Luciana Inés Oklander ^1,2,3* Gabriela Paula Fernández ⁴ Stela Machado ⁵ Mariela Caputo ⁶ Zelinda Maria Hirano ^3,7 Anthony B. Rylands ^3,8 Leonardo G Neves ⁹ Sérgio Lucena Mendes ^10,3 Luciana G. Pacca ¹¹ Fabiano Rodrigues de Melo ^12,3 Italo Mourthe ¹³ Thales Renato Ochotorena De Freitas ^14,15 Daniel Corach ⁶ Leandro Jerusalinsky ^15,16,17,3* Sandro L. Bonatto ^18,5*

• ¹ Grupo de Investigación en Genética Aplicada (GIGA) Instituto de Biologia Subtropical (IBS), UNAM-CONICET., Posadas, Argentina
• ² Neotropical Primate Conservation Argentina, Puerto Iguazú, Misiones., Argentina
• ³ Primate Specialist Group, Species Survival Commission, International Union for the Conservation of Nature, Austin, TX, United States
• ⁴ Centro de Bioinvestigaciones (CeBio-UNNOBA-CICBA) / Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires CITNOBA (UNNOBA-CONICET), Pergamino, Buenos Aires, Argentina
• ⁵ Programa de Pós-Graduação em Ecologia e Evolução da Biodiversidade, Pontifícia Universidade Católica do Rio Grande do Sul., Porto Alegre, Brazil
• ⁶ Servicio de Huellas Digitales Genéticas, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires (UBA) – CONICET, Ciudad autónoma de Buenos Aires, Argentina
• ⁷ Projeto Bugio, Centro de Pesquisas Biológicas de Indaial - CEPESBI, Universidade Regional de Blumenau - FURB, Indaial, Santa Catarina, Brazil
• ⁸ Re:wild, Austin, Texas, United States
• ⁹ Other, Ilhéus, Brazil
• ¹⁰ Instituto Nacional da Mata Atlântica - INMA., Santa Teresa, Brazil
• ¹¹ Centro Nacional de Pesquisa e Conservação de Primatas Brasileiros, Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio/CPB), Cabedelo, Paraíba, Brazil
• ¹² Departamento Engenharia Florestal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
• ¹³ Instituto de Desenvolvimento Sustentável Mamirauá, Tefé, Brazil
• ¹⁴ Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
• ¹⁵ Federal University of Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
• ¹⁶ Centro Nacional de Pesquisa e Conservação de Primatas Brasileiros, Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio), Cabedelo, Brazil
• ¹⁷ Programa Macacos Urbanos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
• ¹⁸ Centro de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul., Porto Alegre, Brazil

The brown howler, Alouatta guariba, endemic to the Atlantic Forest of Brazil and Argentina, is threatened by habitat loss and fragmentation, hunting, and its susceptibility to yellow fever. Two subspecies have been recognized, but their names, validity, and geographic ranges have been controversial. We obtained samples covering the species entire distribution in Brazil and Argentina to clarify these issues by investigating the species’ genetic diversity and structure and assessing its evolutionary history. We analyzed, for the first time, a set of ten microsatellite markers (N=153), plus mitochondrial DNA (mtDNA) segments of the control region (N=207) and cytochrome-b gene (N=116). The microsatellite data support two to three genetic clusters with biological significance. The southern populations (Argentina, Santa Catarina, Rio Grande do Sul) presented a homogeneous genetic component, and populations from São Paulo (SP) to the north presented another component, although most presented ~20% of the southern component. With K=3, SP emerged as a third component while sharing some ancestry with Rio de Janeiro and Argentina. The mtDNA phylogenies revealed three main clades that diverged almost simultaneously around 250 kya. Clades A and B are from central SP to the north and east, while clade C is from SP to the south and southwest. Samples from SP presented haplotypes in all three clades, sometimes in the same population. The demographic history of the species estimated with the Bayesian Skyline Plot of the mtDNA showed a strong expansion ~40–20 thousand years ago (kya) and a strong reduction since the last ~4–2 kya. Although the genetic clusters identified here deserve appropriate management strategies as Conservation Units, the absence of: (i) concordance between the mtDNA and microsatellite data, (ii) reciprocal monophyly in the mtDNA, and (iii) clear-cut non-genetic diagnostic characters, advises against considering them as different taxonomic entities. None of the previous taxonomic proposals were corroborated by our data. Our results elucidate the taxonomy of the Atlantic Forest brown howler, indicating it should be considered a monotypic species, Alouatta guariba. We also clarify the evolutionary history of the species regarding its intraspecific genetic diversity – crucial information for its conservation and population management.