Bird evolution didn’t happen steadily: AI reveals 45 million years of climate-driven changes in skeletons

Birds may look remarkably familiar today, but their skeletons carry clues to a far more turbulent evolutionary history.

A new study from researchers at the University of Michigan has used artificial intelligence and a novel statistical technique to trace how the body shapes of passerine birds changed over roughly 45 million years.

The group, which includes songbirds and more than half of all living bird species, appears to have experienced periods of rapid anatomical change interspersed with much longer stretches of slower evolution.


Several of those evolutionary bursts occurred around major shifts in Earth's climate, suggesting that environmental upheaval may have opened new ecological opportunities for birds and pushed some lineages toward different body forms.

The researchers reconstructed this history by combining thousands of museum specimens with AI-assisted measurements and a new method for studying the skeleton as a connected structure rather than as a collection of unrelated bones.

AI turns thousands of museum specimens into data

The sheer size of the bird family tree made the project difficult to tackle using traditional methods.

The research team examined data covering more than 2,000 passerine species and compiled more than 170,000 skeletal measurements. More than 15,000 museum specimens were photographed and processed, with much of the material coming from the University of Michigan Museum of Zoology.

Instead of measuring every specimen manually, the researchers used an AI system called Skelevision.

The technology was developed through a collaboration between Brian Weeks' laboratory at Michigan and David Fouhey's group at New York University. It was designed to identify and measure bones from photographs of bird specimens.

Each specimen is photographed against a grid that gives the software a consistent scale. Skelevision can then identify roughly a dozen skeletal elements and extract measurements from them.

A single scan takes around 45 seconds.

That speed made it possible to analyse a collection on a scale that would have been extremely difficult for researchers working entirely by hand.

Scientists wanted to know whether evolution happens gradually

The study grew from an old question in evolutionary biology: does evolution usually proceed through small, steady changes, or can species experience relatively sudden bursts of transformation?

Jake Berv, the study's lead author and a postdoctoral researcher at the University of Michigan's School for Environment and Sustainability, focused on the idea of evolutionary radiation.

The concept suggests that when a lineage encounters new ecological opportunities, different species can rapidly adapt to different environments or lifestyles. As those opportunities become less available, evolutionary change may slow again.

The fossil record offers evidence for such episodes, but determining the exact pace of evolutionary change over millions of years can be challenging.

The Michigan researchers approached the problem by looking at the anatomy of living passerine species and using those differences to reconstruct how their body forms changed over deep time.

A new statistical tool tracks the whole skeleton

Measuring individual bones can reveal useful information, but the researchers wanted to understand the bird skeleton as a unified system.

For that reason, Berv developed a statistical approach called bifrost.

The method considers relationships between different parts of the skeleton instead of treating every measurement as an independent characteristic. That matters because changes in one part of an animal's body can be connected to changes elsewhere.

By combining those relationships with the enormous dataset produced by Skelevision, the researchers were able to estimate how quickly passerine body shapes changed at different points in their evolutionary history.

The resulting picture was anything but uniform.

A major evolutionary burst appeared during ancient cooling

One of the strongest signals appeared around 35 million years ago, close to the boundary between the Eocene and Oligocene epochs.

Earth was undergoing a profound climate transition at the time. The relatively warm conditions of the Eocene gave way to a considerably cooler world, bringing major changes to ecosystems and habitats.

The researchers found that passerine body shapes changed at an unusually rapid pace around this period.

The finding does not prove that falling temperatures directly caused the evolutionary acceleration. Climate affects organisms through many interconnected pathways, including changes in food availability, vegetation, habitats and competition.

Still, the timing is striking.

The study suggests that periods of major environmental change may create circumstances in which evolutionary experimentation becomes more intense, allowing some groups to occupy newly available ecological niches.

Evolution also slowed during periods of environmental change

The researchers found evidence of the opposite pattern as well.

Around 15 million years ago, passerine evolution showed a cluster of slower rates of anatomical change. That period also coincided with a significant shift in Earth's geological and environmental history.

The contrast between rapid bursts and prolonged slowdowns challenges the idea that evolutionary change simply accumulates at a constant pace.

Instead, bird evolution appears to have been shaped by a changing rhythm, with environmental conditions potentially influencing when lineages rapidly explore new forms and when that process settles down.

Latitude offers another clue

The researchers then looked beyond geological time and examined the relationship between evolutionary rates and geography.

Another pattern emerged.

Passerines living at higher latitudes, particularly in regions where temperatures fluctuate more strongly across seasons, tended to show faster rates of morphological evolution.

Birds closer to the equator generally showed slower average rates.

The geographic pattern resembles the signal found in the deep-time analysis. In both cases, environments with greater climatic variation were associated with faster changes in body form.

That does not mean temperature alone determines how quickly birds evolve. Evolution is influenced by numerous factors, from competition and food supplies to habitat and reproduction. But the consistency of the pattern gives researchers another reason to investigate the role of environmental variability.

Museum collections hold an evolutionary time capsule

One of the study's broader implications is not limited to birds.

Natural history museums contain millions of specimens collected long before scientists had access to modern imaging, artificial intelligence or large-scale statistical analysis.

Those collections can now be revisited with tools that were unimaginable when many of the specimens were catalogued.

In this case, old bird skeletons became part of a massive dataset capable of answering questions about evolutionary rates across tens of millions of years.

The combination of museum collections and AI also reduces one of the biggest limitations of comparative biology: the amount of time required to collect consistent measurements.

Rather than discarding older specimens because they lack modern digital records, researchers can photograph them and use software to extract comparable anatomical information.

What the findings mean in the era of climate change

The study also offers a reminder of how closely evolution and environmental change can be linked, although the researchers caution against making a direct comparison between today's climate crisis and ancient geological events.

The climate transitions examined in the study unfolded over vastly longer periods than the rapid warming occurring today.

Bird populations cannot necessarily respond to modern climate change in the same way that their distant ancestors responded to environmental shifts millions of years ago.

Evolution itself takes time, while present-day changes in temperature, rainfall and habitat can occur within just a few decades.

That difference is crucial when considering what the fossil and evolutionary record can tell us about the future.

AI gives scientists a new view of bird evolution

The research ultimately combines three things that were previously difficult to bring together: vast museum collections, artificial intelligence and evolutionary modelling.

By measuring thousands of skeletons and reconstructing changes across roughly 45 million years, the researchers found that passerine evolution was not a smooth process. Instead, body shapes appear to have changed at dramatically different speeds depending on the period and environment.

The findings add to evidence that evolution can accelerate when ecological circumstances change, while also showing that those bursts are relatively rare.

More broadly, the study demonstrates how AI can transform natural history collections from rows of preserved specimens into enormous sources of evolutionary data.

For scientists trying to understand how birds responded to Earth's past climate shifts, those collections may now offer something even more valuable than a snapshot of what species looked like: a record of how quickly nature can change when the world around it changes too.