Abstract
<title>Abstract</title> <p>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 strong Neolithic bottlenecks and Bronze Age expansions involving a limited number of successful patrilineages. However, fine-scale maternal demographic patterns have remained unresolved due to small sample sizes and insufficient phylogenetic resolution. Results We assembled a large dataset of 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 phylogenetic trees, identified high-frequency terminal branches and estimated their coalescence ages in three Circum-Baltic populations. We identified numerous rare clades that contributed to the rapid increase in maternal effective population size over the past 2,500 years. 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 male lineages. Phylogenetic links in several subclades suggest long-distance east–west interactions across the East European Forest Belt, involving ancient populations in the forest-steppe contact zones near the Ural Mountains. Conclusions Maternal diversity in the Circum-Baltic region was substantially shaped by Bronze and Iron Age demographic processes. Large population-based mitogenome datasets are essential to resolve fine-scale maternal demographic structure and distinguish population-specific histories.</p>