Posted on 06/03/2010 7:32:55 PM PDT by SeekAndFind
It was 15 months ago that Science carried a story about the completion of a rough draft of the Neandertal genome. Palaeogeneticist Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig was reported as saying "he can't wait to finish crunching the sequence through their computers". It has been quite a long time coming, as it is more than a decade since Paabo first demonstrated it was possible to analyse Neandertal DNA sequences. Earlier reports suggested that Neandertals were sufficiently distinct from humans for them to be classified as a separate species of Homo. The draft genome has more than 3 billion nucleotides collected from three female Neandertals.
"By comparing this composite Neandertal genome with the complete genomes of five living humans from different parts of the world, the researchers found that both Europeans and Asians share 1% to 4% of their nuclear DNA with Neandertals. But Africans do not. This suggests that early modern humans interbred with Neandertals after moderns left Africa, but before they spread into Asia and Europe. The evidence showing interbreeding is "incontrovertible," says paleoanthropologist John Hawks of the University of Wisconsin, Madison, who was not involved in the work. "There's no other way you can explain this"."
Neanderthals once bred with Homo sapiens. (credit PHOTOLIBRARY, source here)
Genetically, then, Neandertals are not altogether extinct. Paabo is quoted as saying: "They live on in some of us". Therefore, the 'Out-of-Africa' model needs revision, as the migrants interbred to some extent with Neandertals and their genetic signatures spread through the migrant populations. According to Rex Dalton in Nature:
"That revelation is likely to revive the debate about whether or not the two groups are separate species, says anthropologist Fred Smith of Illinois State University in Normal, who has studied Neanderthals in Europe. Smith thinks that they are a subspecies of H. sapiens. Now that the genomes can be compared, it will be possible to investigate the genetic roots of some shared features."
This theme is picked up in the pages of New Scientist, and especially noteworthy is the editorial: "Welcome to the human family, Neanderthals". It calls for Neanderthals to be given a warm reception as truly human relatives.
"Svante Paabo, the pioneer of palaeogenetics, equivocated when a reporter asked whether his genome study suggested Neanderthals are the same species as us: "I would more see them as a form of humans that were a bit more different than people are from each other today, but not that much."
Why so shy? Putting aside the vexing question of what defines a species - which flummoxed even Linnaeus and Darwin - it is hard to see why Neanderthals should now be considered as anything other than Homo sapiens. We know that Neanderthals bred with our ancestors and produced fertile offspring, which is one hallmark of a species. And there is plenty more evidence to support giving them the status of Homo sapiens neanderthalis. Neanderthals shared a common ancestor with modern humans around 500,000 years ago. Its descendants went their separate ways as the Neanderthals adapted to colder climes, but then, at least 50,000 years ago, they resumed relations in the eastern Mediterranean, where the two populations met again. This pattern wouldn't necessarily merit separate species status for most animals, so why for us and Neanderthals?"
There is undoubtedly some journalistic enthusiasm here, because the claimed "hallmark of a species" is not valid: hybridisation is not that unusual between species and sometimes it occurs between genera (within the same family). This in itself is not a decisive argument. However, when we combine genetics, morphology and behaviour, the picture looks much clearer.
"There is, of course, more to the concept of being human than ecology and genetics: we are human because we think, talk, love and believe. It is impossible to know the mental life of a Neanderthal, but there is reason to think that it was not so different from our own. The Neanderthal genome differed little from ours, encoding fewer than 100 changes that would affect the shape of proteins. True, some of these differences occur in genes linked to brain function, but similar variation is found among humans today. Moreover, Neanderthals share with us a version of a gene linked to the evolution of speech, and recent archaeological evidence suggests that their minds were capable of the symbolic representations that underlie language and art. If that's not human, then what is?"
This brings us to why Neandertals have been so misinterpreted over the years. Why has it taken us so long to reject the picture of a brutish, grunting caveman devoid of aesthetics and reason? The Editorial starts with these words: "WE HUMANS like to see ourselves as special, at the very pinnacle of all life. That makes us keen to keep a safe distance between ourselves and related species that threaten our sense of uniqueness. Unfortunately, the evidence can sometimes make that difficult." Is this interpretation valid? Do we like to keep a safe distance between ourselves and anything that threatens our uniqueness? Perhaps we should reflect on on the history of scientific racialism, that portrayed races as occupying different rungs of the evolutionary ladder - was this also to keep a safe distance from races that threatened our uniqueness? Furthermore, is it true that we, the population at large, like to keep this safe distance? Why is it that any reports of animals showing apparent cognitive and creative skills are deemed newsworthy, whereas other studies showing a big divide between humans and animals languish in obscurity? I leave these questions for further thought and reflection.
One thing I have noticed over the years is that people with a design perspective have been far more receptive to the idea that Neandertals were part of the human family. They have been impressed by morphological considerations, but the cultural artifacts of Neandertals have made a big impression. In the early days, these were relatively meager, but more recent years have seen a flowering of reports of Neandertal culture. In this blog, these issues have been explored on several occasions: Burying the view that Neanderthals were half-wits, Darwinist thinking on the origin of religion, The cognitive skills of Stone Age Man, Images of evolution as secular icons, Walks like a man, talks like a man - is it a man?, and Rethinking Neanderthals. There is a pattern here, and it is evident even in the original reception given to Neandertal finds. The Darwinian scientists were looking for intermediates and they found one in Neandertal Man. He was portrayed as an ape-man and used to prop up an evolutionary story of ape-to-man evolution. After it was realised that the original finds were bones from someone deformed by disease, the story did not change much. The icon was too important to lose. Darwinism had created a blind spot for palaeoanthropologists and impaired the progress of science. Those able to make design inferences within science have been ahead of the game, but now the genetic data is published, all have to follow. However, would you believe, the same issue of New Scientist that carried the editorial noted above also had an article with the title: "Neanderthals not the only apes humans bred with". Apes? Really! Outdated traditions do not die when it comes to Darwinism - they just get repackaged!
A Draft Sequence of the Neandertal Genome
Richard E. Green [et al] and Svante Paabo
Science, 328, 7 May 2010: 710-722 | DOI: 10.1126/science.1188021
Abstract: Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
See also:
Dalton, R., Ancient DNA set to rewrite human history, Nature, 465, 148-149, (12 May 2010) | doi:10.1038/465148a
Editorial, Welcome to the human family, Neanderthals, (New Scientist, 12 May 2010)
Gibbons, A., Close Encounters of the Prehistoric Kind, Science 328, 7 May 2010: 680-684.
Of course they are.... we call them democrats.
That revealed that the part of their society that'd written the archive (and later on lost the art of writing) had actually left Yakutia hundreds of years earlier, moved to Nepal, conquered Northern India, produced Buddha, and then, under pressure from resurgent Hinduism, moved back North to Yakutia.
That was about 200 AD.
350 years later (as the Dark Ages started) they mounted up, moved East, and invaded (and conquered) Korea, and then Japan.
The Ko-Jiki reflects what happened next. Today this group still identifiably makes up the original Turkic language group that invaded in the 500s. They became the Daimyo and the Royal Family, and later on incorporated a substantial part of the original native population (the Emeshi) into their ruling elite (as samurai warriors).
When you do a DNA or MtDNA test of Japanese, you have a fair to middling chance of encountering a Yakutian ancestor, or even an Indian ancestor (from that sojourn in Nepal).
Without knowing of this relatively recent Yakutian insurgency it was actually quite difficult to figure out the place of the Yayoi in all this. Note: The Yayoi are clearly of Chinese origin ~ roughly 500 BC+ ~ and share many MtDNA and dental traits with the Yakut people, but they are also obviously not Yakut. The Han Chinese have their cultural identity affirmed about 300 BC with the first (Qin) emperor, but the Yakut are too far North to be of concern to the Han. Most analysts who've taken a good look at the Yakut have long recognized that they were "mysteriously" technologically the equal of the Han Chinese society, but at the same time seemed to prefer to live in the colder North where they herded horses, goats, sheep, yaks AND, lo and behold, reindeer!
The Yayoi arise out of the turmoil in China in that critical 500 BC to 200 AD period. They are simply Chinese who founded colonies in Japan and introduced "organized" rice culture. With Japonica rice being grown throughout the region, it's not likely the Yayoi introduced just Japonica rice ~ maybe Indicum rice ~ but the Japonica was already there. Traces have been found in the North on an Emeshi (Jomon) archaeological site in just the last couple of years.
Now this is all recent stuff. In more ancient times there was a constant flow of people from the Asian mainland to Japan, and from Japan to the Asian mainland. Although the Jomon/Ainu/Emeshi can be tracked through their teeth (they have extra roots on some molars), the Yakuts are not so easily traced.
Going back further ~ to the 5000BC period, you can find Yakut traces along an arc stretching from Yakutia to Eastern Siberia to Alaska to the Americas all the way to Tierra del Fuego.
At that point in time (going backward here) we are dealing with people who are culturally and technologically Yakut, and probably have a sign language, who herd animals ~ including by this time "tame reindeer" who've been developed to help deliver access to the major herds present all across Siberia.
These people move North during warmer climates, and South during colder climates. Moving North they achieve access to the broad arctic slope which allows them to move East and West vast distances ~ from Scandinavia to North America. Moving South they achieve access to the warmer lands South of the Himalaya mountains, as well as the technological developments that've taken place there.
Their counterparts in Europe are the Sa'ami. Detailed DNA examination reveals that the Sa'ami and the Yakuts did achieve total contact on at least one occasion! (Probably a bridal gift arrived with some tame reindeer in exchange for some really great furs ~ a "bridal gift" in those days actually consisting of "the bride").
It is presumed that similar movements occurred during the period of maximum glaciation ~ and this is always referred to as "ice age contact".
One of the reasons for classing early Yakut as "turkic" is that they appear to have been the first East Asian people to have horses. Odds are good that the horse moved East in China the same way it moved North from Spanish colonies to the American Great Plains.
Seems to me you're working overtime to emphasize that our DNA "glasses" are one-tenth of one percent empty.
I'm simply pointing to the fact: the DNA-glass is 99.9% "full" of identical DNA base-pairs.
You say there are five times more differences in genetic markers between humans and Neanderthals than amongst humans.
I'm only pointing out that the numbers of base-pair differences -- 3 million out of 3 billion total -- is the same between humans and Neanderthals as it is amongst various humans.
And I'm not disputing your time-line of divergences at all.
Clearly Neanderthals were more distantly related than our more recent out-of-Africa ancestors.
The issue here is: how "human" were Neanderthals?
Answer: plenty human -- human enough to:
So even if Neanderthals were not our human "brothers," they still were genetic cousins, and, so it appears, kissing cousins at that. ;-)
Just as coyotes and wolves would be ‘cousin’ species, although more distantly related.
And it is not five times more difference just in genetic markers, it would be, overall, about five times more differences over all the DNA of the genome.
If the absolute difference in DNA of the genome among humans was 3 million out of 3 billion total base pairs, you would expect, when comparing humans and neanderthals, around 9-15 million base pair differences out of that 3 billion, not the same 3 million.
It is the total amount of differences in the genome, or via comparison of neutral genetic regions, that one derives that the time line of divergence, one that (in this case) agrees nicely with the fossil record.
If there were the same number of base pair differences, it would imply an equal time of divergence. But the amount of difference between a human genome and a neanderthal genome should be three to five times more than the amount of difference between any two human’s genome, which would indicate their divergence around five times longer ago (less than 100,000 years ago, compared to some 500,000 years ago).
Can only go by what I read, and the following report is over 3 years old, but note the numbers:
"The results from the new studies confirm the Neanderthal's humanity, and show that their genomes and ours are more than 99.5 percent identical, differing by only about 3 million bases."This is a drop in the bucket if you consider that the human genome is 3 billion bases," said Edward Rubin of the Lawrence Berkeley National Laboratory, who led one of the research teams.
For comparison, the genomes of chimpanzees, our closest living relatives, differ from humans by about 30 million to 50 million base pairs."
Note the figure of "differing by only about 3 million bases." They then miscalculate this as one-half of one percent, when it should be one-tenth of one percent.
Here is a newer report saying:
"A newly released study published in Science magazine raises new questions about ancient life by concluding much of the DNA from Neanderthal specimens is "within the variation of present-day humans for many regions of the genome." "
Point is, I've seen nothing yet suggesting that Neanderthal nuclear DNA differences were more than 3 million base pairs, or more than the variances amongst modern humans. Of course, these would not be the same 3 million differences.
So again I ask: if it's "human" for humans to vary by 3 million amongst ourselves, why is it not quite "human" for Neanderthals to also vary from us by 3 million base pairs?
Thanks. I knew you’d have an interesting addition.
Now where is the data that says that inter-human variability is similarly 99.5%? I have heard more like 99.9%.
http://www.biotechniques.com/multimedia/archive/00002/BTN_A_000112275_O_2509a.pdf
So the 0.5% genomic difference we see between human and neanderthal is about one fifth less between human populations, or 0.1%.
This is exactly what one would expect if they diverged from humans some 500,000 years ago, rather than any two human populations, which would have a most recent common ancestor at least within the last 100,000 years.
A Neanderthal could probably move in, settle down, and no one would notice ~ except for his wife's four breasts and his bulbous skull ~ but I guarantee no one here would say a thing! Well, maybe a comment about "My word is that guy big ~ 700 pounds?!"
I think this business of having a genetically driven "square" heart is something that must have arisen in the depths of the Ice Age when people were not as well dressed as they are today ~ and no central heat either.
Oh, yeah, he'd no doubt drive only SUVs. We got a lot of those guys!
There are hundreds of genes that needed modification so that people could consume milk all their lives, or to develop the light skin necessary to life in the higher latitudes.
Now it's reported that the Chinese have some gene modifications that facilitate their use of "tone" in language, and to eat rice more efficiently. Just a few weeks ago I read about a group of Vietnamese people who appear to be genetically modified so that the ONLY grain they can consume is rice ~ it's kind of like having a super Celiac condition. No wheat, rye, barley, corn, etc. I have not yet heard if they are limited to eating Japonica, or can they eat both Japonica and Indicum (rice comes in two species in case you missed that ~ not just to varieties ~ they are different plants entirely).
All the attributes that is used to describe Neanderthals can be found scattered throughout the human population today. For example, (I've read) some of the Australian Aboriginies have brow ridges that even exceeds that of the Neanderthals.
While Neanderthal probably did not consume milk other than from their mothers, they probably crunched a lot of bones and marrow. Also, their pale skin, redhead, blue eyed traits made it especially easy for them to utilize what little sun their were exposed to to form Vitamin D in their skin and absorb it for bone building. When our European ancestors, had a white skin gene mutation, it accelerated their ability to move north, but some also probably bred with Neanderthals and got the redhead, pale skin gene which also facillitated their move north. Thus there are probably two distinct classes of “white” people. Would be interesting to see genetic research on that. I think my late husband probably had some of those Neanderthal genes. Scotish ancestry, acute sun sensitivity.
allmendream: "Now where is the data that says that inter-human variability is similarly 99.5%? I have heard more like 99.9%."
That 99.5% is a miscalculation.
The operative number here is "3 million bases", which should calculate to 99.9% identical DNA.
These are the same numbers as amongst modern humans.
Here is my previous post on this subject.
It references this report, from which here is the "money quote":
"Nucleotide diversity is based on single mutations called single nucleotide polymorphisms (SNPs)."The nucleotide diversity between humans is about 0.1%, which is 1 difference per 1,000 base pairs.[4][5][6]
"A difference of 1 in 1,000 nucleotides between two humans chosen at random amounts to approximately 3 million nucleotide differences since the human genome has about 3 billion nucleotides.
"Most of these SNPs are neutral but some are functional and influence phenotypic differences between humans through alleles.
"It is estimated that a total of 10 million SNPs exist in the human population of which at least 1% are functional"
In simple English: any two modern humans can differ by up to one-tenth of one percent of their 3 billion DNA base pairs, or about 3 million SNPs. Amongst the entire human population are about three-tenths of one percent (10 million SNPs) total DNA diversity.
Current estimates of Neanderthal vs. modern Human SNPs are also around 3 million.
These would not, of course, necessarily be the same 3 million differences -- excepting potentially 1% to 4% resulting from alleged interbreeding.
Naturally, you might argue that 3 million Neanderthal SNPs is way too few, the number is underestimated, it has to be higher given the time-spans involved.
Yes, you could argue that, but so far 3 million SNPs is still the number, and it makes Neanderthal DNA 99.9% -- not 99.5% -- identical to modern humans. ;-)
SNP’s are differences in genetic regions, not over the entire genome. As such, one can say based upon the supposed “miscalculation” that our GENETIC DNA is some 99.9% the same. That is not in any way a miscalculation that our GENOME DNA is only 99.5% the same.
Similarly, our GENETIC DNA is 98.5% similar to a chimpanzee, but over our entire GENOME we are some 96% similar to a chimpanzee.
It is common that people outside of science mistake the two numbers, and confuse and/or conflate the two. You are not the first to make this common mistake.
The end result of a genomic comparison puts our similarity with neanderthals at 99.5%, while any two human beings are 99.9% similar.
Exactly what one would expect if we diverged from them some 500,000 years ago, while any two human populations diverged, at most, 100,000 years ago. A 0.1% genomic DNA difference between any two modern humans is about a 0.5% genomic difference between a human and a neanderthal.
Thanks for the interesting post.
The Neanderthals had one ~ the red/yellow allele, and white folks got two ~ the red/yellow and the brown/black allele.
The blue-eyed trick is not unique to humans. Arctic dogs have blue eyes, and barring horizontal gene transfer, they must have come by the series of mutations that make that possible all on their own.
Now, for light skin ~ that takes a bunch of mutations, some of which are tied into the adult ability to consume milk. I haven't seen any information that says the Neanderthals have all of them, but they did have essentially the same major genes suppressing pigment as West Asians (white folks), but not the same genes that are used in East Asians to suppress pigmentation.
I will take a wild guess that the Neanderthals had one or more of the alleles that causes "intermittent Scandinavian porphyria". They were more than likely diabetic ~ 'cause all that extra sugar in your system serves as antifreeze.
I see only one set of numbers reported here.
This report's language clearly equates the units of measure for SNPs, nucleotides and "base pairs":
"Nucleotide diversity is based on single mutations called single nucleotide polymorphisms (SNPs)."The nucleotide diversity between humans is about 0.1%, which is 1 difference per 1,000 base pairs.[4][5][6]
"A difference of 1 in 1,000 nucleotides between two humans chosen at random amounts to approximately 3 million nucleotide differences since the human genome has about 3 billion nucleotides."
This report clearly says that human genetic diversity amounts to 3 million out of 3 billion base pairs, or .1%.
The report on Neanderthals says they are "more than 99.5 percent identical, differing by only about 3 million bases".
There is no suggestion here that they are talking "apples and oranges".
No explanation of how 3 million bases amongst humans is somehow different from 3 million bases between Neanderthals and humans.
In both cases the denominator must be our 3 billion base pairs, making the identical nucleotides 99.9%.
So, as far as I can see, this is only a discussion of "apples".
Now if you wish to introduce "oranges" into the discussion, then you will have to explain just what an "orange" is, how it differs from an "apple" and, most important, how that somehow changes the denominator of 3 billion base pairs to some other number -- a number which mathematically reduces the identical DNA of Neanderthals & humans to 99.5%.
This will be interesting... ;-)
"It is estimated that approximately 0.4% of the genomes of unrelated people typically differ with respect to copy number. When copy number variation is included, human to human genetic variation is estimated to be at least 0.5% (99.5% similarity)."
Ooooops, there's an "orange", showing human DNA only 99.5% identical. Wouldn't want to get that mixed up with those other "apples," would we?
Obviously a 0.5% difference over 3 billion base pairs is 15 million, not 3 million.
So how did that same source get both figures? They are obviously confused, or leaving out a critical bit of info.
Do you have a source for human variability similarly being 99.5%? The figures both you and I have cited have given it as 99.9%.
Either way, the data I have cited has given the human similarity as 99.9% and the neanderthal-human similarity as 99.5%. This is exactly what you would expect if the most distantly related human populations shared a common ancestor within the last 100,000 years, but neanderthals branched off some 500,000 years ago. Five times as much genetic difference, almost all of it in ‘neutral’ DNA regions of the genome.
I notice that you got the latter part also from the same Wiki entry that gave the human similarity as 99.9%.
Human neanderthal similarity is 99.5%.
Five times as much difference, as one would expect from them branching off some 500,000 years ago, while all human populations share a common ancestor some 100,000 years ago.
And that is the point I've tried to make in all these exchanges.
.5% equates to 15 million DNA differences, not 3 million, and yet the only solid number I've seen regarding Neanderthals is 3 million base pair differences.
In everything else we agree -- 15 million for Neanderthals is the number we might expect. It's just that I haven't seen it reported yet. When I do, then will concede the point.
And your larger point is also correct -- that these numbers can be more complicated than it might at first seem.
An example of that is the question of "copy number" which turns out to increase intra-human genetic diversity from .1% to .5%.
So it is important that we know which numbers we are talking about before we start throwing them around.
But finally, let me suggest to you a possible reason why the reports are telling us that Neanderthal DNA is only 3 million base pairs different from human DNA.
This could be the case, couldn't it, even if our common ancestors lived 500,000 years ago -- if there was significant interbreeding between those last living Neanderthals and some of our earlier human ancestors.
Wouldn't a bit of trogloditic hanky-panky tend to reset the genetic clocks on both sides? ;-)
As anyone with a calculator can tell you a 0.5% difference over 3 billion base pairs is 15 million not 3 million. Making the report that a 99.5% difference between humans and neanderthals adding up to 3 million base pair difference an obvious error.
Journalists. They don't know much about science, and apparently they cannot do math either.
What WAS reported in actual science journals, unfiltered by journalists, was that the human neanderthal similarity is 99.5%, and using the same criteria, human similarity is around 99.9%.
This is what one would expect when all the data supports humans sharing a recent common ancestor within the last 100,000 years, while neanderthals split some 500,000 years ago. And those are the numbers from actual science papers from actual scientists.
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