H16: An Introduction

Co-Admin for H16: Paul Malysz email

FTDNA-hosted site is mtDNA Haplogroup H Project: H16

Mitochondria are semi-independent entities found in human cells. They work to produce energy for the cell.

Mitochondrial DNA is inherited only from our mothers. Every child inherits a colony of mitochondrial DNA from their mother in her egg cell. The male sperm cell has its own mtDNA. In humans, it does not survive to be passed on.

Mitochondrial DNA is made up of a control region and a coding region. The control region is further divided into two segments. Because the control region has a higher mutation rate than the coding region the segments are called the hypervariable regions. In most journal articles hypervariable region will be abbreviated to HVR. Thus they are HVR1 and HVR2.

Mitochondrial DNA is abbreviated to mtDNA.

A mutation is a change in the mtDNA sequence. Mutations are described in terms of the first human mtDNA to be fully sequenced. Because it was sequenced at Cambridge University it is called the Cambridge Reference Sequence, CRS.

This is an example of a change at the third place in the mtDNA. The change in the sample is shown in bold.

There are are multiple ways to write this. The first is to give the position and then the change: 003C. The second is to give the normal value for CRS, the position, and then the change: T003C. When talking about a single change the second method is clearer. When describing all of the changes found in a sample though it is quicker to use the first method. Some papers place both the normal CRS value and the mutation value after the position. They then indicate the change with an arrow: 003T→C.

An insertion is when an additional segment is added to the DNA sequence. Insertions are described by writing the position, a period, the insertion point and the name of the new segment. Here is an example of the common insertion 315.1C.

Insertions are highly variable and may occur in variable degrees in the same person.

A deletion is when a single segment is removed from the DNA sequence. Deletions are described by writing the position and a minus sign, ”-.” Here is an example of the common pair of deletions at 522 and 523.

Deletions are highly variable and may occur in variable degrees in the same person.

A transition is when one segment is changed to another of the same type.

A→G, G→A, T→C, and C→T are transitions. Here is an example of the transition A263G.

Transitions do not happen that often but they are more frequent than transpositions.

A transposition is when a segment changed to another of the opposite type.

A→T, T→A, C→G, and G→C are transpositions. Here is an example of the transpositon A227T.

Transpositions are uncommon.

A haplotype is a list of the mutations for an individual in relation the the CRS. The haplotype may be the HVR regions or the entire mtDNA sequence.

A Haplogroup is a collection of related samples. mtDNA Haplogroups are usually defined by changes to the slower coding region. Haplogroup H is defined by two mutations, A2706A and C7028C. Because the CRS was an H these two defining mutations will not show up on a list of coding region mutations for Hs.

Here is a typical list of coding region mutations for an H16.

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All Haplogroups interconnect forming a single tree of decent from our common formother.

L → L1 → L3 → N → R.

R is a Macro-Haplogroup whose daughter populations span much of the Northern Hemisphere.

Based on the tree from the National Genographic Project public partition database, Behar 2007, this is a basic outline of the R Macro-Haplogroup tree.

• R {C12705C}
  • R*
  • R0* {G11719G} [aka pre-HV]
    • HV* {C14766T}
      • H {C7028C}
      • V {G4580A}
  • B {8280-}
  • R9 {3970}
  • TJ
    • T {G13368A}
    • J {A12612G}
  • U {A11467G}
    • K {A1811G,G9055A,A12308G,G12372A}

• H {A2706A,C7028C}
  • H*
  • ..
  • H16 {C10394T}
  • ..

Any H16s found in Finnilä would have been classified as H* or H(xH1,xH2).

• Phylogenetic network for European mtDNA.
  Finnilä S, Lehtonen MS, Majamaa K
  Am J Hum Genet68p1475-84(2001 Jun)

Any H16s found in Hernstadt would have been classified as H* or H(xH1,xH2,xH3). One H16 was sequenced but not identified. See GenBank Sequences page for the sequence which only included Coding Region, no HVR.

• Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups.
  Herrnstadt C, Elson JL, Fahy E, Preston G, Turnbull DM, Anderson C, Ghosh SS, Olefsky JM, Beal MF, Davis RE, Howell N
  Am J Hum Genet70p1152-71(2002 May)

No H16 was found in study samples. Study covered H1-15.

• The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool.
  Achilli A, Rengo C, Magri C, Battaglia V, Olivieri A, Scozzari R, Cruciani F, Zeviani M, Briem E, Carelli V, Moral P, Dugoujon JM, Roostalu U, Loogväli EL, Kivisild T, Bandelt HJ, Richards M, Villems R, Santachiara-Benerecetti AS, Semino O, Torroni A
  Am J Hum Genet75p910-8(2004 Nov)

Study focused on rapid forensic identification by choosing common European HVR results and looking for coding region differences. Study used anonymized samples from the U.S. Armed Forces DNA Identification Laboratory. 10394 was included as a study site. Seven (7) sequences with 10394T were published to Genbank from this study. See GenBank Sequences page for the sequences.

• Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians.
  Coble MD, Just RS, O'Callaghan JE, Letmanyi IH, Peterson CT, Irwin JA, Parsons TJ
  Int J Legal Med118p137-46(2004 Jun)

The mt-H test at FamilyTreeDNA does not include an H16 test. Those who are H16 will be classified as an H*.

This study restricted itself to H1 through H11, so excluded the H16's from Herrnstadt 2002 coding region sequences used in the study.

• Disuniting uniformity: a pied cladistic canvas of mtDNA haplogroup H in Eurasia.
  Loogväli EL, Roostalu U, Malyarchuk BA, Derenko MV, Kivisild T, Metspalu E, Tambets K, Reidla M, Tolk HV, Parik J, Pennarun E, Laos S, Lunkina A, Golubenko M, Barac L, Pericic M, Balanovsky OP, Gusar V, Khusnutdinova EK, Stepanov V, Puzyrev V, Rudan P, Balanovska EV, Grechanina E, Richard C, Moisan JP, Chaventré A, Anagnou NP, Pappa KI, Michalodimitrakis EN, Claustres M, Gölge M, Mikerezi I, Usanga E, Villems R
  Mol Biol Evol21p2012-21(2004 Nov)

Defined H16, characterized by C10394T, which is supported by seven complete genomes from Coble 2004. Study started with 2214 unrelated and anonymized blood samples from Tyrol, Austria. Of these, 859 were Haplogroup H. Table 4 shows H16 occurring 17 times, making up 2.0% of samples.

• Dissection of mitochondrial superhaplogroup H using coding region SNPs.
  Brandstätter A, Salas A, Niederstätter H, Gassner C, Carracedo A, Parson W
  Electrophoresis27p2541-50(2006 Jul)

Study did not identify H16 directly in study, but is included in supplementary material which drew from previous published work.

• Origin and expansion of haplogroup H, the dominant human mitochondrial DNA lineage in West Eurasia: the Near Eastern and Caucasian perspective.
  Roostalu U, Kutuev I, Loogväli EL, Metspalu E, Tambets K, Reidla M, Khusnutdinova EK, Usanga E, Kivisild T, Villems R
  Mol Biol Evol24p436-48(2007 Feb)

Project membership contains a mixed group of results. There are those who have taken only a basic test placing them in Haplogroup H with HVR1 results. There are some who have extended their testing to HVR2. Many have taken the mtDNA Full Genome Sequence test that includes all of the control and coding regions.

All results considered in this section come from members who have taken ether the mtDNA Haplogroup H subclade test, mt-H, or the mtDNA Full Genome Sequence test, FGS, and are positive for the H16 mutation.