Unprecedented study redraws birds' tree of life

A new gene map of nearly all living bird species has shaken the avian evolutionary tree, scattering some of the feathered dinosaur descendants to new perches and adding odd flourishes to their tales.

Parrots perch closer to songbirds, pigeons have fallen to bottom branches, a tiny wren shares a murderous lineage with the eagle, and the pencil-legged flamingo nests near the deep-diving grebe, according to a series of studies published online in the journal Science.

The four-year, multimillion-dollar effort, which mapped the whole genome covering 48 bird species — 45 of them never mapped before — provides an enormous database for research that affects human health. Chickens, finches and pigeons are commonly used in laboratories, offering insight into human brain and fetal development, environmental risks and speech impediments.

The effort by more than 200 researchers at 80 institutions worldwide would have taken about 400 years for one computer to accomplish, and culminated with the simultaneous publication of 28 studies. Researchers said they expect many new findings to emerge over the coming months.

With more than 10,000 species, birds are the most diverse class of four-limbed vertebrates on Earth, and for centuries have fascinated humans, who have domesticated them for food, trained them as hunters, caged them for companionship, used them to detect deadly gas in coal mines or just stared at them.

"In addition to being very charismatic, birds are also the living descendants of dinosaurs," said Tom Gilbert, head of the evolutionary genomics section of the Natural History Museum of Denmark and an author on several of the studies. Nonetheless, Gilbert said, "it's been very, very hard for people to work out the simple relationship between different orders of birds."

By mapping 45 new genomes from each of 30 bird orders, the Avian Phylogenomics Consortium reordered that tree and opened paths toward a better understanding of humans. One study showed remarkable analogies between genes involved in vocal learning of birds and speech areas of human brains, for instance.

The methods pioneered by the consortium could revolutionize the way genome data are analyzed, said mathematician and computer scientist Tandy Warnow of the University of Illinois at Urbana-Champaign.

"We may actually change the trees on other groups, such as mammals, when we reanalyze them with better methods," Warnow said.

Still, for ornithologists and back yard birders, the immediate effect of the studies was to be found in their potential to resolve — or extend — long-standing debates over the dinosaur descendants. Researchers now suggest birds experienced several parallel "big bang" radiations into a wide array of species shortly after the extinction of the land-based dinosaurs some 66 million years ago.

Since then, distinct bird species twice independently gained the ability to learn sounds — hummingbirds and the ancestor of parrots and songbirds. At least two other times, branches lost vocal learning — among the New Zealand wrens and a group that includes antbirds and manakins, according to the studies.

Other birds, such as the emu and ostrich, jettisoned flight, and almost all lost their right ovary.

"We are suggesting that the common ancestor of core land birds was an apex predator, and that this predatory trait has been lost several times," Jarvis said.

On a smaller scale, there finally appears to be an answer to why hens don't have teeth: The common ancestor of all birds lost a handful of genes regulating teeth about 116 million years ago, leaving descendants to evolve horny beaks and a digestive tract that grinds food, one study said.

In the end, the overall genome was a third as small as those of most mammals, said Guojie Zhang, head of comparative genomics at the National Genebank of the Beijing Genomics Institute-Shenzhen.

The studies showed it contains about 1.05 billion to 1.26 billion base pairs, which form the lattice of DNA's double helix (that's about a third the size of the human genome).

"The bird genome has experienced a massive gene loss," Zhang said. "We found that 1,600 genes are completely missing from all bird genomes." Some of those are considered crucial to other animals, including genes regulating flexible lungs, and those associated with sexual organs, Zhang said.