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Author Topic: Neanderthal vs. Moderns: A cautionary statement.  (Read 2156 times)
Jacques Cinq-Mars
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« on: August 30, 2002, 09:39:55 AM »

All,

The following abstract points to the danger of taking at face value or being overly enthusiastic about many of the statements (made by various workers, in the last few years) contending – on the basis of mtDNA sequencing, analyses, and comparisons – that Neanderthals and early AMH were sufficiently different (genetically speaking) to be categorized as two separate species. This is supported by a number of other recent comments (various authors and personal communications) also pointing out the enormous analytical and corollary interpretative difficulties that can result from yet-to-be fully controlled problems of contamination and an equally poorly understood, complex set of diagenetic modifications. Incidentally, it should be noted that such modifications are likely to vary immensely in time as well as from one archaeological deposit to another. In this regard, mention can be made of a number of recent observations regarding the fact that undisturbed bone remains found in relatively stable (through time) cold, northern environments are less likely to have undergone the complex and, sometimes, massive diagenetic changes that are exhibited by bones recovered in temperate and, particularly, increasingly southern environments where diagenetic modifications are known to have rendered the bones unfit for C14 dating and, perforce, molecular types of study. Perhaps it is time for some molecular analysts dealing with matters of human evolution to begin factoring in some of these taphonomic realities.

Jacques Cinq-Mars

Molecular Biology and Evolution 19:1359-1366 (2002)

A Reanalysis of the Ancient Mitochondrial DNA Sequences Recovered from Neandertal Bones.

Gabriel Gutiérrez*, Diego Sánchez{dagger} and Antonio Marín*

*Departamento de Genética, Universidad de Sevilla, Spain;
{dagger}Instituto de Biología y Genética Molecular, Universidad de Valladolid, Spain

Recent reports analyzing mitochondrial DNA sequences from Neandertal bones have claimed that Neandertals and modern humans are different species. The phylogenetic analyses carried out in these articles did not take into account the high substitution rate variation among sites observed in the human mitochondrial D-loop region and also lack an estimation of the parameters of the nucleotide substitution model. The separate phylogenetic position of Neandertals is not supported when these factors are considered. Our analysis shows that Neandertal-Human and Human-Human pairwise distance distributions overlap more than what previous studies suggested. We also show that the most ancient Neandertal HVI region is the most divergent when compared with modern human sequences. However, the opposite would be expected if the sequence had not been modified since the death of the specimen. Such incongruence is discussed in the light of diagenetic modifications in ancient Neandertal DNA sequences.
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lagarvelho
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« Reply #1 on: August 30, 2002, 11:34:42 PM »

Jacques:

Has anyone responded to this yet?  I should think some in the field might feel challenged. . . .
Anne G
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Daryl Habel
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« Reply #2 on: August 31, 2002, 01:11:35 AM »

Dear Anne,

I would think so, also.  But I've been invading the Jackson bars tonight, so it's dangerous out there.  But the thread caught my interest, so I'll follow it tomorrow (that is, unless the Jackson 6'5" group catch me an throw me in jail) in which case my reading the answers will have to wait ntil Sunday.

I'm sure you know what I mean.

Regards,
Dar

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Daryl Habel
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lagarvelho
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« Reply #3 on: August 31, 2002, 01:02:43 PM »

Dar:

I get the picture.  And I think I can wait patiently until Sunday  <vbg>
Anne G
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Greg
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« Reply #4 on: September 03, 2002, 11:06:59 AM »

It seems to me that despite the problems, the bias in data that would be predicted by MRE vs. OOA or any other hypothesis can be used to evaluate different models. If the DNA is all messed up, then there would be no consistency in results.  If the DNA is somewhat messed up, there may be non-random but fuzzy results.  That seems to be what we are typically seeing, and in a manner that supports Neanderthals as a pretty distant population vis-à-vis living humans.  
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lagarvelho
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« Reply #5 on: September 03, 2002, 06:49:54 PM »

Greg:

I guess I would say in reply that Neandertals show distinct mtDNA, and nobody questions that.  How "distant" the actual DNA configuration may have been(since we don't have any nuclear DNA from Neandertals to work with, and since apparently mtDNA can mutate pretty fast), depends on what you think of as "distant".  And I guess I will leave it at that and let the "experts"(real or otherwise)argue this one out.
Anne G
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John Goodrum
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« Reply #6 on: September 08, 2002, 03:13:19 PM »

More from Klein & Takahata -


“For those who do not read scientific reports, the journalists conveyed the message in no uncertain terms as a clear home run for the multiregionalists in their match against the uniregionalists.  In reality, however, the [Lake Mungo 3] sequence does not support any such conclusions.  The position of the sequence on the phylogenetic tree depends on the choice of extant H. sapiens sequences included in the sample and on the tree drawing method used.  In many trees, both the LM3 and the numt sequences position themselves within the cluster of contemporary human sequences and, as the authors themselves admit, “trees in which the LM3/insert lineage branched before the MRCA of contemporary human sequences were not significantly more likely than trees in which this lineage diverged after the MRCA of contemporary human sequences.”  In other words, you can take the tree that you find most appealing and the authors obviously preferred the one showing the LM3/numt sequences to be outside the cluster of extant human sequences.  However, even if one were to accept this placement as genuine, it would still not provide evidence for the multiregional and against the uniregional hypotheses.  It could be interpreted alternatively as evidence that mtDNA lineages existed in prehistoric H. sapiens that no longer persist in contemporary humans.  The extinct lineages may have been replaced by the ancestors of the currently existing lineages which spread through the human species either by random genetic drift or by selection acting on one or several of the genes borne by the nonrecombining mtDNA molecules.

Of course, the same reservations must also apply to the interpretation of the Neandertal sequences.  Their position outside the cluster of modern human sequences is largely reproducible and independent both of sampling and the method used.  Nevertheless, it by no means provides evidence that Neandertals did not contribute genes to the H. sapiens gene pool and hence that they were “replaced” by modern humans.  The apparent absence of H. neanderthalensis mtDNA variants in the H. sapiens gene pool could reflect the possible extinction of Neandertal lineages by drift or selection following the initial mixing of the two gene pools.  Moreover, in the collection of contemporary human sequences, there are pairs that differ from each other to a greater extent than certain contemporary human sequences differ from the Neandertal sequences:  the minimum number of substitutions between Neandertal and contemporary human mtDNAs is 13, whereas the maximum number of substitutions in comparisons between mtDNAs of living humans is 22.  This observation is, of course, inconsistent with the conclusion that H. neanderthalensis and H. sapiens were two distinct, noninterbreeding species, because if they were, any overlap in mtDNA variation between them should have been removed by evolution subsequent to species divergence.  Although the inconsistency can be explained by postulating multiple changes that obscure the phylogenetic signal at some nucleotide sites, it can be argued - as the proponents of the multiregional hypothesis indeed have done - that this explanation is an ad hoc postulate introduced to avert the downfall of the uniregional hypothesis.  In all fairness, therefore, of the conclusions reached by Krings and coworkers and echoed by Ovchinnikov and his associates, only one is warranted:  the sequences are most likely of Neandertal origin.  The rest are overinterpretations reflecting a subjective bias toward the uniregional model.  Viewed objectively, neither the Neandertal nor the ancient Australian sequences resolve the controversy regarding the origin of modern H. sapiens.  Indeed, it is doubtful that mtDNA studies ever will.  Despite the fanfare that accompanied the publication of the sequences of Neandertal and other fossil mtDNA sequences, the actual contribution of these sequences to the resolution of scientific questions has thus far been minimal.”

-- Klein & Takahata, _Where Do We Come From? The Molecular Evidence for Human Descent_, Springer-Verlag 2002, p307-8.


JG


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Bob Stimson
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« Reply #7 on: October 12, 2002, 07:51:58 PM »


It seems to me that despite the problems, the bias in data that would be predicted by MRE vs. OOA or any other hypothesis can be used to evaluate different models. If the DNA is all messed up, then there would be no consistency in results.  If the DNA is somewhat messed up, there may be non-random but fuzzy results.  That seems to be what we are typically seeing, and in a manner that supports Neanderthals as a pretty distant population vis-à-vis living humans.  


I'm a layman, and these are layman comments:

It would seem that Neandertals would have to be pretty distant from living humans. The paper "Y genetic data support the Neolithic demic diffusion mode," cited elsewhere in this forum, posits that local hunter-gatherers contributed less than 30% to the original [European] settlements. Now consider that  AMHs coming into Europe were probably much more numerous than the Neandertals and assume, for the sake of argument, that even if there was interbreeding the "swamping" effect would put the Neandertal contribution to the AMH hunter-gatherer gene pool at, say, 10%

Now stir this relatively small contribution (10% of 30%), drift-wise and influx-wise, for the 20,000+ years after the demise of the Neandertals and before the influx of neolithic farmers. Then factor in more millennia of subsequent population growth. As the results of any modeling (I do know about models) of this process would indeed be "fuzzy," we're going to have to look pretty hard for the Neandertal contribution to the modern gene pool. Even so, various visible morphologic and discernible mental Neandertal characteristics could still crop up in modern Europeans, even though the corresponding strips of DNA either have not yet been identified or are so dilute that they never will be.

Wolpoff seems correct in claiming that the one thing people will always do is interbreed, and if they are interfertile (ahh, there's the rub, NPI) there's going to be a contribution whether the geneticists legitimize it or not. As I've said before on other forums, there's a guy right on my street that has a great big nose. And I also know a few people with short attention spans and quick tempers. And some of them even have red hair!
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lagarvelho
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« Reply #8 on: October 12, 2002, 08:55:57 PM »

Bob:

Well, with regard  to "Neandertal characteristics" in modern populations, I suppose you can say the jury is still out.  On the one hand, last year Rosalind Harding came up with the suggestion that Neandertals contributed red hair to certain European populations on the "edge".  Others, such as Chris Stringer deny this contention.  Who is right?  I don't know.  I do think that if, as Wolpoff suggested in his "Paleoanthropology", that Neandertal populations as a whole were pretty darn small,  then the likelihood, statistically speaking, of their contributing *any* genes to modern populations is kind of small, but it could be. . . .And like you, I've seen people that have some awfully big noses.  Incidentally, where I live, at least, I've done "mind-experiments" where I've mentally "morphed" certain people I see on the street, into Neandertals.  It's really not that hard to do if you are reasonably familiar with Neandertal morphology.  I've done it on men and women, and some of the men are perfectly handsome specimens of modern humanity, and some of the women are rather attractive female specimens of modern humanity.  I don't know if anyone else has done such a thing, but it may be that what constitute Neandertal characteristics in some modern populations are very subtle things that most people don't even look for.
Anne G
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Bob Stimson
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« Reply #9 on: October 14, 2002, 04:02:55 PM »

Anne:

Thank you for your charitable comments and for not jumping on me over the examples I chose in order to illustrate my point that a Neandertal genetic contribution to the modern gene pool would be so slight that it would be result in isolated characteristics, of which some might be physically visible and some might be expressed only in obscure behavioral ways that would probably never be definitively identified. I see, by the fact that buttons were included to modify or delete my comment, that these examples were not received entirely in the spirit I intended.

I meant no disparagement of unfortunate people with short attention spans and/or quick tempers or of those with red hair. I chose these examples because they were handy and could be expressed concisely. Before I go on, Let me root through the box of uncatalogued articles I&#8217;ve collected as possible ways to promote verisimilitude in the Neandertal-Cro-Magnon adventure novel I&#8217;m writing, and also let me expand briefly on these controversial and complicated issues. Bear in mind that in each case other researchers have disagreed.

Here is where I got my admittedly simplistic ideas. &#8220;Neandedrtals &#8216;R&#8217; We,&#8221; www.research.ukans.edu/explore/v1n2/neander.html informs us that David Frayer and others consider it quite thinkable that there&#8217;s a bit of Neandertal genetic material in us. Red or ginger hair was posited by Rosalind Harding as reported in &#8220;Redheads are Neanderthal,&#8221;www.thetimes.co.uk/article/),,2-115198,00.html. (Please don&#8217;t blame me if some of these strange-looking URLs do not work; I&#8217;m transcribing them carefully.) ADHD has been attributed, though IMHO not plausibly, to Neandertals in &#8220;The Neandertal Theory,&#8221; www.rdos.net/eng/asperger.htm). Neandertal&#8217;s quick tempers were posited in &#8220;Behaving Like Neandertals,&#8221; www.washingtonpost.com/wp-dyn/articles/A31521-2002Apr22.html.

As I said, I seized on these ideas because they could be concisely allude to in my comment, not because I was trying to advocate them. Now let me try to pick a more positive, though less explicit, example of how a dilute Neandertal genetic contribution could be expressed non-morphologically in hard-to-pin-down mental characteristics. To this end I will focus on left-handedness. Again, remember that I am not advocating these ideas; I&#8217;m just illustrating a point.

About 11 percent of modern people are left-handed: &#8220;Linkage and Lefties,&#8221; www.nature.com/nature/view/021003.html. &#8220;Left-Handedness: Curse, Blessing or Anomaly of Nature,&#8221; www.geocities.com/Athens/Acropolis/1684/lefthand.html points out that the right half of the brain is the center where the visual, spatial and intuitive processes are directed, whereas the left half controls language, logic, and linear thinking. &#8220;Study suggests one gene separates right-handers from lefties,&#8221; www.augustachronicle.com/stories/073097/fea gene.html (note that this URL, rightly or wrongly, includes a blank space)
cites Amar J.S. Klar&#8217;s conclusion that people who have the gene he calls RGHT &#8220;are right-handed and those without it have a 50-50 chance of being either right-handed or left-handed. &#8220;Study: Left-handers have different brains,&#8221; Http://seattletimes.nwsource.com/html/healthscience/134415110 left05.html (note the URL has another of those annoying blanks) posits that &#8220;People who grow up left-handed have a different, more flexible brain structure than those born to take lie by the right hand,&#8221; and that &#8220;There reallyh is a difference in brains that results a more symmetric brain in left-handers, where the two side are more equal.&#8221; &#8220;Being Left-Handed,&#8221; www.his.com/~pshapiro/left.handed.html points out that some of history&#8217;s most creative minds have been left-handed, including Ludwig van Beethoven, Benjamin Franklin, Isaac Newton, Albert Einstein, Charlie Chaplin, Bobby Fischer, Bob Kylan, Paul McCaartney, and Wynton Marsalis [it does not list right-handed geniuses, he he]. &#8220;Are there psychotic Neanderthals amongst us?&#8221; http:cogprints.ecssoton.ac.uk/archive/00000060/00/crow.htm points out that J.T. crow has a different explanation the Sklar for laterization and cerebral dominance, feeling that it comes from an autosomal gene that is X-Y homologous and that the responsible speciation event took place in Homo sapiens, which he obviously equates with AMHs, about 50,000 years ago, which would exclude Neandertals (all this is bound up in his theory of language). Further, I read omewhere, and I can&#8217;t find it in my rat&#8217;s nest, that the scratches on Neandertals&#8217; incisors, from cutting off hunks of meat, indicate that left-handedness was more prevalent among them than in modern people.

All this could be taken (stretch &#8230;. stretch &#8230; wait for it) to suggest that some of the more flexible thinkers and more creative people among us could have received that gift as a result of the Neandertals&#8217; contribution to the modern gene pool.

Why didn&#8217;t I use this example in place of the rather pejorative-sounding ones that I resorted to? Because it takes too long to postulate it.

In choosing more facile examples, I certainly did not mean to disparage anyone. My point was simply that the Neandertal genetic contribution, while probably faint if it exists at all, could still express itself in our modern-day physical and mental makeup in ways that are hard to detect and impossible to ascribe with any certainty.

Nya! Now can I join the circus?
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