A major Y-chromosome haplogroup R1b Holocene era founder effect in Central and Western Europe

Abstract

The phylogenetic relationships of numerous branches within the core Y-chromosome haplogroup R-M207 support a West Asian origin of haplogroup R1b, its initial differentiation there followed by a rapid spread of one of its sub-clades carrying the M269 mutation to Europe. Here, we present phylogeographically resolved data for 2043 M269-derived Y-chromosomes from 118 West Asian and European populations assessed for the M412 SNP that largely separates the majority of Central and West European R1b lineages from those observed in Eastern Europe, the Circum-Uralic region, the Near East, the Caucasus and Pakistan. Within the M412 dichotomy, the major S116 sub-clade shows a frequency peak in the upper Danube basin and Paris area with declining frequency toward Italy, Iberia, Southern France and British Isles. Although this frequency pattern closely approximates the spread of the Linearbandkeramik (LBK), Neolithic culture, an advent leading to a number of pre-historic cultural developments during the past ≤10 thousand years, more complex pre-Neolithic scenarios remain possible for the L23(xM412) components in Southeast Europe and elsewhere.

Figure 1

(a) Phylogenetic relationships of haplogroup R binary polymorphisms studied. The names of six polymorphisms whose phylogenetic positions were determined in representative-derived samples, but not surveyed in the entire sample collection are indicated in italics. Dashed lines indicate basal haplogroup branches that were not observed. The YCC nomenclature labels reflect the exclusion of the P25 SNP from the phylogeny given its innate instability. The asterisk (^*) refers to the unresolved status of the phylogenetic haplogroups beyond the specified marker. (b) Approximate locations of the 118 studied populations appear as circles on the map that are proportional to sample sizes, the smallest n=9 and the largest n=522. (c–o). Spatial-frequency distributions of haplogroup-frequency data. Each map was obtained by applying the frequencies from Supplementary Table S4 for 10355 individuals distributed in 118 population samples that are either new or updated to the present phylogenetic-resolution level from literature (references listed in the Supplementary Table 4) plus R-M269 data from Cruciani et al for North African points. Data concerning the strong U152 founder effect signal with identical haplotypes in Northern Bashkirs is excluded from the plots. The frequency data were converted to spatial-frequency maps using Surfer software (version 7, Golden software Inc., Cold Spring Harbor, NY, USA), following the Kriging procedure.

Figure 1

(a) Phylogenetic relationships of haplogroup R binary polymorphisms studied. The names of six polymorphisms whose phylogenetic positions were determined in representative-derived samples, but not surveyed in the entire sample collection are indicated in italics. Dashed lines indicate basal haplogroup branches that were not observed. The YCC nomenclature labels reflect the exclusion of the P25 SNP from the phylogeny given its innate instability. The asterisk (^*) refers to the unresolved status of the phylogenetic haplogroups beyond the specified marker. (b) Approximate locations of the 118 studied populations appear as circles on the map that are proportional to sample sizes, the smallest n=9 and the largest n=522. (c–o). Spatial-frequency distributions of haplogroup-frequency data. Each map was obtained by applying the frequencies from Supplementary Table S4 for 10355 individuals distributed in 118 population samples that are either new or updated to the present phylogenetic-resolution level from literature (references listed in the Supplementary Table 4) plus R-M269 data from Cruciani et al for North African points. Data concerning the strong U152 founder effect signal with identical haplotypes in Northern Bashkirs is excluded from the plots. The frequency data were converted to spatial-frequency maps using Surfer software (version 7, Golden software Inc., Cold Spring Harbor, NY, USA), following the Kriging procedure.

Figure 2

Regression plots of coalescent times for S116 lineages vs distance from (a) Paris and (b) Munich. Population codes: France (fra); Germany (ger); England (eng); Switzerland (swz); Netherlands (net), Ireland (ire); Denmark (den); Italy (ita); Slovakia (slk); Sweden (swe); Greece (gre); Romania (rom); Poland (pol); Hungary (hun); Slovenia (slo).

Figure 3

Principal component analysis by haplogroup R1b sub-clades: (a) M269^*, L23, M412^*, L11^*, U106, S116^*, U152 and M529 sub-haplogroups with respect to total M269, and (b) by collapsing the 118 populations into 34 regionally defined populations. We excluded populations when the total R1b frequency was <5% or the count was less than n=5. Population codes: Austria (AUT); Belarus (BLR); Crete (CRE); Croatia (CRO); Czech Republic (CZE); Denmark (DNK); England (ENG); Estonia (EST); France (FRA); Germany (GER); Greece (GRC); Hungary (HUN); Ireland (IRL); Italy (ITA); Komis from Perm Oblast, Russia (KOM); Kosovo (KOS); Northeast Caucasus (NEC); Netherlands (NLD); Poland (POL); Portugal (PRT); Romania (ROM); Russians from Russia (RUS); Serbia (SER); Southern Bashkirs from Bashkortostan, Russia (SB); Southeastern Bashkirs from Bashkortostan, Russia (SEB); Southwestern Bashkirs from Bashkortostan, Russia (SWB); Slovakia (SVK); Slovenia (SVN); South Sweden (SSW); Spain (ESP); Switzerland (SWI); Tatars from Russia (TAT); Turkey (TUR); Ukraine (UKR).