Experiences with Family Finder and PF

[c_thompson_68]

For those of you who are expecting to find Native American Indian (NA) ancestry from Population Finder (PF), which FTDNA chipset are your results from? Is it the Affymetrix chipset or the Illumina chipset?

From the Affy Chipset, I am estimated to be 19.20% Native American (Central American) as my birth-father is from Mexico (I am an adoptee).

[bkilpatrick]

"Where do you find out about sending the raw files to Dr McDonald?

Yes, and what is the process of sending raw data to Dr. McDonald and are we talking about FF raw data, Mtdna or Ytdna results? If they are included, do they have to be tested at the FGS level?

My PF results are not accurate by any means, and am wondering if the FF raw data can be better analyzed. I hope so.

I learned about Dr. McDonald on this forum, which is where I found his e-mail, I think. (Or perhaps it was another blog.) In any case, I sent him an e-mail to ask about participating and he kindly agreed. I contacted him at

mcdonald (at) scs.uiuc.edu

I don't know about mtdna or ytdna; I just sent FF raw data. You'd have to ask him, I guess.

Good luck!

[Yaffa]

For those of you who are expecting to find Native American Indian (NA) ancestry from Population Finder (PF), which FTDNA chipset are your results from? Is it the Affymetrix chipset or the Illumina chipset?

From the Affy Chipset, I am estimated to be 19.20% Native American (Central American) as my birth-father is from Mexico (I am an adoptee).

You are showing NA because your family is from Mexico. Most Mexicans are Indian. It does not matter Affy or Illumnia. FTDNA only has some NA samples for Central and South America not North America. Many people who claim North American Indian do not match Asian or Central/South American Indian on PF. Not all tribes will have same DNA and FTDNA does not have most tribal DNA to compare others to. The US tribes are not giving up their DNA and I cant say I blame them. Without their samples and other populations FTDNA is missing no way to attempt to get accurate admixture on a person. I dont see it being accurate any time soon if they can not use or do not have all populations to use in their calculations on PF. Also everyone inherits different DNA from their ancestors so you could turn up Indian while you may have siblings that dont or visa versa.

[Yaffa]

I'm having the same problem - am Native, but not even a perceptible amount is coming up. Something is amiss, and other threads have addressed this...although FTDNA has not.

Just curious how close or far back are your Indian ancestors? Does your tribe have a blood % with enrollment?

[DelawareNative]

I don't want to get into a discussion over blood quantums for Indian tribes, and I do understand that many tribes don't want to 'give up' their DNA samples. Really, I totally get it. However...these are the days where DNA cannot be locked up anymore.

There are plenty of Cherokees, for example (and I list them because they are great in number), that are sending in their DNA swabs to get tested for all kinds of things, and so in theory, lots of Cherokee-specific DNA is out there, it's just a matter of figuring what it is - not that there is a specific anything that makes one a Cherokee strictly based on DNA - see, we could get into a heavy discussion, but I'm just saying that people other than Cherokee, like me, have submitted samples for other NA tribe(s)...only FTDNA doesn't know what it is yet, and can't ascribe them to any NA population, much less specific tribes. I think DNA Tribes has more NA population samples to compare, and their testing compared to FTDNA would be an apples to oranges thing because FTDNA just doesn't physically have all the NA samples that DNA Tribes has, if I understand it correctly. Doesn't make FTDNA inferior, just difficult to nail down NA DNA.

Hey FTDNA - can you work out a partnership with DNATribes to test the NA DNA for you??

[Yaffa]

I don't want to get into a discussion over blood quantums for Indian tribes, and I do understand that many tribes don't want to 'give up' their DNA samples. Really, I totally get it. However...these are the days where DNA cannot be locked up anymore.

There are plenty of Cherokees, for example (and I list them because they are great in number), that are sending in their DNA swabs to get tested for all kinds of things, and so in theory, lots of Cherokee-specific DNA is out there, it's just a matter of figuring what it is - not that there is a specific anything that makes one a Cherokee strictly based on DNA - see, we could get into a heavy discussion, but I'm just saying that people other than Cherokee, like me, have submitted samples for other NA tribe(s)...only FTDNA doesn't know what it is yet, and can't ascribe them to any NA population, much less specific tribes. I think DNA Tribes has more NA population samples to compare, and their testing compared to FTDNA would be an apples to oranges thing because FTDNA just doesn't physically have all the NA samples that DNA Tribes has, if I understand it correctly. Doesn't make FTDNA inferior, just difficult to nail down NA DNA.

Hey FTDNA - can you work out a partnership with DNATribes to test the NA DNA for you??

I was just asking how far back or how close to you your Indian ancestors were only because it may or may not show up on a test the further back you go.

There are 3 different Cherokee nations and all have different criteria for enrollment. Many of them are mixed so its hard getting a % on their DNA just like some of us who are mixed. The Eastern Band have a blood quantum for enrollment where Oklahoma does not. As long as your direct line ancestor is on the Dawes roll and accepted you can be a Cherokee tribal member in Oklahoma. Today you could be genetically 100% European but still be Enrolled Cherokee because you had one 3rd great grandparent on the Dawes as an accepted tribal member. Having one 3rd great grandparent who was Indian, good chance it might not show up on a % test.

Someone posted in a previous thread they need full blooded Indians to DNA test and do a study to get the DNA accurate and there aren't too many of those left.

[DelawareNative]

3 of my 4 grandparents were NA - the 4th I can't confirm all his history, so unknown. None were enrolled in any tribe because they could be considered "white by law", so they hid under the radar and passed as whites most of the time. Skin color doesn't hide dem red bones, though!

For example, one Maternal GGF was listed on his WW2 Draft Registration as a "Negro" with a "Dark brown" complexion, as were 2 of his brothers, and he was NA with dark skin (and could have SSA, don't know, but it didn't pick up on PF, either). My other Maternal GGF was only ever listed as "white" in the US Censuses, but genealogists have confirmed him to be NA from both sides of his family (and I saw him numerous times and can confirm he was NA). These are just two examples, but it's a tangled family tree and I'm trying to sort it all out. Family Finder should help with this. I'm hoping to find my tribes by comparing my DNA against "known" genealogy, but am prepared that there are plenty of "known unknowns", LOL.

My Paternal Grandmother > my father > me > my son = are all NA:

[Yaffa]

I have not personally traced your family to say what is accurate. If I remember you stated getting a Middle East % which could be Indian since FTDNA does not have American Indian DNA to compare to. I know people who were Portuguese who claimed Indian. I have seen free African Americans claim Portuguese and or Indian. It was slightly safer than claiming African. Portugal was one of the biggest salve ports and Im sure many of them spoke Portuguese. Some of these people too get Middle Eastern % on PF and other tests.

Right now FTDNA's biggest % of Indians tested are coming from Mexico where most of those people are at least 1/2 Indian or close to.

FTDNA would need DNA from Full Blooded Indians from the US to see what their samples look like and if they are different from people coming from Central and South America. With admixture it is much harder to pin what is what on these tests without having solid samples. to compare to

[c_thompson_68]

You are showing NA because your family is from Mexico. Most Mexicans are Indian. It does not matter Affy or Illumnia. FTDNA only has some NA samples for Central and South America not North America.

Actually, only my birth-father is Mexican as my birth-mother is a U.S. citizen of European descent. It was not until a few years ago that I was able to verify my birth-father is Mexican because my birth records are sealed by the state in which I was born. After I got my non-ID information from the children’s home that placed me for adoption, I was able to locate my half-brother a year ago (same birth-mother), and like me he is half-Mexican as well because of his father.

Concerning the Native American DNA, there are similarities between NA and Asians. Both typically have the Epicanthic eye fold, and share other similar physical traits with Eastern Asians. If FTDNA does not have the DNA samples of U.S. and Canadian NA tribes, then their DNA should still (in theory) be more similar to the NA tribes (Central America, South America, Inuit) and to Asians (crossing the bearing sea) than to Europeans. The possible exception that I have heard about is mtDNA haplogroup X, which is found primarily among the Druze (Middle East) and Algonquian peoples of North American. I believe it is considered to be pre-Columbian in origin. Also, I have heard that if a scenario exists where the last 100% Native American Indian existed in a person’s genetic line more than 6 generations ago, it is difficult to detect using Population Finder because of the percentage being too low to detect. Maybe PF will develop higher resolution tests in the future that are capable of detecting a low percentage of NA more than 6 generations ago.

Anyway, my autosomal DNA test estimates from AncestryByDNA 2.5 (2005) were as follows:

• European: 66%
• Native American: 29%
• Sub-Saharan African: 5%
• East-Asian: 0%

After retesting with the FTDNA Affymetrix chipset (2011), the estimates changed to:

• Europe (Western European): 62.65%
• Native American (Central American): 19.20%
• Middle East: 18.15%

The middle east classification is not a surprise as my Y-DNA is J2-M319 (J2a4d) which is found primarily among Crete (Minoan), Moroccan Jews, and Iraqi Jews (http://m172.blogspot.com/2008/10/dif...-subclade.html). It has also been found rarely among other Hispanics / Latinos, and so this causes me to wonder if my birth-father could have been a Sephardic Jew, or of some other middle-eastern ancestry along with the Native American and Spanish ancestry.

So I asked FTDNA about the difference in the test results and I received this explanation:
“AncestrybyDNA uses about 170 SNP's to define your deeper ancestry. We are using something on the order of 95,000 SNP's (Affy) for that purpose.”

So the middle east classification (FTDNA Affy) appears to have replaced some of the NA and all of the Sub-Saharan African percentage. The European percentage is almost unchanged. When I receive the Illumina upgrade Population Finder (PF) results later this week, it would be interesting to see if the percentages or classifications show any changes.

[Yaffa]

Because your father's line is from Mexico, you seem to be matching the Indian samples FTDNA has. Many in the Mexico project also get Middle Eastern. Some of it could be unk Indian markers and some Spaniard. no one is really sure. None of them seem to be getting Asian %. Even people who claim AI in the US don't seem to be getting Asian but are given Middle Eastern % on PF.

Without having Tribal DNA from the US who knows how they would turn out on a PF test.

On my Illumina -My Indian % went slightly higher on PF. My Middle Eastern from affy has now disappeared and replaced with a Very High Orcadian French %. I know this is not accurate but they dont have enough solid samples of many populations to possibly make it accurate at the moment and why this test is Beta.

You being adopted your best luck of finding your father is your Y DNA and getting a close relative match on the Family Finder part of the test.

[DelawareNative]

Great insight - my ME could be anything at this point. We may have to wait a bit more as tweaks occur, but we have FF results until then.

*sigh*

[Darkwriter]

Thank you...

Thank you, Daniel72, for explaining why the PF results are so rough.

Thank you, bkilpatrick, for Dr. McDonald's contact info for requesting participation in the BGA Project:

In any case, I sent him an e-mail to ask about participating and he kindly agreed.

I politely asked the same of Dr. McDonald and he has obliged me as well. I am looking forward to his analysis!

Thank you all!

[smallaxe]

DelawareNative
I don't need to tell you Delaware tribal history, but others may not be aware that the Delawares have been in contact with whites for a long time. In fact, it's a testament to the Delaware people that they have been able to retain a distinct identity after so many years of turmoil and displacement. If you read the first hand accounts of early Rocky Mountain trappers, you quickly pick up on the close association they had with the Delaware, who often made up part of the trapping parties, and were held in extremely high regard by the white trappers.

But this this long interaction, and sometimes close association with whites provides ample opportunity for long term admixture occurring. And the mechanism of DNA transmission from generation to generation means that the DNA of some ancestors beyond 4 generations may not be present or at a detectable quantity, and beyond 5 generations there are many ancestors that are not present genetically. So it may be partly attributable to the roll of the dice that no NA DNA is being picked up for you.

Another problem is that there are not as many SNPs that are clearly distinguishable as NA by the frequency of allele occurrences. It is harder to identify NA segments in a map of a person's chromosomes. Sub Saharan African DNA by comparison, has many more SNPs whose allele frequencies are distinctly African. This is exacerbated by the lack of good, un-admixed samples from which to derive NA allele frequencies. So I think it is possible for someone to have some NA DNA that is undetectable because it happens to be in areas of the DNA where there are insufficient SNP markers suitable for identifying it as NA DNA.

Related to the above, I'm currently studying some areas of my Aunt's DNA that Dr. McDonald identified as Middle Eastern (we have no known Middle Eastern ancestry, or even any southern European ancestry). Interestingly, one of the MidEast segments is exactly adjacent to a small NA segment. By examining the actual SNPs and their allele population frequencies in that are of the chromosome, I want to see if it's possible that NA DNA might be getting attributed to other populations (or vice versa).

The final possibility is that your test results were contaminated or swapped inadvertently. Mistakes do happen. Have you looked into retesting? Or have you been able to corroborate that the results are likely yours because of matches to people confirmed to be related to you on paper?

[Yaffa]

DelawareNative
I don't need to tell you Delaware tribal history, but others may not be aware that the Delawares have been in contact with whites for a long time. In fact, it's a testament to the Delaware people that they have been able to retain a distinct identity after so many years of turmoil and displacement. If you read the first hand accounts of early Rocky Mountain trappers, you quickly pick up on the close association they had with the Delaware, who often made up part of the trapping parties, and were held in extremely high regard by the white trappers.

But this this long interaction, and sometimes close association with whites provides ample opportunity for long term admixture occurring. And the mechanism of DNA transmission from generation to generation means that the DNA of some ancestors beyond 4 generations may not be present or at a detectable quantity, and beyond 5 generations there are many ancestors that are not present genetically. So it may be partly attributable to the roll of the dice that no NA DNA is being picked up for you.

Another problem is that there are not as many SNPs that are clearly distinguishable as NA by the frequency of allele occurrences. It is harder to identify NA segments in a map of a person's chromosomes. Sub Saharan African DNA by comparison, has many more SNPs whose allele frequencies are distinctly African. This is exacerbated by the lack of good, un-admixed samples from which to derive NA allele frequencies. So I think it is possible for someone to have some NA DNA that is undetectable because it happens to be in areas of the DNA where there are insufficient SNP markers suitable for identifying it as NA DNA.

Related to the above, I'm currently studying some areas of my Aunt's DNA that Dr. McDonald identified as Middle Eastern (we have no known Middle Eastern ancestry, or even any southern European ancestry). Interestingly, one of the MidEast segments is exactly adjacent to a small NA segment. By examining the actual SNPs and their allele population frequencies in that are of the chromosome, I want to see if it's possible that NA DNA might be getting attributed to other populations (or vice versa).

The final possibility is that your test results were contaminated or swapped inadvertently. Mistakes do happen. Have you looked into retesting? Or have you been able to corroborate that the results are likely yours because of matches to people confirmed to be related to you on paper?

Per Delawarenative they were hoping that PF would pin the tribe their ancestors are from since their are no records stating tribe on their ancestors. However no DNA test can prove tribe. Free African Americans also claimed Indian because it was safer. They state their records are stating Negro and white but other researchers can prove the line is Indian (no tribe). Being that there seems to be no solid proof their ancestors are Indian, how do you claim your ancestors are Indian? This is where Y and MT DNA come in handy where DNA would be solid proof of having a possible Indian ancestor.. PF has me classified as Pima/Maya but my ancestor is not of either tribe. So PF is not even pinning my ancestors tribe with accuracy. I can also tell you that my MT-DNA is matching to other tribes that are not my ancestors tribe so again DNA does not prove tribe, only paper does.

[bkilpatrick]

Thank you, Daniel72, for explaining why the PF results are so rough.

Thank you, bkilpatrick, for Dr. McDonald's contact info for requesting participation in the BGA Project:



I politely asked the same of Dr. McDonald and he has obliged me as well. I am looking forward to his analysis!

Thank you all!

You are welcome, and good luck! Let us know what you learn. (Dr. McDonald seems to work quickly

Blair