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Genes from our extinct relatives live on in modern humans

February, 2017

Inuits sitting on top of furs on a snowy landscape

Photo credit: Wikimedia

While all humans are remarkably similar at a genetic level — on average any two individuals' genomes are 99.9% identical — those differences that do exist manifest themselves in the dazzling spectrum of human diversity. From a lithe tribesperson of the Kalahari, to a freckled redhead from Ireland, to a sleek-haired, ruddy-cheeked inhabitant of the Tibetan plateau, Homo sapiens come in many different shapes, sizes, hues, and appearances. While we tend to notice differences that are easy to spot, other "stealth" variations in human populations are not necessarily observable from physical appearance alone. For example, many people of African descent are resistant to infection from malaria, while that trait is much rarer among those who hail from other parts of the world.  Now new research into Arctic-dwelling Inuit populations points to a surprising origin for one such "stealth" trait — the ability to tolerate frigid temperatures.

Where's the evolution?

Just as other organisms have evolved adaptations that aid survival and reproduction in their unique environments — finches evolving beaks shaped to eat the seeds that are plentiful, moths evolving wings that blend in with the bark of the trees where they sit — so too have different human populations experienced natural selection shaping them in response to their environments.  Random mutations occur, some of these mutations affect the traits of the organism that carries it, and sometimes the organism lives in an environment where that altered trait aids survival and reproduction. When that happens, the frequency of the mutation increases, generation by generation, as the descendants of the original carriers multiply in the population. That is the essence of evolution by natural selection. And that is how, for example, malaria-resistant African populations came about: a random mutation that happened to confer resistance to its carrier occurred, and when that mutation wound up in an individual living where malaria was common, that person left more offspring (who were also likely to carry the mutation) than did others. Additional traits adapting humans to different local environmental conditions are shown in the figure below.

diagram showing a global distribution of adaptive traits

Figure titled Global distribution of locally adaptive traits. Adapted from Strength in small numbers by Sarah Tishkoff, illustrated by A. Cuadra/Science and Megan Rubel/Univ. of Pennsylvania 2015, Science, Vol. 349, Issue 6254, pp. 1282-1283 DOI: 10.1126/science.aad0584

One might expect the same to have happened among the Inuit with genes that affect cold tolerance. These indigenous people live in places where winter means an average daily temperature of around -20° F and only a few hours of light each day. Any trait that might help someone eke a living out of such a harsh environment would surely have been favored by natural selection. Indeed, researchers recently scanned the Inuit genome looking for areas that seem to have been acted on by natural selection and honed in on a few regions. One area contains genes that affect how the body processes fatty acids, which makes sense given that the seafood upon which the Inuit depend is unusually high in polyunsaturated fatty acids. Another contains genes related to body fat distribution and the storage of fat in a form that helps generate heat, a trait that could make all the difference in the frigid Arctic winter.

While the Inuit's fatty-acid processing gene variants seem to have evolved via the accumulation and selection of random mutations in human ancestors, the fat distribution gene variants have a different source. The region of the genome that contains these genes is remarkably similar in sequence to the DNA of an ancient human relative that lived alongside Neanderthals — the Denisovans.

Denisovans are known only from a one finger bone and a couple of teeth found in a Siberian cave, but the DNA preserved in these 40,000 year old relics has revealed surprising insights about early human relatives. While we don't know what Denisovans looked like, we do know a fair amount about their sex lives. Denisovans interbred with Neanderthals, with another human relative whose physical remains have yet to be discovered, but whose DNA traces were found in the Denisovan genome, and with our human ancestors.

It is likely that the cold-tolerant genes shaping body fat distribution and the storage of heat-generating fat evolved through natural selection in Denisovans or a close relative of Denisovans (possibly because the chilly environments these lineages inhabited) and then wound up in ancestral humans through breeding. Denisovan evolution may have assembled the genes piecemeal, but it seems that ancient humans acquired them wholesale in an already adapted form. And as humans spread out across the planet they took these handy gene variants with them. In populations that settled in cold regions (like the ancestral Inuits), the gene variants were favored by natural selection and rose to high frequency. In populations inhabiting warmer climes, the gene variants remained rare.

With improvements in DNA technology and better techniques for recovering ancient DNA, we are discovering more genes in modern humans that came to us from our extinct relatives. The percent of human DNA that comes from ancient interbreeding events varies population by population: some modern human genomes contain up to 5% Denisovan DNA. And the gene versions contained in these bits of borrowed DNA do a variety of things. Some seem to be deleterious for us and were selected against, but others (like the Inuit fat-related genes) seem to have been helpful and allowed humans to thrive in the diverse environments we occupy today.

Read more about it

Primary literature:

  • Racimo, F., Gokhman, D., Fumagalli, M., Ko, A., Hansen, T., Moltke, I., ... Nielsen, R. (2016). Archair adaptive introgression in TBX15/WARS2. Molecular Biology and Evolution. DOI 10.1093 read it
  • Sankararaman, S., Mallick, S., Patterson, N., and Reich, D. (2016). The combined landscape of Denisovan and Neanderthal ancestry in present-day humans. Current Biology. 26: 1241-1247. read it
News articles:

Understanding Evolution resources:

Discussion and extension questions

  1. Review some background information on natural selection. Explain how a cold tolerance gene variant would spread through an early human population living in the Arctic.  Make sure to include the concepts of variation, selection, and inheritance in your explanation.
  2. In your own words, describe the difference between a gene variant that arises by mutation and one that arises by interbreeding.
  3. What effect does each process (mutation vs interbreeding) have on the level of genetic variation in the population?  Are both processes essentially random in terms of which genetic variants are introduced to the population? Explain your answers.
  4. Review the biological species concept. Explain whether humans, Neanderthals, and Denisovans should be considered the same or different species according to this definition and why.
  5. Advanced: Review several other species concepts. For each concept, explain whether humans, Neanderthals, and Denisovans should be considered the same or different species and why.
  6. Advanced: Research another human trait shown on the map in the article above, and write a short paragraph explaining what the trait is, what population it is present in, what its genetic basis is, and what environmental factors seem to have favored that trait.
Related lessons and teaching resources

  • Teach about the spread of mutations in human populations: In this case study from DNA to Darwin, college students investigate the origin and action of mutations that are thought to have arisen in human populations in response to selection pressure from malaria.
  • Teach about physiological adaptations in humans: In Adaptation to Altitude, a set of sequenced lessons from the Smithsonian, high school and college students learn how to devise an experiment to test the difference between acclimation and adaptation; investigate how scientific arguments show support for natural selection in Tibetans; design an investigation using a simulation based on the Hardy-Weinberg principle to explore mechanisms of evolution; and devise a test for whether other groups of people have adapted to living at high altitudes.
  • Teach about our relatedness to Neanderthals: In this online activity for grades 9-12, students compare the number of mutations in the mitochondrial genomes of Neanderthals and humans to determine ancestry and relatedness.


  • The 1000 Genomes Project Consortium. (2015). A global reference for human genetic variation. Nature. 526: 68-74.
  • Fumagalli, M., Moltke, I., Grarup, N., Racimo, F., Bjerregaard, P., Jørgensen, M., ... Nielsen, R. (2015). Greenlandic Inuit show genetic signatures of diet and climate adaptation. Science. 349: 1343-1347.
  • Pennisi, E. (2013). More genomes from Denisova Cave show mixing of early human groups. Science. 340: 799.
  • Racimo, F., Gokhman, D., Fumagalli, M., Ko, A., Hansen, T., Moltke, I., ... Nielsen, R. (2016). Archair adaptive introgression in TBX15/WARS2. Molecular Biology and Evolution. DOI 10.1093
  • Sankararaman, S., Mallick, S., Patterson, N., and Reich, D. (2016). The combined landscape of Denisovan and Neanderthal ancestry in present-day humans. Current Biology. 26: 1241-1247.
  • Tishkoff, S. (2015). Strength in small numbers. Science. 349: 1282-1283.