Re: Neanderthals genes

Stephen Jones (sejones@ibm.net)
Wed, 07 Jan 98 05:33:28 +0800

Glenn

On Thu, 01 Jan 1998 21:05:25 -0600, Glenn Morton wrote:

GM>The January issue of Scientific American has an interesting
>discussion of the Neanderthal mtDNA which was purported to prove
>that Neanderthal was not related to modern man. Kate Wong writes:
>"Poplular accounts hailed the research as proof of a recent African
>origin for all modern humans, but has the long-standing debate over
>human origins really been put to rest? Judging from subsequent
>reactions among geneticists and paleoanthropologists, apparently
>not." Kate Wong, "Ancestral Quandry," Scientific American, January
>1998, p. 30

Thanks for this reference too. But AFAIK no one is claiming that
the issue of recent African origin for all modern humans has been
"put to rest." No doubt multiregionalists will still be able to
find alternative explanations to keep their theory alive. But the
cumulative weight of evidence is increasingly against the
multiregional continuity theory. It was already pretty shaky before
this latest Neandertal mtDNA study.

GM>and
>
>"Simon Easteal, a geneticist at the Australian National University,
>observes that chimpanzees and other primates display much more
>within-species mtDNA variation than humans do. Taking that into
>account, he says, 'The amount of diversity between Neanderthals and
>living humans is not exceptional.'

That chimps and other primates display much more within-species
mtDNA variation than humans do, actually argues *against* the
multiregionalist case. If Neandertals were very close to modern
humans then one would expect their mtDNA to have the same lack of
variation as modern humans:

"If you took specimens of a special type of genetic material, known
as mitochondrial DNA, from those two squabbling [gorilla] males,
and then compared them with samples from an Eskimo and an
Australian aborigine, you would uncover a surprising fact. You
would find the latter pair (the humans) are more genetically alike than
the former (the gorillas) . Yet the Eskimo and aborigine live half a
world away from each other in dramatically contrasting
environments. Our two gorilla combatants share the same forest.
Nevertheless, there is more variation in their genetic constitutions
than the most distantly related members of Homo sapiens. When it
comes to genes, 'humans are less different...even than lowland gorillas
living in a restricted geographic area of west Africa,' state a team of
Harvard University anthropologists, led by Professor Maryellen
Ruvolo, in a paper in the Proceedings of the National Academy of
Sciences in 1994. Nor is this phenomenon restricted to Homo sapiens
and Gorilla gorilla gorilla (as the lowland gorilla is imaginatively
classified). The Harvard team's research on chimpanzee and orang-
utan mitochondrial DNA has also revealed these species to be
considerably more diverse than Homo sapiens. It is not the gorilla,
nor the chimpanzee, nor the orang-utan, that is unusual, however.
Each enjoys a normal spectrum of biological variability. It is the
human race that is odd. We display remarkable geographical
diversity, and yet astonishing genetic unity." (Stringer C., & McKie
R., "African Exodus", 1997, p113)

GM>"Moreover, many scientists think that too much has been made of
>this very short segment of mtDNA, which came from a single
>individual. The evolutionary history of mtDNA, a lone gene, is only
>so informative. 'You can always construct a gene tree for any set
>of genetic variation,' says Washington University geneticist Alan R.
>Templeton. 'But there's a big distinction between gene trees and
>population trees,' he cautions, explaining that a population tree
>comprises the histories of many genes.

Granted, this is only a short segment of mtDNA from a single individual
but I wonder what would have been the multiregionalists' reaction if it
had shown no differences between this Neandertal and modern humans? I am
sure they would have shouted it from the rooftops as proof of their
theory!

GM>"In fact, examinations of modern human nuclear DNA undermine the
>out-of Africa model by suggesting that some genes have non-African origins.
>Univeristy of Oxford geneticist Rosallind M. Harding studies variation in
>the betaglobin gene, certain mutations of which cause sickle-cell anemia and
>other blood diseases. Harding found that one major betaglobin gene lineage,
>thougth to have arisen more than 200,000 years ago, is widley distributed in
>Asia, but rare in Africa, suggesting that archaic populations in Asia
>contributed to the modern gene pool. And studies of the Y chromosome by
>Michael F. Hammer, a geneticist at the University of Arizona, indicate that
>prehistoric population dynamics were much more complicated than simple
>replacement. His results reflect migrations both out of and back into
>Africa.

I note the "*thought* to have arisen more than 200,000 years ago"!
Dates of genetic change based on assumed constant rates of so-called
molecular clocks must surely be conjectural, especially when we
cannot examine the genetic material from so long ago. But in any
event, I would have thought that the above can be easily accounted
for by normal genetic variability of small Homo sapiens populations
in Africa (the gene is "rare in Africa" but not non-existenmt) and
founder effects of the particular Homo sapiens group which radiated
out from Africa into Asia. There is no requirement that the
ancestral African Homo sapiens populations were all genetically
identical.

In any event the following genetic evidence seems decisive for the
Out-of-Africa theory:

"...people have been found to possess a variable number of
repetitions of a little section of five bases, CTTTT. (There are a
total of three billion bases that make up the six-foot length
gossamer strands of DNA that are coiled inside a single cell.) Some
people have between four to fifteen copies of this little genetic
stammer. Again, this variation has no bearing on a person's genetic
well-being. Now when you look at people living in sub-Saharan
Africa, you observe a simple pattern. Individuals have every variety
of deletion or non- deletion along with any variety of number of
CTTTT repeats. For example, one person may have a chromosome
containing the CTTTT sequence repeated eight times as well as a
deletion and another person may have a chromosome with the CTTTT
sequence repeated twelve times with no deletion. There are many
combinations of numbers of repeats and deletions and non-deletions in
sub-Saharan Africa. Outside this region - in other words, throughout
the rest of the world - you see something very different.
Chromosomes with deletions have only one pattern of CTTTT repeats, a
sixfold one, while non-deletion chromosomes only have CTTTTs
reiterated five or ten times. In other words, Africa shows complete
variability. The rest of the world does not. And there is only one
feasible explanation: that the small wave of settlers who set off
from their African home to conquer the world was made up of a tribe
or group of African Homo sapiens among whom only those who possessed
a chromosome 12 had a sixfold CTTTT repetition. They carried this
combination out to the world 100,000 years ago, and now scientists
have picked up its signal like a discarded genetic calling card.
(Think of those chromosome 12 variations as a set of genetic
dominoes, in which a blank represents the deletion, while the other
numbers represent the different repeat possibilities, say a one for a
fivefold, two for a sixfold, etc. People in Africa are made up of a
mixture of the entire variety of dominoes that have a blank: a
blank-zero, a blank-one, etc. However, those in the rest of the
world have only one: the blank-two.) 'This says one thing,' states
Professor Kidd: It says the rest of the world was peopled from one
sub-set of Africans, the ones who had a deletion associated with a
six-unit repeat on their chromosome 12, or the ones with a
non-deletion and five and tenfold repeat. It also says that only one
wave of these people was responsible. And thirdly, it allows us to
put a fairly accurate date on that emigration: around 90,000 years
ago." (Stringer & McKie, pp129-130)

GM>"Both Hammer and Harding think the overall picture emergin from
>the seemingly inconsisten genetic data best fits one of the
>'intermediate' models of human evoution such as the assimilation
>model engineered by Northern Illinois University paleoanthropologist
>Fred H. Smith. According to Smith's model, the patterns visible in
>the fossil record suggest that both expansion out of Africa an
>genetic interchange among populations were at work." p. 32

I would have no problem with an "assimilation model", if it was
proved. It could always be that there was some interbreeding
earlier on between closely related species, such as can occur with
dogs and wolves. But the more normal pattern is that different
species do not interbreed. The data suggesting assimilation and
regional continuity data can be accommodated within the replacement
model.

GM>Smith's view is a variation on Gunter Brauer's hybridize and
>replacement model which is what I find most consistent with the
>entire spectrum of data. In this model, there was a surge of people
>coming out of Africa and there was interbreeding with the local
>populations. The amount varied and in general the local genes were
>swamped by the genes of the invaders. But not all local genes were
>lost. This allows us to explain data like the unique Neanderthal
>H-O mandibular foramen which occurred in no other ancient
>population and which today is almost certainly indicative of
>European descent. Both the archaic and modern Europeans have
>this unique and rare form of the foramen as part of their genetic
>heritage. The percentages are:

>European H-O Normal
> Foramen Foramen
> % %
>
>Neanderthal 53 47
>African Eves 0 100
>Skhul/Qafzeh 0 100
>Early U. Paleolithic 18 82
>Late U. Paleolithic 7 93
>Mesolithic 2 98
>Medieval Europeans 1 99
>~David W. Frayer, "Evolution at the European Edge: Neanderthal
>and Upper Paleolithic Relationships," Prehistoire Europeenne,
>2:9-69, Table 7, p. 31
>
>The african Eves are those who left Africa in the out of Africa
>theory. Skhul/Qafzeh people are the earliest anatomically modern
>palestinians dating around 90,000 years ago. Early upper
>paleolithic people approximately date between 40-25,000 years ago
>and Late upper paleolithic is approximately 25,000 to 10,000.
>Mesolithic is 10,000 to 8,000.

I can't see how this can be decisive. Neandertals were the next closest
species to Homo sapiens and must have shared over 99% of the same
genes. One should therefore expect some similarities to crop up just
by genetic variation, especially among species sharing a common
environment (eg. it may be correlated with cold adaptation, etc). Or
it could be a recessive archaic trait which was slowly being bred
out of both Neandertal and Homo sapiens populations over time.
After all, the Neandertals varied markedly among themselves with
this trait. It would be much stronger evidence if 100% of
Neandertals had this trait. It would also be stronger if greater
than 0% of the Skhul/Qafzeh Homo sapiens had it, since they were
sharing the same land with Neandertals.

One thing that is clear from the Neandertal mtDNA study is that
there was nothing to support a connection between this Neandertal
and modern Europeans:

"But the new data suggest no mixing at all, at least in mitochondrial
genes. "Neandertals in Europe could not have contributed to the
modern mitochondrial genome," says Stanford University geneticist
Luca Cavalli- Sforza. That "destroys one of the fortresses of the
regional continuity model," he says, which postulates that
Neandertals in Europe are among the ancestors of living Europeans.
Indeed, one of the paper's most important findings is that Neandertal
DNA shows no particular similarity to that of Europeans. "If regional
continuity were correct, "we'd assume that Europeans would be
closest [in their sequence] to Neandertals. But the results show
Neandertals are equidistant to all races," says Stringer. As a result,
most researchers who spoke with Science consider the new data as
support for the idea that modern humans replaced, rather than
intermingled with, Neandertals. "The multiregional guys will have a
hard time wriggling out of this one," says Ward." (Kahn P. &
Gibbons A., "DNA From an Extinct Human," Science, 277, 11 July
1997, p177)

[...]

God bless.

Steve

--------------------------------------------------------------------
Stephen E (Steve) Jones ,--_|\ sejones@ibm.net
3 Hawker Avenue / Oz \ Steve.Jones@health.wa.gov.au
Warwick 6024 ->*_,--\_/ Phone +61 8 9448 7439
Perth, West Australia v "Test everything." (1Thess 5:21)
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--------------------------------------------------------------------
Stephen E (Steve) Jones ,--_|\ sejones@ibm.net
3 Hawker Avenue / Oz \ Steve.Jones@health.wa.gov.au
Warwick 6024 ->*_,--\_/ Phone +61 8 9448 7439
Perth, West Australia v "Test everything." (1Thess 5:21)
--------------------------------------------------------------------