A00 is ~208ky old (Elhaik et al. 2014)

A new paper on Y chromosome haplogroup A00 brings its split time to around the time of the emergence of modern anatomical modernity (~208ky) rather than the much earlier date inferred in the original paper. The low mutation rate (used to derive the old date) was also criticized by Wilson Sayers in an arXiv preprint, while Scozzari et al. recently argued for an old Y chromosome phylogeny (and correspondingly low mutation rate).

I suspect that (i) a good fix on the Y chromosome rate by direct methods, and (ii) ancient DNA work might help resolve this controversy fully. (i) will help us estimate times more accurately, and (ii) might document the presence/absence of lineages at particular time points.

In any case, for the time being, we should doubt that A00 represents a non-sapiens introgression event, although the occurrence of the most basal Y chromosome lineage in a West African farmer population still remains a very interesting finding. It's still possible that a finer sieve might yet detect archaic (or late pre-modern) introgressing lineages in modern humans, but A00 doesn't appear to be one of them.

Interesting (and a first?), a Youtube clip by the lead author on the paper:



European Journal of Human Genetics advance online publication 22 January 2014; doi: 10.1038/ejhg.2013.303

The ‘extremely ancient’ chromosome that isn’t: a forensic bioinformatic investigation of Albert Perry’s X-degenerate portion of the Y chromosome

Eran Elhaik et al.

Mendez and colleagues reported the identification of a Y chromosome haplotype (the A00 lineage) that lies at the basal position of the Y chromosome phylogenetic tree. Incorporating this haplotype, the authors estimated the time to the most recent common ancestor (TMRCA) for the Y tree to be 338 000 years ago (95% CI=237 000–581 000). Such an extraordinarily early estimate contradicts all previous estimates in the literature and is over a 100 000 years older than the earliest fossils of anatomically modern humans. This estimate raises two astonishing possibilities, either the novel Y chromosome was inherited after ancestral humans interbred with another species, or anatomically modern Homo sapiens emerged earlier than previously estimated and quickly became subdivided into genetically differentiated subpopulations. We demonstrate that the TMRCA estimate was reached through inadequate statistical and analytical methods, each of which contributed to its inflation. We show that the authors ignored previously inferred Y-specific rates of substitution, incorrectly derived the Y-specific substitution rate from autosomal mutation rates, and compared unequal lengths of the novel Y chromosome with the previously recognized basal lineage. Our analysis indicates that the A00 lineage was derived from all the other lineages 208 300 (95% CI=163 900–260 200) years ago.

Link

New A00 project

A new project dedicated to Y-haplogroup A00 is seeking funding. A00 is the most basal clade of the human Y-chromosome phylogeny and has so far been found in African Americans and Mbo people from Cameroon. This is how the funds raised will be used:

In this campaign, we're seeking the funds we need to launch our first phase of fieldwork in late August, 2013. Our overall research plan includes five field trips to sample peoples in different regions of the country. In the first trip, Matthew will travel to the remote rural villages where he was raised, in the mountainous, forested Nkongho-Mbo region, and collect at least 100 samples from three villages, which will then be sent to a lab to be screened for A00. More in-depth testing will focus on those A00 samples. 

Planning and discussions are underway regarding which labs, probably more than one, will perform both SNP and STR testing on the samples. A full Y-chromosome sequence is on our wish list. This fundraising campaign, our first, will be limited to funding the DNA collection fieldwork. We'll be asking for your donations for lab testing in a separate campaign, in the near future. We need to limit the total amount of each fundraising campaign's goal to a modest amount we have some confidence of achieving within the set time, due to the all-or-nothing system used by Microryza.

 A00 is separated from the rest of mankind by >200 thousand years, but how closely related are different A00 chromosomes? It is necessary to have multiple samples to attempt to answer that question; I think it is quite probable that A00 is not limited to the area of Cameroon where it was discovered, but it probably makes sense to focus on it, since it is most likely to yield additional A00 samples given a sample size of 100.

A full Y-chromosome sequence of an A00 chromosome would also be very useful, since it would allow us to estimate its divergence from the A0-T remainder of mankind more securely.

The $2,500 they are seeking to launch their first field trip seems like a bargain to me.

Criticism of Y-chromosome Adam old age

... has just appeared on the arXiv. This refers to the paper by Mendez et al. announcing the basal clade A00 of the phylogeny and estimating a TMRCA for Y-chromosome Adam of 237-581ka.

The author argues that such an old age is inconsistent with neutral theory, although that assumes no population structure in the origin of modern humans; it may very well be that A00 introgressed into the modern human gene pool via an admixture event from a different African population.

The best evidence for the authors' of the original paper choice of mutation rate is their estimate that the common ancestor of all Eurasians being ~63ky vs. ~39ky using the faster rate. While a date between these two can be probably accommodated, the ~39ky age seems difficult to accept, given that Homo sapiens had arrived in various parts of Eurasia by the mid-40ky's and had been admixing with Neandertals 47-65ky BP; a higher date would also be more in line with age estimates of Eurasian mtDNA macro-haplogroups M and N.

In any case, it's probably a good idea to get a better handle on the mutation rate: Mendez et al. rely on the autosomal rate, adjusting for the Y-chromosome; while the faster rate derives from a single Chinese deep pedigree study.

arXiv:1304.6098 [q-bio.PE]

Timing of ancient human Y lineage depends on the mutation rate: A comment on Mendez et al

Melissa A. Wilson Sayres (Submitted on 22 Apr 2013)

Mendez et al. recently report the identification of a Y chromosome lineage from an African American that is an outgroup to all other known Y haplotypes, and report a time to most recent common ancestor, TMRCA, for human Y lineages that is substantially longer than any previous estimate. The identification of a novel Y haplotype is always exciting, and this haplotype, in particular, is unique in its basal position on the Y haplotype tree. However, at 338 (237-581) thousand years ago, kya, the extremely ancient TMRCA reported by Mendez et al. is inconsistent with the known human fossil record (which estimate the age of anatomically modern humans at 195 +- 5 kya), with estimates from mtDNA (176.6 +- 11.3 kya, and 204.9 (116.8-295.7) kya) and with population genetic theory. The inflated TMRCA can quite easily be attributed to the extremely low Y chromosome mutation rate used by the authors.

Link

Extremely old (237–581 kya) root of human Y-chromosome phylogeny

I had mentioned this research before, and now it has officially been published. There are three things to be excited about this new paper:

First, it forces us to consider the possibility of either (i) archaic admixture in Africa, or (ii) a much more ancient time depth of modern humans than the first fossils from Ethiopia dated to about ~200 thousand years ago.

Second, it underscores the importance of collaboration between academia and regular folk, since it was the combined contributions of academics, genetic genealogists, and the owners of the new A00 basal Y-chromosomes that made this new discovery possible.

And, third, it shows that the extraordinary can be discovered without contacting isolated tribes or seeking human bones in remote regions, but rather through careful scrutiny of large volumes of data for the proverbial needle in the haystack.

The paper developed a model of Y-chromosome mutation based on the estimate of Kong et al. Significantly, though:

If we were to use the higher mutation rate (1.0x10^-9 per base per year6) rather than a realistic range derived from whole-genome sequencing (4.39x10^-9  -   7.07x10^- 9), the estimated TMRCA for the tree incorporating A00 as the basal lineage would be 209 kya, which is only slightly older than current estimates of the TMRCA of mtDNA and the age of the oldest AMH fossil remains. We note, however, that the higher mutation rate produces an estimate for the common ancestor of all non-African Y chromosome haplogroups (C through T) of ~39 kya6 (i.e., versus ~63 kya for the mutation rate used here).

A 39kya common ancestor for Eurasian Y-chromosomes makes no sense, since we now know for sure that by that time, the differentiation of Eurasians was already well on its way and modern humans in remote parts of the Old World have been documented much earlier than that time.

A ~63kya common ancestor, on the other hand, fits nicely with my "two deserts" theory of modern human origins, according to which the ancestors of Eurasians faced an ecological crisis in Arabia when it became much drier post-70kya; that seems like a most opportune time for the major Eurasian bottleneck and the corresponding coalescence of Eurasian Y-chromosomes to a single man. And, while there is no a priori reason for Y chromosomes and mtDNA to behave similarly, the age of the "older" Eurasian ur-mother, haplogroup N at 59 thousand years, with presumably an older ancestor within mtDNA haplogroup L3 founding the Eurasian population.

Also, if modern human-Neandertal admixture had occurred  "most likely 47,000–65,000 years ago", then the expansion of modern Proto-Eurasians within a 70-60kya timeframe north Out-of-Arabia would have brought them in contact with their northern Neandertal neighbors. On the other hand, it would be incredible if modern humans experienced admixture with Neandertals but were still much later a very small population (to allow for the coalescence of their Y-chromosomes to one man ~39kya).


So, in summary, the mutation rate used by the authors seems consistent with what we know about an important calibration point of the human story.

But, who were the people in Africa responsible for the introgression of A00 chromosomes? Mendez et al. used the haplotype of the African American A00 individual and discovered his patrilineal kin among the Mbo of Cameroon, who are Bantu farmers. 

I have observed before that Pygmies and Bushmen represent only a tiny fraction of pre-existing African genetic diversity, the part that had not yet been absorbed into the farmers' expanding population by the time that Africa came to the attention of of modern science. We see traces of Pygmy and Bushman ancestry in some African farmers, and there were probably other groups, no longer extant as distinct ethno-cultural entities, but, nonetheless, surviving as genetic fragments in the genomes of the farmers.

Thus, while it still makes sense to study the surviving hunter-gatherers of Africa who make up perhaps a percent or less of the population of Africa, it may be equally important to study different groups of African farmers who may possess a much richer treasure trove (albeit diluted) of such "Palaeoafrican" ancestry.

Finally:

Although the stochastic nature of the evolutionary process can explain the aforementioned incongruences, the extreme age and rarity of the A00 lineage point to the possibility of a highly structured ancestral population, consistent with recent work on the autosomes.40,41,43,44 This could take the form of long-standing population structure among AMH populations45 or archaic introgression from an archaic form into the ancestors of AMHs.46 Interestingly, the Mbo live less than 800 km away from a Nigerian site known as Iwo Eleru, where human skeletal remains with both archaic and modern features were found and dated to ~13 kya.47 Further surveys in sub- Saharan Africa and in the African Diaspora might uncover more diverged basal lineages, which will help to disentangle some of the complex evolutionary processes that shape patterns of Y chromosome diversity.

AJHG 10.1016/j.ajhg.2013.02.002

An African American Paternal Lineage Adds an Extremely Ancient Root to the Human Y Chromosome Phylogenetic Tree 

Fernando L. Mendez et al.

We report the discovery of an African American Y chromosome that carries the ancestral state of all SNPs that defined the basal portion of the Y chromosome phylogenetic tree. We sequenced ∼240 kb of this chromosome to identify private, derived mutations on this lineage, which we named A00. We then estimated the time to the most recent common ancestor (TMRCA) for the Y tree as 338 thousand years ago (kya) (95% confidence interval = 237–581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils. The extremely ancient age combined with the rarity of the A00 lineage, which we also find at very low frequency in central Africa, point to the importance of considering more complex models for the origin of Y chromosome diversity. These models include ancient population structure and the possibility of archaic introgression of Y chromosomes into anatomically modern humans. The A00 lineage was discovered in a large database of consumer samples of African Americans and has not been identified in traditional hunter-gatherer populations from sub-Saharan Africa. This underscores how the stochastic nature of the genealogical process can affect inference from a single locus and warrants caution during the interpretation of the geographic location of divergent branches of the Y chromosome phylogenetic tree for the elucidation of human origins.

Link

FTDNA draft Y-chromosome phylogeny

A draft of the Y-chromosome phylogeny, including the newly discovered basal A00 clade has been posted by FTDNA. Hopefully some progress can be made in the F portion of the tree, where currently there are subclades F1,F2,F3,G,H, and IJK. Determination of the bifurcation structure within F will doubtlessly be instrumental in informing our understanding of the dispersal of F descendants, which, according to the age of this major Eurasian haplogroup, are closely linked to the Upper Paleolithic event in Eurasia.

Investing in whole-genome sequencing of one individual from each of these clades would be very helpful in determining this structure. Of course, there are already the Complete Genomics data which include haplogroup G and various IJK descendants, so we now need to identify some F1,F2,F3, and H samples and give them the WGS treatment.

A00 at FTDNA2012: history in the making?

I've been following the #FTDNA2012 tag on twitter where Dr. Mike Hammer has been  talking about A00, the new most basal clade of the human Y-chromosome phylogeny. Apparently, 338ky old Y-chromosome ancestor for modern humans, at 98% confidence, with most basal clade found in western Cameroon and in African Americans separated by ~500 years from Cameroonian chromosome.

Root of human Y-chromosome phylogeny is now much older than both mtDNA Eve and first modern human fossils.

Conference attendees feel free to correct/supplement my understanding of what was said.

UPDATE: With respect to the confidence interval, Bonnie Schrack says:

The 338,000 years ago figure was the median (middle) of the confidence interval, which I believe was 95%, and not 98%. The lower limit of the confidence interval was still a bit over 200,000, I think -- that is, still before the time when fossils have been found showing fully anatomically modern features. Mike specifically said that even if the true age of A00 varied by 10 or 20% from the estimate, it would still be before the time when anatomically modern humans are thought to have appeared. I don't remember the upper limit too clearly, but as I recall, it was over 500,000 ybp.

UPDATE II: There is some uncertainty about the level of significance, with different people remembering anything from 90-98%. Some newer information from Tim Janzen:

Michael gave a TMRCA estimate of 338,000 years with a confidence interval range of 246,000 and 563,000 years for the A00/A0 node. He gave a TMRCA estimate of 202,000 years with a confidence interval range of 133,000 to 366,000 years for the A0/R-M269 node.

I guess we will have to wait for the publication to see the exact numbers, but it certainly appears that A00 branched off from the rest of mankind at an age that is much earlier than the next most basal clade (A0).