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Thread: H1c3 Y Full tree mtdna update

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    H1c3 Y Full tree mtdna update

    The mtdna section of the Y Full tree, has today updated its information. The Mtdna haplogroup H1c, is now showing new dating, as formed 3500 ybp (years before present,) and a time of most recent common ancestor is now 2100 ybp ( TMRCA ).

    Mtdna new dates for H1c3 are formed 800 ybp, and TMRCA is 650 ybp.

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    Quote Originally Posted by Paul333 View Post
    The mtdna section of the Y Full tree, has today updated its information. The Mtdna haplogroup H1c, is now showing new dating, as formed 3500 ybp (years before present,) and a time of most recent common ancestor is now 2100 ybp ( TMRCA ).

    Mtdna new dates for H1c3 are formed 800 ybp, and TMRCA is 650 ybp.
    The last update's from YFull tree Mtdna, informed on 11th May 2019, that Mtdna H1c3, was now formed 1,300 ybp, with a new TMRCA of 1,050 ybp. It also dated H1c as being formed 15,100 ybp, with a TMRCA of 7,500 ybp.
    Last edited by Paul333; 05-14-2019 at 10:29 PM.

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    Ive just been browsing through my '23 & Me' ' raw data', and I have References regarding SNP Markers, that may or may not 'help me move further downstream of my mtdna 'H1c3' Haplogroup.

    I have a Marker SNP of i4001356, with a Genomic position of 16176, with Variants C or T, my Genotype C.

    I have another Marker SNP of i4001236, with a Genomic position 16362, with Variants C or T, my Genotype T


    The reason I ask is that I came across two further downstream subclades of Mtdna,H1c3, one H1c3a, and the other H1c3b.

    H1c3a is defined with a SNP marker C16176 T

    H1c3b is defined with a SNP marker T16362 C

    How can I find out if the information I have regarding my raw data above fits any of these further two downstream subclades of H1c3, or is this information of no use for these, and therefore rules me out.

    Thanks for any help
    Last edited by Paul333; 06-09-2019 at 01:23 AM.

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    Quote Originally Posted by Paul333 View Post
    Ive just been browsing through my '23 & Me' ' raw data', and I have References regarding SNP Markers, that may or may not 'help me move further downstream of my mtdna 'H1c3' Haplogroup.

    I have a Marker SNP of i4001356, with a Genomic position of 16176, with Variants C or T, my Genotype C.

    I have another Marker SNP of i4001236, with a Genomic position 16362, with Variants C or T, my Genotype T


    The reason I ask is that I came across two further downstream subclades of Mtdna,H1c3, one H1c3a, and the other H1c3b.

    H1c3a is defined with a SNP marker C16176 T

    H1c3b is defined with a SNP marker T16362 C

    How can I find out if the information I have regarding my raw data above fits any of these further two downstream subclades of H1c3, or is this information of no use for these, and therefore rules me out.

    Thanks for any help
    Have you tested with anyone else? 23andme doesn't test the full mtDNA genome and even if they did not all reads are 100% accurate. Since you know how to look up the above SNPs I assume you looked up the other positions and found them missing from your raw data. That would be because they weren't tested. The only way to find out if you are positive or negative for them is to get tested for them which means you have to get an FTDNA full sequence mtDNA test or a Yseq mtComplete test.

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    Thanks for the reply.

    I have tested with two companies Living DNA, & 23 & Me. I only got 7 Basic mtdna SNPs,with Living DNA. The 23 & Me Raw Data information, is more confusing to understand. I also had a 17 STR test, that could not identify my Y Haplogroup.

    On the YFull M tree I found only five numbers similar to the ones above under the H1c3 entry. In regard to the two most common lower subclades the two numbers I have come across, I have one for each for them, as above.

    Regarding the other three, I do not have A16219G for H1c3a, and do not have T16189C for H1c3b, and regarding the other, T146C! for H1c3a I also do not have this, even though it looks incomplete. There are astrisks against some of these, and the T146c!, has its exclamation mark at the end.

    On checking the raw Data today, I have to correct the H1c3b SNP Marker entry above 'SNP i4001236', to the following -

    - SNP Marker i3001888, with Genomic position 16362, Variants C or T, and my Genotype T.

    There are some further down Subclades, but these two have been known for some time.

    Regarding the above is the Genotype T placed at the beginning of the number or the end ?, and what, which or where does the variants C-T go.??

    I do intend to test further as I said, but for now I will wait a while and hope for developments, before I decide which way to go, but regarding MTDNA, will I have any further data, that could, or would take me any further.

    Its confusing, with the information I have.

    I also found a further downstream reference today, on the YFull Mtree for Mtdna H1c3b1, which includes the identifying SNP Marker A13933G.

    I have in my Raw Data a similar SNP Marker i5050661 with Genomic position '13933', variants A or G with my Genotype 'A'. this reference is for H1c3b1, which is further downstream.
    Last edited by Paul333; 06-09-2019 at 04:43 PM.

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    Quote Originally Posted by Paul333 View Post
    Thanks for the reply.

    I have tested with two companies Living DNA, & 23 & Me. I only got 7 Basic mtdna SNPs,with Living DNA. The 23 & Me Raw Data information, is more confusing to understand. I also had a 17 STR test, that could not identify my Y Haplogroup.

    On the YFull M tree I found only five numbers similar to the ones above under the H1c3 entry. In regard to the two most common lower subclades the two numbers I have come across, I have one for each for them, as above.

    Regarding the other three, I do not have A16219G for H1c3a, and do not have T16189C for H1c3b, and regarding the other, T146C! for H1c3a I also do not have this, even though it looks incomplete. There are astrisks against some of these, and the T146c!, has its exclamation mark at the end.

    On checking the raw Data today, I have to correct the H1c3b SNP Marker entry above 'SNP i4001236', to the following -

    - SNP Marker i3001888, with Genomic position 16362, Variants C or T, and my Genotype T.

    There are some further down Subclades, but these two have been known for some time.

    Regarding the above is the Genotype T placed at the beginning of the number or the end ?, and what, which or where does the variants C-T go.??

    I do intend to test further as I said, but for now I will wait a while and hope for developments, before I decide which way to go, but regarding MTDNA, will I have any further data, that could, or would take me any further.

    Its confusing, with the information I have.

    I also found a further downstream reference today, on the YFull Mtree for Mtdna H1c3b1, which includes the identifying SNP Marker A13933G.

    I have in my Raw Data a similar SNP Marker i5050661 with Genomic position '13933', variants A or G with my Genotype 'A'. this reference is for H1c3b1, which is further downstream.
    The RSIDs such as i3001888 are really irrelevant. It's the position, genotype, mutation and subclade that matters. Even the exclamation mark is just additional information that simply means it's a back mutation for that specific subclade.

    The mutation is noted as the ancestral allele, the position, the derived allele. If you have the ancestral allele in your genotype then you are negative for the mutation. If you have the derived allele for your genotype then you are positive. So for T16362C which defines H1c3b means that if your genotype is T then you are negative (ancestral). If C then you are positive (derived). Since you have Genotype T then you are negative (ancestral).

    For A13933G you are negative since you have the ancestral allele of A for your Genotype.

    If you are negative for a mutation then you are negative for the subclade so you can then ignore those subclades. If the position is missing from the 23andme raw data it means it wasn't tested. There is nothing more you can do at the moment if it is missing.
    Last edited by ArmandoR1b; 06-09-2019 at 10:32 PM.

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    Quote Originally Posted by ArmandoR1b View Post
    The RSIDs such as i3001888 are really irrelevant. It's the position, genotype, mutation and subclade that matters. Even the exclamation mark is just additional information that simply means it's a back mutation for that specific subclade.

    The mutation is noted as the ancestral allele, the position, the derived allele. If you have the ancestral allele in your genotype then you are negative for the mutation. If you have the derived allele for your genotype then you are positive. So for T16362C which defines H1c3b means that if your genotype is T then you are negative (ancestral). If C then you are positive (derived). Since you have Genotype T then you are negative (ancestral).

    For A13933G you are negative since you have the ancestral allele of A for your Genotype.

    If you are negative for a mutation then you are negative for the subclade so you can then ignore those subclades. If the position is missing from the 23andme raw data it means it wasn't tested. There is nothing more you can do at the moment if it is missing.
    Thank you
    That helps me a lot to understand these

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    Regarding the lower subclades of H1c3, Ive just been checking some raw data again, and I have come across two similar SNP markers in my Raw Data for H1c3a, that I missed, but think I am positive for, these are both 23 & Me raw data references,(1) i 4001356 16176 C, and (2) i705670 16176 C,. the position is 16176 and the genotype is C for both.

    On the Yfull tree for H1c3a, there are three identifying SNP's (1) T146c!,(2) 'C16176T', and (3) A16219G. Two of these I am negative for as discussed ( T146C!, and A16219G )above, in earlier posts, but I do have two SNP Markers for C 16176. How is this worked out, does the two C 16176 positives I have mean I have the subclade H1c3a, or because I have two negatives I do not.

    I am still trying to figure this out, but I came across an entry on the Family Tree British isle Dna by county, and it has kit no 235906, for a lady born in Germany 1467 H1c3a, and comparing her MTDNA entry, she has included in her data the same negative of A16219G, as I have, but the same positive SNP C16176, as I have, but with a T on the end, and she is H1c3a. I have also found another H1c3a, from Northern Ireland, with the same,negative and posative SNPs, living around 1830.

    How do I figure this out, being both positive, and negative, for the same subclade.
    Last edited by Paul333; 06-15-2019 at 08:15 PM.

  11. #9
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    Double post, sorry

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    Quote Originally Posted by Paul333 View Post
    Regarding the lower subclades of H1c3, Ive just been checking some raw data again, and I have come across two similar SNP markers in my Raw Data for H1c3a, that I missed, but think I am positive for, these are both 23 & Me raw data references,(1) i 4001356 16176 C, and (2) i705670 16176 C,. the position is 16176 and the genotype is C for both.

    On the Yfull tree for H1c3a, there are three identifying SNP's (1) T146c!,(2) 'C16176T', and (3) A16219G. Two of these I am negative for as discussed ( T146C!, and A16219G )above, in earlier posts, but I do have two SNP Markers for C 16176. How is this worked out, does the two C 16176 positives I have mean I have the subclade H1c3a, or because I have two negatives I do not.

    I am still trying to figure this out, but I came across an entry on the Family Tree British isle Dna by county, and it has kit no 235906, for a lady born in Germany 1467 H1c3a, and comparing her MTDNA entry, she has included in her data the same negative of A16219G, as I have, but the same positive SNP C16176, as I have, but with a T on the end, and she is H1c3a. I have also found another H1c3a, from Northern Ireland, with the same,negative and posative SNPs, living around 1830.

    How do I figure this out, being both positive, and negative, for the same subclade.
    Since you have C for 16176 that means you are negative for C16176T because your Genotype is the ancestral (negative) allele which means that you are negative for H1c3a. To be positive for a mutation your Genotype has to match the derived (positive) allele which in this case is T. Please ignore RSIDS such as i4001356 and i705670. They have no bearing on positive or negative results.

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