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Thread: Interesting P312 Facts

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    Interesting P312 Facts

    I was curious the other day and while browsing YFull's tree under P312, I noticed some interesting facts.

    There are currently only 7 snps directly below U152. This includes U152*. L2 of course is the largest snp just below U152.
    Below L21 there are only 4 snps, this includes L21*. DF13 is the largest with 24 snps at the next lower level.
    What really stood out was that there are currently 22 snps just below DF27, including DF27*. If Yfull counted ZZ12 as Alex does on his tree, then 18 snps would be just below ZZ12, leaving four outside ZZ12, one of these Z195/Z196, which is the equivalent of L2 and DF13.

    So at first glance, one would make the observation that DF27 has a much wider and quicker spread than the other two large P312 clades. Any thoughts?

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    An incredibly large number of extinctions across all Haplogroups.

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    Quote Originally Posted by Webb View Post
    I was curious the other day and while browsing YFull's tree under P312, I noticed some interesting facts.

    There are currently only 7 snps directly below U152. This includes U152*. L2 of course is the largest snp just below U152.
    Below L21 there are only 4 snps, this includes L21*. DF13 is the largest with 24 snps at the next lower level.
    What really stood out was that there are currently 22 snps just below DF27, including DF27*. If Yfull counted ZZ12 as Alex does on his tree, then 18 snps would be just below ZZ12, leaving four outside ZZ12, one of these Z195/Z196, which is the equivalent of L2 and DF13.

    So at first glance, one would make the observation that DF27 has a much wider and quicker spread than the other two large P312 clades. Any thoughts?
    In general, the tree exhibits a large amount of variation in both the number of branches per node and the number of phylogenetically equivalent SNPs per node - much greater variation than would be expected from single, randomly distributed SNPs. Also, there are generally more branches per node than would be expected if SNPs are randomly distributed at a rate of 1 per ~144 years. Population growth bursts and bottlenecks may account for some portion of the variation, but they are not able to account for all of it.

    The only explanation that is able to statistically make sense of this is if SNPs sometimes occur in runs - in other words, an uneven pace of SNP mutations. Sometimes the gap between SNPs is much greater than ~144 years, and at other times there are many more than a just a single SNP within ~144 years. When the SNPs do occur, they sometimes occur in bursts of not just 1 or 2, but as many as 10 or more.

    Below ZZ12, there was probably a stretch of time significantly greater than ~144 years during which no detectable SNPs occurred.

    This wide variation in the rate of SNPs can be easily seen in parallel branches that, by definition, must be the same age. One branch may contain 20 SNPs while its sibling branch contains only 5.
    Last edited by miiser; 03-29-2016 at 10:58 PM.

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    We need a lot of high quality P312 ancient specimens with high resolution Y-DNA testing results and reliable radiocarbon dating from whenever it really first appeared and 4,200 years ago or whenever the SNPs 1-step downstream from P312 first appeared. It won't be until then that we know whose hypothesis for the runs of SNPs is correct. Rathlin1 was a high quality specimen and was radiocarbon dated to 2026–1885 BC (3976-3835 ybp) and is positive for DF21 which is estimated to have formed 4300 ybp. Bell Beaker Quedlinburg [I0806/QLB 28] is radiocarbon dated from 2296-2206 BC and is P312+ but I don't think the quality was good enough for high resolution results. So there still hasn't been any high quality P312 specimens with reliable radiocarbon dating from close to the period that the SNPs 1-step downstream from P312 first appeared.
    Last edited by ArmandoR1b; 03-30-2016 at 12:58 AM.

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    Quote Originally Posted by miiser View Post
    The only explanation that is able to statistically make sense of this is if SNPs sometimes occur in runs - in other words, an uneven pace of SNP mutations. Sometimes the gap between SNPs is much greater than ~144 years, and at other times there are many more than a just a single SNP within ~144 years. When the SNPs do occur, they sometimes occur in bursts of not just 1 or 2, but as many as 10 or more.
    Is it possible that DF27 diversified so quickly due to natural selection caused by the Iberian climate? As opposed to Central/NW Europe whose client might have better reflected the northern portion of the Pontic Caspian steppe? The 45th parallel appears to be a natural dividing line for red hair frequency, for example-- much lower than the U106 & L21 branches for instance. Obviously y-dna does not tell the whole story, but....


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    I mentioned ZZ12 as a caveat because one well placed snp can change the look of an entire tree.

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    Quote Originally Posted by Webb View Post
    I mentioned ZZ12 as a caveat because one well placed snp can change the look of an entire tree.
    Alex's tree has a few more branches than YFull, simply because his database is larger and so he's seen branches that YFull hasn't yet seen. The number of testers who participate in YFull is pretty small. And I think Alex is willing to take the time to look at SNPs that YFull and others filter out. But Alex's tree has a large enough sample size that I think it's likely he's discovered well over 90% of branches older than 1000 years, approaching 100%. I don't expect we'll see many additional splits in old haplogroups as more samples are added to the tree. I think the structure that we see in Alex's tree is pretty close to the "true" final structure of the tree for extant lineages. And this structure is unmistakably indicative of an irregular rate of SNP distribution. Single, randomly distributed SNPs just aren't capable of producing the tree structure that we have.

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    Quote Originally Posted by ArmandoR1b View Post
    We need a lot of high quality P312 ancient specimens with high resolution Y-DNA testing results and reliable radiocarbon dating from whenever it really first appeared and 4,200 years ago or whenever the SNPs 1-step downstream from P312 first appeared. It won't be until then that we know whose hypothesis for the runs of SNPs is correct. Rathlin1 was a high quality specimen and was radiocarbon dated to 2026–1885 BC (3976-3835 ybp) and is positive for DF21 which is estimated to have formed 4300 ybp. Bell Beaker Quedlinburg [I0806/QLB 28] is radiocarbon dated from 2296-2206 BC and is P312+ but I don't think the quality was good enough for high resolution results. So there still hasn't been any high quality P312 specimens with reliable radiocarbon dating from close to the period that the SNPs 1-step downstream from P312 first appeared.
    Ancient DNA will help nail down the timing of P312's immediate descendants. But even without ancient DNA, the tree structure itself is sufficient to deduce without doubt that the SNP rate has not been uniform. The general tree structure - the large number of branches per node, the large number of phylogenetically equivalent SNPs per node, and the large variation of SNP count between parallel branches - all evident systematically throughout the tree - cannot possibly be generated by single, fully random SNPs.

    Given that the tree structure itself clearly indicates the ubiquitous presence of SNP runs (and, conversely, SNP droughts), it is probable that this irregular distribution is also the explanation for the particular case of DF27 (or rather ZZ12). The only other possible interpretation, capable of generating the observed tree structure, is to argue that nearly all the growth of the P312 population over the past thousands of years has occurred within a small number of explosive, very brief expansions. And this position, while being mathematically consistent with the tree structure, is not credible.
    Last edited by miiser; 03-30-2016 at 05:42 AM.

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    Quote Originally Posted by miiser View Post
    Ancient DNA will help nail down the timing of P312's immediate descendants.
    It will also possibly break up the large run of phylogenetic equivalents of L21 into smaller blocks of SNPs debunking the large run hypothesis.


    Quote Originally Posted by miiser View Post
    But even without ancient DNA, the tree structure itself is sufficient to deduce without doubt that the SNP rate has not been uniform. The general tree structure - the large number of branches per node, the large number of phylogenetically equivalent SNPs per node, and the large variation of SNP count between parallel branches - all evident systematically throughout the tree - cannot possibly be generated by single, fully random SNPs.
    There is no question that the large runs can be caused by "An incredibly large number of extinctions" as stated by Muircheartaigh.

    Quote Originally Posted by miiser View Post
    Given that the tree structure itself clearly indicates the ubiquitous presence of SNP runs (and, conversely, SNP droughts), it is probable that this irregular distribution is also the explanation for the particular case of DF27 (or rather ZZ12). The only other possible interpretation, capable of generating the observed tree structure, is to argue that nearly all the growth of the P312 population over the past thousands of years has occurred within a small number of explosive, very brief expansions. And this position, while being mathematically consistent with the tree structure, is not credible.
    Nothing is clear without the evidence from ancient DNA. All else is speculation.

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    Quote Originally Posted by ArmandoR1b View Post
    It will also possibly break up the large run of phylogenetic equivalents of L21 into smaller blocks of SNPs debunking the large run hypothesis.
    It's theoretically POSSIBLE for new samples to split phylogenetically equivalent blocks of ancient subclades, but not at all likely. As I pointed out, most branches of old haplogroups have already been discovered. At this point, very few added samples will cause splitting of established ancient nodes. The curve of branch discovery is something like a logarithmic curve, approaching a final value as the sample size increases. The curve has already levelled off and we're near the maximum.

    And while there is the slim possibility for new samples to split an ancient phylogenetically equivalent block, new samples are NOT capable of decreasing the number of branches per node. The number of branches per node is already greater than it ought to be for the case of single, randomly distributed SNPs every ~144 years. Additional samples can only have the effect of adding MORE branches to any given node.


    Quote Originally Posted by ArmandoR1b View Post
    There is no question that the large runs can be caused by "An incredibly large number of extinctions" as stated by Muircheartaigh.
    Wrong. Large blocks of phylogenetically equivalent SNPs CANNOT be created simply by a large number of extinctions. ALL the branches inevitably contain a large number of extinct lineages, but they DON'T all contain large blocks of equivalent SNPs. The only way you can generate a large block of SNPs from evenly distributed single SNPs is if a haplogroup is whittled down to literally just a SINGLE surviving lineage.

    Assuming SNPs occur as singular events once per ~144 years - Unless a haplogroup is whittled down to literally a SINGLE individual due to lineage extinctions, there will still be a branch every few generations. If there are even 2 surviving lineages, then there will likely be 2 distinct branches as the result of a SNP somewhere in one of the lineages. Just TWO surviving men within the haplogroup are sufficient to interrupt the block of phylogenetically equivalent SNPs. Suppose a haplogroup is constrained to a bottleneck of 10 men for a thousand years. After a thousand years, you will not have just a single unbranched group of 10 men, all sharing the same block of SNPs. There would still be a SNP every few generations, even among those 10 men, and the most probable outcome is that you would end up with close to 10 different branches among those 10 individuals.

    There may be very rare cases of haplogroups being whittled down to single individual without being whittled down to ZERO individuals. But this is statistically very improbable, and will necessarily be very rare. In most cases, either the haplogroup will retain some number of individuals, even if this number is small, and most of those individuals will be split into separate branches by SNPs occurring every few generations . . . or, the haplogroup will go extinct altogether. The case in which you will see a bottleneck limit a haplogroup to a SINGLE lineage - which is the only case that can generate a large block of unbranched SNPs over hundreds or thousands of years - will be very, very rare.

    And the hypothetical bottlenecks are absolutely NOT capable of explaining away the excessive branch-to-branch variation of SNP count. And neither can this variation be explained away by variability of testing coverage. As with the branch discovery, the SNP discovery is near 100% for the older branches. The sample size is in the hundreds for the major subclades of P312. With sample sizes of each branch in the hundreds, SNP and branch discovery doesn't depend on the test coverage of any single sample, but is cumulative of ALL the samples under that branch so that SNP discovery is near 100%. The structure we see now for P312 is the true structure, and the extreme variation of SNP count is a real, undeniable effect.

    If one assumes single, randomly distributed SNPs every ~144 years, the only interpretation that fits with the tree structure is to believe that all the population growth of P312 has occurred in fits and starts, with a very small number of explosive expansions separated by long stretches of bottlenecks that constrain haplogroups to SINGLE individuals.

    The only reasonable interpretation is that the SNPs are not evenly distributed.
    Last edited by miiser; 03-30-2016 at 02:03 PM.

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