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Text S1.
Correlation of mtDNA haplotypes and estimates of ancestry based on autosomal data
Analyses of autosomal SNP data of Tuscans were carried out in Pardo-Seco et al. ADDIN EN.CITE Pardo-Seco20144545[1]4545454517Pardo-Seco, J.Gmez-Carballa, A.Amigo, J.Martinn-Torres, F.Salas, A.A genome-wide study of modern-day Tuscans: revisiting Herodotuss theory on the origin of the EtruscansPLoS OnePLoS Onee105920992014[ HYPERLINK \l "_ENREF_1" \o "Pardo-Seco, 2014 #4545" 1]. Here we just correlate Tuscan mtDNA haplotypes and their haplogroup adscription with the membership ancestry estimates of these Tuscans in Near East and Europe. As explained in Pardo-Seco et al. ADDIN EN.CITE Pardo-Seco20144545[1]4545454517Pardo-Seco, J.Gmez-Carballa, A.Amigo, J.Martinn-Torres, F.Salas, A.A genome-wide study of modern-day Tuscans: revisiting Herodotuss theory on the origin of the EtruscansPLoS OnePLoS Onee105920992014[ HYPERLINK \l "_ENREF_1" \o "Pardo-Seco, 2014 #4545" 1], the CEU SNP dataset from The 1000 Genome Project (representing a population of European ancestry) and the Near East SNP data published by Behar et al. ADDIN EN.CITE Behar20041052[2]1052105217Behar, D. M.Hammer, M. F.Garrigan, D.Villems, R.Bonne-Tamir, B.Richards, M.Gurwitz, D.Rosengarten, D.Kaplan, M.Della Pergola, S.Quintana-Murci, L.Skorecki, K.Bruce Rappaport Faculty of Medicine and Research Institute, Technion and Rambam Medical Center, Haifa, Israel.MtDNA evidence for a genetic bottleneck in the early history of the Ashkenazi Jewish populationEur J. Hum. Genet.Eur J. Hum. Genet.355-641252004May14722586http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14722586http://www.nature.com/ejhg/journal/v12/n5/pdf/5201156a.pdf[ HYPERLINK \l "_ENREF_2" \o "Behar, 2004 #1052" 2] were used as surrogate ancestral populations for admixture analysis.
The methodology used is explained in detail in Pardo-Seco et al. ADDIN EN.CITE Pardo-Seco20144545[1]4545454517Pardo-Seco, J.Gmez-Carballa, A.Amigo, J.Martinn-Torres, F.Salas, A.A genome-wide study of modern-day Tuscans: revisiting Herodotuss theory on the origin of the EtruscansPLoS OnePLoS Onee105920992014[ HYPERLINK \l "_ENREF_1" \o "Pardo-Seco, 2014 #4545" 1]. In brief, identity-by-state (IBS) values were computed from autosomal SNP data using PLINK ADDIN EN.CITE Purcell20073957[3]3957395717Purcell, S.Neale, B.Todd-Brown, K.Thomas, L.Ferreira, M. A.Bender, D.Maller, J.Sklar, P.de Bakker, P. I.Daly, M. J.Sham, P. C.Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA. shaun@pngu.mgh.harvard.eduPLINK: a tool set for whole-genome association and population-based linkage analysesAm J Hum GenetAm J Hum Genet559-758132007/08/19Genetic Linkage/*geneticsGenome, Human/*geneticsHumansPolymorphism, Single NucleotidePopulation/*genetics*Software2007Sep0002-9297 (Print)
0002-9297 (Linking)17701901http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=177019011950838S0002-9297(07)61352-4 [pii]
10.1086/519795eng[ HYPERLINK \l "_ENREF_3" \o "Purcell, 2007 #3957" 3]. ADMIXTURE software ADDIN EN.CITE Alexander20094362[4]4362436217Alexander, D. H.Novembre, J.Lange, K.Department of Biomathematics, University of California at Los Angeles, Los Angeles, California 90095, USA. dalexander@ucla.eduFast model-based estimation of ancestry in unrelated individualsGenome ResGenome researchGenome Res1655-641992009/08/04*AlgorithmsComputational BiologyEurope/ethnologyGene FrequencyGenetic Association Studies*Genetics, PopulationGenotypeHumansInflammatory Bowel Diseases/ethnology/geneticsJews/ethnologyLikelihood FunctionsModels, GeneticPolymorphism, Single Nucleotide*SoftwareTime Factors2009Sep1549-5469 (Electronic)
1088-9051 (Linking)19648217Research Support, N.I.H., Extramuralhttp://www.ncbi.nlm.nih.gov/pubmed/19648217http://genome.cshlp.org/content/19/9/1655.full.pdf275213410.1101/gr.094052.109eng[ HYPERLINK \l "_ENREF_4" \o "Alexander, 2009 #4362" 4] was used to estimate percentages of admixture in Tuscans considering Europe and Near East as the main source ancestral populations; this software uses a maximum likelihood estimation of individual ancestries from multilocus SNP data.
As shown in the Figure below, all Tuscans have a main European component (represented by CEU) that is on average 79% (95%CI: 78.7-79.4). The Near East component in Tuscans is 21% on average (95%CI: 20.6-21.3). As expected, there is no particular correlation between Tuscan mitogenomes of likely recent Near East origin and the proportion of Near East ancestry measured on the autosomes.
Figure. Ancestry estimates in Tuscan individuals as inferred from autosomal data. Admixture analysis for K = 2; see Pardo-Seco et al. ADDIN EN.CITE Pardo-Seco20144545[1]4545454517Pardo-Seco, J.Gmez-Carballa, A.Amigo, J.Martinn-Torres, F.Salas, A.A genome-wide study of modern-day Tuscans: revisiting Herodotuss theory on the origin of the EtruscansPLoS OnePLoS Onee105920992014[ HYPERLINK \l "_ENREF_1" \o "Pardo-Seco, 2014 #4545" 1] for details. Red color represents the membership ancestry that predominates in Europeans, while green represents the ancestry that is predominant in Middle East. On the right are the mtDNA haplogroup ascriptions of Tuscan haplotypes; green dots point to those mtDNA that are more likely to be of recent Middle East origin as described in the main text.
References
ADDIN EN.REFLIST 1. Pardo-Seco J, Gmez-Carballa A, Amigo J, Martinn-Torres F, Salas A (2014) A genome-wide study of modern-day Tuscans: revisiting Herodotuss theory on the origin of the Etruscans. PLoS One 9: e105920.
2. Behar DM, Hammer MF, Garrigan D, Villems R, Bonne-Tamir B, et al. (2004) MtDNA evidence for a genetic bottleneck in the early history of the Ashkenazi Jewish population. Eur J Hum Genet 12: 355-364.
3. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
4. Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19: 1655-1664.
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