Cardosoetal_Waorani_Suppl_S3

Female genotypes and male haplotypes for 10 X-chromosome STRs in a Waorani population sampl

Age estimates for three Franco-Cantabrian autochthonous haplogroups by using rho (r) statistics.

<p>N: number of complete mtDNA sequences used for the age estimates. Calculations were performed based on the mitogenomes from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067835#pone-0067835-g001" target="_blank">Fig. 1</a> rho: average distance to the most recent common ancestor ⁵⁶ sigma: standard error ⁵⁷.</p

Distribution map of haplogroup U5b1f within the Franco-Cantabrian region.

<p>A) Geographic locations of populations surveyed for haplogroup U5b1f (1. Guipuzcoa, 2. South-West Guipuzcoa, 3. Biscay, 4. West Biscay, 5. Alava, 6. South Alava, 7. Northern Navarre, 8. Central-West Navarre, 9. North-East Navarre, 10. North-West Navarre, 11. Lower Navarre, 12. Labourdin, 13. Soule, 14. Bearn, 15. Bigorre, 16. Chalosse, 17. La Rioja, 18. Burgos, 19. Pas Valley, 20. Cantabria, 21. Aragon, 22. Zaragoza, 23. North-East Spain, 24. Madrid and 25. Périgord-Limousin). Frequency values are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067835#pone.0067835.s004" target="_blank">Table S3</a>. B) Grayscale represents spatial variation in haplogroup frequency, with a peak between northeastern Navarre and Iparralde (French Basque Country), and a gradual decreasing trend towards the borders of the distribution. In evolutionary terms, differences in grayscale within the same geographic territory (e.g. Basque area) imply local genetic differentiation.</p

Maximum parsimony trees of haplogroups U5b, J1c and V including the three autochthonous lineages U5b1f, J1c5c1 and V22.

<p>These trees are extracted from the maximum parsimony phylogenetic tree of 76 complete mtDNA sequences of the Franco-Cantabrian region shown in detail in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067835#pone.0067835.s001" target="_blank">Fig. S1</a>. Mutations are displayed along the branches. All mutations are transitions unless a suffix specifies a transversion (A, C, G, T). Recurrent mutations within the complete phylogeny of the Franco-Cantabrian area are underlined. The prefix ‘‘@’’ indicates a back mutation. Mutational hotspot variants such as 16182, 16183, or 16519, or a variation around position 310 or 523–524, as well as length heteroplasmies were not considered for the phylogenetic reconstruction. All the samples are colored according to their geographic origin, as shown in the legend. For phylogeny construction, five previously published mitogenomes belonging to subhaplogroups U5b1f (JX286537 and DQ156208), J1c5c1 (JQ702776 and JQ704051) and V22 (HQ384212) were included (GenBank accession numbers in the tree). German ethnicity was declared for sample JX286537 in GenBank; however, maternal ancestry in southwestern Europe cannot be ruled out owing to the absence of lineage U51bf in populations outside the Franco Cantabrian area (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067835#pone.0067835.s003" target="_blank">Tables S2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067835#pone.0067835.s004" target="_blank">S3</a>). French B.C. refers to samples from the French Basque Country.</p