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Multiple SNP in haplogroups

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  • Multiple SNP in haplogroups

    I’ve made some tests (waiting for the BigY now) and I’d like to fully (or nearly) understand all the mechanics of haplogroups and SNPs. I see that there are many groups with many associated SNPs (R1b-M269 has 97 or so). A haplogroup should be defined by one SNP, right? Having so many SNP means that all but one correspond to groups further down the tree that are not yet defined, right? But … 97? It’s a bit confusing to me.
    Can you shed a little light on this subject please? Thanks in advance.

  • #2
    When looking at R-M269 in the Haplotree there is a "more" following the SNP name, clicking of it will open a list of equivalent SNPs. There are about 41.

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    • #3
      Ok, there are some places where they have 97. Anyway, the number is not important, what I want to understand is why there are so many SNPs associated with one haplogroup when it should be defined by only one SNP.

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      • #4
        SNPs are like road signs that mark a specific path, with different, smaller tributaries branching off the main highway. They all start out at the same place, but end up at different places.

        A haplogroup is like the interstate highway, a clade is like the county trunk, and a subclade is like a side street.

        Naturally, there are some cities with a denser concentration of streets than isolated country towns.

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        • #5
          Originally posted by Joyodongo View Post
          Ok, there are some places where they have 97. Anyway, the number is not important, what I want to understand is why there are so many SNPs associated with one haplogroup when it should be defined by only one SNP.
          When a lineage goes hundreds of years with very few descendants, within in those hundreds of years, then there isn't any branching but mutations continue to happen and therefore there is an accumulation of SNPs in the people that continued to have descendants. Without lots of descendants within those hundreds of years, and branching from the descendants, then there is no way to know which SNPs are older and which are younger so they are all grouped into a single branch. Every single person alive that is positive for R-M269 is also positive for all of the phylogenetic equivalents of R-M269 when tested for those SNPs.

          YFull estimates the oldest SNPs at the M269 level formed about 13300 years before present and the youngest is TMRCA estimated from about 6400 years before present which is a difference of 6900 years. So YFull estimates that there were about 6,900 years of SNPs that accumulated with only one lineage surviving to modern times.

          The large number of modern people that are positive for R-M269 was due to a population explosion that happened mostly with R-P312 and R-U106 positive people during the Bronze Age. Prior to the Bronze Age there were very few people that were positive for R-M269. That population explosion allowed for there to be a lot of branching with R-P312 and R-U106.

          Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences by Poznik et al. 2016 states "Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations." R-P312 is among the SNPs studied in that academic paper so they also came to the conclusion that there was a population explosion.

          Today The Beaker Phenomenon And The Genomic Transformation Of Northwest Europe by Olalde et al. 2018 will be published. The pre-print uses ancient specimens to show that R-P312 was found among Bell Beaker people but the upstream SNPs were uncommon among people prior to the Bronze Age. So that study also supports a population explosion in the Bronze Age.

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