Hundreds of thousands of years ago, the ancestors of modern humans diverged from an archaic lineage that gave rise to Neanderthals and Denisovans. Yet the evolutionary relationships between these groups remain unclear.
A University of Utah-led team developed a new method for analyzing DNA sequence data to reconstruct the early history of the archaic human populations. They revealed an evolutionary story that contradicts conventional wisdom about modern humans, Neanderthals and Denisovans.
The study found that the Neanderthal-Denisovan lineage nearly went extinct after separating from modern humans. Just 300 generations later, Neanderthals and Denisovans diverged from each other around 744,000 years ago. Then, the global Neanderthal population grew to tens of thousands of individuals living in fragmented, isolated populations scattered across Eurasia.
“This hypothesis is against conventional wisdom, but it makes more sense than the conventional wisdom.” said Alan Rogers, professor in the Department of Anthropology and lead author of the study that will publish online on August 7, 2017 in the Proceedings of the National Academy of Sciences.
A different evolutionary story
With only limited samples of fossil fragments, anthropologists assemble the history of human evolution using genetics and statistics.
Previous estimates of the Neanderthal population size are very small — around 1,000 individuals. However, a 2015 study showed that these estimates underrepresent the number of individuals if the Neanderthal population was subdivided into isolated, regional groups. The Utah team suggests that this explains the discrepancy between previous estimates and their own much larger estimate of Neanderthal population size.
“Looking at the data that shows how related everything was, the model was not predicting the gene patterns that we were seeing,” said Ryan Bohlender, post-doctoral fellow at the M. D. Anderson Cancer Center at the University of Texas, and co-author of the study. “We needed a different model and, therefore, a different evolutionary story.”
The team developed an improved statistical method, called legofit, that accounts for multiple populations in the gene pool. They estimated the percentage of Neanderthal genes flowing into modern Eurasian populations, the date at which archaic populations diverged from each other, and their population sizes.
A family history in DNA
The human genome has about 3.5 billion nucleotide sites. Over time,…