H2: Phylogenetic Trees

mtDNA 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.

Tree diagrams using the mt-H test follow FamilyTreeDNA's nomenclature for that test.

Fluxus is a phylogenetic tree program designed for the creation of network diagrams. The following are median joining network diagrams. Coding region mutations are given a weight of twenty. Insertions and deletions are given a weight of one. All other control region mutations are given a weight of 10. Mutation points are yellow. Nodes that connect multiple possible paths are red. The GenBank sequence AF346980 is used as an outlier.

Its final mutation is shown in blue.

The first tree is constructed using member's hypervariable region one, HVR1, results. The H1 samples available on April 5, 2008 are used.

Next the backbone positioning of each sequence is added.

The next set of tree diagrams are constructed using member's hypervariable region one, HVR1, results. The 223 H1 samples available on March 30, 2008 are used.

Next the backbone positioning of each sequence is added.

Finally mtDNA Full Genome Sequences from the project and GenBank are used.

These are the GenBank sequences.

These are the project sequences.

This is a tree diagram showing both GenBank and project sequences.

• Median-joining networks for inferring intraspecific phylogenies.
  Bandelt HJ, Forster P, Röhl A
  Mol Biol Evol16p37-48(1999 Jan)