Results: 3
1.
Most
parsimonious tree of complete Hg N1b mtDNA sequences. The tree
encompasses the two complete Ashkenazi N1b sequences and one previously
published sequence (Maca-Meyer et al. 2001). The same considerations
detailed in figure 1 are relevant here. Nucleotide positions 11928 and
12092 (bold) were examined in all N1b mtDNAs.
2.
The location of the three Ashkenazi lineages (light blue)
belonging to Hg K in a global set of complete K sequences. For the
network construction, first, a topology network encompassing the 91
branches found in the total set of 121 complete K sequences was drawn
using the same principles described in figure 1. For simplicity, we used
only one complete mtDNA sequence per node, and we indicate only the
coding-region nucleotide positions that are relevant in the context of
the three Ashkenazi lineages K1a1b1a, K1a9, and K2a2a, with the
exception of positions 497, 498D, and 16524, which define K1a, K1c, and
K1a9, respectively. Branch lengths were sometimes distorted to increase
legibility. Then, the topology network was compared with a second
phylogenetic tree of the entire set of 789 K mtDNAs analyzed
hierarchically for the diagnostic mutations (red). All Jews of
North African, Caucasian, Near Eastern, and Spanish-exile ancestry were
aggregated into the category of “non-Ashkenazi Jews.” Likewise, all
non-Jewish samples from Anatolia, the Caucasus, central and southwestern
Asia, and the Near East were aggregated into the category of “West
Asia.” Circle sizes are proportional to the haplotype frequency in the
sample.
3.
Most
parsimonious tree of complete Hg K mtDNA sequences. The tree is rooted
in Hg U* and includes 121 mtDNAs, of which 28 are novel and 93 were
reported elsewhere (12 sequences from Finnila et al. [2001], 1 from
Maca-Meyer et al. [2001], 47 from Herrnstadt et al. [2002] [including
the control-region information that was not reported], 1 from Mishmar et
al. [2003], 28 from Coble et al. [2004], 2 from Palanichamy et al.
[2004], and 2 from Achilli et al. [2005]). The genotyping information
from Finnila et al. (2001) included herein corrects several inaccuracies
that were reported elsewhere for the control-region phylogeny.
Mutations are shown on the branches and are transitions unless the base
change is explicitly indicated. Deletions are indicated by a “D”
following the deleted nucleotide position. Insertions are indicated by a
dot followed by the number and type of inserted nucleotide(s).
Underlined nucleotide positions occur at least twice in the tree. An
asterisk (*) at the end of a nucleotide position denotes a reversion.
The information of the reported samples is presented in table 3. Samples
in blue are from Ashkenazi Jews. Nucleotide positions in red were
assayed in the entire set of 789 mtDNAs belonging to K. To resolve three
possible reticulations, reversions at nucleotide 7082 in sample A01 and
nucleotides 10398 and 11485 in sample H510 and a homoplasy at
nucleotide 7927 for subHg K1a1a and K1a8 were assumed. The tree was
drawn by hand from networks constructed using program Network 4.1.0.0.
We applied the reduced-median algorithm (ρ=2) followed by the
median-joining algorithm (ε=2), as described at the Fluxus Engineering
Web site. The control-region positions were twofold down-weighted, with
respect to coding-region positions. The hypervariable nucleotides 16182
and 16183 in HVS-I and the indels at nucleotides 309, 315, and 524 in
HVS-II were excluded. Coding-region mutations at nucleotides 750, 1438,
1811, 2706, 4769, 7028, 8860, 11467, 11719, and 12308 are not shown
unless reverted. Ethnic designation of the sequences was available for
the sequences reported by Finnila et al. (2001), Maca-Meyer et al.
(2001), Palanichamy et al. (2004), and Achilli et al. (2005), and for
the novel samples reported herein (table 3).
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