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Thread: Explanations for varying rates of Y-Chromosome mutation

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    Explanations for varying rates of Y-Chromosome mutation

    Most of us have seen how certain male lines mutate more/less than others (STR and SNP, even over thousands of years). What are the proposed reasons for this?

    I've heard one theory that deals with endogamy. When a male line procreates within a small population over an extended period of time, this can decrease the rate of mutation. Perhaps it is because there is a limited pool of X-chromosomes with which the Y-chromosome interacts, thereby decreasing the chance of X-to-Y gene conversion (or some other mutative effect caused by the presence of a "foreign" X chromosome that the Y-chromosome has never interacted with before).

    I think this theory attempts to explain the observation that "older" male lines seem to be more stable than "newer" (or more successful) lines. Why when a male line stays in the same place does it mutate less than a line that moves around? The easiest example is R-L151, which has expanded rapidly in the last 4,500 years in Europe and North America (and appears to have supplanted the G haplogroup found in my ancient DNA samples). And my understanding is (and maybe this is all anecdotal) that downstream branches have been observed to mutate relatively quickly.

    After thinking about this theory for a while, I've come up with a related theory that attributes the aforementioned observation to evolution.

    Under this theory, the rate does not actually vary. Lines with large numbers of mutations simply have not had enough time for evolutionary pressures to select them out of the gene pool. Thus, when a male line is successful in the modern era, we observe more mutations. But if we took samples in 10,000 years, we'd find that the surviving lines are those that experienced fewer mutations (since mutations are more likely to result in adverse rather than beneficial effects).

    Curious to hear others' thoughts.

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    I have wondered the same thing... it cannot be a coincidence that basically all of the more "Basal" y-dna haplogroups are found in populations that are:

    a) Genetically "isolated"/endogamous (at least relative to other human groups), and
    b) Spatially "non-mobile", in the sense of having occupied the same ecological niche for many millenia (which would presumably decelerate evolutionary pressure on all portions of the genome, including the Y chromosome)

    Why do Khoisan still overwhelmingly carry y-dna A? Why didn't this mutate much over 100k (or 200k or 300k) years? And the same for y-dna B in Central Africa.

    The Aeta carry P*, P1, and P2. So obviously their y-dna mutated pretty far beyond y-dna "Adam", before suddenly "freezing" in time, with shockingly few downstream mutations dated beyond 30kya or so (around the TMCRA of P*, P1 etc). Is this evidence of an extensive "early" history of movement and admixture with other groups (ie, during first OOA wave), before ultimate isolation/endogamy beginning in the Mesolithic? And the same thing for K2 re: Sahulians?

    Socotra islanders have been reported to harbor 70%+ basal J*, which is dated to 48kya. Again, are they largely a relic population from the "Iberomaurusian" days who just shifted to Semitic languages during the BA? (I think Socotrans may be one of the last un-sequenced modern populations for which autosomal data can still teach us about human origins)

    OTOH the most "downstream" of the major y-dna clades tend to be held by groups that show precisely the opposite pattern-- large-scale movements and admixture with radically different outgroups taking place right down to the common era: Indo-Europeans (R1) and Turkics (N, Q).

    Native Americans would be an interesting case study since they obviously descend from quite mobile, exogamous groups well into the Mesolithic, but following the Bering Strait crossing 15kya, the spatial mobility continued while potential outbreeding was heavily restricted by the population bottleneck. In other words, the one element continued but the other element (exogamy) was substantially controlled for.

    It would be nice to see higher resolution mapping of Native American y-dna--just how many "downstream" nodes are there for Native Q and C? Of course because of European sex bias you'd need to sequence 5-10 self-identified Natives to maybe get 1 genuine Native y-lineage but it would be highly interesting to see the results...

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    This question really depends on the time frame of discussion. For very old branches (over 2,500 years old), there are waves of YDNA replacement via conquest and spread of new technology (farming, metalwork). The patterns vary radically depending on geography.

    Once you get below 2,500 years and getting closer to the genealogical time frame, we are now beginning to understand the mechanics of why mutation rates vary a lot. There are several factors: 1) random statistical variation is the primary cause. The smaller your sample size, the less accurate the estimates based on limited data. For instance years per YSNP are now being reported in the 30 to 60 year range vs. the 130 year range. Also, it depends on your criteria for rejecting YSNP branches that are found in complex areas or insert/deletes; 2) The geography being analyzed plays a significant role as sample size of population varies by several factors. China and the Far East are by far lowest penetration of testing (percent of population tested); The US and other former English colonies are by far the most tested due to higher interest in attempting to make connections back to their European ancestors; 3) There is another major factor - how prolific is your line. Being the conquerors vs. the conquered make a huge difference in the numbers of living testers. L226 which is 1,500 years old has over 1,000 testers at 37 or more markers. L96 which is around 2,500 years old, have only ten known testers; 4) ability to thrive on unlimited access to land (at the expense of the the native population - colonization). My Casey line arrived in South Carolina around 1750 after the massive crop failures caused by harsh weather conditions. Even though Casey ranks in the top 50 Irish surnames in Ireland today, there are more Casey with ties to early South Carolina tested today than all the Caseys that still reside in Ireland today; 5) every geography has its own individual story to tell on how YDNA evolved (people residing between large powerful countries tend to have more blended YDNA and have more constant small waves of influx of new YDNA).

    Only testing of yet larger quantities of archaic remains will shed more light on how YDNA spread across the world. Sample size = accuracy. I do not think the isolation or mobility play much of role as does the massive spread of technology and conquest. During the last ice age to hit Europe, the population of northern Europe fell to zero as no hunter gathers could survive living on top of several miles of ice. However, a small percentage survived via mobility by just walking south to avoid freezing and starving. Until archaic remains were analyzed in great detail, it was believed that R1b were the first to return after the last ice age. That theory was dismissed as no R1b was found for the first few thousand years after the last Ice Age in Europe. R1b from southern Russian allowed those with bronze and horses to almost completely replace the E haplogroup that was at least 25 % of early western Europe after the last ice age. The haplogroup Q was found in significant quantities in Germany are almost entirely replaced. The Vikings replaced around ten percent of the YDNA in Ireland, the Celtic culture allowed more mobility due to common languages and customs. The Ango-Saxon (and Danish) invasion of England replaced ten percent or more of the YDNA in England. There are just constant influxes of new YDNA on a continual basis. Even due to new economic motivations, the number of people claiming Irish ancestry lives in England is about the same as living in Ireland. For every person living in Ireland today, there are ten people living in the United States. Even Canada, Australia and New Zealand have more Irish people living in these former British colonies than live in present day Ireland. So colonization plays a major role in the last 300 years. The middle east was dominated by the Ottoman Empire for centuries - this political control almost certainly had a major effort for ease of YDNA flow. The Irish were recruited by the English to fight Prussians and others. Many of these Irish soldiers were granted land in Poland and Lithuania (where they celebrate St. Patricks Day even today). So there are many smaller waves that are constant.
    Last edited by RobertCasey; 06-11-2018 at 05:14 PM.

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    Is my understanding incorrect or OP? I thought that a person having basal P that isn't Q or R is still having the same number of mutations as happens every generation, just that the P*(xQR) isn't as successful as the one whose got the Q or R mutations. Nobody's is "frozen in time". All the assignments in the charts are retrospective. Number of mutations should still be the same for both P*(xQR) and those with Q and R, just that a group of P* became uber successful and so a subset of P* has an event more recent common ancestor than rest of the P*.

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    Quote Originally Posted by redifflal View Post
    Is my understanding incorrect or OP? I thought that a person having basal P that isn't Q or R is still having the same number of mutations as happens every generation, just that the P*(xQR) isn't as successful as the one whose got the Q or R mutations. Nobody's is "frozen in time". All the assignments in the charts are retrospective. Number of mutations should still be the same for both P*(xQR) and those with Q and R, just that a group of P* became uber successful and so a subset of P* has an event more recent common ancestor than rest of the P*.
    I think we're talking about the same thing, which is why I was using "air quotes" to refer to "newer" and "older" lines. My experience has been that when you look at two branches after they diverged, the more successful branch will have, on average, a larger number of subsequent SNPs. Obviously, they're the same age. EDIT: So while basal P kits should have the same number of mutations as Q or R, they don't.

    Maybe I'm wrong about that. That has been my general observation, and I recall reading somewhere that kits downstream of R-L21 have more subsequent SNPs on average than the rest of the kits downstream of R-P312, even though we know for a fact that R-P312 is older than R-L21.

    Quote Originally Posted by RobertCasey View Post
    I do not think the isolation or mobility play much of role as does the massive spread of technology and conquest.
    Isn't one really just a proxy for the other? Meaning haplogroups that have been extremely mobile, like R1a and R1b, were extremely mobile due to technology and conquest.

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    So only way I can think of that mutation rate is faster in a more prolific/"recent"(lier defined mrca) line than its undefined brother is that the more prolific line besides being more prolific is also reproducing at an earlier age. Example if I am P*(xQR) and my brother is the first R*, and I'm having 1-2 sons while my brother is having 16 sons, and then my sons continue having sons at 25-30 years age while my nephews are having sons maybe 14-15 years old? Maybe prolific-ness has something to do with age at which viable children can be produced, in which case there would end up being more mutations in a person downstream of a R1a than a P*.

    This is like a macro level version of finding a distant uncle (your parents third cousin or something) that's actually younger than you. Pretty comical actually in joint family settings to call them, especially if girls, as auntie lol, because technically you're not wrong.

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    Quote Originally Posted by redifflal View Post
    So only way I can think of that mutation rate is faster in a more prolific/"recent"(lier defined mrca) line than its undefined brother is that the more prolific line besides being more prolific is also reproducing at an earlier age. Example if I am P*(xQR) and my brother is the first R*, and I'm having 1-2 sons while my brother is having 16 sons, and then my sons continue having sons at 25-30 years age while my nephews are having sons maybe 14-15 years old? Maybe prolific-ness has something to do with age at which viable children can be produced, in which case there would end up being more mutations in a person downstream of a R1a than a P*.

    This is like a macro level version of finding a distant uncle (your parents third cousin or something) that's actually younger than you. Pretty comical actually in joint family settings to call them, especially if girls, as auntie lol, because technically you're not wrong.
    I like this theory...a lot.

    More prolific = more desirable/greater fitness = earlier lifetime procreation = more generations = more mutations.

    This would explain why we seem to see one SNP rate per generation across the population in the present, but another across the population over time. And it definitely meshes with the idea that this coincides with pillaging/conquest.

    On a side note, makes me feel better that my slightly higher SNP rate might not mean that I'm sitting on a line that's just waiting to be killed off

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    For more prolific lines - your current sample size is much greater, so you currently observe higher mutation rates. The mutation rates themselves do not change except for random statistical variation for smaller sample sizes. If you are finding TMRCA for very old haplogroups - over 2,500 years, the observed rates are much less since in that time frame, over 99 % of male lines have become extinct just due to random statistical variation. Between, 1,000 years and 2,500 years, for prolific lines (like L226 that is 1,500 years, has 125 Big Y tests and over 1,000 testers with 37 or more markers), I recently had to shift from 70 years per YSNP to 60 years per YSNP from my previous analysis when only there was 35 % less data available. There are a few surname clusters (people who share the same ancestor who first used surnames around 1,000 years ago - Ireland where clan names were first used) that have 100 to 200 testers for just one surname cluster. These people are getting one YSNP per generation (or every 30 years).

    For L226, we also make extensive usage of YSNPs in complex areas and inserts/deletes. If these are removed, our YSNP mutation rate drops by 20 to 40 % depending on which path of the L226 haplotree you look at. YFULL uses 130 years per YSNP as they are estimating older haplogroups and do not allow the usage of YSNPs in complex areas or any inserts/deletes. As a L226 admin, I use 60 years per YSNP for my current sample size. Once my sample size increases another 50 to 100 %, this will surely drop to 50 years per YSNP.

    I know that these adjustments are required due to surname cluster dating. If I do not lower the years per YSNP mutation, YSNP branches become much younger than surname cluster dates. Estimating dates based on surname are much more reliable than YSNPs, so I adjust the YSNP branch mutation rate to minimize the over running of the surname cluster dating. We now have around 25 surname clusters under L226 which helps calibrate the years per YSNP mutation value.

    Another huge adjustment will be made when longer read lengths become available at reasonable costs in the next five to ten years. The YElite2.1 with long read can reveal twice as many base pairs as the Big Y tests. The normal YElite2.1 shows around 30 % more base pairs. So when these tests become the normal due to price reductions, we will see a quick 30 to 100 % increase in YSNP mutation rates.
    Last edited by RobertCasey; 06-12-2018 at 01:25 PM.

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    Quote Originally Posted by RobertCasey View Post
    For more prolific lines - your current sample size is much greater, so you currently observe higher mutation rates. The mutation rates themselves do not change except for random statistical variation for smaller sample sizes. If you are finding TMRCA for very old haplogroups - over 2,500 years, the observed rates are much less since in that time frame, over 99 % of male lines have become extinct just due to random statistical variation.
    I don't see how greater sample size = higher observed mutation rates. We should see a regression toward the mean. As you point out, we'll see random statistical variation for smaller sample sizes, but shouldn't they be scattered equally between high and low outliers? I take it you agree they are not.

    What I like about the "younger-to-procreate" theory is that it also explains why I have not been seeing low outliers, only high outliers, in large samples that represent a long historical period. Before the Big Y platform change, I could see +500 men downstream from U152. It seemed like there was a floor at 17-18 novel SNPs, but the mode was 19-22. Only a handful of kits had fewer than 17 novel SNPs. Some men had 28-32, but no one had 10.

    "Younger-to-procreate" would explain it like this. Some lines went through prolonged periods where the average age of procreation was 20, while the average age for all humans is closer to 30. But no lines go through prolonged periods where the average age of procreation was 40 or older. That just doesn't happen. This would be particularly true in a place like the British Isles, particularly Ireland, where Bronze Age men totally displaced the Neolithic settlers.

    I'm interested in surname clustering, but I wonder, how do you ensure reliability? Some surnames go back to the 11th-13th century, some go back to the 17th century. Are you accounting for this or giving an average date for surname adoption? I'm also interested in the impact of higher resolution testing. Is there a case to be made that large samples skew toward newer tests, and newer tests pick up more SNPs?

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    If the younger to procreate theory does hold water, it would be interesting to understand how that sustains over time. It would have to be a cultural context that allows for such a phenomenon beyond just availability of resources. It might even have very little to do with the so called dominance of the male line and more to do with the resident female population's cooperativity as was noted in the other thread recently about grandma power
    https://www.npr.org/sections/goatsan...ntent=20180607

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