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Iverson ENK. Conservation Mitonuclear Replacement: Facilitated mitochondrial adaptation for a changing world. Evol Appl 2024; 17:e13642. [PMID: 38468713 PMCID: PMC10925831 DOI: 10.1111/eva.13642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 03/13/2024] Open
Abstract
Most species will not be able to migrate fast enough to cope with climate change, nor evolve quickly enough with current levels of genetic variation. Exacerbating the problem are anthropogenic influences on adaptive potential, including the prevention of gene flow through habitat fragmentation and the erosion of genetic diversity in small, bottlenecked populations. Facilitated adaptation, or assisted evolution, offers a way to augment adaptive genetic variation via artificial selection, induced hybridization, or genetic engineering. One key source of genetic variation, particularly for climatic adaptation, are the core metabolic genes encoded by the mitochondrial genome. These genes influence environmental tolerance to heat, drought, and hypoxia, but must interact intimately and co-evolve with a suite of important nuclear genes. These coadapted mitonuclear genes form some of the important reproductive barriers between species. Mitochondrial genomes can and do introgress between species in an adaptive manner, and they may co-introgress with nuclear genes important for maintaining mitonuclear compatibility. Managers should consider the relevance of mitonuclear genetic variability in conservation decision-making, including as a tool for facilitating adaptation. I propose a novel technique dubbed Conservation Mitonuclear Replacement (CmNR), which entails replacing the core metabolic machinery of a threatened species-the mitochondrial genome and key nuclear loci-with those from a closely related species or a divergent population, which may be better-adapted to climatic changes or carry a lower genetic load. The most feasible route to CmNR is to combine CRISPR-based nuclear genetic editing with mitochondrial replacement and assisted reproductive technologies. This method preserves much of an organism's phenotype and could allow populations to persist in the wild when no other suitable conservation options exist. The technique could be particularly important on mountaintops, where rising temperatures threaten an alarming number of species with almost certain extinction in the next century.
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Affiliation(s)
- Erik N. K. Iverson
- Department of Integrative BiologyThe University of Texas at AustinAustinTexasUSA
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2
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Brand JA, Garcia-Gonzalez F, Dowling DK, Wong BBM. Mitochondrial genetic variation as a potential mediator of intraspecific behavioural diversity. Trends Ecol Evol 2024; 39:199-212. [PMID: 37839905 DOI: 10.1016/j.tree.2023.09.009] [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: 05/30/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023]
Abstract
Mitochondrial genes play an essential role in energy metabolism. Variation in the mitochondrial DNA (mtDNA) sequence often exists within species, and this variation can have consequences for energy production and organismal life history. Yet, despite potential links between energy metabolism and the expression of animal behaviour, mtDNA variation has been largely neglected to date in studies investigating intraspecific behavioural diversity. We outline how mtDNA variation and interactions between mitochondrial and nuclear genotypes may contribute to the expression of individual-to-individual behavioural differences within populations, and why such effects may lead to sex differences in behaviour. We contend that integration of the mitochondrial genome into behavioural ecology research may be key to fully understanding the evolutionary genetics of animal behaviour.
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Affiliation(s)
- Jack A Brand
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia; Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden.
| | - Francisco Garcia-Gonzalez
- Doñana Biological Station-CSIC, Seville, Spain; Centre for Evolutionary Biology, School of Biological Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Bob B M Wong
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
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3
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Carter JE, Sporre MA, Eytan RI. Phylogenetic review of the comb-tooth blenny genus Hypleurochilus in the northwest Atlantic and Gulf of Mexico. Mol Phylogenet Evol 2023; 189:107933. [PMID: 37769827 DOI: 10.1016/j.ympev.2023.107933] [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: 04/10/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
As some of the smallest vertebrates, yet largest producers of consumed reef biomass, cryptobenthic reef fishes serve a disproportionate role in reef ecosystems and are one of the most poorly understood groups of fish. The blenny genera Hypleurochilus and Parablennius are currently considered paraphyletic and the interrelationships of Parablennius have been the focus of recent phylogenetic studies. However, the interrelationships of Hypleurochilus remain understudied. This genus is transatlantically distributed and comprises 11 species with a convoluted taxonomic history. In this study, relationships for ten Hypleurochilus species are resolved using multi-locus nuclear and mtDNA sequence data, morphological data, and mined COI barcode data. Mitochondrial and nuclear sequence data from 61 individuals collected from the western Atlantic and northern Gulf of Mexico (N. GoM) delimit seven species into a temperate clade, a tropical clade, and a third distinct lineage. This lineage, herein referred to as H. cf. aequipinnis, may represent a species of Hypleurochilus whose range has expanded into the N. GoM. Inclusion of publicly available COI sequence for an additional three species provides further phylogenetic resolution. H. bananensis forms a new eastern Atlantic clade with H. cf. aequipinnis, providing further evidence for a western Atlantic range expansion. Single marker COI delimitation was unable to elucidate the relationships between H. springeri/H. pseudoaequipinnis and between H. multifilis/H. caudovittatus due to incomplete lineage sorting. Mitochondrial data are also unable to accurately resolve the placement of H. bermudensis. However, a comprehensive approach using multi-locus phylogenetic and species delimitation methods was able to resolve these relationships. While mining publicly available sequence data allowed for the inclusion of an increased number of species in the analysis and a more comprehensive phylogeny, it was not without drawbacks, as a handful of sequences are potentially mis-identified. Overall, we find that the recent divergence of some species within this genus and potential introgression events confound the results of single locus delimitation methods, yet a combination of single and multi-locus analyses has allowed for insights into the biogeography of this genus and uncovered a potential transatlantic range expansion.
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Affiliation(s)
- Joshua E Carter
- Department of Marine Biology, Texas A&M University at Galveston, 1001 Texas Clipper Road, Galveston, TX 77554, United States.
| | - Megan A Sporre
- Department of Marine Biology, Texas A&M University at Galveston, 1001 Texas Clipper Road, Galveston, TX 77554, United States
| | - Ron I Eytan
- Department of Marine Biology, Texas A&M University at Galveston, 1001 Texas Clipper Road, Galveston, TX 77554, United States
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4
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Venit T, Sapkota O, Abdrabou WS, Loganathan P, Pasricha R, Mahmood SR, El Said NH, Sherif S, Thomas S, Abdelrazig S, Amin S, Bedognetti D, Idaghdour Y, Magzoub M, Percipalle P. Positive regulation of oxidative phosphorylation by nuclear myosin 1 protects cells from metabolic reprogramming and tumorigenesis in mice. Nat Commun 2023; 14:6328. [PMID: 37816864 PMCID: PMC10564744 DOI: 10.1038/s41467-023-42093-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/29/2023] [Indexed: 10/12/2023] Open
Abstract
Metabolic reprogramming is one of the hallmarks of tumorigenesis. Here, we show that nuclear myosin 1 (NM1) serves as a key regulator of cellular metabolism. NM1 directly affects mitochondrial oxidative phosphorylation (OXPHOS) by regulating mitochondrial transcription factors TFAM and PGC1α, and its deletion leads to underdeveloped mitochondria inner cristae and mitochondrial redistribution within the cell. These changes are associated with reduced OXPHOS gene expression, decreased mitochondrial DNA copy number, and deregulated mitochondrial dynamics, which lead to metabolic reprogramming of NM1 KO cells from OXPHOS to aerobic glycolysis.This, in turn, is associated with a metabolomic profile typical for cancer cells, namely increased amino acid-, fatty acid-, and sugar metabolism, and increased glucose uptake, lactate production, and intracellular acidity. NM1 KO cells form solid tumors in a mouse model, suggesting that the metabolic switch towards aerobic glycolysis provides a sufficient carcinogenic signal. We suggest that NM1 plays a role as a tumor suppressor and that NM1 depletion may contribute to the Warburg effect at the onset of tumorigenesis.
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Affiliation(s)
- Tomas Venit
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Oscar Sapkota
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Wael Said Abdrabou
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Palanikumar Loganathan
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Renu Pasricha
- Core Technology Platforms, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Syed Raza Mahmood
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Nadine Hosny El Said
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Shimaa Sherif
- Translational Medicine Department, Research Branch, Sidra Medicine, Doha, Qatar
| | - Sneha Thomas
- Core Technology Platforms, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Salah Abdelrazig
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Shady Amin
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Davide Bedognetti
- Translational Medicine Department, Research Branch, Sidra Medicine, Doha, Qatar
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genoa, Italy
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Youssef Idaghdour
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Mazin Magzoub
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates
| | - Piergiorgio Percipalle
- Program in Biology, Division of Science and Mathematics, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates.
- Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box, 129188, Abu Dhabi, United Arab Emirates.
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden.
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5
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Niedziałkowska M, Tarnowska E, Babik W, Konczal M, Gharbi K, Cezard T, Jędrzejewska B. Different waves of postglacial recolonisation and genomic structure of bank vole populations in NE Poland. Heredity (Edinb) 2023; 130:269-277. [PMID: 36944856 PMCID: PMC10163242 DOI: 10.1038/s41437-023-00600-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 03/23/2023] Open
Abstract
Previous studies indicated that in some species phylogeographic patterns obtained in the analysis of nuclear and mitochondrial DNA (mtDNA) markers can be different. Such mitonuclear discordance can have important evolutionary and ecological consequences. In the present study, we aimed to check whether there was any discordance between mtDNA and nuclear DNA in the bank vole population in the contact zone of its two mtDNA lineages. We analysed the population genetic structure of bank voles using genome-wide genetic data (SNPs) and diversity of sequenced heart transcriptomes obtained from selected individuals from three populations inhabiting areas outside the contact zone. The SNP genetic structure of the populations confirmed the presence of at least two genetic clusters, and such division was concordant with the patterns obtained in the analysis of other genetic markers and functional genes. However, genome-wide SNP analyses revealed the more detailed structure of the studied population, consistent with more than two bank vole recolonisation waves, as recognised previously in the study area. We did not find any significant differences between individuals representing two separate mtDNA lineages of the species in functional genes coding for protein-forming complexes, which are involved in the process of cell respiration in mitochondria. We concluded that the contemporary genetic structure of the populations and the width of the contact zone were shaped by climatic and environmental factors rather than by genetic barriers. The studied populations were likely isolated in separate Last Glacial Maximum refugia for insufficient amount of time to develop significant genetic differentiation.
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Affiliation(s)
| | - Ewa Tarnowska
- Mammal Research Institute Polish Academy of Sciences, 17-230, Białowieża, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences Jagiellonian University, 30-387, Kraków, Poland
| | - Mateusz Konczal
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, 60-614, Poznań, Poland
| | - Karim Gharbi
- Edinburgh Genomics, University of Edinburgh, Edinburgh, EH9 3FL, UK
- Earlham Institute, Norwich, NR4 7UZ, UK
| | - Timothee Cezard
- Edinburgh Genomics, University of Edinburgh, Edinburgh, EH9 3FL, UK
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6
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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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7
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Campbell CSM, Dutoit L, King TM, Craw D, Burridge CP, Wallis GP, Waters JM. Genome‐wide analysis resolves the radiation of New Zealand's freshwater
Galaxias vulgaris
complex and reveals a candidate species obscured by mitochondrial capture. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
| | - Ludovic Dutoit
- Department of Zoology University of Otago Dunedin New Zealand
| | - Tania M. King
- Department of Zoology University of Otago Dunedin New Zealand
| | - Dave Craw
- Department of Geology University of Otago Dunedin New Zealand
| | - Christopher P. Burridge
- Discipline of Biological Sciences, School of Natural Sciences University of Tasmania Hobart Australia
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8
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Adaptive mitochondrial genome functioning in ecologically different farm-impacted natural seedbeds of the endemic blue mussel Mytilus chilensis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100955. [PMID: 35065314 DOI: 10.1016/j.cbd.2021.100955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022]
Abstract
We assessed the adaptive contribution of the mitochondrial genes involved with the respiratory chain and oxidative phosphorylation of the blue mussel Mytilus chilensis, a native and heavily exploited species in the inner sea of Chiloé Island, southern Chile. The assembled mitochondrial transcriptome of individuals from two ecologically different farm-impacted natural seedbeds, Cochamó (41°S) and Yaldad (42°S), represented about 4.5% of the whole de novo transcriptome of the species and showed location and tissue (gills, mantle) specific expression differences in 13 protein-coding mitochondrial genes. The RNA-Seq analysis detected differences in the number of up-regulated mitogenes between individuals from Cochamó (7) and Yaldad (11), some being tissue-specific (ND4L and COX2). However, the analysis did not detect transcripts-per-million (TPM = 0) of ND2 and ND5 in gills and ATP6 in mantle samples from Cochamó. Likewise, for ND6 and ATP8 in any sample. Several monomorphic location-specific mitochondrial genetic variants were detected in samples from Cochamó (78) and Yaldad (207), representing standing genetic variability to optimize mitochondrial functioning under local habitats. Overall, these mitochondrial transcriptomic differences reflect the impact of environmental conditions on the mitochondrial genome functioning and offer new markers to assess the effects on mussel fitness of habitat translocations, a routine industry practice. Likewise, these mitochondrial markers should help monitor and maintain adaptive population differences in this keystone and heavily exploited native species.
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9
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Noll D, Leon F, Brandt D, Pistorius P, Le Bohec C, Bonadonna F, Trathan PN, Barbosa A, Rey AR, Dantas GPM, Bowie RCK, Poulin E, Vianna JA. Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation. Sci Rep 2022; 12:3767. [PMID: 35260629 PMCID: PMC8904570 DOI: 10.1038/s41598-022-07562-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/21/2022] [Indexed: 12/21/2022] Open
Abstract
Although mitochondrial DNA has been widely used in phylogeography, evidence has emerged that factors such as climate, food availability, and environmental pressures that produce high levels of stress can exert a strong influence on mitochondrial genomes, to the point of promoting the persistence of certain genotypes in order to compensate for the metabolic requirements of the local environment. As recently discovered, the gentoo penguins (Pygoscelis papua) comprise four highly divergent lineages across their distribution spanning the Antarctic and sub-Antarctic regions. Gentoo penguins therefore represent a suitable animal model to study adaptive processes across divergent environments. Based on 62 mitogenomes that we obtained from nine locations spanning all four gentoo penguin lineages, we demonstrated lineage-specific nucleotide substitutions for various genes, but only lineage-specific amino acid replacements for the ND1 and ND5 protein-coding genes. Purifying selection (dN/dS < 1) is the main driving force in the protein-coding genes that shape the diversity of mitogenomes in gentoo penguins. Positive selection (dN/dS > 1) was mostly present in codons of the Complex I (NADH genes), supported by two different codon-based methods at the ND1 and ND4 in the most divergent lineages, the eastern gentoo penguin from Crozet and Marion Islands and the southern gentoo penguin from Antarctica respectively. Additionally, ND5 and ATP6 were under selection in the branches of the phylogeny involving all gentoo penguins except the eastern lineage. Our study suggests that local adaptation of gentoo penguins has emerged as a response to environmental variability promoting the fixation of mitochondrial haplotypes in a non-random manner. Mitogenome adaptation is thus likely to have been associated with gentoo penguin diversification across the Southern Ocean and to have promoted their survival in extreme environments such as Antarctica. Such selective processes on the mitochondrial genome may also be responsible for the discordance detected between nuclear- and mitochondrial-based phylogenies of gentoo penguin lineages.
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Affiliation(s)
- D Noll
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago, Chile.,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile.,Facultad de Ciencias, Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - F Leon
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - D Brandt
- Department of Integrative Biology, University of California, 3101 Valley Life Science Building, Berkeley, CA, 94720, USA
| | - P Pistorius
- Department of Zoology, 11DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology, Nelson Mandela University, Port Elizabeth, South Africa
| | - C Le Bohec
- CNRS, IPHC UMR 7178, Université de Strasbourg, 67000, Strasbourg, France.,Département de Biologie Polaire, Centre Scientifique de Monaco, 98000, Monaco City, Monaco
| | - F Bonadonna
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier Cedex 5, France
| | | | - A Barbosa
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - A Raya Rey
- Centro Austral de Investigaciones Científicas - Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC-CONICET), Ushuaia, Argentina.,Instituto de Ciencias Polares, Ambiente y Recursos Naturales, Universidad Nacional de Tierra del Fuego, Ushuaia, Argentina.,Wildlife Conservation Society, Buenos Aires, Argentina
| | - G P M Dantas
- PPG in Vertebrate Biology, Pontificia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
| | - R C K Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, 3101 Valley Life Science Building, Berkeley, CA, 94720, USA
| | - E Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile.,Facultad de Ciencias, Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - J A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago, Chile. .,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile. .,Fondo de Desarrollo de Áreas Prioritarias (FONDAP), Center for Genome Regulation (CRG), Santiago, Chile.
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10
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Maduna SN, Vivian-Smith A, Jónsdóttir ÓDB, Imsland AK, Klütsch CF, Nyman T, Eiken HG, Hagen SB. Mitogenomics of the suborder Cottoidei (Teleostei: Perciformes): Improved assemblies, mitogenome features, phylogeny, and ecological implications. Genomics 2022; 114:110297. [DOI: 10.1016/j.ygeno.2022.110297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 01/05/2022] [Accepted: 02/01/2022] [Indexed: 11/04/2022]
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11
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Burton RS. The role of mitonuclear incompatibilities in allopatric speciation. Cell Mol Life Sci 2022; 79:103. [PMID: 35091831 PMCID: PMC11072163 DOI: 10.1007/s00018-021-04059-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 11/03/2022]
Abstract
Aerobic metabolism in eukaryotic cells requires extensive interactions between products of the nuclear and mitochondrial genomes. Rapid evolution of the mitochondrial genome, including fixation of both adaptive and deleterious mutations, creates intrinsic selection pressures favoring nuclear gene mutations that maintain mitochondrial function. As this process occurs independently in allopatry, the resulting divergence between conspecific populations can subsequently be manifest in mitonuclear incompatibilities in inter-population hybrids. Such incompatibilities, mitonuclear versions of Bateson-Dobzhansky-Muller incompatibilities that form the standard model for allopatric speciation, can potentially restrict gene flow between populations, ultimately resulting in varying degrees of reproductive isolation. The potential role of mitonuclear incompatibilities in speciation is further enhanced where mtDNA substitution rates are elevated compared to the nuclear genome and where population structure maintains allopatry for adequate time to evolve multiple mitonuclear incompatibilities. However, the fact that mitochondrial introgression occurs across species boundaries has raised questions regarding the efficacy of mitonuclear incompatibilities in reducing gene flow. Several scenarios now appear to satisfactorily explain this phenomenon, including cases where differences in mtDNA genetic load may drive introgression or where co-introgression of coadapted nuclear genes may support the function of introgressed mtDNA. Although asymmetries in reproductive isolation between taxa are consistent with mitonuclear incompatibilities, interactions between autosomes and sex chromosomes yield similar predictions that are difficult to disentangle. With regard to establishing reproductive isolation while in allopatry, existing studies clearly suggest that mitonuclear incompatibilities can contribute to the evolution of barriers to gene flow. However, there is to date relatively little definitive evidence supporting a primary role for mitonuclear incompatibilities in the speciation process.
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Affiliation(s)
- Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA.
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12
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The genetic drivers for the successful invasive potential of a generalist bird, the House crow. Biol Invasions 2021. [DOI: 10.1007/s10530-021-02684-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Son JM, Lee C. Aging: All roads lead to mitochondria. Semin Cell Dev Biol 2021; 116:160-168. [PMID: 33741252 PMCID: PMC9774040 DOI: 10.1016/j.semcdb.2021.02.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/18/2021] [Accepted: 02/25/2021] [Indexed: 02/07/2023]
Abstract
Mitochondria were described as early as 1890 as ubiquitous intracellular structures by Ernster and Schatz (1981) [1]. Since then, the accretion of knowledge in the past century has revealed much of the molecular details of mitochondria, ranging from mitochondrial origin, structure, metabolism, genetics, and signaling, and their implications in health and disease. We now know that mitochondria are remarkably multifunctional and deeply intertwined with many vital cellular processes. They are quasi-self organelles that still possess remnants of its bacterial ancestry, including an independent genome. The mitochondrial free radical theory of aging (MFRTA), which postulated that aging is a product of oxidative damage to mitochondrial DNA, provided a conceptual framework that put mitochondria on the map of aging research. However, several studies have more recently challenged the general validity of the theory, favoring novel ideas based on emerging evidence to understand how mitochondria contribute to aging and age-related diseases. One prominent topic of investigation lies on the fact that mitochondria are not only production sites for bioenergetics and macromolecules, but also regulatory hubs that communicate and coordinate many vital physiological processes at the cellular and organismal level. The bi-directional communication and coordination between the co-evolved mitochondrial and nuclear genomes is especially interesting in terms of cellular regulation. Mitochondria are dynamic and adaptive, rendering their function sensitive to cellular context. Tissues with high energy demands, such as the brain, seem to be uniquely affected by age-dependent mitochondrial dysfunction, providing a foundation for the development of novel mitochondrial-based therapeutics and diagnostics.
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Affiliation(s)
- Jyung Mean Son
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA,USC Norris Comprehensive Cancer Center, Los Angeles, CA 90089, USA,Biomedical Sciences, Graduate School, Ajou University, Suwon 16499, South Korea,Corresponding author at: Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
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14
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Baldwin HJ, Vallo P, Ruiz AT, Anti P, Nkrumah EE, Badu EK, Oppong SK, Kalko EKV, Tschapka M, Stow AJ. Concordant patterns of genetic, acoustic, and morphological divergence in the West African Old World leaf‐nosed bats of the
Hipposideros caffer
complex. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Heather J. Baldwin
- Institute of Evolutionary Ecology and Conservation Genomics Ulm University Ulm Germany
- Department of Biological Sciences Macquarie University Sydney NSW Australia
| | - Peter Vallo
- Institute of Evolutionary Ecology and Conservation Genomics Ulm University Ulm Germany
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
| | - A. Tonatiuh Ruiz
- Institute of Neural Information Processing Ulm University Ulm Germany
| | - Priscilla Anti
- Department of Wildlife and Range Management Kwame Nkrumah University of Science and Technology Kumasi Ghana
| | - Evans E. Nkrumah
- Department of Wildlife and Range Management Kwame Nkrumah University of Science and Technology Kumasi Ghana
| | - Ebenezer K. Badu
- Department of Wildlife and Range Management Kwame Nkrumah University of Science and Technology Kumasi Ghana
| | - Samuel K. Oppong
- Department of Wildlife and Range Management Kwame Nkrumah University of Science and Technology Kumasi Ghana
| | - Elisabeth K. V. Kalko
- Institute of Evolutionary Ecology and Conservation Genomics Ulm University Ulm Germany
- Smithsonian Tropical Research Institute Balboa Panama
| | - Marco Tschapka
- Institute of Evolutionary Ecology and Conservation Genomics Ulm University Ulm Germany
- Smithsonian Tropical Research Institute Balboa Panama
| | - Adam J. Stow
- Department of Biological Sciences Macquarie University Sydney NSW Australia
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15
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Han KL, Barreto FS. Pervasive Mitonuclear Coadaptation Underlies Fast Development in Interpopulation Hybrids of a Marine Crustacean. Genome Biol Evol 2021; 13:6121088. [PMID: 33502469 PMCID: PMC7947751 DOI: 10.1093/gbe/evab004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2021] [Indexed: 12/21/2022] Open
Abstract
Cellular energy production requires coordinated interactions between genetic components from the nuclear and mitochondrial genomes. This coordination results in coadaptation of interacting elements within populations. Interbreeding between divergent gene pools can disrupt coadapted loci and result in hybrid fitness breakdown. While specific incompatible loci have been detected in multiple eukaryotic taxa, the extent of the nuclear genome that is influenced by mitonuclear coadaptation is not clear in any species. Here, we used F2 hybrids between two divergent populations of the copepod Tigriopus californicus to examine mitonuclear coadaptation across the nuclear genome. Using developmental rate as a measure of fitness, we found that fast-developing copepods had higher ATP synthesis capacity than slow developers, suggesting variation in developmental rates is at least partly associated with mitochondrial dysfunction. Using Pool-seq, we detected strong biases for maternal alleles across 7 (of 12) chromosomes in both reciprocal crosses in high-fitness hybrids, whereas low-fitness hybrids showed shifts toward the paternal population. Comparison with previous results on a different hybrid cross revealed largely different patterns of strong mitonuclear coadaptation associated with developmental rate. Our findings suggest that functional coadaptation between interacting nuclear and mitochondrial components is reflected in strong polygenic effects on this life-history phenotype, and reveal that molecular coadaptation follows independent evolutionary trajectories among isolated populations.
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Affiliation(s)
- Kin-Lan Han
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA.,Department of Biology, University of Washington, Seattle, Washington, USA
| | - Felipe S Barreto
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
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16
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Neverov AD, Popova AV, Fedonin GG, Cheremukhin EA, Klink GV, Bazykin GA. Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins. PLoS Genet 2021; 17:e1008711. [PMID: 33493156 PMCID: PMC7861529 DOI: 10.1371/journal.pgen.1008711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 02/04/2021] [Accepted: 12/07/2020] [Indexed: 11/19/2022] Open
Abstract
The rate of evolution differs between protein sites and changes with time. However, the link between these two phenomena remains poorly understood. Here, we design a phylogenetic approach for distinguishing pairs of amino acid sites that evolve concordantly, i.e., such that substitutions at one site trigger subsequent substitutions at the other; and also pairs of sites that evolve discordantly, so that substitutions at one site impede subsequent substitutions at the other. We distinguish groups of amino acid sites that undergo coordinated evolution and evolve discordantly from other such groups. In mitochondrion-encoded proteins of metazoans and fungi, we show that concordantly evolving sites are clustered in protein structures. By analysing the phylogenetic patterns of substitutions at concordantly and discordantly evolving site pairs, we find that concordant evolution has two distinct causes: epistatic interactions between amino acid substitutions and episodes of selection independently affecting substitutions at different sites. The rate of substitutions at concordantly evolving groups of protein sites changes in the course of evolution, indicating episodes of selection limited to some of the lineages. The phylogenetic positions of these changes are consistent between proteins, suggesting common selective forces underlying them. The mode and rate of evolution of a protein site depends on the effect of its mutations on protein fitness. The fitness effect of a mutation itself can change in the course of evolution for at least two reasons. First, it can be modulated by substitutions occurring at other sites, a phenomenon called epistasis. Second, changes in selection can be non-epistatic, affecting sites independently of one another. Here, we analyse substitutions accumulated by the evolving lineages of the five proteins encoded by the mitochondrial genomes of thousands of species of metazoans and fungi. We show that substitutions at different amino acid sites occur in a coordinated fashion, and this coordination is caused both by epistasis and by episodes of selection affecting groups of sites. We partition each protein into several groups of concordantly evolving sites such that evolution of sites from different groups is discordant, and show that the proteins encoded by the mitochondrial genome consist of coevolving structural blocks. Some of these blocks have a clear functional specialization, e.g. are associated with interfaces between proteins composing respiratory complexes. Together, our results reveal a previously unrecognized complexity in the causes of variation in evolutionary rates between protein sites.
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Affiliation(s)
- Alexey D. Neverov
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology, Moscow, Russia
- * E-mail:
| | - Anfisa V. Popova
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology, Moscow, Russia
| | - Gennady G. Fedonin
- Department of Molecular Diagnostics, Central Research Institute for Epidemiology, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
| | | | - Galya V. Klink
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Georgii A. Bazykin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
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17
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Castellana S, Biagini T, Petrizzelli F, Parca L, Panzironi N, Caputo V, Vescovi AL, Carella M, Mazza T. MitImpact 3: modeling the residue interaction network of the Respiratory Chain subunits. Nucleic Acids Res 2021; 49:D1282-D1288. [PMID: 33300029 PMCID: PMC7779045 DOI: 10.1093/nar/gkaa1032] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/14/2020] [Accepted: 12/08/2020] [Indexed: 12/26/2022] Open
Abstract
Numerous lines of evidence have shown that the interaction between the nuclear and mitochondrial genomes ensures the efficient functioning of the OXPHOS complexes, with substantial implications in bioenergetics, adaptation, and disease. Their interaction is a fascinating and complex trait of the eukaryotic cell that MitImpact explores with its third major release. MitImpact expands its collection of genomic, clinical, and functional annotations of all non-synonymous substitutions of the human mitochondrial genome with new information on putative Compensated Pathogenic Deviations and co-varying amino acid sites of the Respiratory Chain subunits. It further provides evidence of energetic and structural residue compensation by techniques of molecular dynamics simulation. MitImpact is freely accessible at http://mitimpact.css-mendel.it.
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Affiliation(s)
- Stefano Castellana
- Laboratory of Bioinformatics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
| | - Tommaso Biagini
- Laboratory of Bioinformatics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
| | - Francesco Petrizzelli
- Laboratory of Bioinformatics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome 00161, Italy
| | - Luca Parca
- Laboratory of Bioinformatics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
| | - Noemi Panzironi
- Department of Experimental Medicine, Sapienza University of Rome, Rome 00161, Italy
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome 00161, Italy
| | - Angelo Luigi Vescovi
- ISBReMIT Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, IRCSS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
| | - Massimo Carella
- Laboratory of Medical Genetics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG) 71013, Italy
| | - Tommaso Mazza
- Laboratory of Bioinformatics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), 71013, Italy
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18
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Zhou Y, Huang D, Xin Z, Xiao J. Evolution of Oxidative Phosphorylation (OXPHOS) Genes Reflecting the Evolutionary and Life Histories of Fig Wasps (Hymenoptera, Chalcidoidea). Genes (Basel) 2020; 11:genes11111353. [PMID: 33203150 PMCID: PMC7697784 DOI: 10.3390/genes11111353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 11/23/2022] Open
Abstract
Fig wasps are a peculiar group of insects which, for millions of years, have inhabited the enclosed syconia of fig trees. Considering the relatively closed and dark environment of fig syconia, we hypothesize that the fig wasps’ oxidative phosphorylation (OXPHOS) pathway, which is the main oxygen consumption and adenosine triphosphate (ATP) production system, may have adaptively evolved. In this study, we manually annotated the OXPHOS genes of 11 species of fig wasps, and compared the evolutionary patterns of OXPHOS genes for six pollinators and five non-pollinators. Thirteen mitochondrial protein-coding genes and 30 nuclear-coding single-copy orthologous genes were used to analyze the amino acid substitution rate and natural selection. The results showed high amino acid substitution rates of both mitochondrial and nuclear OXPHOS genes in fig wasps, implying the co-evolution of mitochondrial and nuclear genes. Our results further revealed that the OXPHOS-related genes evolved significantly faster in pollinators than in non-pollinators, and five genes had significant positive selection signals in the pollinator lineage, indicating that OXPHOS genes play an important role in the adaptation of pollinators. This study can help us understand the relationship between gene evolution and environmental adaptation.
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19
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The role of selection in the evolution of marine turtles mitogenomes. Sci Rep 2020; 10:16953. [PMID: 33046778 PMCID: PMC7550602 DOI: 10.1038/s41598-020-73874-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 09/11/2020] [Indexed: 11/23/2022] Open
Abstract
Sea turtles are the only extant chelonian representatives that inhabit the marine environment. One key to successful colonization of this habitat is the adaptation to different energetic demands. Such energetic requirement is intrinsically related to the mitochondrial ability to generate energy through oxidative phosphorylation (OXPHOS) process. Here, we estimated Testudines phylogenetic relationships from 90 complete chelonian mitochondrial genomes and tested the adaptive evolution of 13 mitochondrial protein-coding genes of sea turtles to determine how natural selection shaped mitochondrial genes of the Chelonioidea clade. Complete mitogenomes showed strong support and resolution, differing at the position of the Chelonioidea clade in comparison to the turtle phylogeny based on nuclear genomic data. Codon models retrieved a relatively increased dN/dS (ω) on three OXPHOS genes for sea turtle lineages. Also, we found evidence of positive selection on at least three codon positions, encoded by NADH dehydrogenase genes (ND4 and ND5). The accelerated evolutionary rates found for sea turtles on COX2, ND1 and CYTB and the molecular footprints of positive selection found on ND4 and ND5 genes may be related to mitochondrial molecular adaptation to stress likely resulted from a more active lifestyle in sea turtles. Our study provides insight into the adaptive evolution of the mtDNA genome in sea turtles and its implications for the molecular mechanism of oxidative phosphorylation.
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20
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Hill GE. Genetic hitchhiking, mitonuclear coadaptation, and the origins of mt DNA barcode gaps. Ecol Evol 2020; 10:9048-9059. [PMID: 32953045 PMCID: PMC7487244 DOI: 10.1002/ece3.6640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 01/02/2023] Open
Abstract
DNA barcoding based on mitochondrial (mt) nucleotide sequences is an enigma. Neutral models of mt evolution predict DNA barcoding cannot work for recently diverged taxa, and yet, mt DNA barcoding accurately delimits species for many bilaterian animals. Meanwhile, mt DNA barcoding often fails for plants and fungi. I propose that because mt gene products must cofunction with nuclear gene products, the evolution of mt genomes is best understood with full consideration of the two environments that impose selective pressure on mt genes: the external environment and the internal genomic environment. Moreover, it is critical to fully consider the potential for adaptive evolution of not just protein products of mt genes but also of mt transfer RNAs and mt ribosomal RNAs. The tight linkage of genes on mt genomes that do not engage in recombination could facilitate selective sweeps whenever there is positive selection on any element in the mt genome, leading to the purging of mt genetic diversity within a population and to the rapid fixation of novel mt DNA sequences. Accordingly, the most important factor determining whether or not mt DNA sequences diagnose species boundaries may be the extent to which the mt chromosomes engage in recombination.
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21
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Gangloff EJ, Schwartz TS, Klabacka R, Huebschman N, Liu AY, Bronikowski AM. Mitochondria as central characters in a complex narrative: Linking genomics, energetics, pace-of-life, and aging in natural populations of garter snakes. Exp Gerontol 2020; 137:110967. [DOI: 10.1016/j.exger.2020.110967] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 04/11/2020] [Accepted: 05/01/2020] [Indexed: 12/18/2022]
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22
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Wilson RE, Sonsthagen SA, Smé N, Gharrett AJ, Majewski AR, Wedemeyer K, Nelson RJ, Talbot SL. Mitochondrial genome diversity and population mitogenomics of polar cod (Boreogadus saida) and Arctic dwelling gadoids. Polar Biol 2020. [DOI: 10.1007/s00300-020-02703-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Princepe D, De Aguiar MAM. Modeling Mito-nuclear Compatibility and Its Role in Species Identification. Syst Biol 2020; 70:133-144. [PMID: 32497198 DOI: 10.1093/sysbio/syaa044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 01/27/2023] Open
Abstract
Mitochondrial genetic material (mtDNA) is widely used for phylogenetic reconstruction and as a barcode for species identification. The utility of mtDNA in these contexts derives from its particular molecular properties, including its high evolutionary rate, uniparental inheritance, and small size. But mtDNA may also play a fundamental role in speciation-as suggested by recent observations of coevolution with the nuclear DNA, along with the fact that respiration depends on coordination of genes from both sources. Here, we study how mito-nuclear interactions affect the accuracy of species identification by mtDNA, as well as the speciation process itself. We simulate the evolution of a population of individuals who carry a recombining nuclear genome and a mitochondrial genome inherited maternally. We compare a null model fitness landscape that lacks any mito-nuclear interaction against a scenario in which interactions influence fitness. Fitness is assigned to individuals according to their mito-nuclear compatibility, which drives the coevolution of the nuclear and mitochondrial genomes. Depending on the model parameters, the population breaks into distinct species and the model output then allows us to analyze the accuracy of mtDNA barcode for species identification. Remarkably, we find that species identification by mtDNA is equally accurate in the presence or absence of mito-nuclear coupling and that the success of the DNA barcode derives mainly from population geographical isolation during speciation. Nevertheless, selection imposed by mito-nuclear compatibility influences the diversification process and leaves signatures in the genetic content and spatial distribution of the populations, in three ways. First, speciation is delayed and the resulting phylogenetic trees are more balanced. Second, clades in the resulting phylogenetic tree correlate more strongly with the spatial distribution of species and clusters of more similar mtDNA's. Third, there is a substantial increase in the intraspecies mtDNA similarity, decreasing the number of alleles substitutions per locus and promoting the conservation of genetic information. We compare the evolutionary patterns observed in our model to empirical data from copepods (Tigriopus californicus). We find good qualitative agreement in the geographic patterns and the topology of the phylogenetic tree, provided the model includes selection based on mito-nuclear interactions. These results highlight the role of mito-nuclear compatibility in the speciation process and its reconstruction from genetic data.[Mito-nuclear coevolution; mtDNA barcode; parapatry; phylogeny.].
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Affiliation(s)
| | - Marcus A M De Aguiar
- Instituto de Física 'Gleb Wataghin', Universidade Estadual de Campinas - 13083-859, Campinas, SP, Brazil
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24
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Rank NE, Mardulyn P, Heidl SJ, Roberts KT, Zavala NA, Smiley JT, Dahlhoff EP. Mitonuclear mismatch alters performance and reproductive success in naturally introgressed populations of a montane leaf beetle. Evolution 2020; 74:1724-1740. [PMID: 32246837 DOI: 10.1111/evo.13962] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 02/22/2020] [Accepted: 03/13/2020] [Indexed: 12/11/2022]
Abstract
Coordination between nuclear and mitochondrial genomes is critical to metabolic processes underlying animals' ability to adapt to local environments, yet consequences of mitonuclear interactions have rarely been investigated in populations where individuals with divergent mitochondrial and nuclear genomes naturally interbreed. Genetic variation in the leaf beetle Chrysomela aeneicollis was assessed along a latitudinal thermal gradient in California's Sierra Nevada. Variation at mitochondrial cytochrome oxidase II (COII) and the nuclear gene phosphoglucose isomerase (PGI) shows concordance and was significantly greater along a 65 km transect than 10 other loci. STRUCTURE analyses using neutral loci identified a southern and northern subpopulation, which interbreed in the central drainage Bishop Creek. COII and PGI were used as indicators of mitochondrial and nuclear genetic variation in field and laboratory experiments conducted on beetles from this admixed population. Fecundity, larval development rate, running speed and male mating frequency were higher for beetles with geographically "matched" than "mismatched" mitonuclear genotypes. Effects of mitonuclear mismatch were largest for individuals with northern nuclear genotypes possessing southern mitochondria and were most pronounced after heat treatment or at high elevation. These findings suggest that mitonuclear incompatibility diminishes performance and reproductive success in nature, effects that could intensify at environmental extremes.
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Affiliation(s)
- Nathan E Rank
- Department of Biology, Sonoma State University, Rohnert Park, California, 94928.,White Mountain Research Center, University of California, Bishop, California, 93514
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, 1050, Belgium
| | - Sarah J Heidl
- Department of Biology, Sonoma State University, Rohnert Park, California, 94928.,White Mountain Research Center, University of California, Bishop, California, 93514
| | - Kevin T Roberts
- Department of Biology, Sonoma State University, Rohnert Park, California, 94928.,White Mountain Research Center, University of California, Bishop, California, 93514.,Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
| | - Nicolas A Zavala
- White Mountain Research Center, University of California, Bishop, California, 93514.,Department of Biology, Santa Clara University, Santa Clara, California, 95053
| | - John T Smiley
- White Mountain Research Center, University of California, Bishop, California, 93514
| | - Elizabeth P Dahlhoff
- White Mountain Research Center, University of California, Bishop, California, 93514.,Department of Biology, Santa Clara University, Santa Clara, California, 95053
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25
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Reynolds JC, Bwiza CP, Lee C. Mitonuclear genomics and aging. Hum Genet 2020; 139:381-399. [PMID: 31997134 PMCID: PMC7147958 DOI: 10.1007/s00439-020-02119-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/17/2020] [Indexed: 12/25/2022]
Abstract
Our cells operate based on two distinct genomes that are enclosed in the nucleus and mitochondria. The mitochondrial genome presumably originates from endosymbiotic bacteria. With time, a large portion of the original genes in the bacterial genome is considered to have been lost or transferred to the nuclear genome, leaving a reduced 16.5 Kb circular mitochondrial DNA (mtDNA). Traditionally only 37 genes, including 13 proteins, were thought to be encoded within mtDNA, its genetic repertoire is expanding with the identification of mitochondrial-derived peptides (MDPs). The biology of aging has been largely unveiled to be regulated by genes that are encoded in the nuclear genome, whereas the mitochondrial genome remained more cryptic. However, recent studies position mitochondria and mtDNA as an important counterpart to the nuclear genome, whereby the two organelles constantly regulate each other. Thus, the genomic network that regulates lifespan and/or healthspan is likely constituted by two unique, yet co-evolved, genomes. Here, we will discuss aspects of mitochondrial biology, especially mitochondrial communication that may add substantial momentum to aging research by accounting for both mitonuclear genomes to more comprehensively and inclusively map the genetic and molecular networks that govern aging and age-related diseases.
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Affiliation(s)
- Joseph C Reynolds
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Conscience P Bwiza
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
- USC Norris Comprehensive Cancer Center, Los Angeles, CA, 90089, USA.
- Biomedical Sciences, Graduate School, Ajou University, Suwon, 16499, South Korea.
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26
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Jimenez AG, O'Connor ES, Tobin KJ, Anderson KN, Winward JD, Fleming A, Winner C, Chinchilli E, Maya A, Carlson K, Downs CJ. Does Cellular Metabolism from Primary Fibroblasts and Oxidative Stress in Blood Differ between Mammals and Birds? The (Lack-thereof) Scaling of Oxidative Stress. Integr Comp Biol 2020; 59:953-969. [PMID: 30924869 DOI: 10.1093/icb/icz017] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
As part of mitonuclear communication, retrograde and anterograde signaling helps maintain homeostasis under basal conditions. Basal conditions, however, vary across phylogeny. At the cell-level, some mitonuclear retrograde responses can be quantified by measuring the constitutive components of oxidative stress, the balance between reactive oxygen species (ROS) and antioxidants. ROS are metabolic by-products produced by the mitochondria that can damage macromolecules by structurally altering proteins and inducing mutations in DNA, among other processes. To combat accumulating damage, organisms have evolved endogenous antioxidants and can consume exogenous antioxidants to sequester ROS before they cause cellular damage. ROS are also considered to be regulated through a retrograde signaling cascade from the mitochondria to the nucleus. These cellular pathways may have implications at the whole-animal level as well. For example, birds have higher basal metabolic rates, higher blood glucose concentration, and longer lifespans than similar sized mammals, however, the literature is divergent on whether oxidative stress is higher in birds compared with mammals. Herein, we collected literature values for whole-animal metabolism of birds and mammals. Then, we collected cellular metabolic rate data from primary fibroblast cells isolated from birds and mammals and we collected blood from a phylogenetically diverse group of birds and mammals housed at zoos and measured several parameters of oxidative stress. Additionally, we reviewed the literature on basal-level oxidative stress parameters between mammals and birds. We found that mass-specific metabolic rates were higher in birds compared with mammals. Our laboratory results suggest that cellular basal metabolism, total antioxidant capacity, circulating lipid damage, and catalase activity were significantly lower in birds compared with mammals. We found no body-size correlation on cellular metabolism or oxidative stress. We also found that most oxidative stress parameters significantly correlate with increasing age in mammals, but not in birds; and that correlations with reported maximum lifespans show different results compared with correlations with known aged birds. Our literature review revealed that basal levels of oxidative stress measurements for birds were rare, which made it difficult to draw conclusions.
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Affiliation(s)
- A G Jimenez
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - E S O'Connor
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - K J Tobin
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - K N Anderson
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - J D Winward
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - A Fleming
- Department of Biology, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - C Winner
- Department of Biology, Hamilton College, 198 College Hill Road, Clinton, NY 13323, USA
| | - E Chinchilli
- Department of Biology, Hamilton College, 198 College Hill Road, Clinton, NY 13323, USA
| | - A Maya
- Department of Biology, Hamilton College, 198 College Hill Road, Clinton, NY 13323, USA
| | - K Carlson
- Department of Biology, Hamilton College, 198 College Hill Road, Clinton, NY 13323, USA
| | - C J Downs
- Department of Biology, Hamilton College, 198 College Hill Road, Clinton, NY 13323, USA
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27
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Havird JC, Weaver RJ, Milani L, Ghiselli F, Greenway R, Ramsey AJ, Jimenez AG, Dowling DK, Hood WR, Montooth KL, Estes S, Schulte PM, Sokolova IM, Hill GE. Beyond the Powerhouse: Integrating Mitonuclear Evolution, Physiology, and Theory in Comparative Biology. Integr Comp Biol 2020; 59:856-863. [PMID: 31504533 DOI: 10.1093/icb/icz132] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Eukaryotes are the outcome of an ancient symbiosis and as such, eukaryotic cells fundamentally possess two genomes. As a consequence, gene products encoded by both nuclear and mitochondrial genomes must interact in an intimate and precise fashion to enable aerobic respiration in eukaryotes. This genomic architecture of eukaryotes is proposed to necessitate perpetual coevolution between the nuclear and mitochondrial genomes to maintain coadaptation, but the presence of two genomes also creates the opportunity for intracellular conflict. In the collection of papers that constitute this symposium volume, scientists working in diverse organismal systems spanning vast biological scales address emerging topics in integrative, comparative biology in light of mitonuclear interactions.
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Affiliation(s)
- Justin C Havird
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA
| | - Ryan J Weaver
- Department of Integrative Biology, University of Texas, Austin, TX 78712, USA.,Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Liliana Milani
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, 40126, Italy
| | - Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, 40126, Italy
| | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - Adam J Ramsey
- Department of Biological Sciences, University of Memphis, Memphis, TN 38152, USA
| | - Ana G Jimenez
- Department of Biology, Colgate University, Hamilton, NY 13346, USA
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Wendy R Hood
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Kristi L Montooth
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68502, USA
| | - Suzanne Estes
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Patricia M Schulte
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Inna M Sokolova
- Department of Marine Biology, Institute of Biological Sciences, University of Rostock, Rostock, Germany.,Department of Maritime Systems, Interdisciplinary Faculty, University of Rostock, Rostock, Germany
| | - Geoffrey E Hill
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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28
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Milani L, Ghiselli F. Faraway, so close. The comparative method and the potential of non-model animals in mitochondrial research. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190186. [PMID: 31787048 DOI: 10.1098/rstb.2019.0186] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Inference from model organisms has been the engine for many discoveries in life science, but indiscriminate generalization leads to oversimplifications and misconceptions. Model organisms and inductive reasoning are irreplaceable: there is no other way to tackle the complexity of living systems. At the same time, it is not advisable to infer general patterns from a restricted number of species, which are very far from being representative of the diversity of life. Not all models are equal. Some organisms are suitable to find similarities across species, other highly specialized organisms can be used to focus on differences. In this opinion piece, we discuss the dominance of the mechanistic/reductionist approach in life sciences and make a case for an enhanced application of the comparative approach to study processes in all their various forms across different organisms. We also enlist some rising animal models in mitochondrial research, to exemplify how non-model organisms can be chosen in a comparative framework. These taxa often do not possess implemented tools and dedicated methods/resources. However, because of specific features, they have the potential to address still unanswered biological questions. Finally, we discuss future perspectives and caveats of the comparative method in the age of 'big data'. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Liliana Milani
- 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
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29
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Kral LG, Watson S. Preliminary assessment of adaptive evolution of mitochondrial protein coding genes in darters (Percidae: Etheostomatinae). F1000Res 2019. [DOI: 10.12688/f1000research.17552.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Mitochondrial DNA of vertebrates contains genes for 13 proteins involved in oxidative phosphorylation. Some of these genes have been shown to undergo adaptive evolution in a variety of species. This study examines all mitochondrial protein coding genes in 11 darter species to determine if any of these genes show evidence of positive selection. Methods: The mitogenome from four darter was sequenced and annotated. Mitogenome sequences for another seven species were obtained from GenBank. Alignments of each of the protein coding genes were subject to codon-based identification of positive selection by Selecton, MEME and FEL. Results: Evidence of positive selection was obtained for six of the genes by at least one of the methods. CYTB was identified as having evolved under positive selection by all three methods at the same codon location. Conclusions: Given the evidence for positive selection of mitochondrial protein coding genes in darters, a more extensive analysis of mitochondrial gene evolution in all the extant darter species is warranted.
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30
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Gan HM, Falk S, Morales HE, Austin CM, Sunnucks P, Pavlova A. Genomic evidence of neo-sex chromosomes in the eastern yellow robin. Gigascience 2019; 8:giz111. [PMID: 31494668 PMCID: PMC6736294 DOI: 10.1093/gigascience/giz111] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/31/2019] [Accepted: 08/14/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Understanding sex-biased natural selection can be enhanced by access to well-annotated chromosomes including ones inherited in sex-specific fashion. The eastern yellow robin (EYR) is an endemic Australian songbird inferred to have experienced climate-driven sex-biased selection and is a prominent model for studying mitochondrial-nuclear interactions in the wild. However, the lack of an EYR reference genome containing both sex chromosomes (in birds, a female bearing Z and W chromosomes) limits efforts to understand the mechanisms of these processes. Here, we assemble the genome for a female EYR and use low-depth (10×) genome resequencing data from 19 individuals of known sex to identify chromosome fragments with sex-specific inheritance. FINDINGS MaSuRCA hybrid assembly using Nanopore and Illumina reads generated a 1.22-Gb EYR genome in 20,702 scaffolds (94.2% BUSCO completeness). Scaffolds were tested for W-linked (female-only) inheritance using a k-mer approach, and for Z-linked inheritance using median read-depth test in male and female reads (read-depths must indicate haploid female and diploid male representation). This resulted in 2,372 W-linked scaffolds (total length: 97,872,282 bp, N50: 81,931 bp) and 586 Z-linked scaffolds (total length: 121,817,358 bp, N50: 551,641 bp). Anchoring of the sex-linked EYR scaffolds to the reference genome of a female zebra finch revealed 2 categories of sex-linked genomic regions. First, 653 W-linked scaffolds (25.7 Mb) were anchored to the W sex chromosome and 215 Z-linked scaffolds (74.4 Mb) to the Z. Second, 1,138 W-linked scaffolds (70.9 Mb) and 179 Z-linked scaffolds (51.0 Mb) were anchored to a large section (coordinates ∼5 to ∼60 Mb) of zebra finch chromosome 1A. The first ∼5 Mb and last ∼14 Mb of the reference chromosome 1A had only autosomally behaving EYR scaffolds mapping to them. CONCLUSIONS We report a female (W chromosome-containing) EYR genome and provide genomic evidence for a neo-sex (neo-W and neo-Z) chromosome system in the EYR, involving most of a large chromosome (1A) previously only reported to be autosomal in passerines.
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Affiliation(s)
- Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria 3220, Australia
| | - Stephanie Falk
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, Victoria 3800, Australia
| | - Hernán E Morales
- Centre for Marine Evolutionary Biology, Department of Marine Sciences, University of Gothenburg, Göteborg 405 30, Sweden
| | - Christopher M Austin
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3220, Australia
- Deakin Genomics Centre, Deakin University, Geelong, Victoria 3220, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, Victoria 3800, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, Victoria 3800, Australia
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31
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Benayoun BA, Lee C. MOTS-c: A Mitochondrial-Encoded Regulator of the Nucleus. Bioessays 2019; 41:e1900046. [PMID: 31378979 PMCID: PMC8224472 DOI: 10.1002/bies.201900046] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/28/2019] [Indexed: 12/25/2022]
Abstract
Mitochondria are increasingly being recognized as information hubs that sense cellular changes and transmit messages to other cellular components, such as the nucleus, the endoplasmic reticulum (ER), the Golgi apparatus, and lysosomes. Nonetheless, the interaction between mitochondria and the nucleus is of special interest because they both host part of the cellular genome. Thus, the communication between genome-bearing organelles would likely include gene expression regulation. Multiple nuclear-encoded proteins have been known to regulate mitochondrial gene expression. On the contrary, no mitochondrial-encoded factors are known to actively regulate nuclear gene expression. MOTS-c (mitochondrial open reading frame of the 12S ribosomal RNA type-c) is a recently identified peptide encoded within the mitochondrial 12S ribosomal RNA gene that has metabolic functions. Notably, MOTS-c can translocate to the nucleus upon metabolic stress (e.g., glucose restriction and oxidative stress) and directly regulate adaptive nuclear gene expression to promote cellular homeostasis. It is hypothesized that cellular fitness requires the coevolved mitonuclear genomes to coordinate adaptive responses using gene-encoded factors that cross-regulate the opposite genome. This suggests that cellular gene expression requires the bipartite split genomes to operate as a unified system, rather than the nucleus being the sole master regulator.
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Affiliation(s)
- Bérénice A Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation Program, Los Angeles, CA, 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA, 90089, USA
| | - Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation Program, Los Angeles, CA, 90089, USA
- Biomedical Sciences, Graduate School, Ajou University, Suwon, 16499, Republic of Korea
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32
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Hill GE, Havird JC, Sloan DB, Burton RS, Greening C, Dowling DK. Assessing the fitness consequences of mitonuclear interactions in natural populations. Biol Rev Camb Philos Soc 2019; 94:1089-1104. [PMID: 30588726 PMCID: PMC6613652 DOI: 10.1111/brv.12493] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022]
Abstract
Metazoans exist only with a continuous and rich supply of chemical energy from oxidative phosphorylation in mitochondria. The oxidative phosphorylation machinery that mediates energy conservation is encoded by both mitochondrial and nuclear genes, and hence the products of these two genomes must interact closely to achieve coordinated function of core respiratory processes. It follows that selection for efficient respiration will lead to selection for compatible combinations of mitochondrial and nuclear genotypes, and this should facilitate coadaptation between mitochondrial and nuclear genomes (mitonuclear coadaptation). Herein, we outline the modes by which mitochondrial and nuclear genomes may coevolve within natural populations, and we discuss the implications of mitonuclear coadaptation for diverse fields of study in the biological sciences. We identify five themes in the study of mitonuclear interactions that provide a roadmap for both ecological and biomedical studies seeking to measure the contribution of intergenomic coadaptation to the evolution of natural populations. We also explore the wider implications of the fitness consequences of mitonuclear interactions, focusing on central debates within the fields of ecology and biomedicine.
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Affiliation(s)
- Geoffrey E. Hill
- Department of Biological Sciences, Auburn University, United States of America
| | - Justin C. Havird
- Department of Biology, Colorado State University, United States of America
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, United States of America
| | - Ronald S. Burton
- Scripps Institution of Oceanography, University of California, San Diego, United States of America
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Damian K. Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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33
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Banguera-Hinestroza E, Ferrada E, Sawall Y, Flot JF. Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments. Genes (Basel) 2019; 10:E324. [PMID: 31035578 PMCID: PMC6562464 DOI: 10.3390/genes10050324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 01/15/2023] Open
Abstract
More than a decade ago, a new mitochondrial Open Reading Frame (mtORF) was discovered in corals of the family Pocilloporidae and has been used since then as an effective barcode for these corals. Recently, mtORF sequencing revealed the existence of two differentiated Stylophora lineages occurring in sympatry along the environmental gradient of the Red Sea (18.5°C to 33.9°C). In the endemic Red Sea lineage RS_LinB, the mtORF and the heat shock protein gene hsp70 uncovered similar phylogeographic patterns strongly correlated with environmental variations. This suggests that the mtORF too might be involved in thermal adaptation. Here, we used computational analyses to explore the features and putative function of this mtORF. In particular, we tested the likelihood that this gene encodes a functional protein and whether it may play a role in adaptation. Analyses of full mitogenomes showed that the mtORF originated in the common ancestor of Madracis and other pocilloporids, and that it encodes a transmembrane protein differing in length and domain architecture among genera. Homology-based annotation and the relative conservation of metal-binding sites revealed traces of an ancient hydrolase catalytic activity. Furthermore, signals of pervasive purifying selection, lack of stop codons in 1830 sequences analyzed, and a codon-usage bias similar to that of other mitochondrial genes indicate that the protein is functional, i.e., not a pseudogene. Other features, such as intrinsically disordered regions, tandem repeats, and signals of positive selection particularly in StylophoraRS_LinB populations, are consistent with a role of the mtORF in adaptive responses to environmental changes.
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Affiliation(s)
- Eulalia Banguera-Hinestroza
- Evolutionary Biology and Ecology, Université libre de Bruxelles, B-1050 Brussels, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels-(IB)2, 1050 Brussels, Belgium.
| | - Evandro Ferrada
- Center for Genomics and Bioinformatics, Universidad Mayor, Santiago, Chile.
| | - Yvonne Sawall
- Coral Reef Ecology, Bermuda Institute of Ocean Sciences (BIOS), St.George's GE 01, Bermuda.
| | - Jean-François Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles, B-1050 Brussels, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels-(IB)2, 1050 Brussels, Belgium.
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34
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Hill GE. Reconciling the Mitonuclear Compatibility Species Concept with Rampant Mitochondrial Introgression. Integr Comp Biol 2019; 59:912-924. [DOI: 10.1093/icb/icz019] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
The mitonuclear compatibility species concept defines a species as a population that is genetically isolated from other populations by uniquely coadapted mitochondrial (mt) and nuclear genes. A key prediction of this hypothesis is that the mt genotype of each species will be functionally distinct and that introgression of mt genomes will be prevented by mitonuclear incompatibilities that arise when heterospecific mt and nuclear genes attempt to cofunction to enable aerobic respiration. It has been proposed, therefore, that the observation of rampant introgression of mt genotypes from one species to another constitutes a strong refutation of the mitonuclear speciation. The displacement of a mt genotype from a nuclear background with which it co-evolved to a foreign nuclear background will necessarily lead to fitness loss due to mitonuclear incompatibilities. Here I consider two potential benefits of mt introgression between species that may, in some cases, overcome fitness losses arising from mitonuclear incompatibilities. First, the introgressed mt genotype may be better adapted to the local environment than the native mt genotype such that higher fitness is achieved through improved adaptation via introgression. Second, if the mitochondria of the recipient taxa carry a high mutational load, then introgression of a foreign, less corrupt mt genome may enable the recipient taxa to escape its mutational load and gain a fitness advantage. Under both scenarios, fitness gains from novel mt genotypes could theoretically compensate for the fitness that is lost via mitonuclear incompatibility. I also consider the role of endosymbionts in non-adaptive rampant introgression of mt genomes. I conclude that rampant introgression is not necessarily evidence against the idea of tight mitonuclear coadaptation or the mitonuclear compatibility species concept. Rampant mt introgression will typically lead to erasure of species but in some cases could lead to hybrid speciation.
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Affiliation(s)
- Geoffrey E Hill
- Department of Biological Sciences, 331 Funchess Hall, Auburn University, Auburn, AL 36849-5414, USA
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35
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Pleistocene-dated biogeographic barriers drove divergence within the Australo-Papuan region in a sex-specific manner: an example in a widespread Australian songbird. Heredity (Edinb) 2019; 123:608-621. [PMID: 30874632 PMCID: PMC6972870 DOI: 10.1038/s41437-019-0206-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 02/11/2019] [Accepted: 02/23/2019] [Indexed: 11/09/2022] Open
Abstract
Understanding how environmental change has shaped species evolution can inform predictions of how future climate change might continue to do so. Research of widespread biological systems spanning multiple climates that have been subject to environmental change can yield generalizable inferences about the neutral and adaptive processes driving lineage divergence during periods of environmental change. We contribute to the growing body of multi-locus phylogeographic studies investigating the effect of Pleistocene climate change on species evolution by focusing on a widespread Australo-Papuan songbird with several mitochondrial lineages that diverged during the Pleistocene, the grey shrike-thrush (Colluricincla harmonica). We employed multi-locus phylogenetic, population genetic and coalescent analyses to (1) assess whether nuclear genetic diversity suggests a history congruent with that based on phenotypically defined subspecies ranges, mitochondrial clade boundaries and putative biogeographical barriers, (2) estimate genetic diversity within and genetic differentiation and gene flow among regional populations and (3) estimate population divergence times. The five currently recognized subspecies of grey shrike-thrush are genetically differentiated in nuclear and mitochondrial genomes, but connected by low levels of gene flow. Divergences among these populations are concordant with recognized historical biogeographical barriers and date to the Pleistocene. Discordance in the order of population divergence events based on mitochondrial and nuclear genomes suggests a history of sex-biased gene flow and/or mitochondrial introgression at secondary contacts. This study demonstrates that climate change can impact sexes with different dispersal biology in different ways. Incongruence between population and mitochondrial trees calls for a genome-wide investigation into dispersal, mitochondrial introgression and mitonuclear evolution.
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36
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Bernardo PH, Sánchez-Ramírez S, Sánchez-Pacheco SJ, Álvarez-Castañeda ST, Aguilera-Miller EF, Mendez-de la Cruz FR, Murphy RW. Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate. Heredity (Edinb) 2019; 123:359-370. [PMID: 30833746 PMCID: PMC6781153 DOI: 10.1038/s41437-019-0204-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 02/13/2019] [Accepted: 02/18/2019] [Indexed: 12/22/2022] Open
Abstract
Nuclear and mitochondrial genomes coexist within cells but are subject to different tempos and modes of evolution. Evolutionary forces such as drift, mutation, selection, and migration are expected to play fundamental roles in the origin and maintenance of diverged populations; however, divergence may lag between genomes subject to different modes of inheritance and functional specialization. Herein, we explore whole mitochondrial genome data and thousands of nuclear single nucleotide polymorphisms to evidence extreme mito-nuclear discordance in the small black-tailed brush lizard, Urosaurus nigricaudus, of the Peninsula of Baja California, Mexico and southern California, USA, and discuss potential drivers. Results show three deeply divergent mitochondrial lineages dating back to the later Miocene (ca. 5.5 Ma) and Pliocene (ca. 2.8 Ma) that likely followed geographic isolation due to trans-peninsular seaways. This contrasts with very low levels of genetic differentiation in nuclear loci (FST < 0.028) between mtDNA lineages. Analyses of protein-coding genes reveal substantial fixed variation between mitochondrial lineages, of which a significant portion comes from non-synonymous mutations. A mixture of drift and selection is likely responsible for the rise of these mtDNA groups, albeit with little evidence of marked differences in climatic niche space between them. Finally, future investigations can look further into the role that mito-nuclear incompatibilities and mating systems play in explaining contrasting nuclear gene flow.
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Affiliation(s)
- Pedro Henrique Bernardo
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada. .,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada.
| | - Santiago Sánchez-Ramírez
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Santiago J Sánchez-Pacheco
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | | | | | | | - Robert W Murphy
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
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37
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Lee C. Nuclear transcriptional regulation by mitochondrial-encoded MOTS-c. Mol Cell Oncol 2019; 6:1549464. [PMID: 31131297 PMCID: PMC6512917 DOI: 10.1080/23723556.2018.1549464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 11/12/2018] [Accepted: 11/14/2018] [Indexed: 10/27/2022]
Abstract
Cellular stress response is coordinated through the communication between mitochondria and the nucleus. However, whereas mitochondria are regulated by nuclear-encoded proteins, the nucleus was considered ungoverned by mitochondrial-encoded factors. We recently reported that a mitochondrial-encoded peptide directly regulates the nuclear genome upon cellular stress, indicating an integrated bi-genomic cross-communication mechanism.
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Affiliation(s)
- Changhan Lee
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.,USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA.,Biomedical Science, Graduate School, Ajou University, Suwon, Korea
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38
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Lima TG, Burton RS, Willett CS. Genomic scans reveal multiple mito‐nuclear incompatibilities in population crosses of the copepod
Tigriopus californicus. Evolution 2019; 73:609-620. [DOI: 10.1111/evo.13690] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 12/20/2018] [Accepted: 01/11/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Thiago G. Lima
- Department of Biology University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599
- Marine Biology Research Division Scripps Institution of Oceanography La Jolla California 92037
| | - Ronald S. Burton
- Marine Biology Research Division Scripps Institution of Oceanography La Jolla California 92037
| | - Christopher S. Willett
- Department of Biology University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599
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39
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Zhu Z, Han X, Wang Y, Liu W, Lu Y, Xu C, Wang X, Hao L, Song Y, Huang S, Rizak JD, Li Y, Han C. Identification of Specific Nuclear Genetic Loci and Genes That Interact With the Mitochondrial Genome and Contribute to Fecundity in Caenorhabditis elegans. Front Genet 2019; 10:28. [PMID: 30778368 PMCID: PMC6369210 DOI: 10.3389/fgene.2019.00028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/17/2019] [Indexed: 12/16/2022] Open
Abstract
Previous studies have found that fecundity is a multigenic trait regulated, in part, by mitochondrial-nuclear (mit-n) genetic interactions. However, the identification of specific nuclear genetic loci or genes interacting with the mitochondrial genome and contributing to the quantitative trait fecundity is an unsolved issue. Here, a panel of recombinant inbred advanced intercrossed lines (RIAILs), established from a cross between the N2 and CB4856 strains of C. elegans, were used to characterize the underlying genetic basis of mit-n genetic interactions related to fecundity. Sixty-seven single nucleotide polymorphisms (SNPs) were identified by association mapping to be linked with fecundity among 115 SNPs linked to mitotype. This indicated significant epistatic effects between nuclear and mitochondria genetics on fecundity. In addition, two specific nuclear genetic loci interacting with the mitochondrial genome and contributing to fecundity were identified. A significant reduction in fecundity was observed in the RIAILs that carried CB4856 mitochondria and a N2 genotype at locus 1 or a CB4856 genotype at locus 2 relative to the wild-type strains. Then, a hybrid strain (CNC10) was established, which was bred as homoplasmic for the CB4856 mtDNA genome and N2 genotype at locus 1 in the CB4856 nuclear background. The mean fecundity of CNC10 was half the fecundity of the control strain. Several functional characteristics of the mitochondria in CNC10 were also influenced by mit-n interactions. Overall, experimental evidence was presented that specific nuclear genetic loci or genes have interactions with the mitochondrial genome and are associated with fecundity. In total, 18 genes were identified using integrative approaches to have interactions with the mitochondrial genome and to contribute to fecundity.
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Affiliation(s)
- Zuobin Zhu
- Department of Genetics, Research Facility Center for Morphology, Xuzhou Medical University, Xuzhou, China
| | - Xiaoxiao Han
- Center of Reproductive Medicine, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuechen Wang
- Department of Genetics, Research Facility Center for Morphology, Xuzhou Medical University, Xuzhou, China
| | - Wei Liu
- Medical Technology College, Xuzhou Medical University, Xuzhou, China
| | - Yue Lu
- Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China
| | - Chang Xu
- Department of Genetics, Research Facility Center for Morphology, Xuzhou Medical University, Xuzhou, China
| | - Xitao Wang
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Lin Hao
- Department of Urology, Xuzhou Central Hospital, Xuzhou, China
| | - Yuanjian Song
- Department of Genetics, Research Facility Center for Morphology, Xuzhou Medical University, Xuzhou, China
| | - Shi Huang
- School of Life Sciences, Xiangya Medical School, Central South University, Changsha, China
| | | | - Ying Li
- Medical Technology College, Xuzhou Medical University, Xuzhou, China
| | - Conghui Han
- Department of Clinical Medicine, Xuzhou Medical University, Xuzhou, China.,Department of Urology, Xuzhou Central Hospital, Xuzhou, China
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Unraveling the intricate biodiversity of the benthic harpacticoid genus Nannopus (Copepoda, Harpacticoida, Nannopodidae) in Korean waters. Mol Phylogenet Evol 2019; 130:366-379. [DOI: 10.1016/j.ympev.2018.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 09/17/2018] [Accepted: 10/03/2018] [Indexed: 11/18/2022]
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41
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Concordant divergence of mitogenomes and a mitonuclear gene cluster in bird lineages inhabiting different climates. Nat Ecol Evol 2018; 2:1258-1267. [DOI: 10.1038/s41559-018-0606-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 06/13/2018] [Indexed: 02/02/2023]
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42
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Experimental evidence that thermal selection shapes mitochondrial genome evolution. Sci Rep 2018; 8:9500. [PMID: 29934612 PMCID: PMC6015072 DOI: 10.1038/s41598-018-27805-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/04/2018] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are essential organelles, found within eukaryotic cells, which contain their own DNA. Mitochondrial DNA (mtDNA) has traditionally been used in population genetic and biogeographic studies as a maternally-inherited and evolutionary-neutral genetic marker. However, it is now clear that polymorphisms within the mtDNA sequence are routinely non-neutral, and furthermore several studies have suggested that such mtDNA polymorphisms are also sensitive to thermal selection. These observations led to the formulation of the “mitochondrial climatic adaptation” hypothesis, for which all published evidence to date is correlational. Here, we use laboratory-based experimental evolution in the fruit fly, Drosophila melanogaster, to test whether thermal selection can shift population frequencies of two mtDNA haplogroups whose natural frequencies exhibit clinal associations with latitude along the Australian east-coast. We present experimental evidence that the thermal regime in which the laboratory populations were maintained drove changes in haplogroup frequencies across generations. Our results strengthen the emerging view that intra-specific mtDNA variants are sensitive to selection, and suggest spatial distributions of mtDNA variants in natural populations of metazoans might reflect adaptation to climatic environments rather than within-population coalescence and diffusion of selectively-neutral haplotypes across populations.
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43
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Irwin DE. Sex chromosomes and speciation in birds and other ZW systems. Mol Ecol 2018; 27:3831-3851. [PMID: 29443419 DOI: 10.1111/mec.14537] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 02/03/2018] [Accepted: 02/06/2018] [Indexed: 01/01/2023]
Abstract
Theory and empirical patterns suggest a disproportionate role for sex chromosomes in evolution and speciation. Focusing on ZW sex determination (females ZW, males ZZ; the system in birds, many snakes, and lepidopterans), I review how evolutionary dynamics are expected to differ between the Z, W and the autosomes, discuss how these differences may lead to a greater role of the sex chromosomes in speciation and use data from birds to compare relative evolutionary rates of sex chromosomes and autosomes. Neutral mutations, partially or completely recessive beneficial mutations, and deleterious mutations under many conditions are expected to accumulate faster on the Z than on autosomes. Sexually antagonistic polymorphisms are expected to arise on the Z, raising the possibility of the spread of preference alleles. The faster accumulation of many types of mutations and the potential for complex evolutionary dynamics of sexually antagonistic traits and preferences contribute to a role for the Z chromosome in speciation. A quantitative comparison among a wide variety of bird species shows that the Z tends to have less within-population diversity and greater between-species differentiation than the autosomes, likely due to both adaptive evolution and a greater rate of fixation of deleterious alleles. The W chromosome also shows strong potential to be involved in speciation, in part because of its co-inheritance with the mitochondrial genome. While theory and empirical evidence suggest a disproportionate role for sex chromosomes in speciation, the importance of sex chromosomes is moderated by their small size compared to the whole genome.
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Affiliation(s)
- Darren E Irwin
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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44
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Tobler M, Kelley JL, Plath M, Riesch R. Extreme environments and the origins of biodiversity: Adaptation and speciation in sulphide spring fishes. Mol Ecol 2018; 27:843-859. [DOI: 10.1111/mec.14497] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
| | - Joanna L. Kelley
- School of Biological Sciences Washington State University Pullman WA USA
| | - Martin Plath
- Shaanxi Key Laboratory of Molecular Biology for Agriculture College of Animal Science and Technology Northwest A&F University Yangling Shaanxi China
| | - Rüdiger Riesch
- School of Biological Sciences Centre for Ecology, Evolution and Behaviour Royal Holloway University of London Egham Surrey UK
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45
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Koch RE, Hill GE. Behavioural mating displays depend on mitochondrial function: a potential mechanism for linking behaviour to individual condition. Biol Rev Camb Philos Soc 2018; 93:1387-1398. [DOI: 10.1111/brv.12400] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/15/2018] [Accepted: 01/19/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Rebecca E. Koch
- Department of Biological Sciences; Auburn University; Auburn AL 36849 U.S.A
| | - Geoffrey E. Hill
- Department of Biological Sciences; Auburn University; Auburn AL 36849 U.S.A
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46
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Lamb AM, Gan HM, Greening C, Joseph L, Lee Y, Morán‐Ordóñez A, Sunnucks P, Pavlova A. Climate‐driven mitochondrial selection: A test in Australian songbirds. Mol Ecol 2018; 27:898-918. [DOI: 10.1111/mec.14488] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 11/29/2017] [Accepted: 12/08/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Annika Mae Lamb
- School of Biological Sciences Monash University Melbourne Vic. Australia
| | - Han Ming Gan
- School of Science Monash University Malaysia Bandar Sunway Selangor Malaysia
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Waurn Ponds Vic. Australia
| | - Chris Greening
- School of Biological Sciences Monash University Melbourne Vic. Australia
| | - Leo Joseph
- Australian National Wildlife Collection CSIRO National Research Collections Canberra ACT Australia
| | - Yin Peng Lee
- School of Science Monash University Malaysia Bandar Sunway Selangor Malaysia
| | - Alejandra Morán‐Ordóñez
- InForest Joint Research Unit (CTFC‐CREAF) Forest Science Centre of Catalonia Solsona Catalonia Spain
| | - Paul Sunnucks
- School of Biological Sciences Monash University Melbourne Vic. Australia
| | - Alexandra Pavlova
- School of Biological Sciences Monash University Melbourne Vic. Australia
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47
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48
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Krzemińska U, Morales HE, Greening C, Nyári ÁS, Wilson R, Song BK, Austin CM, Sunnucks P, Pavlova A, Rahman S. Population mitogenomics provides insights into evolutionary history, source of invasions and diversifying selection in the House Crow (Corvus splendens). Heredity (Edinb) 2017; 120:296-309. [PMID: 29180719 DOI: 10.1038/s41437-017-0020-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 10/04/2017] [Accepted: 10/06/2017] [Indexed: 11/09/2022] Open
Abstract
The House Crow (Corvus splendens) is a useful study system for investigating the genetic basis of adaptations underpinning successful range expansion. The species originates from the Indian subcontinent, but has successfully spread through a variety of thermal environments across Asia, Africa and Europe. Here, population mitogenomics was used to investigate the colonisation history and to test for signals of molecular selection on the mitochondrial genome. We sequenced the mitogenomes of 89 House Crows spanning four native and five invasive populations. A Bayesian dated phylogeny, based on the 13 mitochondrial protein-coding genes, supports a mid-Pleistocene (~630,000 years ago) divergence between the most distant genetic lineages. Phylogeographic patterns suggest that northern South Asia is the likely centre of origin for the species. Codon-based analyses of selection and assessments of changes in amino acid properties provide evidence of positive selection on the ND2 and ND5 genes against a background of purifying selection across the mitogenome. Protein homology modelling suggests that four amino acid substitutions inferred to be under positive selection may modulate coupling efficiency and proton translocation mediated by OXPHOS complex I. The identified substitutions are found within native House Crow lineages and ecological niche modelling predicts suitable climatic areas for the establishment of crow populations within the invasive range. Mitogenomic patterns in the invasive range of the species are more strongly associated with introduction history than climate. We speculate that invasions of the House Crow have been facilitated by standing genetic variation that accumulated due to diversifying selection within the native range.
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Affiliation(s)
- Urszula Krzemińska
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia. .,Monash University Malaysia Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia. .,Department of Genetics and Animal Breeding, Faculty of Animal Sciences, Warsaw University of Life Sciences SGGW, Warsaw, Poland.
| | - Hernán E Morales
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia.,Department of Marine Sciences, University of Gothenburg, Box 461, Göteborg, SE 405 30, Sweden
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia
| | - Árpád S Nyári
- Department of Ecology and Evolutionary Biology, The University of Tennessee, 569 Dabney Hall, Knoxville, TN, 37996-1610, USA
| | - Robyn Wilson
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia.,Monash University Malaysia Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Beng Kah Song
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia.,Monash University Malaysia Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
| | - Christopher M Austin
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia.,Monash University Malaysia Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia.,School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3220, Australia
| | - Paul Sunnucks
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia.,Monash University Malaysia Genomics Facility, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 47500, Petaling Jaya, Selangor, Malaysia
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