The evolution of the ratite birds has been widely attributed to vicariant speciation, driven by the Cretaceous breakup of the supercontinent Gondwana. The early isolation of Africa and Madagascar implies that the ostrich and extinct Madagascan elephant birds (Aepyornithidae) should be the oldest ratite lineages. We sequenced the mitochondrial genomes of two elephant birds and performed phylogenetic analyses, which revealed they are the closest relatives of the New Zealand kiwi, and distant from the basal ratite lineage of ostriches. This unexpected result strongly contradicts continental vicariance and instead supports flighted dispersal in all major ratite lineages. We suggest that convergence towards gigantism and flightlessness was facilitated by early Tertiary expansion into the diurnal herbivory niche following the extinction of the dinosaurs.One Sentence Summary: Ancient DNA reveals massive Madagascan elephant birds and tiny NZ kiwi are closest relatives, and supports flighted origin of ratites.
Main Text:Despite extensive studies, the evolutionary history of the giant flightless ratite birds of the southern hemisphere landmasses, and the related flighted tinamous of South America, has remained a major unresolved question. The ratites and tinamous, termed palaeognaths due to their shared 'basal' palate structure, form the sister-taxon to all other living birds (neognaths). The living ratites are one of the few bird groups comprised largely of giant terrestrial herbivores and include: the emu and cassowary in Australia and New Guinea; kiwi in New Zealand; ostriches in Africa; and rhea in South America. In addition, two recently extinct groups included the largest birds known: the moa from New Zealand (1) [up to 2-3 m and 250 kg] and elephant birds from Madagascar [2-3 m height but up to 275 kg] (2, 3). Ratites have been believed to have originated through vicariant speciation driven by the continental breakup of Gondwana on the basis of congruence between the sequence of continental rifting and the presumed order of lineage divergence and distribution of ratites (4,5).New Zealand is the only landmass to have supported two major ratite lineages, the giant herbivorous moa and the chicken-sized, nocturnal, omnivorous kiwi. Morphological phylogenetic analyses initially suggested that these two groups were each other's closest relatives (6, 7), presumably diverging after the isolation of an ancestral form following the separation of New Zealand and Australia in the late Cretaceous ca. 80-60 million years ago (Ma) (8). However, subsequent studies suggest that kiwi are more closely related to the Australasian emu and cassowaries (9, 10), while the closest living relatives of the giant moa are the flighted South American tinamous (11-14). The latter relationship was completely unexpected on morphological grounds, and suggests a more complex evolutionary history than predicted by a model of strict vicariant speciation. By rendering ratites paraphyletic, the relationship between moa and tinamous also strong...