://orcid.org/0000-0002-0866-6259)
- David Mahabir
- Dorien de Vries (ORCID: https://orcid.org/0000-0002-6809-0052)
- Anthony Brome Rylands (ORCID: https://orcid.org/0000-0001-6284-248X)
- Rainer Nrshima Deo
- Irune Ruiz‐Gartzia (ORCID: https://orcid.org/0000-0002-2699-7860)
- Lukas F. K. Kuderna (ORCID: https://orcid.org/0000-0002-9992-9295)
- Tomàs Marquès‐Bonet (ORCID: https://orcid.org/0000-0002-5597-3075)
- Sam Shanee (ORCID: https://orcid.org/0000-0001-5573-6208)
- Mareike C. Janiak (ORCID: https://orcid.org/0000-0002-7759-2556)
- Romina Batista (ORCID: https://orcid.org/0000-0002-7030-5227)
- Bernardo Urbani (ORCID: https://orcid.org/0000-0001-5392-9751)
- Amanda Dawn Melin (ORCID: https://orcid.org/0000-0002-0612-2514)
- Robin M. D. Beck (ORCID: https://orcid.org/0000-0002-7050-7072)
- Núria Hermosilla-Albala (ORCID: https://orcid.org/0000-0001-9079-1093)
- Stephen D. Nash (ORCID: https://orcid.org/0009-0007-5267-9958)
- Fabiano Rodrigues de Melo
- Patricia Mendoza
- Rogério V. Rossi
- Jean P. Boubli (ORCID: https://orcid.org/0000-0002-5833-9264)
- Maria N. F. da Silva
- Jeffrey Rogers (ORCID: https://orcid.org/0000-0002-7374-6490)
- Luis M. P. Ceríaco
- João Valsechi
- Richard Sorrillo
- Tomas Hrbek (ORCID: https://orcid.org/0000-0003-3239-7068)
- Felipe E. Silva
- Kyle Farh
Institutions
- Brazilian Institute of Environment and Renewable Natural Resources (BR)
- University of Southern California (US)
- Institució Catalana de Recerca i Estudis Avançats (ES)
- Universitat Autònoma de Barcelona (ES)
- Naturalis Biodiversity Center (NL)
- Université Libre de Bruxelles (BE)
- Universidade Federal de Viçosa (BR)
- University of Calgary (CA)
- Illumina (United States) (US)
- Baylor College of Medicine (US)
- Universidade do Porto (PT)
- Instituto Nacional de Pesquisas da Amazônia (BR)
- Instituto Venezolano de Investigaciones Científicas (VE)
- Universidad Peruana Cayetano Heredia (PE)
- Washington University in St. Louis (US)
- German Primate Center (DE)
- Barcelona Biomedical Research Park (ES)
- Universidade Federal de Mato Grosso (BR)
- Institut de Biologia Evolutiva (ES)
- Centre for Genomic Regulation (ES)
- Bavarian State Collection of Zoology (DE)
- Centro Nacional de Análisis Genómico (ES)
- Instituto de Desenvolvimento Sustentável Mamirauá (BR)
- Institut Català de Paleontologia Miquel Crusafont (ES)
- Bavarian Natural History Collections (DE)
- Alberta Children's Hospital Research Institute (CA)
- Centro de Investigação em Biodiversidade e Recursos Genéticos (PT)
- Hellenic Agricultural Organization - DIMITRA (GR)
- Instituto de Medicina Tropical Alexander von Humboldt (PE)
- University of Salford (GB)
- New York University (US)
- Trinity University (US)
- Universidade Federal do Amazonas (BR)
- Ludwig-Maximilians-Universität München (DE)
Publication Details
- Journal
- Communications Biology
- Published
- 2026-10-30
- DOI
- https://doi.org/10.1038/s42003-026-11187-8
- Primary Topic
- Genetic diversity and population structure
- Type
- article
- Field-Weighted Citation Impact
- 0.00
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