Steve's Genealogy Blog

At the Seventh International Family Tree DNA Conference for Group Administrators, Elliott Greenspan presented a talk on “IT Roadmap 2011: The Year in Review and Looking Ahead.”

Elliott Greenspan

SOURCE:  Elliott Greenspan (Houston, Harris County, Texas); photographed by Stephen J. Danko on 06 November 2011.

The Family Tree DNA GAP (Group Administration Page) 2.0 was launched in November 2010 .  The Family Finder autosomal DNA test platform was changed from Affymetrix chips to Illumina chips in January 2011 .  Family Tree DNA has processed 2.33 PB (petabytes) of matching data for Family Finder.

The SNP (single nucleotide polymorphism) ordering tree was modified, making it easier to order SNPs .  New downstream SNPs were added and the Y-DNA test was expanded from 67 to 111 markers .  Family Tree DNA intends to release new SNPs more quickly.

Family Tree DNA acquired the DNA Heritage Y-DNA (Y chromosomal) database, but not the mtDNA (mitochondrial DNA) database because the two companies did not sequence the same region of mtDNA.

The myFTDNA 2.0 homepage will be released soon .  Project administrators will be able to try the myFTDNA before the project members .  The General Fund is easier to use, a new messaging system from FTDNA to customers has been added, and a new configurable profile for users has been added .  Privacy settings have been added to the profile .  There are specialized resources for each section of the myFTDNA page, Family Finder matches, new images, a link to the profile, and badges .  Y-DNA haplogroup matches have been expanded.

New features allow you to see matches just for a particular project .  A new power search feature has been added, allowing the user to combine the power of all three DNA types in a search .  Family Finder upgrades include new SNPs, fewer false positives, and the ability to upload data from 23andMe (v3 only).

Microalleles can be displayed on GAP charts .  Microalleles are displayed as decimals in three quarter steps: 0.1, 0.2, 0.3 (0.4 is the next higher number of repeats) .  Changes in palindromic markers are now treated as a single step mutation, rather than multiple step mutations, reflecting the number of events rather than the size of the events .  STR (short tandem repeat) values will adhere to NIST standards.

Copyright © 2011 by Stephen J. Danko

At the Seventh International Family Tree DNA Conference for Group Administrators, Michael Hammer, PhD presented a talk on “Neandertals in Our Midst: Just How Modern is Our Genome?”

Michael Hammer

SOURCE:  Michael Hammer (Houston, Harris County, Texas); photographed by Stephen J. Danko on 06 November 2011.

What did Darwin have to say about human evolution?  He avoided the subject .  It was actually Thomas Henry Huxley who discussed evidence as to man’s place in nature.

If all species of the genus Homo (Homo erectus, Homo neanderthalensis, Homo sapiens, among others) are considered humans, did modern man replace older forms or was there gene flow among species that coexisted at one time?  Did archaic forms of humans leave behind DNA evidence?

An indirect method of inferring the past uses contemporary DNA, molecular dating, and single locus phylogeography .  From this type of evidence we know that, since there is greater genetic diversity in Africa, the root of the human evolutionary tree is among Africans .  In Newsweek magazine, on 11 January 1988, the press coined the term “Mitochondrial Eve.”

A direct method of inferring the past uses ancient DNA .  Using this approach, there is no evidence for a Neandertal contribution to mitochondrial DNA (mtDNA).

Analysis of the Y chromosome (Y-DNA) by indirect approaches shows greater African diversity, an African root, with a time to the most recent common ancestor (TMRCA) of about 130 KYA.

Analysis of the X chromosome (X-DNA) by indirect approaches shows a greater Asian diversity, an Asian root, with a TMRCA of about 2 MYA.

The DNA of three Neandertals has been analyzed .  The data from this analysis shows that there was a little interbreeding of Neandertals with Eurasians, but not with Africans.

Evidence shows that after humans left Africa, they bred with Neandertals and then that population interbred with the Denisovians in Melanesia .  There is Denisovian (from the Denisova cave in Siberia) DNA on chromosome 12, a greater Melanesian diversity, and a Melanesian root.

An innate immunity gene STAT2 introgressed (moved from one species to another) from the Neandertal and is positively selected in Melanesia .  Interbreeding of modern man with Neandertals led to an advantage.

Inferring the past using an indirect method involving contemporary DNA, molecular dating, and a computational approach shows that chromosomes 4, 18, and 13 entered African DNA relatively recently, providing evidence for interbreeding of modern man with a now extinct hominid form in Africa.

DNA evidence allows us to reject the theory of recent African replacement.

Bloggers who have discussed Neandertal DNA include John Hawkes.

Copyright © 2011 by Stephen J. Danko

At the Seventh International Family Tree DNA Conference for Group Administrators, Katherine Hope Borges and Alice Fairhurst led a meeting of the Family Tree DNA Chapter of ISOGG (International Society of Genetic Genealogy).

Katherine Hope Borges and Alice Fairhurst

SOURCE:  Katherine Hope Borges and Alice Fairhurst (Houston, Harris County, Texas); photographed by Stephen J. Danko on 06 November 2011.

ISOGG was started in 2005 after the 2004 Family Tree DNA Conference for Group Administrators .  The ISOGG wiki has added the ability to create a book about anything.

There has been increased movement towards regulation of DTC (direct to consumer) DNA tests, especially medical tests.

In a 2011 survey of the ASHG (American Society of Human Genetics), 74% said that DTC tests should not be available for all purposes, 84% were in favor of DTC tests, but consumers should be aware of the limitations .  Regarding the availability of DTC ancestry tests, 60% were in favor, 20% were neutral, and 20% were against.

The ISOGG PAC (Political Action Committee) is not related to money.

California added genetic information to the list of information that people cannot be discriminated against .  The new law (SB559) becomes effective on 01 January 2012 .  This is stronger than GINA (Genetic Information Nondiscrimination Act of 2008) .  GINA failed several times before it was passed.

ISOGG wanted a clearing house to name Y-DNA subclades based on new SNPs (single nucleotide polymorphisms) .  ISOGG needs the help of members to identify new SNPs .  The majority of men in ISOGG are in haplogroup R .  ISOGG prepares a Y-DNA haplogroup map and updates it when new information is available .  This map is in harmony with the YCC (Y Chromosome Consortium), but it is not identical to the Family Tree DNA Y haplogroup map because the Family Tree DNA haplogroup map is updated less frequently than is the ISOGG haplogroup map.

Copyright © 2011 by Stephen J. Danko

At the end of the first day of the Seventh International Family Tree DNA Conference for Group Administrators, those who made presentations answered questions from the audience.

Mike Hammer and Thomas Krahn

SOURCE:  Mike Hammer and Thomas Krahn (Houston, Harris County, Texas); photographed by Stephen J. Danko on 05 November 2011.

Q:  How many generations back is Family Finder accurate?
A:  Five generations

Q:  When will there be a public Genographic Project database?
A:  Soon .  March/April 2012.

Q:  When will Family Finder be able to use the results of 23 and Me?
A:  In 4-8 weeks at a cost of $50.

Q:  Does the Genographic Project still plan to destroy DNA samples not transferred to Family Tree DNA?
A:  Yes .  They will probably do so next year.

Q:  How did ancient people get across the Red Sea?
A:  With climate changes, water levels rise and fall.

Q:  Can Family Tree DNA arrange tours of the Clayton Library?
A:  Yes.

Q:  Can Family Tree DNA extend the 25 year storage period for DNA samples?
A:  Yes, to 50 years.

Q:  Can new SNPs (single nucleotide polymorphisms) distinguish or unite families within the historical range of surnames?
A:  Not yet but, theoretically, yes.

Q:  Are there any STRs (short tandem repeats) on mitochondrial DNA?
A:  Not really, one segment might be considered an STR .  STRs on mitochondrial DNA might be selected against.

Q:  What is the stability of the new Y-DNA markers?
A:  The new markers are single copy, not palindromic.

Q:  Which labs are covering new SNPs?
A:  Various labs.

Q:  How can one explain the Family Finder results when person A matches person B, but person B doesn’t match person A’s parents?
A:  Don’t ignore it, but don’t worry about it.

Q:  Did Turkish farmers make it to Ireland?
A:  We can do SNP testing, but the Western R1b is not found in Armenia.

Q:  Are there passenger manifests that show people leaving the United States?
A:  Not that have survived.

Q:  How were the One-Step search tools created?
A:  Read Deep Linking and Deeper Linking.

Q:  If DNA samples of deceased people are still held by Family Tree DNA, can they still be tested?
A:  Yes, but some older samples no longer work.

Q:  Will a DVD be made of the conference?
A:  Perhaps, after Family Tree DNA reviews the quality of the recordings.

Q:  Can people who tested with the Genographic Project and haven’t transferred their DNA to Family Tree DNA be contacted?
A:  No .  The kits were submitted anonymously.

Q:  What percent of the Y chromosome can be easily sequenced?
A:  20 Mb, part of the p arm and most of the q arm.

Q:  What is the mutation rate of STRs?
A:  About 1 mutation every 500 generations, but there is huge variation.

Q:  Will Family Tree DNA accept results from Ancestry.com?
A:  Family Tree DNA already accepts results from Ancestry.com .  In addition, they will be taking new markers and 23 and Me results, however Family Tree DNA will not be able to provide customer service for results from other companies.

Copyright © 2011 by Stephen J. Danko

At the Seventh International Family Tree DNA Conference for Group Administrators,
Steve Morse, PhD presented a talk on “One Step Webpages Part I: A Potpourri of Genealogical Search Tools”.

Steve Morse

SOURCE:  Steve Morse (Houston, Harris County, Texas); photographed by Stephen J. Danko on 05 November 2011.

Steve Morse’s One-Step Webpages at http://www.stevemorse.org provide tools for searching existing databases with more powerful interfaces than those provided by the database owners. Steve Morse does not generate the databases themselves but, rather, he provides powerful tools to search existing databases.

Some One Step Webpages of genealogical interest include:

• Ellis Island Arrivals
• All New York Arrivals
• One Step Immigration Triangle (Ship Arrivals, Passenger Names, Microfilm Rolls)
• Finding Pictures of Passenger Ships
• Castle Garden Arrivals 1855-189
• Barge Office Arrivals 1890-1891
• Other Ports of Immigration
• US Census Utilities to Find Enumeration Districts
• US Census Utilities to Interpret Occupation Codes
• Births, Deaths, and Vital Records
• Relationship Calculator
• Calendar Conversion
• Time of Sunrise/Sunset
• Zip Codes
• Latitude/Longitude
• Characters in Foreign Languages

Copyright © 2011 by Stephen J. Danko

At the Seventh International Family Tree DNA Conference for Group Administrators,
Peter Hrechdakian presented a talk entitled “The Armenian DNA Project”.

Peter Hrechdakian

SOURCE:  Peter Hrechdakian (Houston, Harris County, Texas); photographed by Stephen J. Danko on 05 November 2011.

The Armenian DNA Project is a large project with 570 members. Historically, Armenia covered a much larger area than it does today and includes several languages.

Armenian DNA exhibits extreme diversity. There are 14 y-DNA haplogroups and 80 distinct clades. Major Y-DNA haplogroups include R1b, J2, G, and J1. Armenians in the R1b haplogroup belong to the older root of R1b, not the Western European root. Armenians come from diverse but ancient origins tied by common language, religion (Christian), and customs.

Armenian mtDNA includes 13 major haplogroups and 70 distinct clades.

Armenians and Assyrians fall into the same Y-DNA and mtDNA haplogroups and Kurdish Jews have similar Y-DNA haplogroups as Armenian.  Iraqi Kurds have a slightly greater East Asian component than other groups in the area.

Copyright © 2011 by Stephen J. Danko

At the Seventh International Family Tree DNA Conference for Group Administrators,
David Pike, PhD presented a talk entitled “Phasing & Other Analysis of Family Finder Results”.

David Pike

SOURCE:  David Pike (Houston, Harris County, Texas); photographed by Stephen J. Danko on 05 November 2011.

David has written a number of utilities for processing unzipped autosomal DNA files from either Family Tree DNA or 23 and Me. The utilities may be found at http://www.math.mun.ca/~dapike/FF23utils/.

Phasing entails separating a child’s alleles inherited from the father from those inherited from the mother. It is one of the more informative used of DNA data and it enables the reconstruction of ancestral chromosomes.

Example:  At a particular locus, the mother’s DNA shows that she has an A and a T, the father’s DNA shows that he has a T and a T, and their child’s DNA shows that (s)he has an A and a T. The child must have inherited the A from the mother, since the father does not have an A at either allele. Therefore, the child must have inherited the T from the father.

If the child has runs of homozygosity (a sequence of bases that are the same in each of the two alleles) such as:

GAGAGCAC
GGGAGCAG

(where A = adenine, C = cytosine, G = guanine, and T = thymine) there may be evidence that the parents are related to each other.

In analyzing the DNA, one may find a discordance. Microdeletions and copy number variations may result in some SNPs having only one allele, in which case the allele is reported twice.

DNA results are reported with 99.99% accuracy. Still, this means that 1 in 10,000 SNPs are miscalled, resulting in genotyping errors.

One may discover actual mutations – de novo mutations in the child.

A child may have a longer match with a cousin than the parent does due to false matches that coincidentally match the cousin.

Phasing a child is straightforward when raw data files are available for the child and both parents. Runs of homozygosity (ROHs) and matching blocks of DNA between relatives can be used to partially phase DNA. One parent and several siblings can also be phased, as can siblings alone, although phasing works better with data from one or both parents. Results may be enhanced if one sibling has already been phased.

Copyright © 2011 by Stephen J. Danko

At the Seventh International Family Tree DNA Conference for Group Administrators, Bruce Walsh, PhD presented a talk entitled “Genetic Genealogy Q&A”. I was particularly interested in this talk because, while I know quite a bit about Y-DNA and mitochondrial DNA (mtDNA), I am relatively new to Family Finder, Family Tree DNA’s version of autosomal DNA analysis.

Bruce Walsh

SOURCE:  Bruce Walsh (Houston, Harris County, Texas); photographed by Stephen J. Danko on 05 November 2011.

Two random people differ at 20 million out of 3 billion bases in their DNA. The differences include short tandem repeats (STRs) which have many alleles (forms) and high mutation rates) and single nucleotide polymorphisms (SNPs) which typically have two alleles and low mutation rates.

Of the 46 chromosomes and mtDNA in humans, 44 chromosomes comprise the 22 pairs of autosomes, the X chromosome, the Y chromosome, and the mt chromosome. The Y chromosome and the mt chromosome are passed from generation to generation intact.

Because the Y chromosome and mt chromosome do not undergo recombination, they are useful for tracing the strict paternal ancestry (father’s father’s father, etc.) and strict maternal ancestry (mother’s mother’s mother, etc.) of an individual, but are not useful for following any other ancestral lines (such as mother’s father’s mother or father’s mother’s father). For these lines of ancestry that are not strictly paternal or maternal, one must analyze the inheritance of the 22 pairs of autosomes.

While the Y chromosome and the mt chromosome are passed from generation to generation intact, the autosomes are recombined or shuffled from one generation to the next. Unfortunately, because of recombination, if two people share a common ancestor, the autosomal DNA shared by those two people is less and less the farther back their common ancestor.

If two people are separated from their most recent common ancestor (MRCA) by one generation, the probability that those two people share at least one intact autosome is 0.99999976 (almost certain). If two people are separated from their MRCA by two generations, the probability is 0.947. If they are separated by three generations, the probability drops to 0.502. Four generations apart, and the probability is 0.158. Six generations, and the probability is 0.01068729. Seven generations, and the probability is only 0.00268211.

Because of recombination, the autosomes usually don’t get passed on to the next generation intact. So, as the autosomes are recombined, blocks of DNA, rather than intact autosomes, are passed on from one generation to the next.

TMRCA – Average Size of Block
1 – 44.06 cM
2 – 19.15 cM
3 – 12.30 cM
4 – 9.07 cM
5 – 7.19 cM
6 – 5.95 cM
7 – 5.08 cM

TMRCA = time to the most recent common ancestor (generations).
cM = centimorgan, a measure of distance in DNA corresponding to a 1% chance of recombination, or approximately 1 million DNA base pairs in humans.

When analyzing autosomal DNA results, the total amount of shared DNA allows an estimate of close relationships (1-3 generations). For more distantly related individuals, the size of the largest block of shared DN is used to estimate relationships.

Common blocks of DNA may be analyzed to determine whether the block of DNA is inherited from the father or the mother. This process is called phasing. The Y chromosome is inherently phased because it is inherited from the father. The X chromosome in males is also inherently phased because it must have been inherited from the mother.

Copyright © 2011 by Stephen J. Danko

After introductory remarks by Bennett Greenspan and Max Blankfeld who announced, among other things, a new collaboration between Family Tree DNA and Archives.com, Spencer Wells, PhD took the podium to present “Genographic Project Update: New from the Field.”

Spencer Wells

SOURCE:  Spencer Wells (Houston, Harris County, Texas); photographed by Stephen J. Danko on 05 November 2011.

The 7 billionth person was born on the earth this year. The National Genographic Project is working with traditional indigenous peoples in a three-part program involving field research, public participation, and a Legacy Fund.

In the field, DNA from approximately 75,000 people from over 1,000 populations has been sampled. Except for the Americas, sampling is going well. North America is the worst. In the public participation part of the project, DNA from about 415,000 people from over 130 countries has been sampled. The Legacy Fund, financed by the sale of public participation kits, has distributed over $1.5 million in 52 grants to countries all over the world. The Legacy Fund supports efforts to raise global awareness about the cultural loss faced by indigenous and traditional communities.

The Genographic Project has generated information about the movement of peoples all over the world. It has discovered that Hungarians have 2-3% Asian (Siberian) DNA. People moved or were isolated by a number of different climactic changes. Such changes allowed people to move from Asia to the Americas by the Bering Land Bridge. Other changes isolated people in refugia in Europe during the Ice Age and isolated people in South Africa because of desertification to the north.

Ancient DNA from central Germany shows that farmers from the Fertile Crescent moved in and replaced hunter-gatherers in Europe. When comparing genetic evolution and language evolution in the same populations, there exists a strong correlation between genealogical dates and language dates. Finally, the Genographic Project is beginning to look at recombination as a new type of genetic marker.

Copyright © 2011 by Stephen J. Danko

I attended the Seventh International Family Tree DNA Conference for Group Administrators which was held on 05 November 2011 – 06 November 2011. I am an administrator for five surname projects at Family Tree DNA:  Busi, Czwalga/Swalga, Danko, Dziurzynski, and Niedzialkowski, and I hoped to learn more about the state of the art in the use of DNA for genealogical purposes.

The program was as follows:

Saturday, 05 November 2011
9:00 AM – Welcome (Bennett Greenspan & Max Blankfeld)
9:30 AM – Genographic Project Update: News from the Field (Spencer Wells, PhD)
10:30 AM – Genetic Genealogy Q&A (Bruce Walsh PhD)
11:15 AM – Breakout Sessions
Phasing & Other Analysis of Family Finder Results (David Pike)
Walk through the Y Update (Thomas Krahn)
2:00 PM – The Armenian DNA Project (Peter Hrechdakian)
2:45 PM – One Step Webpages Part 1: A Potpourri of Genealogical Search Tools (Stephen Morse, PhD)
4:00 PM – Q&A Panel

Sunday, 06 November 2011
8:00 AM – ISOGG (International Society of Genetic Genealogy) Meeting (FTDNA Chapter)
9:00 AM – IT Roadmap 2011: The Year in Review and Looking Ahead (Elliott Greenspan)
9:45 AM – Neandertals in our Midst: Just How Modern is our Genome? (Michael Hammer, PhD)
10:45 AM – DNA of the Three Collas (Peter Biggins & Thomas Roderick)
11:30 AM – One Step Webpages Part II: A Hodgepodge of Lesser Known Gems (Stephen Morse, PhD)
2:00 PM – DNA Tests and the Law – Potential Use of Ancestry Tests for Immigration (Jessica Roberts, JD)
2:45 PM – An Adoptee’s Journey to His Ancestral Surname (Richard Hill, MBA)
3:45 PM – Closing Panel

Copyright © 2011 by Stephen J. Danko