Pitheciidae is a New Word primate family composed of two subfamilies (Callicebinae and Pitheciinae). The three extant pitheciine genera, Pithecia, Cacajao and Chiropotes are all endemic to the Amazon region. Because of the uncertainties about intraspecific relationships, we reviewed the systematics and taxonomy of the genus Chiropotes. The phylogenetic analyses were performed based on Maximum Likelihood and Bayesian Inference, while species delimitation analyses were carried out using multispecies coalescent methods. In addition, we estimated genetic distances, divergence time and the probable ancestral distribution of this genus. Our results support the taxonomic classification of Chiropotes into five species that have emerged during the Plio-Pleistocene. Biogeographic estimates suggest that the ancestor of the current Chiropotes species occupied the endemism areas from Rondonia and Tapajos. Later, subsequent radiation and founder effects associated with the formation of the Amazonian basins have probably determined the speciation events within Chiropotes.

Twenty samples of blood and muscle tissue preserved in alcohol were analyzed in the present study. These included four Chiropotes taxa, C. albinasus (n = 04 samples), C. satanas (n = 03), C. utahicki (n = 05), and C. sagulatus (n = 03), as well as Cacajao melanocephalus (n = 03), Pithecia pithecia (n = 01), and Plecturocebus moloch (n = 01). These samples were obtained from the DNA databanks at the Federal University of Pará (UFPA) in Belém and from the Federal University of Amazonas (UFAM) in Manaus, both in Brazil. The UFPA samples are referenced in previous papers (Rocha et al., 1990; Sampaio et al., 1991; Schneider et al., 1994). Samples from UFAM were obtained from the wild under permits 40217-1 and 5135-1, supplied by the Instituto Chico Mendes de Conservação da Biodiversidade - ICMBio.

The sequences were aligned using ClustalW (Thompson et al., 1994) and edited manually in BioEdit v.7.2.5 (Hall, 1999). PartitionFinder v.1.1.0 (Lanfear et al., 2012) was used to identify the optimal data partitioning and evolutionary models. Phylogenetic analyses were based on Maximum Likelihood (ML) and Bayesian Inference (BI) approaches. Species were delimited using the software Bayesian Phylogenetics and Phylogeography (BPP). In order to estimate the biogeographic history of distributional ranges of cuxius, we used BioGeoBEARS ‘Biogeography with Bayesian (and likelihood) Evolutionary Analysis’ in R Scripts (Matzke, 2013). Six discrete biogeographic areas were defined: Belem (BE), Xingu (XI), Tapajos (TA), Rondonia (RO), Guyana (GU) and Tepui (PA).