Just as bird watchers may use binoculars to add to their species lists, scientists interested in bird evolution may use computational tools to clarify avian lineages. Indeed, such tools have enabled scientists based at the University of Copenhagen, UC San Diego, and Zhejiang University to resolve phylogenetic details that were once indistinct.

The scientists have reported their findings in Nature, in an article titled, “Complexity of avian evolution revealed by family-level genomes.” The article’s co-senior author Siavash Mirarab, PhD, professor of electrical and computer engineering at UC San Diego, declared that the scientists’ goal is to “reconstruct the entire evolutionary history of all birds.”

The goal seems much more achievable now that the scientists have built the largest and most detailed bird family tree to date—an intricate chart delineating 93 million years of evolutionary relationships.

“Using intergenic regions and coalescent methods, we present a well-supported tree but also a remarkable degree of discordance,” the article’s authors wrote. “The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous–Paleogene (K–Pg) boundary.”

The authors continued, “We discovered sharp increases in effective population size, substitution rates, and relative brain size following the K–Pg extinction event, supporting the hypothesis that emerging ecological opportunities catalyzed the diversification of modern birds. The resulting phylogenetic estimate offers novel insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.”

By updating the family tree for birds, the scientists show evolutionary patterns that formed following the cataclysmic mass extinction event that wiped out the dinosaurs 66 million years ago. These patterns reflect the adaptive mechanisms that drove avian diversification in the aftermath of this pivotal event.

The work is part of the Bird 10,000 Genomes (B10K) Project, a multi-institutional effort that aims to generate draft genome sequences for about 10,500 extant bird species.

At the heart of these studies lies a suite of algorithms known as ASTRAL, which Mirarab’s lab developed to infer evolutionary relationships with unprecedented scalability, accuracy, and speed. By harnessing the power of these algorithms, the team integrated genomic data from over 60,000 genomic regions, providing a robust statistical foundation for their analyses. The researchers then examined the evolutionary history of individual segments across the genome. From there, they pieced together a mosaic of gene trees, which were then compiled into a comprehensive species tree. This meticulous approach enabled the researchers to construct a new and improved bird family tree that delineates complex branching events with remarkable precision and detail, even in cases of historical uncertainty.

“We found that our method of adding tens of thousands of genes to our analysis was actually necessary to resolve evolutionary relationships between bird species,” Mirarab noted. “You really need all that genomic data to recover what happened in this certain period of time 65–67 million years ago with high confidence.”

To drive the work forward, Mirarab’s laboratory designed computational methods to run on powerful GPU machines. The laboratory also ran its calculations on the Expanse supercomputer at the San Diego Supercomputer at UC San Diego.

The researchers also looked at the effects of different genome sampling methods on the accuracy of the tree. They showed that two strategies—sequencing many genes from each species, as well as sequencing many species—when combined are important for reconstructing this evolutionary history.

“Because we used a mixture of both strategies, we could test which approach has stronger impacts on phylogenetic reconstruction,” said Josefin Stiller, PhD, professor of biology at the University of Copenhagen and lead author of the Nature paper. “We found that it was more important to sample many genetic sequences from each organism than it was to sample from a broader range of species, although the latter method helped us to date when different groups evolved.”

The impact of this work extends far beyond studying the evolutionary history of birds. The computational methods pioneered by Mirarab’s laboratory have become one of the standard tools for reconstructing evolutionary trees for a variety of other animals.

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