Just as with modern Homo sapiens, the genome of a single individual cannot tell us exactly what genes and traits are specific to all Denisovans. Yet, just one genome can reveal the genetic diversity of an entire population. Each of our genomes contains information about generations far beyond those of our parents and grandparents, said David Reich, a researcher at the Massachusetts Institute of Technology–Harvard University Broad Institute and a co-author on the paper. Scientists can compare and contrast the set of genes on each chromosome—passed down from each parent—and extrapolate this process back through the generations. "You contain a multitude of ancestors within you," Reich said, borrowing from Walt Whitman.
The new research reveals that the Denisovans had low genetic diversity—just 26 to 33 percent of the genetic diversity of contemporary European or Asian populations. And for the Denisovans, the population on the whole seems to have been very small for hundreds of thousands of years, with relatively little genetic diversity throughout their history.
Curiously, the researchers noted in their paper, the Denisovan population shows "a drastic decline in size at the time when the modern human population began to expand."
Why were modern humans so successful whereas Denisovans (and Neandertals) went extinct? Pääbo and his co-authors could not resist looking into the genetic factors that might be at work. Some of the key differences, they note, center around brain development and synaptic connectivity. "It makes sense that what pops up is connectivity in the brain," Pääbo noted. Neandertals had a similar brain size–to-body ratio as we do, so rather than cranial capacity, it might have been underlying neurological differences that could explain why we flourished while they died out, he said.
Hawks counters that it might be a little early to begin drawing conclusions about human brain evolution from genetic comparisons with archaic relatives. Decoding the genetic map of the brain and cognition from a genome is still a long way off, he notes—unraveling skin color is still difficult enough given our current technologies and knowledge.
New sequencing for old DNA
The Denisovan results rely on a new method of genetic analysis developed by paper co-author Matthias Meyer, also of M.P.I. The procedure allows the researchers to sequence the full genome by using single strands of genetic material rather than the typical double strands required. The technique, which they are calling a single-stranded library preparation, involves stripping the genetic material down to individual strands to copy and avoids a purification step, which can lose precious genetic material.
The finger bone—just one disklike phalanx—is so small that it does not contain enough usable carbon for dating, the researchers note. But by counting the number of genetic mutations in a genome and comparing them with other living relatives, such as modern humans and chimpanzees, given assumed rates of mutations since breaking with a last common ancestor, "for the first time you can try to estimate this number into a date and provide molecular dating of the fossil," Meyer said. With the new resolution, the researchers estimate the age of the bone to 74,000 to 82,000 years ago. But that is a wide window, and previous archaeological estimates for the bone are a bit younger, ranging from 30,000 to 50,000 years old. These genetic estimations are also still in limbo because of ongoing debate about the average rate of genetic mutations over time, which could skew the age. "Nevertheless," the researchers noted in their paper, "the results suggest that in the future it will be possible to determine dates of fossils based on genome sequences."
This new sequencing approach can be used for any DNA that is too fragmented to be read well through more traditional methods. Meyer noted that it could come in handy for analysis of both ancient DNA and contemporary forensic evidence, which also often contains only fragments of genetic material.