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Ancient DNA Links Native Americans With Europe

10/27/2013

 
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Last year I received an invite to attend the Paleoamerican Odyssey conference that was held last week in Santa Fe, New Mexico. I declined knowing that it would have been difficult to find the necessary funding for yet another trip across the ocean this year. However, my good friend and colleague Dr. Alessandro Achilli from the University of Perugia (Italy) was able to go and wrote me immediately after attending the presentation where these results were shared. Now I really wished I would have gone!

The study that will come out in the prestigious journal NATURE shortly (as of today it is in press), describes the genetic analysis of a 24,000 year old skeleton found in Siberia. The complete genome was sequenced, including the paternally inherited Y chromosome and the maternally inherited mitochondrial DNA. The results were not quite what was to be expected. The young boy DNA showed no relationship to Easter Asians, but 1/3 of the genome in common with Native American populations and the rest with Europeans. Even the Y chromosome and mitochondrial DNA look European as they belong to haplogroups R and U respectively. The report from SCIENCE included the following comment from the leading researcher:
"The finding suggests that about a third of the ancestry of today's Native Americans can be traced to western Eurasia, with the 
other two-thirds coming from eastern Asia, according to a talk at [the meeting "Paleoamerican Odyssey" in Santa Fe, NM on 16–20 October 2013] by ancient DNA expert Eske Willerslev of the University of Copenhagen. It also implies that traces of European ancestry previously detected in modern Native Americans do not come solely from mixing with European colonists, as most scientists had assumed, but have much deeper roots."

It is obvious that these data and findings will have major implications with regard to our understanding of Native American origins and colonization events. Moreover, it opens a lot more questions on a topic that for so many was already closed. For sure, there is so much more to learn about how and when the ancestors of Native Americans arrived to the Western Hemisphere. Although the DNA in this particular study refers to a very ancient specimen, the presence of European DNA in the Americas that predates the arrival of Europeans within the last 500 years poses some serious new consideration with regard to be able to discern any sort of Old World DNA in the Americas from the time of the first arrivals all the way through the millennia to our days. Can European DNA found in modern and ancient Native Americans be immediately dismissed as being for sure post-Columbian? Can we discern European DNA introgression in the America's gene pool from 20,000 years ago, 10,000 years ago, 3,000 years ago, or 1,000 years ago? 

Native American genetics got all of a sudden a lot more exciting! It will be interesting to see what the future will bring.

Genographic Project's New GENO 2.0 DNA test

8/20/2012

 
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Recently, the National Geographic's Genographic Project launched a new DNA test kit called GENO 2.0. It is an autosomal DNA test that covers very specific nuclear SNPs providing information about the history of our genes including a survey of our paternal line (Y chromosome), maternal line (mitochondrial DNA), and the deep ancestry written in the autosomes. It will link our DNA to the history of humankind as it started in Africa tens of thousands of years ago, all the way to the present time. I just ordered my own test, even though they won't be shipped until the end of October. This test will also compare genes between humans and apes, and even Neandertals, looking for surviving rare genetic links between our species and our closest relatives in the evolutionary tree.

National Geographic has a strong pro-evolution agenda, which continues to stimulates all sort of interesting thoughts in religious arenas about harmonizing the biblical creation account with evidence (particular genetic evidence) from science pointing to evolution (something that I have also speculated about in the past). Interestingly, just today, someone in a forum that does not like LDS beliefs mentioned me in a dissatisfied manner stating that "an LDS scientist speculates if those in the past were even human." Believe it or not, I don't think I am the first one that postulated that there were hominids more than 6,000 years ago, but I am flattered if someone would think so.

Here is a video by the Genographic Project introducing the new test.


I got published! (but not as you would think)

2/8/2012

 
What is almost as good as publishing a paper in a peer-reviewed journal? What about getting your own DNA sequence published! This happened to me last year in the American Journal of Human Genetics (IF = 11.680) by the group at the Universita' La Sapienza in Rome, Italy. The article "A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa" by Cruciani F., et al. brings the coalescence time of the common male ancestor of anatomically modern humans back to an additional ~70k years from the previously accepted ~60k estimate. One of the "ancient" male-inherited Y chromosome haplotypes employed in this study was indeed mine! (See image below). 

I previously included something about the "weirdness" of my Y chromosome in the treatise I published on the issue of DNA and Book of Mormon (FARMS Review, 1, 2010, pp.191-227). At that time, this is what I wrote about it:
"I was born and raised in Italy and can trace my paternal ancestry back several generations to the mid-seventeenth century AD. However, my Ycs belongs to haplogroup C, which has a frequency in southern Europe of less than 1 percent. Haplogroup C is mostly found in east Asia with a branch (C4) found among the aborigines of Australia. How did haplogroup C become part of my paternal ancestry? One possibility is that it is a remnant from an ancient military expansion from the East (e.g., Mongols or Huns) that reached to northern Italy."

Having worked in the molecular anthropology and genetic genealogy arenas for the past decade, it was natural that I wanted to run some analyses on my own DNA and learn about my genetic origins. However, the journey turned out to be a lot more fascinating and complex than expected. Earlier results from specialized labs placed my haplotype all over the Y chromosome phylogenetic tree. I was first assigned to haplogroups F, J, R, and I, with different level of confidence. Ultimately, I had my DNA tested at Stanford University (Dr. Peter Underhill's lab), with the Genographic Project, at the University of Pavia, Italy (Prof. Ornella Semino's lab), and at the University La Sapienza in Rome, Italy (Prof. Rosaria Scozzari's lab). Each lab performed extensive SNP testing on my Y chromosome and the consensus was that I belonged to a yet to be classified lineages within the C branch of the Y chromosome phylogeny. My Y chromosome was temporarily placed in the paragroup C*. The publication in the AJHG last year is an additional step forward in understanding something about the intricate history and origin of my paternal lineage, which is not only very rare in the general worldwide population, but it is also very ancient in origin. The journey continues...
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Figure 1 from "A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa" by Cruciani F., et al. AJHG, June 2011, pp.814-818. The single Y chromosome lineage belonging to haplogroup C is my own.

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