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Author Topic:   Multi-regionalism and Probability
sfs
Member (Idle past 2534 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 16 of 30 (388406)
03-05-2007 10:06 PM
Reply to: Message 4 by Jon
03-02-2007 2:12 AM


Re: Ahem :: Clearing up Some Points
quote:
ut of Africa:
The Out of Africa hypothesis (OOA) states that H. sapiens evolved in Africa about 100,000 years ago, and then migrated outward to where populations of H. erectus and H. neandertalensis were living. The sapiens then out competed/killed off the native populations and took their place. Separate racial characteristics, such as skull features (mentioned in OP), then evolved to what they are today. It claims that mtDNA variation supports the idea.
Multi-regional:
The Multi-regional hypothesis (MH) states that after H. erectus, H. neandertalensis, etc. moved from Africa, their populations, though separated, continued to interact and breed. In a sense, they became a "world population," and not just separate populations in complete isolation. On a global scale then, modern humans--which are considered in MH to be only a variety of the entire H. sapien line that they believe includes erectus and neandertalensis--evolved from these other populations. Evidence for MH comes from the "ginger gene", and fossil similarities between regional skull characteristics, especially those found in Asian H. erectus populations and modern populations.
An Out of Africa model is supported not just by mtDNA, but by X, Y and autosomal data. As far as genetics is concerned (and genetics is very powerful here), full multiregional models are dead. The choice at this point is between complete genetic replacement by African migrants and merely large-scale replacement. The bulk of loci point to an African origin. A few loci look like they may represent introgression from archaic Homo outside the African line, although none are considered conclusive. (One of the most suggestive, if I remember correctly, is the chromosome 17 inversion found by deCODE Genetics.) I have never seen a strong case made that MC1R (the "ginger gene" you referenced) is in this category. The link you posted is hard to do anything with, since it's just a news report, with no attached paper. The scientist quoted, Rosalind Harding, doesn't seem to have published anything supporting this claim. The paper she (and others) did publish on MC1R (Am. J. Hum. Genet. 66:1351-1361, 2000 -- a fine paper) doesn't reach any such conclusion; it finds the European variants in the gene to have an age consistent with other loci examined.
Estimates of total genetic diversity lead to the same conclusion. The effective population size of humans 100 - 200 thousand years ago was 10-15,000. It is very hard to see how a population that small could have been spread out across Africa, Europe and Asia while still maintaining the high levels of gene flow needed to keep regional differentiation in check.

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1.61803
Member (Idle past 1504 days)
Posts: 2928
From: Lone Star State USA
Joined: 02-19-2004


Message 17 of 30 (388594)
03-06-2007 4:00 PM
Reply to: Message 10 by kuresu
03-02-2007 5:27 PM


Re: Oliver!!! i want somore!!
Hello..
quote:
A hypothesis is worthless when grounded in such unprovable assumptions.
Agreed..but I can assure it does not stop theorist from generating some doozys...to include String theory and it's spin offs or the mating habits and rituals of extinct taxa. It sucks when the facts get in the way of a good hypothesis.
Edited by 1.61803, : typos

"One is punished most for ones virtues" Fredrick Neitzche

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Jon
Inactive Member


Message 18 of 30 (388778)
03-07-2007 4:59 PM
Reply to: Message 16 by sfs
03-05-2007 10:06 PM


Re: Ahem :: Clearing up Some Points
An Out of Africa model is supported not just by mtDNA, but by X, Y and autosomal data. As far as genetics is concerned (and genetics is very powerful here), full multiregional models are dead.
Are they, really?
quote:
Recent research suggests that variation in Y-chromosome DNA is relatively low, and a hypothetical ”Adam’ ... may have lived at an even younger date than the hypothetical mitochondrial ”Eve’.
In whatever way these "scientists" are reading the DNA evidence, they are making a mistake. The genetics should show a rather agreeable date, but it shows really old mtDNA populations, and relatively younger Y-chromosome DNA populations; this is only explainable if we realize that current methods for genetic reading are semi-(if not entirely)-flawed.
I believe that the genes that define our sapiens variation may, indeed, have arisen mostly in African populations, but that these genes (not the individual creatures themselves) spread through interbreeding, slowly becoming incorporated into already existing populations of what we would call H. erectus, and slowly altering what is really the erectus variety of Humans to become the modern variety. Other "human" traits could also have arisen in other population outside of Africa, and spread to the rest of the erectus world.
And then:
quote:
In [the case of beta-globin, the DNA coding for which is found on chromosome 11], there are beta-globin types found in modern Asians, but not Africans, which appear to have been evolving their distinctive patterns for at least 200,000 years. This would suggest local continuity in Asia, which goes back well beyond the time of the supposed ”Out of Africa’ dispersal.
Genetic studdies seem glitchy at best for OOA, and at the far end, seem to support MH moreso.
Now, I should really be puting this in my report . Laters.
Max
________________
Chris Stringer and Peter Andrews. The Complete World of Human Evolution (New York: Thames & Hudson Inc., 2005), 177.
Ibid., 177.

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jar
Member (Idle past 394 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 19 of 30 (388787)
03-07-2007 5:19 PM
Reply to: Message 18 by Jon
03-07-2007 4:59 PM


Re: Ahem :: Clearing up Some Points
In whatever way these "scientists" are reading the DNA evidence, they are making a mistake.
And you base that revelation on??????????
The genetics should show a rather agreeable date, ...
Why?
... but it shows really old mtDNA populations, and relatively younger Y-chromosome DNA populations;
Correct.
this is only explainable if we realize that current methods for genetic reading are semi-(if not entirely)-flawed.
Why?
Would it not be possible to have a bottleneck incident where many males came through but few females? After that point in time all the descendants would carry the genes of those few women but also of any of the men.
Would it not be possible at some later time to have a bottleneck incident where many women came through but few males. After that point in time all the descendants would carry the genes of those few men but also of any of the women.

Aslan is not a Tame Lion

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sfs
Member (Idle past 2534 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 20 of 30 (388818)
03-07-2007 10:47 PM
Reply to: Message 18 by Jon
03-07-2007 4:59 PM


Re: Ahem :: Clearing up Some Points
quote:
Are they, really?
Yes, they're really dead. Pushing up daisies.
quote:
In whatever way these "scientists" are reading the DNA evidence, they are making a mistake. The genetics should show a rather agreeable date, but it shows really old mtDNA populations, and relatively younger Y-chromosome DNA populations; this is only explainable if we realize that current methods for genetic reading are semi-(if not entirely)-flawed.
Sorry, but that's wrong -- there are several reasons for the Y chromosome and mtDNA to have different ages. One is different effective population sizes. It is common for human males to take multiple mates, meaning the number of breeding males is smaller than the number of breeding females; smaller effective population size implies a smaller expected age of the locus.
Natural selection may also be quite important on both the Y and mtDNA. Since neither recombines, an advantageous mutation anywhere on either will sweep the entire chromosome to fixation with it, dramatically lowering the diversity and the age estimate. This is why neither the Y nor mtDNA is a good clock for measuring demographic history.
Finally, even if no other processes are at work, the random variation in the age for a single locus (and mtDNA and the Y each act as a single locus) is very large. The expected time to the most recent common ancestor for these loci is N/2, where N is the effective population size. The estimated N for humans is in the range of 10 to 15 thousand, giving an expected age of ~100 - 150 thousand years. The standard deviation on the age, however, for different loci is also equal to N/2, so the expectation is for 100,000 +/- 100,000 years. Finding one at 70,000 and one at 180,000 (or whatever particular estimates you like) is not surprising at all.
quote:
In [the case of beta-globin, the DNA coding for which is found on chromosome 11], there are beta-globin types found in modern Asians, but not Africans, which appear to have been evolving their distinctive patterns for at least 200,000 years. This would suggest local continuity in Asia, which goes back well beyond the time of the supposed ”Out of Africa’ dispersal.
Even under a purely Out of Africa model (which there's no reason to believe is correct), one would expect to find some loci that look like they root outside Africa (see Takahata, Lee and Satta, "Testing Multiregionality of Modern Human Origins", Mol Biol Evol. 2001 Feb;18(2):172-83.) There are indeed some loci that look like they represent an archaic non-African admixture (although I haven't seen betaglobin proposed that way that I can remember -- what paper does the book cite?), and that may be what they are; a better example might be the X-linked locus discussed in Garrigan D, Mobasher Z, Severson T, Wilder JA, Hammer MF, "Evidence for archaic Asian ancestry on the human X chromosome",
Mol Biol Evol. 2005 Feb;22(2):189-92. But the large majority show Africa as the root. So a contribution of 5 or 10 percent of non-African ancestry is quite plausible, but 50% is not.

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Jon
Inactive Member


Message 21 of 30 (389288)
03-12-2007 12:33 PM


MtDNA Report Finished:
My report:
Extension was given by instructor for the report, so I removed the link for now
It should serve as an effective response to questions about why I do not find mtDNA evidence convincing as absolute proof for OOA.
I would like to ask that this report does not recieve the same treatment as my last I posted. Do not attack the style of the report, or how it's written, or the language used, or the conventions, or its straigh-forwardness/lack thereof. Instead, I want to address its content, and how the argument pertains to the subject of this thread. I am not posting this paper as an effort to show off my writing any more than a post on the boards could be seen as such an effort. It is, like any post, meant to convey the information, and it is the information on which I am hoping you will all focus. Why I post this as a paper instead of as a standard post is simply for the fact that I have already written this once, and do not wish to do so twice.
Jns
Edited by Jns, : halvzees, onzees, twozees! :-
Edited by Jns, : Removed link.

In considering the Origin of Species, it is quite conceivable that a naturalist... might come to the conclusion that each species had not been independently created, but had descended, like varieties, from other species. - Charles Darwin On the Origin of Species

Replies to this message:
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 Message 27 by fallacycop, posted 03-12-2007 2:15 PM Jon has replied

  
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 22 of 30 (389292)
03-12-2007 1:29 PM
Reply to: Message 21 by Jon
03-12-2007 12:33 PM


Re: MtDNA Report Finished:
First, mtDNA codes for”or produces”very few things in our body; save for an occasional protein, mtDNA is completely useless3
This is just stupid. Without mtDNA you wouldn't have any functional mitochondria and you wouldn't be alive. You wouldn't just be ill or have a severe developmental defect you would never have got beyond being a one celled zygote.
This just seems as if you have no idea what mitochondria are.
Without mixture from the father, the only variations arising in mtDNA are natural mutations resulting from copying mistakes during conception.
This isn't right, there is no particular significance to conception. It would be more correct to say mtDNA only accrues mutations arising in the maternal germ line. It might also be a good idea to say why this is and why mtDNA is actually unique, i.e. it is seperate from the nuclear genome and contained in multiple copies in the mitochondria of the cell.
It is also thought that there are some rare cases of contribution of paternal mtDNA, which might be at least as big if not a bigger problem for estimates based on an assumption of solely maternal pattern of inheritance than your variations in population density would be.
Because mtDNA doesn't code for many things, these mutations continue to be passed on, i.e., people don't die from the mutations, and so live to pass them on.
Again this is wildly wrong. I think what you may need to do is specify that this analysis focuses on a particular stretch of mtDNA called the
Control region which doesn't code for any proteins and where mutations are usually considered to be neutral but what is true for the control region is certainly not true for all of the mtDNA. I don't know if this research was based on the control region, but that is the only way I can see any of your statements actually being anything other than plain wrong.
Just a few preliminary thoughts.
TTFN,
WK
Edited by Wounded King, : No reason given.

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fallacycop
Member (Idle past 5521 days)
Posts: 692
From: Fortaleza-CE Brazil
Joined: 02-18-2006


Message 23 of 30 (389293)
03-12-2007 1:46 PM
Reply to: Message 19 by jar
03-07-2007 5:19 PM


No need for bottleneck
There is no need for any bottlenecks at all to explain the evidence.
Picture a culture where mem regularly kill all the men from neighbough tribes, but leave the womem alive (and pregnant). Not to hard to imagined, is it?
That would lead naturally to a population for which the genetic analysis of the Y-chromossome's DNA would seem to tell us a different story then the genetic anaysis of the mitochondrial DNA.
In fact, it would most probabily give us a more recent "ADAM" and a more ancient EVE.

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jar
Member (Idle past 394 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 24 of 30 (389294)
03-12-2007 1:51 PM
Reply to: Message 23 by fallacycop
03-12-2007 1:46 PM


Re: No need for bottleneck
Isn't that still a bottleneck?
Whether the cause of the disproportionate presence is due to intentional actions or some naturally occurring event, isn't the end result the same.
Edited by jar, : No reason given.

Aslan is not a Tame Lion

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fallacycop
Member (Idle past 5521 days)
Posts: 692
From: Fortaleza-CE Brazil
Joined: 02-18-2006


Message 25 of 30 (389295)
03-12-2007 2:05 PM
Reply to: Message 24 by jar
03-12-2007 1:51 PM


Re: No need for bottleneck
Isn't that still a bottleneck?
I wouldn't call it a bottleneck because in the scenario I described there isn't necessarily a sharp decrease in the human population. Just a series of sporadic genocydes (like Ruanda or Sudan in modern days).
If you add to it the fact that most genocydes were directed towards men, but left many womem alive, you get the result of selectively reducing the Y-chromossome's variability
Edited by fallacycop, : typo

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Jon
Inactive Member


Message 26 of 30 (389297)
03-12-2007 2:06 PM
Reply to: Message 22 by Wounded King
03-12-2007 1:29 PM


Re: MtDNA Report Finished:
My apologies for the incorrect information. That information was taken primarily from the source cited in footnote one of page 2.
Their information on mtDNA is that it is, indeed, rather pointless. I will definately take what you said into my mind, but as for the paper it should not be too big a concern, as the primary points still apply, only they apply in regards to the "control region," instead of to all of the mtDNA strand--I would assume that it is this region that is used in mtDNA analysis of population history.
Jon

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fallacycop
Member (Idle past 5521 days)
Posts: 692
From: Fortaleza-CE Brazil
Joined: 02-18-2006


Message 27 of 30 (389298)
03-12-2007 2:15 PM
Reply to: Message 21 by Jon
03-12-2007 12:33 PM


Re: MtDNA Report Finished:
Jns, there is an important aspect to this mitochondrial study that you have not addressed at all.
The study doesn't simply count the number of mitochondrial variants.
It also measures the genetic distance between them (this can be taken as a proxy for how long ago the two lineages diverged (whithin statistical fluctuations of course)).
And it turns out that all the lineages outside of Africa are more closely related to each other when compared with the lager variety found in Africa.
How do you explain that with your model?

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Jon
Inactive Member


Message 28 of 30 (389302)
03-12-2007 2:37 PM
Reply to: Message 27 by fallacycop
03-12-2007 2:15 PM


Re: MtDNA Report Finished:
quote:
How do you explain that with your model?
In my report, I do not argue in favour of any particular model; instead, I argue against the OOA interpretation of mtDNA data. According to mtDNA, either population fluctuations could explain it or OOA. And so, I argue that neither should be assumed correct.
Because the OOA seems to be the currently accepted theory, I decided to focus on it could being wrong slightly more than on why population fluctuations can be equally as wrong.
Jon

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fallacycop
Member (Idle past 5521 days)
Posts: 692
From: Fortaleza-CE Brazil
Joined: 02-18-2006


Message 29 of 30 (389307)
03-12-2007 3:19 PM
Reply to: Message 28 by Jon
03-12-2007 2:37 PM


Re: MtDNA Report Finished:
You didn't address the point I made in my previous post, about the lager genetic variability observed among african populations.
I'll give you another one to think about:
The MtDNA variation observed in Populations around the world allows us (By us I mean the scientists that did the work) to reconstruct a tree of relationships among those populations. It turns out that all the populations outside of Africa end up allocated in one Branch, while the African populations end up in many branches (That's to be expected by the OOA theory, but is hard to understand from the oposing point of view)

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DBlevins
Member (Idle past 3776 days)
Posts: 652
From: Puyallup, WA.
Joined: 02-04-2003


Message 30 of 30 (389315)
03-12-2007 5:20 PM
Reply to: Message 8 by kuresu
03-02-2007 2:20 PM


Re: Ahem :: Clearing up Some Points
I want to see the proof that H. sapiens could in fact interbreed with erectus, neandertalensis, and heidelburgensis. Or for that matter, that erectus and neandertalensis could inertreed, or that erectus and heidelgurgensis could interbreed, or any other combination (seeing as how the MRH requires them all being able to interbreed, from what I understand).
While so far the evidence for hybridization is weak and mtDNA evidence seems to suggest that there was no gene flow between H. neanderthalensis and H. sapiens, it doesn't rule it out entirely. A study done by Clifford Jolly on the Papionina subtribe of monkeys suggests that hybridization can occur between hominine genera that have diverged as long as 4 mya. It is possible that advantageous genes survived as the hybrid zone shifted. (Jolly, CJ. 2001. A Proper Study for Mankind: Analogies from the Papionin Monkeys and Their Implications for Human Evolution. Yearbook of Physical Anthropology. 44: 177-204).
Here is a paper that suggests that there was some hybridization between the populations: Hardy, J. et al. 2005. Evidence suggesting that Homo neanderthalensis contributed the H2 MAPT haplotype to Homo sapiens. Biochemical Society Transactions. 33: 582-585
quote:
ABSTRACT: The tau (MAPT) locus exists as two distinct clades, H1 and H2. The H1 clade has a normal linkage disequilibrium structure and is the only haplotype found in all populations except those derived from Caucasians. The H2 haplotype is the minor haplotype in Caucasian populations and is not found in other populations. It shows no recombination over a region of 2 Mb with the more common H1 haplotype. The distribution of the haplotype and analysis of the slippage of dinucleotide repeat markers within the haplotype suggest that it entered Homo sapiens populations between approx. 10000 and 30000 years ago. However, sequence comparison of the H2 haplotype with the H1 haplotype and with the chimp sequence suggests that the common founder of the H1 and H2 haplotypes was far earlier than this. We suggest that the H2 haplotype is derived from Homo neanderthalensis and entered H. sapiens populations during the coexistence of these species in Europe from approx. 45000 to 18000 years ago and that the H2 haplotype has been under selection pressure since that time, possibly because of the role of this H1 haplotype in neurodegenerative disease.

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