Complete mtDNA phylogenetic tree of subhaplogroup A8.

<p>The tree is rooted in haplogroup N. Mutations are scored relative to rCRS. Four additional complete genome sequences were taken from the literature listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054360#pone.0054360.s003" target="_blank">Table S1</a>. The mutations are transitions, unless suffix (A, C, T or G) that represents the transversion is added. Insertions are marked by an “ins” and deletions are marked by “del” following the position of inserted or deleted nucleotide. Haplogroup names are in boldface. Haplotype names are in green. The mutations that are haplogroup diagnostic are listed below the haplogroup name. Branches consisting haplotypes identified in Slavic populations are highlighted in green.</p

Frequencies of the major mtDNA haplogroups in Poles, Ukrainians and Czechs.

<p>Frequencies of the major mtDNA haplogroups in Poles, Ukrainians and Czechs.</p

Complete Mitochondrial DNA Analysis of Eastern Eurasian Haplogroups Rarely Found in Populations of Northern Asia and Eastern Europe

<div><p>With the aim of uncovering all of the most basal variation in the northern Asian mitochondrial DNA (mtDNA) haplogroups, we have analyzed mtDNA control region and coding region sequence variation in 98 Altaian Kazakhs from southern Siberia and 149 Barghuts from Inner Mongolia, China. Both populations exhibit the prevalence of eastern Eurasian lineages accounting for 91.9% in Barghuts and 60.2% in Altaian Kazakhs. The strong affinity of Altaian Kazakhs and populations of northern and central Asia has been revealed, reflecting both influences of central Asian inhabitants and essential genetic interaction with the Altai region indigenous populations. Statistical analyses data demonstrate a close positioning of all Mongolic-speaking populations (Mongolians, Buryats, Khamnigans, Kalmyks as well as Barghuts studied here) and Turkic-speaking Sojots, thus suggesting their origin from a common maternal ancestral gene pool. In order to achieve a thorough coverage of DNA lineages revealed in the northern Asian matrilineal gene pool, we have completely sequenced the mtDNA of 55 samples representing haplogroups R11b, B4, B5, F2, M9, M10, M11, M13, N9a and R9c1, which were pinpointed from a massive collection (over 5000 individuals) of northern and eastern Asian, as well as European control region mtDNA sequences. Applying the newly updated mtDNA tree to the previously reported northern Asian and eastern Asian mtDNA data sets has resolved the status of the poorly classified mtDNA types and allowed us to obtain the coalescence age estimates of the nodes of interest using different calibrated rates. Our findings confirm our previous conclusion that northern Asian maternal gene pool consists of predominantly post-LGM components of eastern Asian ancestry, though some genetic lineages may have a pre-LGM/LGM origin.</p> </div

Complete mtDNA phylogenetic tree of haplogroup H6.

<p>The schematic tree is based on phylogenetic tree presented on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054360#pone.0054360.s002" target="_blank">Figure S2</a>. Time estimates (in kya) shown for mtDNA subclades are based on the complete genome substitutions <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054360#pone.0054360-Soares2" target="_blank">[42]</a>. The circle size is proportional to the number of individuals sharing the haplotype. Geographical origin is indicated by different colours: green - central and eastern Europe (Czech Republic, Poland, Russia, Slovakia, Ukraine); yellow – southern Europe (Italy, Spain); red – western Europe (Austria, Germany, Netherlands); blue – northern Europe (Denmark, Finland, Ireland, United Kingdom, Orkney Islands); black – Near East (Israel, Jordan); grey – America (Philadelphia); white - unknown origin.</p

Complete mtDNA phylogenetic tree of subhaplogroups L.

<p>The tree is rooted in haplogroup L0. Mutations are scored relative to rCRS. The mutations are transitions, unless suffix (A, C, T or G) that represents the transversion is added. Insertions are marked by an “ins” and deletions are marked by “del” following the position of inserted or deleted nucleotide. Haplogroup names are in boldface. Haplotype names are in green. The mutations that are haplogroup diagnostic are listed below the haplogroup name. Complete mitochondrial genome sequences taken from the literature are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054360#pone.0054360.s003" target="_blank">Table S1</a>. Branches consisting haplotypes identified in Slavic populations are highlighted in green.</p

Complete mtDNA phylogenetic tree of haplogroup H5.

<p>The schematic tree is based on phylogenetic tree presented on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054360#pone.0054360.s001" target="_blank">Figure S1</a>. Time estimates (in kya) shown for mtDNA subclades are based on the complete genome substitutions <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054360#pone.0054360-Soares2" target="_blank">[42]</a>. The circle size is proportional to the number of individuals sharing the haplotype. Geographical origin is indicated by different colours: green - central and eastern Europe (Czech Republic, Poland, Russia, Slovakia, Ukraine); yellow – southern Europe (Italy, Spain); red – western Europe (Austria, Germany, Netherlands); blue – northern Europe (Denmark, Finland, Ireland, United Kingdom, Orkney Islands); violet – Africa (Tunisia); black – Near East (Israel, Jordan); pink – southern Caucasus (Armenia, Georgia); grey – America (Philadelphia); white - unknown origin.</p

MDS plot based on FST statistics calculated from mtDNA HVS1 sequences for population samples from northern, eastern, central and western Asia.

<p>Linguistic affiliation of populations is indicated by different colors: Turkic group of Altaic family – in red, Mongolic group of Altaic family – in yellow, Tungusic group of Altaic family – in green, Northern group of Chukotko-Kamchatkan family – in blue, Indo-Iranian group of Indo-European family – in purple, Chinese group of Sino-Tibetan family – in grey, language isolate – in black.</p

Diversity indices and neutrality tests for the studied populations based on HVS1 variability data.

a<p>Sample size.</p>b<p>Sequence diversity (H) and standard error (SE).</p>c<p>Number of different haplotypes and percentage of sample size in parentheses.</p>d<p>Number of segregating sites.</p>e<p>Average number of pairwise differences (Pi) with standard error (SE).</p>f<p>All P values are <0.05 (for Tajima's D) and <0.02 for Fu's F_S), except where noted.</p

Complete mtDNA phylogenetic tree of haplogroup B4'B5.

<p>This schematic tree is based on phylogenetic tree presented in Figure S1. Time estimates (in kya) shown for mtDNA subclusters are based on the coding region substitutions <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032179#pone.0032179-Perego1" target="_blank">[11]</a>, coding region synonymous substitutions <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032179#pone.0032179-Soares1" target="_blank">[19]</a> and complete genome substitutions <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032179#pone.0032179-Soares1" target="_blank">[19]</a>. The size of each circle is proportional to the number of individuals sharing the corresponding haplotype, with the smallest size corresponding to one individual. Geographical origin is indicated by different colors: northern Asian – in blue, central Asian – in pink, eastern Asian – in red, Indian – in grey, European – in white, Mainland southeastern Asian - in orange, Island southeastern Asian – in yellow, Oceania – in green, and Native American – in purple.</p

Multiple Cox regression model for prediction major adverse cardiac events (MACE: the composite of acute coronary syndrome, stent thrombosis and cardiac death).

<p>HTPR: high on treatment platelet reactivity.</p