Detailed Tree of U5b3 in the Context of Haplogroup U5
The tree includes 52 complete mtDNA sequences and illustrates sub-haplogroup affiliations. The position of the revised Cambridge reference sequence (rCRS) 51 is indicated for reading off sequence motifs. MtDNAs were selected through a preliminary sequence analysis of the control region and an RFLP survey in order to include the widest possible range of internal variation of haplogroup U5b3. The sequencing procedure and phylogeny construction were performed as described elsewhere. 4,14,15 Sequences 1–9, 13–14, 18–19, 21, 24–52 are new while the others have been previously reported (Table S1). Mutations are shown on the branches; they are transitions unless a base is explicitly indicated. The prefix “@” designates reversions, whereas suffixes indicate: transversions (to A, G, C, or T), indels (+, d), gene locus (∼t, tRNA; ∼r, rRNA; ∼nc, noncoding region outside of the control region), synonymous or nonsynonymous changes (s or ns), and heteroplasmies (R, Y). Recurrent mutations are underlined. The variation in number of Cs at np 309 was not included in the phylogeny: sequences 2, 4–5, 24, 30, 34–38, 47–49, 51–52 harbored 309+C, whereas sequence 50 harbored 309+CC. Additional information regarding each mtDNA is available on Table S1. Time estimates shown for clades are averaged distance (ρ) of each haplotype with respect to the respective root. The first value has been obtained by considering one coding-region substitution every 4610 years, whereas the second one assumes 7650 years per synonymous transition.

Spatial Frequency Distribution of Haplogroup U5b3 and Geographical Locations of Populations Surveyed
Populations and corresponding frequency values are listed in Table S2.

Median-Joining Network of HVS-I Haplotypes Observed in 152 U5b3 mtDNAs
Eighty-three mtDNAs are from the literature and a subset of these (N = 32) were not included in the population frequency table (Table S2) because population sample sizes were undefined. We constructed the tree by using the Network 4.510 software program (http://www.fluxus-engineering.com). The numbers (plus 16000) on the connecting branches refer to the revised reference sequence 51 and indicate mutations. These are transitions unless the base change is explicitly indicated; the prefix “@” designates reversions. Mutations in italics are most likely erroneous and were disregarded in the calculation of diversity measures. The size of each circle is proportional to the haplotype frequency and geographical origins are indicated by different colors. Fifty-five mtDNAs are from Sardinia; 23 are from Italy [continental Italy (N = 20) and Sicily (N = 3)]; 17 are from Iberia [Spain (N = 11), Portugal (N = 2) and Balearic Islands (N = 4)]; 33 are from Western Europe (excluding Iberia) [Belgium (N = 1), Denmark (N = 1), England (N = 6), France (N = 4), Germany (N = 3), Iceland (N = 3), Ireland (N = 3), Netherlands (N = 2), Norway (N = 1), Scotland (N = 6), Switzerland (N = 2), and Wales (N = 1)]; 19 are from Eastern Europe [Croatia (N = 4), Bosnia (N = 2), Bulgaria (N = 1), Crete (N = 1), Czech Republic (N = 4), Estonia (N = 1), Hungary (N = 2), Montenegro (N = 1), Poland (N = 1), and Slovakia (N = 2)]; and five are “Others” [Armenia (N = 1), Iraq (N = 1), Algeria (N = 1), and Morocco (N = 2)].