The genetics of ancient Africa and a mysterious human population

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In a hurry? Here’s what you need to know:

• Homo sapiens first appeared nearly 200,000 years ago in Africa

• At that time, we weren’t the only humans around

• Other human groups—like Neanderthals—may have assimilated with anatomically modern humans outside of Africa, and it’s likely that other archaic humans did the same within Africa

• Research into the DNA of modern African populations shows signs of an unknown “ghost” human group that left a genetic legacy in modern African genomes

In 1977, two phonographic records were sent hurtling into space, carrying with them the sounds of life on Earth. The idea is that any life existing beyond our planet will one day hear the recordings and learn about us—or at least be inspired to find out who we are. But who we are is a complex matter. There was a time when we thought that modern humans were the sole survivors in a prehistoric “war of worlds” which brought Neanderthals, Homo sapiens, and other human groups together in conflict. Recent genetic findings cast significant doubt on this story and instead offer a new narrative—one that starts in the heart of Africa and involves a human population that’s clouded in mystery. This is the story of how modern humans came to be.

Africa is currently home to more than 1.2 billion people and is the world’s most linguistically and genetically diverse continent. Such a melding of human cultures is a relic of Africa’s rich past, which includes the birth of our species approximately 200,000 years ago [1,2]. Then, as now, Africa was a melting pot of various human populations—the only difference being that back then, it was different species of humans that were coming together [1-6].

So far, we know next to nothing about this “ghost” group of humans.

Homo sapiens—anatomically modern humans—are within the group of primates that collectively form the genus Homo, which comprises humans past and present. This may sound strange because the only humans alive now are Homo sapiens, but throughout time there have been multiple different human species including Homo neanderthalensis, Homo erectus, Homo heidelbergensis, Homo helmei, Homo naledi, and others that were spread out across the African and Eurasian continents [1-3, 7-9].

Scientists used to believe that we left Africa, battled with the inferior Neanderthals, and ultimately came out on top as the only humans remaining. Genetic research has shown us differently by revealing the presence of Neanderthal DNA in modern human populations, suggesting that Neanderthals may have just been assimilated by Homo sapiens. This joining of different human populations likely took place sometime within the past 30,000-80,000 years, which means anatomically modern humans had coexisted with Neanderthals for a relatively small amount of time before they began to assimilate9. This is important because members of Homo sapiens were coexisting with other human groups for at least 100,000 years in the African continent before this, and yet there has been no evidence of a significant genetic legacy from these other archaic humans within Africa. Until a few years ago, that is.

Mosaic evolution in Africa

For hundreds of millenia before the rise of anatomically modern humans, various human groups had been evolving in the African continent. Fossil records show us that some genetically determined features associated with modern humans (large skulls, pelvic structure, finger length, and so on) were evolving in different human groups.

Like a genetic mosaic, these features eventually coalesced and formed what we know as anatomically modern man. In the process, other species of humans living in Africa were still there and may have contributed to the evolving genetic pool [4,5,14].

Research into ancient human populations has shown that there were likely no Neanderthal populations that entered Africa and left a lasting genetic mark—meaning that people from the African diaspora are less likely to have Neanderthal DNA relative to non-African populations [1,5,6,9]. However, genetic studies have found signs of a mysterious human group that coexisted with early Homo sapiens in Africa and left a genetic signature that’s persisted in the DNA of modern Africans. So far, we know next to nothing about this “ghost” population of humans. What we do know is that one mysterious human group may have lived in central Africa. Like in the case of Neanderthal DNA in non-Africans, there is some evidence that this archaic human DNA may have provided some advantage (such as a stronger immune system) to anatomically modern humans. Current research indicates that between 2-7% of the DNA in some modern African people may come from this unknown archaic human group [10-13].

Part of the reason we know very little about the genetics of archaic humans in Africa has to do with the preservation of DNA. In the extreme climates of Africa, DNA is more likely to degrade and break down within ancient human remains which makes it difficult for researchers to extract DNA from them [6,10,11]. Another complicating factor is that the bulk of genetic research has been done using DNA from people of European descent—a practice which limits our understanding of genetics and ancestry in other populations. Efforts are currently being made to increase diversity in genetic research that will hopefully shed further light on African prehistory. As technology improves and genetic studies expand to include more representative genomes, research will be focusing on identifying these mysterious human figures and better understanding how their DNA may be influencing life today. Learning more about human history and genetics within Africa is more than an interesting science endeavor—it brings us closer to understanding who we are as humans.

References

1. Nielsen, Rasmus et al. “Tracing the Peopling of the World through Genomics.” Nature 541.7637 (2017): 302–310. PMC. Web. 14 July 2018.

2. Stinger, Chris. “The origin and evolution of Homo sapiens” Philosophical Transactions of the Royal Society B 371.1698 (2016): 2015023. PMC. Web. 7 August 2018.

3. Campbell, Michael C. et al “The peopling of the African continent and the diaspora into the new world” Current Opinions in Genetics and Development 29 (2014): 120–132. PMC. Web. 7 August 2018.

4. Campbell, Michael C. et al “AFRICAN GENETIC DIVERSITY: Implications for Human Demographic History, Modern Human Origins, and Complex Disease Mapping” Annual Reviews of Genomics and Human Genetics (2008), 9: 403–433. PMC. Web. 7 August 2018.

5. Skoglund, Pontus. et al “Reconstructing Prehistoric African Population Structure.” Cell (2017), 171(1):59-71. Web. 7 August 2018.

6. Wolf, Aaron B. et al “Outstanding questions in the study of archaic hominin admixture” PLoS Genetics 14.5 (2008): e1007349. PMC. Web. 7 August 2018.

7. Berger, Lee. et al “Homo naledi and Pleistocene hominin evolution in subequatorial Africa” eLife, 6 (2017): e24234. PMC. Web. 7 August 2018.

8. Foley, Robert A. et al “Homo naledi and Pleistocene hominin evolution in subequatorial Africa” Philosophical Transactions of the Royal Society B (2016), 371(1698): 20150229. PMC. Web. 7 August 2018.

9. Sankararaman, Sriram et al. “The Date of Interbreeding between Neandertals and Modern Humans.” Ed. Joshua M. Akey. PLoS Genetics 8.10 (2012): e1002947. PMC. Web. 14 July 2018.

10. Hammer, Michael F. et al “Genetic evidence for archaic admixture in Africa” Proceedings of the National Academies of Science. USA (2011): 15123–15128. PMC. Web. 7 August 2018.

11. Durvasula, Arun and Sankararaman, Sriram “Recovering signals of ghost archaic admixture in the genomes of present-day Africans” Cold Spring Harbor Laboratory (2018): doi: https://doi.org/10.1101/285734. BioRxiv. Web. 7 August 2018.

12. Hsieh, PingHsun. et al “Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies” Genome Research 26.3 (2016): 291–300. PMC. Web. 7 August 2018.

13. Xu, Duo. et al “Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation” Molecular Biology and Evolution 34.10 (2017): 2704–2715. PMC. Web. 7 August 2018.

14. Scerri, Eleanor M.L. et al “Did Our Species Evolve in Subdivided Populations across Africa, and Why Does It Matter?” Trends in Ecology & evolution (2018). Web. 7 August 2018.