Multidimentional Scaling Analysis (MDS) plot of R_ST values from Y chromosome STR haplotype frequencies showing genetic affinities among 29 populations from eastern, central and southern Europe.

<p>The stress value for the MDS plot is 0.056. Original references, number of samples and haplotypes and name codes for all populations included in the analysis are listed in Table S3. Symbol designations are as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053731#pone-0053731-g002" target="_blank">Figure 2</a>. The ellipses are drawn around the clusters of east/central European (eastern and western Slavic) (I), southeast European (Balkan-Carpathian) (II) and Italian (III) populations. While the Cheg Albanian population is a genetic “outlier” among southeast European populations, geographically it belongs in the Balkan-Carpathian cluster (indicated by an arrow).</p

Median-joining networks showing phylogenetic relationships of the Moldavian, Romanian and Ukrainian Y-haplotypes within haplogroups I-M423 (A) and R-M17* (B).

<p>Networks were constructed from 17 STRs for haplogroup R-M17* and 15 STRs for haplogroup I-M423 as described in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053731#s2" target="_blank">Materials and Methods</a>. For each network, the smallest circles represent a count of one individual. Branch lengths are proportional to the number of mutational steps separating two haplotypes.</p

Geographical location of the samples analyzed.

<p>Geographical location of the samples analyzed.</p

PCR-RFLP protocols developed for P15, v13, U8 and M423 markers.

<p>F refers to the forward primer, and R refers to the reverse primer for a particular locus.</p>a<p>PCR annealing temperature in C°.</p>b<p>PCR product size in base pairs.</p>c<p>RFLP fragments in base pairs.</p>d<p>Mismatched primer (mismatched bases are underlined).</p

Sample size (N), haplogroup counts and diversity in the population groups studied.

a<p>The phylogeny of haplogroups is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053731#pone.0053731.s001" target="_blank">Figure S1</a>.</p><p>Relative haplogroup frequencies are given within parentheses.</p><p>H, haplogroup diversity; SD, standard deviation.</p

AMOVA calculation results for 10 Y-STRs.

a<p>Twenty nine populations (the same as in MDS analysis) were pooled into five groups defined according to ethnicity (Moldavians, Romanians, Eastern and Western Slavs, Italians) or geography (Balkans) (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053731#pone.0053731.s004" target="_blank">Table S3</a>).</p

Principal Component Analysis (PCA) plot of Y chromosome haplogroup profiles showing genetic affinities among 28 populations from eastern, central and southern Europe.

<p>Original references, number of samples and name codes for all populations included in the analysis and their haplogroup frequencies are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0053731#pone.0053731.s002" target="_blank">Table S1</a>. Moldavian populations are indicated by stars; north Mediterranian groups by diamonds; eastern and central European populations including Ukrainians from Moldova by circles, and north Balkan groups including Romanians by squares.</p

Additional file 1: Figure S1. of Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe

Quality control process. (PDF 25 kb

Additional file 3: Table S1a. of Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe

List of samples included in “Extended” dataset. Table S1b List of samples included in “Core” dataset. Table S1c List of samples included in “Ancient” dataset. Table S2 Results of ADMIXTURE for K = 9. Table S3 Results of ADMIXTURE for K = 6, 7, 8. Table S4 Results of f3 test. Table S5 Results of IBD sharing analysis in 1–3 cM and 4–10 cM bins. Table S6 Total amount of shared IBD between populations. Table S7 Standard residue of linear regression analysis of distance-IBD sharing. Table S8 Distance and shared IBD between pairs of populations. Table S9: Results of f3 outgroup test with ancient samples. (XLSX 482 kb