quote:Originally posted by the lioness,: So now that we have the DNA your theories must take that into account first and foremost.
Looking at ancient DNA to determine ancient population origins can be misleading. Let’s look at dna of Ust-ishim and Clovis-Anzick man as it compares to modern populations.
Although it is clear that Ust-ishim was T2b3, the popular press claims he belonged to the haplogroup U clade. Look at the cousins of Ust-ishim it is these modern people who belong to the U clade that are his cousins. See: http://www.fi.id.au/2014/11/ust-ishim-ancient-dna-has-matches-with.html
Look at the Clovis-Anzick DNA matches to modern people.
What does this mean? It means that researchers may be reporting results that have been contaminated and that they may only be giving us results that match their expectations of how the data should look.
IN relation to Anzick man Felix Immanuel noted that:
quote:
Just a quick recap, I processed the raw data for Clovis-Anzick-1 and uploaded into GEDMatch and to my surprise, there are matches as near as 3rd to 4th cousins. Now, that's a real problem because, the matches are to a DNA sample older than 12500 years. This is practically impossible and very mysterious.[/img] I will investigate step-by-step and see what are all the possibilities and failure points, which could solve the problem. But before that, we need to be absolutely sure that these matches are indeed valid. From the matches, I requested for phased kit and I indeed got one - Thanks to Mario Diaz and Veronica.
Clearly, an IBD segment of 5 cM above 500 SNPs with total IBD segments around 10+ cM cannot be 12500 years old. This is a fact and can be verified using known relationships in families and DNA companies are using these benchmarks all along for showing genetic matches. This fact is more than enough to conclude that the Clovis-Anzick-1 sample is not actually ancient. My best guess is, the infant boy's sample is just from the last century and it was wrongly labeled as 12500 years old or the sample got contaminated.
posted
^^^Above was written by a software designer "Felix" with no education in genetics who has a blog "This is purely my opinion on what I can see but I could very well be wrong." speaking about various details Clyde doesn't understand and is using this to dismiss any DNA analysis that he doesn't like
Analyzing the Native American Clovis Anzick Ancient Results Posted on September 23, 2014 Roberta Jestes dna-explained.com
This ancient DNA truly is the gift that keeps on giving.
Today, Felix Chandrakamur e-mailed me and told me that the Anzick results were not yet fully processed at Gedmatch when I performed a “compare to all.” He knows this because he knows when he uploaded the results, and after they were finished, he ran the same compare and obtained vastly different results. I am updating my original article to point to this one, so the data will be accurately reflected.
In fact, the results are utterly fascinating, take your breath away kind of fascinating. Felix wrote an article about his findings, Clovis-Anzick-1 ancient DNA have matches with living people!
While finding what appear to be contemporary matches for the Anzick child may sound ho-hum, it’s not, and when you look at the results and the message they hold for us, it’s absolutely astounding.
Felix ran his comparison with default values of 7cM. This is the threshold that is typically utilized as the line in the sand between “real” and IBS, matches – real meaning the results are and could be, if you could find your common ancestor, genealogically relevant. In this case, that clearly isn’t true.
The exception to this rule is heavily admixed groups, such as Ashkenazi Jewish people who are related to every other Askhenazi Jewish person autosomally. It seems, looking at these results, that this is the same situation we find with the 12,500 year old Anzick child and currently living people. This population had to be painfully small for a very long time and the DNA had to exist in every person within that population group for it to be passed in segments this large to people living today.
After receiving Felix’s e-mail, of course, I had to go back and run the compares again. In particular, I wanted to run the one to many, as he had.
I began at the 1cM level and noticed that I received exactly 1500 results, which seemed to me like a cutoff – not an actual number of matches. So, I upped that threshold to 2, then 3, then 4, then 5, then 6, then finally to the default of 7. It was only at 7, the IBS/IBD default, that the results were under the 1500 threshold, at 1466.
1466 current matches?????
This is absolutely amazing. The Anzick child lived about 12,500 years ago in Montana. How are 1466 matches to currently living people possible?
Many of these matches are to people from the southwest and Mexico today. They are not, for the most part, from eastern Canada.
Let’s take a look at what we found.
In the 1466 results, as Felix mentioned, the closest matches match at current “cousin” levels to Anzick. The highest 7 matches that show haplogroups are haplogroup Q1a3a. Unfortunately, with the constant renaming of the haplogroups recently, it’s difficult to interpret the haplogroup exactly, which is why we’ve gone to SNP names. Looking at some of the names and e-mails, several appear to carry Spanish surnames or be from Mexico or South America.
Of the 1466 results:
2 were Y haplogroup C 79 were Y haplogroup Q 520 carried a mitochondrial DNA haplogroup of A, B, C, D, M or X Of the 79 haplogroup Q carriers, 52 also carried a Native mitochondrial haplogroup. A total 549 individuals out of 1466 carried at least one Native American haplogroup, or about 37.5%. That’s amazingly high. Of these closest matches who are Y haplogroup Q, they also all carry variant Native American mitochondrial DNA haplogroups as well, so these people may not be heavily admixed. In other words, they may be almost “pure” Native American.
In order to test this theory, I entered the number of the kit that rated the highest in terms of total cM at 160.1 with the largest segment at 14.8. You can click on the images to enlarge.
As you can see, this individual is very nearly 100% Native American.
The second individual on the list, who may be from Guatemala, also carries almost no admixture.
Of the highest 21 matches that listed any haplogroup information, all have either or both Native Y or mitochondrial DNA haplogroups.
Out of curiosity, I ran the first person on the list who had neither a Native American Y or mitochondrial haplogroup – both being European.
As you can see, below, they are still clearly heavily Native American, but clearly admixed.
I moved to the last person of the 1466 on this list whose DNA matched at a total of 7cM, who did not carry a Native haplogroup. This individual, below, is more heavily admixed.
Lastly, I ran the same admixture tool on the last person, who had a total of 7cM matching that did have a Native American mitochondrial haplogroup.
Not surprisingly, the individual with almost no non-Native admixture is much more likely to carry the ancient segments in higher percentages than the individuals who are admixed. This again strongly suggests that at one point, these segments were present in an entire group of Native people and may still be present in very high numbers in people who carry no admixture.
Out of curiosity, and assuming that these first two individuals are not known to be related to each other, I ran them against each other in a one to one comparison.
There were no matches at the default values, but by dropping them just a little, to 5cM and 500 SNPs, they match on 6 segments.
It looks like they should match on chromosome 17 at the 700 SNP/7 cM default threshold.
At 200 SNPs and 2cM, there were 67 segments. These are clearly ancient in nature and size, but matching just the same. By lowering the threshold to 100 SNPs and 1cM, they share a whopping 990 segments.
Indeed, these two men very clearly share a lot of population specific DNA from the ancient people of the New World, including that of Anzick male child who lived in Montana 12,500 years ago.
_________________________________
Comments:
hungrybuffalo on September 23, 2014 at 2:30 pm said: Hi Roberta.... So what do you think is going on here, have I hidden native-American ancestry, or do European populations (sometimes) carry a common DNA from a shared ancestor of the Anzick child ?
robertajestes on September 23, 2014 at 3:47 said: Probably common Asian populations, but we’re still sorting through this.
UBBFriend: Email this page to someone!
Printer-friendly view of this topic