Reconstructions of a Neanderthal man, left, and woman at the Neanderthal museum in Mettmann, Germany. (Martin Meissner/AP)

Most human genomes harbor small fragments of Neanderthal DNA, the legacy of prehistoric hanky-panky between our ancestors and their hominid cousins.

For the most part, that inheritance has been detrimental. Research suggests that as much as 10 percent of the human genome was inherited from archaic hominids other than Homo sapiens, but the majority of that material was weeded out by tens of thousands of years of natural selection. The DNA that does remain has been blamed for increasing risk of depression, Type 2 diabetes, Crohn’s disease, lupus, allergies, addiction and more.

Vanderbilt researcher Tony Capra talks about his research regarding the presence of Neanderthal genes in the genomes of a significant population of adults of European ancestry. (Vanderbilt News and Communications)

But geneticists Fernando Racimo, Davide Marnetto and Emilia Huerta-Sanchez wanted to find evidence that our archaic inheritance actually does us some good. They went looking for instances of adaptive introgression — a phenomenon in which a newly introduced piece of genetic material is so beneficial that it quickly radiates out into the entire population.

“Nobody has yet done a systematic survey of adaptive introgression around the world,” said Racimo, a geneticist at the New York Genome Center and lead author on the study. “We were able to confirm some previous findings and report examples that have never been found before.”

Their results, published in the journal Molecular Biology and Evolution this week, suggest that humans have inherited helpful genetic variants associated with fat storage, respiration, skin pigmentation, liver function, immune response and keratin production.

These scraps of DNA come from both Neanderthals and Denisovans, another hominid known only from a few remains found in Russia. Tens of thousands of years after these species went extinct, their DNA may still be helping us survive the modern world.

Exactly why that's happening is unclear. The statistical tool that Racimo and his colleagues developed was designed to scan thousands of human genomes from all over the world and pinpoint sections among certain populations that bore more resemblance to the DNA of archaic humans than that of other Homo sapiens — in other words, examples of adaptive introgression. Presumably, these variants spread throughout populations because they gave us some advantage. For example, a known instance of adaptive introgression that was confirmed by Racimo's study can be found in Tibetans (whose genome is about 5 percent Denisovan): Members of the mountain-dwelling society have a genetic variant that helps them breathe at high altitudes that is closely related to a Denisovan gene and is completely missing in the genomes of nearby Han Chinese individuals.

But most human traits come from a complex combination of genes, making it a lot more difficult to figure out exactly what makes the inherited genetic material beneficial.

“For a lot of these selection scans you can speculate based on the gene function but the actual adaptive reason is much harder to understand,” said Racimo, who was a PhD student at the University of California at Berkeley at the time of the study.

Racimo has his suspicions about the benefits of two of the genes he and his colleagues discovered: These variants are found in Native American, Eurasian and Denisovan populations and have to do with the production of fat tissue.

“We have an idea of what they are doing,” he said, cagily. But those findings are due to be published in another paper, so he couldn't say more. 

The main takeaway from the study, Racimo said, is that we owe more to our Neanderthal and Denisovan relatives than we think. For years, conventional wisdom about these archaic humans is that they were weaker, dumber and less evolutionarily fit than modern humans and that's why they died out. But Racimo believes that other hominid species could have actually helped humans.

“Archaic humans expanded out of Africa before modern humans, so they had a lot more time to adapt to the particular conditions of Europe and Asia,” he said. “A shortcut to adapt to these conditions, instead of waiting for the mutations to occur, is to obtain the genetic material from these archaic human groups who were established for a long time.”

For example, the genes associated with immunity may have helped Homo sapiens resist the new pathogens they encountered as they spread around the globe.

Lest you start feeling too warm and fuzzy about ancient human-Neanderthal relations, this issue of Molecular Biology and Evolution contains a study looking at another portion of our archaic inheritance: genital warts. According to a genetic analysis of HPV16, a strain of Human Papillomavirus, the disease was likely passed to modern humans who had sex with Neanderthals or Denisovans after leaving Africa.

You win some, you lose some.

Read more:

‘Hobbits’ died off earlier than we’d thought — and we may have killed them

Sequencing the genome creates so much data we don’t know what to do with it

Ancient human bones show evidence of a hungry hyena encounter

Bad heart to bad habits: Blame your Neanderthal DNA

Human and Neanderthal love affair is traced back to Israel, 55,000 years ago