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Tao M, Chen J, Cui C, Xu Y, Xu J, Shi Z, Yun J, Zhang J, Ou GZ, Liu C, Chen Y, Zhu ZR, Pan R, Xu S, Chen XX, Rokas A, Zhao Y, Wang S, Huang J, Shen XX. Identification of a longevity gene through evolutionary rate covariation of insect mito-nuclear genomes. NATURE AGING 2024:10.1038/s43587-024-00641-z. [PMID: 38834883 DOI: 10.1038/s43587-024-00641-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 05/02/2024] [Indexed: 06/06/2024]
Abstract
Oxidative phosphorylation, essential for energy metabolism and linked to the regulation of longevity, involves mitochondrial and nuclear genes. The functions of these genes and their evolutionary rate covariation (ERC) have been extensively studied, but little is known about whether other nuclear genes not targeted to mitochondria evolutionarily and functionally interact with mitochondrial genes. Here we systematically examined the ERC of mitochondrial and nuclear benchmarking universal single-copy ortholog (BUSCO) genes from 472 insects, identifying 75 non-mitochondria-targeted nuclear genes. We found that the uncharacterized gene CG11837-a putative ortholog of human DIMT1-regulates insect lifespan, as its knockdown reduces median lifespan in five diverse insect species and Caenorhabditis elegans, whereas its overexpression extends median lifespans in fruit flies and C. elegans and enhances oxidative phosphorylation gene activity. Additionally, DIMT1 overexpression protects human cells from cellular senescence. Together, these data provide insights into the ERC of mito-nuclear genes and suggest that CG11837 may regulate longevity across animals.
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Affiliation(s)
- Mei Tao
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China
- Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou, China
| | - Jiani Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chunlai Cui
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yandong Xu
- Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Hangzhou, China
| | - Jingxiu Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Zheyi Shi
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiaqi Yun
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Junwei Zhang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guo-Zheng Ou
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chao Liu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zeng-Rong Zhu
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ronghui Pan
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Suhong Xu
- Zhejiang University School of Medicine, Hangzhou, China
| | - Xue-Xin Chen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Antonis Rokas
- Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Yang Zhao
- Zhejiang University School of Medicine, Hangzhou, China
- Zhejiang Provincial Key Lab of Genetic and Developmental Disorders, Hangzhou, China
| | - Sibao Wang
- New Cornerstone Science Laboratory, CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
| | - Jianhua Huang
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, China.
- Centre for Evolutionary and Organismal Biology, Zhejiang University, Hangzhou, China.
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2
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Zhang D, Jakovlić I, Zou H, Liu F, Xiang CY, Gusang Q, Tso S, Xue S, Zhu WJ, Li Z, Wu J, Wang GT. Strong mitonuclear discordance in the phylogeny of Neodermata and evolutionary rates of Polyopisthocotylea. Int J Parasitol 2024; 54:213-223. [PMID: 38185351 DOI: 10.1016/j.ijpara.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/03/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
The genomic evolution of Polyopisthocotylea remains poorly understood in comparison to the remaining three classes of Neodermata: Monopisthocotylea, Cestoda, and Trematoda. Moreover, the evolutionary sequence of major events in the phylogeny of Neodermata remains unresolved. Herein we sequenced the mitogenome and transcriptome of the polyopisthocotylean Diplorchis sp., and conducted comparative evolutionary analyses using nuclear (nDNA) and mitochondrial (mtDNA) genomic datasets of Neodermata. We found strong mitonuclear discordance in the phylogeny of Neodermata. Polyopisthocotylea exhibited striking mitonuclear discordance in relative evolutionary rates: the fastest-evolving mtDNA in Neodermata and a comparatively slowly-evolving nDNA genome. This was largely attributable to its very long stem branch in mtDNA topologies, not exhibited by the nDNA data. We found indications that the fast evolution of mitochondrial genomes of Polyopisthocotylea may be driven both by relaxed purifying selection pressures and elevated levels of directional selection. We identified mitochondria-associated genes encoded in the nuclear genome: they exhibited unique evolutionary rates, but not correlated with the evolutionary rate of mtDNA, and there is no evidence for compensatory evolution (they evolved slower than the rest of the genome). Finally, there appears to exist an exceptionally large (≈6.3 kb) nuclear mitochondrial DNA segment (numt) in the nuclear genome of newly sequenced Diplorchis sp. A 3'-end segment of the 16S rRNA gene encoded by the numt was expressed, suggesting that this gene acquired novel, regulatory functions after the transposition to the nuclear genome. In conclusion, Polyopisthocotylea appears to be the lineage with the fastest-evolving mtDNA sequences among all of Bilateria, but most of the substitutions were accumulated deep in the evolutionary history of this lineage. As the nuclear genome does not exhibit a similar pattern, the circumstances underpinning this evolutionary phenomenon remain a mystery.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; College of Ecology, Lanzhou University, Lanzhou 730000, China.
| | - Ivan Jakovlić
- College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Fei Liu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; Institute of Aquatic Sciences, Tibet Academy of Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa 850032, China
| | - Chuan-Yu Xiang
- College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Qunzong Gusang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Sonam Tso
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Shenggui Xue
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Wen-Jin Zhu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Zhenxin Li
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China
| | - Jihua Wu
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Gui-Tang Wang
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibetan Plateau, Ministry of Education, School of Ecology and Environment, Tibet University, Lhasa 850011, China; Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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3
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Kang N, Hu H. Adaptive evidence of mitochondrial genes in Pteromalidae and Eulophidae (Hymenoptera: Chalcidoidea). PLoS One 2023; 18:e0294687. [PMID: 37988339 PMCID: PMC10662703 DOI: 10.1371/journal.pone.0294687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
Pteromalidae and Eulophidae are predominant and abundant taxa within Chalcidoidea (Hymenoptera: Apocrita). These taxa are found in diverse ecosystems, ranging from basin deserts (200 m) to alpine grasslands (4500 m). Mitochondria, cellular powerhouses responsible for energy production via oxidative phosphorylation, are sensitive to various environmental factors such as extreme cold, hypoxia, and intense ultraviolet radiation characteristic of alpine regions. Whether the molecular evolution of mitochondrial genes in these parasitoids corresponds to changes in the energy requirements and alpine environmental adaptations remains unknown. In this study, we performed a comparative analysis of mitochondrial protein-coding genes from 11 alpine species of Pteromalidae and Eulophidae, along with 18 lowland relatives, including 16 newly sequenced species. We further examined the codon usage preferences (RSCU, ENC-GC3s, neutrality, and PR2 bias plot) in these mitochondrial protein-coding sequences and conducted positive selection analysis based on their Bayesian phylogenetic relationships, and identified positive selection sites in the ATP6, ATP8, COX1, COX3, and CYTB genes, emphasizing the crucial role of mitochondrial gene adaptive evolution in the adaptation of Pteromalidae and Eulophidae to alpine environments. The phylogenetically independent contrast (PIC) analysis results verified the ω ratio of 13 PCGs from Pteromalidae and Eulophidae increased with elevation, and results from generalized linear model confirm that ATP6, ATP8, COX3, and ND1 are closely correlated with temperature-related environmental factors. This research not only enriched the molecular data of endemic alpine species but also underscores the significance of mitochondrial genes in facilitating the adaptation of these minor parasitoids to plateau habitats.
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Affiliation(s)
- Ning Kang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science & Technology, Xinjiang University, Xinjiang, P.R.China
| | - Hongying Hu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science & Technology, Xinjiang University, Xinjiang, P.R.China
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4
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Iannello M, Forni G, Piccinini G, Xu R, Martelossi J, Ghiselli F, Milani L. Signatures of Extreme Longevity: A Perspective from Bivalve Molecular Evolution. Genome Biol Evol 2023; 15:evad159. [PMID: 37647860 PMCID: PMC10646442 DOI: 10.1093/gbe/evad159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/04/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023] Open
Abstract
Among Metazoa, bivalves have the highest lifespan disparity, ranging from 1 to 500+ years, making them an exceptional testing ground to understand mechanisms underlying aging and the evolution of extended longevity. Nevertheless, comparative molecular evolution has been an overlooked approach in this instance. Here, we leveraged transcriptomic resources spanning 30 bivalve species to unravel the signatures of convergent molecular evolution in four long-lived species: Margaritifera margaritifera, Elliptio complanata, Lampsilis siliquoidea, and Arctica islandica (the latter represents the longest-lived noncolonial metazoan known so far). We applied a comprehensive approach-which included inference of convergent dN/dS, convergent positive selection, and convergent amino acid substitution-with a strong focus on the reduction of false positives. Genes with convergent evolution in long-lived bivalves show more physical and functional interactions to each other than expected, suggesting that they are biologically connected; this interaction network is enriched in genes for which a role in longevity has been experimentally supported in other species. This suggests that genes in the network are involved in extended longevity in bivalves and, consequently, that the mechanisms underlying extended longevity are-at least partially-shared across Metazoa. Although we believe that an integration of different genes and pathways is required for the extended longevity phenotype, we highlight the potential central roles of genes involved in cell proliferation control, translational machinery, and response to hypoxia, in lifespan extension.
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Affiliation(s)
- Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Giobbe Forni
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Giovanni Piccinini
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Ran Xu
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Jacopo Martelossi
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
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5
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Lynch M. Mutation pressure, drift, and the pace of molecular coevolution. Proc Natl Acad Sci U S A 2023; 120:e2306741120. [PMID: 37364099 PMCID: PMC10319038 DOI: 10.1073/pnas.2306741120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 05/09/2023] [Indexed: 06/28/2023] Open
Abstract
Most aspects of the molecular biology of cells involve tightly coordinated intermolecular interactions requiring specific recognition at the nucleotide and/or amino acid levels. This has led to long-standing interest in the degree to which constraints on interacting molecules result in conserved vs. accelerated rates of sequence evolution, with arguments commonly being made that molecular coevolution can proceed at rates exceeding the neutral expectation. Here, a fairly general model is introduced to evaluate the degree to which the rate of evolution at functionally interacting sites is influenced by effective population sizes (Ne), mutation rates, strength of selection, and the magnitude of recombination between sites. This theory is of particular relevance to matters associated with interactions between organelle- and nuclear-encoded proteins, as the two genomic environments often exhibit dramatic differences in the power of mutation and drift. Although genes within low Ne environments can drive the rate of evolution of partner genes experiencing higher Ne, rates exceeding the neutral expectation require that the former also have an elevated mutation rate. Testable predictions, some counterintuitive, are presented on how patterns of coevolutionary rates should depend on the relative intensities of drift, selection, and mutation.
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Affiliation(s)
- Michael Lynch
- Center for Mechanisms of Evolution, Biodesign Institute, Arizona State University, Tempe, AZ85287
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6
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Smith CH, Pinto BJ, Kirkpatrick M, Hillis DM, Pfeiffer JM, Havird JC. A tale of two paths: The evolution of mitochondrial recombination in bivalves with doubly uniparental inheritance. J Hered 2023; 114:199-206. [PMID: 36897956 PMCID: PMC10212130 DOI: 10.1093/jhered/esad004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/19/2023] [Indexed: 03/12/2023] Open
Abstract
In most animals, mitochondrial DNA is strictly maternally inherited and non-recombining. One exception to this pattern is called doubly uniparental inheritance (DUI), a phenomenon involving the independent transmission of female and male mitochondrial genomes. DUI is known only from the molluskan class Bivalvia. The phylogenetic distribution of male-transmitted mitochondrial DNA (M mtDNA) in bivalves is consistent with several evolutionary scenarios, including multiple independent gains, losses, and varying degrees of recombination with female-transmitted mitochondrial DNA (F mtDNA). In this study, we use phylogenetic methods to test M mtDNA origination hypotheses and infer the prevalence of mitochondrial recombination in bivalves with DUI. Phylogenetic modeling using site concordance factors supported a single origin of M mtDNA in bivalves coupled with recombination acting over long evolutionary timescales. Ongoing mitochondrial recombination is present in Mytilida and Venerida, which results in a pattern of concerted evolution of F mtDNA and M mtDNA. Mitochondrial recombination could be favored to offset the deleterious effects of asexual inheritance and maintain mitonuclear compatibility across tissues. Cardiida and Unionida have gone without recent recombination, possibly due to an extension of the COX2 gene in male mitochondrial DNA. The loss of recombination could be connected to the role of M mtDNA in sex determination or sexual development. Our results support that recombination events may occur throughout the mitochondrial genomes of DUI species. Future investigations may reveal more complex patterns of inheritance of recombinants, which could explain the retention of signal for a single origination of M mtDNA in protein-coding genes.
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Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - Brendan J Pinto
- Center for Evolutionary Medicine & Public Health, Arizona State University, Tempe, AZ, United States
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - David M Hillis
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - John M Pfeiffer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - Justin C Havird
- Department of Integrative Biology, University of Texas, Austin, TX, United States
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7
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Princepe D, de Aguiar MAM, Plotkin JB. Mito-nuclear selection induces a trade-off between species ecological dominance and evolutionary lifespan. Nat Ecol Evol 2022; 6:1992-2002. [PMID: 36216905 DOI: 10.1038/s41559-022-01901-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 09/02/2022] [Indexed: 12/15/2022]
Abstract
Mitochondrial and nuclear genomes must be co-adapted to ensure proper cellular respiration and energy production. Mito-nuclear incompatibility reduces individual fitness and induces hybrid infertility, which can drive reproductive barriers and speciation. Here, we develop a birth-death model for evolution in spatially extended populations under selection for mito-nuclear co-adaptation. Mating is constrained by physical and genetic proximity, and offspring inherit nuclear genomes from both parents, with recombination. The model predicts macroscopic patterns including a community's species diversity, species abundance distribution, speciation and extinction rates, as well as intraspecific and interspecific genetic variation. We explore how these long-term outcomes depend upon the parameters of reproduction: individual fitness governed by mito-nuclear compatibility, constraints on mating compatibility and ecological carrying capacity. We find that strong selection for mito-nuclear compatibility reduces the equilibrium number of species after a radiation, increasing species' abundances and simultaneously increasing both speciation and extinction rates. The negative correlation between species diversity and diversification rates in our model agrees with the broad empirical pattern of lower diversity and higher speciation/extinction rates in temperate regions, compared to the tropics. We conclude that these empirical patterns may be caused in part by latitudinal variation in metabolic demands and corresponding variation in selection for mito-nuclear function.
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Affiliation(s)
- Débora Princepe
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Campinas, Brazil.
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Marcus A M de Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas, Campinas, Brazil
| | - Joshua B Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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8
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Weaver RJ, Rabinowitz S, Thueson K, Havird JC. Genomic Signatures of Mitonuclear Coevolution in Mammals. Mol Biol Evol 2022; 39:6775223. [PMID: 36288802 PMCID: PMC9641969 DOI: 10.1093/molbev/msac233] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial (mt) and nuclear-encoded proteins are integrated in aerobic respiration, requiring co-functionality among gene products from fundamentally different genomes. Different evolutionary rates, inheritance mechanisms, and selection pressures set the stage for incompatibilities between interacting products of the two genomes. The mitonuclear coevolution hypothesis posits that incompatibilities may be avoided if evolution in one genome selects for complementary changes in interacting genes encoded by the other genome. Nuclear compensation, in which deleterious mtDNA changes are offset by compensatory nuclear changes, is often invoked as the primary mechanism for mitonuclear coevolution. Yet, direct evidence supporting nuclear compensation is rare. Here, we used data from 58 mammalian species representing eight orders to show strong correlations between evolutionary rates of mt and nuclear-encoded mt-targeted (N-mt) proteins, but not between mt and non-mt-targeted nuclear proteins, providing strong support for mitonuclear coevolution across mammals. N-mt genes with direct mt interactions also showed the strongest correlations. Although most N-mt genes had elevated dN/dS ratios compared to mt genes (as predicted under nuclear compensation), N-mt sites in close contact with mt proteins were not overrepresented for signs of positive selection compared to noncontact N-mt sites (contrary to predictions of nuclear compensation). Furthermore, temporal patterns of N-mt and mt amino acid substitutions did not support predictions of nuclear compensation, even in positively selected, functionally important residues with direct mitonuclear contacts. Overall, our results strongly support mitonuclear coevolution across ∼170 million years of mammalian evolution but fail to support nuclear compensation as the major mode of mitonuclear coevolution.
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Affiliation(s)
- Ryan J Weaver
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA.,Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA
| | | | - Kiley Thueson
- Department of Integrative Biology, University of Texas, Austin, TX
| | - Justin C Havird
- Department of Integrative Biology, University of Texas, Austin, TX
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9
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Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks. Sci Rep 2022; 12:11040. [PMID: 35773462 PMCID: PMC9247169 DOI: 10.1038/s41598-022-15076-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/17/2022] [Indexed: 11/08/2022] Open
Abstract
Mito-nuclear phylogenetic discordance in Bivalvia is well known. In particular, the monophyly of Amarsipobranchia (Heterodonta + Pteriomorphia), retrieved from mitochondrial markers, contrasts with the monophyly of Heteroconchia (Heterodonta + Palaeoheterodonta), retrieved from nuclear markers. However, since oxidative phosphorylation nuclear markers support the Amarsipobranchia hypothesis instead of the Heteroconchia one, interacting subunits of the mitochondrial complexes ought to share the same phylogenetic signal notwithstanding the genomic source, which is different from the signal obtained from other nuclear markers. This may be a clue of coevolution between nuclear and mitochondrial genes. In this work we inferred the phylogenetic signal from mitochondrial and nuclear oxidative phosphorylation markers exploiting different phylogenetic approaches and added two more datasets for comparison: genes of the glycolytic pathway and genes related to the biogenesis of regulative small noncoding RNAs. All trees inferred from mitochondrial and nuclear subunits of the mitochondrial complexes support the monophyly of Amarsipobranchia, regardless of the phylogenetic pipeline. However, not every single marker agrees with this topology: this is clearly visible in nuclear subunits that do not directly interact with the mitochondrial counterparts. Overall, our data support the hypothesis of a coevolution between nuclear and mitochondrial genes for the oxidative phosphorylation. Moreover, we suggest a relationship between mitochondrial topology and different nucleotide composition between clades, which could be associated to the highly variable gene arrangement in Bivalvia.
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10
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Li Y, Altamia MA, Shipway JR, Brugler MR, Bernardino AF, de Brito TL, Lin Z, da Silva Oliveira FA, Sumida P, Smith CR, Trindade-Silva A, Halanych KM, Distel DL. Contrasting modes of mitochondrial genome evolution in sister taxa of wood-eating marine bivalves (Teredinidae and Xylophagaidae). Genome Biol Evol 2022; 14:evac089. [PMID: 35714221 PMCID: PMC9226539 DOI: 10.1093/gbe/evac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/19/2022] [Accepted: 06/05/2022] [Indexed: 11/14/2022] Open
Abstract
The bivalve families Teredinidae and Xylophagaidae include voracious consumers of wood in shallow and deep-water marine environments, respectively. The taxa are sister clades whose members consume wood as food with the aid of intracellular cellulolytic endosymbionts housed in their gills. This combination of adaptations is found in no other group of animals and was likely present in the common ancestor of both families. Despite these commonalities, the two families have followed dramatically different evolutionary paths with respect to anatomy, life history and distribution. Here we present 42 new mitochondrial genome sequences from Teredinidae and Xylophagaidae and show that distinct trajectories have also occurred in the evolution and organization of their mitochondrial genomes. Teredinidae display significantly greater rates of amino acid substitution but absolute conservation of protein-coding gene order, whereas Xylophagaidae display significantly less amino acid change but have undergone numerous and diverse changes in genome organization since their divergence from a common ancestor. As with many bivalves, these mitochondrial genomes encode two ribosomal RNAs, 12 protein coding genes, and 22 tRNAs; atp8 was not detected. We further show that their phylogeny, as inferred from amino acid sequences of 12 concatenated mitochondrial protein-coding genes, is largely congruent with those inferred from their nuclear genomes based on 18S and 28S ribosomal RNA sequences. Our results provide a robust phylogenetic framework to explore the tempo and mode of mitochondrial genome evolution and offer directions for future phylogenetic and taxonomic studies of wood-boring bivalves.
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Affiliation(s)
- Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Marvin A Altamia
- Ocean Genome Legacy Center, Department of Marine and Environmental Science, Northeastern University, Nahant, Massachusetts 01908, USA
| | - J Reuben Shipway
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Mercer R Brugler
- Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret Street, Beaufort, South Carolina 29902, USA
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024, USA
| | | | - Thaís Lima de Brito
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Ceará, Brazil
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA
| | | | - Paulo Sumida
- Departamento de Oceanografia Biológica, Instituto Oceanográfico da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Craig R Smith
- Department of Oceanography, University of Hawai’i at Mãnoa, Hawaii, USA
| | - Amaro Trindade-Silva
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Ceará, Brazil
| | - Kenneth M Halanych
- Center for Marine Science, University of North Carolina Wilmington, North Carolina, USA
| | - Daniel L Distel
- Ocean Genome Legacy Center, Department of Marine and Environmental Science, Northeastern University, Nahant, Massachusetts 01908, USA
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11
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Bever BW, Dietz ZP, Sullins JA, Montoya AM, Bergthorsson U, Katju V, Estes S. Mitonuclear Mismatch is Associated With Increased Male Frequency, Outcrossing, and Male Sperm Size in Experimentally-Evolved C. elegans. Front Genet 2022; 13:742272. [PMID: 35360860 PMCID: PMC8961728 DOI: 10.3389/fgene.2022.742272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
We provide a partial test of the mitonuclear sex hypothesis with the first controlled study of how male frequencies and rates of outcrossing evolve in response to mitonuclear mismatch by allowing replicate lineages of C. elegans nematodes containing either mitochondrial or nuclear mutations of electron transport chain (ETC) genes to evolve under three sexual systems: facultatively outcrossing (wildtype), obligately selfing, and obligately outcrossing. Among facultatively outcrossing lines, we found evolution of increased male frequency in at least one replicate line of all four ETC mutant backgrounds tested—nuclear isp-1, mitochondrial cox-1 and ctb-1, and an isp-1 IV; ctb-1M mitonuclear double mutant—and confirmed for a single line set (cox-1) that increased male frequency also resulted in successful outcrossing. We previously found the same result for lines evolved from another nuclear ETC mutant, gas-1. For several lines in the current experiment, however, male frequency declined to wildtype levels (near 0%) in later generations. Male frequency did not change in lines evolved from a wildtype control strain. Additional phenotypic assays of lines evolved from the mitochondrial cox-1 mutant indicated that evolution of high male frequency was accompanied by evolution of increased male sperm size and mating success with tester females, but that it did not translate into increased mating success with coevolved hermaphrodites. Rather, hermaphrodites’ self-crossed reproductive fitness increased, consistent with sexually antagonistic coevolution. In accordance with evolutionary theory, males and sexual outcrossing may be most beneficial to populations evolving from a state of low ancestral fitness (gas-1, as previously reported) and less beneficial or deleterious to those evolving from a state of higher ancestral fitness (cox-1). In support of this idea, the obligately outcrossing fog-2 V; cox-1 M lines exhibited no fitness evolution compared to their ancestor, while facultatively outcrossing lines showed slight upward evolution of fitness, and all but one of the obligately selfing xol-1 X; cox-1 M lines evolved substantially increased fitness—even beyond wildtype levels. This work provides a foundation to directly test the effect of reproductive mode on the evolutionary dynamics of mitonuclear genomes, as well as whether compensatory mutations (nuclear or mitochondrial) can rescue populations from mitochondrial dysfunction.
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Affiliation(s)
- Brent W. Bever
- Department of Biology, Portland State University, Portland, OR, United States
| | - Zachary P. Dietz
- Department of Biology, Portland State University, Portland, OR, United States
| | - Jennifer A. Sullins
- Department of Biology, Portland State University, Portland, OR, United States
| | - Ariana M. Montoya
- Department of Biology, Portland State University, Portland, OR, United States
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Suzanne Estes
- Department of Biology, Portland State University, Portland, OR, United States
- *Correspondence: Suzanne Estes,
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12
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Hénault M, Marsit S, Charron G, Landry CR. Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance. Genome Res 2022; 32:2043-2056. [PMID: 36351770 PMCID: PMC9808621 DOI: 10.1101/gr.276885.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Mitochondrial DNA (mtDNA) is a cytoplasmic genome that is essential for respiratory metabolism. Although uniparental mtDNA inheritance is most common in animals and plants, distinct mtDNA haplotypes can coexist in a state of heteroplasmy, either because of paternal leakage or de novo mutations. mtDNA integrity and the resolution of heteroplasmy have important implications, notably for mitochondrial genetic disorders, speciation, and genome evolution in hybrids. However, the impact of genetic variation on the transition to homoplasmy from initially heteroplasmic backgrounds remains largely unknown. Here, we use Saccharomyces yeasts, fungi with constitutive biparental mtDNA inheritance, to investigate the resolution of mtDNA heteroplasmy in a variety of hybrid genotypes. We previously designed 11 crosses along a gradient of parental evolutionary divergence using undomesticated isolates of Saccharomyces paradoxus and Saccharomyces cerevisiae Each cross was independently replicated 48 to 96 times, and the resulting 864 hybrids were evolved under relaxed selection for mitochondrial function. Genome sequencing of 446 MA lines revealed extensive mtDNA recombination, but the recombination rate was not predicted by parental divergence level. We found a strong positive relationship between parental divergence and the rate of large-scale mtDNA deletions, which led to the loss of respiratory metabolism. We also uncovered associations between mtDNA recombination, mtDNA deletion, and genome instability that were genotype specific. Our results show that hybridization in yeast induces mtDNA degeneration through large-scale deletion and loss of function, with deep consequences for mtDNA evolution, metabolism, and the emergence of reproductive isolation.
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Affiliation(s)
- Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada;,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, G1V 0A6, Canada;,Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université Laval, Québec, Québec, G1V 0A6, Canada;,Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, G1V 0A6, Canada
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada;,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, G1V 0A6, Canada;,Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université Laval, Québec, Québec, G1V 0A6, Canada;,Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, G1V 0A6, Canada;,Département de Biologie, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Guillaume Charron
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada;,Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université Laval, Québec, Québec, G1V 0A6, Canada;,Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, G1V 0A6, Canada;,Département de Biologie, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, G1V 0A6, Canada;,Département de Biochimie, Microbiologie et Bioinformatique, Université Laval, Québec, Québec, G1V 0A6, Canada;,Quebec Network for Research on Protein Function, Engineering, and Applications (PROTEO), Université Laval, Québec, Québec, G1V 0A6, Canada;,Université Laval Big Data Research Center (BDRC_UL), Québec, Québec, G1V 0A6, Canada;,Département de Biologie, Université Laval, Québec, Québec, G1V 0A6, Canada
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13
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Maeda GP, Iannello M, McConie HJ, Ghiselli F, Havird JC. Relaxed selection on male mitochondrial genes in DUI bivalves eases the need for mitonuclear coevolution. J Evol Biol 2021; 34:1722-1736. [PMID: 34533872 DOI: 10.1111/jeb.13931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/21/2021] [Accepted: 09/05/2021] [Indexed: 12/31/2022]
Abstract
Mitonuclear coevolution is an important prerequisite for efficient energy production in eukaryotes. However, many bivalve taxa experience doubly uniparental inheritance (DUI) and have sex-specific mitochondrial (mt) genomes, providing a challenge for mitonuclear coevolution. We examined possible mechanisms to reconcile mitonuclear coevolution with DUI. No nuclear-encoded, sex-specific OXPHOS paralogs were found in the DUI clam Ruditapes philippinarum, refuting OXPHOS paralogy as a solution in this species. It is also unlikely that mt changes causing disruption of nuclear interactions are strongly selected against because sex-specific mt-residues or those under positive selection in M mt genes were not depleted for contacting nuclear-encoded residues. However, M genomes showed consistently higher dN /dS ratios compared to putatively ancestral F genomes in all mt OXPHOS genes and across all DUI species. Further analyses indicated that this was consistently due to relaxed, not positive selection on M vs. F mt OXPHOS genes. Similarly, selection was relaxed on the F genome of DUI species compared to species with strict maternal inheritance. Coupled with recent physiological and molecular evolution studies, we suggest that relaxed selection on M mt function limits the need to maintain mitonuclear interactions in M genomes compared to F genomes. We discuss our findings with regard to OXPHOS function and the origin of DUI.
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Affiliation(s)
- Gerald P Maeda
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Hunter J McConie
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
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14
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Ghiselli F, Iannello M, Piccinini G, Milani L. Bivalve molluscs as model systems for studying mitochondrial biology. Integr Comp Biol 2021; 61:1699-1714. [PMID: 33944910 DOI: 10.1093/icb/icab057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The class Bivalvia is a highly successful and ancient taxon including ∼25,000 living species. During their long evolutionary history bivalves adapted to a wide range of physicochemical conditions, habitats, biological interactions, and feeding habits. Bivalves can have strikingly different size, and despite their apparently simple body plan, they evolved very different shell shapes, and complex anatomic structures. One of the most striking features of this class of animals is their peculiar mitochondrial biology: some bivalves have facultatively anaerobic mitochondria that allow them to survive prolonged periods of anoxia/hypoxia. Moreover, more than 100 species have now been reported showing the only known evolutionarily stable exception to the strictly maternal inheritance of mitochondria in animals, named doubly uniparental inheritance. Mitochondrial activity is fundamental to eukaryotic life, and thanks to their diversity and uncommon features, bivalves represent a great model system to expand our knowledge about mitochondrial biology, so far limited to a few species. We highlight recent works studying mitochondrial biology in bivalves at either genomic or physiological level. A link between these two approaches is still missing, and we believe that an integrated approach and collaborative relationships are the only possible ways to be successful in such endeavour.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Giovanni Piccinini
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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15
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Breton S, Ghiselli F, Milani L. Mitochondrial Short-Term Plastic Responses and Long-Term Evolutionary Dynamics in Animal Species. Genome Biol Evol 2021; 13:6248094. [PMID: 33892508 PMCID: PMC8290114 DOI: 10.1093/gbe/evab084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/13/2021] [Accepted: 04/20/2021] [Indexed: 12/15/2022] Open
Abstract
How do species respond or adapt to environmental changes? The answer to this depends partly on mitochondrial epigenetics and genetics, new players in promoting adaptation to both short- and long-term environmental changes. In this review, we explore how mitochondrial epigenetics and genetics mechanisms, such as mtDNA methylation, mtDNA-derived noncoding RNAs, micropeptides, mtDNA mutations, and adaptations, can contribute to animal plasticity and adaptation. We also briefly discuss the challenges in assessing mtDNA adaptive evolution. In sum, this review covers new advances in the field of mitochondrial genomics, many of which are still controversial, and discusses processes still somewhat obscure, and some of which are still quite speculative and require further robust experimentation.
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Affiliation(s)
- Sophie Breton
- Department of Biological Sciences, University of Montreal, Quebec, Canada
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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