Announcement

Collapse
No announcement yet.

The Y-chromosome tree bursts into leaf

Collapse
X
  • Filter
  • Time
  • Show
Clear All
new posts

  • #31
    Originally posted by T E Peterman View Post
    Have the new SNPs from the Big Y been isolated to lower branches of the U106 tree. Of my 96 novel variants (I am R1b L20*), about 1/3 are higher than U152 on the tree. All of the novel variants are new; they haven't been seen before. But it doesn't mean they are outlining new structure beneath the most derived clades on the y-tree. I suspect that Big Y will result in maybe 3 or 4 nested clades under each pre-Big Y terminal clade, but not much more.

    All of the new U106 Big Y SNPs will extend it down to maybe 20 levels deep across the board; maybe deeper in some cases.

    Timothy Peterman
    It still does not answer the question about the R1b Neolthic SNPs. It should be easy for a genetic scientist to define these. A SNP is a mutation or a defect in our dna.Once they establish one of these Neolithic SNPs then they will be able to put a proper TMRCA to a particular subhaplogroup.

    Comment


    • #32
      A few more thoughts I will offer here. 135 years is about the length of 4 male generations. This tells me that with each new generation, there is a 25% chance that the son will carry a new SNP. So if a man has 4 sons, does this mean there is a 100% chance that one of them will have an SNP? What if he has 8 sons?

      What is the percentage chance that a son will carry an SNP?

      Perhaps 4 generations means there is a 1/16 chance that a son will carry an SNP. Assume a man has an average of two sons. 2 to the 4th power is 16. So, of a man's 16 patrilineal great-great grandsons, odds are one would carry an SNP. What are the odds that a great-great grandson would happen to carry two SNPs? Would it be 1/256? The answers would have a huge impact on what we are discussing.

      I suspect that most clades yield only two clade divisions, so any clade that is shown with a 2 or higher number, or b or higher letter is probably an illusion caused by the fact that population bottlenecks have eliminated most of the varied lines of descent that could have existed. Take for example, the original carrier of R (M207), we show him with two y-DNA sons, R1 & R2. Chances are, these mutations didn't happen in the same generation. When the first occurred, R should have split into R* & R1*. The second mutation could not have occurred in the R1* patriline. It must have occurred in R* patriline. Calling the second mutation R2* is misleading. Whenever a patriline has an SNP split, both lines of descent should have an indicator that they are after the split. If we go with R1 & R2, then after the first mutation, R* would disappear; but the non-mutated post-split R would look identical to the pre-split R. If the nomenclature were set up right & understood as such by everyone, we could assign each subsequent mutation in the remaining R* population another sequential number, thus R1 would be the first mutation in the R* population, R2 would be the second mutation in the R* population, R3 would be the third mutation in the R* population and so forth. But the tree would show R* split into R* & R1 & then R* would split again into R* & R2 & then R* would split again into R* & R3. Big Y data will perhaps, over time, re-organize multiple clades that seem to appear simultaneously into more of a hierarchy.

      As far as the actual R1 (M173) & R2 (M479), they are separated by their parent clade by maybe 8,500 years (per ISOGG). There must have been a myriad of undetected SNPs in that line of descent. The fact that after 8,500 years, only two R patrilines existed with descendants today, tells us a lot about extinction rates during the years between then & now.

      Timothy Peterman

      Comment


      • #33
        This from Irelandsdna.

        "Arguably, it was the production of primitive wheat and barley that had the greatest impact because it transformed child rearing. As these bands moved around their wide ranges, relocating from summer to winter camps, going on seasonal hunting expeditions they needed to be as mobile as possible. That meant only one baby or toddler could be carried along with the other gear needed. And in an age before contraception, another factor came into play. Infant teeth could be too soft to deal with the hunter-gatherer diet and in order to take in enough protein to grow, babies and toddlers almost certainly breast-fed for much longer, perhaps only being weaned as late as four or five years old. During this lengthy period, breast-feeding mothers were usually infertile.
        What also inhibited the growth of populations were the short fertile lives of most women. There is evidence that women in prehistory began their menstrual cycle later, maybe at the age of 13 to 15, and most surveys of surviving skeletons report that the majority of people died relatively young with few of them reaching their thirties. Over such a short time, most women will have given birth to only three or at most four babies, not all of whom will have reached adulthood. The production of cereals changed this cycle radically.
        When the ears of wheat were dried, and sometimes charred, they could be mashed into a nourishing porridge with animal milk or water. Not required to be masticated, this could be fed to infants and they thrived. This in turn led to earlier weaning – and an explosion in the prehistoric population.
        Eventually change would come which forced movement. It was a revolution in a very meaningful sense and it began some time around 8,500BC in the Near East, the arc known as the Fertile Crescent, from Iraq through Syria to the Levant. There, hunter-gatherers had managed their ranges, encouraging the growth of fruit trees and berry bushes, trying to ensure a continuity of supply. But at some point in the 9th millennium BC, stands of fruit trees became orchards, gardens were planted instead of being the semi-accidental product of self-propagation, and crucially, wild grasses were cultivated as cereals.
        As the population grew after c8,500BC in the Near East, pressure built up. Farming led to a powerful sense of the ownership of land as those who had expended great labour in creating gardens and small fields insisted on their rights. That in turn forced a calculation. In the new world of farming, what was the carrying capacity of the land, how many mouths could its produce feed? When the birth interval halved from four to five years to two or three, that led to a rapid increase in numbers. As more and more land was brought into cultivation, those it could no longer support were forced to move and the techniques of farming began to ripple westwards from the Fertile Crescent, crossing the Bosphorus, the Black Sea or the Aegean to reach Europe where many new markers arose."

        The birth rate was a lot less among the hunter-gatherers and probably infant mortality was high.Less births equals less mutations. This could also be the reason that some branches today have more SNPs than others.

        Comment


        • #34
          1798: This is very true. There were a lot fewer mutation opportunities among hunter-gatherer populations.

          Speaking of demographics... there was probably a massive population explosion about 4,000 to 4,500 years ago in Europe, with the arrival of better tools (ie, bronze) & horses, etc. One man (P311) with many sons, each of whom had even more sons. I have often pondered that the surviving y-lines from that era were those of tribal elites, each with multiple wives & lots of offspring. Today, of course, the royal houses of Europe (as well as commoners) descend from these y-lines. If you go back far enough, there is probably a king (or at least a tribal elite) in everyone's patriline.

          Timothy Peterman

          Comment


          • #35
            Originally posted by T E Peterman View Post
            1798: This is very true. There were a lot fewer mutation opportunities among hunter-gatherer populations.

            Speaking of demographics... there was probably a massive population explosion about 4,000 to 4,500 years ago in Europe, with the arrival of better tools (ie, bronze) & horses, etc. One man (P311) with many sons, each of whom had even more sons. I have often pondered that the surviving y-lines from that era were those of tribal elites, each with multiple wives & lots of offspring. Today, of course, the royal houses of Europe (as well as commoners) descend from these y-lines. If you go back far enough, there is probably a king (or at least a tribal elite) in everyone's patriline.

            Timothy Peterman
            There was a massive population explosion in the Neolithic. I don't buy into the idea that one king had 40 wives and all the children were his. That is a fairy tale. Just look at the number of divorce cases there are today and a lot of men can't keep one woman happy never mind 40. I don't know where people get this stuff. Tribal elites my ear.

            Comment


            • #36
              Is your objection to the concept of tribal elites/ kings being present in Neolithic, Chalcolithic, or Bronze Age Europe? Or is your objection to the speculation that I presented that such tribal elites would have outbred their non-elite countrymen?

              Timothy Peterman

              Comment


              • #37
                Originally posted by T E Peterman View Post
                Is your objection to the concept of tribal elites/ kings being present in Neolithic, Chalcolithic, or Bronze Age Europe? Or is your objection to the speculation that I presented that such tribal elites would have outbred their non-elite countrymen?

                Timothy Peterman
                I don't agree with this concept.One man and 40 wives.

                Comment


                • #38
                  In hunter gatherer society, few men have multiple wives. In early agricultural societies/ incipient state societies, there was a lot more social stratification & multiple wives became common place; especially for those closer to the top.

                  But I doubt very many had more than a handful.

                  Timothy Peterman

                  Comment


                  • #39
                    Originally posted by T E Peterman View Post
                    In hunter gatherer society, few men have multiple wives. In early agricultural societies/ incipient state societies, there was a lot more social stratification & multiple wives became common place; especially for those closer to the top.

                    But I doubt very many had more than a handful.

                    Timothy Peterman
                    Any man can have as many wives as wants. It doesn't mean that all the children will be born to him. I don't mean that in a bad sense but it does happen.

                    Comment


                    • #40
                      Originally posted by T E Peterman View Post
                      A few more thoughts I will offer here. 135 years is about the length of 4 male generations. This tells me that with each new generation, there is a 25% chance that the son will carry a new SNP. So if a man has 4 sons, does this mean there is a 100% chance that one of them will have an SNP? What if he has 8 sons?

                      What is the percentage chance that a son will carry an SNP?

                      Timothy Peterman
                      There is a 75% chance that a son will NOT carry a new SNP, and this is the case for all sons. The probability that none of the sons will carry a SNP is the product, .75*.75*.75*.75, or about 32%. Thus the probability that at least one son will carry a new SNP is thus 68%. It's also possible for one son to carry two SNPs.

                      Comment


                      • #41
                        Originally posted by Ann Turner View Post
                        There is a 75% chance that a son will NOT carry a new SNP, and this is the case for all sons. The probability that none of the sons will carry a SNP is the product, .75*.75*.75*.75, or about 32%. Thus the probability that at least one son will carry a new SNP is thus 68%. It's also possible for one son to carry two SNPs.
                        How can that be? A SNP is a single event.

                        Comment


                        • #42
                          Originally posted by 1798 View Post
                          How can that be? A SNP is a single event.
                          A SNP is a change at a single base, say position 24,576,899 in the Y. Another SNP can occur at say position 36,213,455 in the same child. It would be less common, but it's possible.

                          Comment


                          • #43
                            A new mutation occurs in one germline cell, in this case some precursor to a sperm. What proportion of all the sperm carry the mutation is determined by when in development the mutation occurs. If it occurred very early in the germline of the embryo, it could end up being in all or nearly all sperm, but in those early stages of development there are very few cells, so the occurrence of a mutation is very unlikely. Many more mutations occur later in development during the proliferation of pre-sperm cells in the testicle, which occurs through most of life in men. (There are far more cell doublings in the male germline than female, which is a lot of the reason that the male mutation rate is several times higher than the female.) There is no fixed percentage of male offspring that will get a new SNP, since it depends on what proportion of the sperm have it, and that depends on when in development the mutation occurred.

                            Comment


                            • #44
                              Originally posted by 1798 View Post
                              How can that be? A SNP is a single event.
                              Each SNP is a single event, no one said anything about it being an isolated event.

                              Comment


                              • #45
                                I would have never guessed that the chance of an SNP occurring between father & son is as high as 25%. That means that of my three brothers & I, there is a 68% chance that one of us has a SNP. I assume this means that between my great-great grandfather & I, there is also a 68% chance of a SNP having occurred. By the logic of multiplying 75% times 75%, etc, we never get to 0, so there is never a 100% chance of a SNP occurring.

                                If we want to count SNPs that have occurred among descendants of haplogroup founder to estimate the age of the group, we have to remember that ONLY count SNPs that can be arranged hierarchically. On most SNP trees, this is the number of columns in (not the total SNP count nested under the founder). The diversity of SNPs found under P312 & U106 are both testaments to how rapidly the L11+ population was growing.

                                I have never seen any SNP counting that justifies an age for U106 or P312 that is older than the estimated 4,000 to 4,500 years. The only thing that could support an earlier date for either would be ancient DNA; and samples from an earlier age that contain P312 or U106 have to be found first.

                                Timothy Peterman

                                Comment

                                Working...
                                X