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

Show full item record



Permalink

http://hdl.handle.net/10138/346471

Citation

Översti , S & Palo , J U 2022 , ' Variation in the Substitution Rates among the Human Mitochondrial Haplogroup U Sublineages ' , Genome Biology and Evolution , vol. 14 , no. 7 , 097 . https://doi.org/10.1093/gbe/evac097

Title: Variation in the Substitution Rates among the Human Mitochondrial Haplogroup U Sublineages
Author: Översti, Sanni; Palo, Jukka U.
Contributor organization: Organismal and Evolutionary Biology Research Programme
Finnish Museum of Natural History
University of Helsinki
Department of Forensic Medicine
Date: 2022-07-02
Language: eng
Number of pages: 14
Belongs to series: Genome Biology and Evolution
ISSN: 1759-6653
DOI: https://doi.org/10.1093/gbe/evac097
URI: http://hdl.handle.net/10138/346471
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 C-14-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.
Subject: mitochondrial DNA
haplogroup U
ancient DNA
substitution rate variation
tip-calibration
time-dependence
demography
ANCIENT DNA
HUNTER-GATHERERS
MOLECULAR CLOCKS
RECENT RADIATION
TIME DEPENDENCY
GENOMES SUGGEST
MTDNA VARIATION
MUTATION-RATE
EVOLUTION
SELECTION
1184 Genetics, developmental biology, physiology
Peer reviewed: Yes
Rights: cc_by
Usage restriction: openAccess
Self-archived version: publishedVersion


Files in this item

Total number of downloads: Loading...

Files Size Format View
evac097.pdf 417.0Kb PDF View/Open

This item appears in the following Collection(s)

Show full item record