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Author Topic: Genetic Closeness of the East/West African SNP population clusters (blog source)
Swenet
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quote:
Originally posted by Amun-Ra The Ultimate:

Look at my reply to you just above where it says:

This can also can be observed here (autosomal STR): LINK

Question: why are you even lecturing on these
matters, when you're clearly every bit as ignorant
as the average layperson? You're arguably even
more confused than a layperson who is light years
ahead of you by not carrying the sick baggage that
is causing you to posture as some sort of guru
of African population genetics, when it's obvious
to those in the know that you're at square sub-zero.

Dendrograms are NOT pairwise distance data.
Dendrograms do NOT allow for individual cross-
population comparisons--certainly not the elaborate
cross-comparison information you imagine you've
deduced from them, for several years now.

No more stalling, no more deflecting, no more
confused replies that only serve to demonstrate
the fact that you never had the the faintest clue
what you're talking about, either now or in the
past few years.

Post pairwise distance data RIGHT NOW or admit
that you have no idea what you're talking about.

And NO. I'm under no obligation to offer my opinion
on anything. Why? So the spotlights are off your
crackpot claims and you can sit back and wilfully
reject all the peer-reviewed data I post at a whim,
or simply vacate the thread and start over elsewhere
two days later with the EXACT same disproved crackpot
claims, as you have done for the past two years?
Don't think so.

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Amun-Ra The Ultimate
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^^It's obvious to anybody reading this forum you're the one who is trolling and being an ignorant. You're just like a little baby whining about the FACTS I exposed in this thread without having anything to say, any argumentations, to contradict them.


 -

But for a moment let me speak to the guy behind the Swenet character for a moment. Yes, you typing on the keyboard. What does it change in your life if East and West African have a common origin (for most of their genome) in Northeastern Africa after the OOA migrations? Why are you so mad about the relationship of people from the E-P2 lineages in Africa?

Why are you so upset about it? I don't see how this affect your life.

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Swenet
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Dendrograms are NOT pairwise distance data.
Dendrograms do NOT allow for individual cross-
population comparisons--certainly not the elaborate
cross-comparison information you imagine you've
deduced from them, for several years now.

No more stalling, no more deflecting, no more
confused replies that only serve to demonstrate
the fact that you never had the the faintest clue
what you're talking about, either now or in the
past few years.

Post pairwise distance data RIGHT NOW or admit
that you have no idea what you're talking about
and that your claims are unproven mumbo jumbo
you made up one day.

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Amun-Ra The Ultimate
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I know Swenet is just acting retarded and trolling me but I'll bite, since I like to post about it:

 -
Figure S7: Neighbor-joining tree from pairwise (δμ)2 microsatellite genetic distances between populations

We can see a bigger and more clear image Here (the image is too big for this forum) and in the study linked below.
From The genetic structure and history of Africans and African Americans by Tishkoff (2009)

You can also look at Figure 1 in the main document. The genetic structure and history of Africans and African Americans by Tishkoff (2009) is a peer-reviewed study.

Those are pairwise genetic distances between African and World populations.

Among other thing, we can see most Cushitic speakers being much closer to other African populations like Niger-Kordofanian speakers than non-African populations. Which is evident of course. Genetically speaking they share a common E-P2 origin with Niger-Kordofanian speakers for a large part of their genome.

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Swenet
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quote:
Originally posted by Amun-Ra The Ultimate:
Among other thing, we can see Cushitic speakers being much closer to other African populations like Niger-Kordofanian speakers than non-African populations. Which is evident of course.

Confused little puppy, aren't you? Actual geneticists
have contradicted this, but you went as far as
calling them liars. Armed with what academic sources,
one might ask? Nothing, just pictures and a self-
authored monologue filled with figments from your
own rabid imagination.

But what else do you expect from a known charlatan
who has all the trouble in the world complying with
a request as simple as:

Post pairwise distance data RIGHT NOW or admit
that you have no idea what you're talking about
and that your claims are unproven mumbo jumbo
you made up one day.

--Swenet

Which is not an unreasonable request, seeing as
actual transparent and verifiable work dedicated
to investigating this very issue properly (not by
gawking at dendrograms and making up your own
wishful fairytales, like Mr. Windbag here), has
come to a conclusion radically different from
this charlatan's self-authored quackery:

While this Ethio-Somali IAC is found primarily
in Africa, it has clear non-African affinities

--Hodgson et al 2014

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Swenet
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quote:
Originally posted by Amun-Ra The Ultimate:
From The genetic structure and history of Africans and African Americans by Tishkoff (2009)

quote:
Originally posted by Amun-Ra The Ultimate:
The genetic structure and history of Africans and African Americans by Tishkoff (2009) is a peer-reviewed study.

BTW, anyone who has looked at Tishkoff's Ks can
clearly see that Saharan/West Eurasian blue and
Cushitic purple alternate in some of their analyses.
They are clearly not entirely mutually exclusive,
an idea that Mr. Windbag here just can't seem to
compute for the life of him. Must be too abstract
an idea for his sensory input oriented mind.

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Swenet
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Can't even defend his bankrupt quackery to save his
life; another day has gone by and he's fled the scene
again  - . Can't post pairwise distance data either as
they're not susceptible to the same censorship he
applies to the larger, overall, dataset from the
academics he loves to distort, cut and paste into
his elaborate fairy tales. As a matter of fact,
the quack is omitting a lot of things that he
can't manipulate as data that appears supportive
of his case. For instance, there is a very good
reason why the incompetent quack actively censors
fig S18 when he cites from Tishkoff et al 2009--
the position of the blue OOA affiliated branch as
a side-branch to the Cushitic cluster refutes the
dogsh!t out of the tired faith-based crap he's
known for polluting forums with:

 -

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Swenet
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Moreover, maybe the chronic liar wants to explain to
the forum why why he posts figure S7 and S14 from
Tishkoff 2009, but never the four remaining dendrograms/
trees (Figure 1, S8, S18, S21). Of the latter trees
that include non-African populations, all show non-
Africans as an outgrowth of populations whose
ancestors have inhabited the exit points of Africa
along the Indian Ocean since the MSA, in accordance
with tried and tested OOA theory that the Amun-Ra
quack hates so much.

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He holds a cluster view on genetics, opposed to the clinal reality. But the strange thing is why are these studies making 'trees' in the first place? This would require divergence/cladogenesis via speciation, or a high level of reproductive isolation. Above diagram states "clades". Very odd. There are no clades in the putative human species. A clade is a monophyletic group.
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quote:
Originally posted by Swenet:
[QB] I agree with some of the things you're saying. But
simple logic dictates that the feasible hypotheses
among assimilation are, effectively, just variants of
OOAT, not MRT. Any self-respecting origin theory
that falls under assimilation has to take in account
the empirical evidence that human genes
predominantly come from a single source, or it
will fall under orthodox MRT (which predicts that
human genes will structure according to region,
with interregional exchanges) and become
falsified by default.

Check my reply here where this was already raised. I think this is a misunderstanding of MRE, which from the beginning allowed for accumulated genes of any population to be dominated by the largest population via gene flow or population movement:

"Based on these findings and the hypothesis of a larger long-term African population, I suggest that the multiregional model predicts that biological distances based on many traits will show that recent modern fossil samples are more similar to earlier samples from Africa than they are to samples from the same geographic region. I also suggest that regional continuity will be found in a small number of traits, but not all traits." (Relethford, 2001)

"My findings may seem contradictory to the prediction of regional continuity under a multiregional model, which is that the greatest similarity over time will be within regions. However, this prediction would be contradictory only if we expect all traits to show a pattern
of regional continuity. However, proponents
of the multiregional model do not suggest that all traits will show continuity. In reality, regional continuity is expected only for some traits as the result of genetic drift and selection acting to maintain high frequencies of a trait within a region
. (Relethford, 1998)

Also it should be remembered MRE predated most of modern genetics. It was formulated 30 years ago (Wolpoff et al., 1984). This was before the 1987 Cann study on MtDNA. MRE as a model is still primarily based on morphological regional continuity because this is easier to show with fossils. Trying to demonstrate regional continuity with genetics is harder because there are more assumptions involved and then you would have to identify the alleles or whatever for specific craniometric regional traits.

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Swenet
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I will look into Relethford's work, following your
suggestion, but isn't he a revisionist? Last time I
checked, early MRT said that there was no special
role for Africa in at least some of these regions.
Wolpoff said at no point was there an intrusion of
African AMHs in the East Asian record. We now
know that's unequivocally false (re: the genepool
of all modern humans has a single source). From
my perspective it looks like certain MRT proponants
switched to a more defensible position following
mounting evidence that original MRT is at odds with
genetic evidence; it's definitely not a concidence
that your citations of Relethford date to when
population genetics took off.

And what I find disingenuous about this is that
they never announced their concessions (i.e. the
ones that kept giving African AMHs an increasingly
bigger role in the origin of holocene humans);
when Tishkoff and others falsified the predictions
of early MRT in the 90s, they were told they had
misunderstood MRT, but didn't specify that this
'misunderstanding' (if you can call it that) was
because THEY silently shifted the points of
contention around by allowing for more contributions
from African AMHs relative to regional archaics.
They then called the new thing MRT, even though
it wasn't the same as the MRT that was juxtaposed
with OOA early on--the MRT everyone thought they
were arguing against.

But again, don't you end up with a variant of OOA
when you acknowledge that global holocene humans
ended up with an overwhelmingly African origin for
their ~22k genes?

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Read this debate about clarification from 1996 between Wolpoff and Tishkoff.

quote:
The multiregional model originally postulated that most genes in Asian populations derived from H. erectus populations living in the area for more than a million years. Recently, however, the model has become more vague and less quantitative, and allows for considerable contributions of genes recently flowing out of Africa. This current version of the multiregional model is merely a restatement of the assimilation models proposed by Smith et al. (1) and Bräuer (2). The crux of the problem is the amount of gene flow. As pointed out by Stoneking (3), complete replacement out of Africa and completely independent origins from previously separated populations are the extremes of a continuum of hypotheses, with the modern African contribution varying from 100% to 0%.
- Tishkoff

The problem with this statement is that MRE never originally predicted "most genes in Asian [European, Javan] populations derived from H. erectus populations" in their own regions:

quote:
Multiregional evolution began with the hypothesis that, as the world outside of Africa was first colonized, a pattern of genetic diversity developed that contrasted
greater amounts of genetic variability at the center of the human range with greater, though differing, homogeneities at the sparsely inhabited edges (4, 5). We anticipated (4, 5) that Africa, the original center, was a much more densely occupied region. Therefore, while recognizing that gene flow is always multidirectional, the multiregional model proposed that, for most of human evolution, its expected direction was often asymmetrical, largely outward from the center (6). A corollary of this is the expectation that genetic variation in Africa was always greater than elsewhere because of the larger populations, reduced selection at the species' center, and the ecological variation created by Africa's
geographic spread from north to south (7). Variation in the more peripheral human populations reflected small, oscillating, population sizes.

- Wolpoff

Its true to say that MRE from the start (Wolpoff et al., 1984 and Thorne's earlier papers) argued for more gene flow from Africa (as part of "centre and edge" evolution). But at the same it is true they were not committed to putting an estimate/percentage on it. They wrote in 1984 that: "It makes no sense, in our view, to argue about whether gene flow or selection or drift predominated" since MRE involves all of these regardless of quantity. So MRE theoretically is compatible with 99%> genes from Africa, and <1% in situ drift/selection at the peripheral edge populations accounting for regional continuity in certain cranial features. I agree though that no MRE proponent considered it this low, but they were never specific about the % of any regional continuity - just as long as it existed.

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Swenet
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quote:
Originally posted by Dead:
The problem with this statement is that MRE never
originally predicted "most genes in Asian [European,
Javan] populations derived from H. erectus populations"
in their own regions:

What do you make of this, then?

Quote:
"Our examinations of the Chinese specimens found no
anatomic evidence that typically African features
ever replaced those of the ancient Chinese in these
regions. Instead there is a smooth transformation
of the ancient population into the living peoples
of east Asia.
"
--Wolpoff 1992

Tishkoff's data did, in fact, falsify many of Wolpoff's
ideas, including that one. Slightly off-topic: I
just read the letters you posted, and she is also
right that it would be strange for contemporary
late pleistocene human populations all over the
old world to remain one big semi-panmictic population
for millions of years. This doesn't happen in
nature, in any species. We modern humans of today
are barely starting to do it, but we have technologies
and practices that nullify extremely large distances
and promote globalization.

Did Wolpoff reply in detail to the last letter
elsewhere in his work or did I just witness
Wolpoff's objections get nuked by Tishkoff et al?
Talk about overkill! [Razz]

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Stringer (2014) also quotes this:

"The evolutionary patterns of three different regions show that the earliest ‘modern’ humans are not Africans and do not have the complex of features that characterize the Africans of that time or any other [...] There is no evidence of specific admixture with Africans at any time, let alone replacement by them."
- Wolpoff et al., 1994

While understanding gene flow is multidirectional, MRE always acknowledged more African migrations than any other region, but it never estimated a percentage in terms of accumulated genes (via a migration matrix model). This was obviously a mistake, which is why Stringer and Tishkoff have been misled and possibly see a contradiction.

Relethford (1998) correctly points out that there is an incorrect assumption of MRE that it proposes "most of the genes in Europe would derive from Europe, most genes in Asia would derive from Asia, and so on". He simply shows with a migration matrix model:

"[This] problem arises from equating per-generation endogamy with accumulated ancestry over many generations."

Looking at the fossil data, MRE was though certainly revised. In the 80s/90s it proposed far too many regional traits. We're now looking at very few (4-5 in each region) as tested by Habgood, which is why MRE has shifted towards Assimilation or is a "weak" Multiregionalism.

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I will accept it would have been the 'autochthonous' inhabitants of each region that were assimilation into the African gene-pool, not vice-versa. But there was never total replacement: "regional continuity is expected only for some traits as the result of genetic drift and selection acting to maintain high frequencies of a trait within a region" -- Relethford.

The 4 European regional traits in question are horizontal-oval (H-O) shaped mandibular foramen, mastoid tubercle, suprainiac fossae and nasion projection (BNL/NOL). But I also see nasal narrowing as a 5th regional European trait (this was also recognised by Frayer et al. 1993).

 -

Frayer, D. W. (1992). Evolution at the European edge: Neandertal and upper Paleolithic relationships. Préhistoire Européene/European Prehistory 2, 9–69.

In regards to the H-O mandibular foramen:

"The trait appears to be a European marker since it is very rare outside Europe, where it is found in only one fossil mandible from Africa, Asia, or Australia. Yet, the H-O mandibular foramen is common in European Neanderthals (53%) and in early Upper Palaeolithic [European] people (18%)" (Frayer, 1997)

Stringer concedes:

"Nevertheless, as mentioned above, we are ready to consider all documented evidence for regional continuity, and we assume that some trait might finally turn out the be reliable evidence for continuity. Among them could be the horizontal-oval (h-o) mandibular foramen" (Brauer & Stringer, 1997)

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Swenet
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Not to dwell on this too long (I'm only posting on
this site to counter Amun Ra's endless cycle of
deliberate efforts to lie and deceive, running off
when held accountable and repetition of same
campaign of lies and manipulations elsewhere),
but that's the whole problem with MRT. As Tishkoff
has noted, there is no quantitativeness to MRT.
When you remind MRT proponents of the fact that
MRT originally meant anagenesis of regional archaics
into living Old World populations and collective
contributions to collective modernity, they realize
the inherent vulnerability, and claim they stood
for a preponderance of African ancestry and Africa-
mediated physical and behavioural modernity all
along. MRT proponents hover between these two
claims depending on convenience.

But note that the idea of substantial African
migrations over a period of 1.9 millions of
years, as you're suggesting, doesn't necessarily
jive with assimilation. African AMHs were only
around for ~10% of this duration and migrated out
of Africa during only ~5% of this duration; therefore,
the vast majority of these hypothetical exchanges
between Africa and other regions necessarily
involved unrelated African archaics. Moreover,
these exchanges with Africa, whether involving
African archaics or AMHs, were never envisioned
to substantially interfere with the evolution of
regional archaics to the extent necessitated by
assimilation and OOAT:


Today distinctive populations maintain their
physical differences despite interbreeding and
population movements; this situation has existed
ever since humans first colonized Europe and Asia

--Thorne and Wolpoff 2003

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Swenet
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Despite posting elsewhere on the forum, the lying,
deceptive quack who calls himself Amun-Ra hasn't
reared his head here for three days, lol. He keeps
calling me and others dishonest racists, but, yet,
when push comes to shove and he's asked to put
money where his mouth is, this liar repeatedly
escapes ongoing discussions (which he'll later
manipulate as "victories" on his part) and starts
over elsewhere with the same debunked propaganda.

What's taking you three days, lying charlatan?

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