Variation in the Substitution Rates among the Human Mitochondrial Haplogroup U Sublineages

Abstract

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.

Keywords: ancient DNA; demography; haplogroup U; mitochondrial DNA; substitution rate variation; time-dependence; tip-calibration.

Fig. 1.

Distribution of the mean values of ¹⁴C dates among the ancient samples per subhaplogroups. Bolded bars within boxes display median values and boxes represent upper and lower quartiles. Whiskers illustrate the lowest and highest values whereas circles show the outliers.

Fig. 2.

Schematic illustration of different data sets used in three distinct scenarios. (A) Blue = analysis containing only aDNA sequences, (B) orange = analysis containing aDNA sequences and contemporary sequences, and (C) green = analysis containing aDNA sequences, contemporary sequences, and R-outgroup.

Fig. 3.

Molecular rates for the different haplogroups under scenarios A, B, and C. Scenario A: only aDNA sequences, scenario B: aDNA sequences and contemporary sequences, and scenario C: aDNA sequences, contemporary sequences, and R-outgroup. Distributions represent 95% highest posterior density of the molecular rates (ucld.Mean). All values are ×10⁻⁸ substitutions/site/year. For detailed information see supplementary table S5, Supplementary Material online.