Wednesday, October 8, 2014

NextGen Sequencing and yDNA

Genetic genealogy got its start in 2000 and yDNA dominated the first decade. mtDNA entered the scene late in that decade but has two difficulties to overcome. The first is that it is a fairly blunt instrument with only 16,569 locations to differentiate among all of us. It is good for deep ancestry but has yet to demonstrate it has potential to differentiate among related individuals. Second, to date there there have not been hundreds of thousands test their complete mitochondria -- the only level at which mtDNA seems to have much genealogical value.

By 2010 23andMe and FTDNA led the way into exploring the largest areas of our DNA -- the autosomes. These two pioneers were joined in this marketplace in 2012 by AncestryDNA. Now more than a million atDNA test kits have been sold by these three companies and the pace is accelerating. 

Autosomal DNA is great for defining close relationships -- at least when those relationships have existed within the last several few generations. Therefore it can be very useful to genealogists. However, since it is recombined in each intergenerational transfer, it soon loses its power of discernment as we investigate backward in time. This is the hottest growth area in DNA testing for genealogy and likely will continue to be so for some time. Women are on equal footing when it comes to testing autosomes.

In 2014 yDNA is making a comeback. It offers by far the longest segments of unrecombined DNA in our genomes. Therefore, it offers the best tool for looking into our deep ancestry. Although it may seem politically incorrect to say so, the less than seventeen thousand locations on our mtDNA cannot begin to be as informative as the more that fifty million locations on our yDNA. Unfortunately only men can be tested. NextGen sequencing technology is now making it possible to read SNPs at several million locations on our yDNA. This far exceeds the hundred or so ySTRs that were being sequenced by earlier technology just a couple of years ago. 

As a result of NextGen technology, tests like BIG Y, Full Y and Chromo2 have burst onto the scene. Although the prices of such tests are already coming down somewhat, they are still pricey compared to atDNA tests. However, the amount of data that they discover will take us a while to fully organize and analyze. 

Traditional genealogy emphasized starting with the present and building carefully and methodically back into the past inhabited by our ancestors. These new tests have allowed us to reverse our focus and work from prehistory down toward genealogical times. In a few cases they have already allowed us to intersect with our traditional documentary research. This trend will greatly accelerate as we get more skillful at interpreting the information written in our yDNA.

Even in earlier and simpler times we could begin to sketch the flow of our ySNPs from yADAM down toward the present. Five years ago I was offered an overview of how my SNPs and thus my paternal ancestors had migrated down to the last several thousand years. Below is how deCODEme illustrated my paternal descent down to haplogroup R1b -- the largest in Europe:

[Click on the chart to expand.]

The SNP tsunami that flows from these powerful new tests is allowing us to fill in gaps in charts like the one above. More importantly they are allowing us to build down toward the present. I will extend this SNP flow down to the last millennium in my next post.



  1. It's not "Full Y", it's "Y Elite". I agree with all the rest :)

    1. Thanks Leon for updating my terminology.
      In a related matter, over on Facebook Jim Owston questioned whether 23andMe launched in 2010 or 2009. My recollection is that 23andMe Relative Finder was in expanded Beta during the last quarter of 2009 and was officially "public" in February, 2010. Does anyone have information that would correct this?