Tree of life for modern birds revealed

The largest and most complete study pinpoints timing of evolution

AUSTRALIAN MUSEUM

2 April, 2024, Sydney; In a world first, a team of international scientists including three Australians, Al-Aabid Chowdhury and Professor Simon Ho from University of Sydney, and Dr Jacqueline Nguyen from Australian Museum and Flinders University, have determined the family tree of modern birds and pinpointed the timing of their evolution. Their findings have been published today in Nature.

The largest study ever undertaken of modern bird genomes, the scientists combined genomic data of more than 360 bird species with data from nearly 200 bird fossils to reconstruct the most well-supported Tree of Life for modern birds.

The research revealed that most modern bird groups appeared within a very small evolutionary window of only 5 million years. These findings support the hypothesis that birds made the most of opportunities after an asteroid struck earth 66 million years ago wiping out the dinosaurs.

The comprehensive study was led by Assistant Professor Josefin Stiller from the University of Copenhagen, along with Associate Professor Siavash Mirarab from the University of California, San Diego and Professor Guojie Zhang from Zhejiang University.

“Our study has resolved some previous disputes about the bird family tree and added new nuance to the textbook knowledge of bird evolution,” Assistant Professor Stiller said.

Earlier studies had already established that the 10,000 species of living birds form three major groups. About 500 species belong to the flightless ratites group or the landfowl-waterfowl group, however all other birds form a third large and diverse group called Neoaves.

The latest study has been able to establish deeper understanding of relationships in the Neoaves group, which itself contains 10 major sub-groups of birds. These include the colourfully named ‘Magnificent Seven’, including cuckoos, doves, and flamingos, along with three ‘orphan’ groups of birds whose ancestry has long been uncertain.

Professor Ho, who specialises in evolutionary biology at the University of Sydney, said the research has worked out the evolutionary relationships of the major bird groups.

“With such a huge amount of genome data, our study has been able to provide the clearest picture of the bird family tree so far, particularly among the ‘Magnificent Seven’ and three ‘orphan’ bird groups, which make up 95% of bird species,” Professor Ho said.

Australian Museum and Flinders University avian palaeontologist, Dr Jacqueline Nguyen, said the fossil information was used to work out the timescale of the bird family tree.

“By combining evidence from nearly 200 bird fossils, we were able to pinpoint an extremely important period of bird diversification that happened immediately after the extinction of the dinosaurs,” Dr Nguyen explained.

The genomes also reveal a new grouping of birds that the researchers have named ‘Elementaves’, inspired by the four ancient elements of earth, air, water and fire. The group includes birds that are successful on land, in the sky, and in water. Some birds have names relating to the sun, representing fire. Penguins, pelicans, swifts, hummingbirds and shorebirds are among the birds that have been placed in Elementaves.

Two of the most well-known groups of birds in Australia, the passerines (songbirds and relatives) and parrots, share a very close relationship. Songbirds include familiar birds such as magpies, ravens, finches, honeyeaters and fairy-wrens. They originated in Australia about 50 million years ago and have become the most successful group of birds, making up nearly half of all bird species worldwide.

Despite the enormous scale of the latest genome study, there is one mystery that continues. The researchers were unable to work out the relationships of the hoatzin, a distinctive bird that is only found in South America and is the sole survivor of its entire lineage.

The findings are the outcome of nearly a decade of research involving scientists from across the globe working together on the Bird 10,000 Genomes Project (B10K), which aims to sequence the complete genomes of every living bird species.

Chief scientist and Director of the Australian Museum Research Institute, Professor Kris Helgen, said that genomic tools have precipitated one of the great revolutions in biological sciences.

“The global scientific community has come together to champion impressive genome projects like Bird 10K. Efforts like these can address long-standing questions about evolution, in this case for all living species of birds. They do this by drawing on new genetics techniques, expertise on anatomy and the fossil record, and carefully curated DNA samples, which are stored behind-the-scenes in the collections of natural history museums in Australia and around the world,” Professor Helgen said.

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JOURNAL

Nature

DOI

10.1038/s41586-024-07323-1

METHOD OF RESEARCH

Data/statistical analysis

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Complexity of avian evolution revealed by family-level genomes

ARTICLE PUBLICATION DATE

2-Apr-2024

We’ve had bird evolution all wrong

A frozen chunk of genome rewrites our understanding of the bird family tree

Peer-Reviewed Publication

UNIVERSITY OF FLORIDA

Flamingo — IMAGE:
A GREATER FLAMINGO IN MALLORCA, SPAIN. UNRAVELING A GENETIC MYSTERY REVEALED THAT FLAMINGOS AND DOVES ARE MORE DISTANTLY RELATED THAN PREVIOUSLY THOUGHT.
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CREDIT: DANIEL J. FIELD

An enormous meteor spelled doom for most dinosaurs 65 million years ago. But not all. In the aftermath of the extinction event, birds — technically dinosaurs themselves — flourished.

Scientists have spent centuries trying to organize and sort some 10,000 species of birds into one clear family tree to understand how the last surviving dinosaurs filled the skies. Cheap DNA sequencing should have made this simple, as it has for countless other species.

But birds were prepared to deceive us.

In a pair of new research papers released today, April 1, scientists reveal that another event 65 million years ago misled them about the true family history of birds. They discovered that a section of one chromosome spent millions of years frozen in time, and it refused to mix together with nearby DNA as it should have.

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.”

Braun supervised an international team of collaborators led by Siavash Mirarab, a professor of computer engineering at the University of California San Diego, to publish their evidence that this sticky chunk of DNA muddied the true history of bird evolution. Mirarab and Braun also contributed to a companion paper published in Nature that outlines the updated bird family tree, which was led by Josefin Stiller at the University of Copenhagen.

Both papers are part of the B10K avian genomics project led by Guojie Zhang of Zhejiang University, Erich Jarvis of Rockefeller University, and Tom Gilbert of the University of Copenhagen.

Ten years ago, Braun and his collaborators pieced together a family tree for the Neoaves, a group that includes the vast majority of bird species. Based on the genomes of 48 species, they 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, the scientists 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,” Braun said.

Investigating this spot, Braun’s team 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.

Braun’s team 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,” 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,” Braun said. “I think there are cases like this out there for other species that are just not known right now.”

This work was supported in part by the National Science Foundation.

A wompoo fruit-dove in Queensland, Australia. Unraveling a genetic mystery revealed that flamingos and doves are more distantly related than previously thought.

CREDIT

Daniel J. Field

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