January 22, 2014

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

22 comments:

MOCKBA said...

After the Khazar / Armenian folly / fiasco, I would be very hard pressed to take yet another shout "they got it all wrong" from Elhaik seriously...

אחיקם גדליהו ישעיהו בן הלל said...
This comment has been removed by the author.
Dienekes said...

Guys, the blog policy is "Use facts and arguments." Whether the Khazar theory is right or wrong (I believe I criticized that inference myself when it came out) is not really relevant to whether this particular piece of work is right or wrong. So, please discuss this paper on its own merits rather than on something irrelevant.

terryt said...

"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".

I think the authors make a basic mistake here. Why is it absolutely essential that the split between A00 and the 'main' Y-DNA line has to have happened in 'anatomically modern Homo sapiens'? The anatomically modern aspect of our genes has nothing at all to do with Y-DNA. It is the product of gene shuffling over the last 2 million years.

MOCKBA said...
This comment has been removed by a blog administrator.
samw said...


Whatever Elhaik has written before, what are we to make of this, from the press release for this latest paper:

http://www.eurekalert.org/pub_releases/2014-01/uos-pi012214.php?
---------
"Dr Elhaik added: "We have shown that the University of Arizona study lacks any scientific merit.

"In fact, their hypothesis creates a sort of 'space-time paradox 'whereby the most ancient individual belonging to Homo sapiens species has not yet been born. If we take the numerical results from previous studies seriously we can conclude that the past may be altered by the mother of 'Adam' deciding not to conceive him in the future, thus, bringing a retroactive end to our species.

"Think of the movie Back to the Future, when Marty was worried that his parents would not meet and as a result he wouldn't be born - it's the same idea. ..."
--------

It's "the same idea" as Back to the Future? Really?

Grognard said...

Or it means there was no out of africa.

It's probably just wrong, because we have found neanderthal hang off of A00 as well and so the idea that A00 came out of africa long after neanderthal existed and then differentiated is just silly.

Dienekes said...

@MOCKBA,

I repeat that we should evaluate the study on its own merits. Certainly external factors might influence our a priori opinion on it (e.g., who wrote it or where it appeared), but ultimately it boils down to the facts and arguments.

Dienekes said...

It's probably just wrong, because we have found neanderthal hang off of A00 as well and so the idea that A00 came out of africa long after neanderthal existed and then differentiated is just silly.


No Neandertal Y chromosomes have ever been published to this is wrong.

Dienekes said...

I think the authors make a basic mistake here. Why is it absolutely essential that the split between A00 and the 'main' Y-DNA line has to have happened in 'anatomically modern Homo sapiens'?

This is true, but the older the basal Y-chromosome split is, the more likely it is to represent a non-modern element. No one would argue that a 30ky split in modern humans happened in non-AMH, but a 350ky split might have, since there were no AMH around then (or they weren't the only ones around )

This may not be an important question in the grand scheme of things, and Y-Adam is just one guy whose Y chromosome got lucky. Still it's interesting to know when/where he might have lived and what he may have been like.

MOCKBA said...

I understand, Dienekes. I just wish you would have warned your readers that researching the authors, and reviews about the authors, may land them in trouble with System Administrators. We have policies against visiting white supremacist websites, and it's mighty unpleasant to violate this rules out of misguided curiosity!

Dienekes said...

>> I just wish you would have warned your readers that researching the authors, and reviews about the authors, may land them in trouble with System Administrators.

"Stay on topic" is the first instruction at the top of the comments window.

Grognard said...

Dienekes - it's just not been released yet. According to one of john hawks's blogs it's in the works and iirc it hangs off of A00.

terryt said...

"Still it's interesting to know when/where he might have lived and what he may have been like".

Absolutely.

Unknown said...

Ok let's start with the abstract:
- The confidence intervals for the new and old estimates overlap - they are not statistically different
- The coalescent time of a single locus can easily predate a speciation event. Anyone with a basic evolutionary genetics background knows this.
- While *on average* the coalescent times of two independent loci with be the same, the variance is large, so there is no reason to expect the point estimates of the coalescence times for the mt and NRY to be the same
- Mendez et al actually gave very similar dates as them using the Cruciani mutation rate if you read the paper and supplemental

I could go on, but I won't, since this paper and its authors are full of it.

Hans said...

«Dienekes - it's just not been released yet. According to one of john hawks's blogs it's in the works and iirc it hangs off of A00.»

I don't find the article. Do you have a link?

Daniel Szelkey said...

Haplogroup I2a1b is at least 10 thousand years old (ancient dna). Perhaps we could assume how old haplogroup A00 is a by seeing how many times older it is than haplogroup I2a1b. However, before 100kya people on average may have matured faster, so in neolithic times most males might have been 30-35 when they had their kids, on average, 100kya they may have been as young as 15 but then again perhaps polygamy may have been more rampant in early hunger gatherers. This would lead to a possibility that most males had fathers at least 35 least older than them. It is impossible to tell whether A00 is 150 kya or 500kya, without ancient dna, and or studies of early stone age polygamy patterns.

terryt said...

"The coalescent time of a single locus can easily predate a speciation event. Anyone with a basic evolutionary genetics background knows this".

Exactly. In fact most seem to believe that just such a single locus event suddenly gave rise to 'modern' humans. That is so unlikely as to be not even worth considering. There was no sudden moment when a group of 'archaic' humans woke up one morning and found they were suddenly 'modern' humans. As a result there is no need at all to assume the earliest surviving Y-DNA, or even mt-DNA, were actually members of the first population of modern humans (whatever that term means).

Dienekes said...

I repeat that there are no Neandertal Y-chromosomes published (or even blogged about or otherwise leaked).

Debbie Kennett said...

Joe Pickrell has done a nice blog post correcting the misconception in this paper that Y-chromosomal Adam has to coincide with anatomically modern humans:

http://jkplab.org/2014/01/26/y-chromosome-adam-may-not-have-been-human/

One of the authors of the paper has replied in the comments section.

terryt said...

"Joe Pickrell has done a nice blog post correcting the misconception in this paper that Y-chromosomal Adam has to coincide with anatomically modern humans"

Thanks. Quote:

"The implicit assumption here (the reason Elhaik et al. find the numbers “extraordinarily early” and “astonishing”) is that the individual carrying the most recent common ancestor of all human Y chromosomes (AKA “Adam”) should be an anatomically modern human. Amusingly, Elhaik et al. argue that to claim otherwise is analogous to claiming you have a unicorn in your backyard. But there is simply no reason that “Adam” must be a human. At the top of this post I’ve put a figure showing a hypothetical Y-chromosome genealogy superimposed on a hypothetical human phylogeny. In this (of course hypothetical) example, “Adam” existed well before the diversification of modern humans; this type of scenario is perfectly compatible with basic population genetic theory. From the point of view of population genetics, there is absolutely no reason that the common ancestor of all human Y chromosomes must have existed in an individual that we would identify as 'human'".

That fits exactly with what I said in my first comment here.

andrew said...

"From the point of view of population genetics, there is absolutely no reason that the common ancestor of all human Y chromosomes must have existed in an individual that we would identify as 'human'"

But, there must be some modern human who is the earliest modern human man to have human Y chromosomes that are ancestral to all modern human Y chromosomes if these kind of human Y chromosomes are found in any modern humans.

Generally, we are concerned with the age of TMRCA (the most recent common ancestor) of people having a genetic trait, and not of the first person to have that genetic trait (which is unknowable). Pickrell is playing games by conflating the TMCRA concept with the non-equivalent "first man to have this genetic trait" African Adam concept. An African Adam with Y-DNA A00 very likely was an archaic hominin rather than an AMH (who knows by how many generations and at that point definitional issues make the point a fuzzy one). But, TMCRA estimates between the runner up Y-DNA A lineage and A00 can inform our estimates of when modern humans started to have A00 and how.

The first modern human to have this Y-DNA A00 would have had male descendants whose Y-DNA over the generations would begin to mutate at a determinable rate per generation. What seemed to make A00 so notable is that there is no evidence in modern populations of a lot of intermediate steps on the mutation trail between A00 and the next most basal modern human Y-DNA A lineages. There seemed to be more mutations distinguishing A00 from all other modern humans than between any other known two mutation number adjacent Y-DNA lineages in modern humans. Something it seemed, had killed off all but a handful of about two thousand generations of male descendants of the bearers of A00 who went on to have descendants who are patriline ancestors of all other modern human men.

Is that possible? Yes. Is it particularly probable? No.

In that scenario, introgression of A00 from archaic humans who are already known to have introgressed autosomal DNA into Africans within the last 20kya or so in the same general geographic region would seem more plausible.

But, the new study says that the gap in age of TMCRA of A00 and the next most basal Y-DNA hg A clade was much smaller by more than an order of magnitude than earlier claimed due to methodological mistakes by the first research group. Thus, now, A00 looks only a little bit older than the runner up and A00 as a basal modern human lineage rather than as an archaic introgression, seems more plausible.