We were so wrong about bird evolution

Approximately 65 million years ago, a colossal asteroid collided with Earth, triggering the extinction of terrestrial dinosaurs, which also obviously included the iconic Tyrannosaurus rex. However, after this cataclysm, avian creatures began to thrive. With over 10,000 bird species currently inhabiting Earth, the term “flourish” might even be an understatement. Yet, organizing these birds into a coherent family tree has posed a monumental challenge due to their vast numbers and the complexities of their evolutionary history.

Recent advancements in genomic sequencing and analysis have started to unravel the intricate story of avian evolution. Two studies, published on April 1 in the journals Proceedings of the National Academy of Sciences (PNAS) and Nature, shed light on a genetic anomaly approximately 65 million years old (exactly when that asteroid hit) that has obscured scientists’ understanding of avian evolutionary history. Specifically, a section of one chromosome failed to undergo expected mixing with adjacent DNA, impeding the construction of a detailed bird family tree.

According to a statement: “This section, just two percent of the bird genome, convinced scientists that most birds could be grouped into two major categories, with flamingos and doves as evolutionary cousins. The more accurate family tree, which accounts for the misleading section of the genome, identifies four main groups and identifies flamingos and doves as more distantly related.”

“My lab has been chipping away at this problem of bird evolution for longer than I want to think about,” said Edward Braun, Ph.D., the senior author of the paper published in the Proceedings of the National Academy of Sciences and a professor of biology at the University of Florida. “We had no idea there would be a big chunk of the genome that behaved unusually. We kind of stumbled onto it.”

In 2014, technological progress enabled researchers to construct a family tree for Neoaves, a group encompassing the majority of bird species. By analyzing the genomes of 48 species, they divided Neoaves into two primary categories: one comprising doves and flamingos, and the other encompassing all remaining bird species.

In the latest study, genetic analysis involving 363 bird species revealed a revised family tree, indicating four main groups and uncovering the true genetic relationship between flamingos and doves. This revelation stemmed from identifying a specific region in the chromosomes where genes had not undergone expected mixing over millions of years. This lack of recombination, a process essential for genetic diversity, resulted in a fraction of the bird genome remaining unchanged over time.

Two mutually exclusive bird family trees. The top family tree lumps flamingos and doves, in blue and teal respectively, closely together, while the bottom family tree does not. The top family tree was built around distortions in bird genomes that date back to the extinction of the dinosaurs. The bottom family tree is likely more accurate, after accounting for these genomic anamolies. Credit Edward Braun

“When we looked at the individual genes and what tree they supported, all of a sudden it popped out that all the genes that support the older tree, they’re all in one spot. That’s what started the whole thing,” Braun said.

The implications of this genetic anomaly extend beyond birds, potentially existing in other organisms as well. By harnessing computational algorithms like ASTRAL, researchers reconstructed evolutionary relationships among 363 bird species, accounting for approximately 92% of all bird families. This updated family tree illuminated evolutionary patterns following the Cretaceous-Tertiary Extinction, revealing increases in population size, substitution rates, and relative brain size among early birds.

The research, conducted as part of the Bird 10,000 Genomes (B10K) Project, aims to sequence the genomes of around 10,500 living bird species, further enriching our understanding of avian evolution. By leveraging computational models and expanding genomic data, scientists continue to piece together the intricate tapestry of bird evolutionary history.

“We discovered this misleading region in birds because we put a lot of energy into sequencing birds’ genomes,” Braun said. “I think there are cases like this out there for other species that are just not known right now.”