8th Annual Conference on Genetic Genealogy – Day 2

ISOGG FTDNA Chapter Meeting

Sunday morning at the conference always starts with a meeting of the International Society of Genetic Genealogists (ISOGG) FTDNA Chapter.  ISOGG President Katherine Borges reminded everyone that ISOGG is a free support network for genetic genealogists.  Upon joining ISOGG, members receive an invitation to the ISOGG mailing list.  Katherine reminded everyone that ISOGG is self-supporting and hosts booths.  They maintain speakers list.  If you speak on Genetic Genealogy, please submit your name.

Alice Fairhurst is in charge of the ISOGG Y-SNP tree.  She pleaded with the audience for volunteers to help administrate the tree.  There are just a few people who struggle to keep up with everything on a voluntary basis outside of their regular jobs, which often includes engineering and IT positions.  Alice shared changes that we can expect, including migrating ISOGG to a more powerful server and utilizing an SQL database.  The tree will remain in its current style through 2012 and she is not sure if they will be able to get the new tree up in January.  It is still too early to say.

It is going to be very important to learn SNP names, as subclade names may change as new discoveries are found on the Geno project.  The new system is going to be parent / child.  She said, “The explosion in knowledge in the last two years has been tremendous.”  Many universities and students are now using the ISOGG tree and routinely send notes of thanks to the group for all they’ve done and are doing.  The ISOGG page that receives the most hits is the Index to Y-DNA SNPs.

Brian Swann, the ISOGG European Coordinator for England and Wales, has a Ph.D. in Chemistry with a specialty in mitochondria.  He shared that the UK Who Do You Think You Are conference is the largest in the world, with 11,000 – 17,000 attendees.  Wow!  FTDNA has sponsored the DNA area at that conference for several years.  Typically kits sell out by Sunday and then they have to pass out order forms.  This is great for those of us with roots in the British Isles.

Recruiting individuals for projects is always a challenge and Brian gave some tips about how to approach the British.  Adverts in journals and bulletin boards sometimes work.  It may be useful to cold call.  We’re going to have to start doing it if we want to build our projects.  Get to know people and build trust and you will improve your recruitment for project participants.  Also, make sure that your home page is universal, rather than targeted to an American audience.  The Guild of One Name Studies can be a good resource to look for candidates.

Looking at surnames is important.  Brian gave some helpful tips for researching in the UK:

• Look at surname atlases
• Read Debbie Kennett’s new Surname Handbook about surnames and how to research origins of UK surnames
• Use Facebook to contact people (something I’ve had great success with)
• Use Cyndislist to find local Family History Societies in the UK
• Find phone numbers via 192.com or the UK equivalent of whitepages.com

One startling statistic sheds some light on a growing problem that is only going to get worse.  About half the people in Britain who have children don’t marry.  This makes family history more difficult and it’s only going to continue to get worse as this becomes more and more common.

mtDNA Community – A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from Its Root

Dr. Doran Behar presented a paper that was published in the American Journal of Human Genetics and I will do my best to share, although much of it is over my head.  Mitochondrial DNA is not one of my stronger areas.  Dr. Behar told us that NCBI currently has 16,214 complete mitochondrial sequences and, of those, about 6,500 can be attributed to Family Tree DNA.  Kudos to citizen science.  That is outstanding!

Dr. Behar explained that we need a reference sequence to compare results and say in a concise way what is in the result.  The Cambridge Reference Sequence  has been used and was a landmark study but it was randomly chosen and creates a number of practical problems.  The reference is not necessarily “normal”.

There are tools available on mtDNA Community called FASTmtDNA and mtDNAable.  You can post your sequence in NCBI because that is an accepted host but sharing on mtDNA community does not upload to NCBI.  You can ask mtDNA Community to help you upload your results to NCBI by checking a checkbox.

A Highly Divergent Y Chromosome Lineage: Implications for Human Evolution and the Y Chromosome Tree

This presentation was a collaboration between Michael Hammer, Thomas Krahn, and Bonnie Schrack.  Dr. Hammer started out with a teaser, letting us know that they would be revealing a highly divergent Y chromosome lineage.  They are now able to sequence a whole plate with the same sequencing primer.  The 1,500 wells can all go on the sequencer and get a score for each of the samples.  The sequencing machine shoots out sequencing traces and each needs to be reviewed manually for differences from the reference sequence.

Bonnie talked about successes in the A project, which are greatly due to the tremendous financial supporters of the project.  Bonnie has been kind enough to share her powerpoint and presentations on her new website here.  It definitely explains things better than I ever could!

 

Thomas Krahn told the story of a Friday when he and Astrid did two Walk the Y tests on parallel and ended up staying until 6am.  There were 52 derived markers where the Walk the Y customer matched old African samples from Mike Hammer.  These African samples will now be known as A00.

Mike Hammer explained that if they know the root and the time to most recent common ancestor (TMRCA) and where they’ve been sampled in the natural population, and there are derived lineages in other locations, then they can infer the stories of where ancestors lived in the past.  He says that the newly discovered A00 haplogroup is 67% older than anything previously known.  He estimates 338,000 years with a 98% confidence level.  About 500 years between the Cameroonian A00 sample and the South Carolina A00 sample is in line with the Atlantic  slave trade.  This discovery will surely bring about lots of new questions!

A Tale of Two Families – Findings from the FTDNA Surname Project VAN TUYL

Retired engineer Rory Van Tuyl, project administrator for the Van Tuyl project, told how he was able to make some discoveries within his project.  Records-based phylogeny had identified three Van Tuyl branches.  Rory used Monte Carlo Simulation and the Walsh Infinite Alleles Theory to show that there is no constant mutation rate.  Rory used Y-Search and put in the ancestral haplotype and then one by one added changes from the ancestral to the Van Tuyl haplotype.  He found that the Van Tuyls share a specific set of seven alleles that comprise their family haplotype.  He said that using similarities rather than differences is a powerful analytical tool.  He was able to do the same for another set of Van Tuyls and, while they exhibited a similar family haplotype pattern, their pattern did not match that of Rory’s family.  Rory said that we should not try to estimate TMRCA from Y-STR data.

IT Update

The moment we’d all been waiting for!  Elliott Greenspan got up to speak and the Twitter feed went crazy.  Elliott did a quick year in review, talking about added features for General Fund, SNP maps, and third-party data.  FTDNA processed 2.33 petabytes of matching data in 2011 including 16.8 million segments.

Some things that Family Tree DNA plans to do include:

• Allow uploads of Ancestry data once it is released, just as they have done with 23andMe.
• Allow display of micro alleles on gap charts this year in footer soon
• Add palindromic matching soon
• For mtDNA, they will be upgrading all HVR1 to new roots
• Upgrading to build 15 for all FMS.
• New dashboard will be released after December.
• Family Tree Viewer will be an upgrade to view your gedcom and will help in future things for phasing and will allow more data.
• Population finder will have more populations and faster upgrades
• Chromosomal painting
• New Family Finder feature x matching and browsing with filters
• Remove restriction on “in common with”
• Ability to select 5 matches and push to Chromosome browser
• Ability to filter by block – i.e. find all people with that specific block at least 4cm as long as they start or end in that block.
• Phasing 2 versions – with one parent or two or go much further! Use aunts, uncles, cousins and match them against the Family Finder database to triangulate (So exciting!!!!)
• FTDNA developers work group for customers with technical skills

I’m happy!  There was really so much great news from Elliott!

Question & Answer Session

Q: Are there any plans for Android?
A: FTDNA is a .net shop so it doesn’t work well.  If anyone has any idea for an apps, Elliott will definitely listen, whether it’s Android, Apple, etc.

Q: Will Gedcoms that have been uploaded to project participant kids be gone?
A: It will still use a combined Gedcom.  There will not be a data wipe so it will still be there but just not displayed.

Q: Can you remove the 5 limit on the chromosome browser?
A: It would be very hard to see colors.  As far as segment downloads, we can do it if you want.  (Loud applause!!!  The people want it!)

Q: Can you make it so that people can do “in common with” without a confirmed relation condition?
A:  Yes, it’s coming.  (I asked Elliott that last year.  Thank you, Elliott!  It’s worth waiting for.)

Q: If 4-5cM is the minimum to be taken seriously, then why is there a 7.7cM cutoff?
A: There are currently 1,300 matches that don’t have that large of a block.  It has to do with confidence that is based on supporting blocks.

Q: Is a set of APIs going to be available for data mining?
A: NO!!! Bennett is offended.  (Audience was pleased with Bennett for his answer.)

Q: Will there be advanced tools for monthly fees?
A: As long as they can, they not have any extra fees.  It is one fee for life.  However, if the person who asked would like, Max can certainly make special arrangements for that person.

Q: Will you upgrade Y-Search for all DYS markers?
A: Sorry, FTDNA does not have enough resources.

Q: What is FTDNAs source of ethnic data in Family Finder?
A: FTDNA purchased the application from Doug McDonald.  The next version will replace current information with lists of countries of known origin of individuals.  This information is in the FAQs.  Everyone should read them!

Q: What is the best web browser for FTDNA?
A: FTDNA is tested for all browsers.   Internally, they use Chrome.

Q: Can you do Y-DNA testing and a Walk the Y on an orangutan and bonobo?
A: Sure, if someone wants to provide the sample and sponsor it.

Q:What is the future of testing for FTDNA at the University of Arizona now that Geno 1.0 has ended?
A: FTDNA has a state of the art lab in Houston.  (Do they ever!!!)  The University of Arizona is still very connected via Mike Hammer.  97% of the testing now takes place in Houston.  Geno 2.0 will be run completely in Houston.

Q: Can you fix the email blacklist?
A: If emails bounced, there is a presumption of spamming.  If a company spams enough, they will get blocked by the service provider.  This is the reason for the blacklist.  If you have inadvertently ended up on it, call or email and it can easily be fixed.

Q: Will 23andMe data be functional in the new features of chromosome browser?
A: Yes.

Q: Will lower resolution tests like mt HVR1 and Y-12 be dropped?
A: FTDNA would like to offer just FMS, Y-37, 67, and 111 from the perspective of having the data but there are other considerations, a primary one being purchasing power.  Everyone wants the highest number of people in projects but cost would be a deterrent and drive some people out of the market.

To Dr. Behar
Q: Can a project admin see if a member’s FMS is in NCBI?
A: Dr. Behar hopes that an admin can see the number only if it is approved in a transparent manner such as on the website, not via private communication.  This is important for privacy.

Bennett
Q: What is the value of 67 and 111 marker tests?
A: Use the least amount of data you can to get the most.  “We try to make sure you don’t spend money that you have.”  He did not want to allow the 111 marker test to be purchased without first purchasing the lower marker tests but after much arm twisting, he is finally submitting.

Rory
Q: How did you derive the ancestral haplotypes?
A: Do a Google search and an FTDNA page will come up with the haplotypes.  List members then filter excel data, sort by subclade, separate by hand with 37 or 67 vertical columns.  He determined modal haplotype locus by locus.

Mike Hammer
Q: Do all chimps or gorillas have identical Y-DNA?  Is there diversity like there is in humans?
A: Yes, they all have different sequences.  They have looked at lots of chimps and they’re more polymorphic than humans are.  Occasionally, the same site might be polymorphic between chimps and humans.  It would be best to have 10 chimp Walk the Y samples and not use polymorphic results but not doing this would not ultimately damage the study results.

Q: Are there dates for the 2013 conference?
A: Bennett jokingly asked a staff member to go book November 2-3, 2013, but I sure wouldn’t bet the farm!