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J1c5a1 (Mitochondrial DNA)

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This project is a meeting place for users who share the J1c5a1 Mitochondrial DNA haplogroup, which means they are related along their maternal lines. Users in this group may want to share their family trees with each other to find overlaps and merge duplicate profiles in order to join or expand the World Family Tree and discover new relatives.

Introduction to Mitochondrial DNA

Are you new to the use of mitochondrial DNA (mtDNA) in genetic genealogy? Need an introduction? Here are some links that can help:

About the mtDNA J1c5a1 Haplotype

Haplogroup J1c5a1 was established between 500 and 7,600 years (source). This range is very wide because few J1c5a1 individuals were represented in the scientific study that generated the estimate. J1c5a1 is a subclade of J1c5, which is widespread in Europe, so J1c5a1 probably arose somewhere in this region.

Below are links to information about the J1c5a1 mitochondrial DNA (mtDNA) haplogropups, or the higher haplogroups in which it belongs (e.g. J, J1, J1c5).

Haplogroup J1c5a1

Haplogroup J (mtDNA)

J1c5a1 Mutations

Below is the history of cumulative mutations leading from "Mitochondrial Eve" (the RSRS reference sequence), though intermediary haplogroups, that finally led to the J1c5a1haplotype. It is based on the most current information at the time of this writing (in Nov 2016; see PhyloTree.org - mtDNA tree Build 17, 18 Feb 2016). All other mutations you may have beyond those listed, including recurrent mutations, may be used to further extend the mtDNA tree within J1c5a1.

Coding-region mutations (np 577-16023) are shown in regular font; control-region mutations (np 16024-576) in bold italic. Mutations between parenthesis () are recurrent/unstable or are as yet uncertain based on current data. Mutations followed by an exclamation point ! are back mutations, reversions of the sequence to the original letter from an earlier haplogroup. The path from the RSRS sequence to J1c5a1 includes three back mutations (C182T->T182C! G15301A->A15301G! G10398A->A10398G!).

If you have your complete mtDNA sequence through Family Tree DNA's "mtFull Sequence" test, then on the RSRS Values tab of your mtDNA Results page at the ftDNA website, the "extra mutations" listed are those that appeared after the founding of haplogroup J1c5a1 and may be used to further extend the mtDNA tree within J1c5a1.

"Mitochondrial Eve" (RSRS)
  ↳L to L3 - C146T C182T T4312C T10664C C10915T A11914G G13276A G16230A C152T A2758G C2885T G7146A T8468C C195T A247G A825t T8655C A10688G C10810T G13105A T13506C G15301A A16129G T16187C C16189T G4104A A7521G T182C! T3594C T7256C T13650C T16278C A769G A1018G C16311T
  ↳N - G8701A C9540T G10398A C10873T A15301G!
    ↳R/R2'JT - T12705C T16223C T4216C
      ↳JT - A11251G C15452a T16126C
        ↳J - C295T T489C A10398G! A12612G G13708A C16069T (C16519T)
          ↳J1 - C462T, G3010A
              ↳J1c - (G185A), (G228A), T14798C
                ↳J1c5 - A5198G
                  ↳J1c5a - T2387C, C10192T
                    ↳J1c5a1 - A10598G

Note: C16519T is not listed as a characteristic J mutation in PhyloTree.org (mtDNA tree Build 17, 18 Feb 2016) and in the Haplogroup.org data derived from it, but all the kits in the J mtDNA project at ftDNA and the published sequences listing for J mtDNA at haplogroup.org include it. Therefore it has been added to the above tree based on the assumption that it is characteristic for haplogroup J.

PhyloTree.org omitted C16519T because it also appears in other lineages, and therefore is not distinctive or definitive for any mt-haplogroup. The PhyloTree.org (Build 17, 18 Feb 2016) page for JT specifically says "The mutations 309.1C(C), 315.1C, AC indels at 515-522, A16182c, A16183c, 16193.1C(C) and C16519T/T16519C were not considered for phylogenetic reconstruction and are therefore excluded from the tree." It's not specifically stated why variants at 16519 were omitted, although it usually happens because a variant is so unstable that it's impossible to create an unambiguous tree when including it. However, based on extensive genotyping within the J-mtDNA lineage, it appears fairly stable and near-universal within the J-mtDNA haplogroup subclades.

A Deeper Tree Analysis

Using the extra mutations (beyond the founding of J1c5a1), an extended tree within the J1c5a1 haplogroup can be constructed. The trees below use the data from people who have joined the J mtDNA haplotype project at FamilyTreeDNA.com or are listed on the J1c5a1 page at haplogroup.org.

The data as of Nov 2016 gives an ambiguous result due to either the presence of a back mutation in 309.1C or the independent appearance of the same mutation T16325C in two lineages. Note that variant 309.1C is specifically omitted from the PhyloTree.org tree (Build 17, 18 Feb 2016), presumably because it is so unstable that including it makes constructing an unambiguous tree impossible. Also, T16325C appears independently in three places of the Phylotree.org JT diagram and 19 places in the mtDNAcommunity.org tree. Therefore, both might be particularly unstable and best omitted from tree construction.

Given all that, if we include 309.1C and 16325 then the two alternative trees that can be constructed are:

A10598G = J1c5a1 (Hg Id: Hap5012287)
  ↳316 (Hg Id: Hap5022927)
  ↳315.1C (Hg IDs: Hap5013425)
    ↳A185G! (Hg IDs: Hap5013054)
    ↳7270, 9449 (Hg IDs: Hap5004846)
    ↳5460, 5843 (Hg IDs: Hap5002354)
    ↳11197, 14207 (Hg IDs: Hap5001744)
    ↳6413 (Hg IDs: Hap5004094)
      ↳C16126T! (Hg IDs: Hap5001279) [the order of 6413 and C16126T! might be reversed]
    ↳9007 (Hg IDs: Hap5013022)
    ↳11860 (Hg IDs: Hap5013509, Hap5012558)
    ↳16209 (Hg IDs: Hap5013635, Hap5013722)
    ↳522.1A, 522.2C(ftDNA kits: 199299, 448290)
      ↳G228A (ftDNA kits: 166418, 306722, 315340, N74345, 300656, 271173, 248114, 158642, 194658, 333581, 62528)
        ↳309.1C (ftDNA kit: 543017)
          ↳C16256T (ftDNA kit: 411206)
          ↳T16325C (ftDNA kits: N14893, 252327)
            ↳309.0! (ftDNA kits: 107729, 290771, 422591, 399330)

-OR-

A10598G = J1c5a1 (Hg Id: Hap5012287)
  ↳316 (Hg Id: Hap5022927)
  ↳315.1C (Hg IDs: Hap5013425)
    ↳A185G! (Hg IDs: Hap5013054)
    ↳7270, 9449 (Hg IDs: Hap5004846)
    ↳5460, 5843 (Hg IDs: Hap5002354)
    ↳11197, 14207 (Hg IDs: Hap5001744)
    ↳6413 (Hg IDs: Hap5004094)
      ↳C16126T! (Hg IDs: Hap5001279) [the order of 6413 and C16126T! might be reversed]
    ↳9007 (Hg IDs: Hap5013022)
    ↳11860 (Hg IDs: Hap5013509, Hap5012558)
    ↳16209 (Hg IDs: Hap5013635, Hap5013722)
    ↳522.1A, 522.2C(ftDNA kits: 199299, 448290)
      ↳G228A (ftDNA kits: 166418, 306722, 315340, N74345, 300656, 271173, 248114, 158642, 194658, 333581, 62528)
        ↳T16325C (ftDNA kits: 107729, 290771, 422591, 399330)
        ↳309.1C (ftDNA kit: 543017)
          ↳C16256T (ftDNA kit: 411206)
          ↳T16325C (ftDNA kits: N14893, 252327)

Hg ID Hap5002916 (309.1C, 315.1C, 1709, 16325) adds an additional layer of ambiguity, since it includes 16325 but is missing G228A. It may be indicating that 16325 is indeed highly unstable and arose independently in three J1c5a1 lineages (supporting the second tree), or that Hap5002916 has a A228G! back mutation (and is within and supports the first tree).

If both 309.1C and 16325 are omitted from the analysis, the resulting tree is:

A10598G = J1c5a1 (Hg Id: Hap5012287)
  ↳316 (Hg Id: Hap5022927)
  ↳315.1C (Hg IDs: Hap5013425)
    ↳A185G! (Hg IDs: Hap5013054)
    ↳7270, 9449 (Hg IDs: Hap5004846)
    ↳5460, 5843 (Hg IDs: Hap5002354)
    ↳11197, 14207 (Hg IDs: Hap5001744)
    ↳6413 (Hg IDs: Hap5004094)
      ↳C16126T! (Hg IDs: Hap5001279) [the order of 6413 and C16126T! might be reversed]
    ↳9007 (Hg IDs: Hap5013022)
    ↳11860 (Hg IDs: Hap5013509, Hap5012558)
    ↳16209 (Hg IDs: Hap5013635, Hap5013722)
    ↳522.1A, 522.2C(ftDNA kits: 199299, 448290)
      ↳G228A (ftDNA kits: 166418, 306722, 315340, N74345, 300656, 271173, 248114, 158642, 194658, 333581, 62528, 107729, 290771, 422591, 399330)
        ↳309.1C (ftDNA kits: 543017, N14893, 252327)
          ↳C16256T (ftDNA kit: 411206)

Supporting Notes

Haplotype or Haplogroup. A haplotype is set of genes or mutations in genes that are inherited together, typically named by a defining gene or marker in the set. Because gene mutations arise cumulatively in a lineage, the final mutation in a particular lineage implies the presence of all the ones appearing earlier to it. A haplogroup, as the term is used in genetic genealogy, is the group of all people who inherited and carry that haplotype. The same label is used to define both, so the "H1bw haplotype" defines who is in the "H1bw haplogroup."

HVR1 & HVR2. The two hypervariable regions on the mitochondrial chromosome show higher mutation rates than the rest of the mtDNA. However, it is still a very, very low mutation rate compared to autosomal DNA. HVR1 runs from nucleotide 16001 to nucleotide 16569, and HVR2 runs from nucleotide 00001 to nucleotide 00574. Because most of the mutations that define H1bw are not within those two regions, only full mitochondrial sequencing can definitively place a person in the H1bw haplogroup. HVR1+HVR2 sequencing alone can typically only generate a prediction for a person's major haplogroup (e.g. "H").

RSRS or rCRS. The RSRS and rCRS are standardized mitochondrial DNA (mtDNA) sequences that are used as common references for comparing with other mtDNA sequences. By using a reference sequence, other mtDNA sequences can then be described more simply by just a list of the differences vs. the reference sequence, instead of by their whole sequence.

The "RSRS" is the Reconstructed Sapiens Reference Sequence, was introduced in 2012, and is generally considered the current, superior standard. The "rCRS" is the Revised Cambridge Reference Sequence and was the major human mtDNA reference sequence for many years, but generally has been superseded by the RSRS.

The RSRS keeps the same numbering system as the rCRS, but represents the ancestral genome of Mitochondrial Eve, from which all currently known human mitochondria descend. RSRS mutations are usually named as a letter (the "ancestral" value, from the reference sequence) followed by a number (the location) followed by a letter (the mutated or "derived" value). rCRS mutations are usually presented as a number followed by a letter (the derived value), without the ancestral value prefixed. Mutation names like "309.1C" indicate a DNA insertion of one "C" at location 309.

The Mitosearch database uses rCRS values, and therefore does not easily lend itself to the type of tree/breadcrumb display used above. To compare rCRS mutations to the ones listed above, you must first convert the rCRS results to RSRS format.

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