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Resolving the absolute timescale of phylogenetic trees stipulates reliable estimates for the rate of DNA sequence evolution. For this end, various calibration methods have been developed and studied intensively. Intraspecific rate variation among distinct genetic lineages, however, has gained less attention. Here, we have assessed lineage-specific molecular rates of human mitochondrial DNA (mtDNA) by performing tip-calibrated Bayesian phylogenetic analyses. Tip-calibration, as opposed to traditional nodal time stamps from dated fossil evidence or geological events, is based on sample ages and becoming ever more feasible as ancient DNA data from radiocarbon-dated samples accumulate. We focus on subhaplogroups U2, U4, U5a, and U5b, the data including ancient mtDNA genomes from 14C-dated samples (n = 234), contemporary genomes (n = 301), and two outgroup sequences from haplogroup R. The obtained molecular rates depended on the data sets (with or without contemporary sequences), suggesting time-dependency. More notable was the rate variation between haplogroups: U4 and U5a stand out having a substantially higher rate than U5b. This is also reflected in the divergence times obtained (U5a: 17,700 years and U5b: 29,700 years), a disparity not reported previously. After ruling out various alternative causes (e.g., selection, sampling, and sequence quality), we propose that the substitution rates have been influenced by demographic histories, widely different among populations where U4/U5a or U5b are frequent. As with the Y-chromosomal subhaplogroup R1b, the mitochondrial U4 and U5a have been associated with remarkable range extensions of the Yamnaya culture in the Bronze Age. Introduction Results - MtDNA Haplogroup U Genomes - Substitution Models Chosen - Molecular Rate Estimates - Dependability of the Rate Estimates - Comparison of Divergence Time Estimates with Previously Published Estimates Discussion - Time-Dependency Shown With Different Data Sets - Lineage-Specificity in Mutation Rates - Other Potential Causes for Rate Variation among Lineages - Different Demographic Trajectories of Hg-U Sublineages - Range Expansion a Plausible Explanation for Higher U5a Rate Conclusion Materials and Methods - Data Analysis Methods

Human ancient DNA studies have revealed high mobility in Europe’s past, and have helped to decode the human history on the Eurasian continent. Northeastern Europe, especially north of the Baltic Sea, however, remains less well understood largely due to the lack of preserved human remains. Finland, with a divergent population history from most of Europe, offers a unique perspective to hunter-gatherer way of life, but thus far genetic information on prehistoric human groups in Finland is nearly absent. Here we report 103 complete ancient mitochondrial genomes from human remains dated to AD 300–1800, and explore mtDNA diversity associated with hunter-gatherers and Neolithic farmers. The results indicate largely unadmixed mtDNA pools of differing ancestries from Iron-Age on, suggesting a rather late genetic shift from hunter-gatherers towards farmers in North-East Europe. Furthermore, the data suggest eastern introduction of farmer-related haplogroups into Finland, contradicting contemporary genetic patterns in Finns. Results - Authenticity of ancient-DNA results. - Radiocarbon datings. - MtDNA data and haplotypic variation. - MtDNA haplogroup composition at the ancient sites. - Differences in haplogroup composition between the sites. - Genetic distances among sites and to contemporary Finns. - Main haplogroup frequencies in space and time. - Genetic affinities of ancient Finns to other ancient and contemporary populations. Discussion - Genetic layers of mitochondrial variation among the Iron Age and Medieval Finns. - The ancient distribution of mtDNA lineages contradicts the contemporary east-west divergence. - Bidirectional expansion of agriculturally oriented populations into Finland?. Materials and methods - Sample selection. - Reference populations used in comparative analyses. - Sampling. - Extraction of ancient DNA. - Mitochondrial capture and sequencing. - Processing of the sequence data. - Authentication of ancient DNA and haplogroup assignments. - Radiocarbon dating. - Statistical analyses.