Among the most controversial questions in vertebrate evolution are the pattern and timing of the emergence of extant lineages of birds. New basal fossils from the Eocene of North and South America, evaluated in comprehensive combined phylogenetic datasets including molecular sequence data, challenge previously long held ideas about the biogeographical shifts occurring over the Cenozoic histories of avian lineages and their potential drivers. Two of the best exemplars of Paleogene penguins yet recovered, from the middle and late Eocene of Peru, reveal that penguins invaded low latitudes over 30 million years earlier than prior data supported. It was previously proposed that penguins originated in high southern latitudes and arrived at equatorial regions relatively recently, after the onset of late Cenozoic global cooling and increases in polar ice volume. Phylogenetic analysis places the new Peruvian species outside the extant penguin radiation and supports two separate dispersals to equatorial regions (paleolatitude ~14° S) by the late Eocene. Fossil evidence strongly contradicts patterns inferred from molecular divergence dates.

From the Eocene of North America, Green River Formation fossils from multiple ‘higher land bird' clades suggest significant extinct New World diversity for lineages with species depauperate Old World extant distributions. For example, two newly identified fossil mousebirds (Coliiformes) support an extensive New World distribution in the Eocene. They reveal that the clade persisted in North America until at least latest Eocene cooling. Analysis of a complete skeleton of a new stem roller species (Aves, Coracii) supports, for the first time, a possible New World origin for the lineage. Questions of broad patterns and potential climate drivers for extant avian biodiversity require phylogenetically evaluated fossils and combined analyses.