September 06, 2011

East Eurasian mtDNA in Ukrainian Neolithic and Bronze Age

Jean M links to a Master's thesis, which discovered the following:
While most of our samples possessed mtDNA haplotypes that can be linked to European and Near Eastern populations, three Neolithic and all three Bronze Age individuals belonged to mtDNA haplogroup C, which is common in East Eurasian, particularly South Siberian, populations but exceedingly rare in Europe. Phylogeographic network analysis revealed that our samples are located at or near the ancestral node for haplogroup C and that derived lineages branching from the Neolithic samples were present in Bronze Age Kurgans. In light of the numerous examples of mtDNA admixture that can be found in both Europe and Siberia, it appears that the NPR and South Siberia are located at opposite ends of a genetic continuum established at some point prior to the Neolithic. This migration corridor may have been established during the Last Glacial Maximum due to extensive glaciation in northern Eurasia and a consequent aridization of western Asia. This implies the demographic history for the European gene pool is more complex than previously considered and also has significant implications regarding the origin of Kurgan populations.
Unfortunately the thesis is under embargo until next year. We'll have to wait and see whether this research stands up to closer scrutiny by ancient DNA experts. The detection of a haplogroup that is quite rare in Europe today makes it difficult to envision a scenario in which contamination may have produced a spurious result, however.

The Dnieper-Donets population was described as robust Europeoid by Soviet anthropologists as was the Andronovo/Afanasevo tradition further east. It is interesting that Mongoloid admixture has been detected in both groups. I would not have guessed that this would have extended that far west and south. It seems that M. G. Levin may have been right when he stated that the Mongoloid elements penetrated far into eastern Europe.

It will certainly be interesting to discover how the Mongoloid component in the gene pool of the Northern Pontic steppe became diluted until the present. James Mallory argued at great length in a recent talk about the impossibility of Balkan influences on the steppe. I would bet that there were influences from the both the Balkans and the Caucasus, as well as the Transcaspian arrival of Iranic speakers in the 1st millennium BC, ultimately from their Bactria-Margiana source.

UPDATE:


On the Origin of Mongoloid Component in the Mitochondrial Gene Pool of Slavs, B. A. Malyarchuk, M. A. Perkova, and M. V. Derenko (pdf)
Concerning the population of Eastern Europe, it should be noted that the forest zone of Eastern Europe was the area of intense population admixture [35]. It seems likely, that formation of the complex of Mongoloid traits happened not later than in Upper Paleolithic. For this reason, it is suggested that East Siberian populations could have much time for migration to Eastern Europe [35]. The number of such migrations still remains unclear, since in the northwest of Eastern Europe Mongoloid component is detected 10000–8000 years ago; in Dnepr–Donetsk tribes, 7000–6000 years ago, and on the territory of Ivanovo oblast (Sakhtysh), 6000–5000 years ago [35, 36].


It seems, once again, that physical anthropology and genetics are consistent with each other.

33 comments:

n/a said...

I see no reason to believe the presence of haplogroup C indicates a "Mongoloid component". Stephen Oppenheimer sees C/Z mtDNA entering Mongoloids as part of an "intrusive" element "likely to have arrived from farther west in Asia, along with the eastern spread of the Upper Palaeloithic technology that appeared in Kara Bom in the Russian Altai 43,000 years ago." If this is correct, the presence of C in robust steppe Caucasoids would not be surprising. Oppenheimer has C/Z originating in western South Asia and entering Central Asia "round the western end of the Himalayas" 40-50,000 years ago, whereas Mongoloids (and "real" East Eurasian haplogroups) ultimately originate in SE Asia.

terryt said...

A couple of interesting comments:

"mtDNA haplogroup C, which is common in East Eurasian, particularly South Siberian, populations but exceedingly rare in Europe".

And German has been arguing that C is ancient European.

"In light of the numerous examples of mtDNA admixture that can be found in both Europe and Siberia, it appears that the NPR and South Siberia are located at opposite ends of a genetic continuum established at some point prior to the Neolithic. This migration corridor may have been established during the Last Glacial Maximum due to extensive glaciation in northern Eurasia and a consequent aridization of western Asia".

The migration route was quite possibly also open before the Last Glacial Maximum. That would certainly explain the Y-hap C and mtDNA N distribution.

eurologist said...

"our samples are located at or near the ancestral node for haplogroup C"

I find that hard to swallow, especially with the current, old estimates for C - which make sense given the populating of the Americas. See also Dienekes' entry in December 2010 about Derenko et al.:
http://dienekes.blogspot.com/2010/12/post-glacial-expansions-of-mtdna.html

A near basal neolithic lineage would require some extremely small population niche over 30,000 to 60,000 years (depending on what age estimate you believe).

Waggg said...

Let's remember that an haplogroup mtDNA N9a was found in the neolithic remains of the Körös culture in Hungary :

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015214

"The early presence of mtDNA lineages of eastern Asian ancestry in Europe is further confirmed by the discovery of a N9a haplotype in a Neolithic skeleton from the Szarvas site, located in southeastern Hungary that belonged to the Körös Culture, which appeared in eastern Hungary in the early 8th millennium B.P. [29]."

Didier said...

This finding might bring support to the view of those thinking that R1b/R1a are from central Siberia.

Dienekes said...

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015214

"Haplogroup C peaks over 50% among Yukaghirs of northeastern Asia, central Siberian Yakuts and Evenks as well as East-Sayan Tofalars. Its frequency is persistently above 20% in Altaian, West-Sayan and Baikal region populations and drops to 13% or less among Chukchis, Eskimos and Itelmens in the east, Altaian Kazakhs, Shors, and Oroks in the south, and Khants and Kets in the west. The diminishing line (frequencies under 5%) goes through the Turkic and Finno-Ugric populations of the Volga basin, further south through the populations of the Caucasus and western Asia. In the southern direction the decline of haplogroup C frequency is almost as sharp as in the west direction: it is very common in Mongolia (15%) and most of the populations of central Asia (7–18%), but occurs as rarely as 1–5% in Korea, China, Thailand, Japan, Island southeastern Asia and India. Haplogroup C is detected at a very low frequency in several populations of eastern and central Europe and virtually absent in western Europe and Africa (Table S1)."

...

"The average sequence divergence of the 174 C complete genome corresponds to a coalescence time estimate of 27.37 (19.55; 35.44) kya when using the sequence variation of the entire genome and 26.33±6.58 when only synonymous mutations are considered [19] (Table S3)."

...

The present-day variation of haplogroups C and D suggests that these mtDNA clades had already expanded before the LGM, with their oldest lineages being present in the eastern Asia.

...

"It appears that European branch C5c1 is more differentiated, as far as two of three sequenced Polish mtDNAs formed a separate branch (C5c1a), defined by a coding region mutation at np 7694. The relatively large amount of internal variation accumulated in the Polish branch of C5c would mean that C5c1 arose in situ in Europe after the arrival of a C5c1 founder mtDNA from southern Siberia, and that C5c1 affiliation is a marker of maternal Siberian ancestry. The phylogeny depicted in Figure S1 provides additional information concerning the entry time of the founder mtDNA – the age of C5c node is estimated as 9.7 (3.17; 16.49) kya when using the sequence variation of the entire genome, and 9.2±4.74 when only synonymous mutations are considered (Table S3). "

"Importantly, we have not found in northern Asia any genetic signatures of sufficient antiquity to indicate traces of pre-LGM expansions, that originated from the Upper Paleolithic industries that were present both in the southern Siberia and Siberian Arctic, and that date back to ~30 kya, well before the LGM [1], [34], [36]."

Dienekes said...

This finding might bring support to the view of those thinking that R1b/R1a are from central Siberia.

First of all, we don't have Y-DNA data on the NPR population yet.

Second, under the hypothesis that this population belonged to R1, the mtDNA evidence (presence of C in Neolithic and all Bronze Age samples) is inconsistent with large-scale demic movements from the steppe that largely replaced the northern/central European Neolithic population as haplogroup C is "virtually absent in western Europe and Africa (Table S1)." (http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015214)

I see no reason, at present, to accept Klyosov's theories about R1a/R1b from the Altai. The most likely point of origin of R1 is between the Caspian sea and the Indian subcontinent. This would explain the R1b concentration on the west and southern coasts of the Caspian, the R1a concentration north and east of it, and would also bring R1 in close proximity to its sister clade R2, to the south and east.

n/a said...

Dienekes,

Haplogroup C mtDNA has likely been subject to selection relating to extreme cold, meaning those dates likely underestimate its age. Selection could also play a role in the low frequencies in living Europeans.

Effects of purifying and adaptive selection on regional variation in human mtDNA

The relative frequency and amino acid conservation of internal branch replacement mutations was found to increase from tropical Africa to temperate Europe and arctic northeastern Siberia. Particularly highly conserved amino acid substitutions were found at the roots of multiple mtDNA lineages from higher latitudes. [. . .]

On the basis of this biogeographic analysis, we would expect haplogroups A, C, D, and X to have been subjected to much greater cold stress than haplogroup B or African macro-haplogroup L. Accordingly, the I/T ratios of the arctic haplogroups A, C, D, and X (0.91 to 2.91) were all greater than B (0.75) or L (0.70), and the RFI values of haplogroups A and X were significantly greater than that of L (P 0.05) (Table 2). Moreover, the CII values of haplogroups A (53%) and C (73%) were much higher than B (31%) or L (36%), with the CI of C being the highest of any haplogroup (Table 2). Hence, the mtDNA variation of haplogroups A, C, D, and X has been strongly influenced by adaptive selection, whereas that of haplogroup B has not. [. . .]

The Siberian sub-haplogroup C also contained two conserved root variants: ND4 at nt 11969A (A404T) (CI 85%) and cytochrome b (cytb) at nt 15204C (I153T) (CI 85%).


http://www.ufrsdv.u-bordeaux2.fr/siteIML/Maste2biosante/Master2biosantecours/articles/Genet%20Hum-4oct-2.pdf

Mutation Rate Switch inside Eurasian Mitochondrial Haplogroups: Impact of Selection and Consequences for Dating Settlement in Europe

This analysis revealed a new coalescence age for R at 54.500 years, as well as several limitations of standard dating methods, likely to lead to false interpretations. These findings highlight the association of a striking under-accumulation of synonymous mutations, an over-accumulation of non-synonymous mutations, and the phenotypic effect on haplogroup J. Consequently, haplogroup J is apparently not a Neolithic group but an older haplogroup (Paleolithic) that was subjected to an underestimated selective force. These findings also indicated an under-accumulation of synonymous and non-synonymous mutations localized on coding and non-coding (HVS1) sequences for haplogroup R0, which contains the major haplogroups H and V. These new dates are likely to impact the present colonization model for Europe and confirm the late glacial resettlement scenario. [. . .]

Similarly, we propose that the J lineage had the same mutation rate as the other lineages, but preferentially accumulated non-synonymous mutations, possibly due to positive selection of non-synonymous mutations in a cold environment. In fact, it was previously proposed that the non-synonymous mutation of the J haplogroup would promote heat production by decoupling oxidative phosphorylation, thus constituting a mitochondrial adaptation to cold weather [6].


http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0021543

This paper estimates a coalescence age of 31kya for C, but estimates ages of 40kya for its sister haplogroup Z and 58kya for CZ.

Dienekes said...

It's not extremely cold in Europe, certainly not in relation to Siberia.

But, even if we assume that C's age was kept down by cold, that would not explain why it is more diverse at the eastern end of its distribution compared to Europe; we would expect the opposite to be true.

Moreover, if C was long established among Paleolithic Europeans, we would expect to see it throughout Europe, but in fact it is absent in most of Europe and occurs at an extremely low frequency in eastern Europe.

It could be argued that C's frequency may have been reduced by negative selection, but, again, C is absent in all the available ancient DNA samples from Europe so far.

Haplogroup C is more diverse and occurs at higher frequency among Mongoloids today. It must certainly present among north Mongoloids at the time of the colonization of the Americas.

The simplest explanation with the available evidence is that C was introduced into Europe much later than its Paleolithic colonization, otherwise we would see deep time depths and a wide distribution in Europe, like we see with U which is ubuiquitous and has deep time depths. The origin of C could only have been from Siberia, which was occupied during the Paleolithic by Mongoloid groups, until the spread of steppe groups from the west brought Caucasoid types during the Eneolithic and Bronze Age.

This paper estimates a coalescence age of 31kya for C, but estimates ages of 40kya for its sister haplogroup Z and 58kya for CZ.

31ky is similar to 27ky reported by the other paper. Moreover:

"The largest diversity of sister haplogroup C has been reported in Korea (100%) followed by central Asia (86%), and northern China (78%–74%). Therefore, C can be considered a clade with a Northeast Asian radiation [18]. Representatives of subhaplogroup Z extend from the Saami [4] and Russians [51] of west Eurasia to the people of the eastern peninsula of Kamchatka, the Russian Far East [52]. Its largest diversities are found in Korea (88%), followed by northern China (73%), and central Asia (67%), compatible with the hypothesis of central-east Asian origin of radiation for this haplogroup [18] (Fig. S5)."

n/a said...

"It's not extremely cold in Europe, certainly not in relation to Siberia."

That's the point. MtDNA that throw off more heat at the expense of efficiency are likely to be adaptive among hunter-gatherers living in the far north or in the middle of an ice age, but maladaptive among agriculturalists with expanding populations to feed in more temperate climes/times.

"But, even if we assume that C's age was kept down by cold, that would not explain why it is more diverse at the eastern end of its distribution compared to Europe; we would expect the opposite to be true."

If C has been selected against in Europe, the surviving lineages probably represent a non-random sample.

"C is absent in all the available ancient DNA samples from Europe so far."

Based on the results reported here, that's no longer true. If it really turns out to be the case that "our samples are located at or near the ancestral node for haplogroup C", that's particularly instructive. C1 has also been found in a Neolithic Syrian.

"31ky is similar to 27ky reported by the other paper."

And for reasons explained in the haplogroup J paper, these numbers (based on synonymous mutations) almost certainly underestimate the actual age.

I've never seen any physical anthropological evidence for Mongoloid admixture in the Dnieper-Donets people. I don't read Russian, so I can't evaluate the claims cited in the Malyarchuk paper.

German Dziebel said...

"three Neolithic and all three Bronze Age individuals belonged to mtDNA haplogroup C, which is common in East Eurasian, particularly South Siberian, populations but exceedingly rare in Europe."

Notably, Bronze Age South Siberians were close to Amerindians craniologically. http://onlinelibrary.wiley.com/doi/10.1002/%28SICI%291096-8644%28199902%29108:2%3C193::AID-AJPA5%3E3.0.CO;2-V/abstract

@Terry

"And German has been arguing that C is ancient European."

Having C1e, a separate clade closely related to Amerindian C1, in Icelanders and now another C lineage in Bronze Age East Europeans makes my argument stronger. In both cases, these lineages form separate clades, which again suggests that they represent ancient, pre-agricultural "sediments" in Europe characteristic of small-scale population demographies.

@n/a

"Haplogroup C mtDNA has likely been subject to selection relating to extreme cold, meaning those dates likely underestimate its age. Selection could also play a role in the low frequencies in living Europeans."

This makes sense. But whatever the reasons for lower alellic diversity it doesn't mean recent age. The patchy distribution of mtDNA C, Z, D and X in Europe, in addition to Y-DNA Q suggests antiquity because ancient demographies best preserved in historical Amerindians were characterized by low population size.

@ Dienekes

"Haplogroup C is more diverse and occurs at higher frequency among Mongoloids today. It must certainly present among north Mongoloids at the time of the colonization of the Americas."

Wishful thinking, as always.

"It seems, once again, that physical anthropology and genetics are consistent with each other."

As in the case of the elevated frequencies of "Mongoloid"/Amerindian shovel-shaped incisors in Upper Paleolithic Europeans and in Catalhoyuk (etd.ohiolink.edu/send-pdf.cgi/Pilloud%20Marin.pdf?osu1253574143)

Annie Mouse said...

WOW, so genetic evidence from the area that may have been the centre of the Neolithic and/or Bronze age expansion. I would love to know what the other haplogroups are. Could be very interesting.

I have no problem with mitochondrial C being part of the pre-Neolithic Gravettian flow along the snowline from Europe to East Asia (in either direction). It makes sense that the women who travelled were close to the node (spreading nodal women across the migration area) with the variants occuring later once they were in new areas. Perhaps they should however be a bit divergent after 10,000 years though (Gravettian-> Neolithic).

The paucity of C in modern Europe however tells us that the WOMEN of Neolithic or Bronze Ukraine did NOT overrun Europe genetically. Admittedly we are looking at small numbers (3/10 Neolithic, 3/3 Bronze age). But still to show continuity between the Neolithic and Bronze age, they probably were a major part of the genetics of the region at the critical time.

princenuadha said...

" spreading nodal women across the migration area"

Lol for using the term nodal women.

Dienekes said...

That's the point. MtDNA that throw off more heat at the expense of efficiency are likely to be adaptive among hunter-gatherers living in the far north or in the middle of an ice age, but maladaptive among agriculturalists with expanding populations to feed in more temperate climes/times.

It depends on whether evolution was driven by positive selection _for_ specific cold-adapted lineages wtihin C in Siberia, or negative selection _against_ C.

The persistence of C among Amerindians throughout the Americas ...

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001764

... is particularly interesting in that regard. Amerindian ancestors must certainly have been cold-adapted because of their migration route, but C has not apparently been lost to them even though they ended up living in some really hot climates. So, it seems that it is not C itself that is cold adapted, but lineages within C, or, at least mtDNA is mutable enough to lose its cold adaptations.

If Amerindians could fare well with it, I don't see why Europeans would not. Also, presumably the first humans who ventured to the north carrying C mtDNA were not cold-adapted yet, but they became so by selection of specific C subgroup(s). So, overall it seems to me that both gain and loss of function is not an exceptional event in mtDNA evolution.

Another consideration is that C was apparently present at substantial frequencies in the Neolithic and even Bronze Age in these populations, i.e., long after the LGM. The Bronze Age is closer to us than it is to the end of the last glaciation; so, if thermoregulation is the culprit, it is surprising that C persisted through a greater length of time (until the Bronze Age), only to disappear in a shorter length of time (from the Bronze Age to the present, and indeed to the various historical ancient DNA samples from Europe that match the modern pattern with respect to it).

Hector said...

MtDNA HG C's origin in any other place than East Asia is non sensical since its sister clade M8a is present only in East Asia.

Mongloid traits are derived forms. That is to say, an acient remain exhibiting a Mongoloid morphology is likely to harbor a substantial monoloid genetic component. But the other way around is not true. An individual can be genetically Mongoloid(or affilated with such) without showing any mongoloid traits. The prime example would be Ainu.

German Dziebel said...

"MtDNA HG C's origin in any other place than East Asia is non sensical since its sister clade M8a is present only in East Asia."

Hg C could have originated in the Americas. If it arrived to the Americas from East Asia, then why earlier, more diversified and more frequent M haplogroups didn't? The New World has a unique collection of haplogroups found at low frequencies in Eastern and Western Eurasia. It's unlikely they were brought to the New World, while others did not. If, however, hgs C, B, D, A and X represent a back migration from the Americas, then everything becomes nice and clear.

German Dziebel said...

"MtDNA HG C's origin in any other place than East Asia is non sensical since its sister clade M8a is present only in East Asia."

MtDNA hg C could evolve in the New World. America has a unique collection of mtDNA haplotypes that are rare in Eastern and Western Eursia. If hg C came to America from East Asia, then why older, more frequent and more diversified more basal M, N and R haplogroups did not?

terryt said...

"Hg C could have originated in the Americas".

As a result of a disagreement with Maju I've just looked at these American mtDNAs. Seems that the American C haplogroups are derived, the C1s along with one of the C4s: C4c.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015214

"If it arrived to the Americas from East Asia, then why earlier, more diversified and more frequent M haplogroups didn't?"

Because they were not present in the region from which the migration began. C1 met the requirements. Its 'sister clades are C4 and C5 are present in 'Northern Asia' with C5 in 'Southern Siberia' and C7 in 'South Asia'.

"If, however, hgs C, B, D, A and X represent a back migration from the Americas, then everything becomes nice and clear".

We strike the same problem with the other haplogroups. They are all 'downstream' haplogroups. American A is A2, a haplogroup within A4. Sister haplogroup to A3, A7, A9 and A11. These other As are spread through Central Asia between Tibet and the Lake Baikal region, so the route must have passed nearby. American B is B2, a subclade of B4b, an East Asian haplogroup. American D is D1, just one of a large number of D's, and D4h3, also East Asian. American X is the derived X2a, the most westerly of the American haplogroups.

All this stongly indicates that the haplogroups are immigrants into America, from North/Central Asia.

German Dziebel said...

"Because they were not present in the region from which the migration began."

Terry, your whole reasoning is flawed. This is not your fault, however; it's the fault of wrong phylogenies that you're looking at.
E.g., mtDNA B2 is not found in North Asia, so by your logic, it's not supposed to be in the New World. But in fact it's very frequent there. B2 is also very frequent in Polynesians, while B4 is not found in either the New World or Oceania. This suggests strongly that B2, which has a much wider geographic distribution and higher frequencies in two widely separated regions should be ancestral to B4 and not the other way around.

"American X is the derived X2a..."

First, Amerindians have another one of those, namely Xg (see Perego 2009 and PhyloTree). Second, no hg X has ever been found in areas of the Old World adjacent to the New World. Hence, again your logic is falsified.

"American A is A2, a haplogroup within A4. Sister haplogroup to A3, A7, A9 and A11."

So, why didn't Amerindians pick up all those haplogroups, too? According to you, Amerindians cherry-picked one-two lineages out of every clade within both M and N macrohaplogroups. Since most genetic publications support a single entry into the New World, this selectivity becomes an impossible assumption to believe in. Notably, the same can be said about the purported exit from Africa: why did non-Africans pick up only M and N, which are not found in Africa, out of a dozen of earlier and more diversified and more widespread ones in Africa?

"American D is D1, just one of a large number of D's.."

So, why isn't D1 found in Asia, while most other Ds aren't found in the Americas?

I'm just identifying all the problems with the serial bottleneck out of Africa and into the Ameircas idea. If we look at the linguistics picture, we'll see that the whole phylogenetic order in genetics publications is reversed. And the little distributional details around individual haplogroups show it!

terryt said...

"Terry, your whole reasoning is flawed. This is not your fault, however; it's the fault of wrong phylogenies that you're looking at".

The phylogenies seem reasonably well accepted, by most.

"B2 is also very frequent in Polynesians, while B4 is not found in either the New World or Oceania."

As far as I'm aware B2 is not found in Polynesians. Most Polynesians are B4a. According to Phylotree B2, which is American, is really a subgroup of B4b, various clades of which (as far as I'm aware) are found in various parts of Northern Asia.

"Amerindians have another one of those, namely Xg (see Perego 2009 and PhyloTree)".

Which is another subclade of X2 though, so hardly surprising that some accompanied X2a.

"no hg X has ever been found in areas of the Old World adjacent to the New World. Hence, again your logic is falsified".

But X's distribution is very patchy anyway, and if it was one of the original mtDNAs that accompanied Q on the voyage from Central/SW Asia to America it is hardly surprising that it would have remained very thinly spread along the route, and easily replaced by eastern haplogroups that later became more widespread.

"So, why didn't Amerindians pick up all those haplogroups, too?"

The question is more properly asked the other way round. Why would they pick up every single haplogroup, especially if the route to America was very narrow?

"According to you, Amerindians cherry-picked one-two lineages out of every clade within both M and N macrohaplogroups".

I wouldn't use the expression 'cherry-picked' but they could hardly be expected to pick up a completely representative sample of Northern Asian haplogroups. The following is na old but good paper on early American haplogroups (specifically Y-haps, but it covers mtDNA as well) which you are probably familiar with:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1377800/pdf/10053017.pdf

"why did non-Africans pick up only M and N, which are not found in Africa"

Pick up? M and N are really subclades of L3, which is very common in Africa.
Presumably M and N are the only L3 haplogroups that made it out.

"out of a dozen of earlier and more diversified and more widespread ones in Africa?"

Presumably the exit was very difficult. Only a few made it out. The same with the exit from Asia to America. And to the wider Pacific. Just a selection of haplogroups made the trip.

"So, why isn't D1 found in Asia, while most other Ds aren't found in the Americas?"

It would not actually have been D1 that made it to America. According to Phylotree D1 is just one of 17 branches of D4(xD4'5). Many of the others are found in various parts of Asia. Presumably just a few basal D4s entered America where drift in the small population reduced the variation to just one: D1.

"the little distributional details around individual haplogroups show it!"

We must remember that haplogroups don't tell the full story. And even just considering them we must remember that the human population has not simply steadily increased. Any population of constant size will lose haplogroups through drift alone. As a result some haplogroups end up with a long 'tail' of mutations. The populations containing them remained small and isolated and of constant size. A diversification of haplogroups indicates a population expansion, usually as a result of being able to enter a so-far unexploited region. Such as Eurasia, South Asia, Northern Asia, America or the wider Pacific.

German Dziebel said...

"The phylogenies seem reasonably well accepted, by most."

Terry, you treat phylogenies as if they were made by God. In fact, they were made by a small group of humans. And humans err. Genetic phylogenies were built with an eye on archaeology/paleoanthropology and not with an eye on linguistics. If they followed the linguistics lead - high diversity in America and Oceania, low diversity in Africa and Europe - the tree would've been different. As an example of a radically different tree, see this autosomal model: http://www.dnatribes.com/populations.html (p. 4 of the pdf in the bottom of the page). As the Denisova find demonstrates, archaeology/paleobiology is a poor predictor of deep-rooting genetic lineages. A hominid species from which we only have a pinkie and a tooth and which we found only a couple of years ago, supposedly contributed up to 95% of HLA genes to Asians, Amerindians and Papuans.

"As far as I'm aware B2 is not found in Polynesians. Most Polynesians are B4a. According to Phylotree B2, which is American, is really a subgroup of B4b, various clades of which (as far as I'm aware) are found in various parts of Northern Asia."

Okay, this must be the current nomenclature. But my point remains: there are no B4 lineages in the areas adjacent to America. And there're no Siberian groups that have all Amerindian markers attested at the same time, while there're Amerindians with A, X, B, C and D lineages at the same time.

"Pick up? M and N are really subclades of L3, which is very common in Africa.
Presumably M and N are the only L3 haplogroups that made it out."

This is precisely how myths are made. M and N aren't found in Africa, while M1 and U6 are, so how could you say that they made it out if the data shows that they made it in? L3 is likely just a subclade of M or N, if you flip a couple of mutations around. Then it would fit the growing amount of data of a substantial non-African admixture in Africa that didn't affect Paleoafricans such as Bushmen.

"Presumably the exit was very difficult. Only a few made it out. The same with the exit from Asia to America. And to the wider Pacific. Just a selection of haplogroups made the trip."

"But X's distribution is very patchy anyway, and if it was one of the original mtDNAs that accompanied Q on the voyage from Central/SW Asia to America."

You've been reading the Bible too much, Terry. This is not a scientific model.

"According to Phylotree D1 is just one of 17 branches of D4(xD4'5)."

A typical case of sub-lineage diversification under the pressure to colonize new environments! Again, flip a couple of mutations around, and you'll get a tree with D1 as an outlier to all the 17 branches of D4. This would be natural and plausible. Once the ice melted 10,000 years ago, all of these lineages poured out of the Americas into East Asia. On the other hand, one single D1 lineage out of 17 making it to the New World, with no D1 left in the Old World, is a pure fantasy.

terryt said...

"there are no B4 lineages in the areas adjacent to America".

But there are B4 lineages in Japan and Korea, and if B arrived in America by sea they surely would have come via somewhere near Japan. And haplogroups do get replaced occasionally. Families get pushed around, even today.

"And there're no Siberian groups that have all Amerindian markers attested at the same time"

Most likely because not all American mtDNA haplogroups came from the same place. They were picked up along the way, exactly as the link I provided yesterday suggested.

"there're Amerindians with A, X, B, C and D lineages at the same time".

How's this for a provisional order of pickup, from west to east: X, A, C, D, B?

" M and N aren't found in Africa"

No, but plenty of their 'sisters' are.

"M1 and U6 are, so how could you say that they made it out if the data shows that they made it in?"

You seem to be influenced by some 'Noah's Ark' theory of human expansion. Everyone came from a single region and migrated unidirectionally. Humans have been moving backwards and forwards around the world since Homo erectus first emerged. M1 and U6 are a product of back movement into Africa.

"Then it would fit the growing amount of data of a substantial non-African admixture in Africa that didn't affect Paleoafricans such as Bushmen".

But the back movement of M1 and U6, along with other R-derived haplogroups and (possibly) Y-hap E takes care of that problem.

"You've been reading the Bible too much, Terry. This is not a scientific model".

It's basically the model that Karafet et al proposed.

"Again, flip a couple of mutations around, and you'll get a tree with D1 as an outlier to all the 17 branches of D4".

Which mutations do propose 'flipping around'?

"one single D1 lineage out of 17 making it to the New World, with no D1 left in the Old World, is a pure fantasy".

I see it as quite obvious, and likely. I can't understand why you cannot see it as so.

terryt said...

"flip a couple of mutations around, and you'll get a tree with D1 as an outlier to all the 17 branches of D4".

I suppose that if the 2092 and 16325 mutations occurred after D4a'b'c'd'e'f'g'h'i'j'k'l'm'n'q's had left America you might be able to make a case. But surely it is just as likely that D is a 'typical case of sub-lineage diversification under the pressure to colonize new environments' as it expanded north overland from South China, with just one small group being able to invade America.

German Dziebel said...

"How's this for a provisional order of pickup, from west to east: X, A, C, D, B?"

"But there are B4 lineages in Japan and Korea, and if B arrived in America by sea they surely would have come via somewhere near Japan."

And what happened to X in Northeast Asia? And why would proto-Amerindians swing by Japan and Korea on their way from West Asia?

"You seem to be influenced by some 'Noah's Ark' theory of human expansion. Everyone came from a single region and migrated unidirectionally. Humans have been moving backwards and forwards around the world since Homo erectus first emerged. M1 and U6 are a product of back movement into Africa."

Terry, you're trying to sling Bible metaphors back at me but they won't fly. Only derived M and N lineages are found in Africa. There're no L lineages outside of Africa. There're no pre-M and pre-N lineages in Africa. There's no trail of earlier vs. later M and N lineages fanning out from a source region in Africa through West Asia to the rest of the globe. M and N seem to suddenly expand in East Asia, with M1, N1 and U6 finally ending up in Africa.

"But the back movement of M1 and U6, along with other R-derived haplogroups and (possibly) Y-hap E takes care of that problem."

Y-DNA E back migration is much more dramatic than the M1 and U6 migration. To match the footprint of Y-DNA E in Africa, we need to talk about the whole L2'3'5''6 cluster. This would leave us with L0 and L1 to parallel Y-DNA A and B. I date this back migration into Africa at 40,000.

"I suppose that if the 2092 and 16325 mutations occurred after D4a'b'c'd'e'f'g'h'i'j'k'l'm'n'q's had left America you might be able to make a case. But surely it is just as likely that D is a 'typical case of sub-lineage diversification under the pressure to colonize new environments' as it expanded north overland from South China, with just one small group being able to invade America."

You're right on with the mutations. But your last scenario wouldn't fit linguistics or archaeology (Clovis points were moving northward and not southward in the Americas at the end of the ice age). My scenario brings all the interdisciplinary data into alignment.

"I see it as quite obvious, and likely. I can't understand why you cannot see it as so."

Because it's simplistic and teleological, Terry. You have to perform the same reduction multiple times to make it work, so that only one lineage out of several diversified clades entered America, from several widely separated different areas. My model is very simple and evolutionary: once populations enter a new territory, they diversify and disperse in all directions. X went to Western Eurasia, C, D and A took a middle road, while B descended down the coast. This event happened 12-10,000 years ago and brought "Mongoloid" genes and the phenotype to the Old World. All the cultural and biological "similarities" between Amerindians and East Asians stem from this back migration from the New World. Prior to 12,000 years, America uniquely "owned" all these lineages just like Africa owns "L0/L1" and West Euroasia "U".

terryt said...

"And what happened to X in Northeast Asia?"

Probably swamped by the later movement north of other haplogroups, especially C and D.

"And why would proto-Amerindians swing by Japan and Korea on their way from West Asia?"

Again that's what Karafet et al showed for Y-haps. Japan is on any route by sea from Asia to America, although I'm sure that by no means all American haplogroups arrived via the coast.

"Terry, you're trying to sling Bible metaphors back at me but they won't fly".

Hang on. It was you who first wrote, 'You've been reading the Bible too much, Terry'.

"There're no pre-M and pre-N lineages in Africa".

Yes there is. Both M and N have the mutations 769 and 1018, known as L3.

"There's no trail of earlier vs. later M and N lineages fanning out from a source region in Africa through West Asia to the rest of the globe".

No. But there is a trail of M and N lineages fanning out from SW Asia to the rest of the world.

"To match the footprint of Y-DNA E in Africa, we need to talk about the whole L2'3'5''6 cluster"

Why?

"I date this back migration into Africa at 40,000".

Something else we agree on.

"only one lineage out of several diversified clades entered America, from several widely separated different areas".

And I think that fits the most likely scenario. Y-hap Q was able to enter the as yet uninhabited region Central Asia steppe, then began an eastward movement. As it moved it first of all carried mtDNA X but along the way mixed with people living along the southern edge of its route east. It progressively picked up other mtDNAs until by the time it entered America it had accumulated several of them. Later other groups were also able to move north, ultimately largely replacing the haplogroups that had been able to enter America.

"once populations enter a new territory, they diversify and disperse in all directions".

I agree completely. But Y-hap Q was restricted in its northward movement by ice sheets and in its southward movement by already inhabited regions.

"X went to Western Eurasia"

I'm fairly sure that X originated in Western Eurasia.

"B descended down the coast".

I'd place B's movement as being up the coast.

German Dziebel said...

"Probably swamped by the later movement north of other haplogroups, especially C and D."

Even if this is so, it means it wasn't substantial in the first place. Hence, the chances it would get picked up are slim. Plus why didn't it get lost in the New World for a similar reason?

"although I'm sure that by no means all American haplogroups arrived via the coast."

Pretty much all genetic publications argue for a single entry of all Amerindian haplogroups together in one wave with subsequent in situ differentiation.

"Yes there is. Both M and N have the mutations 769 and 1018, known as L3."

That would make them sister haplogroups. Again, as humans colonized Africa, they expanded into a dozen L3 sublineages.

"But there is a trail of M and N lineages fanning out from SW Asia to the rest of the world."

You meant to write SE Asia? Because there's no trail of lineages from SW Asia. There are no earlier branches of M or N in SW Asia and there proliferation doesn't begin until East Asia. Same for Y-DNA: which Y-DNA C lineages are found in SW Asia?

""To match the footprint of Y-DNA E in Africa, we need to talk about the whole L2'3'5''6 cluster"

Why?"

Because E is everywhere in Africa and is found there at high freuqncies, while M1 and U6 are narrowly regional and low frequency.

"And I think that fits the most likely scenario. Y-hap Q was able to enter the as yet uninhabited region Central Asia steppe, then began an eastward movement. As it moved it first of all carried mtDNA X but along the way mixed with people living along the southern edge of its route east. It progressively picked up other mtDNAs until by the time it entered America it had accumulated several of them. Later other groups were also able to move north, ultimately largely replacing the haplogroups that had been able to enter America."

I understand this is your belief. Now you just need to prove it. Interpretation is not proof. Name one or two archaeological cultures in Siberia that match your scenario.

""X went to Western Eurasia"

I'm fairly sure that X originated in Western Eurasia.

"B descended down the coast".

I'd place B's movement as being up the coast."

Too bad, genetics doesn't equip us with the facts that have a compelling power.

terryt said...

"Even if this is so, it means it wasn't substantial in the first place".

I agree. It wasn't substantial in the first place, probably because the route through Central Asia between the inhabited region to the south and the extremely cold region to the north.

"Plus why didn't it get lost in the New World for a similar reason?"

This is the sort of scenario that I think most likely. Y-hap Q set off east with mtDNA X. We would expect the more adventurous males would be first into any new hunting region. Many of these would be uninhabited but occasionally hunters would meet up with people already there. From them they would gather other mtDNA lineages, such as A. This would reduce the proportion of X females whether many As or just a few joined up. The process would be repeated as the combined population continued east. When mtDNA C joined the proportion of X and A would again be appropriately reduced, and so on.

"Pretty much all genetic publications argue for a single entry of all Amerindian haplogroups together in one wave with subsequent in situ differentiation".

And that is completely possible under the above scenario.

"That would make them sister haplogroups".

Which is exactly what they seem to be.

"You meant to write SE Asia? Because there's no trail of lineages from SW Asia".

There is actually. Basal N haplogroups X, N1'5 and N2 are all SW Asian, as is M1.

"which Y-DNA C lineages are found in SW Asia?"

None. The closest is C5 in Northwest South Asia. C's place in SW Asia is taken by G, IJ and F3 as, basically M's place is taken by N.

"Because E is everywhere in Africa and is found there at high freuqncies, while M1 and U6 are narrowly regional and low frequency".

We cannot assume that Y-hap E spread through Africa only with mtDNA haplogroups that had entered with it.

"while M1 and U6 are narrowly regional and low frequency".

And to me are much more likely to have spread with Y-hap R1b1c.

"Too bad, genetics doesn't equip us with the facts that have a compelling power".

True. We can only interpret the haplogroup trees with the information as we presently understand it. My 'belief' closely fits those trees but yours requires considerable alteration of those trees.

German Dziebel said...

"Y-hap Q set off east with mtDNA X."

I agree they are distributionally similar.

"This is the sort of scenario that I think most likely. Y-hap Q set off east with mtDNA X. We would expect the more adventurous males would be first into any new hunting region. Many of these would be uninhabited but occasionally hunters would meet up with people already there. From them they would gather other mtDNA lineages, such as A. This would reduce the proportion of X females whether many As or just a few joined up. The process would be repeated as the combined population continued east. When mtDNA C joined the proportion of X and A would again be appropriately reduced, and so on."

Are you the writer behind the "The Sons of the Bear Clan"? I brought up the unlikelihood that X was lost across the swaths of East Asia where all the major "lineage collecting" for a journey to America took place, but survived in America. You respond by telling another story.

"There is actually. Basal N haplogroups X, N1'5 and N2 are all SW Asian, as is M1."

You know very well, Terry, that all these lineages are no more basal than other N lineages. A back migration from America and East Asia to SW Asia and North Africa fits with all other data.

"C's place in SW Asia is taken by G, IJ and F3 as, basically M's place is taken by N."

Good observation. I also noticed how M and N swap frequencies in different regions.

"Which is exactly what they seem to be."

So, it means not ancestral. Hence, the fact that there're more sisters in Africa doesn't mean humans came from Africa. Even L0 and L1 are not ancestral to others - just more divergent, which can be caused by other factors than age/nativity to Africa.

"And to me are much more likely to have spread with Y-hap R1b1c."

Agree. So we have M1 and U6 corresponding to R1b1, while Y-DNA E corresponding to mtDNA L2'3'4'6.

"My 'belief' closely fits those trees but yours requires considerable alteration of those trees."

Duh, the trees are based on this very belief! It's irrefutable that the belief in a recent origin of Amerindians and in the great antiquity of Africans had been firmly in place before mtDNA was sequenced. So belief drives science when it comes to human origins! "Considerable alteration," instead, means science drives belief. Which side are you on, Terry?

Dienekes said...

A reminder that "Out of America" theory of human origins should be argued elsewhere than the comment section of this blog.

German Dziebel said...

Agree. How about I guest blog about it in the main body of your blog, Dienekes? I'm sure you wouldn't mind.

Dienekes said...

Agree. How about I guest blog about it in the main body of your blog, Dienekes? I'm sure you wouldn't mind.

I mind. Blogspot is free, so get your own.

German Dziebel said...

"I mind. Blogspot is free, so get your own."

Dude, I have three blogs, 2 books and a sense of humor.

terryt said...

"I brought up the unlikelihood that X was lost across the swaths of East Asia"

Why is it 'unlikely'?

"You know very well, Terry, that all these lineages are no more basal than other N lineages".

They are no less basal either.

"It's irrefutable that the belief in a recent origin of Amerindians and in the great antiquity of Africans had been firmly in place before mtDNA was sequenced".

True. But that contradicts your comment, 'A back migration from America and East Asia to SW Asia and North Africa fits with all other data'. Obviously most see the data as fitting a different scenario.

"So belief drives science when it comes to human origins!"

As it does for all other scientific endevour.