April 25, 2016

Bursts in human male demography

From the paper:
When the tree is calibrated with a mutation rate estimate of 0.76 × 10-9 mutations per base pair per year9, the time to the most recent common ancestor (TMRCA) of the tree is ~190,000 years, but we consider the implications of alternative mutation rate estimates below. Of the clades resulting from the four deepest branching events, all but one are exclusive to Africa, and the TMRCA of all non-African lineages (that is, the TMRCA of haplogroups DE and CF) is ~76,000 years (Fig. 1, Supplementary Figs. 18 and 19, Supplementary Table 10, and Supplementary Note). We saw a notable increase in the number of lineages outside Africa ~50–55 kya, perhaps reflecting the geographical expansion and differentiation of Eurasian populations as they settled the vast expanse of these continents. Consistent with previous proposals14, a parsimonious interpretation of the phylogeny is that the predominant African haplogroup, haplogroup E, arose outside the continent. This model of geographical segregation within the CT clade requires just one continental haplogroup exchange (E to Africa), rather than three (D, C, and F out of Africa). Furthermore, the timing of this putative return to Africa—between the emergence of haplogroup E and its differentiation within Africa by 58 kya—is consistent with proposals, based on non–Y chromosome data, of abundant gene flow between Africa and nearby regions of Asia 50–80 kya15.
I've long argued for the Y-chromosome haplogroup E migration into Africa and it is nice to see this common-sense interpretation finally adopted. Too much focus has been placed on figuring out which routes modern humans took out of Africa, and not at all to figure out how Eurasian males came to overwhelm the African Y-chromosome gene pool so decisively. The Eurasian migration into Africa must have taken place in the ~70-60kya window, constrained by the D/E split and  the deepest intra-African E splits. I think that the Out-of-Arabia scenario I outlined in 2012 continues to make a lot of sense. It would be awesome to get data from the first Later Stone Age people from Africa which are probably the best bet to trace this migration from Eurasia into Sub-Saharan Africa.

Nature Genetics (2016) doi:10.1038/ng.3559

Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences

G David Poznik et al.

We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations.

Link

16 comments:

Romulus said...

I think it is very interesting that the expansion of R1b clades seems to directly precede the Beaker era rather than overlap with it.

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eurologist said...

The timings of the tree seem to be reasonably well calibrated at the 25%-of-total-to-shortish range - although older dates might still be underestimated, given that a linear relationship was assumed (whereas for surviving lineages, a relationship with a faster effective mutation rate over time might be expected).

Dienekes already pointed out the haplogroup E y-DNA arguments and implications. It is worthwhile to note that this paper dates a single CT-M168 to before 105,000 ya, i.e., it looks like none of its brother groups survived the entrance into Eurasia at later times. Of course, that is not unusual.

In addition, Terry will be satisfied with: "Three new features of the phylogeny underscore the importance of South and Southeast Asia as likely locations where lineages currently distributed throughout Eurasia first diversified," and the details of that (e.g., "This finding enabled us to define a new mega-group, GHIJK-M3658, whose subclades include the vast majority of the world’s non-African males."

Lank said...

This interpretation ignores the fact that DE* is found in West Africa. African DE* has been shown to be quite divergent from the D and E lineages, close to the root of DE, and hence rather close to the age of CT. In other words, a migration into Africa of DE is only slightly more simple than an out-of-Africa migration of CT-derived lineages.

It also ignores the carefully calibrated ages of mtDNA M and N to 47-55 kya, and the clear dispersal of proto-Eurasians since 50-55 kya, as seen in genetics (Ust'-Ishim from 45 kya has pan-Eurasian affinities, and relatively recent Neanderthal admixture) and archaeology.

So no, an into-Africa migration of Y-DNA E is not necessary. Actually, I would argue it's the least likely scenario when the evidence is considered in its entirety.

SeanF said...

Any thoughts on the 'Genghis Khan of the Yamna' suggested by the Tyler-Smith et al paper, as transmitted to the lay press?

http://www.telegraph.co.uk/science/2016/04/25/half-of-british-men-descended-from-one-bronze-age-king/

Apparently somewhere in the paper is the possibility that half of Western European men are descended from one Bronze Age Indo-European leader.

Federico Abascal said...

I've read this entry and the corresponding article with much interest (I am new to the fascinating world of Y and mt haplogroups). There is something I do not understand. It is said that the most parsimonious scenario is that haplogroup E originated out of Africa and then came back to Africa; the alternative scenario would imply three different lineages (D, C, and F) going out of Africa. I understand we are comparing 1 event vs 3 events (and that is more parsimonious) but if we consider the distribution of haplogroup E within Africa (it is everywhere), an out-of-Africa origin doesn't look very parsimonious either. I would really like to understand this.

Moreover, many things with the Y haplogroups do not look parsimonious. For example that haplogroup D (the sister group to haplogroup E according to the phylogeny) is restricted to Asia.

I am also wondering if the phylogenetic tree could be wrong? Bootstrap supports are very strong, but bootstrap supports are known to be higher with very large matrices. I am wondering if the same topology is recovered using different regions of the Y chromosome.

Thanks for this very nice blog!

Federico Abascal said...

I've read this entry and the corresponding article with much interest (I am new to the fascinating world of Y and mt haplogroups). There is something I do not understand. It is said that the most parsimonious scenario is that haplogroup E originated out of Africa and then came back to Africa; the alternative scenario would imply three different lineages (D, C, and F) going out of Africa. I understand we are comparing 1 event vs 3 events (and that is more parsimonious) but if we consider the distribution of haplogroup E within Africa (it is everywhere), an out-of-Africa origin doesn't look very parsimonious either. I would really like to understand this.

Moreover, many things with the Y haplogroups do not look parsimonious. For example that haplogroup D (the sister group to haplogroup E according to the phylogeny) is restricted to Asia.

I am also wondering if the phylogenetic tree could be wrong? Bootstrap supports are very strong, but bootstrap supports are known to be higher with very large matrices. I am wondering if the same topology is recovered using different regions of the Y chromosome.

Thanks for this very nice blog!

Maju said...

We must calibrate always with age(CF)=100-125 Ka. The archaeological evidence for that date range is overwhelming nowadays (Aterian in India dated to 98 Ka BP, several H. sapiens findings in East Asia dated to c. 100 Ka BP, clear bracket for the early "Arabo-Palestinian" OoA phase in those dates) and also the geostructure of A0, like A00 does not match with that of mtDNA, strongly suggesting that they are pre-Sapiens introgresions acquired in the process of migration to West Africa (this is unquestionable for A00 but A0 has pretty much the same distribution, so...)

This implies adding 30-60% to all age estimates in this paper, assuming everything else is correct.

Dienekes said...

We must calibrate always with age(CF)=100-125 Ka.

That is rather arbitrary. We have a good handle on the Y-chromosome mutation rate now (both from aDNA calibration and Icelandic pedigrees) and it doesn't support such a very early age. The indisputable event in human history is the spread of modern humans across Eurasia and Australia c. 50kya and the dates of this paper seem to correspond to that event quite well.

The archaeological evidence for that date range is overwhelming nowadays (Aterian in India dated to 98 Ka BP, several H. sapiens findings in East Asia dated to c. 100 Ka BP, clear bracket for the early "Arabo-Palestinian" OoA phase in those dates)

That is all contested and also you can't assume that the earliest AMH in different parts of Eurasia "stuck". There is counter-evidence that some of them didn't really (such as the Oase1 heavily Neandertal-admixed people from Europe that "did not contribute substantially to later humans in Europe")

BillyBoy said...

As an alternative, CT could have arisen in east africa (where mtL3/L4 diversity is greatest). A group that gave rise to CF migrated to asia (perhaps after a prolonged stay in Arabia). The CT group that remained in Africa became DE. DE (with mtM) later migrates to asia. In this manner, there is no back migration to aftrica of E (or DE), but two (2) OOA migrations. The positive of this theory is that it is consistent with mt diversity, although I am not sure if the dates of y diversity match up well with L3 diversification.

terryt said...

"In addition, Terry will be satisfied with: 'Three new features of the phylogeny underscore the importance of South and Southeast Asia as likely locations where lineages currently distributed throughout Eurasia first diversified'.

Thanks for that information. I haven't read the paper as I'm too mean to pay!

"This finding enabled us to define a new mega-group, GHIJK-M3658, whose subclades include the vast majority of the world’s non-African males."

I have seen that bit about GHIJK somewhere.

"It also ignores the carefully calibrated ages of mtDNA M and N to 47-55 kya, and the clear dispersal of proto-Eurasians since 50-55 kya, as seen in genetics (Ust'-Ishim from 45 kya has pan-Eurasian affinities, and relatively recent Neanderthal admixture) and archaeology".

But those dates clash with the settlement of Australia, which must be somewhat earlier than 45 kya, or even 55 kya. Unless the surviving haplotypes there are not from the original arrivals. And Ust'-Ishim is Y-DNA K2a^, which is considerably downstream from GHIJK and so formed some time after the spread through much of Eurasia.

"So no, an into-Africa migration of Y-DNA E is not necessary. Actually, I would argue it's the least likely scenario when the evidence is considered in its entirety".

I disagree. It is difficult to explain the apparently huge distance from Africa of D or C as having left Africa fully differentiated. It is surely far more likely that CT became quite widespread through some ecological region, which included part of both Africa and Eurasia, before the CF/DE split. Then the four branches coalesced in four discrete regions within the wider distribution. That would leave open the possibility that E did arise in Africa but closes that option for the other three.

"It is said that the most parsimonious scenario is that haplogroup E originated out of Africa and then came back to Africa; the alternative scenario would imply three different lineages (D, C, and F) going out of Africa".

The three separate lineages out of Africa proposal doesn't really make sense to me. However the hypothesis I provide above would explain things.

"I am also wondering if the phylogenetic tree could be wrong?"

The tree is adjusted occasionally but is likely to be largely correct. For example the recognition of GHIJK doesn't really alter things that much. However I think the 'molecular clock' is extremely unreliable, especially in the case of mt-DNA.

Maju said...

@Dienekes: I don't think that my claim is arbitrary, just based on different reasons than yours. I just can't believe dates based ONLY on mutation rates but I think that multiple lines of evidence must converge to a single most parsimonious solution and mutation rate based estimates produce nearly always too recent results relative to every other piece of evidence. By these other evidences or indications, I mean not just the growingly important archaeological data (which IMO should be central in our considerations but already mentioned) but also:

1. The burning issue of the realistic age of Pan-Homo split: some studies suggest as much as 13 Ka, with very reasonable minimal dates at 8-10 Ka, while the scholastic inertia tends to insist on 5-6 Ka instead, what does not fit even with the paleoanthropological data anymore (Sahelanthropus was clearly already in the Homo line and is dated to c. 7 Ka BP).

2. The contradictions between the Y-DNA and mtDNA "geostructure" (phylogeny on the map, so to say) and also the parallels, which are many. The contradictions are basically two:

(a) A0 and A00 originate in a different region of Africa than "mtDNA Eve" and her most basal descendants, so IMO they are "pre-Sapiens" lineages introgressed.

(b) The issue of the E male-biased explosion, which I will address in a separate comment but that clearly did not carry along any single mtDNA lineage from out of Africa.

Among the parallels however I can list the following:

(a) MtDNA "Eve" does not fit with Y-DNA "Adam" but with A1-T instead.

(b) MtDNA L2"6 fits well with E (not without issues re. the unusual pruning of male lineages but otherwise it does).

(c) Y-DNA CF fits very well with mtDNA M. Sure, there's also Y-DNA D and L3n (i.e. L3* leading to N or "pre-N") but these must be considered as exceptions, randomly favored by the colonization process of Asia, not core issues.

(d) Y-DNA K2 (K(xLT) fits almost perfectly with mtDNA R. Karafet recently demonstrated that Y-DNA K2 must have originated in SE Asia and I have argued that so must have been the case of mtDNA N/R. So IMO they both probably correspond to a secondary but very important "out of SE Asia" expansion, which plausibly happened after the Toba catastrophe opened up many niches and put extra selective pressure not on lineages themselves but on human populations. They may also be related with the early domestication of the dog (which also seems to stem from SE Asia).

"... you can't assume that the earliest AMH in different parts of Eurasia "stuck".

I don't assume anything: I just observe the behavior of the various non-African lineages, both Y-DNA and mtDNA (see here for a more detailed reference) and they do seem to have persisted, not without some changes and sweeps, but all of them specific to Asia. There was no second OoA wave, unattested archaeologically and inconsistent with the most crucial piece of evidence: the Human haploid phylogenies. In order to imagine two waves, we would have to assume that all the genetic evidence for a first wave has been erased (all of it!) and that all the archaeological evidence for a second OoA migration has similarly been wiped out. I just cannot accept either, much less both.

Maju said...

The issue of Y-DNA E is clearly problematic. It would be logical to expect that other lineages within the CT macro-haplogroup would have survived in Africa, as they did in Asia (plus), but that's not the case. Dienekes and myself discussed this issue in 2010 upon the publication of Emery's paper.

For some reason Emery suggested "male bias" not in Africans but in non-Africans, but IMO that doesn't work. The real "male bias" is in Africa and is around the OoA epoch. Why did CT lineages got pruned in Africa and not in Asia? Well, we do not know but I guess that we can make a case for more or less aggressive male-centered expansion with this lineage, that however did not affect the mtDNA distribution in any meaningful way. Basically E guys successfully co-opted all the L2"6 "mtDNA tribes" in Africa (with some Y-DNA A1 also playing a lesser role but otherwise excluding any other Y-DNA line, including E's cousins). This did not affect the migrants in West Asia, which retained E-related lineages (CT and D or pre-D). So far, I think Dienekes would be in approximate agreement.

The disagreement we have is on where did Y-DNA E coalesce. If we only consider Y-DNA "geostructure", then what Dienekes argues for seems correct: the coalescence geography of CT should be in Asia rather than Africa (however it'd be in Arabia, so we are not going too far from Africa in any case). The problem however is that there is not a single mtDNA lineage that would seem to have back-migrated from Asia to Africa before the Upper Paleolithic/LSA: nothing in the "couple" of Y-DNA E (would be L2"6) may have originated outside Africa: neither L2"6, nor L2'3'4'6, nor L2, nor L3, etc. Nothing at all! The most "Asian" of all these lineages is L3 and it has seven basal branches: five in Africa and only two in Asia (M and N).

So from the mtDNA side of things it is clear that the flow was exclusively Africa→Asia, and so it is from the Y-DNA side of things but at a higher and also lower phylogenetic level (getting confusing only at the CT phylogenetic level). Y-DNA E itself appears clearly African, no matter what one may think about its immediate precursors CT and DE, and even DE is probably African: the rare DE(xD,E) has been detected more commonly in Africa, although there's also two instances reported in Tibet (old materials all of them AFAIK). So for me the case is very strong for an African-specific pruning of CT(xE) branches, caused no doubt by a very strong and unusual Y-DNA E dynamism. Unusual dynamism that requires an explanation but an African explanation nonetheless.

My opinion in any case.

Dr. Clyde Winters said...

The idea of haplogroup E resulting in Africa as a back migration seems ludacris to me given the distribution and variety of haplogroup E in Africa.Archaeologists have discovered stone tools on the Arabian Peninsula that suggest that modern humans may have left Africa as early as 125,000 years ago to settle Arabia. This along with other archaeological evidence which clearly indicates that Nubians were continually moving out of Africa into Arabia suggest that haplogroup E probably originated in Africa, not Arabia. The statistical model used by the authors of this article lacks any archaeological evidence indicating a back migration from Arabia into Africa, while there is abundant archaeological evidence for migrations of Nubians into Arabia between 80k-3kya. This leads me to reject the idea of haplogroup E originating in Arabia.

Joe Flood said...

Hm Only just saw this. No the R1b-L11 expansion begins right where it ought to be around 2800BC at the start of the Beaker period. I dont think the authors have done enough analysis or have enough data to show how this continued - but we know it did pretty much up to 1500BC

Regarding E - well I have always thought the idea that everything came again and again out of Africa voided common sense - what was this pump valve driving people out of Africa but not the other way? The CDE split and parsimony does lead one to believe that E must have drifted out of Asia - though why C and D would not come with it remains unexplained.

I think our knowledge of all this is currently minimal and just guesswork. If we cant really work out what was going on in post-Roman times using DNA of modern populations 9and so far we cant), how can we expect to work out events at the dawn of mankind?

Joe Flood said...

SeanF, there is an awful lot of nonsense written on this subject, often by people who ought to know better. Yes a considerable proportion of the population of Europe is descended from one man, no he did not have to be Eureopean or any sort of a king, and it was not 2000 BC, somewhere in the 2800-3000BC range. Nor is there any reason he should have been ' Indo-European' though I think in likelihood he did speak proto-Indo European, along with other languages.

Yes in these expansions they were able to control certain technologies However I think other factors were involved - the spread of diseases, climate change, and possibly natural disasters.

I like the way this paper dispels our Euro-centric predisposiiton; it shows O and E1b to have been by far the most important Y-expansions, though R1b-L11 was late and the fastest of all.