Today was the first day of the 11th conference. I am having trouble loading my large photo files so I’ll publish notes now without them to avoid delay. As usual, these are rough notes that I typed during the conference so if you need clarification, please ask. I may be able to help and if not, I’m sure another attendee can. Enjoy!
Max welcomed everyone to the conference and recognized people who have attended ten conferences and people who have been administrators for ten years. Bennett shared that this is the largest conference that they’ve had. Bennett recognized people who are attending their first conference. Bennett talked about his search for other Greenspans and how he has tested 68 Greenspan men. None of those 68 men matched Bennett. Bennett recently found someone else to test and he was the closest person in the entire database.
Peter Sjolund presented “Y-DNA Research in Scandinavia Maps Family Trees from Medieval Times and the Viking Age.” This summer Sweden passed out Norway in the number of DNA tests for genealogy. Peter is a founder of the Swedish Society of Genetic Genealogy. Today one in a thousand Swedes have tested. Peter showed an example of Family Finder Common Matches Circle made at dnagen.net.
Peter introduced the Bure Family Kinship. It was the work of Johannes Bureus. He has appointed to take reports of all antiquities, or known memories from Sweden. His mother’s family consisted of farmers and he wrote a book including more than 1,000 descendants, using interviews as a source. The book vanished for 300 years but reappeared in the archives of Finland. The Bure Family History has been drowning in fabricated claims of famous history. Using DNA, they were able to make connections 600 years after the fact. They later found a man in America who matched the Bure family but his ancestry was Denmark. They did some research and found evidence of one who went to Norway in the 1540s. This man is likely a descendant of this branch. Another man turned up and traced to the same area but not a farmer. When looking further into the family history, they found one more generation, Herse, and the children Hersesson. They then found more descendants of that generation in the same village of Falmark.
Peter said that this project sends all of their BigY results to Y-Full for analysis. They do a fabulous job for the project. They provide information to help build the family tree with data. They calculate how many years since the common ancestor for each line.
Peter also spoke of his mother-in-law’s brother from the Bergman family who related to the Vorontsov Russian noble family. They tested him to 111 and then began SNP testing. Three years ago, there were not many SNPs available. Now they have more than 90 Big Y tests in the project. They sent the results to YFull.com and paid $49 for the analysis. The results can be used to map migrations within Scandinavia. L1302 went east to Russia and Ukraine and L1301, which is also clearly Viking DNA, went to the British Isles.
In Sweden they have now started an academic project, The Atlas of Ancient Human Genomes in Sweden, a $5 million project. This can connect to the Y DNA data. Peter said they have met with the academics to make sure they are testing the SNPs that are in the project.
Peter provided some tips about “The Way to Create a Big Y Tsunami.” He advocates that if you have already tested and tested your family members, sponsor tests of people close to you for Big Y and it will help you to learn more about your own Big Y test.
There is a woman with mtDNA haplogroup C4a1c who is the only one with that haplogroup in Europe. This is like the Inca or Mayan Indians. Her genealogy stays in northern Sweden until the 1600s but then they were unable to follow it. About a year ago a large study from Russia showed up and there was a large population in Eastern Siberia where almost everyone was C4a1c. These people were the Evenks, who were hunters and reindeer herders who had been there for thousands of years.
Max pointed out that this is a huge contribution to writing the real, unbiased history. That is a very important point to make to your project members. Peter also noted that we need to connect to timelines and geography to make it easier for people to understand and want to be a part of it.
Razib Khan presented “Autosomal & Agamemnon’s face.” He presented a chart showing the sharp decline in the cost of testing. We are currently in the second sharp decline and soon it will not even be a discussion. The first human genome cost $3,000,000. Razib’s son was sequenced in 2014 in utero for $500 with 7x coverage. You can now get high quality medical grade whole genome sequencing for $1,850. Razib believes that half of the American population will have high quality whole genome sequencing by 2025. He consulted with other experts, including Spencer Wells, who believes that this estimate is on the conservative side.
We are still focusing on SNPs instead of WGS because WGS is expensive, takes longer, and oat of it is not informative. We can’t interpret a lot of the variation and it is redundant. Also, more data takes longer to analyze, even on powerful computers.
SNP chip assays survey about 10,000 to 1,000,000 markers. Human chips generally have 500,000 – 1,000,000 markers. Only a minority of human SNPs are captured on a given chip. Many of the markers are intergenic, while the genic ones may not be functional.
Thirty “ancestrally informative markers” give you enough information to tell intercontinental difference, for example, African vs. European. One thousand random SNPs are sufficient for data heavy population assignment at this scale. Ten thousand random SNPs get you most of the way to intra-continental differences, for example China and Japan.
Another issue is imputation. You can gap fill if you know that SNPs are genetically linked. You always have more than 100,000 SNPs if you test 100,000 SNPs because of the way recombination works.
The founder of genomics said to treasure exceptions but exceptions make a tidy story difficult. Autosomal ancestry inference is the Reader’s Digest of your genomic history. If you take thousands of characters and put them into the scaffold of a predetermined plot and reduce them down to fewer than fifty characters, this would be the case.
Razib is working on the second version of MyOrigins right now. It will go up six clusters. The names will not be presented as Razib presented in his slide. Razib talked about why we were getting so many false negative clusters. We will have a northern and southern cluster. In the Siberian cluster, very few customers are going to be Siberian but Siberians turn out to be very important in the history of Eurasia and the New World. Many Native Americans will pick up this. There will be a Sardinian cluster. There will be some new Southern European clusters, The Balkan cluster will be the indigenous group mixed with Balkan people from the north.
Mike Shriver at Penn State is doing research on reconstructing faces with DNA.
David Reich & Eke Willerslev are the Coke & Pepsi of ancient DNA.
Ancient Europe was inhabited by very different people. There were hunters and gatherers who were the oldest ones, the first farmers, and the horse people. The genetic distance between some of these groups was comparable to that between Chinese and modern Northern Europeans.
We know a lot about pigmentation because genes are preserved. They can cause the same effect across all mammals. The gene that makes people “white” is SLC24A5. It explains 35% of the skin color difference between Africans and Europeans. This is not indigenous to Europe. It is entirely absent in Mesolithic Western Europeans, the oldest group. It is present at very high frequencies in both the horse people and the farmers. Looking at the haplotype structure, it’s likely to be from the farmers.
There is a second gene that also makes you light skinned, SLC45A2. If you are heterozygote, you likely have olive skin. Homozygous people likely have very light skin. This was absent in European hunter-gatherers.
Dr. Michael Hammer from the University of Arizona presented “R1B and the Peopling of Europe: an Ancient DNA Update.” As of 2014, there were 15 sites and 74 samples of ancient European DNA. This year we have more than 160 samples.
There are about 85 million SNPs that have been identified in the human genome. In 2014 we had the first study to fully sequence genomes of Neolithic and Mesolithic Europeans.
There are three basic European Ancestral Components, WHG, EEF, and ANE.
Who were the ANE and how did they make such a large contribution to the European Gene Pool? It turns out that R1b into Europe can be traced to the ANE. There are two laboratories publishing this year in the June issue of Nature, both reaching the same conclusion. Massive migrations from the Russian Steppe in the Bronze Age represents the third major source of genetic material found in Europeans today. Dr. Hammer also showed the work of Allentoft et al. “Genomics Supports Steppe Contribution to Bronze Age Europe.” Their conclusions are summarized on the bottom of the slide. He also showed that “Yamanaka genetic contribution to Neolithic European Gene Pool” and their conclusions. He looked at the way the two studies agreed. The Haak paper noticed that there was a resurgence of the hunter-gatherer ancestry during the Middle Neolithic 7,000 – 5,000 years ago.
Dr. Hammer worked with Rui at Family Tree DNA to find Bronze Age Y-chromosome SNPs in Europeans.
Looking for Western Hunter-Gatherers, they were prominent in Balkans and Macedonia.
It has been a Y Chromosome roller coaster for the last 7-10 years.
Miguel Vilar presented “Genographic 2015: New Markers, New Geno Kit, and Accessing the Database.” The Genographic Project is a multi-year genetic anthropology study that aims to map historical human migration patterns by collecting and analyzing DNA samples from hundreds of thousands of people from around the world. Dr. Spencer Wells launched the program in 2005 and then it was redone in 2012 as Geno 2. They ran out of those tests this year, in 2015.
There are three branches of the project. As of year ten, they have 75,000 indigenous samples, 670,000 public participants, and $2.1M granted through the Genographic Legacy Fund.
In August 2015, they launched Geno 2.0 Next Generation. Instead of using the Geno chip, they are now using the Illumine Omni Express, which looks at 750,000 SNPs instead of 130,000 like Geno 2.0. They have Y, autosomal, and Neanderthal SNPs on there. They took off some Y markers that were repetitive and added new ones, to bring the total to about 17,000. Mitochondrial markers went from 3,000 to 3,500. They removed the Denisovan and improved the Neanderthal.
The price is $149.95 with free shipping and handling, which they believe to be competitive.
Highlights include Deep Ancestry, with thousands of new Y-SNPs and hundreds of new mtDNA SNPs. Regional Ancestry is calculated on 18 Bio-Geographical regions with 60+ comparative populations. Hominim Ancestry has a new Neanderthal estimate based on current literature. The Y-chromosome DNA has about 8,000 new SNPs, many of which we are still placing on the tree. There are hundreds of new mitochondrial DNA SNPs. They are based on Phylotree Build 16 from 2014.
Regional Ancestry expanded from 9 regions to 18 regions.
In the Our Story section, people are represented by dots. The larger dots represent participants who have shared their stories.
The database will be searchable by many options. Some of these include mitochondrial haplogroup, Y haplogroup long or short form, Y-SNP, mtDNA position (SNP), age, place of birth, maternal or paternal POB, maternal or paternal ethnicity, maternal or paternal language, grandpaternal or grandmaternal, and all demographic categories at the same time (i.e. all Irish).
Geographic Project has published almost 60 papers in the last 10 years, and they have already published 5 in 2015.
They also have lots of projects going on in the field. They have 11 new grantees since 2012 doing field work and lab work.
The industry is booming today. There are TV shows, hundreds of Academic Papers, and internet searches for “ancestry” have increased. Multiple DNA tests in the market are selling for less. Complete genomes are almost affordable.
The kit went for presale in June and started shipping in August this year.
Geno 2.0 Next Gen kits can transfer to Family Finder but not the other way. You can transfer for free and unlock for $39.
They have not updated the indigenous samples but they are still in communication with their research centers. They may in the future.
The list of new Y-SNPs can be made available but they are still testing some. They are about 90% done.
Why Geno 2.0 Next Gen? Bennett says he told them that but they did not accept his advice.
If you have the old Geno 2.0 kit, there are new terms and conditions that the Legal Department at Nat Geo has added to the program. You will have to consent to the new online terms and conditions before they will run the kit. This could create a 4 week delay if you don’t check your page to see the new terms and conditions.
They are still trying to figure out if there will be an upgrade for Geno 2.0 but the best they can say now is that it’s a new cheap and the least expensive it’s ever been.
If you were a Geno 2.0 customer, you will not get the new subgroups because they would have to re-run the sample. You can use the website to look at your results, though.
Is it possible to get a Geno 2.0 Next Gen analysis on a sample from Geno 2.0? Yes, if it transferred to FTDNA and the sample is stored.
No personal data will be released. It is all completely anonymous. All you will know is that there was a participant with this haplogroup and SNPs.
Can you use a sample from 1.0 to upgrade to 2.0? Everyone who had transferred from Geno to FTDNA had their sample retained. If you did not transfer, those samples were not retained per contract between Nat Geo and FTDNA.
21st Century Fox bought the media part of Nat Geo. Miguel works for the non-profit society portion, which is retained. There are board members now overlooking the partnership called National Geographic Partners. The non-profit side remains completely society. The kit belongs to the partnership but the database belongs to the society portion.
FTDNA made a business decision that kits purchased for Geno 1.0 will have to re-sign the new terms and conditions and they will be supplied the 2.0 product. This is a benefit to the consumer and allowed FTDNA to eliminate one code.
They attempted to put all Big Y SNPs that didn’t appear to be singleton, that appear to be cladistically significant. onto the chip. (Yes, cladistically is a real word!)
The Big Y SNPs that were harvested and put on the chip are available only through Big Y or this new product. This will represent the greatest offering of any company.
After you transfer your record to FTDNA, you should be able to transfer. They have to get the transfer mechanism ready.
Denisovan testing was eliminated because some scientists felt that it was rushed onto the chip in 2012. There is not much known from the one sample. They had gotten some criticism for having it. They are much more confident about Neanderthal and have more information.
Michael Davila presented “Products – Meet the Director of Product Management.” In 2011, Michael left FTDNA to go into the Oil & Gas field. Bennett and Max asked him to come back this summer to fix some things. The focus going into 2016 is tools. He is listening. Janine will help him prioritize the items and they will get the work done.
Questions:
Is the $149 permanent or is it a sale price for Geno 2.0 Next Gen? He is not sure but it will likely be there through the holidays.
What did Razib mean when R1a displaced? The results are from the latest 8,000 Years of Natural Selection.
The $1,800 full genome is done by what company? Max said that is likely academic pricing.
When will the new extended MyOrigins be available? Will it happen magically on the site? Razib is coming back in December. There are a bunch of populations to add. Bennett is struggling on one population that he got 28 samples for that haven’t been run yet. It may be early or late Q1.
Will FTDNA do anything about surname projects that haven’t been updated in a long time? Max said they are managed by volunteer administrators. If it hasn’t been updated, let them know. Contact Janine. What they normally do is to email the person listed and ask politely why the project is not being updated. If the person does not reply within a certain time, they look for a replacement. If that doesn’t work, they ask World Families, Terry Barton, if they want to take over the project administration. Terry has been taking care of orphan projects for years.
How did Razib get a sample from his son in utero? They did chorionic villi sampling when he was second trimester. It was analyzed for karyotypes. He badgered them into giving him the DNA sample. He later found out that legally they were supposed to give it to him but they didn’t know because no one had ever made such a request.
Will there be updates for British Isles populations? The variations are very small, which makes it difficult. The genetic differences represent minor absorption of local substrate and genetic drift.
When will Gap 2.0 be pulled leaving MyGroups as the only option? Max said, “We’re doomed if we do and doomed if we don’t.” This will need to be left as it is for a while.
When will you do autosomal matching using WGS? Bennett said, “That is someone who is way out there!!!” It needs to be enough people to make it of value. He guesses that we are 3 – 10 years away.
FTDNA participates in several events every year. They have been to Gathering of the Clans in Scotland and they sponsor the DNA area at Who Do You Think You Are Live? in England. They discount the tests a lot in an effort to bring in more diverse testers. They also leave a lot of tests with people locally to sell.
Why is German and British difficult to distinguish? If it’s someone from Austria, for example, they are much different. If it’s Saxony, they are very similar.
Do you have blank test kits for people to take home? Yes, there are bags prepared with five blank kits.
Are there any plans to allow display of data on other sites publicly? If anyone has suggestions, please forward those suggestions. They get many suggestions but they need to prioritize according to what they think will benefit the most participants overall.
Once we obtain a sample, how long does the sample last before we send it back to FTDNA? Once a cheek has been scraped and the tip has been ejected into the vial with the buffer, it should last for years. Once they crack it open and pull the DNA out, it should last for a few years for anything that uses Next Gen sequencing or the microarray. If you had DNA done anywhere five years ago, it may work but it may not work. Some people experienced Big Y results delay because the kit of more than 3 years old sitting in the -20C freezer may experience some degradation and it is not as robust.
Many people ask about using other DNA sources for deceased family members — blood, hair, teeth. Don’t send hair. They don’t do a good job crushing up teeth. If you have a relative who hasn’t died too long ago and he has a yucky, crusty, gross hearing aid, it likely has plenty of DNA. If it’s a year old, they probably can do a hand extraction for an extra fee. Blood is a great source of DNA but if there is a drop or two of blood on something, as long as you don’t take it and get your DNA on that spot of blood, it might be usable.
Miguel said that I and J break off in the Middle East. I is found in Europe. I1 is more common to Scandinavia and I2 in Balkans.
Is there a specific autosomal DNA marker showing Native American ancestry at the 1/16 level? After six generations there is more than 50% chance you won’t have DNA from that ancestor. John Ross, the Cherokee Chief on Trail of Tears, was 7/8 Scottish. Of 300 people that Razib looked at, he found two that were Native American. Even a great great grandparent who was Native American was likely admixed.
Is there an action item to make the Gedcom tree more navigable? Yes, they are working on it. They did a short internal test with about 7 users, that led them to a lot of findings about the settings. That is step 1. Step 2 is the actual tree itself. They will fix it.
Would you advocate using someone else’s Y tree? No, if they haven’t seen a mutation, they can’t confirm it.
Of the 17,000 Y-SNPs on the Geno 2.0, does that represent some kind of 80/20 compromise vs. the Big Y at 4x the price? The best of the SNPs that were known at the time were put on the chip. You have about 80 or 85% conversion rate. Some of the SNPs don’t work and they didn’t intentionally fill up the geographic chip with singleton, which are what you’re going to use to say that you’re most derived on a branch and give you the predictions that you are related in 250 years or 400 years. The Big Y is a discovery project.
Why not drop the Y-12 test? In a selective way they are doing that but they are still leaving it open. There is not an option for Y-12 on the page but administrators can order them for a project.
Does the TIP calculator take into account the stability of the STRs that have mutations? Yes. It considers the known volatility rate.
When will you name newly-discovered Big Y SNPs? Bennett suggested it early on and some people said “NO, NO, NO” but those people are now gone.
There has been a lot of speculation about Sephardic in MyOrigins. There is no representation for that in MyOrigins. If you are in a population that is not in the reference set, it will force a match to the next reference population over. Bennett is looking at this population dataset.