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

[Display omitted] ► 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. The estimation of a robust phylogeny is a necessary first step in understanding the biological diversification of the platyrrhines. Although the most recent phylogenies are generally robust, they differ from one another in the relationship between Aotus and other genera as well as in the relationship between Pitheciidae and other families. Here, we used coding and non-coding sequences to infer the species tree and embedded gene trees of the platyrrhine genera using the Bayesian Markov chain Monte Carlo method for the multispecies coalescent (∗BEAST) for the first time and to compared the results with those of a Bayesian concatenated phylogenetic analysis. Our species tree, based on all available sequences, shows a closer phylogenetic relationship between Atelidae and Cebidae and a closer relationship between Aotus and the Cebidae clade. The posterior probabilities are lower for these conflictive tree nodes compared to those in the concatenated analysis; this finding could be explained by some gene trees showing no concordant topologies between Aotus and the other genera. Moreover, the topology of our species tree also differs from the findings of previous molecular and morphological studies regarding the position of Aotus. The existence of discrepancies between morphological data, gene trees and the species tree is widely reported and can be related to processes such as incomplete lineage sorting or selection. Although these processes are common in species trees with low divergence, they can also occur in species trees with deep and rapid divergence. The sources of the inconsistency of morphological and molecular traits with the species tree could be a main focus of further research on platyrrhines.