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Not Neandertal: Genome from fossil fingers a new, recently extinct human

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fossil human tooth from siberian cave might be from DenisovansWhat can be gleaned from a fragment of a 30,000- to 50,000-year-old finger? With highly sensitive genetic sequencing technology, researchers now claim to have spotted a new form of extinct humans that were neither Neandertals nor modern humans.

Meet the Denisovans, whose existence was deduced not from a skull or piecemeal skeleton, but mostly from DNA recovered from a solitary distal manual phalanx.

Named for the Siberian cave in which the finger bone (likely from a juvenile female) was discovered in 2008, the Denisovans seem to be closer genetically to Neandertals than to modern humans (having likely split off from the Neandertal gene pool some 640,000 years ago and from the Africa-based group that led to modern humans some 804,000 years ago; by contrast humans and Neandertals are proposed to have split 270,000 to 440,000 years ago). The findings were published in the December 23 issue of Nature (Scientific American is part of Nature Publishing Group).

"The fragments of ancient DNA illuminate our understanding of human origins and, like the shadows in Plato’s proverbial cave, give us the broad outlines of ancient human migrations," Carlos Bustamante and Brenna Henn, both of the Stanford University School of Medicine’s Department of Genetics, wrote in an essay published in the same issue of Nature. The researchers behind the new study have not yet proposed a formal Latin name for the Denisovans, but they suggest that the group might have been a widespread eastern analogue to Europe’s Neandertals during the Late Pleistocene.

"The story now gets a bit more complicated," Richard Green, of the University of California, Santa Cruz, and coauthor of the study, said in a prepared statement. "Instead of the clean story we used to have of modern humans migrating out of Africa and replacing Neandertals, we now see these very intertwined story lines with more players and more interactions than we knew of before."

More clues should emerge as more samples are unearthed—and as genetic sequencing technology continues to improve. Eight years before the finger bone was found, a well-preserved, curious-looking tooth was discovered in the same cave. The researchers proposed that the tooth (likely the second or third upper left molar) also came from a Denisovan, though likely from a different individual (a young adult) than the finger bone. The molar is unusually large and more closely resembles the teeth of earlier hominins than it does dentition from Neandertals or modern humans.

Although the tooth did not retain as much endogenous genetic information as the finger bone, it still provided traces of DNA. "The tooth is just amazing," Bence Viola, of the Max Planck Institute for Evolutionary Anthropology and coauthor of the study, said in a prepared statement. "It allows us to connect the morphological and genetic information."

Genetic distinctions
A scan of the mitochondrial DNA from the finger bone (published this March) had indicated that it might have come from a third hominin group, and the new nuclear genome, sequenced to 1.9-fold coverage, provides further support for this hypothesis. "It is almost miraculous how well-preserved the DNA is," Green said. Although northern latitudes have provided some of the best genetic samples, this finger was found in the southern edge of Siberia and contained far more endogenous DNA than expected given its less-frozen location.

The timing of the find was also advantageous. "It was fortuitous that this discovery came quickly on the heels of the Neanderthal genome," Green said.

The Neandertal genome, published in May, revealed that these early humans contributed some 1 to 4 percent of the genetic material found in most non-Africans’ genomes—including those of geneticist George Church and heavy metal rocker Ozzy Osbourne.

The Denisovans, on the other hand, did not seem to mix much with the modern human Eurasian gene pool. However, genetic variants similar to those in the Denisovan genome crop up unexpectedly in the genomes of people in Papua New Guinea, suggesting some mixing with Melanesian ancestors. Denisovan genes might compose as much as 4 to 6 percent of some Melanesian’s genomes, the researchers noted. Such a surprising large north-south connection might indicate that the Denisovans had a large range in the east, as modern humans are thought to have lived on those islands in Oceania for some 45,000 years.

"In combination with the Neandertal genome sequence, the Denisovan genome suggests a complex picture of genetic interactions between our ancestors and different ancient hominin groups," Svante Pääbo, of the Max Planck Institute for Evolutionary Anthropology and coauthor on this and several related papers, said in a prepared statement.

But why this whole group of humans had not previously been detected raises questions. "It could be that other samples are misclassified," Green said, noting that the finger bone had previously been thought to have come from a modern human. And the unclear origins of the small "hobbit" remains (Homo floresiensis) found on the Indonesian island of Flores and dated to about 17,000 years old suggest there might be more recently extinct human relatives yet to be found.

"This study fills in some of the details, but we would like to know much more about the Denisovans and their interactions with human populations," Green said. "And you have to wonder if there were other populations that remain to be discovered. Is there a fourth player in this story?"

Image of tooth courtesy of David Reich et al.,
Nature





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  1. 1. JamesDavis 10:01 am 12/23/2010

    I think scientists are beginning to realize that modern human is not the only intelligent bipedal who has ever lived on this planet and we are certainly not the most intelligent species who has ever lived here. They have found pieces of stone, thousands of years old, with cuttings in them that are so complex our scientists can’t even figure out how they did it. So, keep looking and maybe in this new Earth cycle coming up we will figure out how many intelligent bipedals have lived on this planet and why they are no longer here mingling with us modern humans.

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  2. 2. Bill Case 10:46 am 12/23/2010

    Just a speculative question. All cultures seem to have some version of "little people" or "fairies" or "trolls" etc. I wonder if this is a folk memory of other smaller hominids that co-existed with early humans at some time?

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  3. 3. Bill Case 10:55 am 12/23/2010

    Forgot to tick the email response.

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  4. 4. Lotusface 12:02 pm 12/23/2010

    What if it is the same species, but we have lost our way. What if our technological "advancements" have actually been the decline of humanity all this time instead of the rise? What if our true destiny is to be at one with nature, the masters of balance and harmony and able to be present without destroying our surroundings? What if our seeking of convenience has doomed nature itself? I feel that we do have the potential to act with nature as opposed to against it, but society and individual greed are in the drivers seat now.

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  5. 5. Lotusface 12:40 pm 12/23/2010

    What I want to know is what was going on approximately 10,000 to 50,000 years ago, who was building the various henges throughout the world, carnac in france, the mortarless "melted" stone work in South America and all of the other ancient monuments built referencing the constellations as they passed the horizon approximately 10,000 years ago(due to the 26,000 year migration of the Earths axis, the constellations slowly drift across the horizon; and this is measurable)

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  6. 6. Vasilie 3:16 pm 12/23/2010

    It would be interesting to know what land masses existed, their relative conformation, long.and lat. displacement, magnetic alignments, and what if any continental subductions have occured in the intervening ages when said hominids existed. One is tempted to overlook these various possible effects and assume that the earth’s topography was as it is today. Also, were there warmer climatic conditions to have encouraged the existence or movement to so called ‘ northern climes ‘.

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  7. 7. jtdwyer 3:39 pm 12/23/2010

    It seems that ‘we’ were at least refining our spoken language and developing our ability to symbolically represent both physical and abstract information for the purpose of communication and reasoning. Pretty important stuff…

    Another question: if the population of modern humans was diminished from about 1M to maybe less than 10,000 by the effects of the Toba supervolcano eruption in Indonesia around 70k years ago, how could the human Hobbit have survived anywhere in that neighborhood, to be found on the Indonesian island of Flores up to 17,000 years ago?

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  8. 8. basudeba 7:04 pm 12/23/2010

    The finding is not surprising. We have a copy of one ancient book with us which describes life forms over the ages. According to the book, the present human form came into existence around 3100 BC. Before that the life forms changed in three phases around 843,000 BC, 2.14 million BC. The different life forms described in the book in detail resemble the anthropological findings.

    According to the co-lateral texts, the development of life forms is based on the development of support limbs. We may call these as "feet". The first life forms that originated were having hairy extensions, which can be described as innumerable "feet". Gradually the number of "feet" were reduced to 100, 16, 8, 6, 4 and finally 2. In this sequence, monkeys evolved immediately before human beings, as they can walk with two feet, though not as normally as human beings. That is the correct interpretation of evolution of human form and not the Darwinian interpretation, which is still a postulate.

    basudeba.

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  9. 9. elisevil 1:22 am 12/24/2010

    As far as the ubiquity of little people in human mythologies, there is also the vast variety of drugs humans have used for various reasons.

    I have just heard the likely basis for elves and little reindeer (Norway?) in our Santa Claus stories. Northern shamen depended on reindeer to eat, metabolize, and urinate an important mind changing drug that would kill humans if eaten straight. This substance causes the human mind to see other beings as about 1/3rd size and give the sense of flying! And I am sure they travelled by sled throughout their very long and snowy winters.

    The reality of other related homo species is becoming clear, but there are many ways to develop mythology other than simply through clear-headed reality.

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  10. 10. Quinn the Eskimo 1:06 pm 12/24/2010

    How do we *know* these "little" people are extinct? Really?

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  11. 11. gbcjjj 6:49 am 12/26/2010

    All the current history of the man on earth begins
    in Africa, but this is only the current history-based in remains preserved in an atmosphere and a very
    favorable environment to keep the fossils. Nothing stops the man may have originated in another region of the world, but we can not detect it by not preserving
    fossils by climatic and environmental conditions
    inappropriated.Our historical knowledge is fragmented and circumstantial, but isn’t necessarily the true fact, only an attempt to explain to organize our thinking.

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  12. 12. bucketofsquid 3:17 pm 12/27/2010

    So which book is this? It would be nice to actually confirm what you say as based on reality and not the wanderings of a fanciful imagination.

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  13. 13. bucketofsquid 3:23 pm 12/27/2010

    If you take the time to trace back the word roots of most of these "mythical" people such as elves you will find that they were actual ethnic groups and the names for themselves evolved into descriptions of mythical creatures. For example the Sidhe. It just means a person of a specific set of Celtic tribes. This gave rise to the stories of the lords of Underhill and later to the Banshee. Banshee originally translated to "woman of the Celts" in English. If we remember that most people don’t view other ethnic groups as truely human this is easily understandable. In the modern era we are starting to change this but it is still a rather common mind set. For specific examples look up Rawandan, Burundian, Cambodian, Serbian and other recent genocides.

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  14. 14. bucketofsquid 3:24 pm 12/27/2010

    We know because they are delicious and taste just like chicken.

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  15. 15. Quinn the Eskimo 12:53 am 12/29/2010

    Barbecue or breaded? Sweet and Sour or Garlic Butter?

    See? So many questions. How do we actually know? I looked in the frozen section, next to chicken, nada. Still looking.

    Tho, I Googled Little People on a stick recipies! Got some good ideas!

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  16. 16. mikesmtn 7:32 pm 12/30/2010

    This is so fascinating. I really believe through time there was so much more interaction between migrating groups of early humans than what we think we know. I’ve heard scientists say that populations were so low that contacts were unlikely. I think that’s narrow-minded. People find each other, no matter how vast the landscape. By the way I’m not at all surprised at the connection between these northern groups and the populations of the SW Pacific Islands. Cool stuff.

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