January 01, 2015

Y-chromosome tree bursts to leaf (Hallast, Batini, Zadik et al. 2014)

This is an extremely important study of Y-chromosome variation, the most intriguing part of which are the copious references to a yet to come manuscript:
Elsewhere (Batini C, Hallast P, Zadik D, Maisano Delser P, Benazzo A, Ghirotto S, Arroyo-Pardo E, Cavalleri GL, de Knijff P, Dupuy BM, Eriksen H, King TE, López de Munain A, López-Parra AM, Milasin J, Novelletto A, Pamjav H, Sajantila A, Tolun A, Winney B and Jobling MA, submitted.) we have described an NGS-based MSY phylogeny based on 5,996 SNPs ascertained in 334 human Y chromosomes comprising 17 population samples from Europe and the Near East, focused on illuminating the origins and histories of European patrilineages.
Anyway, the current paper is openly available, so do read it if you haven't already. Of interest to long-time readers of this blog is this bit:
Generally, the STRs perform poorly, giving a wide variety of TMRCAs for nodes with similar SNP-based dates, and correlation coefficients consistently below 0.6. Considering the variables described above: 1) ASD generally outperforms rho, and choice of rooting method (ancestral or modal) makes little difference. For rho, rooting through the ancestral haplotype performs much worse than through the modal haplotype; 2) removal of RM-YSTRs, and STRs showing repeat array complexity, does not have a major influence on relationships between SNP- and STR-based estimates of TMRCA, and the effects depend upon how the root is specified; and 3) the evolutionary STR mutation rate consistently overestimates, and the pedigree rate underestimates, the TMRCAs of nodes (fig. 4a). As expected, the pedigree mutation rate performs better for young nodes (less than 10 ka; supplementary table S6, Supplementary Material online), whereas the evolutionary rate performs better for older nodes.
Mol Biol Evol (2014) doi: 10.1093/molbev/msu327

The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades

Pille Hallast, Chiara Batini, Daniel Zadik et al.

Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes.

Link

89 comments:

terryt said...

What we seem to be looking at is two separate expansions outside Africa, not 'from' Africa. The first is a CF/DE separation, presumably indicating some sort of expansion resulting in geographic separation and isolation. Followed almost immediately by the C/F separation, again probably indicating geographic isolation. The D/E separation follows soon after.

Much later we see an almost simultaneous expansion of all four branches, with C being somewhat later than the other two while F's expansion is particularly rapid and widespread. To me this is obviously completely separated from, and unrelated to, the first expansion. In other words the basal haplogroups formed during the first expansion had rapidly become widely dispersed before the second expansion. The question arises as to how widely dispersed. To me it seems likely that E had become isolated in Africa, F somewhere near the Caucasus and both C and D somewhere far to the east.

eurologist said...

"yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported"

This is indeed astonishing - although not quite qualitatively reflected in the paper's analysis.

"TMRCA for the entire tree is approximately 126 ka, and that for the DR node 49 ka, which correlates reasonably well with the date of the colonization of Eurasia."

Or, based on fossils and stone tools and paleoclimate studies is about a factor of 2, wrong.

"The TMRCA of hg R is 19ka"

Well, we know pretty much for sure it is older than ~35ka - so why make all these statements based on a wrong mutation rate, then? P here is estimated as ~24ka, while based on Ust-Ishim, it needs to be close to 45ka. Why not use a chronology based on known dates rather than one based on fantasy?

The factor of two adjustment seems to be about right, which also brings the I1 and 12-expansions into the beginning of agriculture in central and north-central Europe - adoption of farming by some "lucky" male HGs?

"one possibility could be higher or lower average paternal age in a particular region"

That is a very unlikely factor for different mutation rates between haplogroups, given that the male mutation rate scales linearly with age and with an insignificant offset - meaning that the mutational load is pretty much independent of average paternal age (all such groups produce roughly the same mutation rate per time period).

A much more likely reason is a widely different population number history.

Mark Moore (Moderator) said...

Eurologist: Why is it that you think the fossils and stone tools and paleoclimate data invalidate this genetic data (or maybe I should say interpretation of data)? This is not my field but it seems to me that fossils and tools can only tell us that someone was there, they can't tell us that they were the ancestors of a given haplogroup. I remind you of "Mungo Man" who many thought was the ancestor of today's Australian aborigines but once they got genetic evidence from him turned out to be from a line with no living descendants. Maybe the genetic evidence is telling us something similar about some of the other fossil and tool evidence?

mickeydodds1 said...

Back to an old question that has haunted this site for many a year.
Is y DNA haplotype E ultimately of African or Eurasian ancestry?
German Dziebel, terryt, where are you?

eurologist said...

Why is it that you think the fossils and stone tools and paleoclimate data invalidate this genetic data (or maybe I should say interpretation of data)?

Mark,

I don't. Note that the TMRCA timing scale is not a result of the genetic data - the absolute scale is an external input. Pedigree mutation rates are horribly unreliable (i) because they cover too few generations, and (ii) because over many hundreds of generations, most (combined) mutations likely no longer allow sufficiently viable offspring - i.e., only a small fraction of mutational lineages make it, resulting in a much slower effective mutation rate.

The best absolute scaling method available today is comparing to well-dated ancient DNA, keeping in mind that for any ancient result found more "modern" lineages could have been and probably were alive at the same time (i.e., even this method only provides an upper limit on the mutation rate, with the actual rate likely yet slower).

It is a shame that virtually no one seems to be using it.

Ponto said...

I consider it rather futile to guesstimate the ages of haplogroups by fixating on R1b, R1a and I1. It is like studying the workings of a modern internal combustion motor car by studying an array of catalytic converters and the car's exhaust pipe. Fixating on common European haplogroups, two of which have Asian origins and naturalized in Europe due to metal age migrations, the R1 family, and ignoring everything else does nothing to show how the haplogroups really originated. Dating things without a proper root is not going to be accurate whether rate is chosen.

I am disappointed.

terryt said...

"Is y DNA haplotype E ultimately of African or Eurasian ancestry?"

It is impossible to tell at this stage whether E formed from DE within Africa or outside it. Personally I think it most likely that the geographic spread of C'D'E'F's ancestor included northern Africa and much of Eurasia. The four branches coalesced in separate regions within that geographic spread.

Mike Thomas said...

Terry- what do you mean by "coalesced"?

German Dziebel said...

@mickeydodds1

It's pretty clear that hg E has an extra-African origin. It's fully nested within a Eurasian clade CDEF and it shows a special affinity to just one of them, namely D, which has a very specific and narrow East Asian distribution. At the same time, no such special affinity exists between hg E and hgs A and B. Hgs A and B are too divergent and African-specific to be considered native to modern human gene pool. Most likely, they got absorbed into DE-carrying First Modern Africans from a now-extinct archaic hominin substrate.

Grey said...

@terryt

"What we seem to be looking at is two separate expansions outside Africa, not 'from' Africa."

Makes sense I think, rapid expansion into the sub-tropics followed by adaptation to these various new environments once arrived at a destination.

If effective population is the key then places where HGs had the highest population densities might be the source regions for the later four way expansion.

.

"Is y DNA haplotype E ultimately of African or Eurasian ancestry?"

My guess would be the border zone so north Africa to Egypt to Arabia and maybe Levant also.

.

@eurologist

"which also brings the I1 and 12-expansions into the beginning of agriculture in central and north-central Europe - adoption of farming by some "lucky" male HGs?"

I think that's likely given the very long periods of time LBK seems to have had a stable border with HGs. If the European colonization of Australia had stalled half way across for a thousand years or so would Aborigines have picked up sheep herding?

It doesn't even need Aborigines plural as all you need is one clan to adapt and then that clan can expand into HG territory - which might tie in with the I1 bottleneck.

Another condition might be that this adaption initially required a combination of HG + herding to be viable and so farmers switching to just herding alone wasn't enough.

One easy way it could happen is through a captive.

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Annie Mouse said...

"Why is it that you think the fossils and stone tools and paleoclimate data invalidate this genetic data (or maybe I should say interpretation of data)?"

To make things crystal clear. Eurologist is, I think, referring to the Mal'ta boy aged 24kya who is haplogroup R. So The TMRCA of 19kya for R is wrong, assuming Mal'ta is correctly dated, which is likely. Therefore R must be greater than 24kya.

The rate assumptions used for the genetic calculation are most probably, wrong or statistically unsound.

A similar situation arises for mDNA H. The subclade H6 is estimated to be much older than the estimates for H, which is clearly impossible. This is chiefly because the genetic calculations for H are biased by the younger H1 and H3, and thus unsound.

mooreisbetter said...

To PONTO:

HALLELUJAH! You are so right.

The majoritarian bias, whether conscious or subconscious, in DNA studies, is revolting.

Basically DNA as a hobby skews Northwest European. The big testing centers are the first to acknowledge that their average customer is an upper-income Anglo from Britain or the US.

The scientists too. A large proportion of the surnames on the papers are from places where R1b is the main lineage.

Thus we see these wildly biased reports and a focus on R1b that is borderline pathological.

There are widely developed theories on every clade of R1b, even to the absurd level of some clades claiming to represent historical tribes like the Cimbri.

Meanwhile, other lineages, even in Europe, there is nothing. Bubkes! For example, T1. How did it get there? There was never a Horn of Africa migration into Europe, so what does explain T1 spread?

And the E lineages. They are present in Ancient DNA, yet most people still tie to farming.

Etc. I can only imagine how crappy it is to be of a non-European lineage, when even the minor or secondary European lineages are so well nigh ignored, compared to R1b.

terryt said...

"the Mal'ta boy aged 24kya who is haplogroup R. So The TMRCA of 19kya for R is wrong, assuming Mal'ta is correctly dated, which is likely. Therefore R must be greater than 24kya".

That is not the only dating problem either. Ust'-Ishim is far older than any sort of K would be as far as the authors are concerned.

"Basically DNA as a hobby skews Northwest European".

Quite. And even East Asian researchers tend to skew results for that region too.

"what do you mean by 'coalesced'?"

Many haplogroups have a string of mutations separating them from their closest relatives. Strictly speaking a haplotype cannot be considered as belonging to a particular haplogroup unless it has all those mutations. As those four basal groups were forming outside Africa their individual ancestors would have been moving round, perhaps considerably. Therefore we can say that in all likelihood the four actually finally coalesced in separate regions. Until that time other branches obviously formed but have not survived, or at least are yet to be discovered.

"If effective population is the key then places where HGs had the highest population densities might be the source regions for the later four way expansion".

That is the position I have long held.

"It's pretty clear that hg E has an extra-African origin. It's fully nested within a Eurasian clade CDEF"

It is far from 'pretty clear'. The region the CDEF clade was spread around quite probably included the semi-open grassland of northern Africa as well as a similar habitat that stretched through much of Eurasia. Eurasian E is confined to just a small sampling of the multiple E haplogroups although it is possible they spring from an early immigrant to that continent. As Grey said, 'My guess would be the border zone so north Africa to Egypt to Arabia and maybe Levant also'.

"it [E] shows a special affinity to just one of them, namely D, which has a very specific and narrow East Asian distribution".

Which indicates to me that DE had a very wide distribution, which may have stretched from northern Africa to northestern Tibet. My guess is that as climate cooled drastically the survivors were left at either end of the original DE distribution.

"Hgs A and B are too divergent and African-specific to be considered native to modern human gene pool".

Hmmm. What do your African-American acquaintances think of that concept?

aniasi said...

"I can only imagine how crappy it is to be of a non-European lineage, when even the minor or secondary European lineages are so well nigh ignored, compared to R1b."
@mooreisbetter

Thank you. I am surprised that even non-profit research is obsessed with European R & mt H clades, yet provides little resolution on Asia, which holds more than half of the world's population.

On that same note, has anything come from the Rakhigarhi DNA? I would like to see how the first attempt at ancient South Asian DNA fits into the phylogeny we have today.

eurologist said...

"One easy way it could happen is through a captive."

Grey,

Or something more mundane - the combination of famine and the resulting loss of population cohesiveness caused by flooding (an almost yearly event, today) and a local clan lacking male offspring (occurring at a high rate in every population).

Early Central European agriculturalists settled on the floodplains of major rivers and their major tributaries, for numerous economical reasons (e.g., solely picking fertile Loess soils and choosing sites with periodically flooded brush land, which is yet more fertile and much more easily cleared compared to mature trees).

Currently, the Danube and Elbe-Saale river valleys suffer devastating flooding almost on a yearly basis - despite modern flood controls. Even if these events only happened every 100 - 500 years, their effect would have lasted one to two generations at the minimum, making it very plausible that bright, adaptable HGs would have given and taken the chance to jump in. And that with a one-to-two generation advantage in local population expansion - which is huge.

Gaspar said...

@annie

IIRC, Malta boy is reclassified as MA-1 now.
Born after R but before R1 and R2 formed.

@Ponto
I agree, its pointless in try to establish when R1 emerged if the other haplogroups preceeding it do not make logical sense of age.

Mike Thomas said...

Thanks for the reply Terry

I was also curious as I what some of the commentators on this blog think about the apparent "incontrovertible" evidence of copper age , north-eastern derived ANE-rich , probably R1 associated diffusion espoused by other blogs ? Are these conclusions premature?

German Dziebel said...

@TerryT

""Hgs A and B are too divergent and African-specific to be considered native to modern human gene pool".

Hmmm. What do your African-American acquaintances think of that concept?"

Did you ever ask Polynesians what they think about Y-DNA hg C2 coming from extinct "Papuans"?

You should also invite Native Americans and talk to them about the Bering Strait theory.

terryt said...

"Did you ever ask Polynesians what they think about Y-DNA hg C2 coming from extinct 'Papuans'?"

An interesting little fact here is that Maori almost universally accept their deep origin lies in Taiwan and they are a mix of people formed along the route from there out into the Pacific. They don't see any problem there. And Papuans carrying Y-DNA C2 are hardly 'extinct'. The haplogroups is common in Southern Wallacea, western New Guinea and in parts of Melanesia. Where on earth do you get the idea it is extinct? Are you making things up again?

"You should also invite Native Americans and talk to them about the Bering Strait theory".

I agree some people have such a fragile hold on their identity they cling to traditional stories. Australian Aborigines, for example, are very reluctant to accept their distant ancestors ever lived anywhere but in Australia. I guess both Native Americans and Australian Aborigines have both been so marginalised they cling to ancient myths against all the evidence. But you cannot claim Y-DNAs A and B are somehow pre-human. As far as I'm aware members of both haplogroups are able to freely interbreed with other members of the species carrying different haplogroups.

Slumbery said...

terryt: It is a possibility (thought I find it unlikely at this point) that the Y-DNA A vs. BT or even the B vs. CT split pre-dates the arbitrary time limit for anatomically modern humans and these lines were reintroduced to the modern human population by mixture with archaic Africans. In this limited sense A and B can be "pre-human".

You are completely right however that the fact that they are present in modern human populations makes this terminology rather weird. Plus ultimately every Y-Hg has pre-human origin, since humans have a pre-human origin, without a any sudden genetic border anywhere in time.

Egyptsearch 2.0. said...

As far as Y-Chromosome E goes, I find it interesting that the restructuring of DE to a more basal position relative to CF (as announced by Karafet et al 2008) often goes unmentioned. The fact that DE now phylogenetically exhibits a branching pattern more consistent with a split before OOA cannot be ignored. Moreover, Tishkoff et al 2009 report low levels of Cushitic ancestry in populations from greater Australia. While not sampled therein, the Onge seem to carry this same ancestry as well. This would be a good candidate of a post OOA DE (and D[?]) migration along the southern coasts of Asia. With distinct African ancestry along the southern coasts of Asia (and possibly African lithics, if Paul Mellars' observations in this area hold up to future scrutiny), the onus is now on advocates of a backmigrating E, to explain these data in a way that fits these data as well or better.

German Dziebel said...

@Egyptsearch 5.9.

"restructuring of DE to a more basal position relative to CF (as announced by Karafet et al 2008) often goes unmentioned. T"

I don't know where you got that. The topology is still the same. E (African) and D (Asian) are still linked at M145 and opposed to P143-linked C and F (broadly non-African), all linked at M168. Andaman islanders are relatively recent migrants from northeast India close to where Tibetans have high frequencies of hg D, and this is far from any coast.

Annie Mouse said...

IMO we do not pay enough attention to North Africa. It is possible that OOA is really Out of Sub Saharan Africa (OOSSA). It makes sense that the early humans might have travelled up the Nile rather than across to Saudi. They could have sat in North Africa for a period (rather than the Mid
East) with populations expanding out from there at different times. Would explain some aspects of E and is not inconsistent with what little archaeology that we have.

Egyptsearch 2.0. said...

@German Dziebel

By stating the obvious, it seems you've departed from the matter at hand. Lets refocus to the here and now. It cannot escape anyone who follows the literature in this subject area that many academics (e.g. Klyosov), apparently still haven't gotten the memo as late as 2014, that phylogenetic trees with E casually slid in the midst of (or next to) CF lineages, are dated by default.

Like I said earlier, DE underwent a phylogenetic shift from sharing a node with CF to a placement more basal to this. And there is a tendency (as seen in your own reply, for instance) for proponents of a back-migrating E to act like this is somehow not directly relevant to the discussion at hand.

This post-Karafet et al 2008 placement makes D even more incongruous in CF-dominated Asia than was already suggested back in the early '00s by the special relationship of the former, with E.

capra internetensis said...

B is as distantly related to CDEF as R1 is to R2 (about 30 thousand years apart). BCDEF forms a fairly deep node within A1b. It's very unlikely that the carriers of CDEF were modern humans and B weren't, though the oldest clades of A might well be archaic.

Egyptsearch, what are you talking about? The tree in Karafet et al 2008 puts DE as a sister clade to CF, both descendents of CDEF. Nothing has changed since then.

Nobody mentions it because it's common knowledge. And Klyosov? Isn't he some self-published crank never cited by anyone but himself?

The latest study, that of Hallast, finds DE to be slightly younger than CF (9 SNPs vs 2 SNPs after CDEF), but in any case the split of D from E appears to have occurred only a short time (a few thousand years) after the split of CF from DE. The coalescence of the individual C, F, D, and E clades is much later - probably the break up of E is about 15 thousand years after that of DE. There is an enormous stretch of time for people have gone out of or into Africa. So who knows what happened.

I really don't follow how E forming a clade with DE makes a back-to-Africa E migration *less* likely, though.

Annie Mouse said...

Karafet age arguments dont cut it. DE is going to be older than E so long as the tree is right. An older age for E just means that DE is older than expected from the guestimates. Similarly mDNA H cant be younger than H6, as has been suggested.

In the DE argument I found the following useful.

"In a study of over 8000 men worldwide including 1247 Nigerians, Haplogroup DE* was possibly observed in 5 Nigerian males and no more (5/1247). However, the study's authors caution that "the apparently paraphyletic status of this haplogroup, and hence the conclusions of nested cladistic analysis, are also likely to be illusory" and that "the only genealogically meaningful definition of the age of a clade is the time to its most recent common ancestor, but only if DE* is paraphyletic does it also become automatically older than D or E in this sense."[7] More recently, one example of DE* was possibly found amongst the Nalu in Guinea Bissau (1/17). The DE* sequence of this individual differs by one mutation from the DE* sequence of the Nigerian individuals. This indicates common ancestry, though the phylogenetic relationship between the two lineages was not determined in this particular study.[8] A 2008 study detected DE* in two individuals from Tibet (2/594).[9] The paragroup DE* in africa is probably a divergent form of E while the paragroup DE in Tibet probably is a more divergent form of D, or (possibly but not likely) this DE* may simply be a subclade of E or D with a back mutation. This has happened before for example the F* in India is really H some of the K* in Timor Melanesia is really P the NO* in China is really N and the R* in Northern pakistan is really R2 [10]

Haplogroup DE is found in Africa (Haplogroups E and DE*) and East Asia (Haplogroups D and DE* and E*) but is largely absent in between these two regions. The presence of DE across widely separated regions has confounded investigators trying to reconstruct the migration of humans from Africa to Asia. At some time, there was an extinction of DE lineages in West, South and Central Asia. Autochthonous DE lineages are absent in India, an important region in the dispersal of humans in Asia. However DE lineages have been detected in relict populations of the Andaman Islands. Underhill et al. 2007, suggest the possibility that deleterious mutations in some DE carriers may explain the extinction of DE lineages in India.[11]
"

Also:


"E-M96*[edit]

The most basal lineage, paragroup E-M96*, has been reported in 2 Amharas from Ethiopia,[14] a single Bantu-speaking male from South Africa,[1] amongst pygmies and Bantus from the Cameroon/Gabon region,[12] in two individuals from Saudi Arabia[15] and in some Syrians and Lebanese individuals according to Zalloua et al. (2008), but possibly only the Arabian, Lebanese and Syrian individuals are real E-M96*, because the discovery of the V38 SNP by Trombetta et al. (2011) has, in theory, resolved the previously reported cases of E-M96* in Africa (most studies which reported E-M96* in Africa only tested for the M2 SNP but not for the recently-discovered upstream V38 SNP) and, given the paucity of the downstream M2 sub-clade in Eurasia, it is highly unlikely that the reported E-M96* is E-V38*.
"


In summary D is found only in asia. E in Africa and Asia. Basal E (E-M96)is only confirmed in Syria, Arabia and Lebanon (Asia, technically). The Tibetan and Nigerian DEs look to be back mutations of D and E respectively(I would have liked to confirm this by looking at the individuals minor SNPs). Which leaves the ancestral DE found only in the Andamans, an ancient OOA population.

So on balance DE still looks like OOA or OOSSA. With E back migrating into East Africa from the southern Mediterranean. In my opinion.

Sequence details may change this.

terryt said...

"humans have a pre-human origin, without a any sudden genetic border anywhere in time".

A point that is lost sight of in almost all discussions on human evolution.

"Andaman islanders are relatively recent migrants from northeast India close to where Tibetans have high frequencies of hg D, and this is far from any coast".

I agree totally. Andaman Islanders are certainly not some 'remnant' population from a Paleolithic acoastal migration from Africa to Australia.

terryt said...

"DE underwent a phylogenetic shift from sharing a node with CF to a placement more basal to this".

It now makes sense that DE formed a little before CF. The haplogroups D and E seem to lie at the extreme geographic extremes of the CDEF clade (East Asia and Africa respectively) while C and F seem to lie somewhere between those extremes. This implies the CF expansion was somewhat later than that of DE. But not too much later, and before the DE split according to the present diagram.

"The paragroup DE* in africa is probably a divergent form of E while the paragroup DE in Tibet probably is a more divergent form of D"

Makes sense.

"DE lineages have been detected in relict populations of the Andaman Islands".

Or, more likely, a divergent form of D.

"At some time, there was an extinction of DE lineages in West, South and Central Asia".

Somehow I doubt an extinction in South Asia. That region has any number of surviving haplogroups and there seems no reason for extinction. Central Asia on the other hand has ample region for numerous extinctions. I don't think DE was ever part of the South Asian collections as shown by, 'Autochthonous DE lineages are absent in India, an important region in the dispersal of humans in Asia'.

"Underhill et al. 2007, suggest the possibility that deleterious mutations in some DE carriers may explain the extinction of DE lineages in India".

Of course there is another explanation but it doesn't involve any great southern coastal migration, a position some seem reluctant to abandon.

"It's very unlikely that the carriers of CDEF were modern humans and B weren't"

I agree. But it ultimately comes down to your definition of 'modern human', and where do you draw the line. The change towards modernity seems to have been much more gradual than has usually been thought to be the case in the past.

"There is an enormous stretch of time for people have gone out of or into Africa. So who knows what happened".

A further point is that I think it extremely unlikely that the four haplogroups remained within just a small region near Africa until after the diversification of all four haplogroups. I certainly see no problem for K2, for example, to have reached SE Asia before P formed from it.

Egyptsearch 2.0. said...

@Capra Internetensis
Not that I think it'll settle the matter, but where exactly in that paper did you get those mutation distances to CT? You seem to be right as far as the larger distance between CT->DE than CT->CF, as well as your interpretation of Kafaret et al's tree, re: DE and CF being depicted as equidistant to CT.

While processing your post, I had an epiphany. It's not physically possible for a dendrodram to display a fork pattern and have one of the branches be older. This is not what I was arguing a few posts ago, but the implications that follow from this self-evident fact affect my argument; what it ultimately means is that hg ages or proximity to CT will never settle this.

If a study claims one to be older than the other, they're talking about an upstream mutation on one branch being estimated to be older than the parallel mutation on the other branch. But for our intents and purposes this is immaterial as it amounts to semantics; its not the same as saying the general DE people are older than the general CF people or vice versa.

At present the best argument for whether DE is or isn't African, lies in mtDNA L3, L4 and L6. Since nothing in Y-DNA A-T (xCT) can be considered to be a male correlate of mtDNA L6, L4 and L3, CT can't be entirely Eurasian. You'd either have to also make these three mtDNAs back-migrants to Africa (and it would be extremely entertaining to see someone bend over backwards to make that case), invent extinct hgs for these L types to mate with, or accept parts of CT as African. No such thing as population-wide LDR in the MP (or any other epoch for that matter).

terryt said...

"It's not physically possible for a dendrodram to display a fork pattern and have one of the branches be older"

In a way it is possible. The age of original branching must coincide but dating of individual haplogroups is from the time the particular haplogroup diversifies. A 'parent' haplogroup may fork into two but one (or even both) may not undergo an immediate expansion, although I would guess that the branch that escapes the original region of origin usually expands as soon as it escapes. The other may remain in the original region giving rise to a series of non-surviving haplogroups. Its own expansion may occur some time after the other branch has parted. Meaning that is when that branch 'originated' because until that time it has not yet accumulated the mutations that make up the haplogroup as we recognise it today. From the paper we see that CF split from DE at a certain time but after that C split from F almost immediately whereas it was some time after that CF/DE split that D and E parted from each other.

"At present the best argument for whether DE is or isn't African, lies in mtDNA L3, L4 and L6".

I don't see any reason why a particular mt-DNA should be intimately associated with a particular Y-DNA except in the case where a particular population is the first into a previously uninhabited region. I believe most a far too ready to look for connections that may not even exist.

"CT can't be entirely Eurasian".

I think it almost certainly is. CT has a long period of separation from B before it begins its own diversification. The difficulty lies in determining which haplogroup moved back into Africa: DE or E?

Egyptsearch 2.0. said...

@Terry
When I said "branch", I was talking about a single outgrowth of a particular node. These branches (again, not the mutations they harbor, like DE and CF) have the same ages simply because terms like "first" and "second" don't apply when you look at two branches that grow out of a node. Taking the analogous example of a river delta, one would not say distributary A splits earlier from the main stream than distributary B . Relevance? The ages of DE and CF or their mutational distances to CT are not informative of which of the two populations is older, but rather, of some of the things you talked about in your last post.

I'm not sure I understand the relevance of your objection. I'm not speculating or venturing into the unknown here; I'm taking the data as it is. The claim being made here is that the African Y chromosomes are "likely" restricted to Y-DNA A-T(xCT). My answer to that is, populations who split from the human tree prior to the emergence of Y-DNA CT also split from the human tree prior to roughly contemporary mtDNA L3'4'6. If you make CT emerge outside of Africa, this leaves you with little to mate with for L3'4'6, until DE backmigrates. If your solution is that L3'4'6 mated with other Y chromosomes not part of Y chromosome Adam, you're confronted with the fact that CF eventually leaves Africa with descendants of L3'4'6; indicating that there was no seperation between L3'4'6 and CT after Y DNA A-T(xCT) went their seperate ways.

You'll have to take both as backmigrants or postulate both as residing in Africa and the former scenarios leads to discrepancies. For instance, there is very little difference between mtDNA M and N and the nearest African clades, indicating that Africans and OOA populations split very abruptly. There is every reason to expect the paternal side to mimic these specifics. But if you accept only A-T(xCT) as African, there is a huge disconnect on the paternal side as A-T(xCT) and CT are not closely related (as you admitted yourself). How would you make that work without jumping through all sorts of hoops?

Annie Mouse said...

Is an old man, who has a child in his dotage, made younger by the birth? I suppose some actual men might claim it does.

For me a Y haplogroup is actually dated by his formation. The mutations in his descendants just allow us to get an estimate of his age. But the Y haplogroup is potentially immortal and may have many sons in his lifetime. If his oldest sons die out leaving no trace then he will appear to be younger, but he isn't. It is our illusion. He will always be older than his oldest son.

Most of his sons (branches) will be DIFFERENT ages, except the rare twins with two separate mutations. Although in periods of expansion they may appear to be the same age.

terryt said...

"If you make CT emerge outside of Africa, this leaves you with little to mate with for L3'4'6, until DE backmigrates".

No, not at all. Y-DNAs A and B remained in Africa. And I think we can assume that mt-DNAs M and N emerged from Africa with CT.

"If your solution is that L3'4'6 mated with other Y chromosomes not part of Y chromosome Adam"

No need to postulate anything like that. Members of 'Y chromosome Adam' were still present.

"there is very little difference between mtDNA M and N and the nearest African clades, indicating that Africans and OOA populations split very abruptly".

I assume they did so. Just one Y-DNA line and just two mt-DNA lines were able to leave Africa. Once they had done so descendants of each were able to move back into Africa and a few more African lines were able to emerge as well.

"How would you make that work without jumping through all sorts of hoops?"

I don't see any hoops at all. I see it as simple.

"For me a Y haplogroup is actually dated by his formation".

Technically a particular 'haplogroup' doesn't exist until the last common mutation in the line rather than when it separates from its nearest relation. The difference between the two can be substantial.

terryt said...

I compiled some thoughts on the matter the other day. I strongly suspect that the branches are formed at times of increased aridity following times of expansion during climate amelioration. In other words the bases of the split indicate expansion and the period of mutations leading to the fully-formed haplogroups represent times of isolation in different regions within the original expansion. Many branches would have become extinct at such times. When the leaves on the tree are examined from this perspective the whole tree makes complete sense.

In other words CT emerged from Africa during a relatively wet period but Africa and Eurasia became separated genetically with a return of aridity. And so on for the other branches and periods of mutation accumulation.

Egyptsearch 2.0. said...

@Terryt

Like I said, there is no record of A-T(xCT) heavy African population which have mtDNA L3'4'6, independent of introgressions. There is also no record of mtDNA L3'4'6 heavy populations which have A-T(xCT) that cannot be explained as admixture. The proposed link of L3'4'6 females with A-T(xCT) males therefore isn't supported by any the findings in the literature.

The groups that are today dominant and diverse in A-T(xCT), left the rest of the human tree >100kya. Although remnant B lineages are likely to have travelled with the rest of the human tree henceforth, as you correctly suggest, the available data suggests that most of these reunited with populations that already split off >100kya (e.g. B2b is found in Khoisan and it is much younger than pre-existing mtDNA L0; B2a, B2b and B1 are found in West/Central African hunter gatherers, and they're much younger than pre-existing A1a and A1b).

Note, furthermore, that none of these reunions of Y-DNA BT males with pre-existing populations in South and West/Central Africa left a trace of mtDNA L3'4'6, but they did leave a trace in the form of other mtDNAs, which seem to have been L1 and L2 (note that L2 is a sister clade of L3'4'6). It therefore seems likely that a lot of the B carrying males (I'm not sure about Y-DNA A as I haven't seen any evidence of it playing a role near the MSA/MP exit points of Africa) had left the region by then and headed towards West/Central and South Africa. But even if some of them stayed, the record of their contact with pre-existing West/Central Africans only gives mtDNA L1 and L2 as likely candidates, not mtDNA L3'4'6.

terryt said...

"there is no record of A-T(xCT) heavy African population which have mtDNA L3'4'6, independent of introgressions".

Does that matter? We can be sure that Y-DNA E has largely replaced earlier haplogroups through wide swathes of Africa. And there are numerous populations that do contain both A/B Y-DNA and L3'4'6 mt-DNA. Although perhaps most can be explained as being the result of admixture there is no real reason to suppose that in many cases they were not associated before the expansion of E.

"B2b is found in Khoisan and it is much younger than pre-existing mtDNA L0; B2a, B2b and B1 are found in West/Central African hunter gatherers, and they're much younger than pre-existing A1a and A1b".

Which counters your claim. Khoisan groups do have E Y-DNA and L3 of course.

Egyptsearch 2.0. said...

@Terryt

Y-DNA E did replace many Y chromosomes, but I'm not sure that fully explains the paucity of these lineages in northeast Africa, under the proposed scenario that L3'4'6 mated with A-T(xCT). The impact of E on West Africa was much stronger than on East Africa frequency wise, and even there we find indigenous A and B clades in populations who are approaching fixation in E. We also find a seemingly local A clade (A3a) in East Africa with relatively little effort, so these hypothetical northeast African B lineages should still show up, albeit in low frequencies. But given the fact that all three foundational B clades of which we have records are equatorial and South African, and given the fact that B is a sister clade of CT, everything is much easier to understand if one accepts that B reunited with AMHs that lived to the south, after the emergence of the BT node, while L3'4'6 and CT's immediate ancestor stayed. I think you were much better off arguing that L3'4'6 mated with North African Y chromosomes, as there currently is little leeway in the data to make differentiation of B in northeast Africa work.

To my awareness, Khoisan don't have L3 or E that cannot be understood as influences of Bantu, Nilo Saharan and Afro-Asiatic speaking farmers and pastoralists. And which of my own claims did I counter with that argument?

terryt said...

"Y-DNA E did replace many Y chromosomes, but I'm not sure that fully explains the paucity of these lineages in northeast Africa"

It would if E's expansion began in East Africa. I agree E does seem to be especially common in West Africa but to me it appears to be primarily a Sahelian haplogroup. It has not penetrated the deep forest to any great extent except as a farming hapologroup. A and B on the other hand look to me more like a fringe forest haplogroup with invasion of the deeper forest in places. It may simply be the case that CT was able to exploit the more open grassland and so was able to emerge from Africa. Obviously mt-DNAs M and N emerged from Africa with whatever elements of CT has escaped. But the division between B and CT is so great and so prolonged that to me it looks as though the two branches must have been well and truly isolated from each other for a very long time. That is unlikely to be the case if CT remained anywhere within Africa.

There is no such huge split in the mt-DNA lines except within L3. That haplogroup may also have been a Sahelian haplogroup but for some reason the A and B haplogroups associated with it may have been more susceptible to replacement than the Y-DNAs in the more forested regions.

One thing we certainly cannot assume is that A and B were somehow 'pre-modern' while E was fully modern. The same goes for the various L mt-DNAs. There was no problem with genetic intermingling.

Egyptsearch 2.0. said...

"Obviously mt-DNAs M and N emerged from Africa with whatever elements of CT has escaped."

I think we're going in circles. By now my view that CT is roughly contemporary with L3'4'6 (not M and N) should have been disputed but it seems like you disagree and didn't say so (or I may have missed it). Do we agree here or not? As I said earlier, the split of L2 and L3'4'6 (sister clades) clearly mimics the split of B and CT (sister clades), respectively. My argument is that these splits are informative of the same MP/LSA event. Do you agree? If not, what is against it?

"But the division between B and CT is so great and so prolonged that to me it looks as though the two branches must have been well and truly isolated from each other for a very long time. That is unlikely to be the case if CT remained anywhere within Africa."

See above. When one accounts for the possibility that the current distribution of B is not a red herring from mother nature that distracts from the "real" prehistoric distribution of B (as you seem to think), but instead, actually represents where the B branch travelled back to and differentiated, the "discrepancy" you speak of would cease to exist; CT would then simply be a northeast African hg, while B reunited with southerly AMHs. Again, this is confirmed by the distribution patterns of all foundational B clades, while evidence of an LSA/MP expansion of B in North Africa is, to my awareness, utterly lacking. Most B they have is B2a1a, which is way too young for it to have played a role in this time frame. These same West/Central African people also have the oldest L2. How would you explain that these Central African people (as opposed to northeast Africans) have the only early L2 and the only early B, if not that these two travelled south after the emergence of the BT node? Before you answer, please look at mtDNA and Y chromosome trees and observe that the L2 and L3'4'6 split mimics the B and CT split in all relevant specifics.

terryt said...

"Do we agree here or not?"

Yes. That is probably the case. But it is doubtful that CT was the only Y-DNA associated with L3'4'6.

"the split of L2 and L3'4'6 (sister clades) clearly mimics the split of B and CT (sister clades), respectively. My argument is that these splits are informative of the same MP/LSA event. Do you agree? If not, what is against it?"

I don't agree. CT to me is obviously Eurasian, not African, therefore it is probably associated far more closely with M and N rather than L3 as a whole.

"evidence of an LSA/MP expansion of B in North Africa is, to my awareness, utterly lacking"

Not really. From the diagram presented in 'Y-Chromosome Tree Bursts into Leaf' we see that Y-DNA B begins its expansion at almost exactly the same time as CT does. Whatever climatic conditions allowed one expansion allowed the other. The difference is that B keeps gradually expanding (diversifying) whereas once CT forms its separate branches it once more begins period of contraction and isolation. By that time DE had presumably entered Africa and formed E.

"Most B they have is B2a1a, which is way too young for it to have played a role in this time frame".

By the time B2a1a formed B had already divided into B1 and B2. B2 had divided into B2a and B2b. B2a had divided into B2a1 and B2a2. And B2a1a is 'brother' to B2a1b. Surely that indicates considerable expansion and diversity before B2a1a was able to begin its big expansion.

terryt said...

"How would you explain that these Central African people (as opposed to northeast Africans) have the only early L2 and the only early B, if not that these two travelled south after the emergence of the BT node?"

I see no reason at all why particular Y-DNA should be associated with particular mt-DNA except when populations are moving into previously uninhabited regions. Certainly in the case of Polynesia we see the dominant male and female lines originating in different regions of island SE Asia.

I have long held the idea that biological evolution is the product of the subtle, and not so subtle, interplay of inbreeding and hybrid vigour. Consequently I see no reason at all why the surviving Y-DNA and mt-DNA need have come from a single population. To me it is quite possible that the mt-DNA that originally accompanied Y-DNA 'Adam' has become extinct. As has the Y-DNA that originally accompanied mt-DNA 'Eve'. We know for sure in the case of Neanderthals and Denisovans that both mt-DNA and Y-DNA have become extinct. To that extent I agree that Y-DNA BT is intrusive to mt-DNA L, or more realistically, mt-DNA L is intrusive to Y-DNA BT.

To me Y-DNAs A and B are very much West African, probably from just east of the Adamawa Highlands. The female line looks originally much more eastern, certainly east of Lake Chad and possibly as far east as Kenya/Ethiopia.

To me the most likely scenario is that a population carrying L1, which had moved west of L2''6, mixed with the population carrying BT somewhere on the forest margin immediately east of the Adamawa Highlands. From there both A and B, but especially BT, were able to expand through a less arid Sahara Desert and a small subsection was able to emerge from Africa. In fact on reflection I think it is worth reconsidering Dienekes' Persian Gulf hypothesis.

terryt said...

Sorry. One more comment:

"the split of L2 and L3'4'6 (sister clades) clearly mimics the split of B and CT (sister clades), respectively".

The mt-DNA line fails to show the sudden diversification followed by isolation that the B/CT split does. It just shows a gradual and continuous diversification and expansion within Africa with just two insignificant branches of L3 having made it out of the continent. It was obviously very difficult to leave. It is therefore unbelievable that three of the four branches within CT could move out en mass leaving just one behind in Africa. That is totally unlike the mt-DNA evidence.

Egyptsearch 2.0. said...

Typo correction: I mixed up 'LSA' with 'MSA' in my previous post. Of course, the epoch that parallels the MP is the MSA, not the LSA.

@Terryt

"I don't agree. CT to me is obviously Eurasian, not African, therefore it is probably associated far more closely with M and N rather than L3 as a whole."

If by this you mean that CT and M and N are contemporary, this can't be the case, because CT is much older than M and N. Since throwing out age estimates has the potential to cause trivial disagreements, let's just keep it simple: CT emerges at >50% of the duration of the Y tree and the same can't be said of M and N. Both of these trees can be superimposed with no problem because it's demonstrable that both roots have comparable ages and started expanding from the same geographical region.

"Not really. From the diagram presented in 'Y-Chromosome Tree Bursts into Leaf' we see that Y-DNA B begins its expansion at almost exactly the same time as CT does."

Even entertaining the applicability of your reading of the situation, for a second, there is little in what you're saying that necessarily favours a north-bound or a south-bound expansion of B. But I don't see how your reading applies given the dates Hallast et al 2014 reported for the B2 sublineages you're mentioning, which are reported to start differentiating at least 10kya later than CT. It looks like you're trying to make up for a lack of MP/MSA B in North Africa by discussing patterns that are much, much more equivocal.

"I see no reason at all why particular Y-DNA should be associated with particular mt-DNA except when populations are moving into previously uninhabited regions."

If the BT node splits up into CT and B, and on the maternal side the same thing happens around the same time, this has to be seriously considered and cannot be dismissed. Moreover, B and L2 are found in high doses in the same West/Central African populations, while their the sister branches of both of these (L3'4'6 and CT) are found linked in high doses in northeast African populations and OOA populations. These are the reasons for making the links you say you don't see, but which are clearly there.

"To me the most likely scenario is that a population carrying L1, which had moved west of L2''6, mixed with the population carrying BT somewhere on the forest margin immediately east of the Adamawa Highlands."

The pattern of how L0a'b'f'k lineages were 'shed' one by one along the "coasts" of the Indian Ocean from South Africa to the Horn suggests that L2'3'4'6 and BT were nowhere even near West Africa, and that L1, L2 and B 'detached' from this main body to reunite with pre-existing South African and Central African AMHs, somewhere along this eastern African expansion towards East Africa. I can't say too much about this, as I'm in the process of writing a blog post, but to understand some of the things I'm saying one really needs to have a full understanding of all African hgs and how various African mtDNA and Y chromosomes were linked in the Middle and Upper Palaeolithic. To try to link CT with M and N seems like a complete mismatch when you follow these lineages from South Africa ~120kya to northeast Africa ~70kya.

terryt said...

"you mean that CT and M and N are contemporary, this can't be the case, because CT is much older than M and N".

Really? On what grounds do you claim that to be the case? I don't think anybody can have a clear idea of the age of any particular haplogroup until more ancient DNA is uncovered. Until such time I wouldn't be in a hurry to claim any dates. For example it has recently been shown that Y-DNA K2 must be much older than earlier calculated.

"Both of these trees can be superimposed with no problem because it's demonstrable that both roots have comparable ages and started expanding from the same geographical region".

I think you're making some huge assumptions there. As I've tried to point out, there is no reason why we need assume the two branches started together in the same place. In fact there is no reason why we need assume both left Africa together. Either male or female line could have left first and bred with people already outside Africa.

"But I don't see how your reading applies given the dates Hallast et al 2014 reported for the B2 sublineages you're mentioning, which are reported to start differentiating at least 10kya later than CT".

The dates given in the paper for K2 are obviously wrong. I wouldn't rely too heavily on their other dates either. In fact from the diagram itself B splits into B1 and B2 at almost exactly the same time as CT begins to break up.

"It looks like you're trying to make up for a lack of MP/MSA B in North Africa by discussing patterns that are much, much more equivocal".

Don't forget that the Sahara Desert has been uninhabitable for much of human history. Only occasionally has it allowed exchange between Eurasia and Africa, until efficient boating was invented.

"The pattern of how L0a'b'f'k lineages were 'shed' one by one along the "coasts" of the Indian Ocean from South Africa to the Horn"

On what grounds do you claim it was in that direction? To me L0 looks clearly invasive into southern Africa and doesn't reach there until some time after the split between L1 and L2''6. In fact close to the time of the split between L1b and L1c and the split between L5 and L2'3'4'6. If anything the movement of L is from somewhere near Kenya with the L0 branch moving slowly south from there. In fact L0d's actual expansion almost coincides with L3's. Besides which L0d is the only exclusively South African mt-DNA within L0 with the others having a strong East African presence from Ethiopia southwards.

terryt said...

"I'm in the process of writing a blog post"

Let me know when it's up. I'll certainly enjoy reading it and looking at your ideas.

terryt said...

A further comment:

"The pattern of how L0a'b'f'k lineages were 'shed' one by one along the 'coasts' of the Indian Ocean from South Africa to the Horn"

I've been considering your hypothesis of a northward movement of L. To be honest I used to think that myself but improvements in the phylogeny indicate otherwise. I may be using an old phylogeny here but Maju did an excellent job of African mt-DNA here:

http://leherensuge.blogspot.co.nz/2010/03/reviewing-mtdna-l-lineages-notes-l2-and.html

If your hypothesis was correct we should see a progressive geographic pealing off of the haplogroups. That's not what we see.

Yes. L0 separates first, but is that because it left a central region or is it because the others left it behind? The next split is actually L1 which, apart from widespread downstream haplogroups, certainly gives the impression of being an ancient West African haplogroup. Did mt-DNA Eve's descendants move north from southern Africa through West Africa to Ethiopia? Or is L0 a southward push from a central region and L1 a westward push from the same region?

"suggests that L2'3'4'6 and BT were nowhere even near West Africa, and that L1, L2 and B 'detached' from this main body to reunite with pre-existing South African and Central African AMHs"

L2'3'4'6 and BT need be nowhere near each other. Some time back you wondered what Y-DNA these eastern mt-DNA L haplogroups bred with. On checking once more I see that Y-DNA A1b1 fits the bill perfectly. A1b1b is spread right down the east coast of Africa from Ethiopia to South Africa.
In fact A1b1a is, like mt-DNA L0d, specifically Khoisan. It is very tempting to see L0's arrival in southern Africa as being simultaneous with that of A1b1a. That places A1b1a's expansion through southern Africa at the same time as L0d's diversification. In other words, around the same time as L3's expansion and diversification.

BT could well be referred to as A1b2. That would place the L3 expansion with A1b1 and BT, not with E.

terryt said...

Another connection between mt-DNA and Y-DNA is provided by the north-western Pygmies. From Maju's diagrams it is obvious that the earliest modern mt-DNA to enter the deeper jungle and form a Pygmy population is L1c1a1 and L1c1a2, a fairly downstream haplogroup. The main Y-DNA associated with Pygmies in the region is B, especially B2. The formation of this group of Pygmies appears to post-date the diversification of L3, and its presumed exit from Africa. Perhaps the population was pushed deeper into the forest by an increased aridity which separated African and Eurasian branches of BT.

Egyptsearch 2.0. said...

@Terryt

"Really? On what grounds do you claim that to be the case? I don't think anybody can have a clear idea of the age of any particular haplogroup until more ancient DNA is uncovered"

I'm not talking dates; I'm talking contemporaneity. This doesn't require any specific dates. To me this its obvious, but you never know, so I'll ask: do you agree that if patterns in the Y-DNA and mtDNA trees can be shown to correlated, CT has to be older than M and N, given their respective positions along the length of their respective trees?

"I think you're making some huge assumptions there. As I've tried to point out, there is no reason why we need assume the two branches started together in the same place."

If it can be demonstrated that both trees expanded towards North Africa around the time of BT, we know that parts of RSRS and AT were at least linked at the time of BT. If it can be demonstrated that they were linked at the time of A2-T, we know they were together at least since then, and so on. If you feel I'm saying something that's falsifiable (and I've made plenty of falsifiable predictions), the stage is all yours to provide data that contradict my claims.

"The dates given in the paper for K2 are obviously wrong. I wouldn't rely too heavily on their other dates either. In fact from the diagram itself B splits into B1 and B2 at almost exactly the same time as CT begins to break up."

If by "diagram" you mean figure 3, your comments can only pertain to B2. Unless I'm missing something, B1 was not taken into account in this paper and so we have no way of knowing when Hallast et al consider B as a whole to have started breaking up. Another thing: in my previous post I thought you were referring to the break up of B2 subclades relative to CT subclades. But if you're talking about B itself, your comments don't appear to be generalizable beyond Hallast 2014, because trees don't consistently depict this pattern across studies. In fact, according to Scozzari et al 2014, when other B lineages are included, the B node gets pushed back to a point close to BT, which is way, way earlier than CT.

"On what grounds do you claim it was in that direction? To me L0 looks clearly invasive into southern Africa and doesn't reach there until some time after the split between L1 and L2''6."

On the grounds that are in effect everywhere. L0a'b'f'k is largely non-Khoisan (it's Southeast African to East African), while L0d and L0k are Khoisan. The pattern in which L0a'b'f'k subclades are found along the coast in the direction of East Africa is as follows: L0k, L0f, L0b and L0a, with their ages also decreasing in that order (i.e. in the direction of East Africa). This is not consistent with back migration of L0 towards South Africa, and that's an understatement. I would tell you that A2-T and L1 + L2'3'4'6 mirror this L0 pattern in age and other specifics, but earlier discussion of this fact led to you shrugging it all off as a mere "assumption".

"Let me know when it's up. I'll certainly enjoy reading it and looking at your ideas."

I'll keep you in the loop. ;)

terryt said...

"I'll keep you in the loop".

Thanks. I'm certainly interested in trading ideas on the subject.

"do you agree that if patterns in the Y-DNA and mtDNA trees can be shown to correlated"

Not necessarily. Y-DNA can move independently of mt-DNA on occasions. It is less certain that mt-DNA can move independently of Y-DNA but it may be possible.

"CT has to be older than M and N, given their respective positions along the length of their respective trees?"

I think we are probably more sure of the tree lengths in Y-DNA but we are far less sure of the branch lengths within mt-DNA. Besides which I think it is a shaky assumption to think that branch lengths always indicate relative age. Although mutations are quite possible regular the replacement of parent haplogroups by descendant haplogroups is far more random.

"If it can be demonstrated that both trees expanded towards North Africa around the time of BT"

Could have been earlier. A1a is present in much of western Africa beyond the Cameroons and so probably had moved deeper into the savannah early in its development. A1b on the other hand seems to be more eastern with A1b1a being primarily Khoisan.

"If it can be demonstrated that they were linked at the time of A2-T"

A2 appears to have been dropped. Are you thinking A1b2?

"B1 was not taken into account in this paper"

And that is a problem. But in referring to K2* I meant that every branch before K must be earlier than the date calculated in the paper.

"the B node gets pushed back to a point close to BT, which is way, way earlier than CT".

But CT undergoes a considerable period of isolation before itself expanding. That is unlikely to be in Africa as all African haplogroups appear to keep gradually expanding and diversifying.

"L0a'b'f'k is largely non-Khoisan (it's Southeast African to East African), while L0d and L0k are Khoisan".

And every other L haplogroup is non-Khoisan. To me that indicates L0d is the outsider.

"This is not consistent with back migration of L0 towards South Africa"

I don't think we're talking 'back migration'. It looks to be an expansion from a more northerly point of origin. I agree that A1b1a-V50 is very likely associated with this arrival in southern Africa but A1b1b is widespread in eastern Africa and all other A haplogroups, including B, are primarily West African (A00, A0, A1a).

Egyptsearch 2.0. said...

@Terryt

I can't help but notice that several of my points were left unaddressed

Are you saying that if the roots of mtDNA and Y-DNA have approximately the same age, CT will not be much older than M and N? Please confirm. Again, CT emerged >50% of the age of the Y chromosome root, while M and N emerged much later along the length of their tree. I'm not really sure what you mean when you contrast "branch lengths" with what I said, but if you note that if you disagree with this, your arguments elsewhere fall apart.

"Could have been earlier. A1a is present in much of western Africa beyond the Cameroons and so probably had moved deeper into the savannah early in its development. A1b on the other hand seems to be more eastern with A1b1a being primarily Khoisan."

I don't see the relevance of this. You said it was purely an assumption that hgs can be linked together. I replied that if consistent patterns can be observed that make sense, this won't be a mere assumption. You then start talking about A1b and A1a. Do you really think mimicry between the Y chromosome and mtDNA trees is somehow less substantive than what you see as contemporaneity between B and CT in a single dendrogram (which isn't even a consistent finding across studies) or any of your other arguments, e.g. L0 being East African, B being North African, etc?

"And that is a problem."

So, given the fact that it only depicts a single B branch, do you agree that fig 3 in Hallast et al 2014 is a far cry away from depicting the differentiation of B compared to the differentiation of CT?

"That is unlikely to be in Africa as all African haplogroups appear to keep gradually expanding and diversifying."

This is a bit of a circular argument (i.e. you're reasoning within a paradigm others don't subscribe to, to begin with). Right now, it is your assumption that early CT is really as comparatively naked as it seems to be the case today. My position is that early CT(xDE) evolution in Africa died out. So, from my perspective, the relative differences you're observing are certainly not a discrepancy, but expected, considering only Eurasian (and not African) CT[xDE] lineages were run in fig 3.

"And every other L haplogroup is non-Khoisan. To me that indicates L0d is the outsider."

There was no such thing as every other haplogroup back then; most were coalesced in L1'2'3'4'5'6. But, that aside, you don't address my point that L0a'b'f'k moved towards northeast Africa in a manner that suggests that L0 was originally specific to South Africa. I'm not sure you understand the gravity of the situation. For L0k, L0f, L0b, and L0a to be found along the Indian Ocean coasts in the direction of East Africa in this order, and for them to have radiated from East Africa, they must have done so back in time. Either that or there is some other explanation, which I'm asking you to provide.

terryt said...

Two parts sorry.

"if the roots of mtDNA and Y-DNA have approximately the same age, CT will not be much older than M and N? Please confirm".

Why would the roots of mtDNA and Y-DNA necessarily have approximately the same age? I see no reason at all for that assumption. As I've tried to point out the two lines seem to have originated in two different regions within Africa and so there is no reason why they should be the same age.

"CT emerged >50% of the age of the Y chromosome root, while M and N emerged much later along the length of their tree".

Given the above that is no evidence for anything. Besides which the trees' ages can by no means be accurately calculated. Therefore you cannot base any idea of relationship on theoretical tree ages.

"I don't see the relevance of this. You said it was purely an assumption that hgs can be linked together".

I also said that is the case 'unless' a population is moving into a previously uninhabited region. To me it is obvious that no modern haplogroups were present west of the Niger River, or even west of the Adamawa Highlands, in ancient times. Because both Y-DNA A1a and mt-DNA L2a seem specifically present in the western Sahel I would guess they arrived there together. Just as it is reasonable to suppose that Y-DNA C1b2 accompanied mt-DNA B4a1a into the wider Pacific.

"do you agree that fig 3 in Hallast et al 2014 is a far cry away from depicting the differentiation of B compared to the differentiation of CT?"

Yes. It suggests that B continued gradually expanding and diversifying while CT underwent a considerable period of isolation before eventually itself expanding. Where do you believe that isolation occurred? Perhaps it was in northern Africa somewhere but it cannot have been in sub-Saharan Africa because every other African Y-DNAs were apparently able to diversify.

"Right now, it is your assumption that early CT is really as comparatively naked as it seems to be the case today".

If some time in the future we find other branches between the BT split and CT's expansion I will certainly change my mind. But as it stands CT certainly was unable to expand and so diversify for a considerable time.

"considering only Eurasian (and not African) CT[xDE] lineages were run in fig 3".

What African CT(xDE) lines are your referring to? As far as I'm aware the only ones are much later arrivals than the original CF diversification, in which case they make no difference to the dendrogram.

"My position is that early CT(xDE) evolution in Africa died out".

But the is absolutely no eveidence for that. In fact theevidence argues against it as other African haplogroups survived very well. Besides which we have to deal with the evidence as it is, not make up stuff to fit what we believe.

"There was no such thing as every other haplogroup back then; most were coalesced in L1'2'3'4'5'6".

OK. I'll rephrase it. No haplogroup derived from the other branch, L1'2'3'4'5'6, is present in southern Africa except as later arrivals. And let's not forget that by the time the specifically L0d began diversifying (indicating to me its actual arrival in southern Africa) L1'2'3'4'5'6 had diversified into L1a, L1b, L5a, L5b, L2, L6 and L3'4 was about to split. To me that indicates most of the action occurred way north of southern Africa.

terryt said...

Continued:

"you don't address my point that L0a'b'f'k moved towards northeast Africa in a manner that suggests that L0 was originally specific to South Africa".

I don't believe the evidence shows that to be the case. L0 splits from L1'2'3'4'5'6 early in the piece but from that alone we can't tell which branch was the mover. Within L0 the first split is L0d/L0a'b'f'k. At roughly the same time we have L1b forming L1a and L1b and L5 splitting from L2'3'4'6. There was more going on than just an expansion in southern Africa. I agree that within L0d/L0a'b'f'k the first to split off is L0k which is present in southern Africa but also in Yemen. The split between L0k1 and L0k2 is quite recent. What is L0k2 doing in Yemen? L0f1 is southern African but L0f2 is primarily Ethiopian, close to where the bulk of L1'2'3'4'5'6(xL1) haplogroups appear to be centred. Lastly, the L0a'b. Again we find Lob in Ethiopia and L0a widespread through much of the Sahel region about the same time as L3 also began expanding through much of the Sahel region.

The above certainly does not unequivocally indicate mt-DNA L0'1'2'3'4'5'6 originated in southern Africa, especially since the first split within L1'2'3'4'5'6 is a West African haplogroup, not even an East African one. The evidence is just as easily explained as being the result of a gradual expansion south from some centre north of southern Africa. Similarly L1's pattern is easily explained as being a gradual expansion west from a similar region which started somewhat after L0 began its southward movement.

Egyptsearch 2.0. said...

"Why would the roots of mtDNA and Y-DNA necessarily have approximately the same age?"

Out of goodwill, I'll take the bait of this distracting question and cite the reference sooner than I planned to (see Poznik et al 2013), but I'm not interested in getting into that right now. Too much leeway for shifting goalposts. What I want to get into is whether you agree that contemporaneity of Y chromosome and mtDNA roots would make mutations along both trees with a similar distance relative to their roots, contemporaneous as well.

"Perhaps it was in northern Africa somewhere but it cannot have been in sub-Saharan Africa"

Depends on what one means with 'SSA'. One of the African gateways to Eurasia that could have been used by CT positive males during OOA is in SSA. I agree though that an origin deep in inner Africa of pre-CT doesn't seem supported at this point.

"What African CT(xDE) lines are your referring to?"

None. What I was getting at, is that it's a circular argument that CT didn't expand gradually, because you derived that assumption from a pool of Eurasian CT positive Y chromosomes that made it out of Africa (i.e. M9, P123, M216, etc). In my scenario of an African CT I would expect there to be a paucity of pre-M213 CT lineages, because there is an inherent bias in only running CT lineages that made it out of Africa. Do you understand this point?

"But the is absolutely no eveidence for that. In fact theevidence argues against it as other African haplogroups survived very well. Besides which we have to deal with the evidence as it is, not make up stuff to fit what we believe."

I'm not saying that there is direct evidence for African CT(xDE). The point was that the supposed "gradual expansion" pattern you perceive to be lacking in CT, which you're treating as favourable to your point, doesn't favour your point because it would be equally expected in my scenario. See my point above.

"I don't believe the evidence shows that to be the case. L0 splits from L1'2'3'4'5'6 early in the piece but from that alone we can't tell which branch was the mover."

I wasn't basing my interpretation of a South African origin of L0 on any of that nor does any of that trump my argument (if it does, I'll be glad to hear how). I guess I'll just try it again. How do you explain the decreasing 1) age and 2) distance from East Africa of L0k, L0f, L0b and L0a, if these hgs radiated from East Africa?

terryt said...

Sorry. Two posts again:

"What I want to get into is whether you agree that contemporaneity of Y chromosome and mtDNA roots would make mutations along both trees with a similar distance relative to their roots, contemporaneous as well".

Possibly, but certainly not consistently. The first problem will be finding ALL the relevant mutations. The next step will require a huge assumption: that mutations replace pre-existing versions at a constant rate.

"Depends on what one means with 'SSA'"

Surely that always means, 'south of the Sahara Desert'.

"One of the African gateways to Eurasia that could have been used by CT positive males during OOA is in SSA".

What gateway is that? Surely the most likely explanation is an emergence through the Sinai at a time of climate amelioration.

"I agree though that an origin deep in inner Africa of pre-CT doesn't seem supported at this point".

Thank you.

"it's a circular argument that CT didn't expand gradually, because you derived that assumption from a pool of Eurasian CT positive Y chromosomes that made it out of Africa (i.e. M9, P123, M216, etc)".

No. I derived it from the very long tail, which may or may not be directly related to time, but certainly indicates a lengthy period during which a tail developed on the basal CT line, as shown in fig. 3. No haplotypes survive during the apparently very long time between the B/CT branch and the CT diversification. The tail has nothing to do with M9, P123, M216, mutations that occurred ononce CT was able to expand and diversify. It's possible other lines survived for a time, and it's possible they formed within Africa, but CT itself must have formed outside Africa.

"In my scenario of an African CT I would expect there to be a paucity of pre-M213 CT lineages, because there is an inherent bias in only running CT lineages that made it out of Africa. Do you understand this point?"

There is no way to include CT lineages that didn't make it out of Africa because none have survived. Surely that is the simple truth.

"The point was that the supposed 'gradual expansion' pattern you perceive to be lacking in CT, which you're treating as favourable to your point, doesn't favour your point because it would be equally expected in my scenario. See my point above".

I can't see at all how whether BT gradually or not alters the fact that the CT branch looks to be a Eurasian haplogroup. How does it favour your viewpoint? Please explain. C, D, E and F must have sprung from a single individual at some point.

terryt said...

Continued:

"How do you explain the decreasing 1) age and 2) distance from East Africa of L0k, L0f, L0b and L0a, if these hgs radiated from East Africa?"

I don't see point 1) as holding up to any examination. Yes, L0k is the oldest branch but its expansion looks relatively recent with one branch in the Khoisan and one in Yemen. To me that looks like a coastal haplogroup that reached both places with the movement by sea along the East African coast. Probably no more ancient than the arrival of Southeast Asians in Madagascar. We can't draw any conclusions as to where it originated, which may be in neither place it is found today. The next branch, L0f, is similarly widespread. From Ethiopia to South Africa with surviving members at each end of its possible original distribution. This time the split looks earlier than that of L0k1/L0k2 but presumably was land based. Again no real clue as to its region of origin. In fact that split is perhaps contemporary with the L0a/L0b split. Again one branch in Ethiopia (L0b) and one which fairly soon became widespread from Kenya to Chad (L0a). No real indication of a sequence of expansion dates from south to north. Or even from north to south.

As for 2) all four haplogroups have representatives in East Africa as far north as Ethiopia> I grant a possible exception in the case of L0k but it is present in Yemen which sort of indicates an origin not too far from Ethiopia.

terryt said...

Sorry. Further thoughts on this question:

"What I want to get into is whether you agree that contemporaneity of Y chromosome and mtDNA roots would make mutations along both trees with a similar distance relative to their roots, contemporaneous as well".

I don't think sound conclusions will come from lining up branch lengths. However if you find it possible to concede for a moment that the population containing both Y-DNA Adam and mt-DNA Eve lived in a relatively confined space, but not necessarily in the same part of it, you can see regions where the two lines do come together.

My best guess is that the population was confined to the region north of the Congo River on a strip between the Adamawa and Ethiopian Highlands. Y-DNA near the western end and mt-DNA near the eastern end. Regions to the west, northeast and south were not occupied, at least by that population. The two lines first met where L1 had formed at the western end of L's geographic spread, where it met the several A Y-DNA haplogroups already present there. Meanwhile L0 had formed at the southern edge of L's geographic spread but had not actually entered southern Africa. L5 became isolated at the northeastern edge of L's geographic spread but had not actually entered Ethiopia.

The male and female lines mixed and Y-DNA A1 began to spread through L's geographic spread. In the form of A1a-V161 it took L2 west outside the original population's geographic range. In the form of A1b1a-V50 it took L0d into South Africa, and in the form of A1b1b1-M28 it took L5 into Ethiopia (and possibly L6 and L4 as well.

Somehow A1b2 became involved and both it and A1b1 took L3 over much of Africa and even beyond.

Egyptsearch 2.0. said...

"Possibly, but certainly not consistently. The first problem will be finding ALL the relevant mutations."

Really? Then feel free to point to research where improvements in these areas led to consistent changes in tree topology.

"No. I derived it from the very long tail, which may or may not be directly related to time, but certainly indicates a lengthy period during which a tail developed on the basal CT line, as shown in fig. 3."

Understood. But I think the same applies on the other side of the CT mutation: molecular patterns don't indicate geography. In fact, the exact same pattern exists in between the A2-T and BT nodes, without necessitating anything spectacular.

"There is no way to include CT lineages that didn't make it out of Africa because none have survived."

True, but that doesn't take away that the pattern I thought you were speaking of is just as open to the interpretation you were trying to exclude.

"I can't see at all how whether BT gradually or not alters the fact that the CT branch looks to be a Eurasian haplogroup."

The goalpost of why CT "looks" like a Eurasian hg has shifted over time. Note that now we also know that M and N aren't even of the same age, further weakening the case that CT is a contemporary of both M and N.

"I don't see point 1) as holding up to any examination."

Let me get this right. Are you saying that the mere detection of sparse L0 clades beyond where they're most common and diverse complicates the basic procedures of inferring hg origin?

"I don't think sound conclusions will come from lining up branch lengths."

Branch lengths are underlain by tree-informative variants, and the fact that they're scalable is the basis of all of this. Your own arguments in this comment section have leaned on this principle. The only difference is you were doing it with one locus and I'm doing it with two loci. I invite you to motivate your objection with references to research that attest to difficulties in what I'm doing. What you will find is that they're doing the same thing.

terryt said...

"Then feel free to point to research where improvements in these areas led to consistent changes in tree topology".

I'm sure the phylogenies are largely fairly accurate these days but I doubt the whole sequence of mutations has been discovered.

"molecular patterns don't indicate geography".

No. But a diversity centred on a particular region does. And, unless you're going to postulate wholesale extinction, can be regarded as an accurate indication as to point of spread.

"The goalpost of why CT 'looks' like a Eurasian hg has shifted over time".

In what way? It has always been the case that just one of the four branches can be considered 'African' and even that branch has non-African representatives. I am one of those who sees those last as being sub-branches rather than basal however.

"Note that now we also know that M and N aren't even of the same age, further weakening the case that CT is a contemporary of both M and N".

I'm not sure that we 'know' M and N aren't the same age, just that their age of diversification is not the same. Some recent research did indicate N branched off before L3 had formed but I'm not sure how widespread acceptance of that is.

"Are you saying that the mere detection of sparse L0 clades beyond where they're most common and diverse complicates the basic procedures of inferring hg origin?"

Yes. The presence of a haplogroup is far more indicative of spread than is its proportion in a population. Where it is most common sometimes indicates an arrival in a previously unexploited region where it was able to multiply.

"Branch lengths are underlain by tree-informative variants, and the fact that they're scalable is the basis of all of this".

Well let's see your attempt to correlate the Y-DNA and mt-DNA lines. For a start I see a huge problem with placing Y-DNA A00 in South Africa.

terryt said...

I think I see a major assumption you are making that is wrong. You assume Y-DNA Adam and mt-DNA Eve lived side by side when they first appeared. To me that is a hangover from the Victorian idea of evolution: the survival of the fittest. We can safely assume they were not the only two haplotypes in the population, no matter how widespread it was. And certainly there were other haplotypes outside that population, and even outside Africa.

We can assume from this post that Y-DNA can move through populations without carrying associated mt-DNA, at least to a great extent:

http://dienekes.blogspot.co.nz/2015/02/a-story-of-69-ancient-europeans.html

I see no reason why a similar situation would not hold for the very beginning of surviving haplotype origins.

To me it is obvious from both phylogenies that the two lines did not merge until mt-DNA L1c's expansion and diversification. According to Maju's posts this was soon followed by, in turn, the expansion of L0 haplogroups, then L2 haplogroups, then L4 and then L3. It would make sense to fit those mt-DNA expansions to particular Y-DNA expansions rather than try to fit the two lines together right from their origin.

Egyptsearch 2.0. said...

@Terryt

"You assume Y-DNA Adam and mt-DNA Eve lived side by side when they first appeared."

Y-DNA Adam and mtDNA Eve are shaky terms that are susceptible to root revisions. So no, I don't subscribe to this view per se. It's not necessary for any of my arguments that they lived side by side beyond the points in their evolutionary history I've specified earlier.

"I'm sure the phylogenies are largely fairly accurate these days but I doubt the whole sequence of mutations has been discovered."

One doesn't have to look far to see the irrelevance of this objection. The abstact and full text of Hallast et al 2014, among other papers, explicitly state repeatedly that your objection is not considered relevant here, at least not to the extent that you're suggesting.

"It has always been the case that just one of the four branches can be considered 'African' and even that branch has non-African representatives."

CT was considered Eurasian because the only African candidate within it was considered to be a very young and, moreover, E was considered to be a subclade of D. This has all been refuted. Addtionally, CT being Eurasian was considered likely as E was thought to be a candidate tag along of R-V88 and other later backmigrants--this has also been refuted.

"I'm not sure that we 'know' M and N aren't the same age,"

See Behar et al 2012. Huge difference between M and N, but, presumably, you have to count from RSRS to get a consistent result (which makes sense given mtDNA M's considerable branch heterogeneity). The M mutation emerges at roughly ~68% of the evolutionary duration of RSRS.

"Yes. The presence of a haplogroup is far more indicative of spread than is its proportion in a population. "

Indicative of spread? What does that have to do with anything? There is no diversity, differentiation or age of L0k in Yemen or Ethiopia, whatsoever. L0f doesn't center in Ethiopia in either frequency or diversity. At the end of the day, the 'epicentres' corresponding with 4/5 L0 branches are found in the direction of Ethiopia and this stretched L0 path correlates negatively with age, while the remaining basal L0 branch (L0d) is South African.

"For a start I see a huge problem with placing Y-DNA A00 in South Africa."

It's a mistaken assumption that the discovery of additional surviving branches on either tree hampers my observation that RSRS mimics A-T from A2-T onwards (see my first point in this post).

terryt said...

"Y-DNA Adam and mtDNA Eve are shaky terms that are susceptible to root revisions".

It is surely irrelevant what you call the root haplogroups. There is still no necessity that the male and female root both lived at the same time and in the same place.

"CT was considered Eurasian because the only African candidate within it was considered to be a very young and, moreover, E was considered to be a subclade of D. This has all been refuted".

'All been refuted'? I don't think so. No African CT branch is other than very young and I don't remember E ever being considered 'a subclade of D'. From the first discovery of the YAP mutation it has always consisted of two branches as far a I'm aware.

"The M mutation emerges at roughly ~68% of the evolutionary duration of RSRS".

As far as I'm aware the M mutation actually begins branching at ~68% of the evolutionary duration of RSRS. That doesn't mean its ancestor split from N at that time. The two may have a far more ancient common ancestor. The date of a particular haplogroup's final formation and beginning of its expansion and diversification can considerably post-date its separation from its closest relation.

"Indicative of spread? What does that have to do with anything?"

Surely any particular haplogroup has to have originated somewhere within its parent's geographic spread. Haplogroups don't suddenly materialise out of thin air.

"There is no diversity, differentiation or age of L0k in Yemen or Ethiopia, whatsoever".

Exactly. Which indicates its arrival in one (or perhaps both places) is quite recent. As I said, 'To me that looks like a coastal haplogroup that reached both places with the movement by sea along the East African coast. Probably no more ancient than the arrival of Southeast Asians in Madagascar. We can't draw any conclusions as to where it originated, which may be in neither place it is found today'.

"L0f doesn't center in Ethiopia in either frequency or diversity".

Totally irrelevant, because that is not what I said. What I said was, 'The next branch, L0f, is similarly widespread. From Ethiopia to South Africa with surviving members at each end of its possible original distribution'.

"the 'epicentres' corresponding with 4/5 L0 branches are found in the direction of Ethiopia and this stretched L0 path correlates negatively with age, while the remaining basal L0 branch (L0d) is South African".

As I explained above, I do not see that as being the case. You have just demonstrated that you are unable to make a convincing case for that view. I agree L0d is 'South African' but its actual presence there appears to be no more ancient than the formation of both L1a and L1b in West Africa and L5 towards Ethiopia. And is possibly no more ancient that the formation of L2, L6 and even L4. In other words by the time L0 can be securely place in southern Africa the L clade as a whole had become very widespread within Africa.

"It's a mistaken assumption that the discovery of additional surviving branches on either tree hampers my observation that RSRS mimics A-T from A2-T onwards (see my first point in this post)".

Well, let's see your correlations.

Egyptsearch 2.0. said...

@Terryt

“It is surely irrelevant what you call the root haplogroups.”

Since it’s possible for more deep-rooted branches to have survived on one tree than others, MRCAs can be pushed back lopsidedly relative to less preserved trees constructed from other loci. Are you sure you want to make this a point of contention? This is an elementary concept most would take for granted.

“There is still no necessity that the male and female root both lived at the same time and in the same place.”

It's clear now that you're just repeating yourself here and not addressing what I'm saying. I never said they needed to be together at all times. The fact of the matter is that both trees are expected in principle, to have the same age under similar evolutionary conditions. This is a very basic idea no one I know in the field would call into question. You are on your own with your objection.

“and I don't remember E ever being considered 'a subclade of D'.”

See Hammer’s early work.

“As far as I'm aware the M mutation actually begins branching at ~68% of the evolutionary duration of RSRS. That doesn't mean its ancestor split from N at that time”

Your interpretation could very well be correct, but if M’s expansion started later, as you suggest, the situation doesn’t improve from your perspective. It would mean that the M that partook in OOA looks substantially younger than the mtDNA N that partook in OOA, and that CT looks older than than both, for reasons already mentioned.

“Surely any particular haplogroup has to have originated somewhere within its parent's geographic spread.”

The problem is that Yemeni L0k2 doesn’t lie in or near its parent’s epicentre; its clearly a geographical outlier and resides in a haplotypic network that is made up of South Africans. Hence, why I’m scratching my head for several days now, trying to figure out why you’re treating this geographical outlier as informative of the distribution of the rest of L0k. Given that Yemenis may have up to ~60% mtDNA L types, there is nothing noteworthy about their possession of L0 subclades.

“As I explained above, I do not see that as being the case. You have just demonstrated that you are unable to make a convincing case for that view.”

It's not a case I'm making; it's already public knowledge. Data documenting this is uncontroversial and widespread (e.g. Rito et al 2013, Rosa & Brehem 2011). The onus is on you to pick up where I left off several posts ago in a way that doesn’t involve paltry red herrings such as Yemeni possession of L0k and Ethiopian possession of L0f2. These aren’t incongruent with my observations.

terryt said...

"Since it’s possible for more deep-rooted branches to have survived on one tree than others, MRCAs can be pushed back lopsidedly relative to less preserved trees constructed from other loci. Are you sure you want to make this a point of contention? This is an elementary concept most would take for granted".

I have taken it for granted. That is why surviving mt-DNA and Y-DNA lines can be so different in region of origin.

"The fact of the matter is that both trees are expected in principle, to have the same age under similar evolutionary conditions. This is a very basic idea no one I know in the field would call into question".

It may be a basic idea for you, but it is wrong. It would only be so if the particular species evolved from a completely genetically isolated extremely small population. That situation is so unlikely to be the case during the evolution of any species there is no need to consider it. The idea that new species arise from sudden dramatic improvements in small populations is a hangover from Victorian times and even Darwin's own ideas of the superiority of European Man, specifically English man, with no consideration of the role women play in evolution. Species evolve by isolation, selection and subsequent mixing of populations. Not by the simple survival of the fittest view of the Victorians.

" if M’s expansion started later, as you suggest, the situation doesn’t improve from your perspective. It would mean that the M that partook in OOA looks substantially younger than the mtDNA N that partook in OOA"

Rubbish. It would mean that M remained isolated and unable to expand from soon after it left Africa while N (which also has a string of mutations before branching, but not as many as does M) was able to actually expand further much earlier than was M. The ancestors of both could well have emerged from Africa together.

"CT looks older than than both, for reasons already mentioned".

If CT was able to expand more widely before either M or N did so could easily explain such an apparent discrepancy. And, before you object, remember there were othe rhuman populations outside Africa at the time and we know they have contributed genes to the modern human gene pool. We also are fairly sure that males tend to lead population expansions. For example many European males moved far ahead of European females in America, and often had children with the indigenous inhabitants.

"The problem is that Yemeni L0k2 doesn’t lie in or near its parent’s epicentre; its clearly a geographical outlier and resides in a haplotypic network that is made up of South Africans".

I have tried to point out that its haplogroup network is far from exclusively South African. Just L0d can be so described. The other L0 haplogroups are far more widespread although confined to the eastern region of sub-Saharan Africa.

"Given that Yemenis may have up to ~60% mtDNA L types, there is nothing noteworthy about their possession of L0 subclades".

Exactly. I never claimed L0k as a whole is from Yemen. The other L haplogroups in Yemen come from various regions within Africa and are presumably relatively recent arrivals. The expansion of other African mt-DNA haplogroups has presumably considerably disrupted the older haplogroup survival, less so in South Afrioa. Because of that the presence of L0k1 in the Khoisna is not a reliable indicator of the haplogroup's origin either.

terryt said...

"The onus is on you to pick up where I left off several posts ago in a way that doesn’t involve paltry red herrings such as Yemeni possession of L0k and Ethiopian possession of L0f2. These aren’t incongruent with my observations".

Righto. I think you originally claimed L originated in South Africa because its earliest branch, L0, is primarily found there and nearby. I'm prepared to accept that for now but the remainder of the L phylogeny argues very much against an origin of L in South Africa. Unless you're going to claim some magic transportation for the next branch, L1, an obviously West African haplogroup. That is one sudden jump for any haplogroup.

The next branch, L5, also mysteriously appears in Egypt, Ethiopia and Chad, again nowhere near South Africa. That jump is not so spectacular as that of L1 but still spectacular enough.

With L2 we do find South African representatives, but almost certainly the product of the Bantu expansion of some 3000 years or so ago. And L2's expansion is extremely widespread through Africa, appearing to be the earliest mt-DNA to reach the Atlantic far west.

Neither L6 nor L4 show any indication of having originated anywhere near South Africa either although I concede that by the time they appear mt-DNA L had become widespread.

From consideration of the whole L phylogeny is seems as though it didn't originate in South Africa, although one branch reached that region quite early. Another branch reached West Africa almost as early. Presumably the two originated reasonably near each other as they share a common ancestor. To me the obvious conclusion is that they originated somewhere between West and South Africa, as did almost all the other L haplogroups. In other words what we see is the result of a 'pump' from some central region with haplotypes developing on the margins and later expanding independently further beyond that margin.

terryt said...

A third post. Sorry. I've just checked Rito et al 2013. I hadn't seen it before and so thanks. A couple of quotes:

"We propose that the last common ancestor of modern human mtDNAs (carried by “mitochondrial Eve”) possibly arose in central Africa ~180 ka, at a time of low population size. By ~130 ka two distinct groups of anatomically modern humans co-existed in Africa: broadly, the ancestors of many modern-day Khoe and San populations in the south and a second central/eastern African group that includes the ancestors of most extant worldwide populations".

And presumably from that central/eastern African group another group soon split off to the west (L1). And:

"Two south to east migrations are discernible within haplogroup LO. One, between 120 and 75 ka, represents the first unambiguous long-range modern human dispersal detected by mtDNA and might have allowed the dispersal of several markers of modernity. A second one, within the last 20 ka signalled by L0d, may have been responsible for the spread of southern click-consonant languages to eastern Africa, contrary to the view that these eastern examples constitute relicts of an ancient, much wider distribution".

Nothing about originating in South Africa. In fact:

"It is intriguing that the deepest geographically restricted branches of the tree – L0, L1 and L2’6 – evidently originated in southern, central and eastern Africa respectively"

I note the author uses 'central' which is a better description than my 'west' as L1 is not present beyond the Adamawa Highlands.

The earlier Rosa & Brehem paper predates the restructuring of the phylogenies and so is nowhere near as useful as the later paper.

Egyptsearch 2.0. said...

@Terryt

“It would only be so if the particular species evolved from a completely genetically isolated extremely small population.”

How is what you say here mutually conclusive with what I said. Please clarify.

“Rubbish. It would mean that M remained isolated and unable to expand from soon after it left Africa while N (which also has a string of mutations before branching, but not as many as does M) was able to actually expand further much earlier than was M.”

This suggestion would require OOA populations to get separated into M and N groups with surgical precision, since N’s early growth would have been retarded as well if it were under the evolutionary conditions you’re invoking for M. Looking for evolutionary mechanisms that produce such unnatural hg schisms will land you right into fairyland, because they don’t exist.

“If CT was able to expand more widely before either M or N did so could easily explain such an apparent discrepancy.”

Why would CT be able to expand earlier than M or N if they mated together? You’re shooting yourself in the foot with that one, because that is impossible. Looks like you’re running out of alternatives to my observation of CT-L3’4’6 contemporaneity.

“I have tried to point out that its haplogroup network is far from exclusively South African.”

No offense, but given the choice between what you point out and what L0k’s actual haplotype network says (e.g. Rito et al 2013, fig. 2), what do you think I’ll accept, the data or your words? The only individuals in the L0k network that aren’t South African, are undifferentiated, distant geographical outliers that are inappropriate for (re)assessing L0k’s prehistoric distribution. What you say in regards to L0k clashes with the entire literature (the most recent mention-worthy paper being Barbieri 2013).

“From consideration of the whole L phylogeny is seems as though it didn't originate in South Africa,”

It goes back to my earlier reminder that L1, L2, L6, etc. aren’t contemporaries of L0a’b’f’k’d. It makes little sense to speak of L5, L1 etc. when one speaks of L0 (the latter isn’t an individual hg). And sure, Rito et al 2013 have their own interpretations regarding their own data. But I’m basing my views on their results, not necessarily their interpretations thereof (although I did consider them).

terryt said...

Thanks for drawing my attention to the Rito et al 2013 paper (actually Pereira and Soares). In spite of the authors' best efforts I still see a couple of huge problems placing L0's origin in South Africa.

Surely it is almost unbelievable that no surviving modern human mt-DNA lines reached the Tanzania/Kenya region for as much as 100,000 years after the mt-DNA L MRCA. A region that was apparently so supportive of Australopithecus and Homo. erectus. One would also expect Lakes Victoria, Tanganyika and Nyasa to have provided refuge even during the most arid times.

Secondly it is difficult to conceive of any climatic event that would split the modern mt-DNA into regions as separate geographically as South Africa and Chad/Sudan, with no survivors in between.

However I do see a solution to the problem. Perhaps humans had clung to the edge of the retreating jungle in the Congo Basin during a period of increased aridity. With a return of moister conditions and the expansion of jungle to the Rwanda/Burundi highlands the population became divided into northern and southern groups. I have no idea if climate data supports this scenario. But even in this case the southern group would not be 'South African' as such but rather Angola/Zambia and the southern Congo. It would be from that region that L0d moved south (or was pushed south) while the other L0 haplogroups entered Tanzania from Zambia through the highland region, spreading north from there. That scenario actually fits the L0 phylogeny presented in the Pereira Soares paper perfectly.

terryt said...

"This suggestion would require OOA populations to get separated into M and N groups with surgical precision"

You are proposing exactly that in the case of L0 and L1''6. Why the different perspective?

"since N’s early growth would have been retarded as well if it were under the evolutionary conditions you’re invoking for M".

On what grounds do you believe that to be necessary? Surely if two L3 haplogroups emerged from Africa and became isolated in different regions within Eurasia one line could easily be prevented from expanding immediately for any number of reasons.

"Why would CT be able to expand earlier than M or N if they mated together? You’re shooting yourself in the foot with that one"

Once more you're stuck with some sort of Garden of Eden hypothesis. As demonstrated by your comment:

"How is what you say here mutually conclusive with what I said. Please clarify".

Even the Pereira Soares paper specifically places the Y-DNA MRCA at twice the age of the mt-DNA MRCA. What do you propose the modern human Y-DNA line bred with before the modern human mt-DNA line appeared? Modern humans obviously did not 'from a completely genetically isolated extremely small population'. CT would surely have been able to breed with any human group it met anywhere. We know humans bred with Neanderthals for a start and so either the mt- or Y-DNA line must have done so.

"No offense, but given the choice between what you point out and what L0k’s actual haplotype network says (e.g. Rito et al 2013, fig. 2), what do you think I’ll accept, the data or your words?"

I'd advise you to read the paper again.

Egyptsearch 2.0. said...

@Terryt

"You are proposing exactly that in the case of L0 and L1''6. Why the different perspective?"

The post-RSRS split is a natural one, because the split itself symbolizes two populations who went separate ways. The split in your scenario involves two incipient lineages within the same panpictic population that somehow got completely compartmentalized.

"Surely if two L3 haplogroups emerged from Africa and became isolated in different regions within Eurasia one line could easily be prevented from expanding immediately for any number of reasons."

But, as you originally suggested, they left Africa together; how did the M and N lineages become completely devoid of each other, so that whatever happened to M in your scenario had no apparent effect on any extant N and vice versa.

"Once more you're stuck with some sort of Garden of Eden hypothesis. As demonstrated by your comment:"

I think you misunderstood my point. I'm not excluding the possibility of cross mixture of various AMH lines (which likely happened in Eurasia and North Africa). CT's older age makes it natural for it to expand earlier than M and N, so my point was that your acceptance of earlier expansions of CT than M and N undermines your claim that they were contemporary. Before you disagree, remember that we were discussing CT, M and N defined as nascent mutational tips, not as also including their downstream mutations. Since you started invoking expansions as explanations for the age discrepancies a few posts ago, you were necessarily, and unwarrantably, talking about the latter, not the former.

"Even the Pereira Soares paper specifically places the Y-DNA MRCA at twice the age of the mt-DNA MRCA."

Lol. This concept is way too basic to argue over. Listen: if both trees don't have the same age, as you proclaim, the resulting cosmic incongruity that male and female lines don't have to have the same TMRCAs to the African archaic to which they ultimately coalesce, is yours to iron out.

"I'd advise you to read the paper again."

Are you suggesting that the paper suggests an origin of L0k outside of southern Africa?

terryt said...

"Are you suggesting that the paper suggests an origin of L0k outside of southern Africa?"

But not in 'South Africa'.

"The post-RSRS split is a natural one, because the split itself symbolizes two populations who went separate ways. The split in your scenario involves two incipient lineages within the same panpictic population that somehow got completely compartmentalized".

We know the L3 split was multiple with lines diversifying through much of the northern part of Africa. It would surely be no surprise if two L3 lines emerged from Africa, perhaps together but later became separated. Perhaps north and south of the Persian Gulf.

"so that whatever happened to M in your scenario had no apparent effect on any extant N and vice versa".

What do you actually see as the problem? If the two were separated it is surely quite easy to imagine one as being able to expand considerably before the other with the return of a more amenable climate.

"Before you disagree, remember that we were discussing CT, M and N defined as nascent mutational tips, not as also including their downstream mutations. Since you started invoking expansions as explanations for the age discrepancies a few posts ago, you were necessarily, and unwarrantably, talking about the latter, not the former".

I think diversification is always an indication of geographic expansion. Within a group geographically isolated usually just one haplogroup takes over, often a descendant haplogroup. That explains the long mutation tail found in many lineages. If CT managed to emerge from Africa before either M or N it is quite possible that the separate mt-DNA expansions are associated with separate CF and DE Y-DNA expansions although the DE that returned to Africa and became E may not have involved any Eurasian mt-DNA line.

"if both trees don't have the same age, as you proclaim, the resulting cosmic incongruity that male and female lines don't have to have the same TMRCAs to the African archaic to which they ultimately coalesce, is yours to iron out".

You are ignoring facts. This from the paper:

"The modern human mtDNA tree split first at ~180 ka (the age of the 'mitochondrial Eve' MRCA)"

"However, the recent identification of the much deeper A00 lineages, combined with the slower mutation rate calibrated from complete-MSY data, now suggests an MSY MRCA of almost 350 ka"

"Based on fossil evidence, eastern Africa has often been considered the most likely location for the emergence of AMH".

"An analysis of the tree of the human male-specific Y-chromosome (MSY) with improved resolution located the root in central/west Africa, albeit with few data as yet"

"We propose that the last common ancestor of modern human mtDNAs (carried by “mitochondrial Eve”) possibly arose in central Africa ~180 ka, at a time of low population size".

"It is often assumed that the age of the Most Recent Common Ancestor (MRCA) of modern mtDNAs, 'mitochondrial Eve', points to the timing of the appearance of modern Homo sapiens, but this is unwarranted unless there was a speciation bottleneck, the evidence for which is weak"

"indeed the search for a single origin for AMH may prove to be a mirage [1,2]. Modern Homo sapiens may indeed have arisen by 'multiregional evolution' within Africa"

terryt said...

Sorry. More thoughts on the matter although not concerning Y-DNA I'm afraid. An exanination of the data presented in the Pereira Soares paper is actually capable of answering the problem presented in the paper:

“The mtDNA tree is geographically structured at the deepest, basal level, with L0 branching in southern Africa and L1’6 in eastern/central Africa. This implies a dispersal between one region and the other, and clearly 'mitochondrial Eve', carrying the MRCA of human maternal lineages, must have lived in a specific location ~180 ka, but as noted before [21,28] that location is difficult to recover phylogeographically in the absence of the discovery of any further deep lineages. A 'centre-of-gravity' argument might suggest an origin in central Africa”

'A dispersal between one region and the other', but no indication of in which way. But the authors go on to say:

“A 'centre-of-gravity' argument might suggest an origin in central Africa”

So that's a clue. Also:

“It is intriguing that the deepest geographically restricted branches of the tree – L0, L1 and L2’6 – evidently originated in southern, central and eastern Africa respectively”

There is no reason at all to suppose the groups carrying these three haplogroups were originally other than reasonably close to each other. In other words it is unlikely they would have moved particularly far from the region of common origin.

“The modern human mtDNA tree split first at ~180 ka (the age of the 'mitochondrial Eve' MRCA) into L0 and a second branch comprising L1-L6 (referred to as L1’6)”

I think everyone accepts that. Concerning L1''6:

“Its deepest split within L1’6 is between L1 and L2’6 at ~150 ka”

Interestingly the authors provide no date for the split between L0d and L0a'b'f'k, nor between L0d1'2 and L0d3, while providing a reasonably full list of dates for the L0a'b'f'k branches. They do claim L0a'b'f'k itself splits at 120,000 years, and judging from the tree that is considerably before the split, indicating expansion, within L0d. That last looks to be at around 75,000 years, and therefore L0d may not have actually reached 'South Africa' until that date. However they do say:

“L0a’b’f’k dates to ~120 ka, and splits again to give rise to L0k and L0a’b’f (Figure 1 and 2). L0k does not begin to diversify in the tree until ~40 ka and seems to be rare (Figure 3F), concentrated in the northerly Ju and Khwe”.

Rare, but slightly northern. Again there is no reason to expect a huge geographic distance between L0d and the next branches, L0k and L0f:

“Although L0k1a is almost restricted to Khoesan groups [29], L0k1b is mostly present in Bantu-speaking populations from Zambia [29,72], and this is even more true for L0k2”.

That places L0k in Zambia, not South Africa.

“Either scenario remains consistent with an ancient origin of L0k in the south”.

Not inconsistent with an origin further north either though. In fact more likely.

“By contrast, the subclade L0a’b’f, which dates to ~90-95 ka, has a most likely origin in eastern Africa. The frequency distribution of the deepest subclade of L0a’b’f, L0f, is centred on Uganda/Tanzania”.

We're left with a situation similar to that regarding the comments on L0, L1 and L2''6. In other words it is intriguing that the deepest geographically restricted branches of the L0 tree – L0d, L0k and L0a'f – evidently originated in southern Africa, Zambia and Tanzania/Uganda respectively. Again there is no reason at all to suppose the groups carrying these three haplogroups were originally other than reasonably close to each other.

Egyptsearch 2.0. said...

"But not in 'South Africa'."

Barring the moments where I wanted to be more specific, I've mainly divided Africa into broad West/Central, North and South Africa regions throughout this discussion. Clearly, I didn't mean to place L0k specifically within the superfluously narrow confines of the borders of the South African state.

"It would surely be no surprise if two L3 lines emerged from Africa, perhaps together but later became separated."

What is the point of replying to my post if my post addresses your earlier claim that M and N "emerged" from Africa together and you're going to present an entirely new suggestion and pass it off as akin to what you said earlier. It also wasn't just about them becoming separated; it was about it becoming completely compartmentalized.

"If CT managed to emerge from Africa before either M or N it is quite possible that the separate mt-DNA expansions are associated with separate CF and DE Y-DNA expansions"

Maybe, but the fact of the matter is that not even this scenario helps your case that CT was a contemporary of M or N. All these self-contradicting speculations you cook up only seem motivated to protect your cherished apriori assumptions about CT being non-African. It's funny how everything I'm telling you leads to further denial of the reality that CT look substantially older; you just hop from one speculation to the next and end up changing the topic in the process. Nascent mutations can't expand or contract, and such demographic patterns therefore can't explain the age differences under discussion.

"You are ignoring facts. This from the paper:"

You're the one who is systematically ignoring things. I've said several times in several different explanations that the age of trees are subject to revision. It seems like this stuff goes over your head because you keep bringing up the age of the pushed back MSY tree. Unless you're of the very bizarre belief that the human mtDNA molecule popped into existence with the natal day of mtDNA Eve, who cares that Rito et al don't match RSRS with A00? It's beyond irrelevant. I also didn't cite Rito et al for their views; I cited them for their statistical results, re: the distribution of various L0 branches from southeastern to East Africa. Unless you falsify my points, you're just rope tugging (I could just as easy post my sources and go tit for tat but that won't lead anywhere). You completely failed to address the gaping discrepancy inherent in your claim, namely, the resulting inability of both trees to coalesce to the same archaic humans.

terryt said...

"You completely failed to address the gaping discrepancy inherent in your claim, namely, the resulting inability of both trees to coalesce to the same archaic humans".

I told you very early in the discussion that I see no reason at all why they should 'coalesce to the same archaic humans'.

"I didn't mean to place L0k specifically within the superfluously narrow confines of the borders of the South African state".

I accept that position. But 'south of the Congo River', which we could call 'southern Africa', actually comprises the majority of sub-Saharan Africa.

"I've mainly divided Africa into broad West/Central, North and South Africa regions"

Southern Africa; south of the Congo, west/central: north of the ZCongo, north: ?. North of the Sahara? I would prefer the third region to be called northeast Africa: northeast of the Congo and including Egypt south to Tanzania.

"and you're going to present an entirely new suggestion and pass it off as akin to what you said earlier. It also wasn't just about them becoming separated; it was about it becoming completely compartmentalized".

Aren't all the L3 haplogroups completely compartmentalized. Some have eventually become very widespread but they appear originally to have developed in quite specific regions.

"It's funny how everything I'm telling you leads to further denial of the reality that CT look substantially older; you just hop from one speculation to the next and end up changing the topic in the process".

So where, and what time, do you propose CT appeared?

"I've said several times in several different explanations that the age of trees are subject to revision".

In fact I think it very unlikely that such a thing as a molecular clock exists. Sure, it can place a minimum age on a haplogroup but can provide no clue as to the maximum age. I don't think I have anywhere relied on 'age' of haplogroup except where you seem to believe it is significant. Phylogeny is a much better indication of expansions, if not timing of such expansions.

"Unless you're of the very bizarre belief that the human mtDNA molecule popped into existence with the natal day of mtDNA Eve, who cares that Rito et al don't match RSRS with A00? It's beyond irrelevant".

Hang on. It was you who first made the claim that Y-DNA could be closely correlated with mt-DNA. You now seem to be agreeing that it can't be.

akb said...

Do Sub Saharans lack Neandertal or not?

Egyptsearch 2.0. said...

@Terryt

“I told you very early in the discussion that I see no reason at all why they should 'coalesce to the same archaic humans'.”

They’ll have to converge in some archaic human. Since speciation prevents the introgression of highly divergent lineages, all introgression into our ancestral population will simply point back to the same common ancestor(s).

“Southern Africa; south of the Congo, west/central: north of the ZCongo, north: ?. North of the Sahara?”

I think of West/Central Africa and East Africa as meeting North Africa somewhere in the Sahel and meeting South Africa near the northern edge of the Mega Kalahari. I view the West/Central Africa and East Africa dividing line as existing along the Chad/Sudan border.

“Aren't all the L3 haplogroups completely compartmentalized. Some have eventually become very widespread but they appear originally to have developed in quite specific regions.”

I don’t see any of them as having undergone non-random founder effects where one set of a particular type ended up in one founding population and another set in another founding population.

“So where, and what time, do you propose CT appeared?”

As I said, I think the split of the branches on which B and CT mutated, mimics the split of the branches on which L2 and L3’4’6 mutated; the emergence of CT at >50% between A2-T and the present, matches the same specifics on the maternal side, with L3’4’6 appearing at ~50% between RSRS and the present. South Africans have basal lineages of both trees (i.e. A2, L0d), while the rest of the world has the rest. I can’t give a date for the age of L3’4’6 because of the inconsistent methodologies across studies. But usually it’s at 50%. So in Rito et al’s dating table it would likely clock in at ~90kya (180kya/2=90kya), which broadly matches CT in Scozzari et al 2014 at ~167kya/2=~83.5kya. I consider the region of origin to be somewhere near the African side of the Red Sea.

“Hang on. It was you who first made the claim that Y-DNA could be closely correlated with mt-DNA. You now seem to be agreeing that it can't be.”

What I’ve been trying to get across is that there has been a lopsided increase in the MRCA of the Y chromosome while the mtDNA MRCA hasn’t followed suit. If A2-T mated with RSRS, as is the case in my view, logically, one would need branches that are older than RSRS to find a suitable candidate that could have mated with A00 and A1a.

“In fact I think it very unlikely that such a thing as a molecular clock exists.”

See Hallast et al 2014, table S4. How do you explain the similar branch lengths of all the macro hgs, If not as a function of time?

Egyptsearch 2.0. said...

Make that Hallast et al 2014, table S8 and (easier to decipher than table S4).

terryt said...

"Since speciation prevents the introgression of highly divergent lineages"

But the lineages within tropical Africa are extremely unlikely to have been 'highly divergent' at any time, even during H. erectus times.

"all introgression into our ancestral population will simply point back to the same common ancestor(s)".

But I'd be very surprised if at least some of our genes don't go back to erectus times. After all we share many genes with other mammals, and even with fungi. It is proving more and more difficult to decide when the change from 'ancient' to 'modern' actually occurred certainly when considering only Africa. Outside that continent it is perhaps a little easier.

"I don’t see any of them as having undergone non-random founder effects where one set of a particular type ended up in one founding population and another set in another founding population".

I do, although all L3(xNM) branches seem centred near Ethiopia. L3a is basically confined to Ethiopia. L3b'f looks primarily centred near Lake Chad before expanding. L3c'd'j looks somewhere between the above two before it expanded. L3e'i'x'k looks to be centred on eastern Ethiopia to start with. L3h is difficult to decide but L3h2 is Ethiopian.

"the emergence of CT at >50% between A2-T and the present"

A2 no longer exists. Do you mean A1b1?

"South Africans have basal lineages of both trees (i.e. A2, L0d)"

The first A lineage into southern Africa looks to be A1b1a-V20. Although A1b1b-M32 is present in the Khoisan it is widespread in eastern Africa and therefore is not necessarily, or even likely to have, an early southern African presence. A1b1b2a is primarily southern African though but its presence there almost certainly post-dates that of A1b1a.

"I consider the region of origin to be somewhere near the African side of the Red Sea".

I agree.

"one would need branches that are older than RSRS to find a suitable candidate that could have mated with A00 and A1a".

But the female lines they bred with need not have survived to the present day.

Egyptsearch 2.0. said...

@Terryt

“But the lineages within tropical Africa are extremely unlikely to have been 'highly divergent' at any time, even during H. erectus times.”

I agree, but it doesn't matter what the timescale is; all homo mtDNA and MSY (including Neanderthal and Denisovan) are expected to ultimately coalesce in a hominin population. What other sources could our uniparental MRCAs possibly have? You deny that they coalesce in the same population, but provide no source as to where else either could have come from.

“But I'd be very surprised if at least some of our genes don't go back to erectus times.”

I’m not sure what you mean. I was talking about Erectus when I said “archaic humans”. You don't think of Erectus as an archaic human? Like I said, introgressed lineages will simply point to the same common ancestors because the only (sub)species we can mate with successfully share our common ancestors.

“I do, although all L3(xNM) branches seem centred near Ethiopia. L3a is basically confined to Ethiopia. L3b'f looks primarily centred near Lake Chad before expanding.”

The way I see it, these L3 clades inflated in the respective populations before or on arrival via well understood processes. For instance, I think that the L3k population had the same hg profile as the LSA population from which it departed--I don't see this split as creating L3k on one side and non-L3k on the other side.

“A2 no longer exists. Do you mean A1b1?”

No. See Scozzari et al 2014 and their predecessors for the MSY hg naming convention I use. A2 would correspond with A1b1a1.

“But the female lines they bred with need not have survived to the present day.”

Right, so the added antiquity A00 brings to the table is not a discrepancy from my point of view. I wasn't planning on discussing this right now, but some of these mtDNAs actually did survive. The geneticists just stopped investigating them for some reason. Possibly because they saw it as a threat to orthodox OOA. In 1995 a 540 bp vestige of an otherwise extinct mtDNA was found to have survived (intact) on chromosome 11 of a substantial amount of living humans. In 2001 part of this 540 bp vestige was observed in Lake Munga 3's aDNA and its phylogenetic relationship to RSRS suggests that it's a sister branch to RSRS. This means that they combine to form a root that is more ancient than RSRS. In my view, this lineage was among the lineages that populated the North African MSA (and spilled over into Arabia, India, the Levant, etc.) before the CT population arrived in northeast Africa.

terryt said...

"A2 would correspond with A1b1a1".

Thanks. That's considerably downstream from A1b1. Remember that BT is effectively A1b2.

"You deny that they coalesce in the same population, but provide no source as to where else either could have come from".

Just take a look at the phylogenies. I've told you before that the Y-DNA almost certainly originated in Central/West Africa while the mt-DNA line almost certainly originated considerably east of that region, perhaps almost as far as Ethiopia/Sudan.

"all homo mtDNA and MSY (including Neanderthal and Denisovan) are expected to ultimately coalesce in a hominin population"

Of course. But we have plenty of examples in the modern lines where the mt-DNA and Y-DNA lines come together from two completely separate reions, then combine and expand together. I see no reason why the same process should be confined to just modern haploid lineages, or even just to the haploid lineages. It has been pointed out by several scientists that in effect each separate gene has its own separate history.

"I wasn't planning on discussing this right now, but some of these mtDNAs actually did survive. The geneticists just stopped investigating them for some reason".

Interesting. I have always thought it was an unjustified assumption that both the mt- and Y-DNA deeper origin lay exclusively in Africa. Especially when we consider that at a deeper level modern human mt-DNA is closer to Neanderthal than to Denisova mt-DNA. That could easily indicate the ancestor of the modern mt-DNA line had entered Africa from Eurasia some time after after branching off the Neanderthal line. To me there is no evidence Neanderthals formed from any sort of African line, but from a Eurasian Denisova-like line.

Egyptsearch 2.0. said...

@Terryt

"Thanks. That's considerably downstream from A1b1. Remember that BT is effectively A1b2."

Right. It exhibits the exact same phylogenetic relationship to AT(xA2) as L0d does to L(xL0d). This is another instance of the uniparental mimicry I've been making a case for.

"I've told you before that the Y-DNA almost certainly originated in Central/West Africa"

No, you said that A00 likely originated in West/Central Africa. Do you really not know the difference between A00 and the point where MSY connects with all other hominin MSY? Earlier, when you insinuated that the mtDNA molecule was younger than A00, simply because RSRS is younger than A00, you made the same puzzling argument. Again, you provide no additional source for early hominin MSY and mtDNAs that would justify your objection that MSY and mtDNA don't have the same age. And no matter how often I try to address your erroneous treatment of MSY and mtDNA as equalling A00 and RSRS, you keep reverting back to this mix up. Any scenario in which A00 was separated spatially from the ancestor of RSRS can only be understood as a separation that was preceded by the emergence of a shared ancestor, for reasons I already explained numerous times.

"But we have plenty of examples in the modern lines where the mt-DNA and Y-DNA lines come together from two completely separate reions, then combine and expand together."

This has no relevance to the fact that all lineages coalesce in the same early hominin population, and that this makes it inevitable that they would have the same TMRCAs (after accounting for evolutionary forces that may cause differential growth patterns).

terryt said...

"It exhibits the exact same phylogenetic relationship to AT(xA2) as L0d does to L(xL0d)".

In other words you see you see A1b1 connected with L0d, B connected with L1and CDEF connected with L2''6. What about Y-DNA A1b1b? I would say A1b1b1 is more likely to be connected with L2''6 than is CDEF, and A1b1b2b to be connected with L3 than is CDEF.

"Again, you provide no additional source for early hominin MSY and mtDNAs that would justify your objection that MSY and mtDNA don't have the same age".

All age estimates I have seen for the earliest surviving branches of the two lines show A00 to be much older than L0''6. Do have alternative dates?

"Any scenario in which A00 was separated spatially from the ancestor of RSRS can only be understood as a separation that was preceded by the emergence of a shared ancestor, for reasons I already explained numerous times".

But that 'shared ancestor' may considerably predate the development of modern humans. I agree the two lines have come together but that mixing may be far from simple.

"and that this makes it inevitable that they would have the same TMRCAs"

I believe you are making a huge assumption here.

Egyptsearch 2.0. said...

@Terryt

“In other words you see you see A1b1 connected with L0d, B connected with L1and CDEF connected with L2''6. What about Y-DNA A1b1b? I would say A1b1b1 is more likely to be connected with L2''6 than is CDEF, and A1b1b2b to be connected with L3 than is CDEF.”

When I say that A2 mimics L0d, I’m specifically talking about A1b1a(1), not A1b1. In fact, the way I see it, both A1b1a and A1b1b contribute to this mimicry. A1b1a does so by being a candidate mate for L0d and A1b1b does so by being a candidate mate for L0a’b’f’k. In this scenario, A1b1b could have followed L0k when it reunited with South African AMHs. A1b1a and A1b1b clearly group together before joining A1b2/BT under the A1b node. The same pattern can be observed for L0d and L0a’b’f’k; both join first within L0, before joining L1’2’3’4’5’6 under the RSRS node. So yes, I agree with you here.

“All age estimates I have seen for the earliest surviving branches of the two lines show A00 to be much older than L0''6. Do have alternative dates?”

What does the age discrepancy between RSRS and A00 have to do with extant lineages going back to the same hominid population, indicating that they must have spent the same amount of time to make it to our day and age? Your only way out of this reality is to invoke lineages that we already know couldn’t have introgressed.

“But that 'shared ancestor' may considerably predate the development of modern humans. I agree the two lines have come together but that mixing may be far from simple.”

Mixing would not increase the amount of archaic common ancestors. Does the presence of Y chromosome E and A-M13 in Europe increase the amount of early human common ancestors? E coalesces with native European Y chromosomes at CT, and A-M13 coalesces with European Y chromosomes at A3-T, which would make the amount of early common ancestors stay the same, no matter how much mixing takes place.

“I believe you are making a huge assumption here.”

Someone with familiarity with the literature would not say this. It is population genetics 101 (e.g. Sayres 2013):

http://s4.postimg.org/n3v0zwb19/2015_03_04_10_09_10.png

terryt said...

"When I say that A2 mimics L0d, I’m specifically talking about A1b1a(1), not A1b1".

Why didn't you say so? A1b1a is not AT(xA2). The latter is A1b1. I agree A1b1a is obviously very associated with L0d. But A1b1 is not.

"In fact, the way I see it, both A1b1a and A1b1b contribute to this mimicry".

Except that neither are specifically associated with L0. Just the downstream clades A1b1a and A1b1b2a. In fact I would suggest those two 'Khoisan' lineages entered southern Africa separately.

"A1b1b does so by being a candidate mate for L0a’b’f’k. In this scenario",

Possible. Except it is difficult to place A1b1b's origin in southern Africa. Perhaps eastern Africa. Of course I accept L0a’b’f’k originated in eastern Africa. In fact I very strongly suspect the whole L0 clade did so.

"A1b1a and A1b1b clearly group together before joining A1b2/BT under the A1b node".

Yes. They share a common ancestor, but that ancestor is unlikely to have been anywhere near southern Africa.

"What does the age discrepancy between RSRS and A00 have to do with extant lineages going back to the same hominid population, indicating that they must have spent the same amount of time to make it to our day and age?"

As you say:

"It is population genetics 101"

I would have thought the old idea that new species arise through the expansion of a single, small, suddenly superior population was well and truly deceased by now. As would the idea that haploid DNA serves as a marker between separate species. Unless you're claiming humans are somehow completely different from all other species. I can immediately think of two examples where this idea fails. European and American bison would be expected to share closely related mt-DNA. Not so. Totally different. European bison mt-DNA is far more closely related to that of cattle than it is to American bison. the a-DNA and the haploid DNA don't match up. Similarly for mallard ducks. Eurasian and North American mallards look exactly the same yet their mt-DNA is only distantly related. North American mallard mt-DNA is very closely related to the different-looking other North America Anas species. I see no reason to believe humans spring from a single isolated population at any time in their evolution.

Egyptsearch 2.0. said...

"Why didn't you say so? A1b1a is not AT(xA2)."

When I said “it” as in: "it exhibits the same relationship to AT(xA2) as L0d does to L(xL0d)", it was a continuation of the preceding comment that A2 "corresponds with A1b1a1". But yes, I should have been clearer in communicating this.

"Except that neither are specifically associated with L0. Just the downstream clades A1b1a and A1b1b2a. "

You say “just” as if the situation favors East Africa. There is A3a in Ethiopia, which has no indications of having arrived there with A3b2-M13, and there is the very homogeneous A3b2-M13 in the Sahara, Horn and Nile Valley, which, to my awareness, only coalesces to ~10kya. Specify this fictive ‘abundant A1b1 diversity’ you seem to think exists in East Africa, to the exclusion of South Africa, when South Africa clearly has more A1b1 diversity.

“Of course I accept L0a’b’f’k originated in eastern Africa. In fact I very strongly suspect the whole L0 clade did so.”

Only problem is, not a single shred of evidence advances your conjecture. San have the largest effective population size at the time of the San/non-San split ~120kya, leaving no support for your scenario of a relatively small subset of AMHs leaving East Africa and heading for South Africa.

“Yes. They share a common ancestor, but that ancestor is unlikely to have been anywhere near southern Africa.“

It’s easy to utter that something isn't so because you think it isn't. But based on what do you say this, other than dogma? I rarely see strong data or arguments accompanying your denials, and you often dismiss strong data or uncontroversial data on a whim or you conveniently stop replying to it.

“I would have thought the old idea that new species arise through the expansion of a single, small, suddenly superior population was well and truly deceased by now. ”

Not that I expect a coherent answer from you (I'm past the point of taking for granted that you're well-read in this area), but since the past has shown that addressing this argument of yours will inevitably lead to more fallacious replies from you, I'll just ask you (again): If the organisms that potentially mixed with our ancestral population were hominids, **why** would said introgression stop this mixed pool of lineages from having a shared ancestor in some earlier hominid?

terryt said...

"There is A3a in Ethiopia"

We have established that by A2 you mean A1b1a1, but what do you mean by A3? I notice that A3b2-M13 is now A1b1b2b which is extremely widespread.

"There is A3a in Ethiopia, which has no indications of having arrived there with A3b2-M13"

Of course not. A3a is an earlier branch than is A3b2. If anything A3b2 would have arrived where-ever it is with A3a.

"there is the very homogeneous A3b2-M13 in the Sahara, Horn and Nile Valley, which, to my awareness, only coalesces to ~10kya."

Makes sense. A recent wide expansion and any presence in southern Africa cannot possibly be taken as indicating origin there.

"when South Africa clearly has more A1b1 diversity".

We know there have been several expansions into southern Africa from further north. That certainly would lead to diversity.

"Only problem is, not a single shred of evidence advances your conjecture".

No L haplogroup other than L0 has any real representation in Southern Africa. And even L0 has only L0d as specifically southern African. You mentioned diversity. Africa outside southern Africa has far more L diversity than does southern Africa.

"If the organisms that potentially mixed with our ancestral population were hominids, **why** would said introgression stop this mixed pool of lineages from having a shared ancestor in some earlier hominid?"

Presumably the lineages have at times had shared ancestry. I actually doubt the male and female lines have been separate right from when H. erectus left Africa but, in theory, it is possible.

terryt said...

"But based on what do you say this, other than dogma? I rarely see strong data or arguments accompanying your denials"

I would have thought anyone even slightly interested in evolution would be already aware of this but here goes.

Ducks:

http://sora.unm.edu/sites/default/files/journals/auk/v111n04/p0970-p0978.pdf

http://www.jstor.org/discover/10.2307/2409570?sid=21105592456891&uid=3738776&uid=2&uid=4

http://www.biomedcentral.com/1471-2156/12/99

Bison:

http://mbe.oxfordjournals.org/content/21/7/1165.full

http://www.buffalofieldcampaign.org/habitat/documents/Douglas_bisonDNA.pdf

terryt said...

Another example I couldn't find earlier:

http://www.unz.com/gnxp/complex-speciation-of-equids/

Egyptsearch 2.0. said...

“We have established that by A2 you mean A1b1a1, but what do you mean by A3?”

A3 = A1b1b.

“If anything A3b2 would have arrived where-ever it is with A3a.”

Agree. But this doesn’t bode well for your view that A3-M32 has the antiquity in East Africa needed for it to have donated A3b1-M13 to South Africa. In fact, it’s impossible.

“A recent wide expansion and any presence in southern Africa cannot possibly be taken as indicating origin there.”

Reducing it to merely “a recent wide expansion” would be being dishonest with yourself. The fact is that there is no indication whatsoever that one of the two A3-M32 lineages on which you partly base the indigenousness of A3-M32 in East Africa, has the required antiquity there. The argument could be made that such evidence doesn’t exist for A3a-M28, either.

“We know there have been several expansions into southern Africa from further north. That certainly would lead to diversity.”

A3b1-M51 and A3b2-M13 separate ~70kya per Scozzari et al 2014, so we know that South Africa or East Africa was the recipient of their share of A3b1-M51 or A3b2-M13, after this date. Feel free to point to expansions from East to South Africa immediately following this date. We know that the spread of Howieson’s Poort-related industries to East Africa from South Africa perfectly matches the M51/M13 split. Can you produce a well-attested migration going in the opposite direction?

“No L haplogroup other than L0 has any real representation in Southern Africa.”

As I’ve said many times, L0 is parallel to the L1’2’3’4’5’6 macrohaplogroup; it’s not to some individual haplogroup on par with L1 or L3, no matter how barren it is today. How many times are you planning on making the same misguided point about L0 being a regular haplogroup? Like I said, you have no real evidence to support your claim that L0 originated in East Africa.

“Presumably the lineages have at times had shared ancestry.”

What do you mean? Does the point in thime at which at which all extant lineages in a given population coalesce, have an on and off switch?