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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.

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.

Professor Alan Rogers' Lecture on Evolution at UofU

1/27/2011

 
The following are short notes from a lecture given by Dr. Alan Rogers, professor of Population Genetics and Evolutionary Ecology at University of Utah's Department of Anthropology. The lecture was given on January 27, 2011 in the Gould Auditorium (Marriott Library) on the UofU campus.

EVOLUTION

Why skepticism?
- It is because of the concept of species changing?
- Or, changing into a new species?
- Can a species undergo significant changes?

Few people still doubt it based on micro-evolution examples such as resistance to penicillin and pesticides developed by bacteria and insects respectively.
However, what about new species?
- Doubling, tripling genomes (see the example with Primrose)
It is becoming harder and harder to argue that evolution is limited to only small changes.

Dr. Rogers used the example of the eye to discuss complex adaptation.
- lens vs. retina
- retina useless without lens
- how would selection favor a partial eye?

Charles Pritchard (1866)
- He was the first one to argue that the eye could not evolve.
Charles Darwin (1872)
- He was the first one to refuse Pritchard's argument. However this argument would last.
Weakness of Pritchard's argument:
- The claim is about plausibility. To refute such claim you need to invent a plausible story.
- There is no need for evidence. 
- There is no need for the story to be true.

Hypothetical steps in the evolution of the eye:
A. Eye spot - simple eye, but very sensitive to light from all directions
B. Eye cup - light prevented from extreme angles.
C1. Pin-hole camera eye - forms image, not much light, very dim.
C2. Primitive lens - secrete mucus (easy to produce), denser than H2O, will refract light, only sensitive to direct light found straight ahead of the eye.

Next: improvement of the eye --> Need a vertebrate eye.
Are the steps plausible?
- Yes, they are all found in living organisms today.
- Eye evolution is possible. Pritchard was incorrect.

How did the eye evolve?
- Darwin's prediction: retina evolved earlier then came the lenses --> we can test this hypothesis by looking at living animals.
- We all share common characteristics because we have inherited genes from common ancestors.
We need to start at the basis, the protein level. Opsins are light sensitive proteins. Every animal that sees does so because of the presence of opsins. Similar species have similar opsins.

When cells divide, DNA duplicates. Sometimes the machinery stutter and the DNA is duplicated twice. When you have two copies of the same gene, the new copy may provide new functionality. 

We need to observe what humans have in common with their closer relatives, the apes and old world monkeys. We have one opsin that adapted to dim light and three for color vision. Most mammals only have two for color and this is why they are colorblind. The reason humans, apes and monkeys have three for color is due to the fact that our common ancestor experienced a duplication in the DNA sequences thus resulting in one extra copy for that particularly opsin. 

Evidence of common descent in opsin: closely related species have similar opsin molecules. Humans have similar opsin proteins to insects and cephalopods. 

Crystallins: transparent proteins used in lens and cornea.
- If lenses evolved early, humans and insects should have similar crystallins. But they don't because the lens came later. Insects and cephalopods have very different crystallin proteins from humans.

What about eye morphology?
Vertebrates have eyes that work like cameras. All arthropods have compound eyes (including trilobites). Snails however have a great variety of eyes (they evolved in different varieties). Heteropod sea snail has eyes like slits, with a field vision of 180 degree wide, but just few degrees high. Eye scans are done with rapid movements up and down. 

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