“In this study, a comprehensive overview of all available complete mitochondrial DNA (mtDNA) genomes of the four pan-American haplogroups A2, B2, C1, and D1 is provided by revising the information scattered throughout GenBank and the literature, and adding 14 novel mtDNA sequences. The phylogenies of haplogroups A2, B2, C1, and D1 reveal a large number of sub-haplogroups but suggest that the ancestral Beringian population(s) contributed only six (successful) founder haplotypes to these haplogroups.”
On the heels of my recent post discussing all the interesting information that’s recently entered the blogosphere about genetic genealogy and DNA studies, here are a few more:
Misha Angrist, one of the Personal Genome Project’s “First 10“, wrote an article about the inevitability of DNA sequencing at News Observer. The article is a response to a recent editorial in the NEJM.
John Hawk’s Anthropology Weblog, “Viking Ancestry, Surnames and Medieval Genetics” examines a recent study in Molecular Biology and Evolution “investigating whether the Viking influence on surnames in England is mirrored by Y chromosomes.” It’s a great post, especially for genetic genealogists.
There is so much to talk about, and so little time to write. So I thought I’d do a round-up post to bring these interesting stories to your attention. I hope you enjoy the following:
Of great significance to genetic genealogists, the Wall Street Journal says that as many as 1 in 25 children are the result of non-paternal events! The number seems very high, but it is based on a 2005 report in the Journal of Epidemiology and Community Health studying families in “the U.S., Europe, Russia, Canada, South Africa and several other countries.”
SNP studies are coming out left and right. The recent studies have examined variation among genomes from numerous populations using SNP chips that examine 600,000 or more SNPs. See more at GenomeWeb News, The Spittoon, and Genetic Future. A great quote comes from a discussion of one of these SNP studies at the terrific Dienekes’ Anthropology Blog:
Jesse Woodson James, born September 5, 1847 and died April 3, 1882, was an infamous American outlaw. Despite strong evidence that James was killed on April 3, 1882, some theorized that his death was staged and that he in fact survived to father additional children.
In 1995, researchers set out to use relatively new DNA analysis to examine the rumors surrounding James’ death. They exhumed the body believed to be that of James from the Mt. Olivet Cemetery in Kearney, Nebraska. Although the remains were poorly preserved, the scientists were able to obtain DNA from two of four teeth. They also had DNA from two hairs that were recovered in 1978 from James’ original burial site on the James farm.
The mtDNA HVR1 sequence from the teeth and hairs were identical and belonged to Haplogroup T2, with 5 mutations relative to the CRS (16126C, 16274A, 16294T, 16296T, and 16304C).
What are the chances that Megan Smolenyak would meet and marry a man with the surname Smolenyak without being at least distantly related to him? What if the two surname lines came from the same area of the world? I’m sure that everyone who has heard of Megan has wondered how she came by the double last name.
Megan writes “Did I Marry My Cousin” at Megan’s Roots World to introduce a new segment at Roots Television about how she used genetic genealogy to analyze the question. The segment is available here. I highly recommend stopping by to learn more about this particular use of genetic genealogy, especially since I’m not going to give you the answer!
As I was reading through the GENEALOGY-DNA list from Rootsweb this morning, I came across a great question about the frequency of mutation of mitochondrial DNA (mtDNA).
The listmember asks “I am wondering if anyone would know the odds of having a mutation between my brother and me in our mtDNA. Marker 16163 is G for one of us and A for the other…” This is a great question, and one that I’ve been asked as well.
In response, Ann Turner writes “The mutation rate hasn’t been studied in the detail I’d like to see. The largest study for the hypervariable regions was based on deep-rooting pedigrees from Iceland. They found 3 mutations out of 705 transmission events.”
The study, available here (pdf, HT: Ann Turner) was conducted through deCODE Genetics and Oxford University. They used 26 Icelandic ancestral trees to identify maternally-related individuals, and sequenced 272 mtDNA control regions representing a total of 705 transmission events. The researchers found a total of three mutations, resulting in a mutation rate of 0.0043 per generation, or 0.32/site/1 million years. A previous study (Parsons et al., 15 Nature Genetics 363 1997) found a total of 10 mutations in 327 transmission events for a frequency of 2.5/site/1 million years, and yet another study found 2 mutations in 81 transmissions for a rate of 0.75/site/1 million years (Howell et al., 59 Am J Hum Genet 501). The huge differences in these numbers suggests that much more research needs to be done, probably with a much larger dataset. If I had unlimited funds, I would also be interested to see if there are different mutation rates among haplogroups, as well as a number of other factors.
A report published in the New England Journal of Medicine entitled “Letting the Genome Out of the Bottle – Will We Get Our Wish?” is getting a lot of coverage elsewhere, but I thought I’d add my two cents. The report’s authors are largely concerned with quality control, clinical validity (the actual predictive value of genetic tests), and utility (the balance of family history and genetic testing) of genome scans offered by companies such as 23andMe, deCODEme, and Navigenics. They also suggest that people wait for the science to catch up before purchasing genome scans. There is an NEJM audio interview with Muin Khoury, one of the authors of the study about the subject. Note that this particular report is about medical implications of genetic testing, not about genetic genealogy (two very different topics that were very confusingly jumbled in the recent article “A High-Tech Family Tree” from U.S. News & World Report).
Scientists from the University of Utah have traced a mutation in the adenomatous polyposis coli (APC) gene to a Mr. and Mrs. George Fry, who arrived in the New World aboard the William & Mary around 1630.
The mutation, c.426_427delAT, is believed to increase the carrier’s chances of developing colon cancer from 2 in 3 by age 80, a significant increase from the normal of 1 in 24. The study is available here for FREE – thank you open access – and is entitled “American Founder Mutation for Attenuated Familial Adenomatous Polyposis.”
Scientists traced two branches (from two of the Fry’s four children) of the family back to the Fry family, one in Upstate New York and one in Utah. The family in Utah, with more than 5,000 people, has been the focus of scientific study for over 14 years because of their unfortunately high risk of colon cancer. In fact, members of the Utah branch constitute 0.15% of all colon cancer in the state of Utah!
As of the end of November, the Personal Genome Project has a newly-designed and user-friendly website. Compare the OLD site and the NEW site – what an improvement! Misha Angrist, aka genomeboy.com and one of the “First 10″ aptly called the site “PGP 2.0″.
The new site is extremely well organized and contains information about the project and about participating in the project, if one is so inclined. Since this project will contain so much personal information about each individual that joins, participants will go through an extensive consent process that will include education, physician assistance, and even an online assessment to gauge the participant’s grasp of genetics and the risks of participation, among other things. I know that the team is working feverishly behind the scenes to gather as much information as possible to create an extensive consent protocol.
PLoS Genetics has a new paper (PLoS Genet 3(11): e185. doi:10.1371/journal.pgen.0030185) that examines autosomal microsatellite markers (repeating units of base pairs) from Native American DNA:
“We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberiansâ€”signals of the southward dispersal of human populations from the northwestern tip of the Americas”