Tuesday 8 November 2016

Instructions for Doing a DNA Test

If you are not sure which DNA test is best for you, you should read this first.

When ordering the standard Y-DNA-37 test from FTDNA, always join a project first in order to avail of the $20 discount (the $169 cost gets reduced to $149). This could either be a surname project or a geographic project. For example, go to the Silvermines DNA Project and click on JOIN in the photo and follow the instructions to buy the test. If you have an additional Coupon Code, enter this in the "Enter Coupon Code" box (& hit Apply) before you click on the green Proceed to Checkout button.

When you get your FTDNA test kit, make sure you fill out all the forms correctly. The white registration form is fairly straightforward but it is easy to leave something out. Be sure to check you have done the following:
  1. Put in your full name (maiden name is preferable for women, for genealogical reasons)
  2. Write your email twice - in upper case and lower case letters. This helps the lab staff read it correctly and helps minimise the risk of their emails to you going to the wrong address or bouncing.
  3. Be sure that you have put in the 5 pieces of information about your credit card, namely: the long number (16 digits), the short number on the back (3 digits), the expiry date, your name, your address. People often forget one or more of these! Alternatively you can pay by PayPal.
  4. Take a photo of the form or make a note to your kit number and the test you ordered and the date you ordered it.
  5. Sign the green (or white) consent form - you won't get the full benefit of your results otherwise.

Below is Brad Larkin's excellent video on how to swab (this does not apply to the 23andMe test or the AncestryDNA test as these require saliva samples rather than cheek swabs). The most important considerations are to fast for 1-2 hours before doing the swabbing (so we don't get any food in the sample) and to swab the inside of the cheek for 45-60 seconds (to ensure we get enough cheek cells on the cotton head of the swab). Repeat this procedure for the second sample (for example, using one cheek first for the first sample, and the other one for the second).

Dislodging the head of the swab into the test tube can be a bit tricky so take your time, do it slowly, and apply constant but gentle pressure. Take your time with this.

You should have a pre-addressed orange reply envelope with your DNA kit but if not you can buy a padded envelope to post the kit back to the lab - you can easily pick one up at the post office. Get one with bubble wrap on the inside to ensure the plastic test tubes are safe.

The address for posting back to the FTDNA Lab in Houston, Texas is at the bottom of the white registration form. It is as follows:
FamilyTreeDNA, 1445 North Loop West, Suite 820 Houston, Texas 77008, USA

Postage is a few pounds/euro/dollars. There is no need for a customs form, but if the Post Office insists, be sure to put down "Genealogy kit" and not "DNA kit" (these are not considered biological samples) as this will delay it unnecessarily through Customs in the US.

Here is an alternative video about swabbing ... with music! This video is about the Geno 2.0 test kit from National Genographic (but the same principles apply to the test kits from FamilyTreeDNA and LivingDNA).

Maurice Gleeson
Nov 2016

Tuesday 21 June 2016

Should I upgrade my Y-DNA test to 67 or 111 markers?

If you have done a Y-DNA-37 test with FamilyTreeDNA, you may be wondering if there is any point in testing a higher number of markers (67 or 111) and what would be the benefit of such testing. Is it worth doing it? And if so, why?

Well the answer is yes, but only under certain circumstances. Outside of these circumstances you might be better spending your hard-earned cash on a different DNA test ... or on your favourite ice-cream.

Here are the main reasons for upgrading to Y-DNA-67 or Y-DNA-111:
  1. No or few matches at 37 markers
  2. Lots of matches at 37 markers
  3. To assist the Project Administrator with difficulties in placing you in a group
  4. To more precisely estimate how closely two specific people are related
  5. To help the PA identify the branching pattern within a genetic group 
We will look at each of them in turn, but before we do let's mention a few key considerations about Y-DNA testing in general, how matches are identified, and some of the pitfalls involved in the process.

Some general considerations

I choose 37 markers as the starting point because most people interested in surname research will have tested to this level. Not everyone will however, and some people (especially transfers from the National Genographic Project) will only have tested to 12 markers. Neither of these are particularly useful for surname research (with rare exceptions) so I will only be addressing upgrading from 37 markers to 67 or 111.

Secondly, it is important to be aware of FTDNA's threshold criteria for declaring a match and listing them in your Matches List. These thresholds are based on Genetic Distance (GD) and are illustrated in the table below (see FTDNA's FAQ page and Privacy Policy page).  Having a GD of 4/37 means that the two individuals being compared are 4 steps away from an exact match (which would usually be expressed as 0/37, or sometimes 37/37).

The thresholds for declaring a match can be summarised as: having a GD at or below 1/12, 2/25, 4/37, 7/67, and 10/111. Each threshold value roughly equates to about 10% of the total number of markers. 

It is important to be aware that some people who fall within these thresholds will not be related to you within "a genealogical timeframe" (which we will take to be about the last 1000 years or so). Similarly, some people who fall outside these thresholds WILL be related to you "within a genealogical timeframe".

Also, it is important to appreciate that these thresholds are arbitrary. They are designed to maximise the number of true positives (high sensitivity) and minimise the number of false positives (high specificity). However, some true positives will escape being caught and some false positives will sneak through. And one or the other scenario may affect some people more than others. The question is: how do you recognise this? How do you separate the wheat from the chaff? Your chances of being able to do this are substantially increased by joining the appropriate surname and haplogroup projects and liaising with the Project Administrators because they have better oversight of the totality of the data within a genetic group and also have additional tools that they can use to better define how closely you are related to other people.

Interpreting Genetic Distance is just as arbitrary as defining a threshold for "declaring a match" and our thinking on this subject is likely to change over time. The table below is derived from FTDNA FAQ pages relating to Genetic Distance at 12, 25, 37, 67, and 111 markers respectively. Match Thresholds are highlighted in yellow.

There is some apparent inconsistency at the 111 marker level when comparing the Match Threshold (>/=10) to the interpretation of Genetic Distance (Not Related). If two people with a GD of 10/111 are Not Related, why declare them as a match?

Furthermore, with the advent of SNP testing and our increasing experience from surname and haplogroup projects, there is now strong evidence that these interpretations can be wildly wrong. Even two same-surname individuals with a GD of >10/37 could be related within a genealogical timeframe (Farrell DNA Project, group R1b-GF2). The interpretations above should therefore be used only as a guide.

So now let's look at the specific scenarios where it might be worthwhile upgrading. What follows expands on the advice already given by FTDNA in its FAQ pages.

Scenario 1:  No or few matches at 37 markers

If you have (say) no matches at the 37 marker level, it could be because someone has a Genetic Distance to you of (say) 5/37 ... in other words, there are 5 differences between you both in the first 37 markers. However the threshold for "declaring a match" is 4/37, and so neither of you will appear in the other's Matches List.

But if you both upgrade to 67 markers, and there are no further differences between you on markers 38 thru 67, then the number of differences remains at 5 and the Genetic Distance is written as 5/67, which is above the threshold for declaring a match and thus you will each appear in the other's Matches List.

In short, upgrading to 67 markers has revealed an additional match that was "hidden" at the 37 marker level.

The same scenario may also apply at the 111 marker level. But the big caveat is you can only compare yourself with other people who have upgraded to at least the same marker level. You cannot detect more matches by upgrading to 67 markers if everyone else is still at 37 markers. Of the 238,000 people with Y-DNA-37 data in the FTDNA database, only 33% of them have Y-DNA-111 data.

There are several reasons for why you may have no or few matches:
  • you may be the first person with your Y-DNA signature to do the test
  • your DNA signature may be very rare because you are the last of your line, or few people with that particular signature are left in the world
  • you may have unusual mutations which have moved you away from the rest of your group

Scenario 2:  Lots of matches at 37 markers 

If you have lots of matches at 37 markers, either your Y-DNA signature is very common in the population or you are a victim of Convergence. This is where, just by chance, people have a similar genetic profile to you that makes them fall within the matching threshold, but the common ancestor is 1000's of years ago rather than 100's of years ago. 

Upgrading to higher marker levels will help weed out many of these Convergent matches but may not eliminate them completely. Convergence has been observed with a GD of 3/111 in the Stewart DNA Project (see this YouTube video from 28:50 onwards).

Scenario 3:  To assist the Project Administrator with difficulties in placing you in a group

Sometimes it can be difficult to allocate project members to a specific genetic group within a surname project, for example if the GD is borderline (e.g. 5/37) and/or the member has a surname variant that may or may not be related (e.g Farrell and Harrell).

In these circumstances upgrading to a higher level of markers may provide additional supportive evidence for grouping you in a specific group (e.g. if the GD remained the same at 67 markers, namely 5/67, then this would be stronger evidence for including you in a specific group).

This scenario may be particularly relevant to you if you are in the Ungrouped category in a surname project. If so, ask your Project Administrator if upgrading to 67 or 111 markers would help him or her with the grouping process. 

Scenario 4:  To more precisely estimate how closely two specific people are related

Upgrading to 67 or 111 markers can help provide supportive data of a very close relationship on the direct male line. However, this should probably be done in conjunction with autosomal DNA testing (and even mtDNA testing) as the Y-DNA-111 test on its own is not conclusive.

FTDNA says that over 50% of exact matches at 111 markers (GD = 0/111) are first cousins. Similarly, over half of matches with a GD of 1/111 are 2nd cousins or closer, 2/111 are 4th cousins or closer, 3/111 are 5th cousins or closer, and so on (see full Table here). 

In short, upgrading to 111 markers will give you a better estimate of how close you are related to someone else but will not define it precisely. There will still be quite a broad range around the "best guess". In order to get a more precise estimate of which ancestor on a direct male line is the common ancestor between two people, it may be necessary to do autosomal DNA testing to estimate the degree of kinship, or to additionally test specific selected cousins of one or both matches, in order to triangulate with atDNA testing, or even mtDNA testing (the latter technique was used to identify WWI soldiers found in Fromelles).

Scenario 5:  To help the PA identify the branching pattern within a genetic group

As surname projects mature, some Project Administrators may take on the task of better defining the branching pattern within certain genetic groups within the project. I am attempting this in the Gleason/Gleeson DNA Project (you can see more about it in this YouTube video).

This process of building a Mutation History Tree (or cladogram or phylogram) is not easy and requires a lot of work. It is best done with 111 STR marker data combined with SNP data (e.g. via the Big Y test). In the future, the number of STRs available to test may increase to 500 or more (e.g. via YFULL) and testing out to 500 markers may become the preferred option. Furthermore, this process requires that many people within a genetic group have this data available.  It is thus quite a costly undertaking for group members.

However, defining the branching pattern within a genetic group brings several specific potential benefits. It can more accurately define how long ago different branches of the family broke away from each other, and how closely specific individuals within a family are related. This can be very useful for both historical studies of the family and the personal genealogical research of individual members. It can also indicate where Back Mutations and Parallel Mutations occurred within a particular genetic group, and this furthers our understanding of the nature of these mutations which usually remain hidden.


So if you think you fall into one of the above categories, consider upgrading your Y-DNA-37 results to the 67 or 111 marker level. You can do it in a step-wise fashion as there is (usually) no extra cost in doing it this way rather than upgrading to the highest level all at once.  And this potentially saves you money because all your questions may be answered by simply upgrading to 67 markers only.

If you do not fall into one of the above categories, you may benefit more from some other test, such as Y-SNP testing or autosomal DNA testing. It all depends on the questions you want answered.

Defining the genealogical questions clearly in your own head will enable you to better arrive at the optimal testing strategy to answer your questions.

Maurice Gleeson
June 2016

Monday 16 May 2016

Y-DNA matches with Different Surnames

Why do I have Y-DNA matches that don't have the same surname as me? 

This is a common question that is asked when people first get their Y-DNA results. And there are several explanations for it. The Y-DNA test only compares Y chromosome DNA to other Y chromosome DNA. A “match” between two men usually means one of three Scenarios (bear in mind there are exceptions to every general rule):

Scenario 1. 
The two men are related via a common ancestor who lived some time since the appearance of surnames (e.g. within the last 1000 years or so in Britain & Ireland). And there are several sub-scenarios in this situation:
a) the two men have the same surname - in which case, they are probably related via a common ancestor (who bore that same surname) some time within the last c.1000 years. This is the scenario we are most interested in and forms the basis of surname studies.
b) the two men have different surnames - in which case an NPE may be present i.e. Non-Paternity Event (or Not the Parent Expected). In other words, both men have a common ancestor within the last c.1000 years, but the surname on ONE of their lines (we don’t know which one) has changed over the years because of a secret adoption, or infidelity, or illegitimacy, etc. Postscript: as mentioned in the Comments below, there are many other possible causes for "surname discontinuity". For example, some families adopted new surnames after emigrating to the US, changing the name to perhaps sound more English. And of course some societies adopted inherited surnames quite late (e.g. Turkey in 1934) or not at all (e.g. Iceland, Tibet).
Scenario 2. 
The two men are related before the appearance of surnames (e.g. pre-1000 AD) - in this scenario, the two men will have different surnames (with rare exceptions). This scenario can arise where there has been very little mutation in the DNA over the course of the last c.1000 years or so. Or where there has been a degree of Convergence (see below).

Scenario 3. 
The two men are related but much further back then they look. This is because of Convergence, where the two genetic profiles were identical 10,000 years ago (for example), but then mutate away from each other gradually over the millennia, and then (by chance) start mutating back towards each other so that it looks like the common ancestor is closer than he is (say 500 years ago rather than 10,000 years ago). Convergence is still being studied and not a huge amount is known about how commonly it is encountered. It is likely that it is more common in some haplogroup subclades than in others.

So in the situation where a man matches a man with a different surname, these are either cases of Scenario 1b (NPE) or Scenario 2 (pre-surname match) or Scenario 3 (Convergence). How can you distinguish between these three scenarios? Not easily, but there are certain clues that can help.

If one of the men matches other people with his surname, then it is less likely that his particular surname is the result of an NPE. And if the other man matches nobody with his surname (and there are people with his surname in the FTDNA database that he could potentially match), then the likelihood that an NPE has occurred somewhere along that man's direct male line is higher. On the other hand, if both men match others with their surname, then perhaps this is a case of Convergence.

If the two men have tested to 37 markers (or higher) and are exact matches, then this makes Scenario 1b more likely (i.e. an NPE has occurred somewhere in the past). The likelihood increases if there is an exact match at 67 markers or 111 markers. And on the contrary, the less close the match is (say 4/37 or 3/37), then the more likely this is a case of Scenario 2 (pre-surname match) or Scenario 3 (Convergence).

Looking at the terminal SNP results of a man's matches may give a clue as to which of the three scenarios is most likely to be present. You can examine the terminal SNPs of a man's matches (at the 111 marker level down to the 25 marker level) and see which SNPs are most common among his matches. Then by plotting these SNPs on the haplotree* you can get some indication whether or not there is evidence of Convergence (i.e. the SNPs fall onto different branches of the haplotree) or no evidence of Convergence (all of the SNPs fall onto the same branch of the haplotree). If there is no evidence of Convergence, then this makes Scenarios 1b or Scenario 2 more likely.  In the example below, the terminal SNPs of a man's matches all fall below SNP L226, suggesting that he and his matches all sit on the L226 branch of the haplotree. However, there may be some Convergence further downstream, as two of his matches sit on different branches below SNP FGC5628.

Performing additional downstream SNP testing (e.g. a SNP Pack or Big Y test) will help differentiate between the three scenarios. Here is what you might expect:
Scenario 1b (NPE) - the two men sit on the same downstream branch that is associated with the surname of one of them. The age of the common SNP might be somewhere in the last 1000-2000 years.
Scenario 2 (pre-surname match) - the two men sit on the same branch upstream (i.e. representative of a major subclade of the haplogroup, say L226). The age of the common SNP might be somewhere in the last 2000-8000 years.
Scenario 3 (Convergence) - the two men sit on completely different (i.e. very distantly related) branches of the haplotree and the common SNP is (say) >8000 years old.
If a recent NPE is suspected, autosomal DNA testing can help establish if the two men are closely related (i.e. within the past 5 generations or so).

Using these techniques will help distinguish between the three possible scenarios but in many cases there is unlikely to be a single definitive test that will give you the answer. The best you might be able to hope for is that taking all the evidence together, the balance of probabilities points toward a particular scenario as being the most likely.

Example: Plotting terminal SNP results of a man's matches shows that they all fall below SNP L226
(i.e. no evidence of Convergence before SNP FGC5628)
(click to enlarge)

*I use FTDNA's but you can use others too - ISOGG, the Big Tree, or YFULL's tree

Wednesday 27 April 2016

Which DNA Test is Best for Me?

People frequently ask the question: which DNA test should I do? Well the response is simple: The test that is best for you very much depends on the sort of questions that you would like answers to.

Below is a selection of the typical kind of questions that people ask about DNA testing and some brief answers to them. Be sure to explore the links for more information. Hopefully this will help you understand what each type of test can do and that in turn will help you decide which one is best for you.

How many types of DNA test are there?

There are 3 main tests you could do, and you could test one of several members of your family - it depends on what questions you would like answered:
  • Y-DNA traces your father’s father’s father’s line
  • mtDNA (mito or mitochondrial) traces your mother’s mother’s mother’s line
  • and atDNA (autosomal) traces ALL your ancestral lines and gives you your ethnic makeup.
Note that Y-DNA and mtDNA will only give you information about one ancestral line each, whereas atDNA gives you information on all your ancestral lines (but only has a reach of about 300 years, compared to 200,000 years with the other two types of test). You may wish to look at this YouTube video I made explaining the three types of test in more detail and giving examples of their application to genealogy.

Here’s a few examples of questions you might want answers to and the best test to address each one:

How do I find out about my ethnic origins?
  • atDNA will tell you roughly what percentage of your DNA is from Europe, Asia, Africa, etc. It will also give you rough estimates on a sub-regional level (e.g. "Central Europe" or "France/Germany") but is unlikely to identify a particular country. Currently this ethnic admixture test (also known as biogeographical analysis) only gives crude estimates and will continue to be refined over time. Still, it makes for a pretty picture which the kids can print out and take to school.
  • the general opinion among genetic genealogists is that 23andme gives the best genetic ethnicity estimates, followed by Ancestry, and then FamilyTreeDNA.  None of the tests are accurate enough currently to pinpoint ancestral homelands but they might point you in the right direction. Check out this blog post for more info - Making the best of what's not so good by Judy G Russell, The Legal Genealogist, 22 February 2015.
  • both Y-DNA and mtDNA will tell you where that one particular ancestral line originated (eg Western Europe). And because both go back about 200,000 years to Africa, they will also give you the crude migration routes those particular ancestors took. More nice pictures for the kids school projects.

How do I find out more about my surname and where it came from?
  • do the Y-DNA test. And test the oldest generation, so that would be your father, uncle, or grandfather. If you are male, your Y-DNA should be exactly the same as your father's Y-DNA and your grandfathers, etc all the way back on the direct male line.
  • ... unless there has been an NPE along the way. NPE stands for Non-Paternity Event  or Not the Parent Expected. Common causes are secret adoptions, infidelity within marriage, and illegitimacy. These happen in about 1% of cases per generation.
  • Start off with the Y-DNA -37 test from FamilyTreeDNA and be sure to join any relevant surname or haplogroup projects. You can find these by doing a search for your name on the FamilyTreeDNA website and it will give you a selection of relevant projects for you to join.
  • After reviewing the results of your Y-DNA-37 test, ask the Admins of projects you have joined for advice on what additional testing might be warranted. This could mean upgrading to 67 or 111 markers, or it could mean doing SNP marker testing. The Project Admins will advise.
  • If you want to explore your mother's surname, test her brother. He is the one who inherited the Y-DNA that goes with that surname.
  • You can research ANY surname in your family as long as you test the appropriate male cousin who bears that particular surname.

How do I connect with genetic cousins?
  • Y-DNA will connect you with genetic cousins with whom you share the same surname.
  • mtDNA will connect you with cousins on your mother’s mother’s mother’s line but this is the least useful of all 3 tests - because mtDNA mutates so slowly, even an exact match could mean a common ancestor several thousand years ago (rather than several hundred years ago in the case of Y-DNA).
  • atDNA will connect you with about 500-1000 cousins you never knew existed (if you have European ancestry). It gives you the most "bang for your buck". Most of them will be distant cousins, but you may spot a few familiar names in your list of matches. The majority will be unknown cousins who are related to you via unknown ancestors beyond your ancestral Brick Walls, or they will be "false positive matches" (particularly if the amount of DNA they share with you is small). You will have hours of fun (and I mean hours) trying to figure out how they are connected. This test has “Retirement Plan” written all over it. But there are two important questions to address:
    • who to test?
    • and which company to test with?

Who do I test?
  • Anyone. Anyone can do a DNA test. But it’s always a good idea to test the oldest members of the family first, for two reasons:
    • they will not always be around
    • they have more DNA from particular ancestors than you do
  • Your mother for example would be a generation further back than you, and thus she will have twice the number of matches on your maternal side of the family compared to you … because she has twice as much “DNA from the maternal side of the family” - each generation loses 50% of the DNA from that side of the family, because only half of it is passed on from parent to child. So your Dad would only have (roughly) 25% of his DNA from his grandfather, you would have only 12.5%, and your son would have only 6.25%. The percentage inherited from any one specific ancestor roughly halves with each generation.
  • Testing yourself and a parent helps you isolate which side of the family your matches are from. So if you tested yourself and your Dad for example, any matches you both share in common have to be from his side of the family; and any matches that you have but he doesn’t, have to be from your mum’s side. Of course you could also test your mum to answer this same question, if she is still with us. 
  • FamilyTreeDNA store the DNA samples for 25 years free of charge so this serves as a genetic legacy for future generations - could be important as the science of genetic genealogy progresses (and it has only been around for 15 years or so).

Which company should I test with and how much does it cost?
  • there are 3 companies - FamilyTreeDNA23andme, and Ancestry.com. Each have their pros and cons.
  • Re Y-DNA: if you want to research your surname, then only FamilyTreeDNA offer an infrastructure for surname research. You would have to test with them if you wanted to join the Farrell DNA Project (for example). 23andme will tell you what Y-DNA haplogroup you belong to (useful for knowing your crude migration path out of Africa) but that’s it.
  • Re mtDNA: only FamilyTreeDNA and 23andme offer this test, but not Ancestry. It is of little use for genealogy. 23andme have it as part of their single test (you get Y-DNA, mtDNA, and atDNA all in one test) and FamilyTreeDNA offer it as a separate test. I would start with the mtDNAplus test because it is cheaper ($69) and may give you all the information you need.
  • Re atDNA: whichever company you test with, you should upload your atDNA data to Gedmatch (for free). Anyone can do this and it allows you to compare your data with that of people who have tested with other companies and who have uploaded their data to the Gedmatch website. This allows you to fish in 3 genepools instead of 1 (only partial pools in this instance because not everyone uploads their results to Gedmatch). Also, if you test with Ancestry, you should upload your data to FamilyTreeDNA (for $39) so you are fishing in 2 genepools instead of 1 (complete genepools in this instance).
    • 23andme will give you a medical risk assessment as well as a ton of genetic cousins. However the medical component was suspended in the US by the FDA and only partially restored in 2015. You may get a more comprehensive range of medical data if you order the test via their outlets in Canada, the UK, Ireland, & Australia but you would need to ask them about this as the situation is likely to change. Also, you may have to use a friend with a Canadian address (for example) as a middleman if you are ordering from outside the US (Canada in this example).
    • 23andme give you all 3 DNA tests (Y, mt, and autosomal) for $199 in the US. It is more expensive than the other companies, and the Y-DNA and mtDNA tests give only limited results.
    • Ancestry just give you atDNA (no Y or mtDNA), usually for $99 although it can be $79 in their frequent Sales. There is very limited product support, no tools (such as a chromosome browser), and if you want to explore the results further you will need to upload to Gedmatch/FamilyTreeDNA. Also, no further testing is possible. The big advantage of Ancestry is that you can link your DNA results to your family tree and that will potentially allow you to compare your DNA with everyone else on Ancestry who has also done so. And many but not all have family trees ... so it can make finding the common ancestor a lot easier.
    • FTDNA (FamilyTreeDNA) store your sample for 25 years. Further testing can be done on the sample whenever you want (e.g. Y-DNA or mtDNA, or any future tests). Their atDNA test (called Family Finder) is $99, Y-DNA is $149 (for 37 markers; $129 if you buy it via a surname project) and mtDNA is $69 ($199 for the FMS full sequence).
    • I have tested with all 3 companies. I like FamilyTreeDNA the best and have had most success with them (i.e. my closest matches are on FamilyTreeDNA . My guess is that if you have Irish ancestry you will find most of your close matches on FamilyTreeDNA  If you have US colonial ancestry, you will probably find most of your matches on Ancestry. 
    • The most cost-effective option for atDNA would be to test with Ancestry ($99), then transfer your results for $39 to FamilyTreeDNA, and upload them for free to Gedmatch. The cheapest option outside the US is FTDNA ($99).
    • There are also some other neat websites that offer additional third party functionality that are very useful, DNAgedcom offers some tools and I particularly like Don Worth’s ADSA spreadsheet but historically it has only worked with FamilyTreeDNA results. They are developing it for Ancestry and 23andme.

So which test is best for you? Probably the atDNA test from FamilyTreeDNA or Ancestry if you are interested in general genealogy, or the Y-DNA-37 test from FamilyTreeDNA if you are specifically interested in exploring a particular surname.

Maurice Gleeson
April 2016

Monday 25 April 2016

How to download your Ancestry DNA data and upload it to FTDNA

The DNA test from Ancestry is proving very popular and a lot of people are taking advantage of the low cost of the test, especially when there is a Sale on. Ancestry compares your DNA data to everyone in their database (over 1 million people at this stage) and gives you a list of your "matches" - many of these will be genetic cousins with whom you share a common ancestor who was born sometime in the last 250 years or so.

But you can get a lot more from your Ancestry DNA test if you upload the results to FamilyTreeDNA and take advantage of a second database of potential genetic cousins. FamilyTreeDNA (FTDNA) also have a database close to 1 million people and all these databases are expanding all the time. I have tested with both companies and (as of April 2016) I have 3671 matches with Ancestry and 828 matches with FTDNA. However, being Irish, I find that most of my closest matches are in the FTDNA database, not in the Ancestry database. So it is well worth while fishing in both pools.

The good news is that you can get your top 20 matches in the FTDNA database for free, and for a small fee ($39) you can reveal all your matches. So by paying the $39 transfer fee, you get to swim in two data pools for the price of 1.4 (the usual price of the Family Finder autosomal DNA test at FTDNA is $99).

Here's how you download your Ancestry DNA data and transfer it to FTDNA.

1. Log in to your Ancestry account and click on the DNA tab in the menu at the top.

2. Click on Settings (far right)

3. On the next page, in the box on the right, click on the Download Raw DNA Data button

4. Enter your password in the box indicated, and tick the check box below it ... then click on Confirm.

5. You will get a confirmation message asking you to check your email for a link to download your DNA.

6. Click on the green button in your email to confirm you want to download your raw DNA data.

7. This takes you to a new browser window where you will be asked to click on another green button (Download DNA Raw Data). Click on this (only once) and wait. This can take a while ...

... and be sure to note into which folder the DNA Raw Data file has been downloaded - you will need to access this folder in the next steps.

8. The next step is to upload the raw DNA data to FTDNA (FTDNA's instructions can be found here). Begin by visiting https://www.familytreedna.com/landing/atdna-landing.aspx.

9. New customers must enter their name and email address to get started. If you (or the person whose data you want to transfer) already have an FTDNA account, just click Already have a Family Tree DNA account? (Reminder: Each person needs to have their own kit number.) If you have an existing Y-DNA or mtDNA kit, be sure to sign in to it before launching the process.

Don't forget to click your gender and agree to the Terms of Service & Release Form.

10. Next, click Upload Raw Data to select and upload the raw data file from AncestryDNA from your computer. It is not necessary to unzip the file prior to uploading it.

The first round of results processing takes about an hour or so. An email notification will be sent to your registered email address after the raw data is processed. After the processing is complete, the free Family Finder experience includes:
  • your top matches
  • some Family Finder tools, such as the Chromosome Browser and the Family Finder Matrix. You can use the Chromosome Browser and Matrix with your matches to see the longest block and whether or not they’re an X match.
The free transfer has certain limitations compared to the full functionality you get for the $39 fee:
  • myOrigins is not included (genetic ethnic admixture estimates)
  • you cannot use the “in common with” feature
  • you cannot download any data
  • your results will not be seen by any of your matches

11. The price to unlock all of your matches and myOrigins results is $39. Once you’ve paid or unlocked your full results, it takes 3-5 business days for the full results to be completed.

Saturday 23 April 2016

How to order the YFULL reanalysis of your Big Y data

To order the YFULL test, follow these step-by-step instructions:

1. first get hold of the link to your BAM file by following the instructions here … 

2. then go to YFULL at https://www.yfull.com/

3. click on Order Now at the bottom

4. enter your details
  • check .BAM file and FTDNA Big Y and “Link to a sharing file” and enter the link you previously copied
  • Also tick “I am not a Robot” and the “agree to terms etc”
  • then click "Order now"

5. You should be notified of your results by email in about 4-6 weeks time. At that point, you will be asked to pay for them. Payment will be in roubles as this is a company based in Russia.

6. Once you have the results, you should join any relevant group projects on YFULL so that Haplogroup Project Administrators can see your results. You can join projects by following these simple steps:
  • log in to YFULL with your username / ID number & password
  • click on YFULL in the top left corner
  • click on Groups toward the bottom of the menu list on the left (see below)
  • click on the appropriate group in The Group List
  • click on Join Request in the yellow menu bar at the top
  • follow the instructions 

How to share the link to your Big Y BAM file

If you have done the Big Y test at FamilyTreeDNA, FTDNA provide the facility to download your raw data (in .vcf, .bed, and .BAM files) which allows you to have the data analysed and interpreted by a host of other resources (see this blog post for a selection of them). 

Here is a step-by-step description of how you can download your .vcf and .bed files, and also get the link to your BAM file and share it with other people.

1. Firstly, just SIGN IN to your FamilyTreeDNA account with your kit number and Password.

2. Then click on your Big Y Matches ...

3. Then, click on the blue Download Raw Data button …

4. In the subsequent pop-up box, you will be given the option to submit a request to have your BAM file prepared for downloading. This may take a few weeks to prepare and you should be notified by email when it is ready.

Once the file has been prepared, repeat steps 1-3 above, and now when you click on the Download Raw Data button, you will get a pop-up box with green buttons at the bottom, like in the diagram below.

The "Download VCF" option will download the .vcf and .bed files to your computer, usually as a zipped file or with both files in a folder (about 1.7 mB).

The "Share BAM" option will allow you to copy a temporary link to your BAM file. The file itself is >600 mB in size and is far too big to be sent by email, so sending the link instead allows the recipient to download your file from the FTDNA website directly to their computer, without clogging up your mailbox or theirs.

You can also download your BAM file if you wish but this is >600 mB in size so it will take a while.

5. After clicking on Share BAM, click on the Copy button that appears next (this copies the link to your BAM file) …

6. Now simply paste the copied link into an email (e.g. to send it to James Kane or Alex Williamson) or the appropriate box on an application form (e.g. to send it to YFULL or FGC).

A Comparison of Resources for analysing your Big Y data

There are several very useful resources available to us for interpreting the results of our Big Y tests. Here is a brief summary of what we get and what we don't from each resource - all have their Pros and Cons and all add something to the overall interpretation of the results. Because this is a completely new area of science, and we are on the crest of the wave of scientific discovery, the different analyses from the different sources frequently produce different results, which in turn allow us to ask why and to refine our methodologies further. This will continuously change over time as we understand more, adjust our SNP declaring criteria, and refine our interpretation of the data. We can expect big changes to take place over the next few years.

The discussion below relates to my father's Big Y results and those of other members of Lineage II in the Gleason/Gleeson DNA Project

The presentation of the Big Y results from FTDNA is currently quite limited. This is not surprising as they were the pioneers in this area and their first offering in terms of how the data is presented is now outdated. But this is due to change in the near future when they introduce their new Big Y features. What these are as yet we don't know but we can expect exciting developments over the next few months. The march of progress carries on! 

Currently we are given a list of close matches and the number and nature of Shared Novel Variants with each match (i.e. shared new SNPs), also Known SNPs that are not shared, and SNPs that are unique when comparing just two specific individuals. FTDNA also places us on their own version of the Haplotree (the human evolutionary tree) which tells us what SNPs lie at branching points above our own particular sub-branch.

Confusion arises from a number of different issues, some of them general points, some of them FTDNA-specific:
  • the separation of new ("Novel") SNPs from those already identified ("Known")
  • FTDNA's high threshold criteria for declaring a SNP misses some SNPs
  • often no SNP names are reported, only SNP positions - you have to go to YBrowse.org or YFULL to get specific information regarding the name of SNPs present at a particular location on the Y chromosome.
However, and most importantly, FTDNA provide the facility to download our raw data (in .vcf, .bed, and .BAM files) which allows us to have the data analysed and interpreted by a host of other resources. Details of how to access and share these files can be found here. The "Download VCF" option will download the .vcf and .bed files (about 1.6 mB) and the "Share BAM" option will allow you to copy a temporary link to your BAM file (which is >600 mB in size and so is far too big to be sent by email).

My current position on FTDNA's haplotree with details of SNPs tested
(green, positive; red, negative)
(click to enlarge)

YFULL gives us a more detailed analysis of BAM files and places us on their Y-Haplotree in relation to other people nearby (i.e. who have undergone NGS [Next Generation Sequencing] testing, like the Big Y). It also identifies our terminal SNP (or SNP block), the SNPs at branching points further upstream (and hence the Shared SNPs we have with our neighbours), and the unique / personal / private SNPs that each member possesses (currently).

Over and above FTDNA's analysis, YFULL tells us the following:
  • how many people on adjacent branches have tested and where they are from
  • SNP names and any "equivalent SNPs" (i.e. exactly the same position on the Y chromosome but alternative name)
  • time estimates for the formation of each SNP (and hence the particular branching point)
  • TMRCA estimates for the people in each sub-branch (with 95% Confidence Intervals)
  • information on each SNP including position on the Y, ancestral and derived values, alternative names, and reference sequence. This information can be supplemented by YBrowse.org
  • easier-to-understand presentation of currently unique (personal) SNPs with an estimate of their "quality"
  • data on about 500 STRs including the majority found in FTDNA's 111 marker panel - this can be helpful in calculating TMRCA estimates and narrows the 95% range around the estimate (compared to TMRCAs based on 111 marker data)

The Gleeson Lineage II portion of the YFULL haplotree
(click to enlarge)

Full Genomes (FGC) Analysis
The FGC analysis of BAM files is comparable to the YFULL analysis but their public Y-Haplotree is not user-friendly and is of limited utility. FGC generates the following reports with the underlying files (processed BAM file, mtDNA, and STRs):
  • A detailed analysis of called variants report
  • A variant genotyping report
  • Haplogroup classification
  • Y-STR report, and 
  • mtDNA report

clarifYdna analysis
clarifYDNA will reanalyse your Big Y data for $30 and produces a Y-DNA haplotree report from your results - this will be periodically updated as new data becomes available from other testers.  Reports are in sync with a recent version of the ISOGG haplotree, and are able to indicate which aspects of the phylogenetic structure are robust and which are more tenuous - thus it combines aspects of the Y-haplotree that are both "established" and "provisional / experimental". 

Unfortunately the tree is only available to subscribers and is not available to the public.

Click here for an Example analysis.

Haplogroup Project Administrators 
The Administrators at the Z255 Haplogroup Project, and indeed the Admins of more upstream Haplogroup Projects (e.g. L21, R1b & subclades, etc) are an incredible resource and their respective Yahoo Discussion Groups are great places to post questions and get replies.

John Murphy puts together a regular updated spreadsheet / haplotree for the Z255 group which has an advantage over YFULL's analysis - it incorporates new SNP discoveries from specific SNP Packs and single SNP testing and not just from NGS testing (Big Y, FGC).

The Gleeson Lineage II portion of John Murphy's spreadsheet
(click to enlarge)

Alex Williamson's "Big Tree"
Alex is one of the most important people in the R1b research community and is a champion of data analysis, interpretation, and (most importantly) presentation. His Big Tree website (www.ytree.net) is a masterful display of complex data in a digestible format. He places us on his haplotree so that we can see our terminal SNP (block), SNPs at upstream branching points, and our neighbours on adjacent branches.

Advantages over YFULL include:
  • The Big Tree gives us our neighbours names and places of origin, thus making it easier to form an impression of where a particular sub-branch might have formed and if it is specific for a particular surname.
  • Easy to navigate with lots of additional information by simply clicking on a surname or a SNP.
  • His graphics are superb.
  • His Mutation Matrix allows us to see which SNPs are shared and which SNPs are not between us and our closest neighbours. 
  • His presentation of unique (personal) SNPs gives us not only an estimate of "quality" but also the region of the Y-chromosome in which they are found (this can be useful in judging if this is a true SNP and also how easy it would be test for it in a bespoke SNP Panel)

The (current) 4 branches of the Gleeson Lineage II on the Big Tree

Nigel McCarthy's Z255 Subgroup
Nigel is another pioneer. He is one of the first people to combine SNP markers and STR markers into a single tree. We are lucky enough in the Gleeson Lineage II group that we are closely related to  some of the people in Nigel's McCarthy DNA Project. As a result, Nigel has included us in the Z255 portion of his phylogenic tree (Group E).

Nigel's own SNP analysis is complementary to the ones above and he too will occasionally discover new SNPs that others have not included in their analyses.

Major advantages over previous analyses include:
  • As well as the SNPs, he also presents STR data and the change in STR values at each branching point
  • He includes people who have not been tested on the Big Y (i.e. anyone with Y-DNA-67 or Y-DNA-111 results). As a consequence, his portion of the haplotree contains more Gleeson's from Lineage II than any other tree - 12 members altogether (compared to 9 members on Alex's tree, 9 on John Murphy's, and 6 on the YFULL tree).
  • From Nigel's analysis it is possible to see where Back Mutations and Parallel Mutations occur in the STR markers.

The Gleeson Lineage II members in Nigel McCarthy's Group E of his McCarthy DNA Project

Mike W’s Haplotype Data for R1b-L21
Mike is an administrator of several FTDNA projects and a leader in the genetic genealogy community for a long time. He maintains a very comprehensive spreadsheet that can be downloaded from the Links section of the R1b-L21 project Yahoo group or a smaller version from the Z255 Yahoo group. This spreadsheet collects the STRs for 67 and 111 markers, and SNPs from the Big Ys or other sources. A user can calculate his genetic distance in relation to the complete database and he can infer his haplotype according to the most common haplotype of his closest matches. The spreadsheet also calculates the group mode and several statistics required to characterize a particular group.

James Kane's SNP Matrix
I am new to James' SNP Matrix but it too is a work of art, a magnum opus, not surprising for a 90 mB spreadsheet. Yet again, James' approach to NGS data analysis offers a fresh perspective and can detect possible/probable SNPs that have not turned up in other analyses. Having multiple analyses and interpretations of the same data is a great advantage - it allows us to see points of agreement and points of difference in the various approaches, and ultimately helps us to question the data more intelligently which in turn will lead to better analysis and interpretation.

James’ matrix compares the SNPs of all the participants while the other methods preselect the relevant SNPs. This capability is very important for the identification of new potential SNPs. These can be checked against other analyses for consistency or disagreement. Additionally, it is possible to evaluate unique SNPs or SNPs that belong to a particular group with different levels of quality or if they are part of the combBED area. It also provides positions for both the build 37 (GRCh37) and 38 (GRCh38) human reference genome sequence.

The matrix workbook requires BAMs for inclusion. What the scripts do is visit each file for every variant location and outputs the read depth in a very large combined VCF file. The idea is to remove the ambiguity of BED files. The old HTML based pages did include everything, but became unwieldy. They are being replaced soon.

James also has a blog site and an Experimental Y Tree (currently being updated) with SNP names & their equivalents, surnames, places or origin, and TMRCA estimates.

Everyone who has done the Big Y test should send James a link to their BAM file so he can include you in his analysis. This looks at the data from yet another perspective and helps further with the interpretation. It should help clarify the discoveries from other sources and may even identify some additional SNPs.

Below are the instructions and an explanation that James has put together about sending him your BAM file for analysis and what will happen after that:

What’s needed?
A link to your Big Y BAM file using the “Share BAM” button on your Raw Results page.  Let me know if detailed instructions would be helpful.  Please also include this statement in the email:

As the owner or administrator of FTDNA kit#, [YOUR KIT#], I consent to allow analysis of the Y DNA contained in the provided BAM file.  The results of this analysis may be used the phylogenetic tree of haplogroup R or independent researchers for scientific purposes.

What will be done?
Your BAM will be downloaded and realigned to GRCh38.  This will allow a new VCF/BED to be created and compared with others.  Results will be included in http://www.it2kane.org/matrix/R-P312.html.  When sufficient analysis is available for the branches, it will be possible to include time to most recent common ancestor estimation based on these results.  The new VCF/BED will be provided to those interested.

What won’t be done?
Unlike the commercial 3rd party analysis, you won’t get mtDNA, STR value estimates, or variant naming any time in the near future.

See below for my data use policy.

Raw Data Policies

In light of the recent dust-up between FTDNA and another 3rd party site, I have codified my data usage policies.
1.     VCF/BED files submitted for analysis are made available for other R-L21 researchers using the R1b-L21(S145) Haplogroup and Subclades Y DNA forum hosted on Yahoo.  This aids researchers to correctly assign variants to their related haplogroups.
2.     Raw BAM data is retained in a password protected cloud storage account.  The project recognizes there is a low probability that files may contain data not actually on the Y chromosome, which may reveal medically relevant information about the participant. BAM files may be individually shared with qualified researchers and analysts only after approval of the sample’s owner.
3.     GRCh38 aligned versions of variant calls and BED coverage generated by the project’s bio-informatics workflow can be shared with researchers without the sample owner’s explicit authorization.
4.     FTDNA kit #’s are displayed for convenience of related surname projects or haplogroups in all reporting.  As the identifier is used to log into the FTDNA account this has security implications for the kit owner.  Project members may request reporting on tree or call matrix reports use an internal project id instead.
5.     Project members have the right to request that their raw data is removed from reporting at any time, but shared variants in the tree will be retained.

Some Closing Thoughts
This is a new science and we are still trying to get to grips with it. The pithy saying "Many hands make light work" operates quite nicely in this situation. It is only by looking at the data from a variety of different perspectives that we can hope to understand it better, and quickly. So we should be using all of the above utilities to analyse and interpret our Big Y results. Thanks to the internet, this process (which previously would have taken decades to complete) can now be accomplished in a matter of years thanks to what effectively is a crowd-sourcing approach - a group of citizen scientists working together toward a common goal and employing the power of the internet to communicate and collaborate effectively.

There is still a lot of testing to be done - we need more people to do the NGS tests (Big Y, FGC tests, etc). And we need clever people to develop more tools for analysis, interpretation, & presentation of the data. But as this critical mass of people tested builds, and as our ability to analyse and interpret  and present the data improves, we will begin to reap greater and greater dividends. 

Software packages are being developed to help build combination family trees using SNP data, STR data, and standard genealogy. Already you are able to add DNA markers to your Family Tree on Ancestry. This will advance even further and trees will start to be linked online via downstream SNP markers.

Furthermore, for Irish genealogies at least, we will be able to link some of our family trees to the Ancient Annals and Genealogies, bringing us back to before the time of surnames, back to 900 AD, 800 AD, 700 AD, and even further.

In a few years, when we look back at this time in human history, we will be able to say ...
I was there. 
I contributed to that. 
I helped build the Evolutionary Tree of Mankind. 
And I know exactly where I sit on it.

Maurice Gleeson
German Creamer
Lisa Little
April 2016