What We Can Learn From a New Bird Tree of Life

 

(Sequencing the DNA of more than 10,000 birds could reveal how best to conserve our feathery friends—and when they evolved from dinosaurs)

From Smithsonian Magazine

Kat Eschner

Edited by Vinuri Randhula Silva,

Creating a phylogeny of all bird life will help researchers map birds' evolutionary relationships and create conservation plans. Juniors Bildarchiv GmbH / Alamy

For Charles Darwin, birds offered a window into the process of natural selection—and ultimately, evolution. After observing the remarkable variation of beaks among Galapagos Islands finches in the 1830s, the British naturalist remarked: “Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends.” Yet more than 150 years after Darwin, the evolutionary relationships between birds remain a compelling mystery.

This month, a coalition of university and government bird scientists will begin an ambitious effort to disentangle those relationships with the newly launched Open Wings Project. Funded by the National Science Foundation, the project has the goal of creating a full tree of life, or phylogeny, for the world’s birds. By collecting genetic information for all 10,560 species of birds, researchers hope to create a better picture of how our now-extant avian friends evolved from the dinosaurs that preceded them, and how they might fare in the future.

“We know that there’s unevenness in the avian tree of life,” says Terry Chesser, a research zoologist and member of the USGS Biological Survey Unit who works at the National Museum of Natural History. At some places on the tree, birds speciated away from one another onto different branches much faster than at other places—different lineages diversifying faster and perhaps different rates of change depending on the period of history. Certain characteristics such as plumage or body type are associated with some of those changes, but it’s not known exactly how.

The project also has the potential to alter current understandings of bird evolution, including big questions about when birds started evolving from dinosaurs. Some scientists believe that birds and dinosaurs had begun to separate before the Cretaceous-Paleogene extinction event about 66 million years ago that killed off the land dinosaurs, while others believe that birds and avian dinosaurs had not yet speciated at the time. Creating a complete phylogeny of birds is likely to resolve this dispute, or at least offer new evidence. The OpenWings Project team will be working with a paleontologist to integrate fossil evidence, Chesser says.

The project aims to be the most complete bird tree of life to date, and is the first to be done on a vertebrate animal group. Currently, Chesser says, when people try to assemble a tree for birds, they “end up making a tree with lots of missing data,” and adding in species which don’t have data that states where they should go given their current taxonomies, which were decided based on observational, not genetic characteristics. Another project, B10k, is trying to sequence complete "reference genomes" for all species of birds, but it's only got about 300 so far.

Doing reference genomes is a gigantic task, whereas what the Open Wings Project will do is a bit more manageable, says Rebecca Kimball, an evolutionary biologist from the University of Florida who is a collaborator on the OpenWings Project. It will also be open access, meaning that ornithologists from around the world can use the results–which will be released as they are charted, rather than in one batch at the end of the project–to look deeper at specific branches of the bird family tree. Some lesser-understood groups of birds “deserve more focus than we're going to be able to give them in this large-scale study,” says Kim ball.

“Individually, all of us have species [of birds] that we love and are interested in,” she says, but asking big questions means it’s impossible for the researchers to zero in on specific families of birds in the Open Wings Project. Making the data open-access means that work will likely still get done, she says.

Rufous-naped wrens. The Smithsonian's Division of Birds houses and maintains the third largest bird collection in the world, with over 625,000 specimens. NMNH / Smithsonian Institution

Sequencing genetic information for more than 10,000 total species of bird is still a massive undertaking, and something that only became possible thanks to recent advances in genetic analysis, Chesser says. To conduct this broad-ranging study, the researchers will have to zero in on specific DNA sequences that are called “ultraconserved” regions. These regions of DNA are the ones that have endured from previous speciation events, when new kinds of birds came to sit on new branches of the tree, and offer a way to look back into genetic relationships.

This project wouldn’t be possible without the careful collection and preservation efforts of museums, Chesser says. The OpenWings collaborators represent institutions with vast collections of bird specimens, including the Field Museum of Natural History, the American Museum of Natural History and the Smithsonian Institution’s National Museum of Natural History. They also include rapidly-growing collections at universities—especially Kansas University and the Louisiana Student University’s Museum of Natural Science.

Since the 1980s, Kimball says, museums have been preserving DNA samples from the specimens in their collections along with the treated bodies of the specimens themselves. For many species, this is where the genetic material will come from. In other cases, where specimens were collected before this became the norm, Cresser says they’ll rely on an unexpected part of the birds: their talons. The best way to get genetic evidence from a preserved specimen that’s been found so far, he says, “is to cut off a piece of the pads on the birds’ toes.”

At this point, the project researchers are still figuring out which institutions have specimens of what birds, Cresser says. Most studies of this kind use tens or hundreds of species, he says—like a 2015 study published in Nature that laid the groundwork by making a tree of life for 198 bird species. Coordinating thousands takes a little more work, particularly when you’re on a team representing 10 major participating institutions.

Erich Jarvis, a neuroscientist from The Rockefeller University who leads B10K, told Science's Elizabeth Pennisi that he thinks only a whole-genome approach can generate a robust tree for birds, because it covers all the kinds of genetic information encoded in a bird's DNA. But other scientists acknowledged to Pennisi that it's a marked improvement on what bird researchers have now: that, and it's fully funded, which B10K is not.

“This shows the efficacy and fundamental importance of ongoing museum collection efforts,” says Yale University evolutionary ornithologist Richard Prum, a co-author on the 2015 paper. “This consortium includes most of the biggest natural tissue collections in the world,” says Prum, who is not involved in the Open Wings Project.

Prum adds that it’s about time that someone created a complete avian phylogeny. With new genetic technology, it’s more doable than ever before, even if the scale is unprecedented, he says. After all, the methods already exist: it’s just a matter of putting it all together. This kind of work has the potential to change the way birds are understood, which has implications for their conservation as well as their evolutionary history.

Darwin’s ideas about evolution were based on the observable characteristics of his finches. But beyond those observable characteristics are layers and layers of genetic relationships, and without a working knowledge of genetics these were hidden from him. With this new technology, it is possible to see how even species who look and act different may be closely related. Doing a whole tree will “advance the study of phylogenetics,” Chesser says, but it will also help conservation in a direct way.

“One of the criteria frequently used in conservation planning is phylogenetic distinctiveness,” he says, “such that areas that include species on their own distinct evolutionary branches are often given higher weight in conservation planning.” The OpenWings project will show how phylogenetically distinct different species really are. “This information should be very useful to conservationists in making assessments of what areas or species to prioritize,” he says.