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Carl R. Woese Institute for Genomic Biology

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An international effort involving more than 100 researchers, nine supercomputers and about 400 years of CPU time has yielded the most reliable avian tree of life yet produced, researchers report in the journal Science. The tree reflects the evolutionary relationships of 48 species of birds.

The paper describing the bird family tree is one of eight articles on avian evolution published together in Science. The overall endeavor was coordinated by Erich Jarvis of Duke University; M. Thomas P. Gilbert of the Natural History Museum of Denmark; and Guojie Zhang of the Beijing Genomics Institute at Shenzhen.

Tandy Warnow, Founder Professor of Bioengineering and Computer Science.
Tandy Warnow, Founder Professor of Bioengineering and Computer Science.

The computational effort, led by University of Illinois Founder Professor of Bioengineering and Computer Science Tandy Warnow and University of Texas at Austin graduate student Siavash Mirarab, took more than four years to complete.

“Different parts of the genome can actually have different histories, and this data set had this in abundance,” Warnow said. “We observed significant conflict across the genome, which required the development of new statistical methods in order to develop a robust tree.”

“Figuring out the evolution of birds is really hard,” Mirarab said. “Most of the birds we know today, about 95 percent, belong to the group Neoaves. These birds appeared, it seems, in a period of a few million years. When a lot of new species appear in a short period of time, it makes reconstructing their relationships much harder.”

Many scientists believe this “big bang” of bird evolution occurred about 65 million years ago, just after the Cretaceous-Paleogene extinction, which killed off the “other dinosaurs,” Mirarab said. (Most scientists agree today’s birds are the descendants of a few “avian dinosaurs.”)

The exact timing of major events in bird evolution is still being nailed down, however, said Edward Braun, a biology professor at the University of Florida and a co-author on the paper.

“Our results suggest that modern birds diversified in the wake of the mass extinction that marked the end of the age of dinosaurs, but we cannot exclude the possibility that birds began diversifying before the extinction,” Braun said.

The new study offers evidence, however, that birds diverged more recently than earlier studies had indicated, Warnow said. This finding is more consistent with the fossil record, she said.

The new analysis helps clarify the evolutionary relationships of major groups of birds, showing which groups share more recent ancestors and which are more distantly related to each other.

A key, unexpected finding involves an early event in the evolution of the Neoaves (knee-oh-AY-veez), a group that includes songbirds, raptors, parrots, herons, doves, penguins and most other birds.

“We found in this study something that was different from anything suggested before – a divergence between two groups of Neoaves, groups we call Columbea and Passerea,” Mirarab said. “And what’s really interesting about this divergence is that the group Columbea includes birds that you would not think were related, like flamingoes and pigeons. This means that flamingoes are more closely related to pigeons than they are to pelicans, for example.”

Another interesting finding is that some birds of prey are not as closely related to each other as they are to other species that have very different traits.

“If you look at them, you would think that falcons are more eagle-like than they are parrot-like,” Mirarab said. “But falcons are more closely related to parrots and passerines (a group that includes songbirds) than they are to eagles or vultures.”

Of the birds whose genomes were analyzed, only five were not Neoaves. Chickens, turkeys and ducks inhabit a separate branch of the avian tree. Ostriches and tinamous stem from the most ancient branch on the tree.

Researchers have worked out the evolutionary relationships of dozens of bird species. The findings add to the evidence that some traits – such as vocal learning or foot-propelled underwater diving – evolved independently among different groups of birds. Click for interactive graphic.
Researchers have worked out the evolutionary relationships of dozens of bird species. The findings add to the evidence that some traits – such as vocal learning or foot-propelled underwater diving – evolved independently among different groups of birds. Click for interactive graphic.

The study adds support to the hypothesis that some traits – such as vocal learning or foot-propelled underwater diving – evolved independently among different groups of birds. There also is substantial evidence that the core landbirds – a group that includes songbirds, parrots, falcons, owls, woodpeckers and eagles – share a common ancestor that was an apex predator, at the top of the food chain.

To get these results, the computational team analyzed 14,000 different regions within the genomes of the 48 bird species, looking at both coding and non-coding sites in the genes.

“This was an incredible amount of effort from a huge number of people,” Warnow said. “It took 400 CPU years across supercomputing centers all over the world. This was only achievable because of the expertise of the researchers and the supercomputer centers, and having that much time on them.”

The National Science Foundation, the Howard Hughes Medical Institute and the Guggenheim Foundation funded Warnow and Mirarab. Learn more about the computational approach in this related article from News Bureau.

 

Associated Themes
Biocomplexity
Computing Genomes for Reproductive Health
Infection Genomics for One Health
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Diana Yates.
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L. Brian Stauffer.