Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria

Abstract

Modern European genetic structure demonstrates strong correlations with geography, while genetic analysis of prehistoric humans has indicated at least two major waves of immigration from outside the continent during periods of cultural change. However, population-level genome data that could shed light on the demographic processes occurring during the intervening periods have been absent. Therefore, we generated genomic data from 41 individuals dating mostly to the late 5th/early 6th century AD from present-day Bavaria in southern Germany, including 11 whole genomes (mean depth 5.56×). In addition we developed a capture array to sequence neutral regions spanning a total of 5 Mb and 486 functional polymorphic sites to high depth (mean 72×) in all individuals. Our data indicate that while men generally had ancestry that closely resembles modern northern and central Europeans, women exhibit a very high genetic heterogeneity; this includes signals of genetic ancestry ranging from western Europe to East Asia. Particularly striking are women with artificial skull deformations; the analysis of their collective genetic ancestry suggests an origin in southeastern Europe. In addition, functional variants indicate that they also differed in visible characteristics. This example of female-biased migration indicates that complex demographic processes during the Early Medieval period may have contributed in an unexpected way to shape the modern European genetic landscape. Examination of the panel of functional loci also revealed that many alleles associated with recent positive selection were already at modern-like frequencies in European populations ∼1,500 years ago.

Keywords: Early Medieval; Migration Period; demographic inference; paleogenomics; population genetics.

Fig. 1.

(A) Investigated skulls with strong (Left, AED_1108) intermediate, (Middle, STR_220), and no (Right, AED_92) skull deformation. (B) Location of archaeological sites from which genomes were analyzed (n = 41) on a map of Europe with today’s borders of Germany and the former borders of the western (green) and the eastern (light brown) Roman Empire. Bavarian sample sites (black square) are shown in the Inset. Sites in detail (number of deformed/nondeformed skulls): Altenerding (3/7), Alteglofsheim (1/0), Altheim (0/4), Barbing-Irlmauth (1/1), Burgweinting (1/1), and Straubing (3/9). Five additional individuals from Straubing were defined as intermediate. In addition, reference sites are given with which the Bavarian, Medieval genome data were compared: FN_2 (Freiham near Munich, ∼300 AD), deformed skull VIM_2 (Viminacium in Serbia, ∼550 AD), deformed skull KER_1 (Kerch on the Crimea, 256–401 cal AD), and two Sarmatians PR_4 and PR_10 (Pokrovka in southern Russia, 5th–2nd century BC).

Fig. 2.

Procrustes-transformed PCA of ancient samples using pseudohaploid calls based on off-target reads using an imputed POPRES modern reference dataset. Blue, green, and red male or female symbols are ancient Bavarian individuals with normal, intermediate, and elongated skulls, respectively. Orange circles are Anglo-Saxon era individuals. Large circles are medians for regions, dots are individuals. CE, central Europe; EE, eastern Europe; NE, northern Europe; NEE, northeastern Europe; NEW, northwestern Europe; SE, southern Europe; SEE, southeast Europe; WE, western Europe. Percentage of variation explained by PCs 1 and 2 for modern populations only is 0.25% and 0.15%.

Fig. 3.

Supervised model-based clustering ADMIXTURE analysis for ancient samples based on phased haplotypes for individual 1,000 bp loci from the 5-Mb neutralome. Analysis is based on the best of 100 runs for K = 8, but NC_EUR is the ancestry summed across 1000 Genomes CEU, 1000 Genomes GBR, and GoNL populations (i.e., it represents a northern/central European ancestry). Blue, green, and red male or female symbols are ancient Bavarian individuals with normal, intermediate, and elongated skulls, respectively.

Fig. 4.

Geographic distribution of population assignment analysis (PAA) results on pseudohaploid calls from off-target reads summed across individuals for (A) all Bavarian males, (B) all Bavarian females with normal skulls, (C) all Bavarian females with elongated skulls, and (D) KER_1 and VIM_2.