Genetic Genealogy - verifying the family tree with shared DNA segments

This is an aspect of Genetic Genealogy that I'm sure is well known to some researchers, but that, I'm only just starting to appreciate.  I've been DNA testing for ancestry heavily for a year or two, but my prime interest has been older ancestry, admixture, and population genetics.  All of my early attempts to contact matches through 23andme and GedMatch, resulted in frustrated conversations with North American testers, that had no paper trail back before their ancestors emigrated.  Today, I matched on AncestryDNA with a third cousin.  The DNA prediction was fourth cousin, but the relationship on paper is third cousin.  This was my third match, confirmed by both shared DNA segments, and by a shared paper trail to common direct ancestors.  How cool is that?  Finding that yourself, and other researchers, share segments of the same DNA that appear to have been inherited through recent common descent.  Finding each other through the code of Life that is in our cells, and being able to see where that DNA came from in our family trees!

The image at the top of this post represents the biologically verified tree, as represented by colour shaded areas of my pedigree fan.  This is based on descent from shared ancestry found in DNA matches.  There is always the slight possibility that we share DNA from other unknown or unrecorded routes.  But the probabilities are high, that these shared segments of DNA do come from the known common ancestral roots in our trees.  The stronger the verification, perhaps through multiple matches, the darker the shade.

This discovery of a third cousin on AncestryDNA, combined with my mapping of the correlations between paper trail and DNA matches serves as an incentive to work harder on finding and contacting matches.  I've also spotted common DNA segments with someone that flags up as a fourth cousin ... but according to our shared paper trails, and family lore, should be a second cousin.  I'm trying to get a response from the tester.  But have I uncovered another family secret?

FTDNA (Family Tree DNA) My Origins Autosome Test for Ancestry

I know I should have smiled!  Me, myself sitting outside of the archaeology museum earlier this year, at Sofia, Bulgaria.South-West Europe.

FT-DNA Family Finder My Origins

I haven't posted much coherent lately, because, well, my Life changed, and consequently I've been pretty busy, in a very good way.  However, my exploration into genetic genealogy hasn't ceased at all.  Indeed, I took advantage of the Family Tree DNA (FTDNA) Summer sale, and bought the USD $79 Family Finder test.

No need to send a fresh sample, this was the third test from the sample that I sent to FT-DNA's US lab earlier this year.  FTDNA Family Finder is an autosomal DNA test only, without haplogroup results - but I've tested my Y-DNA to death already, and I know my mtDNA haplotype.  The services supplied include relationship matching, raw file download, and an Ancestry analysis named My Origins.  Hey, for that price, in GBP £, that is el cheapo good value.  And it's a good test, with about 690,000 SNPs tested, against 23andMe's current 577,382.  Smoking.

My prime interests was in 1) comparing the raw data with 23andMe on GEDmatch, and 2) seeing what FTDNA My Origins has to say about my autosomal DNA for ancestry.

So what did I find.

The former, comparing raw data files, I've done.  But briefly, the calculators DO vary for the two files, but not by very much - except maybe, that on Eurogenes K13, the nearest GD on my FT-DNA file is closer to correct - putting SE English closer this time than South Dutch.

The latter?

Family Tree DNA reported My Origins as:

100% European.

Broken into:

36% British Isles
32% Southern Europe
26% Scandinavia
6% Eastern Europe

This is a pretty bizarre result.  36% almost hits dead on my 23andMe Ancestry Composition (spec) result for British Isles (32% before phasing, 37% after phasing with one parent).  Perhaps they are using a similarly biased reference?  I'll blog on that soon as well.

26% Scandinavian is massive.  23andMe AC spec reported 7% before phasing, and 2% after phasing with one parent.

That's pretty much my first report for Eastern European, except for DNA.land's claim of some Balkans (hence my excuse for the above photograph).

but .... 32% Southern Europe, really?  Let's go there next, off to Southern Europe now:



Ancestry and DNA Tests

I'm writing this post in response to a number of comments that I see online with regards to using a commercial DNA test, in order to ascertain ancestry.  Quite often, when someone asks how to find out their family history or ancestry, someone will come back with an answer in the form of "just spit in a vial, send it to Ancestry.com, and they'll tell you".  It's not really that simple, so I'm making this post, to explain how an ancestry DNA test can help, or not help, you discover your ancestry.  Nicely dumbed down I hope, for the beginner.

Traditional Genealogy

Traditional genealogists usually set out to create a genealogy (family history and tree), using interview techniques, artefacts, and oral memories, recorded from older relatives.  Artefacts might for example, include old family medals, or photographs.  They then extend the research, through documentary evidences, such as birth, death, and marriage certificates, church registers, census records, transcripts, electoral rolls, and military records. If they are interested in recording all ancestral information, and not merely a single line such as the surname line, then this research can go on for months, years, even decades.

What you cannot do, is to simply pay a small fee, and your entire family history drops through the letter box in a brown envelope.  It takes years of time to research, collate, and to verify a good family tree.  Most genealogy enthusiasts don't mind this, because they actually enjoy doing the research itself.  It becomes a hobby, even sometimes a passion.

However, a number of commercial DNA companies may give the general public the impression, that you now can simply pay a fee, spit or swab, and your ancestry magically appears for you on a website.  It's big business.  Does it work though?  Exactly what is genetic genealogy?

What is Ancestry and why do we care.

Ancestry can simply be defined as our descent from forbearers.  Why do we care who they were? Which forbearers or ancestors?  How many are there?  How far back?

Of course, not every one does care.  Not everyone cares about history.  But for other's how we define ourselves, our communities, and families, it does matter.  It tells us who we are, where we came from.  It defines us, gives us grounding.  It gives us identity.  Wars have often been inspired by ancestry.  At the same time, a deeper appreciation of the human family, and it's common ancestry, can be used to relate to those elsewhere.  One big family.  Discovering the immense poverty and hardships of our ancestors can help us to appreciate what we have, and to help others in need today.

So what ancestry can we discover?  For those few that merely concentrate on one patriarchal line, it's quite simple to define - the generations of a surname.  However, beyond that one narrow line of descent, few appreciate exactly how much total ancestry that we have.  Lets look at our biological ancestors at each generation:

  • 2 parents
  • 4 grandparents
  • 8 great grandparents
  • 16 great grandparents
  • 32 g.g grandparents
  • 64 g.g.g.grandparents
  • 128 g.g.g.g grandprents
  • 256 g.g.g.g.g grandparents.

These are only your 510 most recent direct ancestors, yet just those generations, will take you back to only around 250 years of family history.  Now add all of the recorded children of these direct ancestors - the great great uncles and aunts to the theoretical family tree.  You're probable going to have a tree of around 1,300 individuals.  That is just for 250 years.  You have a big family  Go back a few more generations, and it will explode before you reach far.  All of those direct ancestors though, are a part of your ancestry.  You'll most likely carry some DNA from most of them.  They are, from a biological perspective, who you are.

By the way, the number of biological ancestors will not continue to increase infinitely.  Because increasingly, you will find couples within your tree that are distant biological cousins of each other.  As this accelerates through thousands of years, that explains how all modern people around the world, all descend from a very small population around 100,000 years ago.

So before considering what DNA can do for genealogy, we need to consider which ancestors matter to us.  Do you just want to know who your biological parents, or grandparents were?  Do you want to know the names, places and social positions of your ancestors over centuries?  Do you want to know which parts of the world that your ancestors lived 500 years ago?  Do you want to know how some of your prehistoric ancestors moved across the globe, thousands of years ago?  Maybe you want to know everything.

Let's now turn to genetics for genealogy, and how DNA tests can answer some of these questions.

There are two main types of DNA tests for ancestry, although they are often incorporated together by commercial companies:

  1. The haplogroups, the Y-DNA and mt-DNA
  2. Autosomal DNA
The Haplogroups

The haplogroups are chains, or markers, that are carried on one of only two strict lines of descent.  They do not apply to your entire ancestry - just two lines.  As we saw above, we have 256 g.g.g.g.g grandparents (unless any of their descendants reproduced together).  Our haplogroups came from only two of them.  Your haplogroup does not define you.  Yet, it's quite odd, because very quickly, many genetic genealogists do relate to them, rather like a hereditary football club.  They do become an identity, only if you enthuse over them.

The Y or paternal haplogroup, follows the strict paternal line.  From father to son.  Women do not have a Y chromosome, so cannot pass it on.  It has to come from the biological father.  However, within this constraint, Y-DNA is particularly useful to genealogists.  It mutates often, both as STRs and less often, as SNPs (snips).  Because of these frequent mutations, it is useful for tracing shared descent with others.  It can also be aligned with surname studies.  The champion commercial DNA company for Y-DNA research, is Family Tree DNA.

The mt or mitochondrial (maternal) haplogroup, follows the strict maternal line.  From mother to children.  Both sons and daughter inherit their mt-DNA haplogroup from their biological mother.  However, only the daughters can pass it down.  Two downfalls to mt-DNA for genealogy.  1) The surname frequently changes, traditionally nearly every generation through marriage. 2) it doesn't mutate as frequently as the STRs of Y-DNA. It is still a useful tool, and can prove descent through the maternal line.  It can also still be used for studies of much deeper, ancient ancestry.

Autosomal DNA

This is the bulk of you DNA.  All of the snips (SNPs), that make up who you are genetically.  You receive approximately 50% from each parent, 25% from each grandparent, 12.5% from each great grandparent.  This subdivision cannot go on forever, and indeed, once you go back much more than six generations, the approximates start to deviate, so that you may have no snips at all from a particular line that joined your family tree over 250 years ago.

The problem with autosomal DNA is that it can be such a mess.  It recombines randomly with every generation.  Therefore, it is much harder to track ancestry in the same way, that we can with the haplogroups.

So how can they be applied for genealogy:

Biological descent

Not everyone knows who their biological parents were, or where they came from.  This is the first use of DNA testing.  It can be used to find, test, or prove recent descent.  The first hurdle of genealogy.  Both haplogroup evidence, and autosomal evidence can be used to prove or determine relationship.

Cousins

Many genetic genealogists, use DNA to find distant, and sometimes not so distant cousins.  The hope is that they can link trees, share knowledge and research, perhaps copies of artefacts.  Therefore an awful lot of genetic genealogy is about tracing genetic relatives, and establishing common ancestry.

There are two main tools:

  • Haplogroup Projects.  The Y haplogroup is favoured for it's frequent STRs, and also for it's link to surnames.  Family Tree DNA projects track the STR and SNP data of it's members, tracking families, relationship, known mutations.  Project administrators at FTDNA can predict relationship to other members in the project.  Your Y cousins.
  • Shared segments.  Autosomal DNA can be used for finding distant cousins.  23andMe for example, have Relative Finder.  Alternatively customers of any commercial DNA company that gives them access to their raw data, can upload that data to GEDMATCH.  At GEDmatch, they can search for other kits, looking for lengths of shared segments (measured in cM - centimorgans) on the autosomes or X chromosomes.  The longer or more segments can be used to indicate shared ancestry.

It is important to understand, that this is not about directly tracing ancestry.  It is only about establishing shared biological ancestry, with other researchers, with which you may be able to share resources.  In the old days of genealogy, we would find distantly related researchers by browsing through annually printed surname interest directories.  Here, the same thing is happening, but we are finding people by comparing DNA.

Ancestry from Autosomes

Most commercial DNA companies providing ancestry information, now use their own propriety calculators to look at the autosomal DNA of their customers for patterns that they can relate to a number of reference populations.  23andMe for example, uses Ancestry Composition to determine what parts of the world, that the ancestors of their customers lived 500 years ago.  They predict from this in percentages of ancestry.

However, it is very much a developing art.  The problem is that genes have been randomly mixing and moving around ever since prehistory.  The customers of these DNA companies want hard facts.  They want their ancestry accurately pin pointed down to modern or ancient nation-states, or to historical populations such as the Vikings or Huns.  Ancestral DNA companies are under pressure to provide this deep ancestry.  However, can they?  Ancestral analysis of DNA can be very enlightening.  It can provide some surprises within a family history.  However, it's accuracy is exaggerated.  It is increasingly successful at predicting ancestry from a particular corner or end of a particular continent.  But it cannot for example, accurately tell French, British, and German ancestry apart to any high accuracy.  It can recognise some populations better than others.  It cannot tell anyone if they had Viking ancestry.

Ancient Ancestry

This is a particular value of the haplogroups.  As we accumulate more and more data on more mutations, as we expand the recorded database, and as we relate that to more ancient DNA extracted from referenced and dated ancient human remains, so we will be able to better explore the population genetics not only in history, but deep into prehistory.

However, it is also becoming increasingly realised, that patterns of ancient admixture can also be detected within the autosomes.  Although Autosomal DNA ancestry calculators claim to reveal relatively recent admixtures over the past 500 years, it is becoming clear that these are being confused by much older patterns of admixture.  These patterns can now be explored and probed on a number of GEDmatch programs.  People can compare their DNA with the kits from ancient DNA, or predict just how much of their ancestry was likely "Western Hunter-Gatherer, or "Early Neolithic Farmer".

In addition, more DNA companies are now measuring for much more ancient admixture with archaic populations such as the Neanderthals.

Conclusion

Genetic Genealogy is fun, great fun.  It is not however, a quick and easy replacement for traditional genealogy.  Unless you get lucky with some comparative Y-DNA in a project, it is not going to directly tell you the names or social status of any ancestors.  It can give you a phylogenetic tree, but not any kind of family tree that you can bore other family members with.

Genetic genealogy can provide some tools to some researchers.  It can test biological relationship.  It can be used to predict some of your ancient history.  For most researchers, particularly those that are able to interview many local family members, search local grave yards, access archives and records - it has no, or little value to the pursuit of collecting ancestors.

I personally love to explore my genetic genealogy. But it is documentary research that provides the names.  Genetic genealogy for myself, is more about the long and ancient journey.

The Iberian Connection

The above photo at A Capela dos Ossos (the bone chapel) in Évora, Portugal. The entire chapel is covered with human bones.  Every wall and pillar is decorated with skulls and bones.  On another wall hangs the mummified remains of a man and child, said to have been cursed. There is a sign at the entrance of the chapel which states "Nós ossos que aqui estamos, pelos vossos esperamos" (Our bones here, await yours).

Genetic Genealogy

I was a sceptic of genetic genealogy, I'll admit it.  Now I'm hooked.  Not because I feel that it has been a way of hooking up with distant cousins, that can help me extend my family tree.  That's not the way that I've used it so far.  Instead, it has provided very different kind of information, that helps me understand who I am, and how I can link my ancestry to known heritage.

I might not have been so hooked, but I've had so many surprises with my 23andMe results.  If my results had been perhaps, dire and boring, then maybe I would have retreated to traditional genealogy and regarded the technique as predictable and uninteresting.  However, what ancestry related surprises did I have?

  • I have a very rare Y haplogroup for NW Europe.  So far predicted to L1b M317.  It will be shared by my brother, my son, one cousin (and his son, and grandson).  Today I sent away a further FTDNA Y111 swab test.  The L haplogroup is mainly concentrated in Southern and Western Asia, from Afghanistan down to Southern India.  My L1b M317 sub clade is concentrated in Western Asia, including Eastern Turkey, Armenia, Georgia, Azerbaijan, the South Caucasus, and Western Iran. A faint trace of it along the length of the Med in Southern Europe, and across Italy, and a slight cluster in central Europe - which apparently, I don't belong to.
  • Autosome Ancestry composition by 23andMe, gave me a very low percentage of "British & Irish", and high percentages of "French & German" and "Scandinavian".  I've explored the possibility that this could reflect early medieval admixture from across the North Sea.  I've looked at the typical Ancestry Compositions of people with a strong recorded English ancestry, and compared them to the results from people with strong Irish ancestry.  That SE English people typically sit somewhere between the Irish, and typical Dutch in Ancestry Composition reinforces my view that this is the case.
  • My mtDNA was H6a1.  Not the most exciting haplogroup, but not the most boring neither.  It allows me to relate to the latest evidences for Eurasian Steppe admixture into Western Europe during the Early Bronze Age.

A Southern European Enigma

I captured the above photo at Cabo Espichel, Portugal.

There was a fourth, further surprise in my 23andme results.  It lay in the autosome.  23andMe AC (Ancestry Composition) on speculative mode, suggested 2.4% Southern Europe, including a prediction of 0.5% Iberian ancestry.  On speculative mode again, it falls on five pairs of chromosomes - but never on both sides.  On standard mode, 0.1% remains, just on one side of pair 21.  This suggests that all of it comes from just one of my parents.

I might think that this was just "background noise", an error in AC.  However, it keeps popping up.  Indeed when I upload my raw data to the program at DNA.land, they predict only 80% North/Central European, and a whopping 15% South European.  It doesn't stop there.  On GEDMATCH, the Eurogene calculators keep suggesting Iberian or South European admixture on their mixed population oracles.  Eurogenes K9 for example, gives me 61% North European, 29% Mediterranean, and 6% Caucasus.

Let's just refer back to my recorded paper ancestry.  I have 190 recorded ancestors, all in England, with English surnames.  No sign of any Roman Catholicism.  I have all sixteen of Generation 6 (G.G grandparents) named.  All born and named English.  No sign of any South European even in the 1,490 people on the entire family tree for my kids.

However, I think that all of the autosome ancestry calculators could be telling me a truth, that I can't see in my known family tree.  If I have a South European ancestor somewhere, whether Iberian or not, then either a) I have not yet found them, or b) they were the biological ancestor of a NPE (non-parental event), a cuckoo.  I have 3 out of my 32 Generation 7 ancestors unnamed - all absent fathers.  I have 15 missing ancestors in Generation 8.  Above that, the representation really starts to decline, although I have some ancestors named up to Generation 11.  Could a South European be in there?  23andMe in speculative mode suggested 2.4%.  That would seem "average" for an ancestor in Generations 7 or 8 (3 to 4 x G grandparent level)  Of course from around that point, "averages" become pointless, and subject to a randomness that can delete entire lineages further up from any surviving DNA.  None-the-less, I could have a South European from around that period - either one of the 18 "missing" ancestors, or a NPE cuckoo.

I'm commissioning a 23andme test for my mother.  Three reasons.  1) she wont be here for ever.  Recording her genome feels valuable and worthy.  2) I want to see how her very dense 100% recorded Norfolk ancestry projects on Ancestry Composition and on GEDMATCH.  3) I want to phase her results against mine.  It will tell me for example, where my "South European" DNA came from - which parent.  It will help me further understand my own genetic ancestry.