The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers

Abstract

The Neolithic transition was a dynamic time in European prehistory of cultural, social, and technological change. Although this period has been well explored in central Europe using ancient nuclear DNA [1, 2], its genetic impact on northern and eastern parts of this continent has not been as extensively studied. To broaden our understanding of the Neolithic transition across Europe, we analyzed eight ancient genomes: six samples (four to ∼1- to 4-fold coverage) from a 3,500 year temporal transect (∼8,300-4,800 calibrated years before present) through the Baltic region dating from the Mesolithic to the Late Neolithic and two samples spanning the Mesolithic-Neolithic boundary from the Dnieper Rapids region of Ukraine. We find evidence that some hunter-gatherer ancestry persisted across the Neolithic transition in both regions. However, we also find signals consistent with influxes of non-local people, most likely from northern Eurasia and the Pontic Steppe. During the Late Neolithic, this Steppe-related impact coincides with the proposed emergence of Indo-European languages in the Baltic region [3, 4]. These influences are distinct from the early farmer admixture that transformed the genetic landscape of central Europe, suggesting that changes associated with the Neolithic package in the Baltic were not driven by the same Anatolian-sourced genetic exchange.

Keywords: Baltic; Neolithic transition; Ukraine; ancient DNA; genomics; population genetics.

Figure 1

Geographic Location and Chronologies for Latvian and Ukrainian Sites Radiocarbon dates (in cal BP) are shown under the sample name. Mean genome coverage is shown in yellow squares, mitochondrial haplogroups in blue squares, and Y chromosome haplogroups for male samples (where discernible) in magenta squares. The chronology of the Latvian site of Zvejnieki is adapted from [21]. The Ukrainian chronology is taken from [18, 22, 23].

Figure 2

PCA and ADMIXTURE Analysis for Ancient Latvian and Ukrainian Samples (A) Ancient data presented in this study as well as published ancient data (see Data S1 for sample details) were projected onto the first two principal components defined by selected modern Eurasians from the Human Origins dataset (see the Supplemental Experimental Procedures). Our Latvian Mesolithic samples cluster tightly together between western and eastern hunter-gatherers in PCA space, whereas the Latvian Neolithic samples are more variable in their position, suggesting impacts from exogenous populations. The Ukrainian Mesolithic and Neolithic samples fall close together between western and eastern hunter-gatherers, suggesting a degree of continuity across the Mesolithic-Neolithic boundary in this region. (B) ADMIXTURE ancestry components (K = 17) [25] for ancient samples showing that the Latvian Neolithic samples do not have the yellow component that dominates in Anatolian and early European farmers. The Latvian and Ukrainian samples presented in this study are displayed in a gray box and at twice the height of the other ancient samples for ease of visualization. The arrow shows an Estonian Bronze Age sample (RISE00) [26] that has a yellow component, suggesting that an early European farmer genetic influence had arrived in the Baltic by the Bronze Age. HG, hunter-gatherer; BA, Bronze Age; W, western; C, Central. See also Figures S1–S4.