Maternal contacts across the Baltic Sea – thousands of mitogenomes reveal maternal genetic structure and recent expansions in the CircumBaltic region
Hovhannes Sahakyan1*, Maere Reidla1, Ene Metspalu1, Ivan A. Kuznetsov2, Rodrigo Flores2, Kadri Irdt Rezzakioğlu1, Olga Utevska1,3, Ajai K. Pathak1,4, Raimonds Rescenko-Krums5, Vita Rovite5, Janis Klovins5, Adam Ameur6,7, Ulf Gyllensten6,7, Estonian Biobank research team8, Anne-Mai Ilumäe1*
1Estonian Biocentre, Institute of Genomics, University of Tartu, Estonia; 2Institute of Genomics, University of Tartu, Estonia; 3Genetics and Cytology Department, V.N. Karazin Kharkiv National University, Ukraine; 4Department of Human Genetics, KU Leuven, Belgium; 5Latvian Biomedical Research and Study Centre, Latvia; 6Department of Immunology Genetics and Pathology, Uppsala University, Sweden, 7Science for Life Laboratory, Uppsala University, Sweden; 8Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia
Background: Present-day European mitochondrial diversity has been interpreted as relatively homogenous, reflecting Mesolithic postglacial expansions from glacial refugia. In contrast, Y-chromosomal diversity shows evidence of pronounced Neolithic bottlenecks and Bronze Age expansions involving a limited number of successful patrilineages.
Study question: To resolve fine-scale maternal demographic history in the Circum-Baltic region.
Methods: We assembled a large dataset comprising more than 9,000 complete mitogenomes from six Circum-Baltic populations and integrated ~5,000 additional phylogenetically related mitogenomes from published sources. Using these sequences, we reconstructed maximum-parsimony phylogenetic trees, identified high-frequency terminal branches and estimated their coalescence ages within the Bayesian phylogenetic analysis framework.
Main results: Maternal diversity in the Circum-Baltic region was substantially shaped by Bronze and Iron Age demographic processes. Temporal changes in maternal effective population size revealed distinct demographic trajectories across populations, with Sweden showing a pronounced decline during the Bronze Age, followed by a steep rise in the late Iron Age. We uncovered elevated sharing of matrilineages between Estonia and Finland, pointing to a maternal genetic component underlying their linguistic affinity that had previously been attributed primarily to shared paternal history. Phylogenetic links in several
subclades suggest long-distance east–west interactions across the East European Forest Belt, involving Bronze Age populations in the forest-steppe contact zones near the Ural Mountains.
Limitations: Limited representation of populations from the Eastern European Plain and the southern Baltic region.
Wider implications: Large population-based mitogenome datasets are essential to resolve fine-scale maternal demographic structure and distinguish population-specific maternal histories, complementing insights from paternal lineages.