Total Pageviews

Wednesday, September 5, 2012

mtDNA Haplogroup H5a1

Today, I want show some data about mtDNA haplogroup H5a1 because there is a Kurdish individual with H5a1 in this Kurdish DNA project.

I analyzed the phylogeny of this haplogroup by using fully sequenced and published mtDNA data from GenBank.

To do so I first downloaded the data from GenBank, then I used CLUSTALW, (mode: slow accurate pairwise alignment) to align the sequences and create a rooted phylogenetic tree with branch length (UPGMA). The data were pasted into CLUSTALW in the Fasta format.

I realized that all the data of Herrnstadt et al. 2002 are lacking the first 577 nucleotides, which is messing up the position of Herrnstadt samples in the trees/network and is messing up the position of the rest. The same effect can be seen with the two samples of Kivisild et al.; they are lacking 236 nucleotides. Thus, I excluded these samples.


Rooted phylogenetic tree with branth length (UPGMA) of H5a1:


The nice thing about CLUSTALW is that it also generates a "dnd file" and an "aln file" of the alignment.

The dnd file can be opened with the Figtree software. In Figtree, I generated another tree of H5a1:



The aln file can be opened with the Splitstree software. In Splitstree4, I generated a network (Convex Hull) of H5a1:

H5a1a (T721C mutation): three individuals in these trees have this mutation [AF346975(Dutch) Ingman; Q983087(Italy) Santoro; HQ659693(Polish) FTDNA]


H5a1b (G11719A mutation): two individuals in these trees have this mutation [AY495167(European) Coble; AY495176(European) Coble]

H5a1c1a (C4095T  G13194A G9055A A2851G mutations): only one individual in these trees has these mutations [HQ663878(Danish) FTDNA]

H5a1d (A8803D mutation): only one individual in these trees has this mutation [AY495171(European) Coble]

H5a1e (A16166G mutation): two individuals from Finland belong to the H5a1e branch [AY339431(Finland) Moilanen; AY339432(Finland) Moilanen].

H5a1f (T961C mutation): one individual in these trees has this mutation [ JN646689(Polish) FTDNA]

H5a1g1 (T16172C, A444G, G9804A, T16311C mutations): two individuals in these trees have these mutations [EU294323 FTDNA; HQ645111(English) FTDNA]. Since HQ645111 has the additional  T1284C and A7517G mutations it belongs to H5a1g1a.

Note: In the Finland DNA project I found one individual (N48161 Mary Anne Bodle, b.1791, Plumstead, Kent) that originated in England and has the same mutations of H5a1g1 HV regions, i.e.  A444G, T16172C, T16311C.

H5a1k (T12864C): two individuals have this mutation [AY495170(European) Coble, GQ983064(Italy) Santoro]


H5a1p (T16093C): three individuals have this mutation [FJ966912 FTDNA, GQ983075(Italy) Santoro, GQ983084(Italy) Santoro]



3 comments:

  1. There are now several h5a1d on ftdna in h5 group. Ireland/England before 1700ish

    ReplyDelete
  2. There are now several h5a1d on ftdna in h5 group. Ireland/England before 1700ish

    ReplyDelete
  3. My father's mother a Fitzgerald is h5a1d tested by virtue of her daughters and grand daughters.
    My research indicates Gerald de Windsor and Nesta Verch Rhys born ca. 1085 – died after 1136 daughter of Rhys ap Tewdwr king of Deheubarth, Wales born ca. 1040 died at the battle of Brecon in April 1093 and Gwladys ferch Rhiwallon are the progenitors of the Fitzgeralds (Irish).

    ReplyDelete