An Unprecedented Flock of Genomes Redraws the Bird Tree of Life

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We may never know what came first -- the chicken or the egg -- but thanks to the largest-ever study of avian genomes, we now know a lot more about where both of them came from.

Analyses of 45 bird genomes, published for the first time this week across 28 papers in Science, Genome Biology, GigaScience and other publications, blows wide open our understanding of how and when birds evolved.

The findings include tantalizing discoveries about how birds lost their teeth, the identity of a predatory ancestor, the evolution of birdsong, and how penguins adapted to Antarctica. Most of all, scientists have now constructed the most reliable avian family tree to date.

“It has been very hard for people to work out the simple relationships between the different orders of birds,” said project leader Tom Gilbert, from the Natural History Museum of Denmark, at a news conference this week. “So we proposed to do this at the biggest level yet -- sequence the genomes of at least one bird species per avian order.”

Knowledge gleaned from the effort enhances our understanding of bird biology and could provide “new insights into the factors that influence bird declines and extinctions,” wrote W. John Kress, Interim Undersecretary for Science at the Smithsonian Institution, in an accompanying editorial in Science.

Avian species are vanishing at an alarming rate, according to the 2014 State of the Birds Report, an annual study by the U.S. government, universities and conservation groups. Bird populations have declined across many key habitats in North America, and 33 species, including the northern bobwhite quail, the grasshopper sparrow and the bank swallow, have lost more than half their global population in the last 40 years.

Notable Discoveries

The 28 studies published this week, the fruits of four years of labor from more than 200 scientists, relied upon nine supercomputers to analyze the 45 new genomes.

“Lots of fundamental questions now can be resolved with more genomic data from a broader sampling,” said Erich Jarvis, a Duke University neuroscientist who led several of the studies, in a statement.

Here are some of the most notable discoveries being published this week:

*Birds’ Big Bang: How and when birds diversified into a wide variety of species, including the 10,000 species alive today, has been a longstanding controversy. Using the new avian genomes, a team at Duke found compelling evidence that modern birds rapidly evolved 66 million years ago, in a “big bang” of evolution, right after the mass extinction event that wiped out the dinosaurs -- rather than before the event. While ancient birds existed before, the big bang marked a surge in diversification.

*Predatory Family: The same Duke team compared the avian genomes to create the most solid family tree of modern birds to date. Past attempts had met with limited success, since scientists used just 10 to 20 genes per species to try to infer species relationships. From the new tree, they concluded that the common ancestor of all birds was an apex predator -- the term for a killer at the top of a food chain. As birds evolved, some of them, such as hawks and falcons, retained predatory traits from that ancestor. Many other species lost them.

*Petite Genome: Bird genomes are known to be small -- only about one-third the size of the human genome. A team from BGI-Shenzhen in China found out why they are so petite by analyzing the 45 new genomes, plus three previously available genomes from the chicken, the turkey and the zebra finch. It turns out that birds have very little repetitive DNA (most other animal genomes are bloated with repeated sequences) and their genomes experienced massive gene loss over time, including the loss of genes essential for human reproduction, skeleton formation and lungs.

*Sex and a Graveyard: Unlike the human Y chromosome, which contains many genes that no longer function, the avian W chromosome is full of active genes that are still evolving among bird species, according to a paper from the University of California at Berkeley. The finding challenges the classical assumption that the bird W chromosome is a gene graveyard like the human Y chromosome, which has lost lots of genes and has remnants of genes that aren’t used anymore.

*Of Birds and Men: Humans and songbirds, unlike other animal species, share brain circuits that are important for speech and song, respectively, according to the Duke team. Singing or hearing a birdsong activates complex gene networks in birds, turning genes on and off in their brains. In fact, about 10 percent of the bird genome is activated and regulated by singing. The researchers found that vocal learning in birds evolved independently at least twice during their evolution -- in other words, different groups of our feathered friends learned to sing independently.

*Going Viral: Mammal species have had 6 to 13 times more viral infections in the past than birds, as detected by remnants of viral DNA in a genome. Scientists at the Duke-NUS Graduate Medical School in Singapore and the University of Sydney said the results suggest that birds are either less susceptible to viral infection or better able to rid themselves of viral DNA after an infection.

*Pulling Teeth: Numerous genetic mutations caused the elimination of enamel in birds, which is why birds today have no teeth, according to a report from Montclair State University in New Jersey, though all birds did descend from a toothy, enamel-capped ancestor. Those mutations and the subsequent loss of teeth began about 116 million years ago.

*Mutant Speedsters: Bird genomes evolved much faster than their closest living relatives, the crocodilians, according to a team at the University of California in Santa Cruz that compared the genomes to those of an alligator, a crocodile and an Indian gharial. Mammals outpaced birds.

*March of the Penguins: The 45 genomes in the project included 2 penguin genomes sequenced for the first time: Adelie and Emperor. Scientists at BGI-Shenzhen gained many insights into how penguins adapt to the hostile Antarctic environment: For instance, both species had expanded gene families of proteins that make up feathers and contained a gene known to be involved in the development of thick skin.

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