COII: a useful tool for inferring phylogenetic relationships among New World monkeys (Primates, Platyrrhini)

In this study we evaluated the performance of the cytochrome c oxidase subunit II (COII) mitochondrial gene as a tool for inferring phylogenetic relationships among platyrrhines. Twenty‐nine COII sequences were examined in seven platyrrhine genera (Alouatta, Ateles, Lagothrix, Brachyteles, Cebus, Saimiri, and Aotus) employing parsimony and distance methods. Phylogenetic signal (g1) was present in all codon positions, despite the transitional saturation detected at the third position. In tree reconstructions bootstrap support values decreased abruptly above the generic level. Parsimony trees based on weighted transversions (tv : ts, 10 : 1) at the third position showed similar topologies. The utility of COII in phylogenetic studies among platyrrhines seems to be limited, due to its low rate of replacement substitutions and a relatively fast saturation of silent substitutions at third codon positions. Our data suggest that its main utility in platyrrhine systematics lies at the intrageneric level.