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The updated family tree, detailed in two complementary papers published today in the journal Nature and the Proceedings of the National Academy of Sciences, reveals patterns in the evolutionary history of birds following the cataclysmic mass extinction event that wiped out the dinosaurs 66 million years ago. The authors observed sharp increases in effective population size, substitution rates and relative brain size in early birds, shedding new light on the adaptive mechanisms that drove avian diversification in the aftermath of this pivotal event. The researchers also closely examined one of the branches of the new family tree and found that flamingos and doves are more distantly related than previous genome-wide analyses had shown.
The updated bird family tree delineating 93 million years of evolutionary relationships between 363 bird species. Image credit: Jon Fjeldså / Josefin Stiller.
“Our goal is to reconstruct the entire evolutionary history of all birds,” said Professor Siavash Mirarab, a researcher at the University of California, San Diego.
The work is part of the Bird 10,000 Genomes (B10K) Project, a multi-institutional effort led by the University of Copenhagen, Zhejiang University and the University of California, San Diego 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 Professor Mirarab and colleagues developed to infer evolutionary relationships with unprecedented scalability, accuracy and speed.
By harnessing the power of these algorithms, they 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,” Professor Mirarab said.
“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.”
The scientists 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 — combined together 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 University of Copenhagen’s Professor Josefin Stiller.
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.”
Mirarab et al. closely examined one of the branches of the updated bird family tree and found that groups including flamingos and doves are more distantly related than previous genome-wide analyses had shown and attributed the result to an unusual region of chromosome 4. Image credit: Ed Braun / Daniel J. Field / Siavash Miarab.
With the aid of their advanced computational methods, the researchers were also able to shed light on something unusual that they had discovered in one of their previous studies: a particular section of one chromosome in the bird genome had remained unchanged for millions of years, void of the expected patterns of genetic recombination.
“Ten years ago, we pieced together a family tree for the Neoaves, a group that includes the vast majority of bird species,” said University of Florida’s Professor Edward Braun.
“Based on the genomes of 48 species, we split the Neoaves into two big categories: doves and flamingos in one group, all the rest in the other.”
“When repeating a similar analysis this year using 363 species, a different family tree emerged that split up doves and flamingos into two distinct groups.”
“With two mutually exclusive family trees in hand, we went hunting for explanations that could tell them which tree was correct.”
“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,” he explained.
“Investigating this spot, we noticed it was not as mixed together as it should have been over millions of years of sexual reproduction.”
“Like humans, birds combine genes from a father and a mother into the next generation.”
“But birds and humans alike first mix the genes they inherited from their parents when creating sperm and eggs.”
“This process is called recombination, and it maximizes a species’ genetic diversity by making sure no two siblings are quite the same.”
The authors found evidence that one section of one bird chromosome had suppressed this recombination process for a few million years around the time the dinosaurs disappeared.
Whether the extinction event and the genomic anomalies are related is unclear.
The result was that the flamingos and doves looked similar to one another in this chunk of frozen DNA.
But taking into account the full genome, it became clear that the two groups are more distantly related.
“What’s surprising is that this period of suppressed recombination could mislead the analysis,” Professor Braun said.
“And because it could mislead the analysis, it was actually detectable more than 60 million years in the future. That’s the cool part.”
“Such a mystery could be lurking in the genomes of other organisms as well.”
“We discovered this misleading region in birds because we put a lot of energy into sequencing birds’ genomes.”
“I think there are cases like this out there for other species that are just not known right now.”
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J. Stiller et al. 2024. Complexity of avian evolution revealed by family-level genomes. Nature, in press;
Siavash Mirarab et al. 2024. A region of suppressed recombination misleads neoavian phylogenomics. PNAS 121: e2319506121; doi: 10.1073/pnas.2319506121
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