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Guide to Patagonia's Monsters & Mysterious beings

I have written a book on this intriguing subject which has just been published.
In this blog I will post excerpts and other interesting texts on this fascinating subject.

Austin Whittall


Wednesday, November 18, 2015

Denisovans. More information on their genetics


A paper by S. Sawyer et al., Nuclear and mitochondrial DNA sequences from two Denisovan individuals, PNAS, doi: 10.1073/pnas.1519905112 Published Nov. 16, 2015 has sequenced the nuclear and mtDNA of two Denisovans. Their findings are the following:


Abstract
Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.


Denisovan teeth
Take note of how large the Denisovan teeth are. From the paper

The paper notes that "Both Denisova 8 and Denisova 4 are very large compared with Neandertal and early modern human molars, and Denisova 8 is even larger than Denisova 4. Only two Late Pleistocene third molars are comparable in size: those of the inferred early Upper Paleolithic modern human Oase 2 in Romania and those of ObiRakhmat 1 in Uzbekistan"


The teeth though primitive looking also seem to differ from H. erectus teeth too. Which is quite interesting.


Denisova 8 is about 60,000 years older than Denisova 3 and Denisova 4 meaning that they are 110,000 years old. This is a long period of time in a same location.


The paper says the following about this long occupation: ", suggests Denisovans were present in the area at least twice, and possibly over a long time, perhaps interrupted by Neandertal occupation or occupations. Denisovans may therefore have been present in southern Siberia over an extended period. Alternatively, they may have been present in neighboring regions, from where they may have periodically extended their range to the Altai.".


The paper ends with an open question: " Given that the high-coverage genome from the Denisovan 3 phalanx carries a component derived from an unknown hominin who diverged 1–4 million years ago from the lineage leading to Neandertals, Denisovans, and present-day humans, it is possible that this component differs among the three Denisovan individuals. In particular, it may be that the older Denisovan population living in the cave carried a larger or different such component. It is also possible that the two diverged mtDNA lineages seen in Denisova 8 on the one hand and Denisova 3 and Denisova 4 on the other were both introduced into the Denisovans from this unknown hominin, as has been suggested for the mtDNA of Denisova 3. However, more nuclear DNA sequences from Denisovan specimens of ages similar to Denisova 4 and Denisova 8 are needed to address this question fully.".



Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

4 comments:

  1. Hi Austin, good succinct summary of the paper despite it being behind a paywall!
    I have a quibble however..
    Comparing your precis with that of John Hawks
    (Link: Another Denisovan from Denisova Cave 18 Nov 2015 here: http://johnhawks.net/weblog/reviews/denisova/sawyer-2015-denisova-8.html)

    "We can’t make too much out of the large size of these third molars, because similarly large teeth do occasionally occur among Upper Paleolithic people."
    He then goes on to mention the Oase 2 specimen and a Neandertal from Obi-Rakhmat, Uzbekistan as having similarly large 3rd molars.

    He continues further down:
    "Is it odd that we have large third molars in some individuals in Eastern Europe and Central Asia, including the Denisovans? I think to answer this we will need a larger sample of fossil humans from other places. There is at least one Chinese third molar specimen from Xujiayao that approaches the size of these large teeth. Perhaps the Chinese specimen is a Denisovan, or maybe this is one morphological extreme that is distributed among Late Pleistocene populations.
    The thing is, if there was one piece of morphological evidence I would throw away and pay no attention to above all others, it’s the morphology of the third molar. It is just enormously variable among living humans and living primates. I wouldn’t trust it to tell us about relationships of hominin groups."

    Furthermore in his review of Reich paper of 2010 (Link: http://johnhawks.net/weblog/reviews/neandertals/neandertal_dna/denisova-nuclear-genome-reich-2010.html) he has this to say on Denisova 3, the other, earlier 3rd molar:
    "What is this tooth?
    The paper identifies the tooth as an upper third molar, or possibly as a second molar. What we can say about it is that it’s relatively large. In fact its length and breadth put it within a size range occupied by australopithecines and early Homo, both H. habilis and H. erectus. There are no distinctive morphological characters that would allow it to be assigned to any taxon.
    What the paper doesn’t point out is that there are Upper Paleolithic specimens that equal or exceed this tooth in size. For example, the measured length and breadth of an upper second molar from Oase, Romania, are larger than this specimen, and the third molar (in the crypt) of that specimen is yet larger. There is an Upper Paleolithic-associated molar from Turkey which is also exceedingly large."
    Therefore it seems that the 'interesting' feature of these large 3rd molars is that they are found across a range of hominins widely separated in both time and geographical location.
    What they can't tell us is with which ancestral hominin population(s) this denticular morphology originated in or about the possible population migrations of those earlier hominins at present.
    The archaeological evidence just isn't there yet.. what we really need is a much more complete Denisovan skeleton.
    Finally you end your post quoting the open question from the Sawyer paper regarding the introgression of "unknown hominin" genetic material into the Denisovan genome on one, or possibly two occasions or maybe even from two different unknown hominins.
    Would you care to speculate on what you believe Sawyer et al were hinting at? What are you own opinions on this?
    NeilB

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    Replies
    1. Hi Neil,
      Thank you for your extensive and very interesting post.
      Your point that the size of the 3rd molar is such that it can span any hominin from an australopithecine to an Upper Paleolithic human is correct. I agree with you that we cannot use it to establish if any given remains belong to a specific hominin group.
      As is usually the case, the lack of specimens is the stumbling block: sample size is simply too small.

      Regarding the "unknown hominin" that may have admixed with Denisovans, It is not H. sapiens or Neanderthal. So that does not leave too many options does it?
      If the admixture took place in Asia it could involve either the Homo erectus that lived in Southeast Asia or the Homo Georgicus (Dmanisi) or other yet unknown hominins that evolved from them.
      The findings in China will surely point the way to this hominin.
      I am growing more and more convinced that Homo erectus did not live in Asia for about 1.5 million years and just die out without a trace.
      The point is that the bitter battle between "Out of Africa" vs. Multiregional evolution was for many years tipped in favor of the O.O.A. field. The genetics seem (ed) to support them. But now the picture is looking far more complicated, with Neanderthals in Asia, with their DNA in all humans (even Africans) with Denisovans admixed in Melanesians.... soon we will find H. erectus DNA in the picture.
      Very interesting times await us.
      Austin

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  2. Hi Austin, I believe the 3 wave out of Africa model to be the best fit for the archaeological and genetic data available at present. As I see it the first wave was Homo erectus senso lato as long ago as c. 2Mya as evidenced by the Dmanisi fossils dated to 1.85 Mya followed by a steady spread as far as north west China and perhaps as far Beringia and the Americas.
    Out of Africa 2 about 1Mya to 0.5Mya for the precursor species to H. neanderthalensis as evidenced by the Sima de los Huesos hominids. Lastly, perhaps beginning as early as 130000 ya archaic Homo sapiens as evidenced, for example by the recent report by Wu et al (2015) The earliest unequivocally modern human teeth in southern China (Link: http://www.nature.com/nature/journal/v526/n7575/full/nature15696.html) and continuing into the old OoA period of fully modern Homo sapiens leaving Africa around 60000 ya.
    Having said that I am not, per se, against a multi-regional model of human origins or even Out of America! The current evidence just supports OoA in three waves with repeated introgression of archaic DNA into modern humans i.e. the braided stream idea. I believe if American Archaeologists took a leaf out of China's book and dug some REALLY deep sites then they'd find evidence of humans in America MUCH earlier.
    What is your take on the current evidence? Have you any preferred model on the origins of humanity?
    On a related theme, having read your blog extensively, I know you are a firm proponent of an early peopling of the Americas, care to speculate on the when and by whom?
    NeilB

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  3. Hello Neil,
    I fully agree with you on the multiple waves out of Africa, evidently a first wave spread into Eurasia ca. 2-1.8 Mya, and the Dmanisi remains are proof of it.
    Later these Asians evolved into the Homo erectus and either them or the "first wave" reached America.
    They also moved back into Africa where their remains are also found.
    In Africa they too evolved and the Sima de los Huesos remains - H. Heidelbergensis arose from their migration O.O.A. becoming Neanderthals and Denisovans. Who surely mixed with the extant hominids that evolved from H. erectus in Asia.
    Then modern Humans appeared. And yes, current evidence does support an African origin, but we are very likely the outcome of crossed mixing between contemporary populations of different origins.
    As usual I must say that we must await new findings and new techniques applied to study existing remains. This will shed more light on the matter.
    An early peopling of America with admixture there and even an O.O. America event is very probable too.
    Austin

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