Hybridisation in human evolution

A press release from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, announces the completion of a genome from a third Neanderthal individual and its release to other anthropological researchers. Using a toe bone found in the same Siberian cave as the finger bone used to reconstruct the genome of a Denisovan, the new analysis is by far the most precise obtained from Neanderthal remains. For the first time it is possible to distinguish copies of the genes inherited by the individual from both parents. In that regard its quality is as good or even better than genomes from present-day humans.  Svante Pääbo, lead scientist at the Institute, hopes that the team will now be able to more deeply penetrate aspects of the history of Neanderthals and Denisovans – the Denisovan genome is of a similar quality – and of the genetic divergence of anatomically modern humans from the common ancestors of all three.

The data release coincided with a review of genetic evidence for interbreeding between early Homo sapiens and other species (Hammer, M.F. 2013. Human hybrids. Scientific American, v. 308 (May 2013), p. 52-57). Michael Hammer of the University of Arizona begins by comparing the main hypotheses for the evolution of fully modern humans. The Out-of-Africa model involves modern people of African origin completely replacing all other human species in and outside Africa. Multi-regional evolution posits archaic populations  originally living in and outside Africa being  gradually assimilated by migration and interbreeding that transferred modern traits everywhere yet retained some regionally distinct features of the archaic groups.

1: 1=Homo sapiens 2=Neanderthals 3=Early Homin...

Modern human migration out of and within Africa relative to the domains of coeval archaic humans 1 = modern humans 2 = Neanderthals 3 = other archaic humans (credit: Wikipedia)

The first model clearly has to be modified as evidence accumulates for some degree of hybridisation with archaic groups outside Africa. The second of the two pre-genome ideas seemed to be rendered obsolete by the DNA evidence for significant interbreeding between early immigrants from Africa and Eurasian and Asian populations of earlier archaic migrants – Neanderthals and Denisovans respectively – whereas modern Africans show no sign of recent contact with these archaic groups. However, not all regions of the genome have been examined for signs of more universal hybridisation.

Hammer cites a 2005 study of DNA sequences in a non-functional region of the X chromosome that pointed towards its origin as far back as 1.5 Ma and entry into the modern genome in East Asia from a species of Homo that had entered the region far earlier than Neanderthals or Denisovans (perhaps Homo erectus). There is similar evidence for fertile interbreeding of modern humans with an archaic species in Africa. Together with the evidence for a degree of Neanderthal-modern interbreeding in the Middle East around 80 to 50 ka, some of whose descendants destined to reach Australasia interbred with Denisovans, probably further to the east, such reports clearly indicate a significant role for hybridisation.

As the source of all human species, Africa had the greatest chance of several of them living close-by at any one time and thus of interbreeding. Hammer and colleagues at the University of California, San Francisco report a 2 percent contribution of genetic material in three sub-Saharan modern populations from archaic humans split-off from them around 700 ka and recombined in moderns at about 35 ka. By chance Albert Perry, an African-American who chose to be genetically profiled commercially, found himself the possessor of a never-before recorded DNA variant in his Y chromosome. It was shown to have branched off the modern genetic tree almost 350 ka ago. His overall Y-chromosome DNA match was with men who live in a small area of Cameroon. Further complicating matters is evidence for a small Neanderthal component in the DNA of Maasai people living in East Africa.

Though still unpublished, fossil evidence unearthed in Nigeria and the Democratic Republic of the Congo of humans with cranial characteristics that bear both modern and archaic features. These are not early moderns but date back to about 13 ka. They imply either that there were still archaic humans cohabiting with moderns recently, or regular interbreeding had been going on for millennia further back in time. Hybridisation is emerging as a complicating factor in human evolution, and possibly one of great importance. It may have conferred immunity to pathogens endemic in new territories entered by modern migrants from Africa, and who is to say what other aspects of fitness? The once favoured Replacement model is looking shaky and will be refuted if more evidence emerges of viable hybridisation between various archaic humans and new arrivals from Africa. The African modern genetic pattern may dominate but the ‘old ones’ maintain a genetic foothold, despite their extinction. It always has to be borne in mind that all the modern genetic lines that emerged from Africa since about 100 ka probably did not survive either: those that did may have done so because they combined with significant traces of humans of much greater antiquity and owe their continuity to that legacy.

More on Neanderthals, Denisovans and anatomically modern humans

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