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 on Thursday 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 2011 an estimated 47 million Americans shelled out nearly $41 billion for transportation, lodging, equipment and other costs associated with birding, according to the US Fish and Wildlife Service.
“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.
“There are lots of disorders that affect speech, and we can’t study nonhuman primates or mice for these,” said study co-author Erich Jarvis, a neurobiologist at Duke University School of Medicine and the Howard Hughes Medical Institute. 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, who headed the effort to crunch the data, using several super-computing centers in the US and abroad.
“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 backyard 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 they 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.
And about 65 million years ago, an apex predator probably gave rise to all the major land birds, from the diminutive finch to the massive terror bird of South America, now extinct, according to the studies.
“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,” said Jarvis, who led the Science study on vocal learning.
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, according to one study.
These characteristics, among others, have been a primary means for sorting bird species until the advent of genetics. But even modern studies, many of which depended on analyzing small DNA segments, sprouted conflicting trees, with species flitting from branch to branch.
That problem, known as incomplete lineage sorting, is particularly acute when so many species develop in a short time, Warnow said. Her team resolved this in part by merging about 14,000 individual genetic trees, she said.
In the end, though, 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.
Despite several parallel “big-bang” speciations, birds have proved to be relatively slow evolvers, the studies found. Their rate of DNA shuffling varies by species, but is lethargic compared with that of mammals.
Among those studied, however, no animal matches the molecular malingering of the crocodilians, which started slow and just got slower. Its genome was included in part to help figure out the link between these toothy aquatic carnivores and birds.
“Birds are dinosaurs; they’re the one lineage of dinosaurs that made it through the mass extinction at the end of the so-called age of dinosaurs, the mesozoic,” University of Florida evolutionary biologist Edward Braun said.
“Their closest living relative is actually crocodilians.” Which bird, then, is closest to the last common ancestor shared with saltwater crocodiles, American alligators and the slender-nosed Indian gharial? Either the chicken or the ostrich, depending on how you look at the genomes mapped by the group.
“It’s actually the chicken that seems to have retained the most ancestral chromosomal organization compared to the other species,” Jarvis said. “At the single nucleotide level, the ostrich is evolving more slowly than the chicken.
These are two different aspects of gene evolution.”
Geoffrey Mohan / Los Angeles Times/TNS
Image credits: Wikimedia Commons