BigY is Working

About a year ago I wrote about the results of my BigY test, the discovery test of large parts of the male y chromosome. I thought it was worthwhile to post an update on my results and to explain why I think the BigY test is working. As a start it’s worth reviewing what has changed with the actual test and how you see your results.

FamilyTreeDNA Changes to the BigY test

Back when I last wrote about the BigY test FamilyTreeDNA were busy with the migration of all results to the latest version of the Human Reference Genome sequence (hg38). This migration is now complete, although it took a little longer than planned. With that complex task completed ftDNA have made a number of changes to their test to enhance testers understanding of their results, specifically:

The BigY test is now the Big Y-500

FamilyTreeDNA have changed the product that they sell. Previously you had to purchase a yDNA Short Tandem Repeat test (hereafter STR) before you could take the BigY test. This has now been bundled together as a single test. At the date of writing this tests $649.

As you will have no-doubt spotted the test has been renamed to the BigY 500. This is because you now get at least 500 STR results. The actual number will depend on the success familyTreeDNA have in reading your DNA. More specifically this means that ftDNA will test 5 “panels” of results that will give you 111 STR results. These panels results are the same as the yDNA STR tests you can order separately from ftDNA. On top of that ftDNA will provide up to 450 addition STR results taken from the results of the BigY sequencing. These are labelled as panel 6 by ftDNA. The 500 STR number is a little bit of a fudge, due to the nature of the Next Generation Sequencing (NGS) used to read your DNA for the BigY test.  FamilyTreeDNA can guarantee that you will get all STR results for the first 5 panels, on panel 6 it depends if, and how often, your DNA was sequenced at the location of these additional 450 STR sequences. As an example I had around half a dozen no-reads within the panel 6 STR results.

In all honesty, at least for myself, the additional STR results don’t matter at all. My closest STR match is a genetic distance of 4 at 37 STR markers, which suggests a shared paternal ancestor (>99% confidence) within 24 generations.

FamilyTreeDNA has a yDNA SNP browser

You can now look in detail at your yDNA test results thanks to the SNP browser that ftDNA have built. You can do this for every named and unnamed SNP that the company have called in your results.

The example below shows the results for my terminal SNP (I-Y89241). It shows that I had seven reads at position 9970322, all good quality and all with a value of T. The Reference value at this position is C.

To be honest it’s not as clear, or as easy to operate, as the yFull product. Their website allows you to see your results via either SNP name or position in the Hg38 build of the SNP. In addition they give you an actual count of the number of reads. Here is my same test result on the yFull website for SNP I-Y89241.

yFull I-Y89241 SNP results. Note the count and named SNPs at this location

FamilyTreeDNA have changed their SNP naming policy

This is really just a technical issue. SNPs were originally usually not named until 3 independent test results confirmed a particular branch. As yDNA testing has become a hobbyist interest there has been pressure to name SNPs early. Everyone, myself included, like to look at their portion of the y Haplotree and say “Yup, that SNP was identified in my results first”.

As a result FamilyTreeDNA now “SNP is being named with one reliable occurrence, BUT, the SNP still is not being placed on the tree without two high quality occurrences.”

(The quote is from the dna-explained.com site run by Roberta Estes.)

FamilyTreeDNA have made their Haplotrees public

This is actually a bit of a two for one offer. Not only have FamilyTreeDNA made their yDNA Haplotree public, but they have also made their Mitochondrial DNA haplotree public. Both trees can show either the complete list of SNPs in a branch OR the location of the testers earliest known paternal/maternal ancestor. The y Haplotree has the additional trick of showing all Surnames of the earliest known paternal ancestor. The location and surname info depends on the information that testers add to their ftDNA profile, so is obviously only as good as the information the testers themselves know.

Development of the y Chromosome Haplotree

The main point of this posting is that I wanted to show how BigY testing is building out the y haplotree. It’s easiest if I show you “before and after” pictures. The top diagram is the I-PH4482 branch of Haplogroup I looked in 2017, and below, how it looks at today (November 2018). Flags are used to indicate the origins of the earliest-known paternal line male ancestor. I’ve done this to help illustrate the geographical diversity of this part of the tree. To put these branches in context the most-recent branch of the trees are probably 1500 old ± 500 yrs.

I-PH4482 branch (c. November 2017). Results based on 5 testers.

I-PH4482 branch (November 2018). Results based on 13 testers.

As you can see there has been significant changes to the tress specifically:

  • A new branch, I-A13740 formed  under I-PH4482 as a result of a new tester matching the existing, Irish-heritage) tester. This new branch contains a significant number (21) of shared variants, suggesting a more recent common ancestor. Since I’ve yet to see any geneticist estimate a date for this common ancestor I’m not going to stick my neck out and suggest a date.
  • A single tester, with French heritage tested positive for some, but not all of the SNPs that used to make up the I-PH2658 branch, thus separating this one result from all other testers with had a common ancestor who had the SNP mutations I-S2273 and I-S2268.
  • A new tester shared 5 SNPs (I-Y89241 plus 4 others) with myself. As a result we both currently have this new terminal SNP position.
  • One tester, with Lithuanian heritage, matches neither the I-S2275 or the I-Y89241 group, however since he had the SNPs I-S2273 and I-S2268 he, at the moment, represents an intermediate branch between I-PH2658 and the I-S2275 and I-Y89241 leaves. Theoretically when he matches another tester he will form a third branch under I-PH4482. Perhaps this is evidence of an increasing population around the time that these branches formed?

The most important thing to note here is that whilst all the 13 testers here share an common male-line ancestors at some point in history, it is so far back in time that it is (virtually) impossible to trace through traditional genealogical research. To look at it another way, none of the testers here, myself included, had any idea we share this common ancestor. Through testing, specifically the BigY 500 test, we have contributed to the development of the I branch of the y chromosome haplotree.

yFull or yEmpty

Last time I wrote about BigY testing I suggested that yFull.com provided useful additional analysis of yDNA results. Given the developments that have occurred at FamilyTreeDNA the question arises if it’s still worthwhile. At this point the most important thing to remember is the FamilyTreeDNA is not the only lab offering NGS sequencing of either your y chromosome or your whole DNA. Labs offering these services include Dante Labs, Full Genomes Corp and ySeq. I’ve seen one person report that they managed to order the Dante Labs “My Full DNA” product for a discount price of $299. Since ftDNA does not offer a service to analyse other yDNA data, then services like yFull and the yDNA analysis from Full Genomes Corp will continue to have a place in the yDNA ecosystem.

Final Thoughts

I’m excited that my yDNA has contributed to the further development of the I Haplotree. As prices continue to reduce we should see further development of all parts of both the yDNA and Mitochondrial DNA Haplotrees. What I personally find interesting is how the contributions from a seemingly random group of testers have built out this part of the I Haplotree.

Haplogroup I1 is considered to have arisen somewhere in Europe, possibly Northern Europe/Scandinavia given that it’s found in high concentrations there. As a result it’s sometimes “branded” as a “Viking” Haplogroup. Personally I’m not a big fan of the idea that specific haplogroups represent specific historical “tribes” as I suspect tribes were based more on cultural connections. However as DNA becomes a common part of the historian/archaeologists toolkit it will be interesting to see if the yDNA Haplotree maps on to the historical record of population genetics.

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