“The interpretation of genetic data is not straightforward,” Chikhi says. “We always have to make assumptions. Nobody takes data and magically comes up with a solution.”
Embracing the uncertainty
Most of the half-dozen population geneticists I spoke with praised Chikhi and Tournebize’s ingenuity and appreciated the spirit of their critique. “Their paper forces us to think more critically about the model we use for inference and consider alternatives,” says Aaron Ragsdale, a population geneticist at the University of Wisconsin–Madison. His own work likewise suggests that the earliest Homo sapiens populations in Africa were probably structured—and that this is the likely reason for genomic patterns that other research groups had attributed to hybridization with a mysterious “ghost lineage” of hominins in Africa.
Yet most researchers still believe that modern humans and Neanderthals did probably have children with each other tens of thousands of years ago. Several pointed to the fact that fossil DNA of Homo sapiens who died thousands of years ago had longer chunks of apparent Neanderthal DNA than living people, which is exactly what you would expect if they had a more recent Neanderthal ancestor. (To address this possibility, Chikhi and Tournebize included DNA from 10 ancient humans in their study and found that most of them fit the structured model.) And while the Harvard population geneticist David Reich, who helped design the statistical test from Pääbo’s 2010 study, declined an interview, he did say he thought Chikhi and Tournebize’s model was “weak” and “very contrived,” adding that “there are multiple lines of evidence for Neanderthal admixture into modern humans that make the evidence for this overwhelming.” (Two other authors of that study, Richard Green and Nick Patterson, did not respond to requests for comment.)
Nevertheless, most scientists these days welcome the development of structured, or “spatially explicit,” models that account for the fact that any given member of a population is usually more closely related to individuals living nearby than to those living far away.
Loosening our attachment to certain narratives of evolution can create space for wonder at the sheer complexity of life’s history.
Other scientists also say that random mating isn’t the only assumption in population genetics that merits scrutiny. Models rarely factor in natural selection, which can also create genetic patterns that look like hybridization. Another common assumption is that everyone’s DNA mutates at the same, constant rate. “All the theory says the mutation rate is fixed,” says Amos, the Cambridge population geneticist. But he thinks that rate would have slowed drastically in the group of Homo sapiens that expanded to Europe around 45,000 years ago. This, too, could have created genomic patterns that other scientists interpret as evidence of interbreeding with Neanderthals.
COURTESY OF 23ANDME
The point here isn’t that a complex model of evolution with many moving pieces is necessarily better than a simple one. Scientists need to reduce complexity in order to see the underlying processes more clearly. But simple models require assumptions, and scientists need to reevaluate those assumptions in light of what they learn. “As you get more data, you can justify more complex models of the world,” says Mark Thomas, a population geneticist at University College London, who wrote a history of random mating in population genetics that highlighted how the field was starting to see it as “a limiting assumption as opposed to a simplifying one.”
It can feel discouraging to couch conversations about the past in confusing terms like “population structure” and “mutation rates.” It seems almost antithetical to the spirit of science to talk more about uncertainty at the same time we are developing powerful technologies and enormous data sets for analyzing evolution. These tools often yield novel answers, but they can also limit the questions we ask. The French archaeologist Ludovic Slimak, for example, has complained that the idea of the inner Neanderthal has domesticated our image of Neanderthals and made it difficult to imagine their humanity as distinct from our own. Investigating Neanderthal DNA is sexier to many young researchers than searching for archaeological and fossil evidence of how Neanderthals actually lived.
Loosening our attachment to certain narratives of evolution can create space for wonder at the sheer complexity of life’s history. Ultimately, that’s what Chikhi and Tournebize hope to do. After all, they don’t believe the question of population structure versus hybridization is either-or. It’s possible, and even likely, that both played a role in human evolution. “Our structured model does not necessarily mean that no admixture ever took place,” Chikhi and Tournebize wrote in their study. “What our results suggest is that, if admixture ever occurred, it is currently hard to identify using existing methods.”
