Species tree estimation for a deep phylogenetic divergence in the New World monkeys (Primates: Platyrrhini)

► We estimate the species tree and embedded gene trees of the platyrrhines using multiple coding and non-coding sequences. ► We explore the conflictive relationship among Aotus and other genera, as well as among Pitheciidae and other families. ► Our species tree shows a closer relationship between Atelidae and Cebidae, and between Aotus and the Cebidae clades. ► The posterior probabilities are lower for these conflictive tree nodes when compared with those of concatenated analysis. ► The topology of our species tree also differs from the previous molecular and morphological studies on the place of Aotus.