title: Phylogenomic evidence for multiple losses of flight in ratite birds.
abstract: Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are large, flightless birds that have long fascinated biologists. Their current distribution on isolated southern land masses is believed to reflect the breakup of the paleocontinent of Gondwana. The prevailing view is that ratites are monophyletic, with the flighted tinamous as their sister group, suggesting a single loss of flight in the common ancestry of ratites. However, phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal that unequivocally places tinamous within ratites, making ratites polyphyletic and suggesting multiple losses of flight. Phenomena that can mislead phylogenetic analyses, including long branch attraction, base compositional bias, discordance between gene trees and species trees, and sequence alignment errors, have been eliminated as explanations for this result. The most plausible hypothesis requires at least three losses of flight and explains the many morphological and behavioral similarities among ratites by parallel or convergent evolution. Finally, this phylogeny demands fundamental reconsideration of proposals that relate ratite evolution to continental drift.
authors.affiliation: Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605, USA.
authors.forename: John
authors.initials: J
authors.lastname: Harshman
authors.forename: Edward L
authors.initials: EL
authors.lastname: Braun
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Braun
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Huddleston
authors.forename: Rauri C K
authors.initials: RC
authors.lastname: Bowie
authors.forename: Jena L
authors.initials: JL
authors.lastname: Chojnowski
authors.forename: Shannon J
authors.initials: SJ
authors.lastname: Hackett
authors.forename: Kin-Lan
authors.initials: KL
authors.lastname: Han
authors.forename: Rebecca T
authors.initials: RT
authors.lastname: Kimball
authors.forename: Ben D
authors.initials: BD
authors.lastname: Marks
authors.forename: Kathleen J
authors.initials: KJ
authors.lastname: Miglia
authors.forename: William S
authors.initials: WS
authors.lastname: Moore
authors.forename: Sushma
authors.initials: S
authors.lastname: Reddy
authors.forename: Frederick H
authors.initials: FH
authors.lastname: Sheldon
authors.forename: David W
authors.initials: DW
authors.lastname: Steadman
authors.forename: Scott J
authors.initials: SJ
authors.lastname: Steppan
authors.forename: Christopher C
authors.initials: CC
authors.lastname: Witt
authors.forename: Tamaki
authors.initials: T
authors.lastname: Yuri