Extensive farming in Estonia started through a sex-biased migration from the Steppe

The transition from hunting and gathering to farming in Europe was brought upon by arrival of new people carrying novel material culture and genetic ancestry. The exact nature and scale of the transition – both material and genetic – varied in different parts of Europe. Farming-based economies appear relatively late in Northeast Europe and the extent to which they involve change in genetic ancestry is not fully understood due to the lack of relevant ancient DNA data. Here we present the results from new low coverage whole genome shotgun sequence data from five hunter-gatherers and five first farmers of Estonia whose remains date to 4,500 to 6,300 years before present. We find evidence of significant differences between the two groups in the composition of autosomal as well as mtDNA, X and Y chromosome ancestries. We find that Estonian hunter-gatherers of Comb Ceramic Culture are closest to Eastern hunter-gatherers, which is in contrast to earlier hunter-gatherers from the Baltics who are close to Western hunter-gatherers. The Estonian first farmers of Corded Ware Culture show high similarity in their autosomes with European hunter-gatherers, Steppe Eneolithic and Bronze Age populations, and European Late Neolithic/Bronze Age populations while their X chromosomes are in addition equally closely related to European and Anatolian/Levantine early farmers. These findings suggest that the shift to intensive cultivation and animal husbandry in Estonia was triggered by the arrival of new people with predominantly Steppe ancestry, but whose ancestors had undergone sex-specific admixture with early farmers with Anatolian ancestry. IDs: MA825 – Sope_d MA826 – Sope_r MA968 – Ardu1_d MA969 – Ardu2 MA971 – Kunila1 MA973 – Kunila2 MA974 – Kudruküla2 MA975 – Kudruküla3 MA976 – Ardu1_r DNA sequencing: DNA was sequenced using the Illumina HiSeq 2500 platform with the 100 bp single-end method. All samples were first sequenced together on one lane, one sample (Sope_r) became part of a Bronze Age project The Rise (Allentoft et al. 2015) and was therefore sequenced many times, and 7 other samples from different individuals with endogenous DNA content over 1% were sequenced further on 8 lanes. Mapping: Before mapping, all sequence files from one sample were merged, the sequences of adaptors and indexes were cut from the ends of DNA sequences using Trimmomatic 0.32 with the option ILLUMINACLIP. Sequences shorter than 30 bp were also removed with the option MINLEN to avoid random mapping of sequences from other species. The sequences were mapped to reference sequence GRCh37 using Burrows-Wheeler Aligner (BWA) and command aln. Additional steps: After mapping, the sequences were prepared for analyses by first converting them to SAM format with BWA command samse. Then the sequences were converted to BAM format, sequences that mapped to the reference sequence were sorted out, and PCR duplicates were removed, all of which was done with samtools 0.1.19.