East Europe in the 12th Century
Black labels mark Russian princedoms which transformed later into the Grand Duchy of Moscow. The map is used by permission of Vladimir Nikolaev (www.ostu.ru/personal/nikolaev). Asterisks designate locations of the present-day populations studied here. Black asterisks mark Russian populations, whereas red and green asterisks mark Ukrainian and Belorussian populations (used for comparative analysis), respectively. Numbers in black asterisks refer to , except for three northern Russian populations (1–3), established after 12th century and not placed on this map.

Location of the Studied Populations
The reliability map inventing areas where concentration of the studied Russian populations is high enough to support correct cartographic interpolation was constructed by software described in . Areas that surrounded the studied populations were estimated as more reliable, considering cumulative distance to all studied locations. Dark gray and gray zones correspond to 99% and 95% confidence space, respectively. The area with 95% probability of correct cartographic interpolation is marked by the gray line in maps at . Numbers of populations refer to .

Distribution of Y Chromosomal Haplogroups R1a, R1b, N3, and N2 in Europe
Panels are described as follows: (A), frequency distribution map of haplogroup R1a; (B), frequency distribution map of haplogroup R1b; (C), frequency distribution map of haplogroup N3; and (D), frequency distribution map of haplogroup N2. The correlogram on each map indicates results of the spatial-autocorrelation analysis of the given haplogroup distribution within the studied Russian area. The Moran's I coefficient was calculated in the PASSAGE program with binary weight matrix with five distance classes. Absciss shows the distance (in hundreds of kilometers); the longest-distance classes is wider because of less number of distant populations. Nonsignificant values are shown as empty circles; significant values are shown as black (p > 0.01) and gray (p > 0.05) circles.
Maps were created with haplogroup frequency data from this study and literature in the GGMAG program package as described in and . Because of different phylogenetic resolution levels of data from literature, not all of them were included for creating all eight maps. If source identified R1a1 and R1(xR1a1) haplogroups, they were taken for the mapmaking as R1a and R1b, respectively. Gray lines mark the studied Russian area.
Population grouping. Most of populations with sample size less than 40 were omitted or pooled. Data on the same group from the different sources with the sample sizes greater than 40 were pooled when exact localities were not specified in all sources. The map scales are different for frequent (R1a, R1b, and N3, 10% scale step) and less frequent haplogroups (the other five, 5% step); for all maps, the first interval indicates virtual absence (less than 1%). The bar graph above the scale shows the portion of the total area covered by the respective scale interval. Abbreviations in the statistical legend indicate the following: K, number of the studied populations; n, number of samples in K populations; and MIN, MEAN, and MAX, the minimal, mean and maximum frequencies on the map.

Distribution of Y Chromosomal Haplogroups I1a, I1b, J2, and E3b in Europe
(A) Frequency distribution map of haplogroup I1a.
(B) Frequency distribution map of haplogroup I1b.
(C) Frequency distribution map of haplogroup E3b.
(D) Frequency distribution map of haplogroup J2.

Synthetic Maps of the Russian Gene Pool
The synthetic maps were constructed from the correlation matrix as described in . Maps A and B are based on frequencies of eight haplogroups in 14 Russian populations; data are from .
(A) The first synthetic map of the Y chromosomal variation. The interpolated frequency distribution maps of individual haplogroups were created, and then the principal components (synthetic maps) were calculated from these interpolated distributions.
(B) The map of the first principal component of the Y chromosomal variation. The principal components were calculated from the raw data in Statistica 6.0 software, and then the values were interpolated so that the map was obtained. Comparing maps A and B allowed an estimation of possible artifacts caused in the map A by the initial interpolation.
(C) The first synthetic map of the classical markers variation. The map is based on frequencies of 35 alleles of 13 loci, studied on average in 39 Russian populations; data came from the Russian Gene Pool databank (see ).

MDS Plot Depicting Genetic, Y Chromosomal, Relationships between 14 Russian Populations

MDS Plot Revealing Different Patrilineal Affinities of Northern and Central-Southern Russians

MDS Plot of the Y Chromosomal Variation, Grouping Regional Subpopulations and Averaged Ethnical Populations of Europe
The aggregate set of populations (specified in the ) was used, except for Croatians (isolated island populations) and Belorussians (data of lower phylogenetic resolution). Regional subpopulations of different ethnic affiliation are marked by signs of different color and shape (small circles, triangles, and cubes) and designated by abbreviations (populations names are those published in the original papers, indicated in the ). Average values for ethnic populations are marked by large circles and bold names. The analysis was performed in Statistica 6.0 program. Axes were omitted from the plot.
Greeks: Gr1, central (Agrinion, Ioannina, Kardhitsa, and Patrai); Gr2, northern (Larisa, Serrai, Thessaloniki); Gr3, isles (Khios, Mitilini); and Gr4, Crete (Iraklion, Khania, Lasithi, Rethimnon).
Italians: I1, northern (Val di Non, Verona, Garfagnana, and Genoa); I2, central (L'Aquila, Pescara, and Avezzano); I3, southern (Benevento, Foggia, and North Gargano); I4, south-eastern (Altamura, Brindisi, Casarano, and Matera); and I5, southwestern (Cilento, Paola, and Reggio Calabria).
Germans: G1, Berlin; G2, Cologne; G3, Freiburg; G4, Greifswald; G5, Hamburg; G6, Leipzig; G7, Magdeburg; G8, Mainz; G9, Muenster; G10, Munich; and G11, Rostock.
Poles: P1, Bydgoszcz; P2, Gdansk; P3, Krakow; P4, Lublin; P5, Suwalki; P6, Szczecin; P7, Warsaw; and P8, Wroclaw.
Ukrainians: U1, Dnepr; U2, eastern; U3, Podol; and U4, western (Lvov and Ivano-Frankovsk).
Finns: F1, Northern Ostrobothnia; F2, Northern Savo; F3, southern (Southwest Finland, Hame, and Satakunta); F4, Karelia (Northern Karelia and Southern Karelia); and F5, Ostrobotnia (South Ostrobotnia and Swedish-speaking Ostrobotnia).
Swedes: S1, Vasterbotten; S2, Blekinge and Gotland; S3, Uppsala and Varmland; and S4, Skaraborg, Ostergotland, and Jonkoping.
Russians: Populations numbers as shown in and . Populations with sample sizes less than 70 were pooled (population 1 with 2, 5 with 6, 7 with 8, and 11 with 13) and marked on the plot as R1,2; R5,6; R7,8; and R11,13, respectively.
Turks: Similarly, population 1 was pooled with 2; 5 with 6; and 7 with 8, and pooled populations were marked on the plot as T1,2; T5,6; and T7,8, respectively.