Systematics and Biodiversity (2011), 9(1): 45–57 Research Article Assessing the molecular phylogeny of a near extinct group of vertebrates: the Neotropical harlequin frogs (Bufonidae; Atelopus)

Neotropical harlequin frogs, Atelopus, are a species-rich bufonid group. Atelopus monophyly has been suggested but intergeneric, interspecific and intraspecific relationships are poorly understood. One reason is that morphological characters of harlequin frogs are often difficult to interpret, making species delimitations difficult. Molecular analyses (DNA barcoding, phylogeny) may be helpful but sampling is hampered as most of the more than 100 Atelopus species have undergone severe population declines and many are possibly extinct. We processed mitochondrial DNA (12S and 16S rRNA) of 28 available ingroup samples from a large portion of the genus ’ geographic range (Bayesian Inference, Maximum Likelihood). Our samples constitute a monophyletic unit, which is sister to other bufonid genera studied including the Andean genus Osornophryne. In contrast to previous morphological studies, our results suggest that Osornophryne is neither sister to Atelopus nor nested within it. Within Atelopus, we note two major clades with well supported subclades, one Amazonian–Guianan Clade (Flavescens-spumarius Clade plus Tricolor Clade) and an Andean–Chocó–Central American Clade (Varius Clade plus all other Atelopus). The first mentioned includes all species that possess a middle ear (i.e. stapes) except for A. seminiferus lacking it (like all remaining Atelopus). Previously proposed species groups based o