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Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing
Published on: February 10, 2023
Mitochondrial Genome Evolution: The Influence of Partitioning, Calibration, and Gene Heterogeneity on Pleurodontan
Matheus M A Salles1, Fabricius M C B Domingos2
1Departamento de Zoologia, Setor de Ciências Biológicas, Programa de Pós-Graduação em Zoologia, Universidade Federal do Paraná, Centro Politécnico, Avenida Cel. Francisco H Santos, Jardim das Américas, Curitiba, PR, 81531-980, Brazil. matheusmaciel.salles@gmail.com.
Journal of Molecular Evolution
|May 30, 2026
Summary
Estimating mitochondrial DNA substitution rates is crucial for evolutionary biology. This study reveals rate heterogeneity across the mitochondrial genome and highlights how partitioning and modeling choices impact estimates, offering a framework for improved molecular dating.
Area of Science:
- Evolutionary Biology
- Molecular Evolution
- Genomics
Background:
- Substitution rate estimates are fundamental for inferring evolutionary timescales and macroevolutionary patterns.
- Mitochondrial DNA (mtDNA) substitution rates are frequently used but often based on limited data or taxa.
- Understanding rate variation across the mitochondrial genome is essential for accurate evolutionary analyses.
Purpose of the Study:
- To estimate substitution rates across the entire mitochondrial genome in 27 pleurodontan species.
- To evaluate the impact of data partitioning, calibration strategies, and model specification on rate estimates.
- To provide a robust empirical framework for improving molecular dating and evolutionary inference in squamates.
Main Methods:
- Bayesian phylogenetic analyses using nearly complete mitogenomes from 27 pleurodontan species.
- Explicit evaluation of different data partitioning schemes (e.g., codon positions, coding/non-coding regions).
- Comparison of calibrated versus non-calibrated analyses and various model specifications.
Main Results:
- Pronounced heterogeneity in substitution rates was observed among codon positions and genomic regions.
- Estimated rates varied from 0.004 to 0.02 substitutions per site per million years.
- Partitioning and modeling choices significantly influence substitution rate estimates, with potential trade-offs between parameter resolution and data informativeness.
Conclusions:
- Mitochondrial DNA substitution rate estimates are sensitive to analytical choices, particularly data partitioning and model selection.
- Calibrated analyses generally produced lower rates but showed overlap with non-calibrated methods.
- The study provides partition-specific rate estimates and emphasizes evaluating model complexity based on data informativeness for robust evolutionary inference.
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