When the first Neanderthal genome was sequenced, using DNA collected from ancient bones, it was accompanied by the discovery that modern humans in Asia, Europe and the Americas inherited about 2% of their DNA from Neanderthals - proving that humans moderns and Neanderthals had interbred after modern humans left Africa. Therefore, it was thought that Africans would be the only ones without Neanderthal ancestry.
In a paper published in the journal Cell, a team of Princeton researchers detailed a new computational method for detecting Neanderthal ancestry in the human genome. Their method, called IBDmix, allowed them for the first time to search for Neanderthal ancestry in African and non-African populations. The project was led by Joshua Akey, a professor at Princeton's Lewis-Sigler Institute for Integrative Genomics (LSI).
This is the first time we can detect the real sign of Neanderthal ancestry in Africans said co-author Lu Chen, a postdoctoral research associate at LSI. And surprisingly it showed a higher level than we previously thought he said.
The method the Princeton researchers developed, IBDmix, takes its name from the genetic principle identity by descent (IBD), in which a section of DNA in two individuals is identical because those individuals once shared a common ancestor. The length of the IBD segment depends on the age of those individuals who shared a common ancestor. For example, siblings share long segments of IBD because the ancestor they share (a parent) is only one generation younger. On the other hand, fourth cousins share shorter IBD segments because their common ancestor (a third great grandparent) is several generations apart.
The Princeton team took advantage of the IBD principle to identify Neanderthal DNA in the human genome, distinguishing sequences that resemble Neanderthals because we once shared a common ancestor in the very distant past (~500,000 years ago). , of which they are similar because we crossed paths in the most recent present (~50,000 years ago). Previous methods were based on reference populations to help distinguish shared ancestry from recent interbreeding, generally African populations that were thought to carry little or no Neanderthal DNA.
However, this dependency could bias Neanderthal ancestry estimates depending on which reference population was used. The Princeton researchers called IBDmix an unreferenced method because it does not use an African reference population. Instead, IBDmix uses features of the Neanderthal sequence itself, such as the frequency of mutations or the length of IBD segments, to distinguish shared ancestry from recent interbreeding. Thus, the researchers were able to identify Neanderthal ancestry in Africans for the first time and make new estimates of Neanderthal ancestry in non-Africans, showing that Europeans and Asians had more equal levels than previously described.
Kelley Harris, a population geneticist at the University of Washington who was not involved in the study, noted that the new estimates of Neanderthal ancestry using IBDmix highlight the technical problem with methods based on reference panels. We may need to go back through a bunch of results from the published literature and assess whether the same glitch has been throwing off our understanding of gene flow in other species her, she said.
In addition to identifying Neanderthal ancestry in African populations, the researchers described two insights into the origin of Neanderthal sequences. First, they determined that Neanderthal ancestry in Africans was not due to an independent interbreeding event between Neanderthals and African populations. Based on the characteristics of the data, the research team concluded that the migrations of ancient Europeans into Africa introduced Neanderthal ancestry into African populations.
Second, by comparing data from simulations of human history with data from real people, the researchers determined that some of the Neanderthal ancestry detected in Africans was actually due to human DNA introduced into the Neanderthal genome. The authors stressed that this human-to-Neanderthal gene flow involved a group of humans that dispersed early out of Africa, which occurred at least 100,000 years ago, before the out-of-Africa migration responsible for modern human colonization of Europe and Asia. and before the interbreeding event that introduced Neanderthal DNA to modern humans. The finding reaffirmed that hybridization between humans and closely related species was a recurring part of our evolutionary history.
While the Princeton researchers acknowledged the limited number of African populations they were able to analyze, they hope their new method and findings will encourage further study of Neanderthal ancestry across Africa and in other populations. As for the overall importance of the research, Chen said:This shows that remnants of Neanderthal genomes survive in every modern human population studied to date .
Fonts
Princeton University / Identifying and Interpreting Apparent Neanderthal Ancestry in African Individuals , by Lu Chen, Aaron B. Wolf, Wenqing Fu, Liming Li and Joshua M. Akey, appears in the Feb. 20 issue of Cell, with an advance online publication on Jan. 30 (Chen et al., 2020, Cell 180 , 1–11, DOI:10.1016/j.cell.2020.01.012).