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How birds evolved is a complex question that has puzzled biologists for decades. A spate of papers in the journal Science provides the clearest picture to date of the avian family tree. By mapping the genomes of 45 bird species for the first time (and using three previously mapped genomes), the researchers were able to more closely trace relationships between species—and to confirm that birds underwent an early, rapid, ‘big bang’ that led to the evolution of the more than 10,000 species we have today.

Over 200 scientists from 20 countries joined together to form the Avian Phylogenomics Consortium, the umbrella organization for the research. The project spanned four years, and yielded 28 separate research papers, all published this week.

“How do birds relate to each other? This was our fundamental first question,” says , lead author on one of the studies, and head of the section for evolutionary genomics at the Natural History Museum of Denmark, during Science’s press conference. 

Most modern-day bird species—95 percent of them—reside on a single branch (or “clade”) of the avian family tree called Neoaves that exists close to the base. The genetic differentiation within this group, however, isn’t very distinct, so ornithologists have been stumped about exactly how the various lineages within it split off as today’s species evolved. 

“There were parts of the tree that were pretty well resolved before this, but when you looked at the base it was very difficult to test relationships,” says , associate professor of biology at the University of Florida. There were so many different theories for how the original splits happened that it was very difficult to rigorously analyze any one idea. Additionally, avian evolution research has previously relied on smaller gene sets, which caused data inconsistencies, further inhibiting any consensus on what the tree looked like.  

For this body of work, the researchers changed the game by using full genome mapping of 48 species, which together encompass all the bird lineages alive today. “What’s impressive here is the number of different species that they’ve done,” says , an evolutionary geneticist at the University of Sheffield who has worked on bird genome projects in the past, but was not involved in the research. “There are almost five-fold as many birds sequenced now.” With this data, the APC were able to reconstruct the avian family tree in unprecedented detail. “This is the biggest DNA sequenced tree ever generated. In this case it’s 30 billion base pairs long,” says , an associate professor of avian neurobiology at Duke University School of Medicine.

What Hurt Dinos Helped Birds

In addition to reconstructing a fuller avian tree, the mapping also helped settle a longstanding controversy over when the mass expansion of Neoaves occurred. Past research has suggested this group evolved somewhere between 10 to 80 million years before the mass extinction that killed the dinosaurs. But the genome project allowed the APC to pinpoint the evolutionary development of Neoaves to about 66 million years ago, meaning the origin of all bird species today likely happened right around the time of the mass extinction that wiped out dinosaurs at the end of the Mezozoic Era. 

“We’re suggesting [the expansion] occurred right at that time, with only a few lineages surviving the mass extinction, and then giving rise to all these Neoaves groups within the last 66 million years,” Jarvis says. The huge species gap left by the dinosaurs likely created an accommodating environment for the widespread expansion of bird species—one that happened very rapidly in evolutionary terms, Jarvis says. 

“All modern orders formed from this radiation within a 10 to 15 million year period, around 50 million years ago,” he adds. 

The reworked avian tree also reveals some unexpected relationships between species that were unknown until recently: Flamingoes are related to pigeons, for example, and even though falcons seem similar to eagles, they’re actually more closely linked to parrots and songbirds. 

The level of detail available in the new avian tree will allow researchers to delve more deeply into avian biology going forward. “We can dig into very specific bird traits and look at the genetic basis of them; things like flight, feathers, vision, olfaction, sexual selection,” Gilbert says. “We hope we can start addressing even more exciting questions—like whether we can infer things about dinosaurs.”

The project will be ongoing, Jarvis says, and could ultimately help researchers map other datasets, including insects, mammals, and plants. Researchers say they’re already seeing noticeable parallels between the avian and mammal genomes.  

“The findings will certainly help people to decide which questions to ask,” says Slate. “This, in a sense, is big toolbox that’s being described.”