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Author Topic:   Neanderthals
JIM
Inactive Member


Message 106 of 159 (59573)
10-05-2003 6:53 PM


The scenario of replacement of Neanderthals by early modern humans is complicated, however, by evidence that the Neanderthals themselves were gradually evolving a modern physique. This raises some intriguing questions: If early modern humans had never existed, would Neanderthals eventually have evolved into a modern form? Is it possible that some Neanderthals actually did evolve into modern humans?
Although early modern humans expanded throughout Eurasia some time between 30,000 and 40,000 years ago, not enough evidence yet exists to prove where they originated or how extensive their expansion may have been. Perhaps Neanderthals in some areas were replaced by modern humans, while those in other regions evolved into modern humans on their own. And if Neanderthals in certain regions were replaced, perhaps some, or maybe even all, of the modern human groups that replaced them had evolved not in Africa, but somewhere in Eurasia, from a Neanderthal stock.
These different possibilities concerning the transition from Neanderthals to modern humans in Eurasia tie into a wider debate on the origin of modern humans in general. Researchers have been puzzling over modern human origins for decades. Numerous explanations have been put forward, but these have tended to lean toward one or the other of two competing theories:
One theory posits that modern humans arose as early as 200,000 years ago in Africa, then spread to the Near East, and then colonized the rest of the Old World. This "Out-of Africa" theory claims that these early modern Africans replaced all indigenous populations of archaic humans, including the Neanderthals, by about 30,000 years ago and that all people living today are descended from these Africans. Support for this theory comes from the fact that fossils of modern humans from Africa and the Near East are much older than those found elsewhere. These fossils are 100,000 to 120,000 years old, and some may be even older. This is long before the period 30,000 to 40,000 years ago when modern humans began appearing in other regions. These early modern Africans and Near Easterners could therefore have served as source populations for subsequent migrations of modern humans.

Replies to this message:
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NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 107 of 159 (59587)
10-05-2003 8:08 PM
Reply to: Message 103 by sfs
10-05-2003 2:55 PM


Of course there is continued debate over the details, we are, after all, dealing with academics. There may never be enough data to settle it once and for all at the detailed level.
[This message has been edited by NosyNed, 10-05-2003]

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NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 108 of 159 (59589)
10-05-2003 8:13 PM
Reply to: Message 106 by JIM
10-05-2003 6:53 PM


The mtDNA and Y chromosome polymorphisms also strongly support the out of africa hypothosis. In addtion, recent archaic h. sapiens find of about 160,000 years ago in africa fit well with the genetic data.
I understand (Nature - Not Found) that there has been enough Neanderthal DNA sequencing done to demonstrate that we have been separate from them for more like 500,000 years.
In addition, I am not aware of any neanderthal evidence in anywhere but Europe. H. erectus is ound in asia and is not the same.
[This message has been edited by NosyNed, 10-05-2003]

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Replies to this message:
 Message 109 by Speel-yi, posted 10-05-2003 10:53 PM NosyNed has replied
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Speel-yi
Inactive Member


Message 109 of 159 (59614)
10-05-2003 10:53 PM
Reply to: Message 108 by NosyNed
10-05-2003 8:13 PM


Alrighty then, battling links from Nature
Nature - Not Found
Quote from abstract:
"Africans have had a huge genetic impact on humanity," he says. "But my analysis really isn't compatible with complete replacement."
Can't post more now...must...watch...stupid...baseball game.

This message is a reply to:
 Message 108 by NosyNed, posted 10-05-2003 8:13 PM NosyNed has replied

Replies to this message:
 Message 110 by NosyNed, posted 10-05-2003 11:17 PM Speel-yi has replied
 Message 112 by sfs, posted 10-06-2003 11:19 AM Speel-yi has not replied

  
NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 110 of 159 (59616)
10-05-2003 11:17 PM
Reply to: Message 109 by Speel-yi
10-05-2003 10:53 PM


I read it. It isn't something that we can judge. It will have to be left to those looking at the detials to arrive at a consensus.
My limited understanding wonders about the use of regular genes that get mixed so much. I'd like to know more of why he choose to use them and why it is ok here when others avoid that.
It doesn't cover the details of "his analysis" so I don't know what the conclusions mean.

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 Message 109 by Speel-yi, posted 10-05-2003 10:53 PM Speel-yi has replied

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Speel-yi
Inactive Member


Message 111 of 159 (59649)
10-06-2003 3:45 AM
Reply to: Message 110 by NosyNed
10-05-2003 11:17 PM


mt DNA is handy because it doesn't recombine during meiosis like chromosomal DNA does, it is also passed only through the female parent to the offspring. Y chromosome DNA also is largely not subject to recombination, so it can be handy as well.
What we see in present day populations is a retention of physical features in humans that have been seen in ancient erectus populations.
http://www-personal.une.edu.au/~pbrown3/dali.html
From the site:
quote:
Wu (1981, 1989) found that most of the cranial dimensions and morphological features of Dali were intermediate between Homo erectus and H. sapiens, with Dali assigned to archaic H. sapiens. Craniofacial anatomy and vault shape are distinct from European Neandertals and earlier European hominids like Petralona and Atapeurca.
What we see is distinct and intermediate forms of hominids that retain features found in modern populations in these geographic areas. Two key words--intermediate and distinct.
What the Out of Africa model proposes is that an isolated population of hominids evolved into modern H. sapiens and then migrated out of Africa to replace the more primative hominids found in those areas. This is an allopatric speciation model and it employs competitive or Gaussian exclusion to explain the sudden disappearance of the erectus types that coincide with the appearance of H. sapiens. Gaussian exclusion only works with 2 separate species that are unable to interbreed and compete for the same niche. It does not work with the same species, if genes are exchanged, then the Out of Africa model falls apart and MRH is the best explanation.
mtDNA can be spread by either migration or gene exchange, it is inconclusive as a means by itself to determine modern origins.
Further, two of the tenets of Darwinism are that 1) populations will have varied traits and 2) that a trait can be selected for by natural selection. Given this, it can be seen that H. erectus could have forms within a population that deviated from the norm enough to be recognized as H. sapiens by modern observers. For an adherant of Regional Continuity, it would not be too surprising to see a specimen dated 160,000 years ago that appeared to be modern since it would still represent a member of an H. erectus that varied from the norm. We could expect to see some forms become more common with reduced selection and possibly become the norm with directional selection.
------------------
Bringer of fire, trickster, teacher.
[This message has been edited by Speel-yi, 10-06-2003]

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 Message 110 by NosyNed, posted 10-05-2003 11:17 PM NosyNed has not replied

Replies to this message:
 Message 113 by sfs, posted 10-06-2003 11:25 AM Speel-yi has replied

  
sfs
Member (Idle past 2533 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 112 of 159 (59715)
10-06-2003 11:19 AM
Reply to: Message 109 by Speel-yi
10-05-2003 10:53 PM


quote:
Quote from abstract:
"Africans have had a huge genetic impact on humanity," he says. "But my analysis really isn't compatible with complete replacement."
There were several significant problems with Templeton's Nature paper, the one he's referring to here. There's good evidence that one of the genes he looked at (MC1R) is under strong purifying selection in Africa and either weak or diversifying selection outside Africa (MC1R controls skin pigmentation), so dating it as if it were a neutral locus isn't right. He redated another locus, increasing its age by an order of magnitude over the age in the original study, but offers no justification for the change. For a more fundamental problem, see
Out of Africa with regional interbreeding? Modern human origins.
Satta Y, Takahata N.
Bioessays. 2002 Oct;24(10):871-5.
Which is largely a response to Templeton's paper.
quote:
Can't post more now...must...watch...stupid...baseball game.
Stupid game? Sounds like you were watching a Red Sox game.

This message is a reply to:
 Message 109 by Speel-yi, posted 10-05-2003 10:53 PM Speel-yi has not replied

  
sfs
Member (Idle past 2533 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 113 of 159 (59718)
10-06-2003 11:25 AM
Reply to: Message 111 by Speel-yi
10-06-2003 3:45 AM


quote:
mtDNA can be spread by either migration or gene exchange, it is inconclusive as a means by itself to determine modern origins.
Yes, but the paper you quoted was about mtDNA haplotypes that arose outside Africa and then increased in some places outside Africa due to selection. You were citing it as if it were evidence that selection had caused the spread of African mtDNA to replace non-African, which it isn't. You also claimed that selection was inconsistent with an Out of Africa model, which isn't true.

This message is a reply to:
 Message 111 by Speel-yi, posted 10-06-2003 3:45 AM Speel-yi has replied

Replies to this message:
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Speel-yi
Inactive Member


Message 114 of 159 (59786)
10-06-2003 5:13 PM
Reply to: Message 113 by sfs
10-06-2003 11:25 AM


quote:
Yes, but the paper you quoted was about mtDNA haplotypes that arose outside Africa and then increased in some places outside Africa due to selection. You were citing it as if it were evidence that selection had caused the spread of African mtDNA to replace non-African, which it isn't.
It has been traditionally viewed that any mtDNA did not have any selective advantage, it was only a passenger carried along by autosomal genetics.
quote:
You also claimed that selection was inconsistent with an Out of Africa model, which isn't true.
Where did I claim this?
My claim is simple: That erectus and sapiens were fully capable of interbreeding, they did not form two separate species in a biological sense.
------------------
Bringer of fire, trickster, teacher.

This message is a reply to:
 Message 113 by sfs, posted 10-06-2003 11:25 AM sfs has replied

Replies to this message:
 Message 117 by sfs, posted 10-07-2003 9:58 PM Speel-yi has replied

  
Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 115 of 159 (59863)
10-07-2003 4:20 AM
Reply to: Message 108 by NosyNed
10-05-2003 8:13 PM


Hi Ned,
There are also some serious problems with the neandertal work (and with ancient DNA from humans and their relatives in general). First, the neandertal mtDNA gives you absolutely no insight as to what the nuclear DNA composition of neandertals were. We only see the maternal line via mtDNA. This is a technical limitation as nuclear sequences from aDNA are difficult to retrieve and have only been done so reproducibly from mammoths and giant ground sloths.
A more serious problem (and one that Svante Paabo and Alan Cooper recently shot themselves in the foot with) is what constitutes an "acceptable" neandertal or cro magnon sequence for example? Paabo made the argument with neandertals but more recently with Cro magnon that if a sequence is retrieved from either and looks modern, there is no way to distinguish it from a modern contaminant. Thus, only divergent sequences are accepted as bona fide neandertal or cro magnon. What the hell kind of science is that then? I know researchers who have pulled out very modern looking sequences from neandertal fossils. The one published Cro magnon sequence is identical (for the portion sequenced) to the first full mtDNA genome published by Anderson and colleagues i.e. plain old normal human mtDNA. These sequences are called into question or outright rejected as valid. So if you can only a priori accept that divergent neandertal or cro magnon (no H. erectus sequence claims have yet been made) sequences are valid the you will a priori determine that they were either a separate species or radically divergent from modern humans...that is just not good science. This was pointed out to Paabo and Cooper by the Italian group that did the Cro magnon sequencing.
My overall point is that one should take the claims made by the ancient DNA community and the human evolution community in general with a grain of salt. They argue as badly as creationists sometimes.

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sfs
Member (Idle past 2533 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 116 of 159 (60011)
10-07-2003 9:49 PM
Reply to: Message 115 by Mammuthus
10-07-2003 4:20 AM


Re: Truncation Selection
quote:
A more serious problem (and one that Svante Paabo and Alan Cooper recently shot themselves in the foot with) is what constitutes an "acceptable" neandertal or cro magnon sequence for example? Paabo made the argument with neandertals but more recently with Cro magnon that if a sequence is retrieved from either and looks modern, there is no way to distinguish it from a modern contaminant. Thus, only divergent sequences are accepted as bona fide neandertal or cro magnon. What the hell kind of science is that then? I know researchers who have pulled out very modern looking sequences from neandertal fossils. The one published Cro magnon sequence is identical (for the portion sequenced) to the first full mtDNA genome published by Anderson and colleagues i.e. plain old normal human mtDNA. These sequences are called into question or outright rejected as valid. So if you can only a priori accept that divergent neandertal or cro magnon (no H. erectus sequence claims have yet been made) sequences are valid the you will a priori determine that they were either a separate species or radically divergent from modern humans...that is just not good science. This was pointed out to Paabo and Cooper by the Italian group that did the Cro magnon sequencing.
I don't see how that follows. If the experiment is done well, the test is one-sided but valid. That is, you can get two answers, "Different from modern humans" and "Can't tell". The Neandertal specimans clearly gave results that were different from modern humans, and reproducibly so. And now that multiple individuals have been tested, there are multiple results, all different from modern mtDNA and clustered together. What alternative hypothesis explains these results?

This message is a reply to:
 Message 115 by Mammuthus, posted 10-07-2003 4:20 AM Mammuthus has replied

Replies to this message:
 Message 119 by Mammuthus, posted 10-08-2003 4:33 PM sfs has replied

  
sfs
Member (Idle past 2533 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 117 of 159 (60012)
10-07-2003 9:58 PM
Reply to: Message 114 by Speel-yi
10-06-2003 5:13 PM


Re: Truncation Selection
quote:
It has been traditionally viewed that any mtDNA did not have any selective advantage, it was only a passenger carried along by autosomal genetics.
What do you mean by "traditionally"? Many analyses have considered the possibility of selection in recent mtDNA and Y evolution. Look at the big Takahata paper on testing multiregionality, or Kaessmann et al's 1999 paper on Xq13.3, or Stumpf and Goldstein's review article on the Y. It has been widely recognized that selection is a possibility that needs to be taken into account when drawing conclusions from any locus (Takahata even modeled it), and especially for mtDNA and the Y, since they're nonrecombining and single-copy.
As for where I got the idea that you thought OoA and selection were incompatible, it was from this:
quote:
The Eve hypothesis postulates that mtDNA was simply carried along with a migrating population. While the MRH states that genes were exchanged and natural selection facilitated the spread of favorable traits found in mtDNA.
(I assume you meant OoA rather than Eve, since a mitochondrial Eve is a feature of any theory of human origins.) "Simply carried along" (especially when contrasted with natural selection) sounds like you're making an absence of selection a postulate of the theory.

This message is a reply to:
 Message 114 by Speel-yi, posted 10-06-2003 5:13 PM Speel-yi has replied

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Speel-yi
Inactive Member


Message 118 of 159 (60045)
10-08-2003 3:03 AM
Reply to: Message 117 by sfs
10-07-2003 9:58 PM


Re: Truncation Selection
Mammuthus said:
quote:
My overall point is that one should take the claims made by the ancient DNA community and the human evolution community in general with a grain of salt. They argue as badly as creationists sometimes.
True, there's a lot of assumptions being made. I find it particularly annoying that some evidence is presented as "proof". The sampling sizes are hmmmm...kinda tiny for some of the conclusions we see. The skeletal remains are interesting, but for a trait to disappear and then reappear really throws a wrench into some of the conclusions about Out of Africa.
sfs said:
quote:
What do you mean by "traditionally"? Many analyses have considered the possibility of selection in recent mtDNA and Y evolution. Look at the big Takahata paper on testing multiregionality, or Kaessmann et al's 1999 paper on Xq13.3, or Stumpf and Goldstein's review article on the Y. It has been widely recognized that selection is a possibility that needs to be taken into account when drawing conclusions from any locus (Takahata even modeled it), and especially for mtDNA and the Y, since they're nonrecombining and single-copy.
The Wilson group in its original study allowed for a population of 20,000 in the group which mitochondrial Eve lived with. This was based on a purely stochastic model and did not include the possibility that selection was involved in mitochodrial genetics. Selection by and large was thought of on the autosomal level.
------------------
Bringer of fire, trickster, teacher.
[This message has been edited by Speel-yi, 10-08-2003]

This message is a reply to:
 Message 117 by sfs, posted 10-07-2003 9:58 PM sfs has not replied

  
Mammuthus
Member (Idle past 6475 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 119 of 159 (60148)
10-08-2003 4:33 PM
Reply to: Message 116 by sfs
10-07-2003 9:49 PM


Re: Truncation Selection
That is fine but then when a sequence comes out like the one from Cro magnon the same group screams it is a contaminant, dont accept it. I know almost all of the people who worked on the various neandertals personally. There were some specimens that gave modern looking sequences i.e. non-divergent. They were dropped because they could not be distingished from contamination. How is that science if you exclude any data that does not fit your hypothesis i.e. humans and neandertals or humans and cro magnon were divergent? It does not matter how many times you verify the divergent samples if you exclude samples that give a different result. I am not claiming that the sequences for the neandertals were incorrect, though a few positions have come into question as DNA damage rather than polymorphism. I am questioning whether it is even possible to do the science at all if you cannot distinguish less divergent sequences from contamination...

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 Message 116 by sfs, posted 10-07-2003 9:49 PM sfs has replied

Replies to this message:
 Message 120 by sfs, posted 10-11-2003 12:42 AM Mammuthus has replied

  
sfs
Member (Idle past 2533 days)
Posts: 464
From: Cambridge, MA USA
Joined: 08-27-2003


Message 120 of 159 (60492)
10-11-2003 12:42 AM
Reply to: Message 119 by Mammuthus
10-08-2003 4:33 PM


My comments were based on the assumption that the tests were done well. If specimens were dropped from the papers because they didn't give the expected results, then the tests were not done well.
(The only person involved that I'm sure I know is Paabo himself, but I've probably met others at meetings. Since I tend not to remember anyone's name unless I'm married to her(*), I'm unlikely ever to know.
(*) I'd include my kids as well, but I sometimes get the younger one mixed up with the guinea pig.)

This message is a reply to:
 Message 119 by Mammuthus, posted 10-08-2003 4:33 PM Mammuthus has replied

Replies to this message:
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