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Thread: Can Last Glacial Maximum evidence help us estimate SNP ages?

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    Can Last Glacial Maximum evidence help us estimate SNP ages?

    yfull estimates of haplogroup ages show a fallow period (between 39,000 and 30,000 BC) when virtually no new surviving y-dna lineages arose, and none of those that did arise seem to be of European origin. This would appear to indicate a human (and especially European) population struggling to survive and on the brink of extinction. Both before and after this period, yfull estimates that new haplogroups arose in substantial numbers.

    The earth (and in particular Europe) is thought to have been at its least hospitable at the time of the Last Glacial Maximum, which is estimated to have occurred between 23,000 and 11,000 BC. This would seem to be the period in which SNP bottlenecks would be most likely to occur and fewer new lineages would be expected to arise.

    So does this suggest that yfull's TMRCA estimates might be exaggerating (approximately doubling) the real ages of SNPs, and that SNPs are generally much younger than they are currently believed to be? Or might there be another reason why a pre-LGM environment might have been significantly less capable of allowing a diverse human gene pool to thrive than the LGM itself?

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    A lack of new branches between 39,000 and 30,000 BC does not mean that there weren't new SNPs and therefore doesn't throw off the real ages of SNPs very much. It's the number of SNPs that are used to calculate the estimated dates of the branches and not the number of branches. Relatively speaking, the YFull date estimates and the date estimates from Poznik et al. 2016 (see the Supplementary Table 10 page 47 of the Supplementary PDF) aren't that far off from each other and if anything, YFull has estimated the SNPs to be somewhat younger than they really are, contradicting your suggestion that YFull's TMRCA estimates might be exaggerating (approximately doubling) the real ages of SNPs.

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    Quote Originally Posted by ArmandoR1b View Post
    A lack of new branches between 39,000 and 30,000 BC does not mean that there weren't new SNPs and therefore doesn't throw off the real ages of SNPs very much. It's the number of SNPs that are used to calculate the estimated dates of the branches and not the number of branches. Relatively speaking, the YFull date estimates and the date estimates from Poznik et al. 2016 (see the Supplementary Table 10 page 47 of the Supplementary PDF) aren't that far off from each other and if anything, YFull has estimated the SNPs to be somewhat younger than they really are, contradicting your suggestion that YFull's TMRCA estimates might be exaggerating (approximately doubling) the real ages of SNPs.
    I think you're missing the point of Epp's comment. Epp can correct me if I'm wrong. But I don't think he's suggesting that there were no SNPs.

    He's suggesting that the glacial maximum might be used as a calibration point to set the number of years per SNP. The dearth of branches pinpoints the time at which the glacial maximum occurred because of the strain it put on the population, resulting in a haplogroup bottleneck, according to the hypothesis. YFull used a similar method to establish their "years per SNP" constant - associating a known historical event at a particular time with a particular node in the tree and taking an SNP count from that node. Epp is simply suggesting that the glacial maximum might be used as a similar calibration point.

    If one accepts that the empty section of the tree does represent the glacial maximum, then it's a valid approach. If this is the case, then this glacial maximum calibration contradicts the calibration currently being used by YFull. As far as I know, YFull has never validated their calibration by comparing it to a second calibration of a different event. I think it's a reasonable concern that the calibration may not be correct, or at least not applicable to all times and places.

    My own opinion is that SNP rate has not been proven to be a fully random process. The SNP rate can vary significantly, beyond what's expected of a random distribution. So the SNP rate within a particular branch and particular time range may not be the same as the SNP rate of a different branch in a different time range. Different calibration standards may, in fact, give different SNP rates.

    Along this same line of reasoning, though, we cannot assume that a block of phylogenetically equivalent SNPs necessarily represents a long period of time without extant branching. It may simply be a large number of SNPs that occurred within a short time. So the dearth of branches mentioned by Epp may not even represent a population bottleneck, but just a clump of SNPs occurring within a normally growing population.

    At any rate, I think Epp's hypothesis is an interesting idea that bears further consideration. I would like to see YFull's calibration validated by additional calibrations to more than one event.
    Last edited by miiser; 07-30-2016 at 10:36 PM.

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    Quote Originally Posted by ArmandoR1b View Post
    A lack of new branches between 39,000 and 30,000 BC does not mean that there weren't new SNPs
    So what does the lack of new branches mean? What are the likely reasons why the new branches would tail off after 40,000 BC and then begin to arise again in significant numbers after 30,000 BC?
    Quote Originally Posted by ArmandoR1b View Post
    It's the number of SNPs that are used to calculate the estimated dates of the branches
    How do we know that the number of SNPs provides an accurate estimate of the dates of the branches?

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    Thanks, miiser. You've explained my thinking better than I have.

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    Quote Originally Posted by epp View Post
    So what does the lack of new branches mean? What are the likely reasons why the new branches would tail off after 40,000 BC and then begin to arise again in significant numbers after 30,000 BC?
    It simply means that the sons of each SNP weren't successful in branching out.

    Quote Originally Posted by epp View Post
    How do we know that the number of SNPs provides an accurate estimate of the dates of the branches?
    We have ancient DNA such as Bell Beaker Germany Osterhofen-Altenmarkt [RISE563] http://www.ancestraljourneys.org/cop...zeagedna.shtml (coverage of 0.329
    per SupplementaryDataTable2 of Lazaridis et al. 2016) who is positive for U152. The Bell Beaker period was c. 2800 – 1800 BC and YFull estimates U152 to have a TMRCA of 4500 ybp (2500 BC). Since the coverage was only 0.329 we don't know which other U152 SNPs was positive for but at least we know that U152 is at least 3800 years old which definitely means YFull's TMRCA estimates are not exaggerating (approximately doubling) the real ages of SNPs.
    Last edited by ArmandoR1b; 07-31-2016 at 07:01 PM. Reason: fixed typo of 1500 BC to 2500 BC

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    Quote Originally Posted by miiser View Post
    I think you're missing the point of Epp's comment. Epp can correct me if I'm wrong. But I don't think he's suggesting that there were no SNPs.
    Actually you missing my point. He used the term lineages for branches. There are multiple SNPs, sometimes many dozens of them in a branch, and those SNPs are used for dating.

    Quote Originally Posted by miiser View Post
    He's suggesting that the glacial maximum might be used as a calibration point to set the number of years per SNP. The dearth of branches pinpoints the time at which the glacial maximum occurred because of the strain it put on the population, resulting in a haplogroup bottleneck, according to the hypothesis. YFull used a similar method to establish their "years per SNP" constant - associating a known historical event at a particular time with a particular node in the tree and taking an SNP count from that node. Epp is simply suggesting that the glacial maximum might be used as a similar calibration point.
    You are both still missing the point. The lack of branches is irrelevant for SNP dating.

    Quote Originally Posted by miiser View Post
    If one accepts that the empty section of the tree does represent the glacial maximum, then it's a valid approach.
    No, it's not. The SNPs average out over time. More branches just mean more people.

    Quote Originally Posted by miiser View Post
    If this is the case, then this glacial maximum calibration contradicts the calibration currently being used by YFull. As far as I know, YFull has never validated their calibration by comparing it to a second calibration of a different event. I think it's a reasonable concern that the calibration may not be correct, or at least not applicable to all times and places.
    Poznik et al. used a different calibration and I provided links to that study and what to look for in that study.

    Quote Originally Posted by miiser View Post
    My own opinion is that SNP rate has not been proven to be a fully random process. The SNP rate can vary significantly, beyond what's expected of a random distribution. So the SNP rate within a particular branch and particular time range may not be the same as the SNP rate of a different branch in a different time range. Different calibration standards may, in fact, give different SNP rates.
    That will be true for short time periods but over a thousand or more years there will be an average.

    Quote Originally Posted by miiser View Post
    Along this same line of reasoning, though, we cannot assume that a block of phylogenetically equivalent SNPs necessarily represents a long period of time without extant branching. It may simply be a large number of SNPs that occurred within a short time. So the dearth of branches mentioned by Epp may not even represent a population bottleneck, but just a clump of SNPs occurring within a normally growing population.
    Some SNPs can occur simultaneously in a person or a few generations but there is no evidence that dozens have happened often enough for the date estimates to be wildly off for branches from thousands of years ago.

    Quote Originally Posted by miiser View Post
    At any rate, I think Epp's hypothesis is an interesting idea that bears further consideration. I would like to see YFull's calibration validated by additional calibrations to more than one event.
    We have the U152 example I provided in my post #6. There are other examples of ancient DNA that can be used to completely refute Epp's hypothesis that "YFull's TMRCA estimates might be exaggerating (approximately doubling) the real ages of SNPs such as Anzick-1 which is about 13,000 to 12,600 calendar years bp and is positive for Q-Z780 which has a TMRCA 14200 ybp. If the YFull estimate were twice the actual age then Anzick would not have been able to have been Q-Z780.

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    A related article on climate extremes and mutation rates
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    Quote Originally Posted by ArmandoR1b View Post
    Actually you missing my point. He used the term lineages for branches. There are multiple SNPs, sometimes many dozens of them in a branch, and those SNPs are used for dating.

    You are both still missing the point. The lack of branches is irrelevant for SNP dating.
    I'm not saying I believe Epp's hypothesis. But it's clear that, in your initial post, the response you made was not an answer to the hypothesis that Epp intended to propose. Whether your points are right or wrong, I think you misunderstood what he was proposing. But let's not dwell on the past...

    Quote Originally Posted by ArmandoR1b View Post
    No, it's not. The SNPs average out over time. More branches just mean more people.

    Poznik et al. used a different calibration and I provided links to that study and what to look for in that study.
    When I say that I'd like a validation of YFull's calibration, I mean a second calibration, using the same technique based on SNPs, for a second historical event. I've read the original paper by YFull. It includes no such validation.


    Quote Originally Posted by ArmandoR1b View Post
    That will be true for short time periods but over a thousand or more years there will be an average.

    Some SNPs can occur simultaneously in a person or a few generations but there is no evidence that dozens have happened often enough for the date estimates to be wildly off for branches from thousands of years ago.
    How long will it take for those differences in rate to average out? In evolutionary biology and bioinformatics, it's pretty much an accepted fact that gamma ray bursts can cause a very large number of mutations, and these events have generated discontinuities in the evolutionary mutation rate. Such events can certainly generate dozens of SNPs within an individual. Do you deny the existence of such events? If such an event occurs once every few thousand years, then a few thousand years is definitely not long enough to average out the rate.

    Quote Originally Posted by ArmandoR1b View Post
    We have the U152 example I provided in my post #6. There are other examples of ancient DNA that can be used to completely refute Epp's hypothesis that "YFull's TMRCA estimates might be exaggerating (approximately doubling) the real ages of SNPs such as Anzick-1 which is about 13,000 to 12,600 calendar years bp and is positive for Q-Z780 which has a TMRCA 14200 ybp. If the YFull estimate were twice the actual age then Anzick would not have been able to have been Q-Z780.
    These specific examples demonstrate that the calibration is not an over estimate - for these specific cases, within this branch and within this time period. But your claim that YFull's dates may actually be an under estimate supports the idea that the calibration rate might be inaccurate, and different calibrations based on different events might give different rates. YFull being a consistent under estimate for many branches, as you claim, indicates a systematic error. A systematic errors means that we are not observing just random variation, but an inaccuracy of the calibrated rate. If the mutation rate is not consistent through history, we should expect a calibration based on a single event to result in over estimates of some nodes and under estimates of other nodes. The under estimation of some nodes does not rule out the possibility of other nodes being over estimated.
    Last edited by miiser; 07-31-2016 at 01:12 AM.

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    Quote Originally Posted by miiser View Post
    I'm not saying I believe Epp's hypothesis. But it's clear that, in your initial post, the response you made was not an answer to the hypothesis that Epp intended to propose. Whether your points are right or wrong, I think you misunderstood what he was proposing.
    His hypothesis is that the LGM needs to be used as a calibration point because he thinks YFull's estimations are off because there is a lack of branching between 39,000 and 30,000 BC and not in the LGM, which is when he expects for there to have been fewer branches (he uses the term lineages). My contention is that the branching is irrelevant because the Poznik dates are similar to YFull's and therefore the need to try and use the LGM as a calibration point is unnecessary. So my initial response was a counter to the data that he uses for his hypothesis. I'm basically saying that low branching between 39,000 and 30,000 BC and not in the LGM is a false cause to needing the LGM as a calibration point and I am also saying it is not an indication that YFull's TMRCA estimates might be exaggerating (approximately doubling) the real ages of SNPs.

    Quote Originally Posted by miiser View Post
    When I say that I'd like a validation of YFull's calibration, I mean a second calibration, using the same technique based on SNPs, for a second historical event. I've read the original paper by YFull. It includes no such validation.
    They calibrated to both Ust-Ishm and Anzick-1 (I had forgotten that they used Anzick-1) so they did it with a pre-LGM specimen and a post-LGM specimen. I also provided the example of a Chalcolithic or Bronze Age specimen and how it's YFull age is not too old. Which other historical event are you looking for?


    Quote Originally Posted by miiser View Post
    How long will it take for those differences in rate to average out? In evolutionary biology and bioinformatics, it's pretty much an accepted fact that gamma ray bursts can cause a very large number of mutations, and these events have generated discontinuities in the evolutionary mutation rate. Such events can certainly generate dozens of SNPs within an individual. Do you deny the existence of such events? If such an event occurs once every few thousand years, then a few thousand years is definitely not long enough to average out the rate.
    Just two dozen SNPs would throw off the dates by about 3,456 years. There isn't that much of a difference with the Bell Beaker.

    Quote Originally Posted by miiser View Post
    These specific examples demonstrate that the calibration is not an over estimate - for these specific cases, within this branch and within this time period. But your claim that YFull's dates may actually be an under estimate supports the idea that the calibration rate might be inaccurate, and different calibrations based on different events might give different rates. YFull being a consistent under estimate for many branches, as you claim, indicates a systematic error. A systematic errors means that we are not observing just random variation, but an inaccuracy of the calibrated rate. If the mutation rate is not consistent through history, we should expect a calibration based on a single event to result in over estimates of some nodes and under estimates of other nodes. The under estimation of some nodes does not rule out the possibility of other nodes being over estimated.
    The range of the error is not so great for me to be concerned about it at the moment. So far there isn't a significant contradiction between historical events and YFull date estimates and the inaccuracy isn't anywhere close to as great as what epp proposed.

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