Mitochondrial Genomic Evidence of Selective Constraints in Small-Bodied Terrestrial Cetartiodactyla

Overview

Journal Animals (Basel)

Date 2024 May 25

PMID 38791652

Authors

Xuesong Mei

Xibao Wang

Xiaoyang Wu

Guangshuai Liu

Yao Chen

Shengyang Zhou

Yongquan Shang

Zhao Liu

Xiufeng Yang

Weilai Sha

Honghai Zhang

Affiliations

Soon will be listed here.

Abstract

Body size may drive the molecular evolution of mitochondrial genes in response to changes in energy requirements across species of different sizes. In this study, we perform selection pressure analysis and phylogenetic independent contrasts (PIC) to investigate the association between molecular evolution of mitochondrial genome protein-coding genes (mtDNA PCGs) and body size in terrestrial Cetartiodactyla. Employing selection pressure analysis, we observe that the average non-synonymous/synonymous substitution rate ratio (ω) of mtDNA PCGs is significantly reduced in small-bodied species relative to their medium and large counterparts. PIC analysis further confirms that ω values are positively correlated with body size (R = 0.162, = 0.0016). Our results suggest that mtDNA PCGs of small-bodied species experience much stronger purifying selection as they need to maintain a heightened metabolic rate. On the other hand, larger-bodied species may face less stringent selective pressures on their mtDNA PCGs, potentially due to reduced relative energy expenditure per unit mass. Furthermore, we identify several genes that undergo positive selection, possibly linked to species adaptation to specific environments. Therefore, despite purifying selection being the predominant force in the evolution of mtDNA PCGs, positive selection can also occur during the process of adaptive evolution.

References

Zurano J, MagalhAes F, Asato A, Silva G, Bidau C, Mesquita D . Cetartiodactyla: Updating a time-calibrated molecular phylogeny. Mol Phylogenet Evol. 2018; 133:256-262. DOI: 10.1016/j.ympev.2018.12.015. View

van der Bliek A, Sedensky M, Morgan P . Cell Biology of the Mitochondrion. Genetics. 2017; 207(3):843-871. PMC: 5676242. DOI: 10.1534/genetics.117.300262. View

Harvey J, Dong Y . Climate Change, Extreme Temperatures and Sex-Related Responses in Spiders. Biology (Basel). 2023; 12(4). PMC: 10136024. DOI: 10.3390/biology12040615. View

Shen Y, Shi P, Sun Y, Zhang Y . Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability. Genome Res. 2009; 19(10):1760-5. PMC: 2765268. DOI: 10.1101/gr.093138.109. View

Bowmaker M, Yang M, Yasukawa T, Reyes A, Jacobs H, Huberman J . Mammalian mitochondrial DNA replicates bidirectionally from an initiation zone. J Biol Chem. 2003; 278(51):50961-9. DOI: 10.1074/jbc.M308028200. View

Bjornerfeldt S, Webster M, Vila C . Relaxation of selective constraint on dog mitochondrial DNA following domestication. Genome Res. 2006; 16(8):990-4. PMC: 1524871. DOI: 10.1101/gr.5117706. View

Wang Z, Yonezawa T, Liu B, Ma T, Shen X, Su J . Domestication relaxed selective constraints on the yak mitochondrial genome. Mol Biol Evol. 2010; 28(5):1553-6. DOI: 10.1093/molbev/msq336. View

Clauset A, Erwin D . The evolution and distribution of species body size. Science. 2008; 321(5887):399-401. DOI: 10.1126/science.1157534. View

Stern D . The genetic causes of convergent evolution. Nat Rev Genet. 2013; 14(11):751-64. DOI: 10.1038/nrg3483. View

10.

Zhao B, Gao S, Zhao M, Lv H, Song J, Wang H . Mitochondrial genomic analyses provide new insights into the "missing" atp8 and adaptive evolution of Mytilidae. BMC Genomics. 2022; 23(1):738. PMC: 9628169. DOI: 10.1186/s12864-022-08940-8. View

11.

Lanfear R, Frandsen P, Wright A, Senfeld T, Calcott B . PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses. Mol Biol Evol. 2016; 34(3):772-773. DOI: 10.1093/molbev/msw260. View

12.

Blanckenhorn W . The evolution of body size: what keeps organisms small?. Q Rev Biol. 2000; 75(4):385-407. DOI: 10.1086/393620. View

13.

Talavera G, Castresana J . Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 2007; 56(4):564-77. DOI: 10.1080/10635150701472164. View

14.

Kumar V, Buragohain S, Deka P, Narayan G, Umapathy G . Non-Invasive Reproductive Hormone Monitoring in the Endangered Pygmy Hog (). Animals (Basel). 2021; 11(5). PMC: 8148191. DOI: 10.3390/ani11051324. View

15.

Montoya J, Lopez-Perez M, Ruiz-Pesini E . Mitochondrial DNA transcription and diseases: past, present and future. Biochim Biophys Acta. 2006; 1757(9-10):1179-89. DOI: 10.1016/j.bbabio.2006.03.023. View

16.

Druzhyna N, Wilson G, LeDoux S . Mitochondrial DNA repair in aging and disease. Mech Ageing Dev. 2008; 129(7-8):383-90. PMC: 2666190. DOI: 10.1016/j.mad.2008.03.002. View

17.

Zhang L, Sun K, Csorba G, Catherine Hughes A, Jin L, Xiao Y . Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats. BMC Ecol Evol. 2021; 21(1):199. PMC: 8565063. DOI: 10.1186/s12862-021-01926-2. View

18.

Wang X, Zhou S, Wu X, Wei Q, Shang Y, Sun G . High-altitude adaptation in vertebrates as revealed by mitochondrial genome analyses. Ecol Evol. 2021; 11(21):15077-15084. PMC: 8571627. DOI: 10.1002/ece3.8189. View

19.

Fennessy J, Bidon T, Reuss F, Kumar V, Elkan P, Nilsson M . Multi-locus Analyses Reveal Four Giraffe Species Instead of One. Curr Biol. 2016; 26(18):2543-2549. DOI: 10.1016/j.cub.2016.07.036. View

20.

Tomasco I, Lessa E . The evolution of mitochondrial genomes in subterranean caviomorph rodents: adaptation against a background of purifying selection. Mol Phylogenet Evol. 2011; 61(1):64-70. DOI: 10.1016/j.ympev.2011.06.014. View