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An Updated Y-DNA Tree at ISOGG

The International Society of Genetic Genealogy (ISOGG) announced today that their Tree Team has completed the 2008 version of the Y-DNA Haplogroup Tree. This revision was a major undertaking, because, as ISOGG states in the version history, “[t]he Karafet et al paper (2008) required a significant revision to the tree and affected all haplogroups.” The reference for this paper is (Karafet T M, Mendez F L, Meilerman M B, Underhill P A, Zegura S L, Hammer M F, (2008).
New Binary Polymorphisms Reshape and Increase Resolution of the Human Y-Chromosomal Haplogroup Tree. Abstract. Genome Research, published online April 2, 2008. Supplementary Material.). From ISOGG’s official release:

MAY 04, 2008 – The 2008 version of the ISOGG Y-DNA Haplogroup Tree is now available online: http://www.isogg.org/tree/. New to the tree is a haplogroup conversion table which is downloadable in MS Word. If you do not have MS Word/MS Office, you can download openoffice.org for a compatible word processing program. Appreciation goes to Richard Kenyon and Charles Moore for their work on compiling this table. ... Click to read more!

Here is the abstract of today’s Y-chromosome haplogroup tree paper in Genome Research, I’m still working to get a copy of the actual paper (unfortunately, it’s not open access at this time):

Markers on the non-recombining portion of the human Y chromosomecontinue to have applications in many fields including evolutionarybiology, forensics, medical genetics, and genealogical reconstruction.In 2002, the Y Chromosome Consortium published a single parsimonytree showing the relationships among 153 haplogroups based on243 binary markers and devised a standardized nomenclature systemto name lineages nested within this tree. Here we present anextensively revised Y chromosome tree containing 311 distincthaplogroups, including two new major haplogroups (S and T),and incorporating approximately 600 binary markers. We describemajor changes in the topology of the parsimony tree and providenames for new and rearranged lineages within the tree followingthe rules presented by the Y Chromosome Consortium in 2002.Several changes in the tree topology have important implicationsfor studies of human ancestry. We also present demography-independentage estimates for 11 of the major clades in the new Y chromosometree. ... Click to read more!

[This is a repost of an article that appeared on May 29, 2007. Since I’m knee-deep in final projects and exams, I thought I’d pull out a popular article from the archives. I hope you enjoy it (again)]:

In Part I, Part II, and Part III of the “You and the $1000 Genome” series we’ve examined the Archon X PRIZE for Genomics, the International HapMap Project, and the ethical issues associated with both. In this final installment of the series we will examine the potential impact of genomic or SNP sequencing and interpretation on both medicine and genealogy (finally, some genealogy for you patient genealogists out there!).

I believe that whole genome sequencing will have myriad uses. In the paper mentioned in Part III of the series (John A. Robertson, “The $1000 Genome: Ethical and Legal Issues in Whole Genome Sequencing of Individuals (pdf).” 2003 The American Journal of Bioethics 3(3):InFocus), Mr. Robertson suggests that demand for personal genome sequencing outside of the medical context could be quite limited. But that view might fail to take into account uses of genomic information other than identifying or predicting disease, such as the genetic genealogy setting. Very few could have predicted 10 years ago that thousands of genealogists would be submitting their DNA for limited sequencing as they are doing today. If information from whole genome sequencing can be used to analyze genealogy (which it surely will be), then this will create an entire niche that will increase commercial demand outside of the medical context. And this is only one such niche. There might be many many more, some of which will only develop after whole genome sequencing becomes economically available. ... Click to read more!

[This is a repost of an article that appeared on May 22, 2007. Since I’m knee-deep in final projects and exams, I thought I’d pull out a popular article from the archives. I hope you enjoy it (again)]:

Over the next week and a half I will be examining the Archon X PRIZE for Genomics, a challenge from the Archon X PRIZE Foundation to foster the development of efficient and inexpensive genomic sequencing. Not only will the X PRIZE for Genomics change the face of medicine, but it will also have an ENORMOUS impact on the field of genetic genealogy, which we’ll discuss in Part IV of the series. Stay tuned for all the information you need to know about the prize, and if you have any thoughts or questions please leave a comment! ... Click to read more!

I’m sorry if I’ve overloaded you on the recent launches of 23andMe and deCODEme, but I think there’s so much to talk about. For a little lightheartedness, read “23andMe Party” from How to Change the World by Guy Kawasaki. Kawasaki describes a friends and family “Spit Party” hosted by 23andMe, and even has a number of pictures from the event.

The party offered attendees the chance to submit their DNA for analysis at a discounted rate. Some of the attendees included co-founders Linda Avey and Anne Wojcicki, at least one Nobel Prize winner, and celebrities Goldie Hawn and Kurt Russell.

Would you like your genome sequenced in a matter of hours for under $100?

An article from GenomeWeb last week, “Complete Genomics, BioNanomatrix to Use $8.8M NIST Grant to Develop ‘$100 Genome’ Platform,” reveals that BioNanomatrix and Complete Genomics have partnered together to share an $8.8 million grant from the U.S. National Institute of Standards and Technology to “develop technology that will be able to sequence a human genome in eight hours for less than $100.”

From the article (don’t worry, I have no idea how these technologies really work either):

“The proposed sequencing platform will use Complete Genomics’ sequencing chemistry and BioNanomatrix’ nanofluidic technology. The companies said they plan to adapt DNA sequencing chemistry with “linearized nanoscale DNA imaging”to create a system that can read DNA sequences longer than 100,000 bases quickly and with accuracy “exceeding the current industry standard.”” ... Click to read more!

Ancestry.com has established a new blog, located at blogs.ancestry.com.  Let me just say that they have excellent taste in WordPress themes (it’s the same as mine)!

If you’re interested, here’s a link to a document from the Edge Foundation, a group designed to promote the discussion of intellectual pursuits. The document is a summary (including video links) of a casual meeting between some fantastic scientific minds (Craig Venter, Freeman Dyson, Robert Shapiro, Dimitar Sasselov, and Seth Lloyd) which took place in late August.

Although Dr. Church doesn’t discuss the Personal Genome Project, his brief discussion about our past and our future is very interesting.  There’s also a summary of the meeting from Gregory T. Huang, an invited journalist.  I see that one of the invited guests was Ting Wu, a researcher at Harvard who has initiated the pgEd (personal genetics education project). ... Click to read more!

Yesterday was another big day for genetic genealogy, with two major announcements.First, as I have previously mentioned, Ancestry.com teamed up with Sorenson Genomics to offer DNA testing.The results of that testing can be, at the owner’s discretion, tied into a new DNA database as well as their massive collection of genealogical source materials.Here’s the official announcement from PRNewswire: “Ancestry.com Enters DNA Genealogy Field Through Exclusive Partnership With Sorenson Genomics: Combines Three Major Pillars of Family History Research – Historical Records, DNA and Family Trees.”Here’s another blurb at Family Tree Magazine.According to one source (CNET News), the $200 test will examine both Y DNA and mtDNA, but that hasn’t been confirmed.It only makes sense to test both, however, especially at that price. ... Click to read more!

Ancestry.com, one of the largest online sources of family trees and genealogy source material, is teaming up with Sorenson Genomics to offer DNA testing.

Ancestry.com has more than 14 million users, meaning that genetic genealogy will be introduced to a huge new group of individuals. Additionally, Ancestry can use the results of this testing to enhance the other databases they already offer – something that the other big testing companies lack.

As of now, the rumored price is to be $200, with no mention of the type of testing to be offered. There’s a lot more information available at Eastman’s Online Genealogy Newsletter, The Jerusalem Post, The Times Daily.com, The Salt Lake Tribune, and The Deseret News.com. Look for the announcement to be made sometime today. ... Click to read more!