Variation in the Substitution Rates among the Human Mitochondrial Haplogroup U Sublineages
| Autor: | Översti, Sanni, Palo, Jukka U. |
|---|---|
| Přispěvatelé: | Organismal and Evolutionary Biology Research Programme, Finnish Museum of Natural History, University of Helsinki, Department of Forensic Medicine |
| Rok vydání: | 2022 |
| Předmět: |
SELECTION
demography MTDNA VARIATION mitochondrial DNA DNA Mitochondrial substitution rate variation RECENT RADIATION Evolution Molecular tip-calibration Genetics time-dependence ANCIENT DNA Humans DNA Ancient Phylogeny Ecology Evolution Behavior and Systematics MUTATION-RATE GENOMES SUGGEST Fossils haplogroup U 1184 Genetics developmental biology physiology Genetic Variation Bayes Theorem EVOLUTION HUNTER-GATHERERS TIME DEPENDENCY Haplotypes MOLECULAR CLOCKS |
| Zdroj: | Genome Biology and Evolution |
| ISSN: | 1759-6653 |
| Popis: | 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 |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|