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  • #16
    I'm already lost

    cacio, I want to make sure I am understanding the table on page 9.

    My numbers all start with a 16 and end with an A, T, C or G, but the numbers in the middle match almost EXACTLY with haplotype H006, or haplogroup L1a1a. The only difference is mine starts with a 129, not 093. The H005 (L1a1) starts with a 129, but is missing the 278 and 293. Does it have to be an exact match? If I give you the numbers, can you tell me which one of these is correct?

    16129A, 16148T, 16168T, 16172C, 16187T, 16188G, 16189C, 16223T, 16230G, 16278T, 16293G, 16311C, 16320T

    If I meet other people with this same sequence, are we closely related or it is still distant? From the same tribe maybe?

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    • #17
      Originally posted by josh w.
      Your L0 results do suggest East African origins for one of at least tens of thousands of your genetic lines.. As the other posts have noted, L0 occurs with some frequency in two East African groups, Ethiopians in the north and the Khosian in the south. This is more than a coincidence. Evidence suggests that some Khosian migrated to what is now Ethiopia.
      Josh: this is where some of my confusion comes in. One of at least tens of thousands of my genetic lines. So where the heck are the other ones? If my brother takes the Y DNA test, his results will show my paternal lineage, correct? Who else would have to take it to get the complete picture?

      So I have descended from either Ethiopians or Khosians? Is there a way to narrow it down?

      Many thanks. I am sorry I have so many questions. I am hoping that within a couple of months I will be able to pass some of this knowledge on to others in a coherent manner.

      Comment


      • #18
        Originally posted by MDV
        cacio, I want to make sure I am understanding the table on page 9.

        My numbers all start with a 16 and end with an A, T, C or G, but the numbers in the middle match almost EXACTLY with haplotype H006, or haplogroup L1a1a.

        Not sure whether it can help you, but there is a direct correspondence between two nomenclatures. Names in the left became obsolete and were replaced by ones in the right:

        L1a -> L0a
        L1f -> L0f
        L1d -> L0d

        L1b and L1c are still valid and make up what now called L1 haplogroup.


        Originally posted by MDV
        16129A, 16148T, 16168T, 16172C, 16187T, 16188G, 16189C, 16223T, 16230G, 16278T, 16293G, 16311C, 16320T
        If it's your sequence, you have tons of exact or close matches throughout Africa (and in African diaspora as well), so I don't think this result may help in your genealogical research. Obviously, the relation is too distant.



        Alvez-Silva 2000 Brasil 3 of 247
        Barbosa 2006 Alagoas, Northeastern Brazil 2 of 110
        Bortolini 1997 Brazil, S., Porto Alegre 2 of 28
        Bouzaid 2005 Egypt 1 of 75
        Brandstaetter 2004 Kenya 3 of 100
        Cerny 2004 Cameroon 6 of 104
        Chen 2000 Khwe 2 of 31
        Coia 2004 Cameroon Bakaka 4 of 50
        Coia 2004 Cameroon Bamileke 1 of 48
        Coia 2004 Cameroon Fali 2 of 41
        Coia 2004 Cameroon Podokwo 1 of 39
        Coia 2004 Cameroon Uldeme 1 of 28
        SWGDAM African-American 9 of 1096
        SWGDAM Hispanic 2 of 662
        Knight 2003 Datoga 1 of 18
        Knight 2003 Sukuma 1 of 21
        Krings 1999 Dinka (Sudan) 1 of 46
        Krings 1999 Egyptians northern 2 of 14
        Krings 1999 Sudanese southern 1 of 79
        Mateu 1997 Sao Tomeans 3 of 50
        Parsons et al., AF African American 1 of 103
        Pereira 2001 Mozambique 10 of 109
        Plaza 2003 Mbundu (Angola) 2 of 44
        Rando 1998 Moroccan non-Berbers 1 of 32
        Salas 2002 Mozambique 22 of 307
        Tajima 2004 Dominicans 1 of 83
        Trovoada 2003 Sao-Tomeans 3 of 103
        Watson 1996 Kikuyu (Kenya) 1 of 25
        Watson 1996 Tuareg (Niger) 1 of 25

        Valery
        Last edited by vraatyah; 31 July 2006, 05:51 AM.

        Comment


        • #19
          Originally posted by MDV
          Josh: this is where some of my confusion comes in. One of at least tens of thousands of my genetic lines. So where the heck are the other ones? If my brother takes the Y DNA test, his results will show my paternal lineage, correct? Who else would have to take it to get the complete picture?
          Y-DNA and mtDNA are quite special for genealogical purposes because they are passed virtually unaltered from father to son (yDNA) or mother to child (mtDNA). Thus, we can get tremendous insight into the history of our strict patrilineal line and matrilineal line. All the rest are virtually untraceable because the rest of your DNA is a random mixture from all your grandparents.


          Testing more family members can expand the picture, but only to a limit. Your brother can reveal the YDNA of your father, and his father, etc. as you surmise.

          Does your mother have a brother? His yDNA will tell you about your mother's father's father's father etc.

          Is your Dad alive? He has mtDNA from his mother's mother's mother etc.

          Testing all four of your grandparents will reveal four yDNA lines and eight mtDNA lines. Finding the right combination of cousins, aunts, and uncles, can fill in even more gaps.

          You have well-endowed trust fund, no doubt

          Comment


          • #20
            MDV:

            regarding HVR and the like. Your mtdna is composed by 16600 letters, HVR is letters 16000 on. In many papers, though, as a shorthand, they leave off the 16. So when you read HVR and see only three digits, add 16 to the front. (instead, HVR2 are letters 0 to 600 or so, so you should not add anything when you see HVR2).

            Your real HVR1 results would be a string of around 600 letters (which you can see on your ftdna page). However, it would be quite cumbersome and difficult to understand to look at the whole list. So the results are reported in a different way. There is a reference sequence (the first person whose mtdna was sequenced), called CRS (common reference sequence). Results for other people are listed as differences from CRS. So in the case of your results, for instance, it means that you have the same as CRS except those 13 letters listed. Eg. you have an A on position 16129, a T on position 16148, etc., whereas CRS has something else in those positions.

            Usually the term "mutation" is used, but they aren't really mutation, they're simply differences. In fact, often, it is CRS who mutated relative to some ancestral value. In general, it's hard to know what was the ancestral value and who mutated, one can only observe the fact that there is a difference.

            Because CRS, obviously enough, was European, usually Europeans have few differences to CRS. Deeper African lineages, which are most distant from the European ones, tend to have more differences (like you). But that's all you can read in the number of differences to CRS.

            As for the table in the paper, you're reading it correctly. You are close enough to those sequences and seem to be L0a1a. Vraatyah, who is a big expert on mtdna, has listed your matches in Africa. As said, your own L0a sequence is most likely not Ethiopian or Khoisan (those would be L0d or L0k). As vraatyah's results show, you have matches in many parts of Africa, although Cameroon seems to have a good deal of them, and Cameroon is also a likely origin for many of the Africans brought to America.

            cacio

            Comment


            • #21
              Originally posted by cacio
              most likely not Ethiopian or Khoisan

              Thanks for the mention. Ethiopia and Yemen should be listed too, 16 of 385 published sequences fall into L0a1, and, as showed on Dr Kivisild diagram, some of them underwent back transition at 16293 which made them somewhat L1a*-looking. On the other hand, Ethiopia is hardly the main source of the African American gene pool.

              Comment


              • #22
                Originally posted by vineviz
                Testing all four of your grandparents will reveal four yDNA lines and eight mtDNA lines. Finding the right combination of cousins, aunts, and uncles, can fill in even more gaps.

                You have well-endowed trust fund, no doubt
                Unfortunately, none of my grandparents are alive. I do have 54 first cousins though, including several males on my mother's side and several males on my father's side. (What can I say? We're a fertile bunch.) I expect they will do nicely, as my mother's brother has two sons and I have two brothers whose DNA will carry my father's lineage. No trust fund here, but we're all well educated and have done fairly well in our careers. I'm sure my cousins can each chip in a few dollars to have a sibling tested. I just have to get them excited about this, so it certainly helps to have all of this data to reference.

                Comment


                • #23
                  Originally posted by vraatyah
                  Not sure whether it can help you, but there is a direct correspondence between two nomenclatures. Names in the left became obsolete and were replaced by ones in the right:

                  L1a -> L0a
                  L1f -> L0f
                  L1d -> L0d

                  L1b and L1c are still valid and make up what now called L1 haplogroup.
                  Thank you Vraatyah - I am starting to understand now why it is so difficult to find L0-specific informaton through available resources. I suppose it was fairly recently that this change occurred?

                  If it's your sequence, you have tons of exact or close matches throughout Africa (and in African diaspora as well), so I don't think this result may help in your genealogical research. Obviously, the relation is too distant.
                  How do we know that the relation is distant? If my sequence (mutations?) are an exact match, I would think we were closely related. Perhaps I am only a few hundred years out of Africa, and that's really not very many generations. I know my grandmothers were in New Orleans in the early to mid 1800s. That's only about four generations ahead of me. Six to eight additional generations back would put us right in the middle of the slave trade. So I could theoretically have cousins in Africa from just 10 great-grandmothers back.

                  Here's a hard one for you:

                  If my recent ancestors, i.e., the past eight generations, were very tribal (for lack of a better word) and if the next eight generations continued the tradition, would they eventually produce a segregant genotype? A new mutation? I can't think of the correct term for an ethnic group that segregates itself and marries within its own community, but this practice was quite common in my family, as the free men of color were not accepted by either Black or White. They were very ... (what is the term??)


                  Alvez-Silva 2000 Brasil 3 of 247
                  So, in 2000, someone named Alvez-Silva tested 247 people in Brasil, and 3 of them have the same sequence that I do, correct? I just want to make sure I understand the references.

                  Comment


                  • #24
                    MDV:

                    vraatyah will be able to give you exact probabilistic statements. But the point is that these mutations are very infrequent, they can happen once every thousands of years. So, yes, you could be related to some of those only 8 generations ago, when your GGmother left Africa. But it could also be many thousand years back.

                    Which relates to your second question. Mutations are totally random events.
                    At some point, somebody has a mutation. If the group lives in isolation, then the mutation may only remain within the group and not be found elsewhere. But as said, it may take thousands of years for a mutation to happen. In the case of your HVR1, vraatyah's data show that there are people in many parts of Africa, which means that the groups is ancient and did not leave in isolation.

                    Of course, there may be mutations outside HVR1 that may help restrict a little bit. But remember that there are only 16000 or so letters in the mtdna. This may sound like a big number, but in fact, it isn't, given that mutations are infrequent, and moreover that most letters are the same for everybody and have not changed since the emergence of modern humans. Actually, the HVR1 is the one usually tested, exactly because it is the area where there are the most mutations. Other stretches of the mtdna tend to have much fewer differences. (The rest of the DNA is immense, so certainly, if you could look around in your chromosomes, there would be mutations somewhere that are shared only by your near relatives. But you'd have to look around your other chromosomes.)

                    cacio

                    Comment


                    • #25
                      Cacio:

                      "...there are people in many parts of Africa, which means that the groups is ancient and did not leave in isolation."
                      I understand what you're saying about isolation. (It's evident that a wide dispersion of this sequence means they were not isolated.) However, I do not understand how this equates to age. How can you tell the groups are ancient?

                      Second (and unrelated) question: Who exactly was used for the CRS model? Is the DNA from a fossilized specimen, a living person, or ???

                      Thanks so much for your patience with my questions. Your valuable expertise is much appreciated. (All of you guys! I am so impressed!!!)

                      Comment


                      • #26
                        MDV, Cacio is correct on the presence of your haplogroup in diverse parts of Africa. I should have been less certain about East African origins. As for the age of your haplogroup, it is determined by the number of mutations from the "grandmother" of all modern humans, the Mtdna "Eve". Some suspect she was from the Khosian population. The Cambridge Reference Sequence simply indicates how anyone tested differs in mutations from an arbitrarily chosen person in England who just happened to be tested by dna researchers. It was totally arbitrary, anyone else could have been chosen for the reference point.
                        There is no possible way to test for most of your genetic lines. Beside your Mtdna lines and a male relative's Ydna lines, it is also possible to test for some autosomal lines which would give you alot more information. There are some technical problems with autosomal tests but DnaTribes' test may be helpful in identifying specific areas of Africa as regions of origin. Ftdna may also come out with an autosomal test in the future. One limitation about autosomal tests is that they can identify ancestral lines but they can"t tell if it is a maternal line or a paternal line.
                        Last edited by josh w.; 31 July 2006, 08:00 PM.

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                        • #27
                          So where/how did they get Mitochondrial Eve's DNA?

                          Comment


                          • #28
                            Mtdna Eve is a sort of "inferred" person, in the sense that she actually lived but cannot be tested. Geneticists can estimate the rate of mutations over time, e.g. per century or per generation. (This is also how time to the most recent common ancestor is estimated). Starting out with the number of mutations in present day humans, they estimate back to when the first mutations appeared. Eve supposedly lived around 150,000 years ago. In effect, she is the most recent common ancestor off all modern human females.
                            Last edited by josh w.; 31 July 2006, 08:43 PM.

                            Comment


                            • #29
                              Josh:
                              you are right that most L0 is to be found in Ethiopia or among the Khoisan. But this particular lineage spread around. An Ethiopian or South African origin for African American is highly unlikely. As the previous papers show, most African Americans originate in West Africa, or, in smaller numbers, from West Central and a little from Mozambique, which is to be expected, these were the areas closer to the Americas, where Europeans had trade routes. Ethiopia in the opposite side, and trade was rather controlled by the Arabs (and in fact, Ethiopian slaves are to be found in the Middle East).

                              MDV:
                              Josh explained already. All lineages go back to this mitochondrial eve, so they are all equally ancient. It's just a matter of how the branches are called. Think of reconstructing the tree of all lineages. They all go back to this woman. When there is a mutation, a branch splits, so you can form a very complex tree with many sub-sub-sub branches. Because humans arose in Africa, all the early branching is to be found in Africa. Only a sub-branch of L3 left Africa. As usual, because Europeans and Americans were studied first, haplogroup names were first assigned for their sub-branches. African lineages were simply lumped under the letter L. More ancient, in this sense, simply means that there are very many sub-branches of L0 that are very diverse among themselves. There is far more genetic diversity among Africans than there is between any group that lived outside Africa.

                              As for this mitochondrial Eve, we only know she existed somewhere in Africa, may be 150K years ago (but the estimation error can be large). But we cannot know what her mtdna was. Possibly, no currently living human has exactly her mtdna, because of mutations. As a side curiosity, you may find it funny to know that the Y-chromosome "Adam" lived in Africa, but he certainly never met mitochondrial Eve: he lived at least 70K years later!

                              cacio

                              Comment


                              • #30
                                Yes, I did indeed find it humorous that Adam never met Eve! But she had to have a mate and I wonder why he didn't leave a trail.

                                The lightbulb just went on for me on the "ancient" thing. If our genes only mutate every 10,000 years or so, then those of us with many mutations are deemed genetically ancient, whereas those with fewer mutations have relatively newer branches and their lineage is not as old. Sorry it took so long for me to get it!

                                This random English guy is bugging me now. Why base a "standard" off some random person? How could they possibly tell how old HIS lineage was if he was the base of the CRS project?

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