Key role of ice age cycles in early human interbreeding

A study published in Science indicates that climatic shifts over the past 400,000 years have influenced Neanderthal and Denisovan interbreeding.

Recent paleogenomic research revealed that interbreeding was common among early human species. However, little was known about when, where, and how often this hominin interbreeding took place. Using paleoanthropological evidence, genetic data, and supercomputer simulations of past climate, a team of international researchers has found that interglacial climates and corresponding shifts in vegetation created common habitats for Neanderthals and Denisovans, increasing their chances for interbreeding and gene flow in parts of Europe and central Asia.

Contemporary humans carry in their cells a small amount of DNA derived from Neanderthals and Denisovans. "Denny," a 90,000-year-old fossil individual, recently identified as the daughter of a Denisovan father and a Neanderthal mother, bears testimony to the possibility that interbreeding was quite common among early human species. But when, where, and at what frequency did this interbreeding take place?

In a recent study published in Science on 10 August 2023, researchers from Korea and Italy have joined hands to answer this question. Using fossil data, supercomputer simulations of past climate, and insights obtained from genomic evidence, the team was able to identify habitat overlaps and contact hotspots of these early human species. Dr. Jiaoyang Ruan, Postdoctoral Researcher at IBS Center for Climate Physics (ICCP), South Korea, explains, "Little is known about when, where, and how frequently Neanderthals and Denisovans interbred throughout their shared history. As such, we tried to understand the potential for Neanderthal-Denisovan admixture using species distribution models that bring extensive fossil, archeological, and genetic data together with transient Coupled General Circulation Model simulations of global climate and biome."

The researchers found that Neanderthals and Denisovans had different environmental preferences to start with. While Denisovans were much more adapted to colder environments, such as the boreal forests and the tundra region in northeastern Eurasia, their Neanderthal cousins preferred the warmer temperate forests and grasslands in the southwest. However, shifts in the Earth's orbit led to changes in climatic conditions and hence vegetation patterns. This triggered the migration of both these hominin species towards geographically overlapping habitats, thus increasing the chance of their interbreeding.

The researchers further used insights gained from their analysis to determine the contact hotspots between Neanderthals and Denisovans. They identified Central Eurasia, the Caucasus, the Tianshan, and the Changbai mountains as the likely hotspots. Identification of these habitat overlaps also helped the researchers place 'Denny' within the climatic context and even confirmed the other known episodes of genetic interbreeding. The researchers also noted that the Denisovans and Neanderthals would have had a high probability of contact in the Siberian Altai during ~ 340-290, ~240-190 and ~130-80 thousand years ago.

To further elucidate the factors that triggered the 'east-west interbreeding seesaw,' the team examined the change in vegetation patterns over Eurasia over the past 400 thousand years. They observed that elevated atmospheric CO2 concentrations and mild interglacial conditions caused an eastward expansion of the temperate forest into central Eurasia, and the dispersal of Neanderthals into Denisovan lands. On the contrary, lower CO2 concentrations and corresponding harsher glacial climate potentially caused a fragmentation of their habitats, leading to lesser interactions and interbreeding events.

"Pronounced climate-driven zonal shifts in the main overlap region of Denisovans and Neanderthals in central Eurasia, which can be attributed to the response of climate and vegetation to past variations in atmospheric CO2 and northern hemisphere ice-sheet volume, influenced the timing and intensity of potential interbreeding events," remarks senior author Axel Timmermann, Director, ICCP and Professor at Pusan National University, South Korea.

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Study of ancient skulls sheds light on human interbreeding with Neanderthals

Research has established that there are traces of Neandertal DNA in the genome of modern humans. Now an exploratory study that assessed the facial structure of prehistoric skulls is offering new insights, and supports the hypothesis that much of this interbreeding took place in the Near East -- the region ranging from North Africa to Iraq.

"Ancient DNA caused a revolution in how we think about human evolution," says Steven Churchill, co-author of the study and a professor of evolutionary anthropology at Duke University. "We often think of evolution as branches on a tree, and researchers have spent a lot of time trying to trace back the path that led to us, Homo sapiens. But we're now beginning to understand that it isn't a tree -- it's more like a series of streams that converge and diverge at multiple points."

"Our work here gives us a deeper understanding of where those streams came together," says Ann Ross, corresponding author of the study and a professor of biological sciences at North Carolina State University.

"The picture is really complicated," Churchill says. "We know there was interbreeding. Modern Asian populations seem to have more Neandertal DNA than modern European populations, which is weird -- because Neandertals lived in what is now Europe. That has suggested that Neandertals interbred with what are now modern humans as our prehistoric ancestors left Africa, but before spreading to Asia. Our goal with this study was to see what additional light we could shed on this by assessing the facial structure of prehistoric humans and Neandertals."

"By evaluating facial morphology, we can trace how populations moved and interacted over time," Ross explains. "And the evidence shows us that the Near East was an important crossroads, both geographically and in the context of human evolution."

For this study, the researchers collected data on craniofacial morphology from the published literature. This ultimately resulted in a data set including 13 Neandertals, 233 prehistoric Homo sapiens, and 83 modern humans.

The researchers focused on standard craniofacial measurements, which are reproducible, and used those measurements to assess the size and shape of key facial structures. This then allowed the researchers to do an in-depth analysis to determine whether a given human population was likely to have interbred with Neandertal populations, as well as the extent of that likely interbreeding.

"Neandertals had big faces," Churchill says. "But size alone doesn't establish any genetic link between a human population and Neandertal populations. Our work here involved a more robust analysis of the facial structures."

The researchers also accounted for environmental variables that are associated with changes in human facial characteristics, to determine the likelihood that connections they established between Neandertal and human populations were the result of interbreeding rather than other factors.

"We found that the facial characteristics we focused on were not strongly influenced by climate, which made it easier to identify likely genetic influences," Ross says. "We also found that facial shape was a more useful variable for tracking the influence of Neandertal interbreeding in human populations over time. Neandertals were just bigger than humans. Over time, the size of human faces became smaller, generations after they had bred with Neandertals. But the actual shape of some facial features retained evidence of interbreeding with Neandertals."

"This was an exploratory study," Churchill says. "And, honestly, I wasn't sure this approach would actually work -- we have a relatively small sample size, and we didn't have as much data on facial structures as we would have liked. But, ultimately, the results we got are really compelling.

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