Thursday, November 15, 2012

Geno 2.0 sample received

I mailed my Geno 2.0 sample over 1 month ago and today I see it has been received and is now in DNA Isolation before being tested.

More information on the Geno 2.0 project is available on this web page:


An interview from last weeks conference in Florence is on JustinTV:

Wednesday, November 14, 2012

Article: Archaic Human Genomics

Archaic human genomics

Todd R. Disotell*
Article first published online: 2 NOV 2012

DOI: 10.1002/ajpa.22159

Copyright © 2012 Wiley Periodicals, Inc.
American Journal of Physical Anthropology
Supplement: Supplement: Yearbook of Physical Anthropology
Volume 149, Issue Supplement 55, pages 24–39, 2012

Neanderthals;Denisovans;introgression;ancient DNA

For much of the 20th century, the predominant view of human evolutionary history was derived from the fossil record. Homo erectus was seen arising in Africa from an earlier member of the genus and then spreading throughout the Old World and into the Oceania. A regional continuity model of anagenetic change from H. erectus via various intermediate archaic species into the modern humans in each of the regions inhabited by H. erectus was labeled the multiregional model of human evolution (MRE). A contrasting model positing a single origin, in Africa, of anatomically modern H. sapiens with some populations later migrating out of Africa and replacing the local archaic populations throughout the world with complete replacement became known as the recent African origin (RAO) model. Proponents of both models used different interpretations of the fossil record to bolster their views for decades. In the 1980s, molecular genetic techniques began providing evidence from modern human variation that allowed not only the different models of modern human origins to be tested but also the exploration demographic history and the types of selection that different regions of the genome and even specific traits had undergone. The majority of researchers interpreted these data as strongly supporting the RAO model, especially analyses of mitochondrial DNA (mtDNA). Extrapolating backward from modern patterns of variation and using various calibration points and substitution rates, a consensus arose that saw modern humans evolving from an African population around 200,000 years ago. Much later, around 50,000 years ago, a subset of this population migrated out of Africa replacing Neanderthals in Europe and western Asia as well as archaics in eastern Asia and Oceania. mtDNA sequences from more than two-dozen Neanderthals and early modern humans re-enforced this consensus. In 2010, however, the complete draft genomes of Neanderthals and of heretofore unknown hominins from Siberia, called Denisovans, demonstrated gene flow between these archaic human species and modern Eurasians but not sub-Saharan Africans. Although the levels of gene flow may be very limited, this unexpected finding does not fit well with either the RAO model or MRE model. More thorough sampling of modern human diversity, additional fossil discoveries, and the sequencing of additional hominin fossils are necessary to throw light onto our origins and our history. Am J Phys Anthropol, 2012. © 2012 Wiley Periodicals, Inc.

Tuesday, November 13, 2012

FTDNA Holiday sale: Now till 31 Dec 2012

As we ended our 8th Annual Genetic Genealogy Conference, several conference participants asked us to start our year-end sale as soon as possible. In answer to those requests we decided to start it immediately:
New Kits Current Price SALE PRICE
Y-DNA 37         $169 $119
Y-DNA 67         $268 $199
mtDNAPlus         $159 $139
mtFullSequence (FMS) $299 $199
SuperDNA (Y-DNA 67 and 
 mtFullSequence) $548 $398
Family Finder         $289 $199
Family Finder + 
 mtDNAPlus         $438 $318
Family Finder + 
 mtFullSequence         $559 $398
Family Finder + 
 Y-DNA 37         $438 $318
 (FF + FMS + Y-67) $837 $597

Upgrades Current Price SALE PRICE
Y-Refine 12-25 Marker $59 $35
Y-Refine 12-37 Marker $109 $69
Y-Refine 12-67 Marker $199 $148
Y-Refine 25-37 Marker $59 $35
Y-Refine 25-67 Marker $159 $114
Y-Refine 37-67 Marker $109 $79
Y-Refine 37-111 Marker $220 $188
Y-Refine 67-111 Marker $129 $109
mtHVR1toMega         $269 $179
mtHVR2toMega         $239 $179
mtFullSequence Add-on $289 $199

To order this special offer, log in to your personal page and click on the Order An Upgrade button in the upper right corner. A link to the login page is provided below. ALL ORDERS MUST BE PLACED AND PAID FOR BY MONDAY, DECEMBER 31, 2012 11:59:00 PM CST TO RECEIVE THE SALE PRICES.

Log In to Order an Upgrade.

Click Here to Order a New Kit.

As always, we appreciate your continued support.

Family Tree DNA
"History Unearthed Daily"

Match statistics from FTDNA, 23andme and AncestryDNA

As of today I have:

467 matches at FTDNA on their Illumina V.3 chip;
1540 matches at 23andme on the Illumina V.2 chip;
1145 matches at 23andme on the Illumina V.3 chip;
2300-2350 matches at AncestryDNA on the Illumina V.3 chip:

Other than known 1st and 3rd cousins I had tested, my closest known matches are at the 3rd cousin level. I have a 2nd cousin match at 23andme who has not answered any invitations in 2 years. I have two predicted 2nd cousin matches at FTDNA who have not replied to emails and do not have pedigrees posted there. I have gotten through the first 27 of 47 match pages at with many matches having either private trees, very small trees, or no trees. Very frustrating.

I spent this past weekend in Houston at the 8th FTDNA DNA Administrators Conference. I'll post a report later this week.

Sunday, November 04, 2012

Abstract from American Society of Human Genetics meeting session

The GenoChip: a new tool for genetic anthropology.

S. Wells1, E. Greenspan2, S. Staats2, T. Krahn2, C. Tyler-Smith3, Y. Xue3, S. Tofanelli4, P. Francalacci5, F. Cucca6, L. Pagani7, L. Jin8, H. Li8, T. G. Schurr9, J. B. Gaieski9, C. Melendez9, M. G. Vilar9, A. C. Owings9, R. Gomez10, R. Fujita11, F. Santos12, D. Comas13, O. Balanovsky14, E. Balanovska14, P. Zalloua15, H. Soodyall16, R. Pitchappan17, G. Arun Kumar17, M. F. Hammer18, B. Greenspan2, E. Elhaik19

1) Mission Programs, National Geographic Society, Washington, DC; 2) Family Tree DNA, Houston, TX; 3) Wellcome Trust Sanger Institute, Hinxton, UK; 4) University of Pisa, Italy; 5) University of Sassari, Italy; 6) National Research Council, Monserrato, Italy; 7) University of Cambridge, UK; 8) Fudan University, Shanghai, China; 9) University of Pennsylvania, Philadelphia, PA; 10) CINVESTAV, Mexico City, Mexico; 11) University of San Martin de Porres, Lima, Peru; 12) Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil; 13) Pompeu Fabra University, Barcelona, Spain; 14) Russian Academy of Medical Sciences, Moscow, Russia; 15) Lebanese American University, Byblos, Lebanon; 16) University of the Witwatersrand, Johannesburg, South Africa; 17) Chettinad Academy of Research and Education, Chennai, India; 18) University of Arizona, Tucson, AZ; 19) Johns Hopkins University, Baltimore, MD.

Background: The Genographic Project is an international effort aimed at charting human history using genetic data. The project is non-profit and non-medical, and through the sale of its public participation kits it supports cultural preservation efforts in indigenous and traditional communities. To extend our knowledge of the human journey, interbreeding with ancient hominins, and modern human demographic history, we designed a genotyping chip optimized for genetic anthropology research. Methods: Our goal was to design, produce, and validate a SNP array dedicated to genetic anthropology. The GenoChip is an Illumina HD iSelect genotyping bead array with over 130,000 highly informative autosomal and X-chromosomal SNPs ascertained from over 450 worldwide populations, ~13,000 Y-chromosomal SNPs, and ~3,000 mtDNA SNPs. To determine the extent of gene flow from archaic hominins to modern humans, we included over 25,000 SNPs from candidate regions of interbreeding between extinct hominins (Neanderthal and Denisovan) and modern humans. To avoid any inadvertent medical testing we filtered out all SNPs that have known or suspected health or functional associations. We validated the chip by genotyping over 1,000 samples from 1000 Genomes, Family Tree DNA, and Genographic Project populations. Results: The concordance between the GenoChip and the 1000 Genomes data was over 99.5%. The GenoChip has a SNP density of approximately (1/100,000) bases over 92% of the human genome and is highly compatible with Illumina and Affymetrix commercial platforms. The ~10,000 novel Y SNPs included on the chip have greatly refined our understanding of the Y-chromosome phylogenetic tree. By including Y and mtDNA SNPs on an unprecedented scale, the GenoChip is able to delineate extremely detailed human migratory paths. The autosomal and X-chromosomal markers included on the GenoChip have revealed novel patterns of ancestry that shed a detailed new light on human history. Interbreeding analysis with extinct hominids confirmed some previous reports and allowed us to describe the modern geographical distribution of these markers in detail. Conclusions: The GenoChip is the first genotyping chip completely dedicated to genetic anthropology with no known medically relevant markers. We anticipate that the large-scale application of the GenoChip using the Genographic Project’s diverse sample collection will provide new insights into genetic anthropology and human history.

You may contact the first author (during and after the meeting) at