Living DNA - June 2017 updates

Living DNA produced their first update.  An update by a "DNA for Ancestry" business can sound like an admission of failure.  To some, it could sound like a recall due to product failure.  "Your previous ancestry was a mistake".  This only applies if you have bought into some marketing campaigns, that autosomal DNA tests for ancestry actually work even close to 100%.  Surprise, they don't!  They are cutting edge, in development, and far from accurate below a Continental level. They are still somewhere in the twilight between being nothing more than a genetic lottery, and actually becoming a tool that is useful.  Therefore "updates" are to be welcomed.  They are a sign that the business wants to improve the test accuracy.  That is to the credit of Living DNA.

My latest results?  First of all, a quick recap on my actual ancestry, as supported by family history, local history, ethnicity, and by a traditionally researched record based family tree that includes over 270 direct ancestors over the past 380 years.  I'm English.  Indeed, all of my direct ancestors, appear to have been South East English.  More precise, I'm East Anglian.  On family history and recorded genealogy, I'd suggest that between 75% and 85% of my direct ancestors over the past three centuries were East Anglian, almost all from the County of Norfolk.  Others on my father's side, if not in East Anglia, still in Southern England.

That I feel, makes me an interesting subject for ancestral auDNA testing.  You see, my ancestry is very localised here in South East England.  DNA tests such as 23andMe that claim to accurately plot ancestry over the past 300 - 500 years should get me.  But they don't.  This is because their algorythms, and reference data set designs fail over different ages.  They also (although they sometimes deny it), fail to discriminate against older population background.  We East Anglians and South East English have been heavily admixed with non-British populations on the European Continent.  Not so much over the past 500 years, so much as over the past few thousand years.

The new Results.

Below are my Living DNA regional ancestry, based on Standard Mode.

Below are my Standard Mode results broken down into sub regions.

Below is a table, comparing my recorded ancestry, with my early Living DNA results in Standard, now my revised results.

Living DNA has now introduced two new modes of confidence called complete and cautious modes.  First the Complete results:

Below are my Complete Mode results in regional:

Below are my Complete Mode results for sub-regional:

Now the Cautious results:

Below are my Cautious Mode results in regional:

Finally, below are my Cautious Mode results for sub-regional:

Conclusions

No auDNA test, by any DNA-for-ancestry company has yet come close to assigning me 100% English or even British.  They don't get me.  23andMe gives me 32-37% "British & Irish".  FT-DNA gives me "36% British".  Therefore, to be fair, Living DNA, giving me 70% "Great Britain or Ireland", give me the best result.  However, Living DNA has started out with the largest, best quality British data-set of any DNA-for-ancestry company, and is often accused of a bias towards Britain in it's results.  If so, then my 70% still looks weak.  They are planning on producing similar quality data sets soon for Ireland, Germany, then France. Therefore any results, will as I started out saying at the beginning of this post, be perpetually progressive.  Businesses that do not improve data sets or algorithms, will not get any better.  They are not progressive.

I get Southern European in other tests besides this one.  Living DNA points to Tuscany.  FT-DNA before a recent update gave me 32% Southern European, although they have revised this down to a little noise from South-East Europe!  23andMe gives me 2% Southern European - but this appears nothing unusual for an English tester.  None-the-less, I am interested in trying to better understand, why some of these tests give me this "Southern European" admixture, for which my family history, local history, and recorded genealogy has absolutely no account.  It equally reflects in ancient calculators that give me a little bit more Neolithic Farmer than for other English, which on average, already have a little more Neolithic Farmer than other British or Irish populations do.

The New Complete and Cautious Modes

How do I feel about these?  At Sub-Regional level, the Complete mode starts to get silly.  For the first time, Living DNA at this level, starts to even suggest some ancestry from Wales, SW Scotland, and Northern Ireland.  Only small percentages - but I just don't buy them.

However, the Cautious Mode, I start to like.  My British ancestry doesn't increase, but it looks more realistic, although with strange enigmatic suggestions still of Italian ancestry in the mix.  At Sub-Regional level, Cautious Mode also looks a little more likely.  My East Anglian remains at 37%, I however, lose Lincolnshire (which does exist in my record), but retain Cornwall.  I think Cornwall unlikely - however, there is just a small hint that something could be there, in surname evidence of a brick-walled great great great grandparent.  So maybe, just maybe.

East Anglia

I seriously doubt that my East Anglian ancestry over the past 300 years genuinely falls much below 75%.  Living DNA only appears to recognise a half of it at 37% - but they claim to be easily able to identify East Anglian DNA.  They call it "Distinct" because of it's high levels of Continental admixture.  They have admitted that based on their early data sets, that it was hard to separate from Germanic.  I don't know why it isn't stronger in my results.  I honestly do believe that the test underplays it on my results, even though it is the strongest of any population in my test results.  My East Anglian ancestors lived mainly in Eastern, Central, and Southern Norfolk.

Living DNA also provide a chart of the Continental "contributing regions" to East Anglian ancestry:

Finally, a chart breaking down their proposal of my British ancestry at Cautious mode:

I'm not disappointed with Living DNA.  That it does identify me as 37% East Anglian is I believe, incredibly good, and far advanced over any other DNA-for-ancestry test.  I'm looking forward to more updates in the future.  Well done Living DNA.

Living DNA - my early results are in!

After a four month wait, my initial results have arrived today from Living DNA.  The wait has, I feel been understandable for a launch company.  The results are still limited to standard mode only.

Living DNA Standard mode

100% European
Regional:
74% Great Britain & Ireland
10% Europe (South)
7% Europe (North and West)
10% Europe (unassigned).

Sub-regional:

39% East Anglia
8% South Central England
5% South East England
5% Lincolnshire

2.5% Cornwall
2.4% North Yorkshire
2% South England
1.9% Devon
1.6% Central England
1.5% North West England
1.3% South Yorkshire
1.2% Northumbria

3.5% unassigned Great Britain & Ireland

10% Tuscany (Europe South)
5% Scandinavia (Europe North and West)
2% Germanic (Europe North and West)
9.7% Europe unassigned.

My initial response?  Enthralled and highly impressed.  A little disappointed that the East Anglia percentage was not higher.  I suggest 77% based on my documentary record.  Living DNA gave it 39%.  I still find that a very good result.

However... let's get this into perspective to 23andMe and FT-DNA tests.  Documentary evidence suggests that I am 100% British over the past 300 years.  23andMe said 32%.  FT-DNA said 36%.  Living DNA gets it so much closer at 74%!  That is a whole lot more accurate.

What about the remaining 26% on regional level, where do Living DNA say that comes from? All European.  It suggests 9.7% unassigned European, 9.6% Tuscan (Southern European), 4.6% Scandinavian, and 2% "Germanic".  The Tuscan is interesting, but I'm not convinced yet that it is not ancient and population based.  The Scandinavian is also most likely ancient - in my opinion.

Two things please and impress me about my results on the sub regional level:

1) Based on documentary research, I estimate that 250 years ago, 77% of my ancestors were in East Anglia.  Living DNA indeed, sees it as by far my largest sub regional percentage.  At 39%, a little low, but very impressive.  They correctly identified me as East Anglian.

My next main region, in my Family Tree, I have circa 12% ancestors from "South Central England".  Living DNA saw this, and it is indeed, my second  largest percentage at sub regional level.  I get South Central England with 7.5% - incredible.  The small "South England" would also tied to this line.

Then I get 5.4% South-East England.  It could be over spill from the East Anglia ancestry, but I do have one 3xgreat grandfather Shawers In London, that I do not know the origins of.  I wonder now?

Then it's "Lincolnshire" with 4.8%.  Brilliant!  I had a 3xgreat grandfather from the southern parts of Living DNA's Lincolnshire sub region.  That fills my documentary record almost perfect.  The small "Central England" percentage would also tie to this line.

Then follows a number of low percentages from all over Southern and Eastern England.  They might tell a story, or might not.  Surprisingly Cornwall and Devon show up in low percentages, as does Yorkshire.  Did my Shawers line actually come from one of those regions?  I have seen Shawers in Devon, Cornwall, Shores in Yorkshire, and Shawers in Lancashire.

2) What is excluded can also demonstrate the accuracy of such a test.  No Welsh, Northumbrian, French, Normand, Irish, Scottish, or Iberian ancestry suggested.  Not that I'd have any objection against descent from any of these, or anywhere - but that this test successfully sees that I am NOT descended from these close regions, is to my mind, a great success, and a vast improvement on any past autosomal DNA tests for ancestry by other businesses.  The truth is, that the English are so like these other populations!

On mtDNA they get my haplogroup down to H6a1a.

They have not yet completed my Y-DNA analysis.  I guess L in an English tester might have thrown them a bit.

No other DNA test has ever existed quite like this.  My initial response is - an amazing test.  The future of autosomal testing for Ancestry.

My Ancestral Events Mapped

Here I map the ancestral events as recorded on my Gramps genealogical database.  These events can be baptisms, marriages, census records, etc.  The larger the dot, the more events for that particular parish.  I have modified images of Southern England from OpenStreetMap.org Copyright attribution-sharealike 2.0 generic.

My Mother's Ancestral Events.

This includes the recorded events for my mother's 134 recorded direct ancestors and siblings.  As you can see, her known ancestry over the past 330 years has been incredibly localised!  All English.  All East Anglian.  Almost entirely in Norfolk - with one line drifting back to nearby Suffolk.  An incredibly dense cluster in East Norfolk, around the River Yare in Broadland.  Sure enough second cousin and third cousin marriages have been detected in her tree.

My Father's Ancestral Events

This includes the recorded events for my late father's 116 recorded direct ancestors and siblings.  A little more travelled over the past 330 years, although I feel that the events record has a bias in research to show this - as indeed, I estimate his known Norfolk ancestry over the past 330 years to amount to at least 70% of his combined heritage.  Nonetheless, some of his lines trace back temporarily to London, then back mainly to Oxfordshire and the Thames Valley.  All South-East English again.

None of this makes my family any more special than any other family anywhere else in the World, with any type of recent heritage and admixture.  Indeed, the English are a particularly admixed population. However, in testing commercial DNA tests for ancestry, I feel that we offer a good reference sample of SE English, and even East Anglian Norfolk.

I'm particularly interested in how these commercial DNA companies are failing to discriminate ancient or population admixture, from recent (350 years) family admixture.  Some populations they are able to detect with some certainty and accuracy.  However, others such as the English, not at all.  They are unable - despite their claims otherwise, to break recent autosomal admixture on lines over the past ten generations, from earlier, sometimes much earlier population admixtures.

I'm looking forward to seeing if the new Living DNA test fares any better, with it's rich British data set.

Living DNA Kit

Well, the kit arrived in good time!  Living DNA only just announced yesterday afternoon, on their Facebook Page, that the first batch of kits were ready for despatch - and it was here in Norfolk this morning!

Unfortunately, I can't activate it until the service goes live on Friday midday.  So I've got to wait a few days.  Ugh.  I also notice that the return address for the completed sample, is back to their base in Frome, Somerset.  So I'm guessing that they'll pile them up until they ship them to the lab in Denmark.  Must be patient!

A new test - LivingDNA test for Ancestry

You might think that following my recent posts, that I've lost all faith in DNA testing for Ancestry.  Not at all.  I just object when people take the analysis results of autosomal DNA tests for ancestry, as infallible truths.  They are clearly not.

So far this year, I have commissioned two 23andMe tests, and three FT-DNA tests, a FullGenomes analysis, and a YFull analysis.  I have also used free analysis at WeGene and DNA.land, and have run three raw files on GEDmatch calculators.  You'd might also think that I've done enough testing for one year!  I thought that as well.  Then a new service just entered the market.

Living DNA Ancestry attracted my commission on two particular points.  1) it has an incredible British reference, that promises to break ancestry composition into 30 British regions - in addition to global analysis.  If it works, then this is a must for people with significant British ancestry.  2) it uses the latest cutting edge test chip.  The latest Illumina chip based on Global Screen Array (GSA).  In addition, it uses a European based lab (Denmark), it tests Y-DNA, mtDNA, and autosomes.  It tests more SNPs on all three counts, than other current chips used by competitors offering autosomal plus tests.  Raw files for the test results will be available for download.

The British Reference

Living DNA will be using a British reference broken down into an incredible 30 regions, across England, Scotland, Wales, Orkney, and Northern Ireland.  The reference uses the much heralded POBI (Peopling of the British Isles 2015) data set.  This project collected 4,500 blood samples from people that could claim four grandparents in the same area, from across the regions of Britain.

A little about the POBI project below:

The British reference does not include the Republic of Ireland.  However, LivingDNA are confident that they have collected a good global reference, and I understand, that they are seeking a similar quality Irish data-set for the future.  

In comparison, other providers of DNA tests for ancestry, only reference to Britain, or the British Isles & Ireland, as a single reference point.  And as can be seen by my previous posts, with limited success.

They also hope to provide imports for formats of raw file from other test companies in the future.  LivingDNA do not themselves currently offer relative matching, or health information.  Their service is for now, primarily for ancestry.

The Chip

They will be using a custom version of the latest Illumina chip technology, the Global Screen Array (GSA).  It is encoded with:

650,000 autosomal DNA SNPs

20,000 Y-DNA SNPs

4,000 MT-DNA SNPs.

In comparison for example, the 23andMe V4 chip scans for:

577,000 atDNA SNPs

2,329 Y-DNA SNPs

3,100 MT-DNA SNPs.

I hope that LivingDNA will also use up-to-date haplogroup nomenclature and information.  23andMe with their V4 chip still use very dated 2009 nomenclature.

So, let's see if this new service is any improvement to my results, compared with the hit and miss of 23andMe, and Family Tree DNA (FT-DNA).  Will they be able to identify and locate my English roots successfully?  What will the improved chip make of my haplogroups?

The Southern European DNA enigma. Option 1. The DNA Analysis is true

My great grandfather Fred Smith, and my great Uncle Lenny.

Option 1.  The DNA Analysis for Ancestry is true

This option supports the commercial DNA for ancestry companies claim, that I have Southern European ancestry.  For this to be the case, my Southern European ancestors must have either a) been hidden in the gaps, the missing ancestors.  b) be NPE (non parental events - biological ancestors that are contrary to recorded ancestors.  Usually male). c) predate my genealogical record over the past 360 years or d) my recorded genealogy is faulty.  I have badly researched my ancestry and have made mistakes.

What gaps are there?  All of my generations are complete to and including my Generation 5.  I have all of the names of my 16 direct ancestors at that generation (great great grandparents).  All appear totally English, of English religious denominations.  Their surnames and location were: Brooker of London (previously Oxfordshire), Shawers of London, Baxter of Norfolk, Barber of Norfolk, Smith of Norfolk, Peach of Norfolk, Barber (again) of Norfolk, Ellis of Norfolk, Curtis of Norfolk, Rose of Norfolk, Key of Norfolk, Goffen of Norfolk, Tammas-Tovell of Norfolk, Lawn of Norfolk, Thacker of Norfolk, and Daynes of Norfolk.

I have photographs of three of them.

Everything looks utterly English - the majority East Anglian.

The gaps start to appear at Generation 6 (G.G.G Grandparents)  Three missing male ancestors - all missing fathers of illegitimate births.  29 out of 32 direct ancestors recorded though.  All appear English again:  

Brooker of Oxfordshire, Edney of Oxfordshire, Shawers of London, Durran of London (previously Oxfordshire), Baxter of Norfolk, Barber of Norfolk, Smith of Norfolk, Hewitt of Norfolk, Peach of Lincolnshire, Riches of Norfolk, Barber of Norfolk, Ellis of Norfolk, Goodram of Norfolk, Curtis of Norfolk, Larke of Norfolk, Rose of Norfolk, Barker of Norfolk, Key of Norfolk, Waters of Norfolk, Goffen of Norfolk, Nichols of Norfolk, Tovell of Norfolk, Tammas of Norfolk, Lawn of Norfolk, Springall of Norfolk, Thacker of Norfolk, Daynes of Norfolk, Quantrell of Norfolk.  Oh, and a "Mary Ann" of Norfolk.

Again, all English, English religious denominations.  Mainly rural working class East Anglian.  No sign of any foreigners.

The record does start to really fall away at Generation 8.  From then on, it's a minority of lines recorded, stretching back to the 1680's.  However, at no where on my record of 207 direct ancestors, do I see anything that looks remotely non-English, never mind Southern European.  No sign of any Catholicism anywhere.

Let's just consider percentages of DNA though.

Each grandparent gives me 25% on average.

Generation 3 (grandparent) 12.5%

Generation 4 (great grandparent) 6%

Generation 5 (great great grandparent) 3%

Generation 6 (G.G.G grandparent) 1.5%

Beyond then genetic recombination starts to really kick in, and you may have zero DNA from any particular ancestral lineage.  It get's washed out.  Only if it comes down from a number of lines is admixture highly likely to survive further back.

23andMe (V4 AC in spec after phasing with one parent) claims that both of my parents had 2% Southern European DNA.  That takes it back to around MY Generation 6 or 7.  Sure, I'm missing 9% of Generation 6, and 20% of Generation 7.  My Southern European ancestors could have admixed then.  But what are the chances of it happening on both sides?  Possible, yes.  I think unlikely though.  No Southern European names or religions passed down.  When was this? Around 1780 to 1820.  Okay, if I want to piece national history into it, how about The Peninsular Wars (1807-1814)?  The Royal Norfolk Regiment took an active part in that campaign.  Could I have (presumably male) ancestors through both of my parents, that brought back Portuguese wives?  It is a possibility.  I'll acknowledge that.  But am I weaving history in order to make it fit the DNA analysis?

FT-DNA (FF My Origins) claims that I have 32% "Southern European" ancestry.  No sign of it in family history or photography.  Too much likeness of recorded fathers.  Okay, maybe it goes further back, but on multiple lines?  I think that we are pushing this one.  What is the chance of so many Southern Europeans given my above recorded or known English ancestry.  It couldn't have happened.

DNA.land gives me 19% Southern European, including 13% Balkan.  The same problem as the FT-DNA analysis.  It just doesn't wash.  It cannot fit.

Therefore I conclude:

  1. FT-DNA and DNA.land claims of my Southern European percentages cannot realistically be explained by gaps or missing ancestors.
  2. 23andMe claims of 2% Southern European could be explained by the missing gaps - just!  But would need quite a coincidence to be on both sides, just in those gaps.

That pretty much covers it for gaps, NPE's, etc.  If any Southern European on the other hand, predates my genealogical record, then it would need to be on multiple lines, and to have lost all sign of Southern European surnames, religions, and traditions.  I haven't seen any history of a mass Southern European migration to England 600 - 400 years ago.

Exploring Gedmatch Eurogenes

The above grave is of my great great grandparents Robert and Ann Smith at Attleborough, Norfolk.

L1b Y-DNA News

First of all, it's looking good on the Y-Front.  My Y111 sample kit has arrived from FTDNA.  I also sent my 23andme V4 raw data to the administrator of the FTDNA Y Haplogroup.  He replied the next day "the raw data confirms that you are positive for M317 and negative for downstream SNPs M349 and M274. A very rare result for a NW European. It will be interesting to see who are your closest matches at 67 and 111 markers.".

So it doesn't look as though my L1b has anything to do with the M349 Rhine-Danube cluster.  I wonder where it comes from, how and when it got into an English ancestry?  It's starting to dawn on me just how rare it is in NW Europe.  European Y-Haplogroup maps and tables simply don't display or list it, because Y-DNA Hg L is not even considered a European Haplogroup, nevermind on British Haplo-maps.  All of those R1b's and I2's.  Not an L in sight.  I can see that having an unusual haplogroup is a mixed blessing.  Sure it's interesting, but no one knows much about it, because there is so little data on it in Europe, and so little research.

I had my first case of disbelief of my L1b Y-DNA on an FTDNA surname project group.  I reported my Y haplogroup as reported by 23andme (using ISOGG 2009) as L2*  The administrator retorted "It is NOT the "L" haplogroup, instead, it is "I".  So I linked her  copy of my 23andMe Paternal line report.  This time she replied  "Goodness gracious Paul. I administer many, many projects and yours is the first "L" You see, it has problems.

Wouldn't it be just great if I found someone else descended from the Berkshire Brookers by their Y line, that had the same haplogroup?

Gedmatch Eurogene admixture results for an Englishman

GEDMATCH offers free tools for analysing the autosome DNA of your raw data, from 23andme or Ancestry.com.  One suite of tools that are useful for analysing population admixture, are the Eurogene.  As an English person, with strong paper English ancestry - including almost certainly early medieval admixture, I thought that I'd get a comparison out of the way.  See which "works" best for my known ancestry and likely heritage.  I'm trying oracles on my 23andMe V4 raw data, for 1. EU Test, 2. K13,and 3. V2 K15.
1. Eurogenes EU Test
Oracle

1 Cornish 4.6
2 English 5.01
3 NL 6.26
4 West_&_Central_German  6.92
5 Orcadian 7.02
6 IE 7.33
7 FR 7.51
8 Scottish 7.95
9 DK 9.39
10 NO 11.57

A bit strange that it sees me as first "Cornish".  I don't know where it got that reference from.  I have no known Cornish ancestry.  However, 2 and 3 are likely.  As a whole it's not a bad prediction, just that the ball landed a bit to the West.
What about mixed populations?  What are it's favourite admixtures between two populations for me?

1   83.7% English  +  16.3% French_Basque  @  3.11
2   79% English  +  21% ES  @  3.17
3   63.7% English  +  36.3% FR  @  3.18
4   80.2% English  +  19.8% PT  @  3.5
5   51.8% FR  +  48.2% Scottish  @  3.54

Okay, not bad - it's given up on the Cornish.  However, it seems to point to France, Spain, and Portugal as a secondary source.  That is eerie, because 23andme threw up a speculative 2.4% South European including 0.5% Iberian.  I do wonder if I actually do have some unrecorded South European ancestry, even Iberian.

2. Eurogenes K13
Oracle

1 South_Dutch 3.89
2 Southeast_English 4.35
3 West_German 5.22
4 Southwest_English 6.24
5 Orcadian 6.97
6 French 7.63
7 North_Dutch 7.76
8 Danish 7.95
9 North_German 8.17
10 Irish 8.22

I like K13.  The Dutch may be there in admixture, and I know that they do often share some common patterns with SE English.  So I can excuse it making it to position 1.  Then in second place, the ball scores a goal.  Yes, I am SE English.  Most of the other suggestions could represent ancient admixture.

How about two population proposals?

1   65.6% Southeast_English  +  34.4% French  @  2.03
2   84.9% Southeast_English  +  15.1% North_Italian  @  2.05
3   63.5% Norwegian  +  36.5% Spanish_Valencia  @  2.06
4   69.7% North_Dutch  +  30.3% Spanish_Valencia  @  2.08
5   87.5% Southeast_English  +  12.5% Tuscan  @  2.09

It's got the SE English spot on, but all of these Iberians again!  Is it trying to tell me something?

3. Eurogenes EU Test V2 K15
Oracle

1 Southwest_English 2.7
2 South_Dutch 3.98
3 Southeast_English 4.33
4 Irish 6.23
5 West_German 6.25
6 North_Dutch 6.79
7 West_Scottish 6.84
8 French 6.85
9 North_German 6.89
10 Danish 7.26

Very good, except again, a bit skewed to SW England.  However, to be fair, I do have some slightly westward ancestors in the Oxfordshire area.  The rest is spot on.
What does it offer as a hybrid?

1   73.9% Southwest_English  +  26.1% French  @  1.27
2   71.8% North_Dutch  +  28.2% Spanish_Cantabria  @  1.3
3   89.7% Southwest_English  +  10.3% North_Italian  @  1.35
4   91.6% Southwest_English  +  8.4% Tuscan  @  1.4
5   86.4% Southwest_English  +  13.6% Spanish_Galicia  @  1.43

Those Spanish again!  Goes for SW English over SE English as the primary ancestral population.

Out of these predictions, my gut feeling is that they are all good for single population match.  On two population mix, they all suggest Iberian minorities.  Either I have an undiscovered South European ancestor, or something else is going on.  Do other English get this?  I can't really pick a winner.