Thursday, 19 January 2017

My Living DNA results Part 2: mtDNA and Y-DNA reports

In my previous post I wrote about my family ancestry maps from Living DNA which showed the regional breakdown of my genetic ancestry in Britain based on an analysis of my autosomal DNA. I'm now reviewing the mtDNA and Y-DNA reports, which have started to be rolled out to some of the early testers at Living DNA.

The mtDNA report is a provisional report based on my own Living DNA test on the Illumina Global Screening Array. Males who take the Living DNA test also receive a report on their Y-chromosome results. As I don't have a Y-chromosome, for the purposes of this blog post I've been given access to a sample report for someone who belongs to haplogroup R1b-U106 (my father's haplogroup).

mtDNA results
The Living DNA test analyses 4,700 mtDNA SNPs. My results show that I belong to haplogroup U4c1. I have also had my full mitochondrial DNA genome sequenced (all 16569 base pairs) at Family Tree DNA. My full sequence results place me in haplogroup U4c1a. For my motherline ancestry I have received four different reports: a coverage map, a history page, a migration map and a phylogenetic tree.

Here is the coverage map which shows the present-day distribution of haplogroup U4, and the frequency of haplogroup U4 in different populations.


Here is the history page which provides background information on haplogroup U4.


Here is the phylogenetic tree which shows my placement on the mtDNA tree.


Here is the migration map which "shows the possible routes your ancient ancestors could have taken, from the point we all shared the same mtDNA (nicknamed “Eve”) to recent times".



Y-DNA results
The microarray chip used by Living DNA covers 22,500 Y-SNPs. The Y-SNPs are currently going through the quality control process, and it will be a few more weeks before the results are ready. Not all SNPs work properly on a microarray chip and it is likely that the actual number of SNPs reported will be reduced. The sample report I've been given is for haplogroup R1b-U106 (my father's haplogroup). U106 is quite high up on the Y-SNP tree but I understand that the test will give a more refined subclade assignment than this, though we don't yet know which SNPs are included on the chip. There are once again four different reports: a coverage map, a history page, a migration map and a phylogenetic tree.

Here is the U106 coverage map.


Here is the history page. I'm told that this is legacy information from the old test site, but that the content will eventually be updated and will be based on the scientific literature.


Here is a screenshot showing the upper branches of the Y-chromosome phylogenetic tree.


You can move the tree around and zoom in on the tree. Here is a close up showing the placement of U106 on the R1b tree.


Here is the migration map which "shows the possible routes your ancient ancestors could have taken, from the point all men shared the same YDNA (nicknamed "Adam") to recent times".


Conclusion
The mtDNA and Y-DNA pages are visually appealing and I like the simplicity of the presentation. The phylogenetic trees are easy to understand. The distribution maps and frequency tables are a very useful feature. It would be helpful to have the full citations with links to the actual papers, though I understand that these will be added in due course. At present the Y-DNA and mtDNA SNPs are not reported but these will also be added.

While it's good to see scientific papers used for the history pages it should be remembered that it's very difficult to provide meaningful information on haplogroup histories and migration. Much of the scientific literature on the subject is highly speculative with conclusions inappropriately drawn about ancient migrations and origins from modern DNA (Balloux 2009, Chikhi 2010, Goldstein and Chikhi 2002). The DNA of living people is not a good proxy for past populations, and direct evidence from ancient DNA is required (Pickrell and Reich 2014). However, we can expect to see many new ancient DNA publications in the coming years which will improve our understanding. I would hope that the Living DNA platform will have the ability to update the reports from time to time as and when new research is published.

The Y-DNA and mtDNA results from the Living DNA test are potentially useful for deep ancestry purposes but don't currently have a direct application for genealogical research. Y-DNA and mtDNA testing for genealogy needs to be done with a company such as Family Tree DNA which has a matching database that allows you to compare your results with other people. However, if you've already taken a Y-STR test at FTDNA and wish to refine your subclade assignment the Living DNA test could be a possible alternative to SNP testing or Y-chromosome sequencing. For SNP discovery and a detailed subclade classification it's necessary to take a Y-chromosome sequencing test (eg, the BigY from Family Tree DNA or the YElite from Full Genomes Corporation) but these tests are still relatively expensive and beyond the reach of the average genealogist.

I suspect genetic genealogists will be taking the Living DNA test primarily for the autosomal DNA family ancestry maps, but the Y-DNA and mtDNA information will be a useful bonus feature. Not everyone is interested in genealogical research and for people who just want an overview of their genetic ancestry then this is an excellent all-round test.

References

Balloux F (2009). The worm in the fruit of the mitochondrial DNA tree. Heredity 104: 419-420.

Chikhi L (2010). Update to Chikhi et al.'s "Clinal Variation in the Nuclear DNA of Europeans” (1998): Genetic Data and Storytelling - From Archaeogenetics to Astrologenetics?" Human Biology 81(5/6): 639-643.

Goldstein DB, Chikhi L (2002). Human migrations and population structure: what we know and why it matters. Annual Review of Genomics and Human Genetics 3: 129-152.

Pickrell J, Reich D (2014). Towards a new history and geography of human genes informed by ancient DNA. Trends in Genetics 2014; 30 (9): 377-389 (subscription required).

8 comments:

Cybele Moon said...

I am totally confused with the different results I got with Family Tree and Ancestry.
Family tree gave me 46% western and cntral european 30% British Isles and 24% middle Eastern (22% Asia minor and 2% North African).

Ancestry made more sense with what I already knew about family some of whom still live in regions that came up! 14% western europe, 21% Britain ( mother from Scotland) and 12% Irish (knew about that too) 2%Scandinavian(not surprising on Isle of Skye and elsewhere)- and here is the big one- 48% Italian/Greek (Father's family southern Italy) with 2% Asia Minor!! Big difference and I don't know what to think! Even the 2% North Africa of Familytree might make sense considering location but no mention in Family Tree of Italian at all and I know Southern Italians often have different DNA from the North (hence Italian/Greek). I'm so confused I wonder if I should test again and with another company- just not sure which one!
(PS I posted this on a very old post of yours and under a different email profile (hana mcmoon) so ignore that)

Cybele Moon said...

PS: I'm haplo group H of course.

Debbie Kennett said...

Hi Cybele

These admixture percentages are not very reliable beyond the continental level though it is possible to detect certain patterns in the data.

I get three very different results from 23andMe, AncestryDNA and Family Tree DNA. See my blog post here and the various links on that page:

https://cruwys.blogspot.co.uk/2015/05/comparing-admixture-results-from.html

Essentially each company has different reference populations. You can only be matched with populations that are in the dataset. Your Italian ancestry is just being reported in different ways. At FTDNA it's subsumed into Middle Eastern, North African, Asia Minor and Western and Central Europe. At Ancestry it's includes in the Italian/Greek percentages.

Living DNA can provide breakdowns between southern and northern Italy. However, the main purpose of doing these tests is for the genealogy matches rather than the admixture percentages.

Cybele Moon said...

Thank you so much for your explanation and for your very interesting blog and information about DNA!!!

Robert said...

Can you tell me where the Fatherline % screenshot comes from?

Debbie Kennett said...

Robert, I was given access to a sample U106 report. The screenshot is from the legacy DNA Worldwide website and I understand that the haplogroup descriptions are in the process of being updated.

Robert said...

The reason I asked was because that Fatherline % is identical in every way to my one. I would have thought these things would be a lot more varied. Can I ask, when did you get it?

Debbie Kennett said...

I got the results a few days before I posted the review. There are a lot of subclades below U106 which should be picked up by the Living DNA test, especially as they have a large number of Y-SNPs. I suspect it will not be possible to give too much information about the individual subclades because it simply doesn't exist.

For U106 you'll get the best information from the U106 Project at Family Tree DNA:

https://www.familytreedna.com/groups/u106/about/background

Make sure too that you join the U106 group on Yahoo. You can join that whether or not you've tested at FTDNA.