Millennia of Mitochondrial Change: Tracing Haplogroup Variation in Lithuania

Background: A comprehensive temporal analysis of mtDNA haplogroup variation across Lithuanian history remains limited. This study investigates the mtDNA variation landscape during the Iron Age by comparing newly reported Iron Age individual mtDNA data with the new data from present-day Lithuanians. Methods: Remains of individuals from the Iron Age Lithuania (n = 101) were processed using standard protocols for ancient DNA processing. For the present-day Lithuanians (n = 279), whole mitogenomes were sequenced. Thirty-six polymorphic sites within the Hypervariable Region I were used for haplogroup assignment, phylogenetic and population genetic analyses. Results: Fifteen distinct haplogroups in the Iron Age and the present-day Lithuanians were identified. Haplogroup R0/H remained the most frequent across time. Haplogroups U, T, and N were prominent in the Iron Age. Haplogroups M and D were introduced after the Iron Age. Phylogenetic and population genetic analyses revealed greater mtDNA diversity in the present-day Lithuanians. Significant difference in molecular variance was observed during the Iron Age. Barring the Viking period, the Iron Age mtDNA variation matched the present-day Lithuanian and European populations. Conclusions: Our study showed that mtDNA variation over time remained stable with some random fluctuations and gained more diversity in the present-day Lithuanians.