‘Ghost’ of mysterious hominin found in West African genomes

Ancestors of modern West Africans interbred with a yet-undiscovered species of archaic human, similar to how ancient Europeans mated with Neanderthals, researchers report.

Credit: Zacarias Pereira da Mata/Shutterstock

Their work helps inform how archaic hominins added to the genetic variation of present-day Africans, which has been poorly understood, in part because of the sparse fossil record in Africa and the difficulty of obtaining ancient DNA.

The authors’ computer modelling technique overcomes these challenges, enabling the discovery of genetic contributions from archaic hominins when fossils or DNA are lacking. Well-established research shows that sequences of Neanderthal DNA are found in modern European populations, and Denisovan DNA appears in Oceanian populations.

Demography relating known and proposed archaic lineages to modern human populations. (A) Basic demographic model
with CSFS fit. W Afr, West Africans; Eur, European; N, Neanderthal; D, Denisovan; UA, unknown archaic [see (18)].
Below, we show the CSFS in the West African YRI when restricting to SNPs where a randomly sampled allele from the
high-coverage Vindija Neanderthal was observed to be derived [Neanderthal (data)], as well as where a randomly
sampled allele from the high-coverage Denisovan genome was observed to be derived [Denisovan (data)]. We also
show the CSFS under the proposed model [Neanderthal (model) and Denisova (model)]. Migration between Europe
 and West Africa introduces an excess of low-frequency variants but does not capture the decrease in intermediate
frequency variants and increase in high-frequency variants. (B) Newly proposed model involving introgression
into the modern human ancestor from an unknown hominin that separated from the human ancestor before
 the split of modern humans and the ancestors of Neanderthals and Denisovans. Below, we show
the CSFS fit from the proposed model, which captures the U-shape observed in the data
[Credit: Durvasula et al. 2020]

These segments arrived in modern humans through introgression, the process by which members of two populations mate, and the resulting hybrid individuals then breed with members of the parent populations. Recent studies have shown that, though modern West Africans do not have Neanderthal or Denisovan ancestry, there may have been introgression by other ancient hominins in their past.

Now, by comparing 405 genomes of West Africans with Neanderthal and Denisovan genomes, Arun Durvasula and Sriram Sankararaman found differences that could be best explained by introgression by an unknown hominin whose ancestors split off from the human family tree before Neanderthals.

The authors’ data suggests this introgression may have happened relatively recently, or it may have involved multiple populations of archaic human, hinting at complex and long-lived interactions between anatomically modern humans and various populations of archaic hominins. The authors call for more analysis of modern and ancient African genomes to reveal the nature of this complex history.

The findings were published in Science Advances.

Source: American Association for the Advancement of Science [February 12, 2020]



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