View Full Version : Neanderthal introgression reintroduced ancestral alleles

25-10-17, 17:16

"Science News (https://www.sciencenews.org/article/mating-neandertals-reintroduced-lost-dna-modern-humans) reports that evolutionary genomicist Tony Capra of Vanderbilt University and his team analyzed the genomes of more than 20,000 people contained in a databank of electronic health records and the 1000 Genomes Project. They found that when a small number of modern humans left Africa some 100,000 years ago, they lost some genes inherited from ancestors shared with Neanderthals. But when Europeans and Eurasians later mixed with Neanderthals, they regained some of these old genes, which can be found in modern African populations, in addition to Neanderthal genes. Capra says Europeans have more than 47,000 of these reintroduced ancestral alleles, and East Asians have more than 56,000 of them."


"Anatomically modern humans (AMHs) interbred with Neanderthals approximately 50,000 years ago, and as a result, ~1–3% of the genomes of modern Eurasians are derived from of DNA introgressed from Neanderthals. Recent studies have focused on identifying and testing the effects of Neanderthal-derived alleles in AMHs, and these introgressed haplotypes have been shown to influence diverse phenotypes in AMHs including risk for many immune, skin, and neuropsychiatric diseases. However, recent analysis of an introgressed Neanderthal haplotype at the OAS locus revealed that the variant responsible for changes in gene expression is a reintroduced ancestral human allele, rather than a Neanderthal-derived allele.

Motivated by this observation of the reintroduction of a functional ancestral allele that was lost in Eurasian populations in the out of Africa bottleneck, we performed a genome-wide search for other lost alleles on introgressed Neanderthal haplotypes in 1000 Genomes Phase 3 European (EUR), East Asian (EAS), and South Asian (SAS) individuals. In each super-population, we identified between ~47,000 and ~57,000 ancestral introgressed alleles. Consistent with the greater levels of Neanderthal DNA in Asian populations, these groups had more reintroduced ancestral alleles. Additionally, we found that nearly 66% of the reintroduced ancestral variants identified in EUR individuals are polymorphic in at least one non-admixed African sub-population (Yoruba, Esan, or Mende). These variants represent an extreme scenario where the ancestral allele was completely lost either before or during the out of Africa transition, and reintroduced by Neanderthal introgression.

Many introgressed haplotypes carry more lost ancestral alleles than Neanderthal-derived alleles. Thus, we hypothesized that these alleles might influence phenotypes in modern Eurasian populations. To explore the potential function of these reintroduced ancestral alleles, we performed a phenome-wide association analysis on the introgressed alleles over more than 20,000 European-ancestry individuals with electronic health record data in Vanderbilt’s BioVU databank. We identified and replicated several novel associations with clinical phenotypes that are likely driven by these reintroduced alleles."

This is the link to the Science article:

"Capra and others have evidence that Neandertal versions of genes make humans more prone to some diseases (https://www.sciencenews.org/article/neandertal-dna-may-raise-risk-some-modern-human-diseases) (SN: 3/5/16, p. 18). Of the thousands of ancestral variants reintroduced into modern humans, only 41 have been linked in genetic studies to diseases, such as skin conditions and neurological and psychiatric disorders, he said. The researchers can’t tell for sure whether the effect is from the ancestral variant or neighboring Neandertal DNA. Capra and Vanderbilt colleague Corinne Simonti’s analyses indicate that the Neandertal DNA is more likely to blame. Many of the ancestral alleles are still present in modern-day Africans, Capra said, “so they’re unlikely to be very, very bad.”

26-10-17, 19:47
Neanderthal genomes do match closes to modern Africans, I think.

26-10-17, 19:58
Neanderthal genomes do match closes to modern Africans, I think.

Wasn't it the exact opposite of that?

27-10-17, 00:21
Wasn't it the exact opposite of that?

Yes and no. I was thinking of the DNA.land results, but I know I've seen other examples where calculators choose African populations for Neanderthals

DNA Land ancestry report for Altai Neanderthal:

As we can see DNA Land chose 2/3 Bushman + 1/3 Pygmy as a surrogate for archaic Homo:



Denisova Hominin is similar, but 1/2 Bushman + 1/2 Pygmy:


They diverged from HSS some time ago and so they do have distinct Alleles, but they still represent an Archaic genotype, which apparently conserved some Alelles from the Common Ancestor of HSS and Neanderthals. This may explain the affinity to African populations that some calculators show, or it may not.