Wednesday, January 22, 2014

Neanderthal DNA Among Modern Humans? How About the Denisovans' DNA ?

In a post two years ago, I noted research conducted at the University of Colorado- Boulder, and UC-Denver, that appeared to scotch two common theories: 1) that the Cro-Magnon exterminated the mentally slower Neanderthals, or 2) that they out -competed for resources by higher reproduction rates.   Based on detailed computer modeling, as well as genetic analysis (from the human genome) the research showed instead that Neanderthals were simply absorbed into modern humans. By "absorbed", I mean that their unique phenotype (see image, e.g. for the skull) became non-existent after extensive interbreeding with the modern humans.

Supporting this was the finding  from a year earlier that 1 to 4 percent of modern human genes, mainly in Eurasian peoples, were "leftovers" from Neanderthals. (Evolutionary biologists consider that residual gene percentage the proof of breeding between the two distinct species before the Neanderthals died out roughly 30,000 years ago)    The computer models had been run over 1,500 generations, based on estimated samples of humans and Neanderthals roving across Europe and Asia. One parameter in the model included the researchers' knowledge that the last ice age forced Neanderthals and modern humans to widen their search for food. The computer models showed interaction, but because there were far more Cro-Magnon (something like a 10:1 ratio) over time than the mating- diluted Neanderthals,  until they emerged as just a minor fraction of our DNA.

Since then the proportions, mating frequencies have been more refined. We now know that 2.5 percent of Neanderthal DNA is found in Asians and Europeans. Two Swiss geneticists - Matthias Currat and Laurent Excoffier - researched how much interbreeding would be needed to end up with so little Neanderthal DNA today and concluded it would require one Neanderthal to mate with a human (Cro-Magnon) to create a child every 30 years.

To have been preserved into modern times, clearly the hybrid offspring would have had to have been accepted - but no one can say how they emerged (in what context) in the first place. It might have been by way of rapes during violent battles between humans and Neanderthals or (more benevolently) when Neanderthals were welcomes into one or more human communities.

A new strategy has been adopted by David Reich, in terms of following the directionality of gene flow.  This is made possible given that human females have two X chromosomes and males have one X and one Y. If Neanderthal females mated with male humans more prominently  Reich notes - they'd provide an X- chromosome to all their children. If Neanderthal males predominated in relations with human females they'd impart  an X chromosome to daughters but none to sons.

Reich hypothesizes that if he were to find an unusually low amount of Neanderthal DNA on the X chromosome, say compared to the other chromosomes, it would be a prime clue that Neanderthal males impregnated human females. Conversely, a high ratio would point the other way, i.e. to Neanderthal great-great grandmothers.

Readers may also recall that roughly a year ago, another specimen hominid was unearthed, packed with DNA (which was then sequenced) and found to be not quite human and not quite Neanderthal.  Geneticists concluded the DNA belonged to yet another hominid group hitherto unknown to science and they dubbed it "Denisovan".  Reich and colleagues applied their same methods (as they did to Neanderthal DNA) to the newcomer genome and discovered the genes were closest to Neanderthals  - but the genome also included many mutations not found in either humans or Neanderthals.

Evidently, Denisovans had diverged from the ancestors of Neanderthals somewhat more recently than the split between Neanderthals and modern humans.   Knowing this, Reich and colleagues looked carefully for Denisovan DNA in the genomes of modern humans. They found it in genomes of two populations, one from New Guinea and another from the nearby island of Bougainville. Reich et al found that at least 5 percent of their DNA came from the Denisovans.

By contrast, Reich et al could not find any trace of Denisovan DNA in Africans, or Europeans or mainland Asians.  They did, however, find vestiges in the genomes of Australian Aborigines and in a people known as the Mamanwa in the Philippines.

The picture that's now emerged is that by the time Neanderthals and Denisovans encountered modern humans their genes had been evolving separately for hundreds of thousands of years.  Despite that, it's possible their DNA is still influencing the health of billions today.  Reich, however, is not ready to take a firm stand because the draft genomes of both Denisovans and Neanderthals still have too many gaps and errors to allow for anything more than conjecture.

More research is in the works, including experiments. As Reich puts it, we can actually perform an experiment to decide, say, whether people with a particular chunk of Neanderthal DNA are faster runners than those without it. Just parse the genetic profiles of different people beforehand, turn 'em loose, then draw conclusions after the race. In the same way experiments can be done to determine, say, whether people with a particular chunk of Denisovan DNA are better at logic puzzles .....or more likely to be atheists.

Stay tuned!

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