The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269

Abstract

Recently, the debate on the origins of the major European Y chromosome haplogroup R1b1b2-M269 has reignited, and opinion has moved away from Palaeolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. Here, we address this debate by investigating frequency patterns and diversity in the largest collection of R1b1b2-M269 chromosomes yet assembled. Our analysis reveals no geographical trends in diversity, in contradiction to expectation under the Neolithic hypothesis, and suggests an alternative explanation for the apparent cline in diversity recently described. We further investigate the young, STR-based time to the most recent common ancestor estimates proposed so far for R-M269-related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates. As a consequence, the existing data and tools are insufficient to make credible estimates for the age of this haplogroup, and conclusions about the timing of its origin and dispersal should be viewed with a large degree of caution.

Figure 1.

Y chromosome tree showing the relationships of SNPs downstream from R-M269 tested in this study. Alternative nomenclature for some SNPs is provided in italics.

Figure 2.

Frequency distributions and variation of Y chromosome haplogroups R-M269, R-S127 and R-M269(xS127) in Europe. The three panels show contour maps based on the frequencies of the different haplogroups found across Europe and western Asia: (a) R-M269, (b) R-S127 and (c) R-M269(xS127). The maps on the left are based on the frequencies of the SNPs in all populations marked on the map (data in electronic supplementary material, table S1 and figure S1). The graphs on the right show the relationship between longitude and bootstrap variance based on 10 STRs for all populations with at least 10 individuals carrying that SNP. The R² and associated p-values are shown for the correlations in the graphs. The population codes are detailed in table 1 and electronic supplementary material, table S1.

Figure 3.

Frequency distributions of R-M269 sub-haplogroups. Contour maps for lineages defined by marker (a) R-S21, (b) R-S145 and (c) R-S28.

Figure 4.

Relationship between time to the most recent common ancestor, T, and mutation rate, μ, for various STR subsets. (a) Estimates of T for the R-S127 haplogroup. Points are labelled with the subset of STRs used to calculate T and are detailed in electronic supplementary material, table S4. (b) The same data, but this time together with estimates of T based on comparisons of Y chromosome A and B haplogroups (see main text).