17 November 2012

Family Tree DNA’s 8th International Conference on Genetic Genealogy, Day 2

Houston, Sunday, 11 Nov 2012

The last day always seems to come so quickly.  There never seems a great deal of time to chat with fellow genealogists so getting to bed late and up early does keep some of us non-morning people dragging a bit!   But the excitement of the day is as good as a cup of coffee!

Alice Fairhurst
Sunday morning was our usual International Society of Genetic Genealogy (ISOGG) meeting.  Alice Fairhurst spoke on the ISOGG Y-DNA tree which started in 2006.  There are now over 2,000 SNPs on the  tree.  The first few years there were 25-30 updates per year; last year over 100.  There are already 73 updates this year so far and that number is that low only because the team clustered some of the updates.  Many people in many countries are involved in helping, but they could use more.  They need help in Q and some other areas.  Due to Geno 2.0 ISOGG tree is going to a stronger database, but will remain the same through December 2012.  The next tree may not be ready in January, however.  Although there is a conversion chart, the new tree will only use terminal SNPs.  Some R1b sub-clades are over 20 letters and numbers, and with Geno they will be much too long.  This ISOGG tree is used by geneticists around the world.
Dr. Brian Swann
Brian Swann from England gave great information and encouragement in his presentation suggesting that people with British genealogy learn how British records work and use them to find probable testers and reconstitute the families.  He stressed checking the 1881 census, the 2055-2006 Birth, Marriage, and Death records now online, and checking for your surname through the Guild of One Name Studies. There are online databases for the UK from 1837-1841 could be a good resource, as well.  Debbie Kennett’s new book Origins of British Surnames can be helpful. Facebook can also be a good source for current contacts.  Join the local family history societies in areas of interest in Britain. Dr. Swann urged that as half the people in Britain who have children do not marry, now is the time to start the reconstruction as it will be more difficult in the future.

Dr. Doron Behar
Dr. Doron Behar spoke on the mtCommunity, referring to his paper:  A Copernican Reassessment of the Human mtDNA Tree from its Roots.   He states that about 16,000 mtDNA sequences on NCBI’s  (National Center for Biotechnology Information) GenBank are from Family Tree DNA customers.  He explained that Chimps are not our ancestor, but when through 6,000 years of evolution and are our contemporaries.  Neanderthals were extinct only 30,000 years ago.  Some of our species interacted with the Neanderthals, we did not evolve from them.  Mankind did not evolve as you see in many online posters.  Dr. Behar’s paper clearly shows that using the rCRS (Revised Cambridge Reference System) gives a skewed vision as more western Europeans have fewer mutations than those of other world areas.  With his paper reconstructing the mtDNA comparison starting with the root and adding such populations as the Neanderthal, we see that there are now fewer mutations for those populations closer to the root and more mutations for those farther from the root which is much more logical.  This new method is termed RSRS (Reconstructed Sapiens Reference Sequence).  With the RSRS, all contemporary mtDNA shows approximately the same number mutations from the root…again, more logical. This change has no effect on the mtDNA tree topology or haplogroup labels.  It will only add or subtract to the number of mutational differences when compared to the root mtDNA.
See the mtDNACommunity website which has over 13,700 full mtDNA sequences so far and is a centralized database allowing sequences to be posted for scientists.  You can add yours.  It is free to all testers from all communities, but only uses complete mtDNA sequences; the full mitochondrial tests.  Each sequence not from FTDNA will be verified for accuracy before uploading.  You will be asked if you want to upload to NCBI so check the option if you do, and FTDNA will upload for you.  If you have already uploaded to NCBI do not do it a second time so you are not duplicated.  You can send your CBI to FTDNA to check. Once you upload your NCBI submission number will be on your profile page.

Dr. Michael Hammer
Bonnie Schrack
Dr. Michael Hammer of the University of Arizona presented the most exciting news of the conference!  Dr. Hammer’s presentation was entitled A highly Divergent Y Chromosome Lineage; Implications for Human Evolution and the Y Chromosome Tree.  Bonnie Schrack, citizen scientist, gave us the back story and suggested that haplotypes that do not fit into the main groups can be gold, and that rare haplotypes can identify new clades.  She found three people in her Y-DNA Haplogroup A project who did not have any designated haplogroup.  After consulting some papers by Cruciani (2011) and Batini (2011), the decision was made to do a Walk The Y (WTY) for one of the members living in Georgia.  More than 40 new SNPs were found with this test, setting a new record.  It also included 32 SNPs discovered by Cruciani in is A1b sample.  A second WTY was done with another member of  her project in Maryland.  For this tester about 24 new SNPs were found, but he shared 18 of Cruciani’s SNPs and 19 of the SNPs found in the tester from Georgia, and 22 new SNPs for his branch.  A third WTY, a candidate from South Carolina, tested negative for all the SNPs previously tested in the other two  testers.
     At this point, Dr. Michael Hammer was brought into the picture.  Over 50 SNPs were derived from this South Carolina sample and about 30 which are ancestral and derived from all other human Y lineages.  Dr. Hammer had seven SNPs matching the WTY testers and these were found in a small section of Western Cameroon.  These new results put the Chimp and Gorilla very distant to modern humans.  Hammer stated that the South Carolina tester who now has a haplogroup of A00 (currently the oldest haplogroup) is 500 years from his Cameroonian A00 cousin, and that the Atlantic slave trade brought his ancestor to the US. This discovery predates the origin of modern human fossils, and this tester’s line could be an archaic population.   Two fossils found at Iwo Eleru (in nearby Nigeria) dated ~13,000 years ago showed archaic features.
Dr. Thomas Krahn
     Dr. Thomas Krahn shared the story of the discovery as he worked with his wife Astrid to see if each newly found SNP had been previously discovered.  After working all day and night, at 4 a.m. they realized they had new haplogroups.  By 6 a.m. they were done checking all the new SNPs.  As a result we no longer have just Haplogroup A, thought to be 60,000 years ago, but we have two haplgroups which came before A, namely A0 and A00.  The A00 haplogroup lived ~338,000 years ago, but could range anywhere between 246,000- 563,000 years ago.  Regardless, this is an astounding find and to know that one of our FTDNA administrators, Bonnie Schrack, was instrumental in calling this to the attention of the geneticists is an outstanding example of the value of citizen scientists.  Several people throughout the world contributed to the cost of WTY tests and were thanked by Bonnie.  This find is truly an important moment in history!

Elise Friedman
Yesterday’s Breakout Groups were repeated today to allow people to attend at least two. I attended Elise Friedman’s group entitled Advanced Group Administration Techniques as a review and to see if there was information new to me.  Without seeing the pages here it would be difficult to describe various aspects.  I suggest that everyone take the Interactive Tour, read the FAQs, click on the FTQL (Family Tree Query Language for compound searches) and the Help icon found on all pages.

A few basics she covered:  
1.  Go to MY ACCOUNT and click on SETTINGS. Check the boxes you want shown on the left.  DISPLAY SETTINGS on the right control what you see.  The bottom of MY SETTINGS has settings for different report pages.
2.  You can create a different email address for each project if you have more than one.  Just add your email address on the CONTACT PAGE and select one for default.
3.  Important:  Go to PROJECT ADMINISTRATION and then click on MANAGING PROJECT.  Fill in the blanks, but click on SHOW SURNAME even if your project isn’t a surname project.  This way it is shown in the list of projects.
4. If you use counters or other logos or icons, put those under JAVASCRIPT.
5.  You can also click on the results page and move members from one subgroup to another, but only in the regular results; not in classic or color.
5.  On the results page you can highlight one line.  I asked for 2-3 to be highlighted and maybe in different colors.  This, in my opinion will help with comparing.
6.  ACTIVITY LOG is new and shows changes in your projects.
7.  It is very important to read the Project Administrators Guidelines and adhere to them.

Rory Van Tuyl’s presentation entitled A Tale of Two Families – Findings from the FTDNA Surname Project Van Tuyl showed how he used Monte Carol simulation and the Walsh Infinite Alleles Theory to show that there was no constant mutation rate.  He suggests that using similarities rather than differences is a powerful analytical technique and not to try to estimate TMRCA from Y-STR data.

Elliott Greenspan
Elliott Greenspan’s presentation entitled IT Road Map covered the accomplishments of this last year and the goals for the coming year. In 2010 FTDNA processed 250 terabytes and in 2011 they processed 2.33 Petabytes of matching data. The latter translates into 16.8 million segments.  This is 50 times more data than last year.  FTDNA has run over 5 million individual tests of all types over the years. The General Fund Invoice Payment was added along with SNP Maps and 23andMe uploads.  As previously mentioned in this blog, FTDNA will allow uploads of Ancestry’s data as soon as it is available.  The “about me” section of the Personal Profile was added and is view-able by your matches when they click on your profile.  Advanced Matches was added in order to compare two different tests at the same time.

The coming year’s goals are quite extensive and very welcomed:
1.  FTDNA will go to Build 37 which is GRAND!
2.  Microalleles will be coming on GAP charts.
3.  Palindromic matches will be added in DYS 459,464 and CDY which will appear as one mutation as they are one event.
4.  New mtDNA haplogroups will see some changes when Geno 2.0 begins getting results.
5.  As the home page causes confusion for new members, the pages will be updated probably in December with items people have not done such as uploading a Gedcom being highlighted.
6.  More badges like Niall of the Nine Hostages will be available.
7.  Uploaded Gedcoms will be searchable and allow for direct input of data.
8.  FTDNA will upgrade Population Finder by adding more populations more often and will have chromosome painting.
9.  FTDNA will have X chromosome matching and browser, but will be different than that of Family Finder as it is inherited differently.
10.  You will be able to select five matches and push to your chromosome browser page.
11. There will be more filter options so you can filter by blocks in Chromosome Browser to see all matches on that block.  Blocks must be at least 4cM and start and end in the same block.
12.  Restrictions on “In Common With” will be removed.
13.  Many of us have asked for phasing over the last couple of years and is it coming!  YEAH!!!  There will be two types of phasing depending upon the availability of testing parents.
14.  Various apps for androids, iPhones, etc. will be added.
15.  FTDNA developers plan to work with a group of customers with tech skills…a developer sandbox.
16.  FTDNA will remove the five person limit for Family Finder downloads so all can be downloaded at one time into CVS or Excel files.  EVERYONE clapped!

What a wonderful list for the coming year!

FTDNA cautioned against using Gedmatch as it shows your matches names.  FTDNA cannot control customers who do this, but feel it could come back to bite you and can cause outside regulation.  They suggested we do not take cM blocks seriously without other supporting information.  They were firm about data mining not being available because of security and people who “connect the dots.”  FTDNA is not planning to drop the 12 and 25 marker test so that those who need to start small can do so.

AND…at the end of the conference FTDNA announced its Holiday Sale earlier than expected.  See my previous post for the sale items and prices.  The sale ends 31 December 2012 and is a great opportunity to upgrade, to add new tests, or to become a first-time tester with the largest genetic genealogy company!

On Monday, FTDNA offered three tours of their “state of the art” lab in Houston.  The equipment automation is amazing, and seeing the process to get our DNA results is fascinating.  The weekly cost of some of the disposable items is astounding!  It is clear why the time and cost we incur is what it is.

No doubt I omitted some information from this lengthy blog.  For that reason, I suggest you also read Roberta J. Estes’ blog DNAeXplained.

Can anyone doubt that history isn't being made on the monumental level?  

16 Nov 2012

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