Friday, January 14, 2022

Study: Mutation Rate Variability across Human Y-Chromosome Haplogroups

 A small post about a relevant study that was published in 2020.

Qiliang Ding, Ya Hu, Amnon Koren, Andrew G Clark, Mutation Rate Variability across Human Y-Chromosome Haplogroups, Molecular Biology and Evolution, Volume 38, Issue 3, March 2021, Pages 1000–1005, https://doi.org/10.1093/molbev/msaa268

A common assumption in dating patrilineal events using Y-chromosome sequencing data is that the Y-chromosome mutation rate is invariant across haplogroups. Previous studies revealed interhaplogroup heterogeneity in phylogenetic branch length. Whether this heterogeneity is caused by interhaplogroup mutation rate variation or nongenetic confounders remains unknown. Here, we analyzed whole-genome sequences from cultured cells derived from >1,700 males. We confirmed the presence of branch length heterogeneity. We demonstrate that sex-chromosome mutations that appear within cell lines, which likely occurred somatically or in vitro (and are thus not influenced by nongenetic confounders) are informative for germline mutational processes. Using within-cell-line mutations, we computed a relative Y-chromosome somatic mutation rate, and uncovered substantial variation (up to 83.3%) in this proxy for germline mutation rate among haplogroups. This rate positively correlates with phylogenetic branch length, indicating that interhaplogroup mutation rate variation is a likely cause of branch length heterogeneity.

From the supplement 

For the Xue et al. (2009) rate, we identified the following haplogroups having significantly lower relative somatic mutation rate: E1b, R1a, and R1b. For these haplogroups, their actual mutation rate may be lower than the Xue et al. (2009) rate, and thus divergence times may be underestimated.

 

Branch length Y haplo
R1b, E1b, and R1a have the shortest branch lengths

 This is YFull's age calculation method:

The second formula uses an assumed mutation rate of 144.41 years (0.8178*10-9, which is the average of the mutation rates of the ancient Anzick-1 sample and of a group of known genealogies, and an assumed age of 60 years for living providers of YFull samples.

Y-Full has the most accurate Y haplogroup tree due to the largest numbers of SNPs utilized, however, they also use a common mutation rate across haplogroups. 

Summary: 

R1b, E1b & R1a Y-chromosomes have lower somatic mutation rates than others due to shorter branch lengths, and therefore expected TMRCA & formation dates of these clades and subclades are most likely underestimated. YFull uses a common mutation rate across Y Haplogroups, therefore its TMRCA and formation dates for R1b, E1b, and R1a (and subclades) are underestimated.






17 comments:

  1. Got to keep this in mind when quoting formation dates for R1a Z93, L657 etc obtained from Yfull.

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  2. Do we have any haxamanish dynasty era genetic profile of Persians?

    Aren't ancient Iranians populations Anatolian rich + IranN?

    Do we have Elamite samples?

    How does the Elamite and Persians relate genetically?

    I was looking into the map and it seems like Kurds occupy the elamite lands whereas Persians are East (North and South) of the zargos.

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  3. I wonder if anyone has looked into it but Islamic Turkic rule of India between 1200-1757ce saw Persian as a court language instead of their native Turkic language.

    I find a similar parallel with pontic-Steppe Scythians who appear to be Europid but spoke Iranian language.

    I wonder if it was their native language to begin with.

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  4. From iran we have hajji firuz chalcolithic, hajji firuz IA, seh Gabi Late Neolithic, seh Gabi chalc, tepe hissar chalcolithic, shahr sokhta

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  5. Which clad are the Scythian R1a? is it any way related to Indian L657 and Iranian m198 m269

    300-200bce samara oblast Scythian culture haplogroup detected was R1a1a1b2a2a .....

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  6. @AshishKaull

    I know that western steppe and eastern steppe had 2 different haplogroups. Western steppe had European while eastern steppe had Z93. This goes to show that language and culture can spread in other ways besides male driven mediation. Not saying it was female mediated as thats not possible.

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    Replies
    1. Thanks.

      What role did Taxila played? What language was used as a medium of instruction etc.

      Delete
  7. If I am not wrong Greek and Aramaic were the languages used for ashokan rock edicts in North Western India ~250bce

    I have been looking into what was spoken in north western India but there is no clarity like we have Pali Maghadi and ardh-Maghadi in Eastern India.


    Gandhari Prakrit was spoken around Afghanistan but still drawing a blank for Punjab and Sindh.

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  8. If oral tradition is anything to go by then Punjab and Sindh were homeland of Sanskrit speakers. Even the Kushans and Northern+Western kshatraps who ruled in these regions patronized Sanskrit.

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  9. Old #Persian Text : 02

    /tuvam kā haya aparam imām dipi[m] patiparsāha taya manā kartam varnavatām θuvām mātaya dra[uga]m maniyāha/


    On what basis have linguists labelled this language old Persian and not Sanskrit? Why not a western dialect of Sanskrit?

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  10. There was a period of severe draught around 2200bce. Vritra slaying and freeing up of rivers myth may be related to this event.


    No rain for decades and then came the thunderer Indra with his thunderbolt and returned life to the imprisoned/dying rivers.

    Here is an interesting mention in Rig Veda 4.18.4

    What strange act shall he do, he whom his Mother bore for a thousand months and many autumns?
    No peer hath he among those born already, nor among those who shall be born hereafter.

    or

    “Aditi speaks: What irregular act has he committed whom (I, his mother), bore for a thousand months and for many years? there is no analogy between him and those who have been or will be born.”

    Though in older Mandala Vritra slaying is related to Agni, I guess.

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  11. @Anonymous

    Unlikely. Those languages come from parkrit. Further west you have gandhari parkrit as well.

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  12. Can any AMT proponent explain to me how come steppe ancestry enter Greece and India around the same time yet language already appears too diverged?

    It's equally impossible to think that the steppe migrants spoke different dialects of steppe language.

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  13. Really interesting !

    It would be interesting to look at the branch lengths of the subclades as well.

    For example E1b and O2a2 have a large spread/tail. What does this mean? Was the branch length large and did it go through a bottleneck with a chance survival of people who happened to have shorter branch length ?

    r2a, L1a spread seem clipped, does that mean its under sampled?

    Would be interesting to see branch lengths of R1a subclades

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  14. A new paper about the population of Britannia. It seems that a new wave arrived at early 1st millennium BCE, bringing of what seems to be the Celts (now this agrees with archeological record). https://www.nature.com/articles/s41586-021-04287-4

    So, the arrival of people from the Steppes in the 3rd millenium may seem less likely to be related to PIE.

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  15. https://www.brownpundits.com/2022/01/18/can-linguistics-prove-amt-reject-oit/#more-16389

    A must read HUGE article dissecting the linguistic case for indo aryan languages with more references than you will ever need.

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  16. I was thinking, if r1a mutation rates are slower, that means L657 would be older. If L657 is dated to sometime around 3100 BCE, could the dispersal and dominance of L657 have to do with the post-Mahabharata situation? If anyone knows about the Mahabharat please tell me what you think about this.

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