Announcement

Collapse
No announcement yet.

Experiences with Family Finder and PF

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #31
    Originally posted by smallaxe View Post
    DelawareNative


    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).
    Interesting. I'm now in the same position, trying to make sense of an unexpected NA that Dr. McDonald identified as one "small but strong" segment (plus a few other spots that are more likely "noise.")

    So how do you go about studying this?

    (Sorry if my question is naive

    Blair

    Comment


    • #32
      Originally posted by Yaffa View Post
      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.
      I had missed that. I made an assumption based on his name. You are correct about determining tribe via DNA. It's hard enough to identify NA vs. East Asian. I don't think any test can identify down to the level of tribe, and if a test claimed it could, I would be highly skeptical. PF is not making that claim. It's only reporting the sample populations a person is most like, and Pima/Maya is about it for North America as far as sample populations go. Y-DNA and MtDNA are good when they are positive for NA haplogroups, but they can't disprove NA ancestry since they represent less than 2% of your ancestry 7 generations back.

      I also agree with what I think you are saying, i.e. that claiming Native American ancestors was the safe explanation among families in the south to explain physical traits actually attributable to African ancestors. This is just my opinion based on doing southern genealogical research for many years. I'm not saying this is the case for DelawareNative, I'm speaking generally now.

      Comment


      • #33
        Originally posted by bkilpatrick View Post
        Interesting. I'm now in the same position, trying to make sense of an unexpected NA that Dr. McDonald identified as one "small but strong" segment (plus a few other spots that are more likely "noise.")

        So how do you go about studying this?

        (Sorry if my question is naive

        Blair
        Here is how I have done it in the past. You open up your raw data file in notepad++ (it's too big for most spreadsheet programs). Find the area using the chromosome and position where the interesting segment is. Select the rows in the segment (plus some before and after the segment) and copy to the clipboard. Now paste that into a spreadsheet, or paste it into a text editor and save it as a .csv file and open that file in a spreadsheet.

        So now you have a spreadsheet showing the data for the area of your genome where the segment of interest is. Select the values in the RSID column (the SNP names that start with "rs"), or if there are many of them select up to 1000 of them at a time. Open the following link in a web browser:
        http://spsmart.cesga.es/
        Check the "CEPH U. Stanford HGDP " box and click the Metasearch button. In the next screen, check the America, Africa, and all the other continental area boxes. In the "Search by SNPs" box, paste the RSID values you copied from your spreadsheet, and then click the "next" button. On the next page, just click the "search" button. After this you will see a page with all the SNPs you pasted, along with pie charts that show the continental frequencies of the alleles. You can look at your values for each SNP in your spreadsheet (remember that A=T and C=G). If there is an SNP that is a good indicator for a continent of interest, and you have the value that is most likely associated with that value, then you can click on the rs name on the left hand side. This will open a web page that tells you everything about that SNP including a more detailed breakdown of population frequencies among the sub-populations, and also other sets of population samples if there are any.

        If you are looking mostly European looking for non-Euro admixture, you can sort your spreadsheet first by alleles (AA, AC, CC, TC, etc), secondly by chromosome, and thirdly by position. Then select a block of heterozygous SNPs (alleles like AC were the two values are different, but not like CC where the two values are the same). These are the most likely SNPs to show admixture. This is because if you are homozygous, then either you're 100% a particular population, or you are 50/50 two different populations, but both alleles are relatively frequent for that SNP. But the heterozygous ones are most likely where you'll find that one of the alleles is infrequent in one population, but frequent in the other, and since you're heterozygous, it supports that you're 50/50 for two different populations. Also note that there are contra-indicators too. For example, if you are homozygous CC at some SNP, but 100% of Africans are AA, then this contraindicates you being part African there. Multiple contra-indicators within a potential segment can put the whole segment into question. Contra-indicators can also be helpful in determining where a real segment starts and ends. Remember that these are all just statistics. Even if it says 0% of Europeans have a particular allele at an SNP, it may actually be 0.2%. That's 2 out of 1000, and you could be one of them. So one SNP is not enough. You need to see a pattern of supporting SNPs.

        I've attached a screen shot of an area where it appears I have a African segment among my mostly European DNA, and another where there is a possible NA segment to show what I mean. I'm heterozygous for all the displayed SNPs. It was hard to find a good screenshot of an NA example, because there are so few good markers, and I'm not sure my segment is really even NA. And the of the ones that show a difference between Euro and NA, there is usually a fair amount of East Asian too, so you can't be sure whether you're seeing actual NA, or Asian bits that sometimes show naturally in Europeans. I added green arrows to that one to point out some possible NA SNPs.

        It's not enough to just find one or two possible SNPs. You need to see that they're consistently showing up throughout the segment, and it has to run over a big enough area (>1 mega base pairs) to be more than noise. I'm a programmer, and I'm currently working on a program that will do this automatically, and that people can run on their own computers so they don't have to send me their raw data.

        Last edited by smallaxe; 27 March 2011, 11:41 AM.

        Comment


        • #34
          Originally posted by smallaxe View Post
          I had missed that. I made an assumption based on his name. You are correct about determining tribe via DNA. It's hard enough to identify NA vs. East Asian. I don't think any test can identify down to the level of tribe, and if a test claimed it could, I would be highly skeptical. PF is not making that claim. It's only reporting the sample populations a person is most like, and Pima/Maya is about it for North America as far as sample populations go. Y-DNA and MtDNA are good when they are positive for NA haplogroups, but they can't disprove NA ancestry since they represent less than 2% of your ancestry 7 generations back.

          I also agree with what I think you are saying, i.e. that claiming Native American ancestors was the safe explanation among families in the south to explain physical traits actually attributable to African ancestors. This is just my opinion based on doing southern genealogical research for many years. I'm not saying this is the case for DelawareNative, I'm speaking generally now.
          With Y and MT DNA, you would have to get Y and MT DNA on each or as many direct line ancestors as you can to tell a full story. Lines dies out. You also cant get Y DNA on women. You cant get MT-DNA on deceased men. You never get the full story.

          To have an Indian ancestor has to be within 500-600 years, its then finding paper where it falls on the tree.

          I can prove my closer relatives great grandparents to me are either Indian or European through Paper and Y and MT DNA. Now going back further to my 5th/ 6th greats or before, my European men do have ties to and I have circumstantial evidence that I might have some free African American in my lines. I have no solid evidence at the moment . These possible free African Americans on my tree going that far back would not show up on a PF test. Im missing marriages. This is where I would need MT-DNA on those missing wives to prove they might have been African.

          as for the Pima/Maya. They have that DNA because they were doing a diabetes study. They say the Pima have one of the highest rates of diabetes. I also read they did a DNA study on the early settlers of Starr County Texas where they too have one of the highest rates of diabetes. Those settlers they claim carry the specific Pima/Maya markers. My ancestors being one of those early settlers although they are not Pima/Maya. Many of my ancestors have died due to serious complications of diabetes in the past. That Pima/Maya marker maybe specific to diabetes????? I have heard that many Indian tribes in general came down with diabetes due to changes in their diet when their natural food sources were taken by invasion by the Europeans.

          Comment


          • #35
            Originally posted by c_thompson_68 View Post
            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.
            Unfortunately, it's not a matter of test resolution. There's no way to increase the resolution, it's already as finely grained as possible, comparing individual base pairs (A, C, G, or T) against known SNPs. The problem is two-fold, and its origin lies elsewhere.

            First, there just haven't been enough people tested, from various populations, to be as accurate as any of us would like. There are better reference populations than the HGDP, namely the HapMap and 1000 Genomes projects. Someday soon, I hope, FTDNA will switch to using one or more of those databases for PF, or even a combination of all of them. Also, as more genetic research is done, new SNPs will be identified that are predominantly found in certain populations. Then it'll be a matter of comparing your data with the new SNPs, which were hopefully tested by the Illumina chip.

            Second, and more significant, is the simple arithmetic of inheritance, and probability. After six generations, the average contribution of each of those 64 ancestors is only 1/64 of your DNA, or a little over 1.5%. After just 5 generations, the probability you inherited DNA from any individual ancestor is about 50/50. Because of DNA recombination, the amount inherited from each ancestor can be much different than the theoretical average. We should have about 25% from each grandparent, but the actual share might be 20%, or it could be 40%. When you go back a few generations, with average contributions in the single digits, the actual contribution could very well be zero. However, even if you didn't match a known ancestry, one of your siblings might.
            Last edited by nathanm; 27 March 2011, 12:08 PM. Reason: copy/paste screwed up entry

            Comment


            • #36
              Originally posted by smallaxe View Post
              Here is how I have done it in the past. You open up your raw data file in notepad++ (it's too big for most spreadsheet programs). Find the area using the chromosome and position where the interesting segment is. Select the rows in the segment (plus some before and after the segment) and copy to the clipboard. Now paste that into a spreadsheet, or paste it into a text editor and save it as a .csv file and open that file in a spreadsheet.

              So now you have a spreadsheet showing the data for the area of your genome where the segment of interest is. Select the values in the RSID column (the SNP names that start with "rs"), or if there are many of them select up to 1000 of them at a time. Open the following link in a web browser:
              http://spsmart.cesga.es/

              ....

              I'm a programmer, and I'm currently working on a program that will do this automatically, and that people can run on their own computers so they don't have to send me their raw data.
              Thanks, I hadn't seen that website before. And keep us posted on your software. (You're not making it Windows specific I hope.)

              Comment


              • #37
                Originally posted by Yaffa View Post
                You cant get MT-DNA on deceased men.
                That's not always the case. Sometimes it's possible to get mtDNA samples from hair. Of course, that presumes you have a hair sample, but keeping them was popular in the 19th century.

                Comment


                • #38
                  Originally posted by nathanm View Post
                  Thanks, I hadn't seen that website before. And keep us posted on your software. (You're not making it Windows specific I hope.)
                  I'm writing it in C# (.NET), so it should run on linux and MaxOS if you have the Mono framework installed.

                  Comment


                  • #39
                    Originally posted by nathanm View Post
                    That's not always the case. Sometimes it's possible to get mtDNA samples from hair. Of course, that presumes you have a hair sample, but keeping them was popular in the 19th century.
                    I have heard you have to have the roots to get useful DNA samples. It probably is much more expensive too if you don't use the standard spit or swab samples.

                    Comment


                    • #40
                      Originally posted by nathanm View Post
                      That's not always the case. Sometimes it's possible to get mtDNA samples from hair. Of course, that presumes you have a hair sample, but keeping them was popular in the 19th century.
                      Well yes if someone has a good DNA sample that might have been left by that deceased male. I dont know any living family of mine who might have DNA samples of hair on deceased relatives. Dont they need the root of the hair not just a clipping of a hair sample??

                      Comment


                      • #41
                        Originally posted by smallaxe View Post
                        I have heard you have to have the roots to get useful DNA samples. It probably is much more expensive too if you don't use the standard spit or swab samples.
                        I heard this also.

                        Comment


                        • #42
                          Originally posted by smallaxe View Post
                          I had missed that. I made an assumption based on his name. You are correct about determining tribe via DNA. It's hard enough to identify NA vs. East Asian. I don't think any test can identify down to the level of tribe, and if a test claimed it could, I would be highly skeptical. PF is not making that claim. It's only reporting the sample populations a person is most like, and Pima/Maya is about it for North America as far as sample populations go. Y-DNA and MtDNA are good when they are positive for NA haplogroups, but they can't disprove NA ancestry since they represent less than 2% of your ancestry 7 generations back.

                          I also agree with what I think you are saying, i.e. that claiming Native American ancestors was the safe explanation among families in the south to explain physical traits actually attributable to African ancestors. This is just my opinion based on doing southern genealogical research for many years. I'm not saying this is the case for DelawareNative, I'm speaking generally now.
                          Where are you researching in the SE? I know there were a lot of Free African Americans in the Granville/Orange/Chatham Area of NC. Some of them claimed Indian when they were African/European Mixed. There were also Indians in the area. Some of them could be tri racial. I also know some of the people in that area did come from Maryland, VA etc. They move south to NC and then west or further south.

                          Comment


                          • #43
                            results from Dr McDonald

                            I received this response about my raw Illumina file from Dr McDonald. See the first post in this thread for my data from FTDNA.

                            As shown below, the quantitative does not discover the Native American.

                            kit 173139-autosomal-o-results.csv
                            Most likely fit is 87.4% (+- 10.8%) Europe (all Western Europe)
                            and 12.6% (+- 10.8%) Europe (various subcontinents)
                            which is 100% total Europe

                            The following are possible population sets and their fractions,
                            most likely at the top
                            French= 0.486 Irish= 0.514
                            French= 0.352 Orcadian= 0.648
                            Orcadian= 0.859 Tuscan= 0.141
                            French= 0.760 Finland= 0.240
                            Irish= 0.779 Tuscan= 0.221
                            Spain= 0.163 Orcadian= 0.837
                            Spain= 0.257 Irish= 0.743
                            French= 0.758 Lithuani= 0.242
                            Orcadian= 0.837 Italian= 0.163
                            Irish= 0.744 Italian= 0.256

                            It shows a typical British person, with a mixture that you are
                            solidly in Britain. The PCA (speckle)plot agrees.

                            However, since you suggested Native American, I looked
                            carefully at that green spot on the chromosomes. It is small
                            but very strong, and quite possibly is real, but still,
                            it is too small to be 99% sure. Maybe 70%.


                            He included a chromosome diagram that shows a small but definite native american area on my chromosome 8, and a speckle diagram showing populations I match.

                            I'm hoping that more DNA data from North American natives will improve the accuracy in the future, but this is very helpful to me.

                            Comment


                            • #44
                              Clarification:

                              -) I'm from Delaware

                              -) I'm Native American physically...and other things mixed in. I believe I'm tri-racial because I've found whites, 'mulattoes' and 'negroes' on many records, so finding anything and everything in my lineage is expected.

                              -) Unless it's a connection we haven't discovered, I'm not from one of Delaware's state recognized tribes. Doesn't make me less "DelawareNative" - just clarifying.

                              -) DNA might carry you specifically to a tribe in North America, or anywhere in the world, depending on any DNA companies' test populations, and of course I'd like to find "my peoples" anywhere in the world they are, indigenous or not. You might be "orcadian" - tribes are merely groups of peoples, not necessarily one in the US that you can "join" by having the right Indian ancestors. I've never said that I'm looking for any specific tribe by way of FTDNA, but I myself can narrow down my people by logical deduction using Family Finder results, Population Finder results (well, maybe not for me yet) and paper trails.

                              -) In speaking with professional genealogists, I've gleaned that I have red ties to Virginia and Maryland at a minimum, and maybe NC. It's a few tribes coming together, not just one relative way down the road; it's several families on both sides from different states. Most people from Delaware are mixed blood of many races, but they either don't know it or don't want to admit it - and that's the truth I have witnessed myself.

                              -) I understand that this is somewhat 'bleeding edge' technology, and my results may vary. Daily.

                              -) I'm a private investigator

                              -) I'm a woman



                              Just the facts, ma'am.

                              Comment


                              • #45
                                I do happen to know that some tribes in VA are considered extinct according to paper. They maybe be out there somewhere but you will not find paper. meaning you cant claim tribe if you dont have paper stating tribe. I do know people who have proven Indian ancestors Though Y-DNA from VA that can not even prove tribe on their ancestors because the tribes they may be of are considered extinct.


                                Being that there are so many tribes. Some may have also branched off each other, some may have records and some dont. In my experience researching it is very rare even if you have an Indian ancestor that you will find a record outside tribal enrollment that will state tribe. If you find a record with a tribe listed outside enrollment you just found the equivalent of the holy grail!


                                My MT-DNA does match 2 federal US tribal members at a distance. Both those tribal members are of different tribes and my ancestor is NOT of either tribe. MT-DNA is solid where % is not and my MT DNA can not prove tribe.

                                % tests cant be accurate if they are not using samples from all populations. This is why PF is in its beta phase and will not be 100 % accurate anytime soon. FTDNA even told me that they dont have enough samples to prove that some DNA is in fact Indian so they may be classified elsewhere in a different population that fits closest at the moment.

                                If someone wants solid proof of confirming they have an Indian ancestor, the best thing they can do is Y and MT-DNA test those lines. It will not prove tribe but will confirm if that one line ancestor is Indian. Especially if your paper fluctuates on race form White, to Negro to Mulatto. All 3 of these does not mean Indian. Usually someone who is listed Mulatto more times than not has African mix in that line. The term Mulatto has a much different meaning than say Mexico. Race classifications in Mexico are actual blood % ( Casta)

                                You might also check surname projects for your ancestors to see if any of your cousin lines may have come forward to DNA test for any of your direct line ancestors that you can not Y and MT DNA test for.

                                I have more than enough proof to claim I am genetically in part Indian but I dont run around claiming I am Indian because I am not a tribal member. I descend from Indians. There is a difference.
                                Last edited by Yaffa; 27 March 2011, 07:09 PM.

                                Comment

                                Working...
                                X