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Bird Phylogeny Reveals Unexpected Relationships

NEW YORK (GenomeWeb News) – A new large-scale study is dramatically altering scientists’ understanding of the evolutionary relationships between different types of birds.
In a paper appearing online today in Science, a team of American researchers sequenced thousands of bases of DNA from each of nearly 170 bird species. Based on their phylogenetic analyses of these birds, which represented all the major living bird groups, the team found evidence to support some previously held views of bird relationships. But other findings revealed unexpected relationships between birds and provided new insights into the evolution of specific bird traits, behaviors, and lifestyles.
“What we wanted to do was provide ourselves — and the rest of the research community — with the roots and the trunk and the tops of the tree of life for birds,” co-lead author Shannon Hackett, associate curator of birds at the Field Museum of Natural History in Chicago, told GenomeWeb Daily News.
Many people think of birds as being very well-studied, co-lead author Rebecca Kimball, a zoologist at the University of Florida, told GenomeWeb Daily News. Indeed, she said, there are numerous studies on bird morphology, behavior, ecology, and genetics — though many of these have focused on just one or two genes.
Even so, evolutionary relationships between the majority of bird species have remained murky, with little consensus amongst researchers about which species are most closely related, Kimball said, adding that some have suggested that bird phylogeny is an unanswerable question.
Undeterred, Hackett, Kimball, and their co-workers from across the US took a genome-wide view in order to try to understand evolutionary relationships between bird species. As part of the Early Bird Assembling the Tree of Life Research Project, the team spent more than five years sequencing and comparing DNA from representatives from all of the main living bird groups.
To do this, they chose species based on their perceived genetic distance from one another determined from previous studies, Hackett said, with the goal of representing each major genetic lineage. These samples were housed at museums and other participating institutions, Kimball said.
All told, the group sequenced an estimated 32 kilobases of nuclear DNA — containing information from 15 different chromosomes — for each of the 169 bird species tested. These included a few protein-coding regions, though the team purposely focused on non-coding regions, particularly introns.
“We targeted sort of regions that evolved more quickly and were under less evolutionary constraint,” Kimball explained. Because the introns are under relatively little selection, they are prone to more sequence differences.
“That was pretty controversial,” Hackett added. That’s because some thought the introns would be too divergent to align. For the most part, though, the researchers were able to align the sequences and make good predictions about evolutionary relationships.
Using this approach, they were able to confirm some previously proposed but hotly debated relationships between birds — including a close link between flamingos and grebes. On the other hand, their findings also revealed some new and unexpected relationships. For instance, they found that a large group of birds called Passeriformes (perching birds or songbirds) were closely related to parrots.
They also discovered unexpected splits within bird groups that were heretofore believed to be related. This included splits within the raptor group, predatory birds such as hawks, eagles, and falcons that look and act similarly. Their results suggest that falcons are not closely related to eagles and hawks.
And, despite their similar prey preferences, owls aren’t closely related to the other raptors either. “We probably have at least three different evolutions of this lifestyle,” Kimball said.
Notably, they also found that birds with other specialized lifestyles — including water birds, noctural birds, and so on — evolved several times. “We’re getting a much better idea about how many times these habitats and lifestyles have evolved,” Hackett said.
Knowledge of these phylogenetic relationships is expected to inform other types of research — on everything from species morphology to ecology — as well. That, in turn, could help biologists, conservationists, and others predict how certain birds will adapt to environmental or ecological challenges. “Understanding how a bird species responds, in part, is facilitated by understanding what it’s related to,” Kimball said.
Despite the new resolution provided by this study, there are still some “thorny issues” at the base of the bird tree of life, Hackett said. The team is currently going back to the most surprising relationships and examining them in more detail by looking at additional representative species and/or by more gene regions. “We are looking at what would happen if we collected much more data,” Kimball said.

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