Neanderthal DNA illuminates split with humans

Posted by: DA Morgan

Neanderthal DNA illuminates split with humans - 10/11/06 04:53 PM

The first comparison of human and Neanderthal DNA shows that the two lineages diverged about 400,000 years ago and that Neanderthals may have had more DNA in common with chimps than with modern humans.

There is ongoing debate over whether the Neanderthals were a separate species, Homo neanderthalensis, or a subspecies of Homo sapiens. The first Neanderthals are thought to have emerged about 350,000 years ago, so the new findings from this DNA analysis strongly favour the theory that modern humans and Neanderthals share a common ancestor but are not more closely related than that.

For more:
http://www.newscientist.com/article/dn10275-neanderthal-dna-illuminates-split-with-humans.html
Posted by: terrytnewzealand

Re: Neanderthal DNA illuminates split with humans - 10/12/06 02:37 AM

I would be very interested to read the actual paper if you can find it. It will not be a simple matter for the scientists to find any appropriate genes. NZ scientists are having trouble finding the difference between holstein and jersey cattle genes. They're working backwards by looking at the F2 and F3 hybrids.

The half million year's separation mentioned in the article is the mitochondrial DNA lines, about the time Homo heidelbergensis began their expansion.

The same mtDNA time scale puts the separation between cattle and bison as twice as long, a million years. Althoughn speciation is unlikely to be simply a function of time hybrids between cattle and bison are fertile. Incidentally, does anyone know anything about domestic cattle ever joining bison herds?

The myDNA evidence on its own is not sufficient to prove no Neanderthal genes survive in modern humans. It would be interesting to know how the scientists chose the genes they looked for. They would be unlikely to find Neanderthal genes in Africans or Polynesians for example. My bet would be that if they have concentrated on stocky Europeans with big noses, blond hair and a tendency for a bulge at the back of their skull they would raise their chances.
Posted by: soilguy

Re: Neanderthal DNA illuminates split with humans - 10/12/06 12:57 PM

Terry:

This study was done on nuclear DNA, not mtDNA. As I recall (and I don't have a photographic memory), mtDNA studies put the split between the species further back in time.
Posted by: terrytnewzealand

Re: Neanderthal DNA illuminates split with humans - 10/13/06 01:29 AM

No, no soilguy. The article DA posted doesn't say what parts of the nuclear DNA they looked at. That's why their own publication would be most interesting. Mitochondrial DNA studies all have the split at 350,000 to 400,000 years so nothing new in this release as yet.
Posted by: soilguy

Re: Neanderthal DNA illuminates split with humans - 10/13/06 12:55 PM

Terry,

So what? All I said was that they looked at nuclear DNA, not mtDNA, in this study.
Posted by: terrytnewzealand

Re: Neanderthal DNA illuminates split with humans - 10/13/06 10:14 PM

Soilguy, you might find this interesting:

http://cogweb.ucla.edu/ep/Templeton_02.html

Of course there is nothing specifically Neanderthal covered but it does show hybridising between Out of Africa and pre-existing human populations.

In my observation the belief in replacement by a single movement "Out of Africa" in influenced by biblical stories about species, including humans, descending from a single couple. We know evolution involves whole populations. Have you had intimate contact with some subspecies of the Judeo-Christian genus of human belief?
Posted by: terrytnewzealand

Re: Neanderthal DNA illuminates split with humans - 10/13/06 10:27 PM

Another one. Covers much the same ground but amplifies the ideas a little:

http://dienekes.blogspot.com/2006/02/alan-templeton-vs-out-of-africa-with.html
Posted by: soilguy

Re: Neanderthal DNA illuminates split with humans - 10/14/06 03:40 PM

Soilguy, you might find this interesting:

http://cogweb.ucla.edu/ep/Templeton_02.html

Of course there is nothing specifically Neanderthal covered but it does show hybridising between Out of Africa and pre-existing human populations.


I have no problem with the idea of multiple emigrations out of Africa. There just doesn't seem to be evidence of interbreeding with Neandertals.

In my observation the belief in replacement by a single movement "Out of Africa" in influenced by biblical stories about species, including humans, descending from a single couple. We know evolution involves whole populations. Have you had intimate contact with some subspecies of the Judeo-Christian genus of human belief?

Judeo-Christian stories are meaningless to this question, in my opinion. I have no stake in whether we (Homo sapiens) interbred with Neandertals or not, if that's what you're asking. I'm only interested in what the pertinent researchers think, and the reasoning behind their thinking. It just seems to me that the genetic evidence that we have to date is contrary to the idea that there was interbreeding between the two types of humans, since the dawn of Homo sapiens.
Posted by: DA Morgan

Re: Neanderthal DNA illuminates split with humans - 10/14/06 05:58 PM

Soilguy is correct TTBOMK. I am not aware of any reports supporting interbreeding.

No doubt we reacted to them the way we react to each other: Genocide.
Posted by: terrytnewzealand

Re: Neanderthal DNA illuminates split with humans - 10/15/06 12:25 AM

Strange that it seems it was only in Europe that modern humans committed genocide against the pre-modern human inhabitants. Was that an indication of the future?
Posted by: samwik

Re: Neanderthal DNA illuminates split with humans - 10/15/06 01:22 AM

Re: "I have no problem with the idea of multiple emigrations out of Africa. There just doesn't seem to be evidence of interbreeding with Neandertals." from -soilguy (I think?)

Anyway, I haven't looked at the links yet but do any of them refer to how all the populations that left Africa before 70,000 yr. ago were probably wiped out by the big volcano back then. Was it Tambura, in Indonesia? I'll go check the web, but there was a sort of "nuclear winter" back then which would explain why our diversity mainly traces back 70,000, except within Africa. Neanderthals probably did survive, being far enough away and better adapted. Basically, they could easily be the only 'out of Africa' group, from our lineage, that survived the volcano.
~Sam
Posted by: samwik

Re: Neanderthal DNA illuminates split with humans - 10/15/06 01:47 AM

Update: Nope, it was Toba; not Tambora.
~Sam

35 x 100 km Toba caldera, the Earth's largest Quaternary caldera, was formed during four major Pleistocene ignimbrite-producing eruptions beginning at 1.2 million years ago. The latest of these produced the Young Toba Tuff (YTT) about 74,000 years ago. The YTT represents the world's largest known Quaternary eruption, ejecting about 2500-3000 cu km (dense rock equivalent) of ignimbrite and airfall ash from vents at the NW and SE ends of present-day Lake Toba. Resurgent doming forming the massive Samosir Island and Uluan Peninsula structural blocks postdated eruption of the YTT. Additional post-YTT eruptions include emplacement of a series of lava domes, growth of the solfatarically active Pusukbukit volcano on the south margin of the caldera, and formation of Tandukbenua volcano at the NW-most rim of the caldera. Lack of vegetation suggests that this volcano may be only a few hundred years old (Chesner and Rose, 1991).

...and speaking of climate change....
Does anyone know the "volcano equivalent" of anthropogenic pollution?
~Sam
Posted by: terrytnewzealand

Re: Neanderthal DNA illuminates split with humans - 10/15/06 02:51 AM

Samwik. Home erectus survived in Southeast Asia until possibly as recently as 30,000 years ago. This is quite near the centre of the eruption and so I doubt the destruction of humanity, or life in general, was as severe as some scientists like to make out.

Re. the studies. They show that modern human genes include some that show a regional origin from over the last 1.7 million years. These variations would not show up regionally if humans genes all came out of Africa in one go at any time since then. But as the writers on the paper on the split between humans and chimpanzees (another post, I forget which) say it may take a long time before their evidence is accepted.
Posted by: terrytnewzealand

Re: Neanderthal DNA illuminates split with humans - 10/15/06 02:58 AM

Samwik. For your interest and edification here is the chimpanzee site again. I've earlier put it in the "Out of Asia - not Africa" on the science discussion forum but it won't hurt to put it in again.

http://www.haverford.edu/KINSC/06Journal/nature04789.pdf#search=%22genetic%20evidence%20for%20complex%20speciation%20of%20humans%20and%20chimpanzees%22

.
Posted by: samwik

Re: Neanderthal DNA illuminates split with humans - 10/15/06 03:36 AM

Yes, and the hobit florensis folks too, I guess. And I should have made it clear that i was talking mostly conjecture or barely hypothetical. Thanks, I'll look at these links.
~Sam
Posted by: samwik

Re: Neanderthal DNA illuminates split with humans - 10/15/06 04:36 AM

Couldn't get that lastlink, but here's an interesting one.
http://human-nature.com/nibbs/02/frost.html

Even if neanders are closer to chimps than us, that'd still mean they were less than 1% different; wouldn't it?
~Sam
Posted by: terrytnewzealand

Re: Neanderthal DNA illuminates split with humans - 10/15/06 09:07 AM

Thanks samwik. Good overall look at the situation. Do you not have acrobat reader? You can download it reasonably easily. You can then read PDF files.
Posted by: terrytnewzealand

Re: Neanderthal DNA illuminates split with humans - 10/17/06 03:46 AM

Samwik, I've read your contribution again and I note:

"In the absence of selection pressures, the current level of hair colour diversity would have taken 850,000 years to develop (Templeton 2002). One would have to conclude that the gene pool of Eastern and Northern Europe is derived mainly from the Neanderthals and even earlier Homo populations. Otherwise, some kind of selection must have favoured these colour polymorphisms."

Interestingly the possibility is immediately disregarded as it doesn't fit the paradigm. The large number of genes contributing to blond hair also indicates a very long period of diversification. When examined the sexual selection explanation falls to pieces. The evidence is more likely to indicate a movement of modern humans into Europe gradually replacing genes for blond hair.

This takes us back to a comment soilguy made:
"Judeo-Christian stories are meaningless to this question, in my opinion."

Soilguy, I was merely pointing out the obvious, that our pre-existing beliefs always influence how we interpret evidence. The Judeo-Christian myths are so deeply embedded in western culture that even atheists are influenced by them.

I don't know if you have read books by Stringer, Olson or Tattersall. Their books are crammed with biblical ideas. They ask such questions as "Why were we the chosen ones?", "What made us so special?" etc. By this argument Tasmanian Aborigines were not human. Australian Aborigines and North American Indians are barely so.
Posted by: samwik

Re: Neanderthal DNA illuminates split with humans - 10/17/06 04:17 AM

I haven't looked into this much, but I'm sure I've heard that it only took about 20,000 years for skin color to change from dark to light (Arican to N.European). But that is with some selection pressures such as the vitamin D/Folic acid paradox. Maybe 850,000 yr. is right, but are there ever no selection pressures?
~Sam
Posted by: terrytnewzealand

Re: Neanderthal DNA illuminates split with humans - 10/17/06 07:00 AM

There is probably almost never no selection pressures. The problem is: what was the selection pressure? From the article you posted we see it's accepted humans in the northern regions ate a lot of meat. This provides vitamin D. Therefore no selection pressure for white skin from that angle.

So-called white people actually turn brown in summer by tanning. For any other creature that had white hair, blue eyes and changed from white to brown with the seasons we'd have no hesitation pronouncing it was an adaption to winter snow. Are we so convinced humans obey a different set of biological rules to all other species that we discount this idea?
Posted by: samwik

Re: Neanderthal DNA illuminates split with humans - 10/17/06 07:58 AM

TTNZ, cool
While I thought the article was interesting, I don't agree with it's conclusions. Firstly it, http://human-nature.com/nibbs/02/frost.html, starts out with "Long intense sunlight favoured a lush growth of mosses, lichens, grasses, and low shrubs that fed mammoths, reindeer, bison, and horses. Despite this high bioproductivity, the loess-steppe confronted...."

It may be long intense sunlight, but it's a lot less intense than in Africa. That is why depigmentation was highly selected for. Vit.D comes from sunlight (synthesized via), not meat. Sunlight degrades folic acid (or folate) and so pigmentation is highly selected for in the African environs. ...and yes, through the wisdom of intelligent design, the dark skin is just dark enough to protect the folate but still make vit.D in Africa & vice versa for the light skin up North.
Lack of folate causes birth defects. Actually I think light skins need to supplement with folate a bit (leafy greens). Musta been hard in the winter months. Maybe all those hair colors came from the increased birth defects.

...and what's this stuff about white hair??
also...dark skin tans too. I think tanning is not a recent adaptation.
I think we follow the same rules, everything is consistent; although I'm sure cultural and psychological selection pressures have added some new rules.

I'll have to read those articles more thoroughly before I post them next time. I can usually follow technical explanations, but I didn't understand any of that genetic stuff.
Thanks,
~Sam
Posted by: TheFallibleFiend

Re: Neanderthal DNA illuminates split with humans - 10/17/06 02:31 PM

I'm not sure how much comparison there is between hair color in humans and fur color in dogs, but here goes. I saw a program on dog evolution some months back: http://www.pbs.org/wgbh/nova/dogs/about.html

It reported on an interesting experiment on foxes that occurred in Russia. They were attempting to produce less ferocious foxes they could release in the wild, but surprisingly they produced foxes with many colors and different sizes, as well. (That was a very small part of the entire program.)
Posted by: TheFallibleFiend

Re: Neanderthal DNA illuminates split with humans - 10/17/06 06:45 PM

More info on the fox experiment:
http://abc.net.au/animals/program1/factsheet5.htm

---

More info on the program from a post I made some time ago on another board:

My daughter and I watched a show about dog evolution on NOVA last night. It was narrated by John Lithgow. Very interesting stuff. The scientists interviewed scoffed at the idea that humans adopted, then domesticated wolves.

Their reasoning goes like this:

1) Dog training and selective breeding are very difficult. They require a lot of resources and some sophisticated knowledge.

2) While archaeological evidence shows that humans and dogs have cohabited for at least 15,000 years, genetic clock evidence indicates that the dog line goes back about 100,000 years.

3) Dog's brains are smaller than wolves' brains.

From these facts some researchers conclude that dogs became at least partially domesticated BEFORE humans adopted them. They suggest that as early human groups began to throw away garbage, some wolves filled a niche by becoming scavengers. (Scavengers generally have smaller brains than predators.) Those scavengers had an evolutionary advantage over the wilder ones who had to struggle much harder to get their food. Over generations, populations of these animals gradually lost their fear of humans and lived alongside them. That is, they became dogs in this process.

An interesting factoid from the show: the earliest dogs seemed to be playthings for royalty and looked a lot like modern salukis.
Posted by: terrytnewzealand

Re: Neanderthal DNA illuminates split with humans - 10/18/06 03:52 AM

Admittedly a biased source but it's the only link I've found at short notice:

http://www.beefyandlamby.co.uk/red-meat.html

One thing we can be sure of. Meat made up a substantial portion of the ancient human diet in Europe. Also I recall that modern vitamin D deficiency does occur in black-skinned people in Europe these days but only in those whose culture demands they cover up in an unnatural manner. Selection for white skin is unlikely to have anything to do with vit. D.

Re. colour change in domesticated animals. I've been aware of the fox phenomenon for some years. Many of the genes were probably already present as recessives in the wild population. They have been able to survive as double recessives through lack of selection pressure. In the wild there is an advantage for animals to look much the same as each other. Any that stand out are likely to be predated quickly. Likewise for animals that are less afraid. Once a colour variation is established in a domestic population there is no selection to eliminate it. The question for hair colour variation in humans is who domesticated them? Was it each other?

I agree totally with the idea that dogs entered human society on their own initiative.
Posted by: samwik

Re: Neanderthal DNA illuminates split with humans - 10/18/06 04:15 AM

TerryT: regarding the part of your reply: "Selection for white skin is unlikely to have anything to do with vit. D."

I found a 2002 Scientific American article (although I know they can be wrong, as with the shower-curtain effect). It is entitled Skin Deep: Throughout the world, human skin color has evolved to be dark enough to prevent sunlight from destroying the nutrient folate but light enough to foster the production of vitamin D. At <http://www.sciam.com/article.cfm?articleID=000B7732-FC72-1D80-90FB809EC5880000>
~The first paragraph ends with: "Recent epidemiological and physiological evidence suggests to us that the worldwide pattern of human skin color is the product of natural selection acting to regulate the effects of the sun?s ultraviolet (UV) radiation on key nutrients crucial to reproductive success."
Not definitive, but certainly plausible I think.
Thanks,
~Sam
Posted by: terrytnewzealand

Re: Neanderthal DNA illuminates split with humans - 10/19/06 03:25 AM

The theory is fine but several questions then arise. Why didn't the same thing happen throughout Northern Eurasia? Why did selection for a white skin colour occur predominantly in the region of northern deciduous forest, a region where the trait is found in many other species? Is the balance between folate and vitamin D that precarious? Wouldn't humans have been fully-clothed by the time they reached north far enough for it to matter?

Re. the pervasive influence of Judeo-Christian beliefs. The Basque philosopher Unamuno recognised the problem when he said that in Spain even atheists are Catholic.
Posted by: samwik

Re: Neanderthal DNA illuminates split with humans - 10/19/06 03:42 AM

I think the changes in skin color took place 50-30 Kya. The exceptions to the theory would be populations that more recently moved to "wrong" latitudes such as the native Americans. Maybe a white, reflective environment fosters darker skin also, like the eskimos (though they are relatively recent too). I'm just speculating here.

ROFL with "The Basque philosopher Unamuno recognised the problem when he said that in Spain even atheists are Catholic."

Thanks alot,
~Sam
Posted by: terrytnewzealand

Re: Neanderthal DNA illuminates split with humans - 10/19/06 06:54 AM

Samwik. Your comments re. reflective environments are widely accepted. East Asians evidently have very little melanin but plenty of keratin in their skin. This reflects sunlight very effectively. The East Asian eyes shape also indicates a reflective environment. Where might these characteristics have evolved? My guess is in the high altitudes of what is now Western China and Mongolia. Both white skin and these East Asian features presumably developed before people had clothes. What evidence do you have they developed only as recently as 50,000 years ago?
Posted by: samwik

Re: Neanderthal DNA illuminates split with humans - 10/19/06 08:01 AM

Okay, just speculation based on the 70Kya date for 'out of Africa' & a 20,000 year time period needed for skin color shift. I'm sure I recall the 20K figure, and I think I heard of that on the PBS Nova program on the Vit.D/folate theory.
I also allowed 20K years for migration first, but this selection is always happening. I imagine that at some point ~60-30Kya populations became stable enough in one region that color shift took place. I probably should have said 40-30Kya +/-20K years.
Neat info. about the keratin and eyes too.
Thanks,
~samwik
Posted by: samwik

Re: Neanderthal DNA illuminates split with humans - 10/19/06 08:15 AM

I thought that was interesting stuff above, about the dogs too.

re: "some wolves filled a niche by becoming scavengers." -FF
re: "In the wild there is an advantage for animals to look much the same as each other. Any that stand out are likely to be predated quickly. Likewise for animals that are less afraid." -TTNZ

I was struck by a thought after reading the two ideas above. Both of Terry's points, would lead those animals to be shunned, or driven out, by the pack; and, if not predated, could likely become FF's "some wolves [that] filled a niche by becoming scavengers."

~Samwik
Posted by: soilguy

Re: Neanderthal DNA illuminates split with humans - 10/19/06 02:02 PM

re: Dogs

I think the Nova program attributed the multiple colors "available" in domestic dogs to testosterone levels. Domestic dogs have lower testosterone levels than wolves, which allows pre-existing color variations to be expressed. (The high testosterone levels in wild wolves has a strong influence on the production of dark pigment.) The "new" colors in dogs occur too quickly for them to have arisen through mutations since domestication.
Posted by: terrytnewzealand

Re: Neanderthal DNA illuminates split with humans - 10/20/06 12:25 AM

Soilguy wrote:

'The "new" colors in dogs occur too quickly for them to have arisen through mutations since domestication.'

Totally agree. I read information on the foxes years ago and the writer stated the changes started happening within just two or three generations. The genes must have already been present. Testosterone levels could well be implicated in colour change. We know that the effect of any particular gene is seldom as simple as we were taught in school.

I think change becomes rapid once selection is reduced because not only do double recessives survive, new combinations of double recessives survive. Colours and patterns that never appear in the wild population can suddenly appear. I think this is the aspect Trilobyte just can't get his head around when he demands a magical series of changes at the same point on the chromosome.

A relaxing of selection pressure, by definition, allows population numbers to build. Resources usually eventually become fewer and selection rears its head once more. Any change in selection pressure can then lead to rapid change in appearance. Punctuated equilibrium.