Principal Component Analysis (47% of the total variance) performed considering mtDNA haplogroup frequencies of the ancient and present-day European and Near East populations.

<p>In green Neolithic populations, in pink Hunter-Gatherer groups (HG), in yellow ancient and present-day Romania groups, present-day European population in blue and present-day Near East population in orange. Interpretation based on the haplogroup frequency has been written on both PC (Absence of haplogroups D, M, C and N on one side of the first component and absence of haplogroup H on the top of the second component). PC1 represents 30% of variance and PC2 represents 17% of variance.</p

Geographic location of ten Romanian sites analyzed in the present study.

<p>(The figure has been provided by M. Rotea and T. Károly).</p

Haplotype (ht) and haplogroup (hg) mtDNA distribution resulting of the analysis of 62 ancient individuals from Romania.

<p>Haplotype (ht) and haplogroup (hg) mtDNA distribution resulting of the analysis of 62 ancient individuals from Romania.</p

Multidimensional Scaling Analysis performed by haplogroup frequencies of the ancient and present-day European and Near East populations.

<p>In green Neolithic populations, in pink hunter-gatherer groups and in yellow ancient and present-day Romanian groups, present-day European population in blue and present-day Near East population in orange. Stress: 0.07553 and RSQ: 0.99071.</p

Prehistoric samples from Romania analysed in the present study: Chronology, Cultural stages (also in Supporting Information S1 Table), Archaeological sites and Sample size (I.D.: Identification name; N analysed: Number of individuals analysed; N rep: number of individuals with reproducibility results).

<p>Prehistoric samples from Romania analysed in the present study: Chronology, Cultural stages (also in Supporting Information <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128810#pone.0128810.s009" target="_blank">S1 Table</a>), Archaeological sites and Sample size (I.D.: Identification name; N analysed: Number of individuals analysed; N rep: number of individuals with reproducibility results).</p

Additional file 1: Table S1. of Genetic affinities among the historical provinces of Romania and Central Europe as revealed by an mtDNA analysis

Contains the detailed description of mitochondrial molecular data of the 714 Romanian sample in the present study. (XLSX 103 kb

Additional file 7: Figure S2. of Genetic affinities among the historical provinces of Romania and Central Europe as revealed by an mtDNA analysis

Specific median networks of haplogroups U, K, M, N, W, V, X, and I. (PDF 1820 kb

Additional file 8: Figure S3. of Genetic affinities among the historical provinces of Romania and Central Europe as revealed by an mtDNA analysis

Interpolation frequency map of haplogroups H, HV, U, K, T, J, N, and W. The figure was constructed by R.C. and F.R. using the Surfer 9.0 application (Golden Software Inc., Golden, CO, USA). (PDF 24007 kb