Journals of a Time Traveller

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?

Here I'm considering the third option to my enigma.  My known ancestry is 100% English.  However, autosomal DNA tests for Ancestry, by commercial companies, and by third party analysis, suggest that I have a mixture of European ancestries, including varying percentages of Southern European.  I'm trying to best explain this phenomena.  In previous posts, I considered 1) that my paper record is incomplete, or biologically incorrect.  2) that something ancient is picked up in analysis of present day English testers - that maybe reflect shared algorithms with ancient admixture, perhaps prehistoric, or Roman.

Now in this post, I consider the third option.  That commercial DNA companies exaggerate their claims to be able to differentiate to any successful degree, between different regions of Europe in my ancestry.  If this is indeed the case, it has significant repercussions for testers for example, in the USA, Canada, Australia, etc.  If they have a poor paper trail, and poorly known ancestry, maybe it's all too easy for them to regard such DNA tests for ancestry, as indisputable and accurate truths.

Commercial DNA companies for Ancestry, are under pressure to supply to market demands.  Their markets have been dominated particularly by USA customers.  Some of them seasoned genealogists with good quality paper trails.  Others, attracted by the easy option to know their ancestry before the, as 23andMe puts it, the Age of Migration before the past few centuries.  Instead of spending a lifetime chasing documents, they can simply send a DNA sample to a company, and know their roots.  People trust the science of DNA testing for ancestry.  That is the demand that commercial companies can cater for.

But what if their abilities to accurately detect ancestry from Autosomal DNA is exaggerated?

Lack of agreement between analysis.

Population References

Is it all Bunk?

The above photograph taken by me, of Neolithic skulls from the Tomb of the Sea Eagles, Orkney.

I'm not the only English person reporting "Southern European" on their Autosomal DNA for Ancestry test results.  I've noticed that on 23andMe, for example, that English often report these strange low percentages of "Southern European" in their ancestry composition results.

There may be something odd about the ancient ancestry of the English, that we do not yet know.  Others have also pointed out that in ancient admixture calculators, that the English receive lower percentages of ANE (Ancient North Eurasian) than do the Irish, Scottish, or other nearby neighbours.  POBI (People of the British Isles 2015) suggested a unknown immigration into Southern Britain during Late Prehistory perhaps from the area that is now France.

Some point to perhaps, more Neolithic survival in lowland Britain, relating perhaps to Sardinian patterns.  Others suggest immigration from Southern Europe and elsewhere during 360 years of Roman occupation.

Option 2 is a possibility - perhaps these is something about English ancestry that we do not yet know about, that confuses the algorithms of commercial DNA companies, when trying to identify our more recent ancestry.

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.

First, a recap

Above photo taken by myself of the Ring of Brodgar, Orkney

I've modified this from a post that I made on a DNA forum, in response to people discussing out-dated origin stories, in response to a thread looking at ancestral composition for the English.  There is so much misinformation out there, and few people actually try to look at the latest evidences.

It starts by looking at the key points of a recent Irish study.

Cassidy, Martiniano, Murphy etal Study of Neolithic and Bronze Age migration to Ireland

http://www.pnas.org/content/113/2/368.full.pdf

https://www.theguardian.com/science/2015/dec/28/origins-of-the-irish-down-to-mass-migration-ancient-dna-confirms

Key points.

• Ancient DNA from earlier Neolithic farmers suggests an origin from the Near East.

• Later DNA from Bronze Age suggests a new population had arrived and dominated, with origins from the Eurasian Steppes, including the present day predominance of Y haplogroup R1b, lactose tolerance, and blue eyes. This displacement event appears to have occurred throughout much of Western Europe. The founder population on the Steppes has been linked to the archaeological population known as the Yamna or Yamnaya.

A background to the Yamna hypothesis to help people understand what the above study supported:

The Yamnaya were a population that existed across the Pontic and Caspian Steppes from what is now Ukraine, to Kazakhistan. They themselves were an admixed population, with ancestry from various different groups of Eurasian hunter-gatherers, and from the ANE (Ancient North Eurasian). They carried a number of successful adaptations, including the use of the wheel, improved selective breeding of horses for both riding and haulage, lactose tolerance, use of horse drawn wheeled carts, and a very successful pastoral based economy revolving around the herding of a number of species of livestock.

They are strongly figured to have carried an Indo-European language into Europe and elsewhere (South and Western Asia). That Indo-European language being the ancestor of the vast majority of modern European languages today. They may have also carried many of the most common haplogroups of modern Europeans, including Y hg R1a, R1b, and some mt hg H types among others.

There is a hypothesis that the earlier peoples of Europe, the Early Neolithic farmers, who had largely descended from early farmers in the Levant / Anatolia, had been suppressed by a number of possible environmental and climatic events. This might have paved the way for such a successful displacement of European populations.

As the descendants of the Yamna swept westwards into Europe during the Copper Age, so they spawned a series of new archaeological cultures including the Corded Ware of Eastern and Central Europe, and the Bell Beaker culture of Western Europe.

The Bell Beaker culture spread from Central Europe to the Western Atlantic Seaboard, and from Portugal up to Scotland. Classic artifacts include archer burials in round barrows, the bell beaker ware pottery, round scrapers, and barbed and tanged arrowheads. It was the dominant culture of Early Bronze Age Europe.

One suggestion is that it spawned the later Iron Age Celtic cultures, including the classic Western Atlantic Seaboard Celtic Culture. This culture may have simply evolved locally and through trade links along that seaboard.

The Irish study above supports the Yamnaya hypothesis. It supports displacement during the Early Bronze Age, and that the present day, fairly homogeneous population of Ireland, largely descends from Copper Age Eurasian Steppe pastoralists.

Okay, so what if we apply that also to the late prehistoric British populations? Scottish and West British today appear to have a close genetic distance to the Irish. How about the lowland SE British? It might be the case, that they had fresh admixture, exchanged with the Continent, and particularly with the expanding Germanic cultures. These events could have occurred even during late prehistory.

Now People of the British Isles (POBI) Study 2015:

http://www.peopleofthebritishisles.org/nl6.pdf

This genetic study looked at the British Isles including Northern Ireland, but excluding the Republic of Ireland. It tested a large sample group of present day British with known local ancestry.

Key points.

• Orkney had the most distinctive population, with a known high percentage of Norse ancestry.

• The Welsh were distinct from the English. However, they were the most diverse group, with a clear division between the North Welsh and South Welsh. Cornwall was also distinctive from English.

• Northern Ireland clusters with Scottish.

• There was no homogeneous shared British “Celtic” population. The Scottish, North Welsh, South Welsh, and Cornish being quite distinct from each other.

• The South-East British (most of the English) were surprisingly homogeneous, although the boundaries of the old Anglo-Saxon kingdoms could still be distinguished.

• The Continental Anglo-Saxon contributiion to present day English people appeared to be circa 10% to 40%. This contradicts Bede's claims of a genocide. The English descend more from earlier British populations than they do from Anglo-Saxon immigrants.

• Although the Norwegian Viking contribution to Orkney was distinctive, the Danish contribution to Eastern England could not be detected. This may be because of the close genetic distance between Danish Viking and some earlier Anglo Saxon settlers makes it impossible to see.

• Although there was no “Celtic Fringe”, the Welsh appear to be closest to the late prehistoric British population.

• Any Iberian contribution appears to be tiny and insignificant.

• There appeared to be a contribution in Southern Britain, particularly in Cornwall, from a population shared today by the North French. This contribution appears to have occurred during late prehistory and is historically unknown.

Okay, so that is suggesting a diversity across the British Isles that extends into Prehistory. A key finding to this thread is that it found the English to be an admixed population, with earlier British ancestry dominating Anglo Saxon ancestry from the Continent.

Finally, I think it is worthwhile bringing up another recent study:

Iron Age and Anglo Saxon Genomes from Eastern England. Schiffels, Haak, etal. 2015.

This qualitative study focused on ancient DNA from a number of Iron Age and Anglo Saxon cemeteries in the Cambridge area of SE England, referenced against modern populations.

Key points.

• The East English derive 38% of their ancestry from Anglo-Saxon immigrants

• The closest genetic distances on the Continent between the Anglo Saxon settlers and present day Europeans was to the Dutch and Danish.

• They found evidence of admixture and intermarrying. Individuals with both Iron Age British, and Anglo Saxon ancestry.

• People of Iron Age British ancestry were adopting and embracing Anglo-Saxon culture and grave goods.

• The richest graves were of local Iron Age British ancestry (with Anglo Saxon cultural artifacts). The poorest graves were recent Anglo-Saxon arrivals.

My conclusion:

• We have to be careful about who we regard as the Celts. A Celtic culture did exist, but it wasn’t necessarily brought to the British Isles and Ireland by an Iron Age people. It may have developed on the Western Atlantic Seaboard from earlier Bronze Age peoples.

• Those Bronze Age peoples, predominantly descended, from Eurasian Steppe Pastoralists, that had swept across Europe, bringing innovations. They are the oldest peoples of Ireland and the British Isles, but they did not form a homogeneous Celtic Fringe. There must be more to it.

• The Anglo-Saxon event in SE Britain was a major and significant migration. However, it was not the genocide of Bede's claims. Hengist and Horsa were clearly mythological origin characters akin to Romulus and Remus.

• The modern day English are an admixed population. They have a foot both in earlier British ancestry, and in Anglo-Saxon / North Sea migration.

Copied from openstreetmap.org and modified under the Open Data Commons Open Database License.  

Bridges and Walls, Snakes and Ladders

I've noticed two perspectives within the broad scope of genealogy where it ties to population genetics.

• Some people, those with nationalistic, right wing political views, frequently look for what divides their ancestry from others.  What defines and ties them to a historical population, or even to a land.  They may well want to prove connection to a romanticised historical group within their part of the world.
• Others - those of a more international, liberal persuasion, instead tend to look for what unites them with other peoples alive today - what connects them within the community of humanity.

I have to confess to being more of the latter.

On Paper

I started out with a pretty well researched paper genealogical record.  A family tree.  A family history.  Researched through oral history, interviews, parish records, state records, and then on to digitalised records in more recent years.  A genealogical database of 1,570 individuals for my kids, and 207 direct ancestors recorded for myself - going back to the 1680s.  My recorded ancestry was 100% English - dominated by the County of Norfolk.  The majority of present day English perhaps have some non-English ancestry, perhaps Irish or Scottish, or something a little further afield.  I didn't find any.  All English surnames, and English denominations.  Some of those surnames however, did echo rather more ancient immigration from across the North Sea.

Autosomal DNA Testing

Autosomal DNA testing for ancestry provided a bit of a surprise.  I took a 23andMe DNA test, along with my mother, who's results I phased with to provide more accuracy.  The 23andMe Ancestry Composition analysis in standard mode didn't simply see me as English, or even as British.  It did see me pretty much as 100% European.  Not a hint of Africa nor Asia within the past several hundred years.  It saw 86% of my autosomal DNA as definitively North-West European.  However, it could only see a mere 17% as distinctly belonging to British & Irish.  So, the ancestry test of my autosomal DNA certainly agreed that I was European, NW European even, but couldn't be sure on how English or even British that I was.

23andMe Ancestry Composition in the very unreliable speculative mode rated my British/Irishness at only 37%.  The highest percentage of focus - but it saw 22% of my autosomal DNA ancestry as French / German, 1% as Scandinavian, and 2% as South European.  So considering my 100% English ancestry on paper, autosomal DNA testing couldn't really be very sure about my ancestry.  Even in speculative mode, it had 34% of my DNA as "Broadly NW European", meaning that it couldn't be sure, but somewhere in that corner of that continent.

Fair enough I suppose.  I've lost a certain amount of faith in any autosome DNA tests for ancestry to be able to pinpoint the English.  You see, even ignoring recent waves of immigration of Irish, Scottish, French, Germans, West Indians, South Asians, etc, etc.  The truth is that the English were already a very admixed population even 1,500 years before present.  Already a mixture of prehistoric populations, immigrants from across the Roman Empire, then from across the North Sea, from the Low Countries, Northern Germany, Denmark, Scandinavia, etc.  23andMe claim that their product reflects your ancestry 500 years ago.  No it does not.  It uses modern reference populations.  Genes have been circulating around the World for a long time.  Autosomal DNA tests for ancestry have really improved.  They are pretty good now for recognising a Continent - sometimes even a corner of a continent, as the source of some ancestry.  But they cannot pinpoint many populations with accuracy, and they cannot pinpoint the English.

So, my paper record said English.  My 23andMe autosome DNA test said North-West European, but couldn't even pinpoint British.  It suggested admixture.  It did however - this is important - only see me as European.  Okay, in Standard Mode, it did have a tiny 0.3% that it failed to assign to Europe, nor anywhere.  It did not see Asian.

Haplogroup DNA Testing

Haplogroups follow two narrow lines of ancestry.  The Y follows the direct paternal line, the MT follows the direct maternal.  They do not represent the bulk of your ancestry.  However, they can tell a more accurate, and longer term story.  Ancestry can be lost in Autosomal DNA within a few centuries.  In addition, it gets messed up through recombination.  Not so with the two haplogroups.  So where did mine come from?

My MT-DNA

There is an awful lot that we will know in future about our haplogroups, that we don't yet know - especially in the case of mt-DNA. However, we do know that my haplogroup, H6a1, did not originate in Europe.

H is common in Europe, and it most likely originated either there, or in South West Asia, during the Upper Palaeolithic. H6 did not originate in Europe.  It may be West or Central Asian in origin.  H6a1 has not been recovered in any ancient DNA within Western Europe.  However, it has been recovered in the DNA of the Yamnaya on the Eurasian Steppes.  For this reason, it is generally thought - based on evidence so far, to have been brought into Western Europe during the Early Bronze Age, by the expansion from the Eurasian Steppes at that time.

It isn't too fanciful - based on this evidence, to imagine that my distant grandmothers belonged to tribes of Early Bronze Age pastoralists, living on the Steppes of what is now the Ukraine.

My Y-DNA

This one has been a cracker for me.  Anyone that has followed my blog, might be getting bored with this.  I've thoroughly tested my Y-DNA.  It's not an exaggeration to suggest that it is quite likely Ancient Persian.  Based on current evidence, I believe that my Y-DNA arrived into England within the last millennia - probably between 350 and 800 years ago.  I'm still working on it's most likely route here.  I do believe that it was most likely still located in the region of Iran circa 1,000 to 2,000 years ago.  My nearest 111 STR match is to a guy in Australia who's paternal line lived in Birjand, Eastern Iran.  We shared a common ancestor around 2,000 years ago.  My terminal SNP is shared on record with only one other man so far - in the world.  He was a Balochi speaker that lives in Makran, SW Pakistan - close to the border with Iran.  The Balochi are believed to have migrated from North Iran between the 5th and 14th centuries AD.

Nomad camp, at the Zagros Mountains, Iran.  By C Whitely on Flickr under Creative Commons License.

A bit more distant, I have a Y cousin in the USA that maybe I shared a common ancestor with 3,000 years ago.  He is of Azores Portuguese descent on his Y line, but he carries a distinct STR marker that has been associated with the Parsi, who migrated to India and Pakistan, but originated in Iran.

And going further back, the Y haplogroup L most likely originated within the area of Iran and Iraq, during the Ice Age.  It would have been carried by Upper Paleolithic hunter-gatherers in that region.  13,000 years, I shared grandfathers with two Pontic Greek Y cousins, who's ancestors lived in Trazbon, Eastern Anatolia.  Maybe one Y ancestral son headed to the Black Sea, the other settled at the Caspian Sea?  The Ice Age was drawing to a close, but with a ferocity and climate instability that drove bands of people apart and into refuges at that time.

The Parsi connection keeps hinting.  They descend from Persians that worshiped the ancient religion of Zoroastrianism.  I've just seen a Y haplogroup study of men in Pakistan.  The background level of Y haplogroup L-M317 sat at 1.1%.  However, in the sample of Parsi men there - it spikes up to 13.3%.  That might not be the route however, of my Y line.  The SK1414 SNP turned up in that same study, but that was found on the Makrani Boluch man that was tested L-M317, not in the 12 Parsi men that also tested positive for L-M317.

Conclusion

I prefer bridges to walls, and that is what I got.  My paper ancestry said 100% English - much of it East Anglian.  I'm quite proud of that, but I'm equally proud of my more distant ancestors that emigrated here.  I've found North Sea admixture, from places such as the Netherlands and southern Scandinavia.  I've found a grandmother in a Bronze Age tribe of pastoralists in the Ukraine.  I've found ancient Persians, descending from hunters of Ibex in the Iran / Iraq region.  I've found distant cousins in the USA, Iran, Pakistan, Australia, and Turkey.

One species, one family.