Tree of life for modern birds revealed
The largest and most complete study pinpoints timing of evolution
AUSTRALIAN MUSEUM
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DR JACQUELINE NGUYEN + PROFESSOR SIMON HO WITH AUSTRALIAN MUSEUM BIRD SPECIMENS
view moreCREDIT: JAMES ALCOCK
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
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
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A GREATER FLAMINGO IN MALLORCA, SPAIN. UNRAVELING A GENETIC MYSTERY REVEALED THAT FLAMINGOS AND DOVES ARE MORE DISTANTLY RELATED THAN PREVIOUSLY THOUGHT.
view moreCREDIT: 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
JOURNAL
Proceedings of the National Academy of Sciences
METHOD OF RESEARCH
Data/statistical analysis
SUBJECT OF RESEARCH
Not applicable
ARTICLE TITLE
A region of suppressed recombination misleads neoavian phylogenomics
ARTICLE PUBLICATION DATE
1-Apr-2024
When did the chicken cross the road? New evidence from Central Asia
New research reveals that chickens were widely raised across southern Central Asia from 400 BCE through medieval periods and likely dispersed along the ancient Silk Road
MAX PLANCK INSTITUTE OF GEOANTHROPOLOGY
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AN EGGSHELL FRAGMENT FROM THE SITE OF BASH TEPA, REPRESENTING ONE OF THE EARLIEST PIECES OF EVIDENCE FOR CHICKENS ON THE SILK ROAD
view moreCREDIT: ROBERT SPENGLER
Chickens are one of the most economically important animals in the world today. However, the story of their origins and dispersal across the ancient world is still poorly understood. In fact, new archaeological techniques have recently led to the recognition that many finds of bones previously thought to represent early chickens in fact belonged to wild birds. Now, in a new publication, an international team of archaeologists, historians, and biomolecular scientists present the earliest clear evidence for the raising of chickens for egg production, and argue that the loss of seasonal egg laying was the main driver for the dispersal of domestic chickens across Eurasia and northeast Africa.
Using eggshell fragments collected from 12 archaeological sites spanning roughly 1500 years, the researchers show that chickens were widely raised in Central Asia from approximately 400 BCE to 1000 CE and were likely dispersed along the ancient Silk Road. The abundance of eggshells further suggests that the birds were laying out of season. It was this trait of prolific egg laying, the researchers argue, that made the domestic chicken so attractive to ancient peoples.
To reach these conclusions, the team collected tens of thousands of eggshell fragments from sites located along the main Central Asian corridor of the Silk Road. They then used a method of biomolecular analysis called ZooMS to identify the source of the eggs. Much like genetic analysis, ZooMS can make species identifications from animal remains such as bone, skin and shell, but it relies on protein signals rather than DNA. This makes it a faster and more cost-effective option than genetic analysis.
“This study showcases the potential of ZooMS to shed light on human-animal interactions in the past,” says Dr. Carli Peters, researcher at the Max Planck Institute of Geoanthropology and first author of the new paper.
The identification of these shell fragments as chickens, and their abundance throughout the sediment layers at each site, led the researchers to an important conclusion: the birds must have been laying more frequently than their wild ancestor, the red jungle fowl, which nests once per year and typically lays six eggs per clutch.
“This is the earliest evidence for the loss of seasonal egg laying yet identified in the archaeological record,” says Dr. Robert Spengler, leader of the Domestication and Anthropogenic Evolution research group and principal investigator on the study. “This is an important clue for better understanding the mutualistic relationships between humans and animals that resulted in domestication.”
Taken together, the new study suggests an answer to the age-old riddle of the chicken and the egg. In Central Asia, evidence suggests that the ability to lay a multitude of eggs is what made the chicken the chicken we know today – a global species of enormous economic importance. The authors hope that this study will demonstrate the potential of new, cost-effective methods and interdisciplinary collaboration to address long-standing questions about the past.
The breathing pore of an ancient eggshell fragment from the medieval site of Tashbulak in Uzbekistan under high power SEM magnification. The morphology of these breathing pours helps with the identification.
CREDIT
Robert Spengler
JOURNAL
Nature Communications
ARTICLE TITLE
When Did the Chicken Cross the Road: Archaeological and molecular evidence for ancient chickens in Central Asia
ARTICLE PUBLICATION DATE
2-Apr-2024
Chicks prove vision and touch linked at birth
Study reveals that newly hatched chicks can instantly recognise objects with their vision, even if they've only ever experienced them by touch.
Newly hatched chicks raised in darkness and allowed to touch either a smooth or bumpy cube for 24 hours instantly recognised the object with their vision upon first exposure to light.
This suggests chicks can link touch and vision without any prior experience combining these senses, challenging the long-held belief that such integration requires learning.
The discovery implies a pre-wired ability in the brain for cross-modal perception, potentially redefining our understanding of animal cognition and sensory processing.
In a study published in Biology Letters, researchers at Queen Mary University of London have cracked a centuries-old philosophical question about sight and touch. Led by Dr Elisabetta Versace, the team used chicks to finally answer the question posed by William Molyneux in 1688: can someone born blind instantly recognize objects by sight after gaining vision?
Molyneux proposed a scenario where a person blind from birth learns to distinguish a cube from a sphere by touch. Would they then be able to recognise these shapes visually upon gaining sight? Studying this question in humans is ethically challenging. However, Dr Versace and her team used chicks, which hatch with well-developed sensory systems.
"Unlike humans and other mammals," explains Dr Versace, Senior Lecturer at the School of Biological and Behavioural Sciences, chicks hatch with developed sensory systems. This allowed us to raise them in darkness and expose them to either a smooth or bumpy object for the first 24 hours of their lives – their first ever tactile experience."
Remarkably, when exposed to light for the first time, chicks that had touched a smooth object preferentially approached the visual representation of a smooth object, and vice versa. This suggests that chicks can inherently link touch with sight, even without any prior visual experience.
"This finding contradicts traditional theories," says Dr Versace. "It suggests our brains are pre-wired to make connections between different senses, even before we have ever used them together."
This breakthrough opens exciting new avenues in understanding how our brains process information across different senses. It could also lead to a deeper understanding of how our senses develop and interact with the world around us.
JOURNAL
Biology Letters
ARTICLE TITLE
First-sight recognition of touched objects shows that chicks can solve Molyneux's problem
ARTICLE PUBLICATION DATE
3-Apr-2024
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