May 14, 2011

Let the Y-STR mutation wars begin!

This should strictly go to the new ESHG abstracts post, but I am sure it will spark a lot of interest, so I am posting it separately. I recently noticed how Y-STR age estimates are dependent on the choice of Y-STRs used, so it will be very interesting to see what Busby and Capelli have come up with.

It is certainly a very good thing to reignite the debate, even though I do believe that Y-SNP based dating in the age of whole genome sequencing will solve many dating problems, especially for old clades of the tree. I have argued at length why the evolutionary mutation rate is wrong, but the more serious problem is the fact that different sets of Y-STRs lead to different age estimates (with slower-mutating ones producing much older ages than fast-mutating ones).

Microsatellite choice and Y chromosome variation: attempting to select the best STRs to date human Y chromosome lineages
G. B. J. Busby, C. Capelli
Recently the debate on the origins of the major European Y chromosome haplogroup R-M269 has reignited, and opinion has moved away from Paleolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. We investigate the young, STR-based Time to the Most Recent Common Ancestor estimates proposed so far for R-M269 related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates. We further expand our analysis to include a worldwide dataset of over 60 STRs which differ in their molecular attributes. This analysis shows that by taking into account the intrinsic molecular characteristics of Y chromosome STRs, one can arrive at a more reliable estimate for the age of Y chromosome lineages. Subsequently, we suggest that most STR-based Y chromosome dates are likely to be underestimates due to the molecular characteristics of the markers commonly used, such as their mutation rate and the range of potential alleles that STR can take, which potentially leads to a loss of time-linearity. As a consequence, we update the STR-based age of important nodes in the Y chromosome tree, showing that credible estimates for the age of lineages can be made once these STR characteristics are taken into consideration. Finally we show that the STRs that are most commonly used to explore deep ancestry are not able to uncover ancient relationships, and we propose a set of STRs that should be used in these cases.


Anatole Klyosov said...

>We investigate the young, STR-based Time to the Most Recent Common Ancestor estimates ... and find evidence for an appreciable effect of microsatellite choice on age estimates.

Here we go again...

There is not and will be no "war on mutations". The issue is solved long ago. There is no "evidence" for any appreciable effect on "age estimates". There are folks, though, who do not know how to examine and verify mutation rate constants based on experimental data, how to separate DNA-lineages, how to count mutations, and how to translate them to time spans to common ancestors.

Anatole Klyosov

McG said...

I recently posted the following entry at DNA Forums:

My studies reveal that variance is a poor model for the Y STR mutational process. Almost all non multi copy markers have greater than 95% of their values as +/-1 of the modal. If we also consider that fully up to 5% of all mutations are multi-step, This implies that most dys loci provide low variance and saturate quickly. This seems consistent with what the authors are saying?

jeanlohizun said...

Dr.Anatole Klyosov

I wonder why you seem so quick to try to discredit the work done by Dr.G.B.B.Busby and Dr.C.Capelli, when you haven't done much work yourself. How can you say that you have done studies on mutation rates, when the only two papers you wrote about mutations rates were partly done off samples from FTDNA projects? Had you had any knowledge of Basques haplogroups you would have seem something is off in the Basque DNA Project you used to prove your so called theory; starting with the fact that most of the samples come from New World people who claim Basque Ancestry, not actual Basques. So if your sample was already flawed then imagine your results. But I guess it is cooler to say that Basques aren't the descendants of those people who painted the murals in the Caves of Altamira, or to claim they were descendants of Turkish speakers. Even though, if Haplogroup R1b1b2 was indeed of recent West Asian origin, that still would leave half of their ancestry (The Maternal one, mt-DNA Hgs) as being of mostly pre-farming European ancestry, so yes they are still the descendants of those people who encounter Neanderthals and did the beautiful paintings in those caves. It is sad that a Doctor like you seems to ignore those facts, or the archeological record (Which shows continued inhabitance since the Aurignacian period). So what makes you think that finding the TMRCA of a sample (Basque DNA Project members) that is already lacking diversity, as they are a subset of actual Basques, gives the actual time when the Basques first arrived to Europe? The other thing is if you were to check Haplogroups frequencies for Basques 1400 ybp (Alzualde et al.2007), and now, you would see that their haplogroup profile hasn't change at all. So how can one assume exponential growth of populations that would bring about founders effect, when Basques in 600 AD were 85.19% R1, including 7.41% R-M153, and the rest was I-M170 at 14.81%. If exponential population growth and drift took place, it most likely happened recently as you claimed, yet their haplogroups composition hasn't really changed that much is the past 1400 years. So I ask you sir, did you take the time to think about the representativeness of your samples as Basques, or about the fact that aDNA studies done on Basques have revealed a different picture from what you concluded in your studies.

eurologist said...

we suggest that most STR-based Y chromosome dates are likely to be underestimates

I am happy to see that, since older dates than what has been published recently in many cases make much more sense (e.g., when looking at the archeological record or autosomal DNA).

Looking forward to something more quantitative.

Anonymous said...

sire kylosove you made very interesting and milestone works however you failed in your logic of connecting languages with hg's since most of old world languages should be connected with neolithic autosomal components and not with paleolithic hg'S

how can african negroid R1b+european caucasoid r1b be turkic when turkic is 2000 years old, connected(as other altaic branches)with mongoloid race and there is no mongoloid input in africa or europe

altaic hg is C3c simply because it was the most present hg around the lake baykal area(wich is assumed to the homeland of proto altaic)
the affinity of caucasoid indo-european+afrasan+kartvelian(nostratic)with uralic+altaic is not genetical(as altaics+uralics are connected with the mongoloid type wich is way more distant to caucasoid than negroid does)but a result of sprachbund+loanwords(into uralic+altaic)from peacefully and naturally expanding (into central asia)caucasoid indo-european farmers+herders+craftsmen+religious leaders+poets
It was very recently(starting around 8-10 th centuries)that unnatural, warfare type invasions of altaic and uralic folks(turks,mongols,magyars)did bring altaic+uralic languages into central+western asia&europe(much like a language shift with no racial,cultural,genetical input from those uralic and altaic hordes)
the original huns were yenisseian(with iranic exonym hun=saddle)[bases on onomastics and some attested words]while european huns were mostly an amalgamation of slaves and germans(again based on onomastics and some attested words)please see the paper below of the historian and linguist xavier tremblay who proves,through study of onomastics and attested words, that xiongnus were iranian while asian huns were yenisseians

The affinity between IE and uralic/altaic is due to a creolisation between native mongoloid uralics and altaics retaining their original grammar with an indo-european lexicon from the expanding indo-europeans.

Genetical affinity can only be established between languages with close grammars and connected with same racial stock(in this case proto IE+proto afrasan+proto kartvelian)

mike said...

Hi Dienekes-The new Capelli and Busby approach is almost certainly the same as that used on the very recent paper on Africa that Capelli also is co-author of. There is a dating section of that paper (a PDF of which is available on the internet) that describes an approach that closely resembles the abstract for the new Capeli and Busby paper you have drawn our attention to.