Abstract
Due to their integral roles in oxidative phosphorylation, mitochondrially encoded proteins represent common targets of selection in response to altitudinal hypoxia across high-altitude taxa. While previous studies revealed evidence of positive selection on mitochondrial genomes of high-altitude Phrynocephalus lizards, their conclusions were restricted by out-of-date phylogenies and limited taxonomic sampling. Using topologies derived from both nuclear and mitochondrial DNA phylogenies, we re-assessed the evidence of positive selection on the mitochondrial genomes of high-altitude Phrynocephalus. We sampled representative species from all four main lineages and sequenced the mitochondrial genome of P. maculatus, a putative sister taxon to the high-altitude group. Positive selection was assessed through two widely used branch-site tests: the branch-site model in PAML and BUSTED in HyPhy. No evidence of positive selection on mitochondrial genes was detected on branches leading to two most recent common ancestors of high-altitude species; however, we recovered evidence of positive selection on COX1 on the P. forsythii branch, which represents a reversal from high- to low-elevation environments. A positively selected site therein marked a threonine to valine substitution at position 419. We suggest this bout of selection occurred as the ancestors of P. forsythii re-colonized lower altitude environments north of the Tibetan Plateau. Despite their role in oxidative phosphorylation, we posit that mitochondrial genes are unlikely to have represented historical targets of selection for high-altitude adaptation in Phrynocephalus. Consequently, future studies should address the roles of nuclear genes and differential gene expression.
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Data Availability
All sequences generated in this study have been deposited in GenBank (Accession Number: MW007749).
Abbreviations
- OXPHOS:
-
Oxidative phosphorylation
- nuDNA:
-
Nuclear DNA
- mtDNA:
-
Mitochondrial DNA
- MRCA:
-
Most recent common ancestor
- bp:
-
Base pairs
- dN:
-
Nonsynonymous substitution
- dS:
-
Synonymous substitution
- LRT:
-
Likelihood ratio test
- BEB:
-
Bayes Empirical Bayes
- P b :
-
Posterior probability
- PROVEAN:
-
Protein Variation Effect Analyzer
- ND:
-
NADH Dehydrogenase
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Acknowledgements
We thank Dr. Daniel Melnikov for providing tissue samples, Sarah Ouellet for her contributions to the initial stages of lab work, and Dr. Teresa J. Crease for her thoughtful comments on the early manuscript drafts. Sequencing was conducted at the AAC Genomics Facility at the University of Guelph.
Funding
This project is funded by Natural Sciences and Engineering Research Council of Canada (NSERC Canada) (Discovery Grant Number 400479 to JF).
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JEA contributed lab work, statistical analyses and drafted the manuscript. JF designed the study, contributed lab work, and edited the manuscript. Both authors read and approved the final manuscript.
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All animal utility protocols are approved by the Animal Care Committee of the University of Guelph (AUP#3886).
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Atlas, J.E., Fu, J. A Re-Assessment of Positive Selection on Mitochondrial Genomes of High-Elevation Phrynocephalus Lizards. J Mol Evol 89, 95–102 (2021). https://doi.org/10.1007/s00239-020-09991-9
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DOI: https://doi.org/10.1007/s00239-020-09991-9