May 10, 2009

X chromosomes and settling of Americas

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American Journal of Physical Anthropology doi:10.1002/ajpa.21084

X-chromosome lineages and the settlement of the Americas

Stephane Bourgeois et al.

Abstract

Most genetic studies on the origins of Native Americans have examined data from mtDNA and Y-chromosome DNA. To complement these studies and to broaden our understanding of the origin of Native American populations, we present an analysis of 1,873 X-chromosomes representing Native American (n = 438) and other continental populations (n = 1,435). We genotyped 36 polymorphic sites, forming an informative haplotype within an 8-kb DNA segment spanning exon 44 of the dystrophin gene. The data reveal continuity from a common Eurasian ancestry between Europeans, Siberians, and Native Americans. However, the loss of two haplotypes frequent in Eurasia (18.8 and 7%) and the rise in frequency of a third haplotype rare elsewhere, indicate a major population bottleneck in the peopling of the Americas. Although genetic drift appears to have played a greater role in the genetic differentiation of Native Americans than in the latitudinally distributed Eurasians, we also observe a signal of a differentiated ancestry of southern and northern populations that cannot be simply explained by the serial southward dilution of genetic diversity. It is possible that the distribution of X-chromosome lineages reflects the genetic structure of the population of Beringia, itself issued from founder effects and a source of subsequent southern colonization(s).

Link

24 comments:

eurologist said...

I remember a while ago I elaborated a bit on my preferred view that the peopling of Europe started ~45,000 years ago via northern Pakistan, Afghanistan, and so on westward, after humans had had time (and need) to develop the tool set to live in the seasonally varying and at times cold and dry conditions, and re-acquainted themselves with efficient big-game hunting (efficient transport of food and water, preservation of food via drying and smoking, and tents and proper fur coats). I also argued that at the same time, this group split and a portion of them traveled East into Kyrgyzstan, South-East Siberia, and eventually Beringia and the Americas.

Although there is mT-DNA data to support this, some criticized it, saying that the majority of peopling happend from the south, via the Chinese coast.

I am glad to see that this paper pretty much shows the strong affinity between Europe and the Americas, as expected from this IMO most straightforweard pouplating model.

While Siberia and Mongolia also show some affinity, they do so to a lesser extend, since they had ~25,000-40,000 years of admixture from the south that neither Europe nor the Americas had, since. Which essentially is the same reason why present-day Afghans, northern Pakistani, and Kyrgyzs have substantially diverged and can no longer be looked upon as the remnant source population of Europe and the Americas.

Maju said...

There are two X-DNA haplotypes that can be said to be shared between Europe/WEA and Native Americans other than the widespread B001, which is most concentrated in NE Asia anyhow. These are:

B003, that is essentially a West Eurasian lineage but also found in North America (one could argue that is post-Colonial admixture - men also carry X-DNA and succesive waves of men from the same origin can actually dominate in this aspect, as it was seen in Colombia). Still B003 has some presence in Central Asia and Siberia and could also be associated to the thinly spread expansion of mtDNA X and also the P (R and Q) Y-DNA connection. Also B003 is derived from B001, what may indicate a double directon of expansion from a common center, much like Y-DNA P.

B006, which is the most interesting one, IMO, as it is believed to be one of the oldest distinct lineages and is shared notably by Basques and Amerindians. But again, this lineage has several subclades (fom an older paper) and again the highest diversity is in Mongolia, with the other subclade (not found in America and less important in Europe) being primarily Asian.

Also B006 in this paper is shown as relevant among Northern Eurasians suggesting a pattern of distribution by the far north or, alternatively, a refugium area for a once more southern connectivity route.

Anyhow, I'm still reading the paper. But for me these connections suggest a Siberian/Central Asian/Mongolian connection - nothing else.

German said...

B006 is the most basal lineage which is virtually absent in Africa (see Zietkiewicz 2003, etc.) and is most frequent in the Americas. In addition to being most frequent in the Americas, it's polymorphic there and is split into two sublineages (_15 and _16), which are mostly concentrated in Europe and Asia. B006-15 is concentrated in North America and Mongolia, while B006-16 is shared between South America, Europe and Asia.

This one of the most recently-found indications that Africa is not the oldest continent, while America very well may be.

X chromosome evidence shows exactly what (Johnson et al. 1983) found for mtDNA (ancestral morph 2-1-1-1 most frequent in the America) and (Schroeder et al. 2009) published for microsatellites (American Model Haplotype coupled with 9-repeat allele most frequent in the Americas).

Maju said...

Word of caution: X-DNA studies are still in their infancy (and growing very slowly) and there is a couple of most important sampling biases:

1. Africa has been so far clearly undersampled.

2. India has not been sampled at all.

B006 anyhow has been found in Africa, albeit at very low levels so far.

German said...

No doubt. But the same pattern seems to recur across multiple systems - both well-studied and nascent, namely high frequency of a lineage that has a great geographic range is typical of the Americas, while Africa is characterized by lineages restricted to Africa. Under the population scenario whereby emigrant population is growing in size faster than the stay-behind population (with no gene flow between the original stay-behind population and the ever-growing emigrant population), Africa is a colonized continent, while America (or another area outside of Africa with the pattern of conservation of archaic lineages similar to that found in the Americas) is the homeland.

Maju said...

No, German. That is not what we find in the other genetic lineages. In Y-DNA and mtDNA, African diversity is clearly at the oldest level of the phylogenetic tree, with Eurasian diversity being derived from this one and Native American diversity derived from that in Asia.

And there's nothing that points to an specifically American origin for B006. Y-DNA Q is also much more common among Native Americans than anywhere else but it is of clear Asian origin. Frequency does not automatically mean origin, much less where a colonization on virgin land is as well documented as in the case of America.

German said...

We discussed the mtDNA situation extensively on www.anthropology.net. African lineages can't be the oldest because they're not found outside of Africa. Geneticists just have to figure out the conditions under which mutation rate increases for certain "hot spots." Under the neutral model, it's population growth plus gene flow that's responsible for this. Under non-neutral model, it's selection. In any case, Africa, like Australia, followed the path of local differentiation.

Y chromosome is a good check for mtDNA phylogenies. With the recent discovery of a slew of D lineages in Asia (including DE), it's clear that all YAP+ chromosomes originated in Asia. And this accounts for more than 50% of African Y-DNA diversity. What's the parallel to this in mtDNA? Probably L3.

Y-DNA Q and C haplogroups are again widely-dispersed lineages found everywhere outside of Africa (they are both YAP-). American Indians harbor all the basal mutations plus, of course, local innovations. This pattern corresponds to long-term isolation of demes with small population sizes.

You think the colonization of the Americas is "well-documented"? Not true. It's over-theorized with coalescence dates ranging from 10,000 to 70,000 years, with no archaeological evidence for a Siberian origin, with no idea how 140 language stocks could emerge from a handful of Siberian and East Asian stocks, etc. No matter how many papers are authored yearly that have "peopling of the Americas" in the title, they all stem from the same assumption. Without testing this assumption all these studies are futile in the long-run.

Maju said...

We discussed the mtDNA situation extensively on www.anthropology.net.

Ah, you are that guy! The one who believes that Humankind must have arisen in America against all evidence just because he thinks that hyper-complex family relationships should be older than the simpler ones found for example among the Bushmen.

Well, I tried to teach you a couple of things back then but eventually had to disengage because we were going nowhere.

African lineages can't be the oldest because they're not found outside of Africa.

African lineages, some of them at least, are certainly found outside Africa: mtDNA M and N are just subclades of L3, even if the nomenclature may make you think something else. And, of course, most L3 sublineages are found in Africa and only two of them make up virtually all non-African mtDNA ancestry. And L3 itself is nothing but a sublineage of other higher level lineages, whose greatest diversity is found in Africa, of course.

I'll discuss more with you whe you make your homework.

Y chromosome is a good check for mtDNA phylogenies. With the recent discovery of a slew of D lineages in Asia (including DE), it's clear that all YAP+ chromosomes originated in Asia.

Y-DNA is slightly different from mtDNA but DE* has not been found only in Tibet but also in West Africa (several locations). The situation remains not fully clarified but surely means that DE spread in Africa and Asia before its fixation in E and D respectively.

Anyhow, DE is sybling of C'F and together (C'DE'F) are sybling of B (only found in Africa) and together Y(xA) are sybling of A, also found almost exclusively in Africa. Top level diversity remains highest in Africa: (2/2 vs 1/2 branches at all levels before OOA) and this is coincident with what we see in mtDNA, though mtDNA is a zillion times more clear and less susceptible radical sweeps than Y-DNA.

And this accounts for more than 50% of African Y-DNA diversity.

No. It accounts for 50% (or probably more) of frequency, which is different than diversity.

Y-DNA Q and C haplogroups...

Mixing apples and oranges here. C is many levels higher in the phylogenetic tree than Q:

C'F > C > C sublineages (like C3)
C'F > F > IJK > K > NOP > P > Q

Understand?

American Indians harbor all the basal mutations plus, of course, local innovations.

OMG! Obviously: they are derived lineages, so they have all the basal mutations plus some more.

You think the colonization of the Americas is "well-documented"? Not true.

It is. Your 70 kya are nothing but speculative nonsense but anyhow 70 kya are nothing when we compare with the c. 200 kya of Africa. The current consensus is of 15 or at most 20 kya. And anyhow is very clear in genetics, regardless of the date, that Native Americans are a derived population from Eurasians.

I won't reply to further comments, as I consider discussing with you a total waste of time. This is more than enough.

German said...

Yes, I'm this guy. A scholar with two doctorates from top-tier universities who actually studied genetics, linguistics and anthropology in some depth and who operates with a database of some 2500 languages. Yes, I'm the one who developed a new theory of human dispersals bringing together kinship studies, linguistics and population genetics into a new synthesis (see my book The Genius of Kinship from 2007). Before trying to teach me a lesson, I suggest you read about genetic phylogenies in the context of population structure and demography. You'll learn about the dependence of phylogenetic interpretations on the assumed population scenarios. In order to understand what really happened in human evolutionary history one needs to arrive at a consensus model satisfying all data patterns coming from extant populations (kinship studies, linguitics and genetics is the best calculus out there) and then build a specific phylogeny for mtDNA or Y-DNA.

American Indians show low diversity but high frequency of certain genetic lineages. Sometimes, as in the case of X-DNA B006, these lineages can easily be showed to be ancestral to the rest of human X-DNA lineages. Sometimes, it takes time to discover which lineages are root lineages and which ones are the result of ancient bottlenecking with subsequent re-expansion.

When coupled with the highest linguistic diversity in the world and the preservation of archaic forms of kinship systems and terminologies, genetic data can be interpreted as favoring an out-of-America scenario provided a certain population dynamic is entertained. This population dynamic is 1) long-term low effective population size in the Americas; 2) no gene flow between America and Asia; 3) population growth and expasion outside of America with gene-flow restricted by distance.

All the more specific points you raise were answered on anthropology.net, e.g., 1) all mtDNA M1 lineages found in Africa are now believed to be result of a back-migration; 2) most of the mutations found on L1, L2 are missing on L3, and most of the mutations found on L3 are missing on M and N; 3) no archaic traces of M and N are found in Africa; 4) L1, L2, L3a-f lineages are not found outside of Africa.

Maju said...

B006 is not ancestral to anything but itself. It's just apparently old (i.e. it splits closer to the root than the other lineages) and that is a phylogeny as good as the one you have for mtDNA (in the best case).

You claim to be an expert in genetics but from your words it's obvious that I, a mere amateur, know more (well, no wonder, I also know more history than my sister who is historian - just because I have real interest). You say:

1) all mtDNA M1 lineages found in Africa are now believed to be result of a back-migration.

Sure, so what?

2) most of the mutations found on L1, L2 are missing on L3, and most of the mutations found on L3 are missing on M and N.

L1 and L2 are not ancestral to L3, so no wonder that some L3 mutations are missing in these other related but distinct lineages. L1 and L2'3'4'5'6 are sisters, L2 and L3'4'6 are also sisters. If I can still count, there are 10 mutations leading to L3 that do not exist in L2 and 26 mutations leading to L3 that do not exist in L1 (source: the most up-to-date mtDNA tree online - originally an academic paper by Owen and Kaiser: doi:10.1002/humu.20921).

There are no mutations leading to L3 missing in M or N, though obviously M and N are defined by further downstream mutations (4 and 5 respectively, same source). If what you claim in this aspect would be true, then you would cause an upheaval in population genetics. But you would need to prove it first.

3) no archaic traces of M and N are found in Africa

Apparently not. But it doesn't matter because they are L3-derived.

4) L1, L2, L3a-f lineages are not found outside of Africa.

That's not exactly correct because through history some of those have actually migrated. You can found occasional L(xM,N) in all Europe and West Asia, either mediated by North Africa or product of colonial times.

Your list of L lineages is outdated anyhow, as you don't ever mention L0 (the oldest branch, common among Khoisan) nor the less important L4 (common among Hadza if I'm correct), L5 and L6.

L6 is pretty curious because it's found in larger ammounts (and enough diversity) in Yemen than anywhere in Africa (where it's extremely rare and apparently restricted to a few Ethiopians), what means that there is at least some L(xM,N) and L3'4'6(xM,N) that is found mostly out of Africa, even if at this moment we can't determine if it's a remnant of the OOA process or a later arrival.

German said...

All haplogroups are distinct from each other. The easiest way to compare them is to look at restriction site mutations. All haplogroups, with the exception of X and I, share a gain at 1715 DdeI. Haplogroups L1 and L2 share a gain at 3592 HpaI and they're unique at that. Haplogroups L3a, b, c share one restriction site gain at 10394DdeI with (macro)haplogroup M and with I, J, K haplogroups and no restriction sites with the rest of the members of (macro)haplogroup N. L3d shares a loss at 10394DdeI with H, T, U, V, W, A, B, X.

For HVR mutations at the "joints" (or better to say disjoints of L1/L2 and L3/M/N) see my exchange with Victor on anthropology.net on May 30, 2008.
The only shared position is 16233.

L3 is an artificially created haplogroup (in the 1990s geneticists noticed that there are African lineages that lack 3592HpaI and declared them ancestral to M and N) with some RFLP mutations shared with some non-African lineages and other mutations shared with other non-African lineages. There's nothing specifically African about L3 as it lacks 3592HpaI characteristic of L1 and L2. You could say that L3 lineages are more closely related to lineages found in M and N macrohaplogroups than to L1/L2 lineages, but it's plain wrong to say that M and N ARE L3.

I consider L3 lineages products of local African differentiation on the basis of some M and N lineages streaming into Africa from Near East and India. They are of later origin than L1 and L2. Again, the exact population dynamic is unclear but a combination of bottleneck, genetic drift and expansion leading to greater effective pop size and hence diversity created this African specificity.

You're right there cases of relatively recent admixture of African lineages in European/Near Eastern and American Indian gene pools. (Good catch on L6, by the way, it's also found in Saudi Arabia at low frequencies.) Some of them happened in southern Europe/Middle East in the past 10,000 years, others in the Americas after 1492. But there's no evidence for any L1, L2 or L3a-f lineages making it out of Africa around 30-50-60,000 years ago and spawning Lx lineages there. Maybe they will be found. But the more people dig in India, Southeast Asia or Australia, the more M and N lineages they find. And there're no archaic M and N lineages in Africa. Geneticists used to think that a couple of Senegalese sequences (at the time when they were tagged AF...) that displayed both RFLP mutations characteristic of M are those archaic M lineages. Now, they are considered results of a back migration into Africa (M1). Same for U lineages.

The majority of M and N lineages emerged after humans had left America. When it comes to origins, size doesn't matter. America retained a subset of M lineages and a subset of N lineages and due to low population size and isolation has not accrued much diversity in them. Allele diversity is a function of effective pop size. The colonization of the Old World required huge demographic resources on the part of the early hunters and gatherers. Population size grew in response to the expansion needs and this affected effective population size (the no. of fertile men and women), which in turn affected diversity levels.

Maju said...

I cannot find the mutations you mention in PhyloTree.

Your usage of "L3a-f" seems to imply that you're using old literature of some sort (no idea which because you provide no references).

... it's plain wrong to say that M and N ARE L3.

It is plain correct. L3 is nowadays defined by mutations in the loci: 769, 1018 and 16311 and these are shared by all L3-letter lineages, as well as by M and N. This is the phylogeny of L3.

But the more people dig in India, Southeast Asia or Australia, the more M and N lineages they find.

Now that you mention, I just got private communication from an Indian man who is L3*. Without further info, it may be a "recent" arrival maybe mediated by West Asia, but I can't discard fully that it's just another remnant of the OOA. As someone mentioned in a recent study, Indian genetic diversity is still largely unknown.

And there're no archaic M and N lineages in Africa.

Why do you insist in this: it is widely known. Your key contention would be that L3 is not ancestral to M and N (and nobody doubts theser are Asian lineages) but the reality is different.

The majority of M and N lineages emerged after humans had left America.

I can only concieve sarcastic comments to this absurd claim, things like "it's so obvious that N derives from B" and nonsenses of the like.

You are building your house beginning with the roof and that's why it's crumbling. Full stop.

German said...

769, 1018 are different between L1/l2 and L3, 16311 is a "hot spot" (M lineages in India show different states there). I'm not even sure if 769 and 1018 are the same across all L3 lineages. I think now they're believed to be the defining L4 mutations.

See Herrnstadt 2002; Kivisild 2004.
Herrnstadt writes: "There
is no single polymorphism that is specific to all L3 hap-
lotypes, although the G15301A polymorphism occurs
in all L2- and L3-haplotype mtDNA sequences (and in
one L1-haplotype sequence), in which it caused a retic-
ulation that was resolved by assuming that it arose in-
dependently on three separate occasions." This 15301 site is also part of the macrohaplogroup N signature but not the macrohaplogroup M signature (see Maji 2009).

There's a lot of noise in the phylogenies. It's just Africans are unique in showing very long branches (if you see their sequences, there're just too many mutations there), which is usually intepreted as a sign of great age. I, on the contrary, can't help but think: what if it's accelerated mutation rate in certain African-specifc parts of mtDNA that has produced these long branches in the past 40,000 years.

For restriction site polymorphisms see all the publications in the 1990s from Ballinger 1990 and Torroni 1992.

I don't start with the roof. I disagree that we should be determining where the roof is and where the base is on tha basis of a single discipline (first archaeology and now genetics). I look at multidisciplinary data vertically: if you believe that human came to America 10,000 years ago, plese explain their levels olf linguistic diversity. If you believe Africa is that old, why are all the archaic kinship systems found in America, Australia and Papua New Guinea, but not in Africa?

Anthropologists of kinship systems have surveyed human kinship diversity for more than 150 years now. Do you think we would have missed some archaic African kinship structures?

Maju said...

IDK, go and find some L3 individual who lacks the following mutations (based on Behar 2008): 769A, 1018A and 16311C.

You say that Herrnstadt found a mutation that could not be an SNP, alright - not the first time probably. But the lineage is still valid because others have resolved that it does have several shared mutations.

If L3 would be invalid for some reason (which is not the case), M and N still share mutations upstream within the following macrohaplogroups:
· L3'4: 182 3594 7256 13650 16278
· L3'4'6: 4104 7521
· L2'3'4'6: 195 247 825A 8655 10688 10810 13105 13506 15301 16129 16187 16189
· L2-6: 152 2758 2885 7146 8468
· L1-6: 182 1048 4312 6185 11914 12007

You have a lot of mutations to disprove before you can demonstrate that M and N are not rooted into a wider lineage, whose greatest diversity is in Africa. Good luck.

It's just Africans are unique in showing very long branches...

Not only. It is mainly a phylogeny regardless of the number of mutations.

... if you believe that human came to America 10,000 years ago, plese explain their levels olf linguistic diversity.

I just happen to believe in Greensberg's Amerindian. I have a lot of trust in Greensberg's methods: if he could solve African linguistic phylogenies (and he did), his methods can be applied elsewhere too.

If you believe Africa is that old, why are all the archaic kinship systems found in America, Australia and Papua New Guinea, but not in Africa? -

I happen to think that Bushmen and Pygmy kinship system is surely much older, precisely because it's simpler. One really needs a lot of time to waste in order to invent such complex kinship systems of the circumpacific region.

Actually I really have a hard time believing those peoples and their kinship systems are for real. Of course they do seem to exist but they imply necesarily a cultural founder effect of some sort, a cultural element that is mostly alien to me (hence innovation, non-natural). Basic kinship is spontaneous and flexible: natural, simple, not too important anyhow because what really matters is alliance, friendship, which may or not be related to kinship.

Anthropologists of kinship systems have surveyed human kinship diversity for more than 150 years now. Do you think we would have missed some archaic African kinship structures? -

You don't seem to know what is archaic and what is not. For you rocket science (complex) is archaic while spear throwing (simple) is modern. I can't agree with that at all.

German said...

Shared mutations can be interpreted both ways.

Kinship phylogenies are a bit more complex than just "complex to simple." In fact, some scholars use the terms "simple" in reference to the American-Oceanic-Australian systems, and "complex" with respect to African systems. These are very relative terms. Some of the Khoisan kinship systems are very much like some archaic, "simple" systems in America and Australia, but not as pure.

I met with Joe Greenberg and his wife Selma many times in Stanford. He was a very passionate and eruditious men. His impact on linguistic typology is huge. His Amerind, Eurasiatic and Indo-Pacific classifications seem absurd to the vast majority of linguists. They're definitely at odds with my kinship data, which shows that Eskimo-Aleut, Na-Dene and Amerind are one "linguistic population." But even if you believe in his Amerind classification, you should know that he didn't have a clue about the age of Amerind. he followed the benchmark dates suggested by archaeology but if those dates were 100,000 YO he would have claimed that the power of his multilateral comparison can easily reach that far. Proto-World etymologies by Ruhlen are based on the same principle. Greenberg's African classification is relatively strong mainly thanks to the earlier work of Westermann, otherwise it's being slowly taken apart by present-day Africanists.

I like the works of Lyle Campbell and Johanna Nichols the most but I have to admit that Ruhlen's application of Greenberg's method to the Ket-Na-Dene connection apparently yielded an essentially correct result. By the way, Ket-Na-Dene is one of those cases when language is a better predictor of an ancient connection than genes.

Thank you for all your thoughts, Luis, I believe.

German said...

A good paper to read, which is not about kinship or linguistics, is Dental evidence on the hominin dispersals
during the Pleistocene, by
M. Martinon-Torres (PNAS, 2007, 104 (33)).

1. The paper discusses how evolution can show both simplification (anterior dental features) and complication (posterior dental features). My kinship data presented in The Genius of Kinship: The Phenomenon of Kinship and the Global Diversity of Kinship Terminologies (Dziebel 2007) documents exactly the same dynamic of ancestral and derived kin terminological traits, with the resulting global cline between Africa and America identical to the one reported by odontologists and geneticists.
2. The paper specifies how African hominin dental variation is full of autapomorphies (unique derived features). In modern human dentition, Bushman canine is an example of this autapomorphic feature. Thinking again vertically, Khoisan languages show a unique phonological feature, namely clicks, which is autapomorphic as it's missing in other languages outside of Africa and probably represents a local sociolinguistic (not a natural phonological development). Kinship shows the same thing for Sub-Saharan Africa in general.
3. The paper makes an important distinction between phenetics and cladistics. Cladistics filters autapomorphies out. Phenetically, Homo sapiens populations appear closer to African hominin populations, while cladistically they're closer to Eurasian hominin populations. One of those archaic anterior Eurasian dental features is shoveling, which is found at its highest frequencies among American Indians and at its lowest frequencies in Sub-Saharan Africa (see also Irish 1998).

The mtDNA lineages such as L0, L1, L2, L3a-f that Luis's referring to are the example of autapomorphic features that are interesting for the evolution of modern humans in Africa but irrelevant for modern human evolution in general as they are derived and African-specific. B006 on X chromosome is one of the clear genetic signals of the emergence of modern humans outside of Africa: it's global in distribution and has high frequencies in the Americas.

The Out-of-America theory introduced in the Genius of Kinship is based on the vertical and interdisciplinary data integration: all available phylogenies and taxonomies, from mythology, kinship, linguistics to population genetics and odontology, seem to contain one message: modern humans emerged in the Old World as a result of a founding migration from the Americas. It's the reversal of the current thinking but facts are more powerful than opinions in the same way as cladistics is better than phenetics.

Maju said...

B006 on X chromosome is one of the clear genetic signals of the emergence of modern humans outside of Africa: it's global in distribution and has high frequencies in the Americas.

But not necessarily high diversity. I have lost my bookmarks and my backup copies with my old defunct computer but from memory these studies on X-DNA, seem to suggest an origin for this trait (highest diversity) in the area of Mongolia/Siberia. Right now I'm not sure if it was B006 or if it was another lineage also shared by Europeans and Amerinidians.

Regarding click languages and other stuff, nobody says that Bushmen are ancestral to the rest of humankind, but rather the first branch to break apart. For some this means that Bushmen migrated southwards from East Africa and for others that the bulk of humans moved northwards from south Africa. I'm more with the later.

I understand that shoveling is an innovative trait, not archaic for the same reasons: it appears surely in East Asia, after humans moved there and is clearly associated with one of the human phenotypes (Mongoloid) and not the others (except where Mongoloid connections can be demonstrated, like in Northern Europe - very influenced by minor Uralic genetics, ultimately from Siberia).

But anyhow all groups innovated: nothing remains static.

Another argument against your far-fetched hypothesis is pigmentation. It is sufficiently well known by now that East Asians (and Amerindians by extension) and West Eurasians followed two different adaptative strategies to lowered UV input (critical for vit. D formation, in turn critical for proper mental development, specially in embryos and infants). This clearly means that West Eurasians are not directly derived from NE Asians.

Similarly, while the tropical peoples of the Old World have very dark color, sing of full adaptation to high UV environments, Native Americans never display such extreme pigmentation, sign that they lost their "black genes" before they returned to the tropics, and therefore could never adapt that perfectly to the tropical climate, not in the 15 thousand years or so they have been over there. They got back some tan but never the really dark color of all other tropical humans. This is a very clear signal of recent arrival from darker latitudes.

German said...

Shoveling is in fact an archaic trait first detected in Australopithecines. It's very pronounced in the Peking man and in Neanderthals. Sinodonts and especially Amerindians have this trait at very high frequencies, while Sub-Saharan Africans have it at low frequencies. All other dental features follow the same pattern. Although Christie Turner considers Sinodont dentition derived from Sundadonts because of the complexity of root and crown and a lot of mass-additive features, this can as easily signify antiquity and retention from hominins. South Asian, European and North African dentition underwent simplification (compare skull gracialization as a general craniometric trend that affected post-Pleistocene skulls), most likely in the last 10,000 years. African dentition is also mass-additive and complex (unlike South Asian and European dentition). It's again a matter of anterior vs. posterior teeth: Sinodonts seem to be complex in the front but simplified in the back, Sub-Saharan Africans the other way around.

I could send you some papers so you can form your own opinion.

You mention that, according to mtDNA and Y chromosome, Khoisans branched off first. But if you look at their pigmentation it's light and it's partially controled by a derived allele. Doesn't fit.

Khoisans have epicanthus, Mongolian spot and light skin, so they seem like an Asian offshoot from the time when some Mongoloid phenotypical features were already in place, while others were still in the making. Their mtDNA and Y chromosome lineages were subject to selective, mutational or other pressures and developed long branches. Although neutral genes are important, especially when it comes to small-scale population reconstructions, it's important to constantly check them against major phenotypical systems, in order to avoid mistaking results of accelerated rate of mutations with truly ancient connections.

B006 was stated to have higher diversity values in Mongolians. True. But any relative age assessment isn't just a matter of allele diversity. Allele diversity depends on eff pop size and hence variable. Relative age assessment is the art and science of diversity levels, frequencies and geographic range of lineage. For instance, all major Amerindian mtDNA haplotypes (A, B, C, D) were found in Mongolians but at very low frequencies. Amerindians, on the other hand, have these lineages at moderate to high frequencies (mutation-drift equilibrium). A population scenario under which a small group of ancient Amerindians ended up in Mongolia and then expanded would manifest itself in Mongolians reducing the frequencies of the original markers and developing new ones. If this process is very speedy diversity levels may end up somewhat higher in Mongolians. But the frequencies would tell a different story.

Maju said...

Maybe it's an archaic trait, guess that debatible, like whatever other trait (prognathism, epicanthic fold, various types of noses, dolicocephaly, etc.) But a grain does not make a granary. Using exactly the same logic, I could perfectly argue that dolicocephaly, most common in Africa by far, is an archaic trait (all archaic hominis and even most archaic modern humans have it) as well, and inversely brachicephaly (most common towards the Pacific) is an innovation.

You mention that, according to mtDNA and Y chromosome, Khoisans branched off first. But if you look at their pigmentation it's light and it's partially controled by a derived allele. Doesn't fit.

I know nothing about the alleles that rule Khoisan pigmentation but it makes all sense that they are fair because they live and have lived for many many milennia in a climatic area comparable to the Mediterranean basin.

Khoisans have epicanthus, Mongolian spot and light skin, so they seem like an Asian offshoot...

Or vice versa. Or a mere accident of similar founder effects in these phenotype features.

B006 was stated to have higher diversity values in Mongolians. True. But any relative age assessment isn't just a matter of allele diversity.

Normally diversity within a lineage is accepted as marker for a likely origin. It's like fleas placed on a spot: they spread all around but most frequently near the origin. The farther the most likely that only some lineages arrive (founder effect).

For instance, all major Amerindian mtDNA haplotypes (A, B, C, D) were found in Mongolians but at very low frequencies.

Actually B is not found in NE Asia. A, C and D are instead. But again the diversity is in the side of Asia in all cases.

A population scenario under which a small group of ancient Amerindians ended up in Mongolia and then expanded would manifest itself in Mongolians reducing the frequencies of the original markers and developing new ones.

Whatever you say this shows that you're green in real knowledge of genetics. If D1 is derived (downstream) of D, D cannot be derived from D1. Of all top tier derived lineages of A, B, C, D and X2, they are most diverse in Asia. Native Americans are in all cases the ones holding the least diversity at the high phylogenetic levels of each shared lineage (by far). This clearly indicates that ALL the Native American lineages started as Asian ones. There's nothing to to argue on this. Native Americans are (originally) just a subset of North and East Asians.

German said...

For Khoisan pigmentation as determined by a derived allele, see Norton Genetic Evidence for the Convergent Evolution of Light Skin in Europeans and East Asians. MBE 2007 24 (3), pp. 716, 719.

It's possible to interpret global clines in genes and phenotypes both ways. True. Let's keep our eyes open to reverse scenarios.

B is not found in NE Asia. True. (But found at low frequencies in Eskimos/Inuits). Mongolia is not NE Asia, though. All American Indians haplotypes with the exception of X are found in Mongolians and a couple of South Siberian groups such as Tuvans and Altaians. At very low frequencies, though.

Like I said, diversity is only one possible parameter to infer age. American Indians are very diverse genetically if we take into account how low their population size was before 1492 as compared to some most genetically diverse parts of the Old World (just check the pop sizes of some of those African and Amerindian tribes listed in genetics publications). Plus right now America is arguably the most diverse continent (first mtDNA studies used African American genes as representing African diversity but not American diversity; imagine we didn't have a clue that America was peopled in 1492), although this diversity is only 500 years old.

mtDNA and Y-DNA are very "green" disciplines. Don't invest yourself too much into them.

Maju said...

Mongolia is not NE Asia, though.

That is just arbitrary decission and depends on context. For example, Mongols are high in Y-DNA, like other NE Asians and unlike most Han, so for this purpose it'd be logical to place them in that area. Often East Asia is just split in two cutting through China and that also makes some sense. You can't define any clear border across Eastern Asia in any case.

Like I said, diversity is only one possible parameter to infer age. American Indians are very diverse genetically if we take into account how low their population size was before 1492 as compared to some most genetically diverse parts of the Old World.

Top level diversity is still higher among much lower density groups, like the peoples of Sahul or Africa. Even such a reduced population like Bushmen probably has more diversity (and certainly more ancient lineages) than Native Americans.

Bushmen have at least L0 and L1 and what do all Eurasians, including Native Americans have? just a small subset of L3.

You're just diverting the issue because you really really really badly want your theory to hold true and are not ready to accept you could be wrong.

If you want to make science you must begin by self-criticism.

German said...

I recommend reading:

R H Ward, B L Frazier, K Dew-Jager, and S Pääbo. Extensive mitochondrial diversity within a single Amerindian tribe. PNAS 1991 October 1; 88(19): 8720–8724.

The point of this paper is that diversity within a single Native American tribe formerly called Nootka is higher than that of !Kung and approximates that of Tokyo (sic!). Similar levels of diversity were reported for Maya.

To be true, some American Indian tribes have reduced diversity levels, e.g., Cayapa in Ecuador. But Fst values (F-statistic is a tool that measures microdifferentiation in cranial and genetic populations) are consistently higher in the New World vs. Old World populations. It's textbook knowledge. High Fst values in the Americas correlate nicely with high levels of linguistic diversity in the Americas.

I'm open to any evidence whatsoever, but I have to admit I hate papers that start by saying that science has established that American Indians came from Siberia and end by confirming it. The origin of American Indians from the Old World is a myth that science inherited from the late Middle Ages with its "New World" cosmology. Scientists have been "proving" an unscientific assumption for 200 years now. What an irony!

Maju said...

It's a 1991 paper! Please...

Native Americans have exactly 5 mtDNA lineages: A, B, C, D and X, all derived ultimately from M (some 35 directly derived lineages) and N (12). Even if C and B are not directly derived from M and N respectively (the sequence is M>M8>CZ>C and N>R>R11'B>B) and NAs only have some of the diversity within those lineages, comparing 5 to 47 gives you the right impression in regard to American and Eurasian relative mtDNA diversity.

When you compare any of the two with Africa it is two vs many dozens.

This discussion is just pointless.

German said...

Unfortunately the scientific community can't fit all its research into one most recent year. That's why some research is published in 1991, other in 2009. They're all valid unless they were disputed and proven wrong.

I see you have interest in ancient population processes. I've suggested to you some of the original articles I'm aware of.