Thursday, 19 May 2022

Evolution News - Tracing Our Cousins the Denisovans

Views of the TNH2-1 specimen.
a. Occlusal, b. inferior, c. mesial, d. distal, e. buccal and f. lingual
Ancient tooth suggests Denisovans ventured far beyond Siberia.

Until recently, the archaic humans, the Denisovans, cousins of the Neanderthals and probably cousins to modern humans, were known only from a few fragments of bone and teeth from a single site - the Denisova Cave in Siberia. One fragment turned out to be from a girl who was the child of a Denisovan father and a Neanderthal mother, showing that the two species co-existed and interbred, at least in Siberia.

Since then, there has been increasing acceptance that, because up to 5% of the genome of many people from South East Asian and Oceania, including Native Australians and people from Papua-New Guinea, is Denisovan DNA, Denisovans probably occupied South East Asia and interbred with modern Homo sapiens as they migrated to and through it.

There was also the intriguing discovery that the genes that help the inhabitants of the Tibetan Plateau live at high altitude were from Denisovans. The initial assumption was that they must have been acquired from people from lower altitudes because Denisovans would probably not have lived on the Tibetan Plateau. This would have meant that the Denisovans must have evolved these genes for a different purpose, possibly related to prolonged physical exertion, and that modern humans exapted them for high altitude survival.

The Xiahe mandible, only represented by its right half, was found in 1980 in Baishiya Karst Cave.
© Dongju Zhang, Lanzhou University
That view was challenged in 2019, when a jawbone, discovered in 1980, proved to be Denisovan on analysis of the proteins extracted from it. Proteins can be reverse engineered to reveal the DNA template that coded for them and that turned out to be Denisovan. The mandible had been discovered in a cave on the Tibetan Plateau, the Baishiya Karst Cave, Xiahe, Gansu, China, showing that Denisovans occupied the site about 160,000 years ago, way before H. sapiens arrived on the scene. Sadly, the paper describing this find, published in Nature lies behind a paywall. In the abstract, the authors say:

The Xiahe specimen provides direct evidence of the Denisovans outside the Altai Mountains and its analysis unique insights into Denisovan mandibular and dental morphology. Our results indicate that archaic hominins occupied the Tibetan Plateau in the Middle Pleistocene epoch and successfully adapted to high-altitude hypoxic environments long before the regional arrival of modern Homo sapiens.

These Denisovan 'high altitude' genes gave the founder population of Han Chinese who migrated to the plateau and interbred with the Denisovans, such an advantage that they would have spread rapidly through the population, especially since one of the effects of altitude sickness that non-carriers of these Denisovan genes experience, is a high proportion of failed pregnancies.

We’ve always assumed that Denisovans were in this part of the world, but we’ve never had the physical evidence. This is one little piece of evidence that they were really there.

Laura Shackelford, Co-author
Palaeoanthropologist
Department of Anthropology
University of Illinois at Urbana-Champaign, Urbana, IL, USA
And now, more detail has been added to the Denisovan story by the discovery of a single tooth, a deciduous tooth of a child - probably a female - in the Tam Ngu Hao 2 (Cobra Cave), a limestone cave in the Annamite Mountains, Laos, dated to 164,000-131,000 years old - a date range which includes the Xiahe specimen’s age. This tooth shows a 'close morphological affinity' with the teeth in the Xiahe jaw, so the researchers are almost certain it is from the same taxon, i.e., that it is Denisovan. If DNA or protein analysis confirm that this is indeed the tooth of a Denisovan child, it will confirm that Denisovans were a widespread and very adaptable species, being present in the tropical forests of Loas in the Middle Pleistocene at the same time they were also present on the high Tibet plateau and the cold northern tundra of Siberia.

It surely can't be much longer before Denisovans are given a respectable binomial scientific name - Homo altai or Homo denisovensis, perhaps?

Copyright: © 2022 The authors.
Published by Springer Nature. Open access. (CC BY 4.0)
The paper describing the Tam Ngu Hao 2 tooth is published, open access, in Nature Communications:
Abstract
The Pleistocene presence of the genus Homo in continental Southeast Asia is primarily evidenced by a sparse stone tool record and rare human remains. Here we report a Middle Pleistocene hominin specimen from Laos, with the discovery of a molar from the Tam Ngu Hao 2 (Cobra Cave) limestone cave in the Annamite Mountains. The age of the fossil-bearing breccia ranges between 164–131 kyr, based on the Bayesian modelling of luminescence dating of the sedimentary matrix from which it was recovered, U-series dating of an overlying flowstone, and U-series–ESR dating of associated faunal teeth. Analyses of the internal structure of the molar in tandem with palaeoproteomic analyses of the enamel indicate that the tooth derives from a young, likely female, Homo individual. The close morphological affinities with the Xiahe specimen from China indicate that they belong to the same taxon and that Tam Ngu Hao 2 most likely represents a Denisovan.

Evidence then of a second archaic hominin in addition to Neanderthals, probably evolving from an earlier migration out of Africa of a common ancestor (probably H. erectus) to both them and H. sapiens, which had not diversified so far as to prevent interbreeding between all three species, although not sufficiently well to justify them being regarded as subspecies or regional variants, judging by the few genes of either that have been retained by modern H. sapiens.

In fact, for much of our shared history, hominins have behaved very much like a ring species, undergoing speciation across a wide geographical range. A snapshot of speciation in progress and entirely inconsistent with the popular Bronze Age origin myth that require a founder couple magically arising out of dirt without ancestry, as though such a thing was even remotely possible. Not a founder couple and not even a founder species, but at least three ancestral species contributing to the modern H. sapiens genome and sharing at least one common ancestor that evolved in Africa, where the genetic evidence shows periods of isolation and partial speciation followed by contact and remixing of the genomes, even before migration up into Eurasia.

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