Maximum parsimony tree of available HV4a1a control region sequences (HVS-I sequence motif: C16221T-C16291T).

<p>This tree includes the ones inferred from the complete genomes considered in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032851#pone-0032851-g001" target="_blank">Figure 1</a>. The area of the circles is proportional to the sample size. Population codes (within circles) are as follows: Iberia: CA = Cantabria (central-northern), CL = Castile León (north-central), BC = Basque Country (central-northern), CM = Castile La Mancha (north-central), AR = Aragón (north-central, GA = Galicia (north-western), AS = Asturias (north-central), NA = Navarra (north-central), France: FR = France, MT = Martinique; Canada: CN = Canada, GP = Gaspesia (south-east), AC = Acadia (south-east), LY = Loyalists (south-east), TI = Prince Edward Island, Tignish (south-east), IT = Italy; GB = Great Britain, RL = Ireland, USA = United States of America, NW = Norway; DN = Denmark; AF = Afghanistan.</p

Map of Europe showing the frequency distribution of haplogroup HV4a1a.

<p>Blue crosses represent the location of the sampling points (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032851#pone.0032851.s001" target="_blank">Table S1</a> for more information). Arrows represent a tentative reconstruction of the pre-historical and historical movements of HV4 and its sub-lineages across Europe and America. The scale indicates the absolute frequency of the HV4a1a mtDNAs in the regions sampled.</p

Molecular divergences and age estimates (Maximum Likelihood and ρ Statistics) for HV4 and its sub-clades.

<p>Delta T indicates the standard deviation computed using the two different age estimation methods.</p>a<p>number of complete mtDNA sequences.</p>b<p>using the corrected molecular clock proposed by Soares et al. (2009) for complete mtDNA genomes which is 0.0074±0.00019 substitutions per site.</p

Maximum parsimony tree of entire mtDNA genomes belonging to haplogroup HV4.

<p>The mutations are displayed along the branches. The position of the revised Cambridge reference sequence (rCRS) is indicated for reading off sequence motifs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032851#pone.0032851-Andrews1" target="_blank">[15]</a>. All mutations are transitions unless a suffix specifies a transversion (A, C, G, T), an insertion (+), a synonymous substitution (s), a mutational change in tRNA (-t), a mutational change in rRNA (-r), a non-coding variant located in the mtDNA coding region (-nc) or an amino acid replacement (indicated in round brackets). Recurrent mutations within the phylogeny are underlined. The prefix “@” indicates a back mutation. Mutational hotspot variants such as 16182, 16183, or 16519, or a variation around position 310 and length or point heteroplasmies were not considered for the phylogenetic reconstruction. Divergence times correspond to the ML estimates reported in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0032851#pone-0032851-t001" target="_blank">Table 1</a>. Population codes (blue squares on top of circles) for the Cantabrian region: BC = Basque Country, CA = Cantabria, AS = Asturias, GA = Galicia, TE = Teruel, VA = Valladolid, SE = Segovia, GU = Guadalajara; FR = France; NA = Navarra.</p

The First Peopling of South America: New Evidence from Y-Chromosome Haplogroup Q

<div><p>Recent progress in the phylogenetic resolution of the Y-chromosome phylogeny permits the male demographic dynamics and migratory events that occurred in Central and Southern America after the initial human spread into the Americas to be investigated at the regional level. To delve further into this issue, we examined more than 400 Native American Y chromosomes (collected in the region ranging from Mexico to South America) belonging to haplogroup Q – virtually the only branch of the Y phylogeny observed in modern-day Amerindians of Central and South America – together with 27 from Mongolia and Kamchatka. Two main founding lineages, Q1a3a1a-M3 and Q1a3a1-L54(xM3), were detected along with novel sub-clades of younger age and more restricted geographic distributions. The first was also observed in Far East Asia while no Q1a3a1-L54(xM3) Y chromosome was found in Asia except the southern Siberian-specific sub-clade Q1a3a1c-L330. Our data not only confirm a southern Siberian origin of ancestral populations that gave rise to Paleo-Indians and the differentiation of both Native American Q founding lineages in Beringia, but support their concomitant arrival in Mesoamerica, where Mexico acted as recipient for the first wave of migration, followed by a rapid southward migration, along the Pacific coast, into the Andean region. Although Q1a3a1a-M3 and Q1a3a1-L54(xM3) display overlapping general distributions, they show different patterns of evolution in the Mexican plateau and the Andean area, which can be explained by local differentiations due to demographic events triggered by the introduction of agriculture and associated with the flourishing of the Great Empires.</p></div

Estimated Ages for Q Sub-Lineages in Native Americans.

<p>SE, Standard Errors.</p>a<p>excluding samples with duplicated loci and micro-variants (partial repeats).</p>b<p>including PV4, 24.3±3.4 without PV4.</p>c<p>including PV4, 23.7±3.7 without PV4.</p>d<p>including or excluding PV2.</p>e<p>one sample from this study and five from the YRHD database.</p>f<p>DYS388 and DYS461 were not genotyped.</p

PCoA plots.

<p>Analyses were performed on 433 Native American haplogroup Q Y chromosomes and based on pairwise, individual-by-individual genetic distances generated from 33 <i>loci</i> Y-STR haplotypes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071390#pone.0071390.s002" target="_blank">Table S2</a>) represented in their (A) geographic (<u>Andes</u>: Bolivia, Chile, Colombia, Ecuador, Peru; <u>C</u>entral <u>America</u>: Costa Rica, El Salvador, Guatemala, Nicaragua, Panama; <u>S</u>outh <u>E</u>ast <u>America</u>: Argentina, Brazil, Paraguay, Uruguay) and (B) sub-haplogroup Q contexts. Ancient DNA (aDNA) matching haplotypes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071390#pone.0071390-Baca1" target="_blank">[75]</a> are indicated by arrows. Three separated (Central American, Mexican and Andean) clusters are indicated by ovals.</p

Observed Frequencies of Haplogroup Q and of its Sub-Lineages.

a<p>Marker described here for the first time.</p>b<p>Grouping due to sample size <10 in single populations. <u>C</u>entral <u>American Isthmus</u>: El Salvador, Guatemala and Honduras; <u>N</u>orthern <u>S</u>outh<u> America</u>: Colombia, Ecuador, Venezuela; <u>S</u>outhern <u>S</u>outh <u>America</u>: Argentina and Paraguay; <u>The Caribbeans</u>: Barbados, Bermuda, Cuba, Dominican Rep., French Guiana, Grenada, Haiti, Jamaica, Martinique.</p><p>The following mutations were surveyed in all potential carrier samples but they were not observed: NTW01, M323, L401 and M19. M199 was only typed in a subset of samples.</p><p>In parentheses, % frequencies.</p

Y-Chromosome Diversity in Modern Bulgarians: New Clues about Their Ancestry

<div><p>To better define the structure and origin of the Bulgarian paternal gene pool, we have examined the Y-chromosome variation in 808 Bulgarian males. The analysis was performed by high-resolution genotyping of biallelic markers and by analyzing the STR variation within the most informative haplogroups. We found that the Y-chromosome gene pool in modern Bulgarians is primarily represented by Western Eurasian haplogroups with ∼ 40% belonging to haplogroups E-V13 and I-M423, and 20% to R-M17. Haplogroups common in the Middle East (J and G) and in South Western Asia (R-L23*) occur at frequencies of 19% and 5%, respectively. Haplogroups C, N and Q, distinctive for Altaic and Central Asian Turkic-speaking populations, occur at the negligible frequency of only 1.5%. Principal Component analyses group Bulgarians with European populations, apart from Central Asian Turkic-speaking groups and South Western Asia populations. Within the country, the genetic variation is structured in Western, Central and Eastern Bulgaria indicating that the Balkan Mountains have been permeable to human movements. The lineage analysis provided the following interesting results: (i) R-L23* is present in Eastern Bulgaria since the post glacial period; (ii) haplogroup E-V13 has a Mesolithic age in Bulgaria from where it expanded after the arrival of farming; (iii) haplogroup J-M241 probably reflects the Neolithic westward expansion of farmers from the earliest sites along the Black Sea. On the whole, in light of the most recent historical studies, which indicate a substantial proto-Bulgarian input to the contemporary Bulgarian people, our data suggest that a common paternal ancestry between the proto-Bulgarians and the Altaic and Central Asian Turkic-speaking populations either did not exist or was negligible.</p> </div

Haplogroup affiliation and non-synonymous nucleotide changes of mtDNAs from LHON and control cybrid and fibroblast cell lines used in this study.

a<p>rCRS refers to the revised Cambridge reference sequence <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007922#pone.0007922-Andrews1" target="_blank">[58]</a>. In addition, all mtDNAs differed from rCRS, which belongs to haplogroup H2a, for A8860G (<i>ATP6</i>) and A15326G (<i>CYTB</i>).</p>b<p>This fibroblast cell line is from the same patient and harbours the same mtDNA as cybrid HL180.</p