Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined approximately 32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.

On tropical Pacific islands, a human-caused "biodiversity crisis" began thousands of years ago and has nearly run its course. Bones identified from archaeological sites show that most species of land birds and populations of seabirds on those islands were exterminated by prehistoric human activities. The loss of birdlife in the tropical Pacific may exceed 2000 species (a majority of which were species of flightless rails) and thus represents a 20 percent worldwide reduction in the number of species of birds. The current global extinction crisis therefore has historic precedent.

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.convergence ͉ flightlessness ͉ Paleognath ͉ homoplasy ͉ vicariance biogeography

Whatever the cause, it is extraordinary that dozens of genera of large mammals became extinct during the late Quaternary throughout the Western Hemisphere, including 90% of the genera of the xenarthran suborder Phyllophaga (sloths). Radiocarbon dates directly on dung, bones, or other tissue of extinct sloths place their ''last appearance'' datum at Ϸ11,000 radiocarbon years before present (yr BP) or slightly less in North America, Ϸ10,500 yr BP in South America, and Ϸ4,400 yr BP on West Indian islands. This asynchronous situation is not compatible with glacial-interglacial climate change forcing these extinctions, especially given the great elevational, latitudinal, and longitudinal variation of the slothbearing continental sites. Instead, the chronology of last appearance of extinct sloths, whether on continents or islands, more closely tracks the first arrival of people.

Birds are prolific colonists of islands, where they readily evolve distinct forms. Identifying predictable, directional patterns of evolutionary change in island birds, however, has proved challenging. The "island rule" predicts that island species evolve toward intermediate sizes, but its general applicability to birds is questionable. However, convergent evolution has clearly occurred in the island bird lineages that have undergone transitions to secondary flightlessness, a process involving drastic reduction of the flight muscles and enlargement of the hindlimbs. Here, we investigated whether volant island bird populations tend to change shape in a way that converges subtly on the flightless form. We found that island bird species have evolved smaller flight muscles than their continental relatives. Furthermore, in 366 populations of Caribbean and Pacific birds, smaller flight muscles and longer legs evolved in response to increasing insularity and, strikingly, the scarcity of avian and mammalian predators. On smaller islands with fewer predators, birds exhibited shifts in investment from forelimbs to hindlimbs that were qualitatively similar to anatomical rearrangements observed in flightless birds. These findings suggest that island bird populations tend to evolve on a trajectory toward flightlessness, even if most remain volant. This pattern was consistent across nine families and four orders that vary in lifestyle, foraging behavior, flight style, and body size. These predictable shifts in avian morphology may reduce the physical capacity for escape via flight and diminish the potential for small-island taxa to diversify via dispersal.B irds on islands helped to inspire the theory of evolution by natural selection (1, 2), and they continue to illuminate its mechanisms (e.g., ref.3). Some studies have reported that the bodies and bills of island birds systematically shift in size, reflecting evolution toward a generalist niche in species-poor communities (4-8). The tendency for island taxa to converge toward intermediate body size after colonizing islands is known as the island rule (4), but this ecogeographic rule has proven to be an inconsistent predictor of evolutionary trends in island bird populations (9-12). Detailed studies of island radiations have revealed idiosyncratic patterns of body size and bill size evolution among species, with morphological changes attributable to taxon-specific changes in foraging ecology (e.g., ref. 12). This inconsistency raises the question as to whether there are predictable evolutionary trends that apply generally to island birds.The most striking evolutionary trend among island birds is the loss of flight. Transitions to flightlessness are rapid and irreversible (13,14), with each instance involving the substantial reallocation of mass from the forelimbs to the hindlimbs and near elimination of costly flight muscles (15-18). More than 1,000 independent lineages of island birds have lost flight, including rails, parrots, pigeons, owls, waterfowl, and passerines (13-1...

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Vertebrate remains recovered from a limestone fissure filling on Antigua, Lesser Antilles, are associated with radiocarbon dates ranging from 4300 to 2500 yr B.P., contemporaneous with the earliest aboriginal human occupation of the island. Nine taxa of lizards, snakes, birds, bats, and rodents (one-third of the total number of species represented as fossils) are either completely extinct or have never been recorded historically from Antigua. These extinctions came long after any major climatic changes of the Pleistocene and are best attributed to human-caused environmental degradation in the past 3500 yr. Such unnatural influences have probably altered patterns of distribution and species diversity throughout the West Indies, thus rendering unreliable the data traditionally used in ecological and biogeographic studies that consider only the historically known fauna.