A complete Neandertal mtDNA genome

Posted 6 January 2009 by Jim Foley

In 1997 the first successful extraction of Neandertal DNA was announced to great fanfare (Krings et al. 1997). This DNA was not from the nuclear DNA (from cell nuclei) which determines most of our physical characteristics, but mitochondrial DNA (mtDNA) from the small energy-producing organelles which are inside all of our cells ¹. It so happens that mtDNA is easier to extract from ancient bones than is nuclear DNA. Krings et al reconstructed a 379 base sequence from the Neandertal mtDNA, out of the full mtDNA length of more than 16,000 bases. Since then, many other researchers have also extracted mtDNA sequences from Neandertal bones (and one team has even recovered some nuclear DNA). Now, for the first time, a complete mtDNA sequence has been recovered, from a 38,000 year old Neandertal fossil from the Vindija cave in Croatia. The results were published in August 2008 in the journal Cell: A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing (Green et al. 2008). Here is one of the most important conclusions from the paper's summary:

Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years.
— Green et al. 2008

The Neandertal mtDNA sequence was compared with mtDNA from chimpanzees and 53 modern humans. The human mtDNA sequences had between 2 and 118 differences from each other. The number of differences between the human mtDNAs and the Neandertal mtDNA varied from 201 to 234. This graph shows the differences between the human, Neandertal and chimp groups, and the human group: This is not unexpected; it confirms the conclusion from the earlier Krings et al. 1997 paper (you can see the equivalent graph from that paper here). In that paper, the 994 human sequences had between 1 and 24 differences from each other (over a partial mtDNA sequence). The number of differences between the human sequences and the Neandertal sequence varied from 22 to 36. Because the minimum distance between any human and the Neandertal (22) was slightly less than the maximum distance between any two modern humans (24), some creationists (e.g. Lubenow 1998) misinterpreted these figures to claim that the 1997 Neandertal mtDNA was within the modern human range. (It was a misinterpretation because it was comparing apples (a minimum distance between N'tals and any human) with oranges (a maximum distance between any two humans)). As an alternative explanation of the data, Lubenow suggested that maybe early humans formed a large population which had far greater genetic variability, most of which had since been lost. This was, at the time, a conceivable conjecture, though not one I would have wanted to bet on. But further study has disproved it; all the subsequent Neandertal mtDNA sequences which have been recovered have been similar to each other, and dissimilar to modern humans. Now that we have a complete Neandertal mtDNA genome, the distinction between the Neandertal and modern human mtDNA is even more striking. It strengthens the view that Neandertals should be designated a separate species Homo neanderthalensis, because even if they could interbreed with the ancestors of modern humans (and they probably could, and possibly did on occasion ³) there does not seem to have been a significant amount of genetic interflow happening between the two populations. We don't find Neandertal mtDNA in modern humans, and vice versa. Humans and Neandertals seem to have split off around 600,000 years ago and developed separately thereafter. For a more in-depth analysis of this paper, see John Hawks' blog entry Complete Neandertal mitochondrial sequence, and selection on human (not Neandertal) mtDNA.

Footnotes

1. mtDNA also has the intruiging property that it is always (or almost always; there is some dispute over this) inherited only from the mother, and not the father. This means that it is useful for determining relationships through maternal lines.

2. The graph shows the Neandertal group between the human and chimp groups. This does not mean that Neandertals are intermediate between humans and chimps. In fact, both are about equally distant from chimps (which is what we would expect from evolutionary theory). The Neandertal group is in the middle because the graph compares each group with modern humans. If instead it had compared each group with the Neandertal mtDNA, then the human group would have been between the Neandertals and the chimps.

3. Just because two individuals can breed does not mean they belong to the same species. Although there are many competing concepts as to what constitutes a 'species', usually it is considered to be a population of individuals that successfully interbreed in the wild. Populations that could interbreed in theory but don't in practice are therefore different species.

References

Krings M., Stone A., Schmitz R.W., Krainitzki H., Stoneking M., and Pääbo S. (1997): Neandertal DNA sequences and the origin of modern humans. Cell, 90:19-30. Green R., Malaspinas A-S, Krause J., Briggs A., et al. (2008) A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing. Cell, 134:416-426. Lubenow M. (1998), Recovery of Neandertal mtDNA: an evaluation. Technical Journal, 12(1):87-97

64 Comments

Terrapin · 6 January 2009

Personally, I think this is fascinating. I wonder what we can learn about these extinct cousins of ours just from the mtDNA. It's amazing to think we went from mediocre mtDNA fragments to a full sequence in just over a decade.

Of course, AiG will probably just put a little blurb in their "News to Note" about how this evidence is biased by evolutionary preconceptions or similar nonsense. Ah well, we'll let the little bugs dance on the end of the stick, it doesn't change the fact that we skewered 'em.

The Curmudgeon · 6 January 2009

Gentlemen, on the basis of this news, let me be the first to proudly say: "I ain't no kin to no Neandertal."

Dave Luckett · 6 January 2009

Can I ask what will seem to the geneticists here a very stupid question?

On the basis of this new evidence - as we have it - would this mean that the Neaderthals are a different species to us? So that the genus Homo would be made up of at least four species, three of them extinct: sapiens, neanderthalis, erectus and habilis (ergastor)?

tresmal · 6 January 2009

Dave Luckett said: Can I ask what will seem to the geneticists here a very stupid question? On the basis of this new evidence - as we have it - would this mean that the Neaderthals are a different species to us? So that the genus Homo would be made up of at least four species, three of them extinct: sapiens, neanderthalis, erectus and habilis (ergastor)?

That depends on which definition (the number of which exceeds the number of species) of species you use.

JimF · 6 January 2009

Even if you use a particular definition of 'species', it's damn near impossible to say how many species of humans existed. Are sapiens, neanderthalensis, antecessor, erectus, ergaster, heidelbergensis, habilis and rudolfensis all different species? You can't easily apply the definition given above (or any definition) to species known only from scanty fossil remains. And genera don't have fixed boundaries in any case - some people would put habilis and rudolfensis in the genus Australopithecus.

Dave Luckett · 6 January 2009

I just realised that it is a stupid question, since it is actually asking to draw a boundary that doesn't really exist as a boundary, a line.

It's like the boundary between sea and land. Where do you draw it? At the bottom of the tide, or the top? Where the highest waves break or along the points that are always covered? Is that tidal lagoon part of the sea or not? Is that half-tide rock an island?

But if the boundary can't be drawn as a line, does that mean that there is no meaning to the terms "land" and "sea"? Of course not.

W. H. Heydt · 6 January 2009

Dave Luckett said: It's like the boundary between sea and land. Where do you draw it? At the bottom of the tide, or the top? Where the highest waves break or along the points that are always covered?

Now *those questions actually have answers.... Where do you draw the line? It depends on what coast you're on. On East and Gulf Coasts of the US, the line is drawn at mean low water (the average height of all low tides). On the West Coast of the US, the line is drawn at mean lower low water (the average of the lower low tide on each day). This is, by the way, why you can get a low tide with a negative value, though it's less common on the West Coast than on the East or Gulf Coasts.

Dave Luckett · 7 January 2009

The point is that the line is drawn because of a convention that has been agreed to. That convention is perfectly reasonable, but it is a convention. The fact that a different convention has been adopted for the two coasts is a demonstration that we are dealing with a human construction, not a division that exists in nature. The same for species. Where we draw the dividing line depends on a human convention, not on nature.

Frank J · 7 January 2009

2. The graph shows the Neandertal group between the human and chimp groups. This does not mean that Neandertals are intermediate between humans and chimps. In fact, both are about equally distant from chimps (which is what we would expect from evolutionary theory). The Neandertal group is in the middle because the graph compares each group with modern humans. If instead it had compared each group with the Neandertal mtDNA, then the human group would have been between the Neandertals and the chimps.
— Jim Foley

That cannot be overemphasized. I have asked people such questions, and they usually get them wrong. The reason is that they think "ladder" not "tree." I can recall thinking that way too.

John Ericsson · 7 January 2009

Frank J said: That cannot be overemphasized. I have asked people such questions, and they usually get them wrong. The reason is that they think "ladder" not "tree." I can recall thinking that way too.

Agreed!

eric · 7 January 2009

Lets complete the trio. How would the graph look if it had compared each homo group to chimps?

Frank J said:
2. The graph shows the Neandertal group between the human and chimp groups. This does not mean that Neandertals are intermediate between humans and chimps. In fact, both are about equally distant from chimps (which is what we would expect from evolutionary theory). The Neandertal group is in the middle because the graph compares each group with modern humans. If instead it had compared each group with the Neandertal mtDNA, then the human group would have been between the Neandertals and the chimps.
— Jim Foley
That cannot be overemphasized. I have asked people such questions, and they usually get them wrong. The reason is that they think "ladder" not "tree." I can recall thinking that way too.

eric · 7 January 2009

eric said: Lets complete the trio. How would the graph look if it had compared each homo group to chimps?

Oops, never mind, Jim already answered that; they're approximately equidistant.

John Kwok · 7 January 2009

Dave, The answer to your question is absolutely yes:

Dave Luckett said: Can I ask what will seem to the geneticists here a very stupid question? On the basis of this new evidence - as we have it - would this mean that the Neaderthals are a different species to us? So that the genus Homo would be made up of at least four species, three of them extinct: sapiens, neanderthalis, erectus and habilis (ergastor)?

Human evolutionary history is quite complicated to say the least. John

Eric Finn · 7 January 2009

Frank J said: That cannot be overemphasized. I have asked people such questions, and they usually get them wrong. The reason is that they think "ladder" not "tree." I can recall thinking that way too.

Neanderthals are not intermediate between humans and chimps. However, that is not the only possible misinterpretation of the graph. The graph appears to indicate that the distribution among humans is rather wide as compared both to the Neanderthal group and to the chimpanzee group. This was exactly my first impression. I thought that it was due to the limited number of individuals (one?) in the Neanderthal group, but surely there should be mtDNA available from chimps. Only later I realized that this graph does not tell much about the variation within the Neanderthal group (in this study), or about the variation within modern chimpanzees. It tells that the locations in mtDNA that differ between two human individuals are likely to be different between any human and either a Neanderthal or a chimp. The graph does tell, however, that the distance between humans and chimps is about tenfold compared to the distance between any two humans.

Peter S. · 7 January 2009

We still need a study of mtDNA from late Homo erectus in Asia (which, despite the species name, may be just as far removed evolutionarily from early Home erectus as Neanderthals and modern humans).

KP · 7 January 2009

Has someone sent a PDF over to the DI? Since they don't bother with such unfruitful activities as actually reading the literature, they probably aren't aware yet. I can't wait to hear their (and AiG's) response to this.

Joshua Zelinsky · 7 January 2009

KP, AIG has already commented on prior mitochrondial DNA studies of neanderthals( http://www.answersingenesis.org/tj/v12/i1/mtdna.asp ) I suspect they will rehash the points made there.

Now onto more substantative issues: Can someone explain why mitochrondial DNA is easier to recover than nucleic DNA? There's no obvious reason to the non-experts like me. The only thing that occurred to me is there are many copies of the same mitochrondrial DNA in each given cell but it isn't clear to me that will be substantial enough to make a difference.

Reed A. Cartwright · 7 January 2009

We have to be careful when comparing modern sequences to ancient sequences. The proper comparison is not between Neanderthals and present humans, but rather between Neaderthals and the our ancestors that are contemporaneous with them. Due to the process of coalescence our mt genomes can (and will) be rather divergent from our ancestors, therefore it is difficult to draw conclusions without the additional information about what the variation in our ancestors was like as well.

Kevin · 7 January 2009

Very cool article.
Some pop-sci questions for the experts:

1) What is the likelihood that nuclear Neanderthal DNA will ever be sequenced in full (is it "just a matter of time", or are there obstacles which might conceivably leave the Neanderthal genome lost to history)?

2) If Neanderthal DNA were sequenced, would there be ethical objections to cloning one?

3) Is there archaeological reason to expect the Neanderthal to have significantly less (or approximately the same) cognitive capacity / language skills of Homo sapiens?

Mark Farmer · 7 January 2009

Kevin said: Very cool article. Some pop-sci questions for the experts: 3) Is there archaeological reason to expect the Neanderthal to have significantly less (or approximately the same) cognitive capacity / language skills of Homo sapiens?

The likely answer is that they were probably pretty comparable to us. They had a complex clan structure and intentional burial of the dead (and perhaps a belief in the afterlife) and similarities in the FOXP2 gene suggest that they possessed complex language skills like our own. http://www.cell.com/current-biology/abstract/S0960-9822(07)02065-9

jasonmitchell · 7 January 2009

re Kevin

until 1983 or so it was believed that Neanderthals could not possibly have similar language skills vs. H. sapiens - because there were no examples of Neanderthal hyoid bones; essential for fine motor control of larynx and tongue. An example of a Neanderthal hyoid was found in 1983 and it is very similar to the hyoid in H. sapiens. Between this evidence and brain case casts there is currently no reason not to believe that Neanderthals (at least anatomically) had vastly different cognitive/ language capabilities. There does seem to big vast cultural differences between Neanderthal and H. sapiens populations that were contemporaneous- there are not many examples of Neanderthal art for example.

JimF · 7 January 2009

Kevin said: 1) What is the likelihood that nuclear Neanderthal DNA will ever be sequenced in full (is it "just a matter of time", or are there obstacles which might conceivably leave the Neanderthal genome lost to history)? 2) If Neanderthal DNA were sequenced, would there be ethical objections to cloning one? 3) Is there archaeological reason to expect the Neanderthal to have significantly less (or approximately the same) cognitive capacity / language skills of Homo sapiens?

1. A fair chance, I think. As is said, some nuclear Neandertal DNA has already been sequenced, by Green and his team in fact. That was a sequence of over a million base pairs, and somewhere recently I read they're working on the full nuclear Neandrtal genome. 2. I think you'd have the exact same ethical considerations as with cloning a modern human. 3. Opinions differ. Neandertals used fire, make sophisticated tools, would have been able to talk and make clothes, buried their dead, so are undoubtedly human in many respects. However they don't seem to have been as innovative with tools, or have done much in the way of art, so there's a widespread suspicion, which I cautiously share, that they weren't quite as smart or inventive as modern humans.

Vaughn · 7 January 2009

Kevin said: Very cool article. Some pop-sci questions for the experts: 1) What is the likelihood that nuclear Neanderthal DNA will ever be sequenced in full (is it "just a matter of time", or are there obstacles which might conceivably leave the Neanderthal genome lost to history)?

I heard the senior author Svante Paabo (sorry I don't know how to add umlauts to the two "a"s) talk about this work this past October, so I can share some information about the first question - Svante said their studies show that DNA degradation and chemical modification begins immediately after death and that all the DNA from an organism is completely deteriorated by one million years after death. 40,000 YO DNA is degraded to pieces averaging 70bp in length. Sequencing of Neanderthal nuclear DNA is ongoing, some work already published, but assembling a 3 billion base sequence from 70bp pieces will take time. My personal guess is that 20 fold coverage will be required to assure accuracy. Svante's conclusion from all the completed DNA sequencing is that there was very little "mixing of DNA" (a weaker way of saying "interbreeding") between Neanderthals and our ancestors. Vaughn

Frank J · 7 January 2009

The proper comparison is not between Neanderthals and present humans, but rather between Neaderthals and the our ancestors that are contemporaneous with them.
— Reed A. Cartwright

Another good point, if only to dispel the "ladder" misconception. Ideally the "chimp" DNA should be a ~30K year old ancestor too. But AIUI, they left few if any fossils, let alone partially preserved DNA, from that era. I often wonder what a field day creationists would have had if for some reason other hominid/hominoid branches fossilized well and Australopithecus/Homo branches didn't.

Henry J · 7 January 2009

Yeah, I guess it's just luck that we're in a genus in which the odds of fossilization are apparently better than one per trillion individuals (although maybe worse than one per billion, if my rough estimates aren't too far off).

Henry

JohnS · 8 January 2009

You were just joking around, Curmudgeon, I'm sure. Still, it fascinates me to conceptualise common ancestry in terms of genealogy.

Thus, on the basis of this news, one of my many-times-great grandmothers who lived about 0.7 Mya, had a child whose descendants are known to us as Neandertals.

Given the common ancestry of all known living species on the planet, I can only conclude that you are admitting to being an alien. If so, I'd love to study this further with you. When can we schedule an autopsy? Er, I mean compete physical exam.

Ron Okimoto · 8 January 2009

Now, we have to try to figure out what the common ancestral population that the 0.66 Mya mtDNA common ancestral sequence came from, and what that population might have become before the Neandertal and modern human lineages split. Was this ancestral population Homo erectus like or more Neandertal or generic Homo sapien? The question of whether we evolved from Neandertals is still open in a sense. As far as I know we do not know what that common ancestral population looked like. Comparing erectus like skulls to Neandertal and modern humans I'd expect that those common ancestors would have looked more like Neandertals than modern humans. What would their classification be?

eric · 8 January 2009

JimF said:
2) If Neanderthal DNA were sequenced, would there be ethical objections to cloning one?
2. I think you'd have the exact same ethical considerations as with cloning a modern human.

That was my initial reaction too, but now I think its wrong. One significant ethical reservation with human reproductive cloning comes from the fact that you are intentionally choosing a reproductive method known to give a very high rate of birth defects when other less risky methods are available. So you are being unnecessarily risky and cruel; you are toying with the potential health of the child for no better reason than to stroke your own ego. And this is not like a difference between, say, a 0.001% chance and 0.01% chance. The chance of a major developmental issue from cloning is still very high (over 50%, I think) in the anmials we clone. While I'm certain other people can list other ethical problems relevant to this case, the ethical problem with human cloning I've cited above is not an issue for Neanderthal because, obviously, there's no other way to produce them.

rijkswaanvijand · 8 January 2009

Maternal lines...
So if Neandertal women were damned ugly, Neadertal men would subsequently choose to mate with human women while human men wouldn't even think of doing the same with Neandertal women..
And we would still see no sign of interbreeding from the mtDNA.
Farfetched?

MrrKAT · 8 January 2009

rijkswaanvijand said: So if Neandertal women were damned ugly,..

What if both women were ugly from others side of view but only sapiens had some fermented juice fruits within and he temporarily saw some very very beautiful Ne-Annes.. ? ;)

Henry J · 8 January 2009

Strange, something in these comments reminds me of "Clan of the Cave Bear"...

KP · 8 January 2009

Joshua Zelinsky said: KP, AIG has already commented on prior mitochrondial DNA studies of neanderthals( http://www.answersingenesis.org/tj/v12/i1/mtdna.asp ) I suspect they will rehash the points made there.

Wow. I scrolled down and down waiting for some "point" to emerge. Apart from misrepresenting the facts somewhat, the argument seems to accept that neanderthals existed and date back to, well, further than the biblical records would allow. Note to newer newcomers than me: consistency is not one of the creationist's strong points...

Now onto more substantative issues: Can someone explain why mitochrondial DNA is easier to recover than nucleic DNA? There's no obvious reason to the non-experts like me. The only thing that occurred to me is there are many copies of the same mitochrondrial DNA in each given cell but it isn't clear to me that will be substantial enough to make a difference.

I'm an ecologist, but my understanding is that mtDNA is used because it has a relatively fast and consistent rate of nucleotide substitutions. So it can be used more like a "molecular clock" if you can tolerate that term, particularly for lineages that diverged relatively recently -- like neanderthals and modern humans. Also, the substitutions will generally be neutral so the additional noise of selection acting on them won't confound things. I'm sure someone will correct me if I'm reaching too far on this or have it wrong in some other way...

JimF · 8 January 2009

Joshua Zelinsky said: Now onto more substantative issues: Can someone explain why mitochrondial DNA is easier to recover than nucleic DNA? There's no obvious reason to the non-experts like me. The only thing that occurred to me is there are many copies of the same mitochrondrial DNA in each given cell but it isn't clear to me that will be substantial enough to make a difference.

Each cell contains 1 copy of our nuclear DNA (in 23 pairs of chromosomes), but it has lots (possibly > 1000) of copies of the mtDNA (http://en.wikipedia.org/wiki/Mitochondrial_DNA). The greater number of mtDNA copies makes it easier to pick up.

MememicBottleneck · 8 January 2009

rijkswaanvijand said: Maternal lines... So if Neandertal women were damned ugly, ...

Now you know why beer is almost as old as humanity.

Ron Okimoto · 8 January 2009

KP said:
Joshua Zelinsky said: KP, AIG has already commented on prior mitochrondial DNA studies of neanderthals( http://www.answersingenesis.org/tj/v12/i1/mtdna.asp ) I suspect they will rehash the points made there.
Wow. I scrolled down and down waiting for some "point" to emerge. Apart from misrepresenting the facts somewhat, the argument seems to accept that neanderthals existed and date back to, well, further than the biblical records would allow. Note to newer newcomers than me: consistency is not one of the creationist's strong points...
Now onto more substantative issues: Can someone explain why mitochrondial DNA is easier to recover than nucleic DNA? There's no obvious reason to the non-experts like me. The only thing that occurred to me is there are many copies of the same mitochrondrial DNA in each given cell but it isn't clear to me that will be substantial enough to make a difference.
I'm an ecologist, but my understanding is that mtDNA is used because it has a relatively fast and consistent rate of nucleotide substitutions. So it can be used more like a "molecular clock" if you can tolerate that term, particularly for lineages that diverged relatively recently -- like neanderthals and modern humans. Also, the substitutions will generally be neutral so the additional noise of selection acting on them won't confound things. I'm sure someone will correct me if I'm reaching too far on this or have it wrong in some other way...

Mostly OK, but mitochondrial DNA actually has less chance of mutations being neutral. There is a hypervariable noncoding region that is part of what is called the D-loop. They went after the hypervariable region first because it gives the biggest bang for the buck. If you can only recover a short sequence of DNA you go after the piece of DNA that will give you the most information interms of differences between two species. There isn't a lot of noncoding DNA in mtDNA. It is packed with two ribosomal RNA genes, enough tRNAs to make the mitochondrial encoded proteins, and 13 protein coding genes with no introns. It does change more rapidly than nuclear DNA, but one of the main reasons why ancient DNA studies go after it is that it is at a high copy number. You might have two copies of any nuclear encoded gene per cell, but mtDNA is only 17 kilobase-pairs and can be around 1% of the DNA in a cell. By comparison the nuclear genome is 3 billion base-pairs. So with mtDNA you have a rapidly evolving piece of DNA that has a bunch of copies per cell (something important when you are looking for surviving DNA sequences in ancient tissue samples).

Jim · 8 January 2009

This makes me wonder what the distant future of humanity holds for us - I think it would be impossible for separate populations of humans to evolve independently now simply because the human population is so mobile and interaction between peoples from every corner of the globe is constant due to modern transportation.

But suppose that we did colonize distant solar systems - given enough time, I wonder what would become of separate humans in vastly different environments. It’s so exciting!

Such is the stuff of science fiction, I suppose, but it’s this kind of research that makes the very best use of human imagination...

Jim · 8 January 2009

MememicBottleneck said:
rijkswaanvijand said: Maternal lines... So if Neandertal women were damned ugly, ...
Now you know why beer is almost as old as humanity.

It's funny 'cause it's true.

Henry J · 8 January 2009

It does change more rapidly than nuclear DNA,

Is that because the organelles reproduce more often than the cell in which they're inmates? Henry

Tinnie · 8 January 2009

rijkswaanvijand said: Maternal lines... So if Neandertal women were damned ugly, Neadertal men would subsequently choose to mate with human women while human men wouldn't even think of doing the same with Neandertal women.. And we would still see no sign of interbreeding from the mtDNA. Farfetched?

Not sure this theory will fly. Leviticus 18:23 Neither shalt thou lie with any beast to defile thyself therewith: neither shall any woman stand before a beast to lie down thereto: it is confusion. Apparently there was a small problem with men picking less than attractive partners several thousand years ago, so much so that the god of the entire universe was forced to address the issue in writing.

KP · 9 January 2009

Ron Okimoto said: Mostly OK, (snip)

Cool! Thanks, Ron!

Marek14 · 9 January 2009

Jim said: This makes me wonder what the distant future of humanity holds for us - I think it would be impossible for separate populations of humans to evolve independently now simply because the human population is so mobile and interaction between peoples from every corner of the globe is constant due to modern transportation. But suppose that we did colonize distant solar systems - given enough time, I wonder what would become of separate humans in vastly different environments. It’s so exciting! Such is the stuff of science fiction, I suppose, but it’s this kind of research that makes the very best use of human imagination...

My guess is that the sexual fetishes will now start to play their part :) Most people who have a fetish (or other strong interest) would prefer a partner with the same (or complementary) fetish. While number of individuals with a given fetish might be low, the global culture makes it easier for them to find each other. And, if sexual preferences have any genetic basis, you have a scenario where sexual selection might be posed to dominate. The preferences would get stronger each generation, until the varying sexual habits cause sympatric separation of humans into multiple species :)

Eric Finn · 9 January 2009

I am still intrigued by the idea of a similar graph, but this time taking the chimpanzee group as a reference. Would it show a wide distribution (how wide) for chimps and two closely-spaced narrow spikes, one for the Neandertals and one for the humans?

R Smith · 9 January 2009

"Is that because the organelles reproduce more often than the cell in which they’re inmates?

Henry"

(Wish I knew how to do a quote box)

It's because certain cells have higher energy requirements than others (stuff like nerves and muscle) and mitochondria are the organelles responsible for utilising oxygen to liberate energy from carbohydrates. The cells that need more energy have more copies of the mitochondria.

eric · 9 January 2009

R Smith said: (Wish I knew how to do a quote box)

Google "html blockquote tag" Other html tags work too, like bold and italics If you are really lazy :-) you can just reply to this post. That lets you see the tags for blockquoting, bolding, and italicizing I used in this post.

Kevin B · 9 January 2009

Eric Finn said: I am still intrigued by the idea of a similar graph, but this time taking the chimpanzee group as a reference. Would it show a wide distribution (how wide) for chimps and two closely-spaced narrow spikes, one for the Neandertals and one for the humans?

Seems a fair bet to me.... As the OP notes, plotting intra- and inter-species difference on the same graph is somewhat misleading. Would it be better to plot the three species as a triangle of dots on the page, with the distance between any pair of dots being the measure of the "average" difference between the two species represented, and the size of each dot representing the variablity within the species? Of course, the modern human and chimp dots would be on a different page to the 38,000 year old Neandertal sample.... Presumably, if it were possible to construct a set of these graphs working back in time when the species diverged, it would tell us something about how they diverged. Incidentally, is the double peak in the human/human difference plot merely an artefact of the data, or does it represent a real drift towards speciation?

eric · 9 January 2009

Kevin B said: Incidentally, is the double peak in the human/human difference plot merely an artefact of the data, or does it represent a real drift towards speciation?

And would this drift lead to human speciation at all, or just a single human species with two distinct types of mitochondria? Or am I completely missing the concept of mtDNA by asking that question?

Henry J · 9 January 2009

To lead to speciation, something would have to discourage interbreeding between the two types, i.e., the difference would have to somehow influence fertility or mate preference.

Henry

JimF · 9 January 2009

Kevin B said: Incidentally, is the double peak in the human/human difference plot merely an artefact of the data, or does it represent a real drift towards speciation?

Neither. Green et al covered that:

Among the humans, the number of differences ranges from 2 to 118, and is bimodal. The peak with a mode around 99 differences contains comparisons that involve at least one member of deep clades containing sub-Saharan African mtDNA. The peak with a mode around 44 differences involves comparisons between individuals outside these clades.

Kevin B · 9 January 2009

JimF said:
Kevin B said: Incidentally, is the double peak in the human/human difference plot merely an artefact of the data, or does it represent a real drift towards speciation?
Neither. Green et al covered that:
Among the humans, the number of differences ranges from 2 to 118, and is bimodal. The peak with a mode around 99 differences contains comparisons that involve at least one member of deep clades containing sub-Saharan African mtDNA. The peak with a mode around 44 differences involves comparisons between individuals outside these clades.

Sometimes the precision of "scientific English" promotes the risk of quotemining. On casual inspection that could read as "sub-Saharan African mtDNA is different to everyone else's." However, am I reading it correctly as "sub-Saharan African mtDNA has much more variation than everyone else's?"

JimF · 9 January 2009

Kevin B said: As the OP notes, plotting intra- and inter-species difference on the same graph is somewhat misleading. Would it be better to plot the three species as a triangle of dots on the page, with the distance between any pair of dots being the measure of the "average" difference between the two species represented, and the size of each dot representing the variablity within the species?

This idea certainly has some merit in this case; it more accurately shows the difference between each pair of groups (at the cost of making it harder to show the details of the pattern of differences in each group. But it quickly breaks down if you want to, say, display lots of species. The problem is that mtDNA sequences diverge in a multidimensional manner (and at a very high dimension), so a two-dimensional graph soon becomes as inadequate as a one-dimensional one as you increase the number of groups you're analyzing.

JimF · 9 January 2009

Kevin B said: Sometimes the precision of "scientific English" promotes the risk of quotemining. On casual inspection that could read as "sub-Saharan African mtDNA is different to everyone else's." However, am I reading it correctly as "sub-Saharan African mtDNA has much more variation than everyone else's?"

Correct. "More variation", at any rate; "much more" might be overstating it.

Henry J · 9 January 2009

However, am I reading it correctly as “sub-Saharan African mtDNA has much more variation than everyone else’s?”

That would make sense, if "everyone else" came from one or a few geologically recent migrations out of that area, and the people in that area had already been diversifying for a long time before that. Henry

JimF · 9 January 2009

MrrKAT said: What if both women were ugly from others side of view but only sapiens had some fermented juice fruits within and he temporarily saw some very very beautiful Ne-Annes.. ? ;)

Funny you should say that. In an earlier paper coauthored by Green about recovery of one million bases of Neanderthal nuclear DNA (Green et al. 2006, Nature 444:330), they say, as part of an analysis comparing N'tal, human and chimp DNA:

... This may suggest gene flow between modern humans and Neanderthals. Given that the Neanderthal X chromosome shows a higher level of divergence than the autosomes (R.E.G., unpublished observation), gene flow may have occurred predominantly from modern human males into Neanderthals. More extensive sequencing of the Neanderthal genome is necessary to address this possibility.

That's only a very tentative result so don't read too much into it, but ... wow.

tresmal · 9 January 2009

So, has anyone written a paper on the role of beer goggles in human evolution?

JimF · 9 January 2009

tresmal said: So, has anyone written a paper on the role of beer goggles in human evolution?

The October 2008 issue of National Geographic had an article about Neandertals, with a reconstruction of a Neanderthal woman as their cover picture. I think you'd need a lethal dose of beer...

tresmal · 9 January 2009

JimF said:
tresmal said: So, has anyone written a paper on the role of beer goggles in human evolution?
The October 2008 issue of National Geographic had an article about Neandertals, with a reconstruction of a Neanderthal woman as their cover picture. I think you'd need a lethal dose of beer...

Ah yes, that would explain why Playboy's "Women of the Pleistocene" issue was such a bust.

Ron Okimoto · 11 January 2009

Henry J said:
It does change more rapidly than nuclear DNA,
Is that because the organelles reproduce more often than the cell in which they're inmates? Henry

There could be various reasons for mtDNA accumulating substitutions at a higher rate. It isn't mutation that we observe, but replacement rate of mutations. There is a population of mtDNA molecules in the cells. A mutation in one has to take over the cell population of mtDNA and make it into the female egg cell. There seems to be some mechanism to do this where only a fraction of the mtDNAs in the cell are chosen for replication. Vertebrate mitochondria may not have effective DNA repair mechanisms. Their polymerase seems to make a higher frequency of transistion mutations than the nuclear polymerases and may make more mistakes overall or they aren't repaired as effectively (the mito DNA polymerase is nuclear encoded and is transported into the mito). There are also the guys that think that the environment of the mitochondria has something to do with the high rate of substitutions. The electron transport chain (the major reason for the existence of the mito is to produce ATP) produces a bunch of free radicals and peroxides as a by-product of the less than 100% efficiency of the system. These may cause DNA damage at a higher rate than is observed in the nucleus.

Jim · 11 January 2009

I assume that Homo S. and Homo N. had a very close common ancestor given their similarities. Do we have clues as to who that could be?

Ron Okimoto · 13 January 2009

Jim said: I assume that Homo S. and Homo N. had a very close common ancestor given their similarities. Do we have clues as to who that could be?

My guess is that the common ancestor between Neandertal and modern humans would have looked more Neandertal-like in the skull. Modern humans are likely the more derived type with their flater face and pentagonal cranium. Neandertal has a skull more like the erectus types that probably coexisted with this common ancestor at that time over 600,000 years ago. Heck, some people might lump the common ancestor with erectus instead of archaic Homo sapiens. Below the neck Neandertals may be the more derived type with a more robust skeleton. More derived just means that those characters have changed more from the ancestral type.

Henry J · 13 January 2009

The October 2008 issue of National Geographic had an article about Neandertals, with a reconstruction of a Neanderthal woman as their cover picture. I think you’d need a lethal dose of beer…

Well, they do say that beauty is in the eye of the beer holder.

Steviepinhead · 13 January 2009

Reed A. Cartwright said: We have to be careful when comparing modern sequences to ancient sequences. The proper comparison is not between Neanderthals and present humans, but rather between Neaderthals and the our ancestors that are contemporaneous with them. Due to the process of coalescence our mt genomes can (and will) be rather divergent from our ancestors, therefore it is difficult to draw conclusions without the additional information about what the variation in our ancestors was like as well.

Perhaps a more detailed explanation of the impact of "coalescence" on the data would clarify Reed's comment, but why don't we have mtDNA sequences from a sufficiently wide sample of anatomically modern humans such that we can, in effect, "correct" for this lack of contemporaneity? Realizing that both anatomically modern humans and Neanderthals go further back in time, let's still draw the "contemporaneous" horizon at 40,000 to 50,000 BP, representing the period of maximum "overlap" in the respective Eurasian ranges of the two hominids. Doesn't the modern human genome contain representative samples of the diversity of that era? After all, Australian aborigines probably took their ancestral copies of human mtDNA into pretty complete isolation > 40 kya, emerging from that isolation only within the last several centuries, a genetic eyeblink. Likewise for the bulk of native americans, who were isolated from the rest of human mtDNA diversity for between 10k and 35k years, depending on which archaeologist you listen to... And subSaharan African mtDNA was relatively isolated from the OoA mtDNA for much of the past 50-60 k years (whence the double peak) -- or, perhaps better put, the OoA groups that budded off, and rebudded, and rebudded, from the subSaharan core population, obtained relative isolation from that parental population... So we have extant populations that effectively split from the parental population, and which went into relatively complete isolation until the Age of "Discovery." And those lineage splits date back more than 10 ky, and as far back as 40-50-60 ky. Accepting that the mtDNA of all these populations has continued to evolve and differentiate over the interim, one would still think that an ancestral anatomically-modern-human mtDNA genome could be reconstructed for approximately 40 to 60 kya? And that this reconstructed genome could be usefully compared with the (admittedly much more limited) sample of Neanderthal mtDNA from roughly the same time period. And, effectively, by modelling the present human variability, isn't that what this the current paper's authors have done?

Doug Watts · 19 January 2009

"However they don’t seem to have been as innovative with tools, or have done much in the way of art, so there’s a widespread suspicion, which I cautiously share, that they weren’t quite as smart or inventive as modern humans."
---

How is this any different from saying that humans from cultures that did not use wheels are not as "smart or inventive" as humans from cultures that used wheels?

Without hard, compelling evidence, this sounds like suspiciously like cultural prejudice.

Henry J · 19 January 2009

What if their art was using materials that don't last for thousands of years? In that case we wouldn't know about it.

JimF · 29 January 2009

Doug Watts said: How is this any different from saying that humans from cultures that did not use wheels are not as "smart or inventive" as humans from cultures that used wheels? Without hard, compelling evidence, this sounds like suspiciously like cultural prejudice.

Henry J said: What if their art was using materials that don’t last for thousands of years? In that case we wouldn’t know about it.

These objections are why I'm cautious. But, if they were doing art, you'd think they'd have done some of it in durable materials over the course of a couple of hundred thousand years. Ditto, if they really were as inventive as modern humans, you'd think there'd be some sign of it, somewhere, somewhen. Recent cultures that didn't use wheels did demonstrate their ingenuity in other ways. Not that Neandertals were without it, but the evidence is indicative (I agree, not conclusive!) to me that they weren't quite on a par with modern humans.