April 06, 2011

Phylogeographic analysis of Y haplogroups A and B

I was skeptical of the recent Out of South Africa paper, and not much later, a new paper suggests that South Africa has been a population sink of Y-chromosomes. Of course, this is compatible with an ultimate origin of mankind in South Africa: it's possible for indigenous South African Y-chromosomes to have been replaced by more recent Y-chromosomes from elsewhere. On balance, however, this weakens the case for "Out-of-South Africa".

The authors make an interesting point:
Finally, our study contributes to the debate on the geographical origin of Homo sapiens in sub-Saharan Africa, providing evidence for the retention of early Y chromosome lineages in East and Central but not in Southern Africa. However, we note that the current absence of significant palaeoanthropological investigation, together with the possibility of different fossil preservation conditions in central Africa, makes the extremely long human fossil record in eastern Africa inconclusive in solving this issue. The screening of Y-chromosomal variation at an increased level of resolution, combined with additional sampling from these regions, is expected to further elucidate the early steps of Homo sapiens in Africa.
I am increasingly skeptical that Homo sapiens really "originated" in a limited geographical region within the global Homo range. Recent evidence has shown increased signs of older anatomical modernity around the world, and has rehabilitated 2/2 of the DNA-tested "archaic" hominins as relevant to the genetic diversity of modern humans. I would say that the focus on East Africa has been largely an artefact of the Great Rift Valley, rather than any strong evidence that modern humans really originated there.

Here is an interesting excerpt from the paper:
Given the limitation related to ASD saturation, some potentially interesting inter-lineage comparisons were beyond the available resolution dictated by the STRs we used. For example, the ASD between A and B clades, which is expected to give an estimate of the Time to the Most Recent Common Ancestor (TMRCA) of the entire human Y chromosome genealogy.
As I mentioned in How Old is Y-chromosome Adam, markers with different mutation rates ("slow" vs. "fast") give widely divergent estimates of the time depth of the human Y-chromosome phylogeny. Fast markers give very low time estimates, and the problem of saturation can indeed be important. On the other hand, using the slowest markers, where the problem of saturation is unlikely to be important results in ages of >150ky and up to 500+ky depending on which clade haplogroup A chromosomes (that are the most basal) are compared with.

This is the first time I've seen the issue of the age of the human Y-chromosome phylogeny mentioned in a scientific paper in a long time, and hopefully it will alert people to the reality that
  • we don't know how old the human Y-chromosome phylogeny is
  • it could be much older than the stuff of National Geographic documentaries and the recent Out of Africa model
I have not looked into the Y-chromosome data released by the 1000 Genomes Project yet (tip me if you have), but I can't help but notice that in the Project's debut paper only the CT part of the tree (i.e., excluding Palaeoafrican haplogroups A and B) was shown.

Assuming that there are some haplogroup A and B chromosomes among the Project's African contingent, and through SNP counting-based age estimation, which is much less problematic thatn Y-STR based molecular clocks, I'm willing to bet that a lot of people will be surprised when the date of Y-chromosome Adam is finally estimated properly.

Mol Biol Evol (2011) doi: 10.1093/molbev/msr089

Signatures of the pre-agricultural peopling processes in sub-Saharan Africa as revealed by the phylogeography of early Y chromosome lineages

Chiara Batini et al.


The study of Y chromosome variation has helped reconstruct demographic events associated with the spread of languages, agriculture and pastoralism in sub-Saharan Africa, but little attention has been given to the early history of the continent. In order to overcome this lack of knowledge, we carried out a phylogeographic analysis of haplogroups A and B in a broad dataset of sub-Saharan populations. These two lineages are particularly suitable for this objective because they are the two most deeply rooted branches of the Y chromosome genealogy. Their distribution is almost exclusively restricted to sub-Saharan Africa where their frequency peaks at 65% in groups of foragers. The combined high resolution SNP analysis with STR variation of their sub-clades reveals strong geographic and population structure for both haplogroups. This has allowed us to identify specific lineages related to regional pre-agricultural dynamics in different areas of sub-Saharan Africa. In addition, we observed signatures of relatively recent contact, both among Pygmies, and between them and Khoisan speaker groups from southern Africa, thus contributing to the understanding of the complex evolutionary relationships among African hunter-gatherers. Finally, by revising the phylogeography of the very early human Y chromosome lineages, we have obtained support for the role of southern Africa as a sink, rather than a source, of the first migrations of modern humans from eastern and central parts of the continent. These results open new perspectives on the early history of Homo sapiens in Africa, with particular attention to areas of the continent where human fossil remains and archaeological data are scant.



Andrew Oh-Willeke said...

The ancient population structure of sub-Saharan Africa that we see evidence of today is of Khoisan more strongly affiliated with A than B, Pygmies more strongly affiliated with B than A. A recent study found what is probably the signature of a third ethnicity in the vicinity of Mozambique that no longer exists in unadmixed form due to recent Bantu expansion. This paper puts the oldest subtypes of A and B in East Africa, which there has long been suspicion was the ancestral origin of the Khoisan before they made their way South.

Pygmies, as I understand it, were historically in the Central African tropics, were split into two groups pre-Bantu expansions, and have had recent admixture with Bantus during their expansion and lost any indigeneous language of their own.

There surely must also either have been a parallel hunter-gather ethnicity that was in West Africa and perhaps the Wet Sahara prior to the appearance of the Y-DNA hg E that are now predominant in these regions, which is pretty much buried almost beyond recognition as traces in the population genetics of later waves of migrants; or pygmies are a refugium of them which is less likely as it is asking for a lot of physical anthrological change in perhaps 10,000 years or so (assuming hg E expansion in the Sahel Neolithic), and as the uniparental lines in Pygmies suggest that they have roots in Central Africa that are older and more regionalized than one would expect in a refugia of West African exile populations culturally adapated to a very different ecology.

So, realistically, you are looking at about four regionally distinct ethnicities non-East African, sub-Saharan populations of hunter-gatherers with hg A or B or both, in the early modern human pre-Out of Africa era, all of which seem to have the deepest roots in East Africa which would have been a more genetically diverse source pool for East African hunter-gatherers - none of which are direct sources for non-Africans. Of these four populations: two of which have extant near pure types left in small undesirable refugia populations, and two of which in more agriculture friendly areas were totally submerged or rendered extinct by some means. There are also some relict old lineage East African hunter-gatherers who aren't particularly admixed who would have made up one or more East African ethnicities with hg A or B or both.

This all seems to make the case of a long line of parallel intermediate modern human types or modern human evolution in Central Africa rather than East Africa seem a stretch before resorting to archaeological preservation issues at all.

Andrew Oh-Willeke said...


Then, the question is what kind of archaic homo interaction would have taken place in any of these regions. One or more species of archaics must have been present in Sub-Saharan Africa at the first Out of East Africa moments, probably at lower population density than the modern humans. The archaics would have had more than a million years to settle into micro-environments across Africa before modern humans came along.

But, given the experience of modern humans elsewhere, archaics were probably gone in Africa before anything other than hg A and hg B existed in Africa, and no one archaic group would have made more than about a 4%-5% contribution to a hg A/hg B population. Those admixtures would be diluted by the same proportions that hg A/hg B have in the respective modern populations today. So, in modern pygmy or khoisan populations one might find as much as 3-4% of archaic traces from their respective archaic encounters, but genetic traces of African archaic homo from lineages other than E should be at an almost impossible to discern faction of a percentage point in most non-Khoisan, non-Pygmy farmer/herder populations of Africa. The vast majority of any African archaic DNA should be about 4% of the Y-DNA macrohg DE percentage restricted to origins from a single population that was ancestral to Y-DNA macrohg DE peoples. But, since that same African archaic homo population could have been the source of admixture with predecessors to Eurasians and some East African hg A and hg B, and since we don't know how genetically diverse low population density African archaic homo would be, it is going to be hard to pin that down as distinct without an ancient DNA sample to compare.

If East African admixture with archaics happened prior to an Out of East Africa moment, and subsequent admixtures left little trace outside Pygmies and Khoisan for the reasons described above, all modern humans should share that archaic DNA. You'd look at what very old looking genetic traces all modern humans, but not Neanderthals, have in common, rather than pitting one group of modern humans v. another.

Ancient DNA from second wave archaic admixture by Pygmies or Khoisan ought to be revealed by looking at non-Pygmy v. Pygmy and by non-Khoisan v. Khoisan, informed by Neanderthal but not decisively directed by Neanderthal.

Nobody in African would have more than 8% ancient admixture as is seen in the Melanesians.

Brandon said...

Andrew, are you trying to achieve some "ethnically correct" synthesis about how all moderns are all equal—and, fortunately, equally archaic?

Ponto said...

You can apply that rational argument to everything dealing with human genetics. Just because you find a lot of something in a certain region does not mean the something originated there. The converse has been applied from the beginning, that finding high J1 in Yemen means J1 originated in South Arabia among the South Arabians of Yemen. Similarly someone finding your remains buried with your favorite iPod does not mean you whilst alive made the thing.

More effort should go into finding exactly where certain human genetic features originated rather than going by the simplistic rule.

eurologist said...

To me it seems that the time window that this paper can reasonably explore really doesn't allow much comment on human origin. I mean, most of the dates are just a few thousand years up to LGM, and thus allow exploration of migrations and populations shifts since then. How can one extrapolate from that to a time a factor of ten farther back? Before the LGM and agricultural migrations mixed everything up, there were at least two, if not three important climatic events. Like the Saharan pump, much of South Africa (south and west of Zimbabwe) also acts as a huge reservoir of population at climatically benign times, followed by times of tiny population islands.

East Africa, including the Southeast all the way to Mozambique, likely was able to hold a much more steady population. However, it could have been a sink anytime the South (or the North!) had a favorable climate and population expansion.

At any rate, the idea of a y-DNA Adam is quite different from that of the origin of modern humans. The latter could have involved much of Africa and also input from Europe and West Asia until ~300,000 ya (let alone after ooA).

terryt said...

"At any rate, the idea of a y-DNA Adam is quite different from that of the origin of modern humans. The latter could have involved much of Africa and also input from Europe and West Asia until ~300,000 ya (let alone after ooA)".

Agree totally.

Ted Kandell said...

The FTDNA haplogroup A Project has two kits who are:
V166- (xA0), L896- (= xA0b), V168- (= xA1a-T), V50- (xA2), M42- (xBT), P97+ (= xBT), SRY10831.1- (xBT)



One of these is N64496, the descendant of Albert Perry, black slave from York Co. South Carolina, who more or less matches an African Y cluster from Buea in Southwest Cameroon:


I would like everyone posting here and anyone who discusses African archaic ancestry to PAY and donate to the FTDNA Haplogroup A Project for the purpose of a Walk on the Y (WOTY) 100k bp sequencing test for kit N64496.



I myself just PAID.
You can too.

I would like everyone to also try to think of ways we can get a full genome sequence for this individual (or another member of the same Y cluster) so we can obtain a reasonably complete full Y sequence.

This is going to tell us something very critical about human origins in Africa.