1
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Nielsen TM, Baldwin J, Danis M, Fedorka KM. Support for Y-compensation of mother's curse affecting lifespan in Drosophila melanogaster. Heredity (Edinb) 2024:10.1038/s41437-024-00726-w. [PMID: 39369145 DOI: 10.1038/s41437-024-00726-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 09/20/2024] [Accepted: 09/23/2024] [Indexed: 10/07/2024] Open
Abstract
Mother's curse refers to male-biased deleterious mutations that may accumulate on mitochondria due to its strict maternal inheritance. If these mutations persist, males should ideally compensate through mutations on Y-chromosomes given its strict paternal inheritance. Previous work addressed this hypothesis by comparing coevolved and non-coevolved Y-mitochondria pairs placed alongside completely foreign autosomal backgrounds, expecting males with coevolved pairs to exhibit greater fitness due to Y-compensation. To date, no evidence for Y-compensation has been found. That experimental design assumes Y-chromosomes compensate via direct interaction with mitochondria and/or coevolved autosomes are unimportant in its function or elucidation. If Y-chromosomes instead compensate by modifying autosomal targets (or its elucidation requires coevolved autosomes), then this design could fail to detect Y-compensation. Here we address if Y-chromosomes ameliorate mitochondrial mutations affecting male lifespan in Drosophila melanogaster. Using three disparate populations we compared lifespan among males with coevolved and non-coevolved Y-mitochondria pairs placed alongside autosomal backgrounds coevolved with mitochondria. We found coevolved pairs exhibited lower mortality risk relative to non-coevolved pairs. In contrast, no such pattern was observed when coevolved and non-coevolved pairs were placed alongside non-coevolved autosomes, as with previous studies. These data are consistent with Y-compensation and highlight the importance of autosomes in this capacity. However, we cannot fully exclude the possibility that Y-autosomal coevolution independent of mitochondrial mutations contributed to our results. Regardless, modern practices in medicine, conservation, and agriculture that introduce foreign Y-chromosomes into non-coevolved backgrounds should be used with caution, as they may disrupt Y-autosome coadaptation and/or inadvertently unbridle mother's curse.
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Affiliation(s)
- Tobias Møgelvang Nielsen
- University of Central Florida, Biological Sciences Building, 4110 Libra Dr., Orlando, FL, 32816, USA
| | - Jaden Baldwin
- University of Central Florida, Biological Sciences Building, 4110 Libra Dr., Orlando, FL, 32816, USA
| | - Megan Danis
- University of Central Florida, Biological Sciences Building, 4110 Libra Dr., Orlando, FL, 32816, USA
| | - Kenneth M Fedorka
- University of Central Florida, Biological Sciences Building, 4110 Libra Dr., Orlando, FL, 32816, USA.
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2
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Nagarajan-Radha V, Beekman M. G × G × E effect on phenotype expression in a non-conventional model organism, the unicellular slime mould Physarum polycephalum. Biol Lett 2023; 19:20220494. [PMID: 36789533 PMCID: PMC9929494 DOI: 10.1098/rsbl.2022.0494] [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: 10/27/2022] [Accepted: 01/26/2023] [Indexed: 02/16/2023] Open
Abstract
In metazoans, the expression of key phenotypic traits is sensitive to two- and three-way interactions between variation in mitochondrial DNA, nuclear DNA and the external environment. Whether gene-by-environment interactions affect phenotypes in single-celled eukaryotes is poorly studied, except in a few species of yeast and fungi. We developed a genetic panel of the unicellular slime mould, Physarum polycephalum containing strains differing in mitochondrial and nuclear DNA haplotypes. The panel also included two strains harbouring a selfishly replicating mitochondrial-fusion (mF) plasmid that could affect phenotype expression. We assayed movement and growth rate differences among the strains across two temperature regimes: 24° and 28°C. We found that the slime mould's growth rate, but not movement, is affected by G × G × E interactions. Predictably, mtDNA × nDNA interactions significantly affected both traits. The inter-trait correlation across the strains in each temperature regime was positive. Surprisingly, the mF plasmid had no negative effects on our chosen traits. Our study is the first to demonstrate genetic regulation of phenotype expression in a unicellular slime mould. The genetic effect on phenotypes manifests via epistatic interactions with the thermal environment, thus shedding new light on the role of G × G × E interactions in trait evolution in protists.
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Affiliation(s)
- Venkatesh Nagarajan-Radha
- Behaviour, Ecology and Evolution Lab, School of Life and Environmental Sciences, University of Sydney, Sydney NSW, 2006, Australia
| | - Madeleine Beekman
- Behaviour, Ecology and Evolution Lab, School of Life and Environmental Sciences, University of Sydney, Sydney NSW, 2006, Australia
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3
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Kyrgiafini MA, Giannoulis T, Moutou KA, Mamuris Z. Investigating the Impact of a Curse: Diseases, Population Isolation, Evolution and the Mother's Curse. Genes (Basel) 2022; 13:2151. [PMID: 36421825 PMCID: PMC9690142 DOI: 10.3390/genes13112151] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 09/08/2024] Open
Abstract
The mitochondrion was characterized for years as the energy factory of the cell, but now its role in many more cellular processes is recognized. The mitochondrion and mitochondrial DNA (mtDNA) also possess a set of distinct properties, including maternal inheritance, that creates the Mother's Curse phenomenon. As mtDNA is inherited from females to all offspring, mutations that are harmful to males tend to accumulate more easily. The Mother's Curse is associated with various diseases, and has a significant effect on males, in many cases even affecting their reproductive ability. Sometimes, it even leads to reproductive isolation, as in crosses between different populations, the mitochondrial genome cannot cooperate effectively with the nuclear one resulting in a mito-nuclear incompatibility and reduce the fitness of the hybrids. This phenomenon is observed both in the laboratory and in natural populations, and have the potential to influence their evolution and speciation. Therefore, it turns out that the study of mitochondria is an exciting field that finds many applications, including pest control, and it can shed light on the molecular mechanism of several diseases, improving successful diagnosis and therapeutics. Finally, mito-nuclear co-adaptation, paternal leakage, and kin selection are some mechanisms that can mitigate the impact of the Mother's Curse.
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Affiliation(s)
- Maria-Anna Kyrgiafini
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| | - Themistoklis Giannoulis
- Laboratory of Biology, Genetics and Bioinformatics, Department of Animal Sciences, University of Thessaly, Gaiopolis, 41336 Larissa, Greece
| | - Katerina A. Moutou
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
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4
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Weaver RJ, Rabinowitz S, Thueson K, Havird JC. Genomic Signatures of Mitonuclear Coevolution in Mammals. Mol Biol Evol 2022; 39:6775223. [PMID: 36288802 PMCID: PMC9641969 DOI: 10.1093/molbev/msac233] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial (mt) and nuclear-encoded proteins are integrated in aerobic respiration, requiring co-functionality among gene products from fundamentally different genomes. Different evolutionary rates, inheritance mechanisms, and selection pressures set the stage for incompatibilities between interacting products of the two genomes. The mitonuclear coevolution hypothesis posits that incompatibilities may be avoided if evolution in one genome selects for complementary changes in interacting genes encoded by the other genome. Nuclear compensation, in which deleterious mtDNA changes are offset by compensatory nuclear changes, is often invoked as the primary mechanism for mitonuclear coevolution. Yet, direct evidence supporting nuclear compensation is rare. Here, we used data from 58 mammalian species representing eight orders to show strong correlations between evolutionary rates of mt and nuclear-encoded mt-targeted (N-mt) proteins, but not between mt and non-mt-targeted nuclear proteins, providing strong support for mitonuclear coevolution across mammals. N-mt genes with direct mt interactions also showed the strongest correlations. Although most N-mt genes had elevated dN/dS ratios compared to mt genes (as predicted under nuclear compensation), N-mt sites in close contact with mt proteins were not overrepresented for signs of positive selection compared to noncontact N-mt sites (contrary to predictions of nuclear compensation). Furthermore, temporal patterns of N-mt and mt amino acid substitutions did not support predictions of nuclear compensation, even in positively selected, functionally important residues with direct mitonuclear contacts. Overall, our results strongly support mitonuclear coevolution across ∼170 million years of mammalian evolution but fail to support nuclear compensation as the major mode of mitonuclear coevolution.
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Affiliation(s)
- Ryan J Weaver
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA.,Department of Natural Resource Ecology and Management, Iowa State University, Ames, IA
| | | | - Kiley Thueson
- Department of Integrative Biology, University of Texas, Austin, TX
| | - Justin C Havird
- Department of Integrative Biology, University of Texas, Austin, TX
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5
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Cui J, Zhang H, Gao X, Zhang X, Luo M, Ren L, Liu S. Correlations of expression of nuclear and mitochondrial genes in triploid fish. G3 GENES|GENOMES|GENETICS 2022; 12:6655693. [PMID: 35924985 PMCID: PMC9434317 DOI: 10.1093/g3journal/jkac197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022]
Abstract
Abstract
The expression of nuclear and mitochondrial genes, as well as their coordinated control, regulates cell proliferation, individual development, and disease in animals. However, the potential coregulation between nuclear and mitochondrial genes is unclear in triploid fishes. The two triploids (R2C and RC2) with distinct mitochondrial genomes but similar nuclear genomes exhibit different embryonic development times and growth rates. They are an excellent model for studying how nuclear and mitochondrial genes coordinate. Here, we performed the mRNA-seq of four stages of embryonic development (blastula, gastrula, segmentation, and hatching periods) in the two triploids (R2C and RC2) and their diploid inbred parents (red crucian carp and common carp). After establishing the four patterns of mitochondrial and nuclear gene expression, 270 nuclear genes regulated by mitochondrial genes were predicted. The expression levels of APC16 and Trim33 were higher in RC2 than in R2C, suggesting their potential effects on regulating embryonic development time. In addition, 308 differentially expressed genes filtered from the list of nuclear-encoded mitochondrial genes described by Mercer et al. in 2011 were considered potential genes for which nuclear genes regulate mitochondrial function. The findings might aid in our understanding of the correlation between mitochondrial and nuclear genomes as well as their synergistic effects on embryonic development.
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Affiliation(s)
- Jialin Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha 410081, Hunan, P.R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Hong Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha 410081, Hunan, P.R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Xin Gao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha 410081, Hunan, P.R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Xueyin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha 410081, Hunan, P.R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Mengxue Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha 410081, Hunan, P.R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha 410081, Hunan, P.R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University , Changsha 410081, Hunan, P.R. China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University , Guangzhou 510642, Guangdong, P.R. China
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6
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Ceriotti LF, Gatica-Soria L, Sanchez-Puerta MV. Cytonuclear coevolution in a holoparasitic plant with highly disparate organellar genomes. PLANT MOLECULAR BIOLOGY 2022; 109:673-688. [PMID: 35359176 DOI: 10.1007/s11103-022-01266-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Contrasting substitution rates in the organellar genomes of Lophophytum agree with the DNA repair, replication, and recombination gene content. Plastid and nuclear genes whose products form multisubunit complexes co-evolve. The organellar genomes of the holoparasitic plant Lophophytum (Balanophoraceae) show disparate evolution. In the plastid, the genome has been severely reduced and presents a > 85% AT content, while in the mitochondria most protein-coding genes have been replaced by homologs acquired by horizontal gene transfer (HGT) from their hosts (Fabaceae). Both genomes carry genes whose products form multisubunit complexes with those of nuclear genes, creating a possible hotspot of cytonuclear coevolution. In this study, we assessed the evolutionary rates of plastid, mitochondrial and nuclear genes, and their impact on cytonuclear evolution of genes involved in multisubunit complexes related to lipid biosynthesis and proteolysis in the plastid and those in charge of the oxidative phosphorylation in the mitochondria. Genes from the plastid and the mitochondria (both native and foreign) of Lophophytum showed extremely high and ordinary substitution rates, respectively. These results agree with the biased loss of plastid-targeted proteins involved in angiosperm organellar repair, replication, and recombination machinery. Consistent with the high rate of evolution of plastid genes, nuclear-encoded subunits of plastid complexes showed disproportionate increases in non-synonymous substitution rates, while those of the mitochondrial complexes did not show different rates than the control (i.e. non-organellar nuclear genes). Moreover, the increases in the nuclear-encoded subunits of plastid complexes were positively correlated with the level of physical interaction they possess with the plastid-encoded ones. Overall, these results suggest that a structurally-mediated compensatory factor may be driving plastid-nuclear coevolution in Lophophytum, and that mito-nuclear coevolution was not altered by HGT.
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Affiliation(s)
- Luis F Ceriotti
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - Leonardo Gatica-Soria
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina
| | - M Virginia Sanchez-Puerta
- Facultad de Ciencias Agrarias, IBAM, Universidad Nacional de Cuyo, CONICET, Almirante Brown 500, Chacras de Coria, M5528AHB, Mendoza, Argentina.
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Padre Jorge Contreras 1300, M5502JMA, Mendoza, Argentina.
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7
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Genome-wide local ancestry and evidence for mitonuclear coadaptation in African hybrid cattle populations (Bos taurus/indicus). iScience 2022; 25:104672. [PMID: 35832892 PMCID: PMC9272374 DOI: 10.1016/j.isci.2022.104672] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/11/2022] [Accepted: 06/21/2022] [Indexed: 11/21/2022] Open
Abstract
The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions, human-mediated selection preferences, and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which diverged 150-500 thousand years ago. Despite extensive admixture, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu biparental and male uniparental nuclear ancestry. This has been interpreted as the result of human-mediated dispersal ultimately stemming from zebu bulls imported from South Asia during the last three millennia. Here, we assess whether ancestry at mitochondrially targeted nuclear genes in African admixed cattle is impacted by mitonuclear functional interactions. Using high-density SNP data, we find evidence for mitonuclear coevolution across hybrid African cattle populations with a significant increase of taurine ancestry at mitochondrially targeted nuclear genes. Our results, therefore, support the hypothesis of incompatibility between the taurine mitochondrial genome and the zebu nuclear genome.
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8
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Sun B, Williams CM, Li T, Speakman JR, Jin Z, Lu H, Luo L, Du W. Higher metabolic plasticity in temperate compared to tropical lizards suggests increased resilience to climate change. ECOL MONOGR 2022. [DOI: 10.1002/ecm.1512] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Baojun Sun
- Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology, Chinese Academy of Sciences Beijing China
- Department of Integrative Biology University of California Berkeley CA USA
| | | | - Teng Li
- College of Resources and Environmental Sciences Nanjing Agricultural University Nanjing China
| | - John R. Speakman
- Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing China
- Institute of Biological and Environmental Sciences University of Aberdeen Aberdeen UK
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
| | - Zengguang Jin
- Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Hongliang Lu
- Hangzhou Key Laboratory of Animal Adaptation and Evolution Hangzhou Normal University Hangzhou People's Republic of China
| | - Laigao Luo
- Department of Biology & food engineering Chuzhou University Chuzhou People's Republic of China
| | - Weiguo Du
- Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology, Chinese Academy of Sciences Beijing China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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9
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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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10
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Allison TM, Radzvilavicius AL, Dowling DK. Selection for biparental inheritance of mitochondria under hybridization and mitonuclear fitness interactions. Proc Biol Sci 2021; 288:20211600. [PMID: 34875196 PMCID: PMC8651416 DOI: 10.1098/rspb.2021.1600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Uniparental inheritance (UPI) of mitochondria predominates over biparental inheritance (BPI) in most eukaryotes. However, examples of BPI of mitochondria, or paternal leakage, are becoming increasingly prevalent. Most reported cases of BPI occur in hybrids of distantly related sub-populations. It is thought that BPI in these cases is maladaptive; caused by a failure of female or zygotic autophagy machinery to recognize divergent male-mitochondrial DNA ‘tags’. Yet recent theory has put forward examples in which BPI can evolve under adaptive selection, and empirical studies across numerous metazoan taxa have demonstrated outbreeding depression in hybrids attributable to disruption of population-specific mitochondrial and nuclear genotypes (mitonuclear mismatch). Based on these developments, we hypothesize that BPI may be favoured by selection in hybridizing populations when fitness is shaped by mitonuclear interactions. We test this idea using a deterministic, simulation-based population genetic model and demonstrate that BPI is favoured over strict UPI under moderate levels of gene flow typical of hybridizing populations. Our model suggests that BPI may be stable, rather than a transient phenomenon, in hybridizing populations.
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Affiliation(s)
- Tom M Allison
- School of Biological Sciences, Monash University, Victoria, Australia
| | | | - Damian K Dowling
- School of Biological Sciences, Monash University, Victoria, Australia
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11
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Powers MJ, Martz LD, Burton RS, Hill GE, Weaver RJ. Evidence for hybrid breakdown in production of red carotenoids in the marine invertebrate Tigriopus californicus. PLoS One 2021; 16:e0259371. [PMID: 34748608 PMCID: PMC8575244 DOI: 10.1371/journal.pone.0259371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/18/2021] [Indexed: 11/21/2022] Open
Abstract
The marine copepod, Tigriopus californicus, produces the red carotenoid pigment astaxanthin from yellow dietary precursors. This ‘bioconversion’ of yellow carotenoids to red is hypothesized to be linked to individual condition, possibly through shared metabolic pathways with mitochondrial oxidative phosphorylation. Experimental inter-population crosses of lab-reared T. californicus typically produces low-fitness hybrids is due in large part to the disruption of coadapted sets nuclear and mitochondrial genes within the parental populations. These hybrid incompatibilities can increase variability in life history traits and energy production among hybrid lines. Here, we tested if production of astaxanthin was compromised in hybrid copepods and if it was linked to mitochondrial metabolism and offspring development. We observed no clear mitonuclear dysfunction in hybrids fed a limited, carotenoid-deficient diet of nutritional yeast. However, when yellow carotenoids were restored to their diet, hybrid lines produced less astaxanthin than parental lines. We observed that lines fed a yeast diet produced less ATP and had slower offspring development compared to lines fed a more complete diet of algae, suggesting the yeast-only diet may have obscured effects of mitonuclear dysfunction. Astaxanthin production was not significantly associated with development among lines fed a yeast diet but was negatively related to development in early generation hybrids fed an algal diet. In lines fed yeast, astaxanthin was negatively related to ATP synthesis, but in lines fed algae, the relationship was reversed. Although the effects of the yeast diet may have obscured evidence of hybrid dysfunction, these results suggest that astaxanthin bioconversion may still be related to mitochondrial performance and reproductive success.
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Affiliation(s)
- Matthew J. Powers
- Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
- * E-mail: (MJP); (LDM)
| | - Lucas D. Martz
- University of California, Scripps Institution of Oceanography, San Diego, CA, United States of America
- * E-mail: (MJP); (LDM)
| | - Ronald S. Burton
- University of California, Scripps Institution of Oceanography, San Diego, CA, United States of America
| | - Geoffrey E. Hill
- Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Ryan J. Weaver
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA, United States of America
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12
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Maeda GP, Iannello M, McConie HJ, Ghiselli F, Havird JC. Relaxed selection on male mitochondrial genes in DUI bivalves eases the need for mitonuclear coevolution. J Evol Biol 2021; 34:1722-1736. [PMID: 34533872 DOI: 10.1111/jeb.13931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/21/2021] [Accepted: 09/05/2021] [Indexed: 12/31/2022]
Abstract
Mitonuclear coevolution is an important prerequisite for efficient energy production in eukaryotes. However, many bivalve taxa experience doubly uniparental inheritance (DUI) and have sex-specific mitochondrial (mt) genomes, providing a challenge for mitonuclear coevolution. We examined possible mechanisms to reconcile mitonuclear coevolution with DUI. No nuclear-encoded, sex-specific OXPHOS paralogs were found in the DUI clam Ruditapes philippinarum, refuting OXPHOS paralogy as a solution in this species. It is also unlikely that mt changes causing disruption of nuclear interactions are strongly selected against because sex-specific mt-residues or those under positive selection in M mt genes were not depleted for contacting nuclear-encoded residues. However, M genomes showed consistently higher dN /dS ratios compared to putatively ancestral F genomes in all mt OXPHOS genes and across all DUI species. Further analyses indicated that this was consistently due to relaxed, not positive selection on M vs. F mt OXPHOS genes. Similarly, selection was relaxed on the F genome of DUI species compared to species with strict maternal inheritance. Coupled with recent physiological and molecular evolution studies, we suggest that relaxed selection on M mt function limits the need to maintain mitonuclear interactions in M genomes compared to F genomes. We discuss our findings with regard to OXPHOS function and the origin of DUI.
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Affiliation(s)
- Gerald P Maeda
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Hunter J McConie
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
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13
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Chen W, Mao X. Extensive alternative splicing triggered by mitonuclear mismatch in naturally introgressed Rhinolophus bats. Ecol Evol 2021; 11:12003-12010. [PMID: 34522356 PMCID: PMC8427577 DOI: 10.1002/ece3.7966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/07/2021] [Accepted: 07/16/2021] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial function needs strong interactions of mitochondrial and nuclear (mitonuclear) genomes, which can be disrupted by mitonuclear mismatch due to mitochondrial DNA (mtDNA) introgression between two formerly isolated populations or taxa. This mitonuclear disruption may cause severe cellular stress in mismatched individuals. Gene expression changes and alternative splicing (AS) are two important transcriptional regulations to respond to environmental or cellular stresses. We previously identified a naturally introgressed population in the intermediate horseshoe bat (Rhinolophus affinis). Individuals from this population belong to R. a. himalayanus and share almost identical nuclear genetic background; however, some of them had mtDNA from another subspecies (R. a. macrurus). With this unique natural system, we examined gene expression changes in six tissues between five mitonuclear mismatched and five matched individuals. A small number of differentially expressed genes (DEGs) were identified, and functional enrichment analysis revealed that most DEGs were related to immune response although some may be involved in response to oxidative stress. In contrast, we identified extensive AS events and alternatively spliced genes (ASGs) between mismatched and matched individuals. Functional enrichment analysis revealed that multiple ASGs were directly or indirectly associated with energy production in mitochondria which is vital for survival of organism. To our knowledge, this is the first study to examine the role of AS in responding to cellular stress caused by mitonuclear mismatch in natural populations. Our results suggest that AS may play a more important role than gene expression regulation in responding to severe environmental or cellular stresses.
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Affiliation(s)
- Wenli Chen
- School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
| | - Xiuguang Mao
- School of Ecological and Environmental SciencesEast China Normal UniversityShanghaiChina
- Institute of Eco‐Chongming (IEC)East China Normal UniversityShanghaiChina
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14
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Greimann ES, Ward SF, Woodell JD, Hennessey S, Kline MR, Moreno JA, Peters M, Cruise JL, Montooth KL, Neiman M, Sharbrough J. Phenotypic Variation in Mitochondria-Related Performance Traits Across New Zealand Snail Populations. Integr Comp Biol 2021; 60:275-287. [PMID: 32589742 DOI: 10.1093/icb/icaa066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial function is critical for energy homeostasis and should shape how genetic variation in metabolism is transmitted through levels of biological organization to generate stability in organismal performance. Mitochondrial function is encoded by genes in two distinct and separately inherited genomes-the mitochondrial genome and the nuclear genome-and selection is expected to maintain functional mito-nuclear interactions. The documented high levels of polymorphism in genes involved in these mito-nuclear interactions and wide variation for mitochondrial function demands an explanation for how and why variability in such a fundamental trait is maintained. Potamopyrgus antipodarum is a New Zealand freshwater snail with coexisting sexual and asexual individuals and, accordingly, contrasting systems of separate vs. co-inheritance of nuclear and mitochondrial genomes. As such, this snail provides a powerful means to dissect the evolutionary and functional consequences of mito-nuclear variation. The lakes inhabited by P. antipodarum span wide environmental gradients, with substantial across-lake genetic structure and mito-nuclear discordance. This situation allows us to use comparisons across reproductive modes and lakes to partition variation in cellular respiration across genetic and environmental axes. Here, we integrated cellular, physiological, and behavioral approaches to quantify variation in mitochondrial function across a diverse set of wild P. antipodarum lineages. We found extensive across-lake variation in organismal oxygen consumption and behavioral response to heat stress and differences across sexes in mitochondrial membrane potential but few global effects of reproductive mode. Taken together, our data set the stage for applying this important model system for sexual reproduction and polyploidy to dissecting the complex relationships between mito-nuclear variation, performance, plasticity, and fitness in natural populations.
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Affiliation(s)
- Emma S Greimann
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Samuel F Ward
- Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, USA
| | - James D Woodell
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | | | - Michael R Kline
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Jorge A Moreno
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Madeline Peters
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Jennifer L Cruise
- Department of Biology, University of St. Thomas, Saint Paul, MN, USA
| | - Kristi L Montooth
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Joel Sharbrough
- Department of Biology, University of Iowa, Iowa City, IA, USA
- Colorado State University, Fort Collins, CO, USA
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15
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Pereira RJ, Lima TG, Pierce-Ward NT, Chao L, Burton RS. Recovery from hybrid breakdown reveals a complex genetic architecture of mitonuclear incompatibilities. Mol Ecol 2021; 30:6403-6416. [PMID: 34003535 DOI: 10.1111/mec.15985] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/29/2021] [Accepted: 05/11/2021] [Indexed: 01/03/2023]
Abstract
Reproductive isolation is often achieved when genes that are neutral or beneficial in their genomic background become functionally incompatible in a foreign genomic background, causing inviability, sterility or other forms of low fitness in hybrids. Recent studies suggest that mitonuclear interactions are among the initial incompatibilities to evolve at early stages of population divergence across taxa. Yet, the genomic architecture of mitonuclear incompatibilities has rarely been elucidated. We employ an experimental evolution approach starting with low-fitness F2 interpopulation hybrids of the copepod Tigriopus californicus, in which frequencies of compatible and incompatible nuclear alleles change in response to an alternative mitochondrial background. After about nine generations, we observe a generalized increase in population size and in survivorship, suggesting efficiency of selection against maladaptive phenotypes. Whole genome sequencing of evolved populations showed some consistent allele frequency changes across three replicates of each reciprocal cross, but markedly different patterns between mitochondrial backgrounds. In only a few regions (~6.5% of the genome), the same parental allele was overrepresented irrespective of the mitochondrial background. About 33% of the genome showed allele frequency changes consistent with divergent selection, with the location of these genomic regions strongly differing between mitochondrial backgrounds. In 87% and 89% of these genomic regions, the dominant nuclear allele matched the associated mitochondrial background, consistent with mitonuclear co-adaptation. These results suggest that mitonuclear incompatibilities have a complex polygenic architecture that differs between populations, potentially generating genome-wide barriers to gene flow between closely related taxa.
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Affiliation(s)
- Ricardo J Pereira
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thiago G Lima
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - N Tessa Pierce-Ward
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Lin Chao
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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16
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Ghiselli F, Iannello M, Piccinini G, Milani L. Bivalve molluscs as model systems for studying mitochondrial biology. Integr Comp Biol 2021; 61:1699-1714. [PMID: 33944910 DOI: 10.1093/icb/icab057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The class Bivalvia is a highly successful and ancient taxon including ∼25,000 living species. During their long evolutionary history bivalves adapted to a wide range of physicochemical conditions, habitats, biological interactions, and feeding habits. Bivalves can have strikingly different size, and despite their apparently simple body plan, they evolved very different shell shapes, and complex anatomic structures. One of the most striking features of this class of animals is their peculiar mitochondrial biology: some bivalves have facultatively anaerobic mitochondria that allow them to survive prolonged periods of anoxia/hypoxia. Moreover, more than 100 species have now been reported showing the only known evolutionarily stable exception to the strictly maternal inheritance of mitochondria in animals, named doubly uniparental inheritance. Mitochondrial activity is fundamental to eukaryotic life, and thanks to their diversity and uncommon features, bivalves represent a great model system to expand our knowledge about mitochondrial biology, so far limited to a few species. We highlight recent works studying mitochondrial biology in bivalves at either genomic or physiological level. A link between these two approaches is still missing, and we believe that an integrated approach and collaborative relationships are the only possible ways to be successful in such endeavour.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Giovanni Piccinini
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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17
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Powers MJ, Hill GE. A review and assessment of the Shared-Pathway Hypothesis for the maintenance of signal honesty in red ketocarotenoid-based coloration. Integr Comp Biol 2021; 61:1811-1826. [PMID: 33940618 DOI: 10.1093/icb/icab056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 12/14/2022] Open
Abstract
For decades, scientists have noted connections between individual condition and carotenoid-based coloration in terrestrial and aquatic animals. Organisms that produce more vibrant carotenoid-based coloration tend to have better physiological performance and behavioral displays compared to less colorful members of the same species. Traditional explanations for this association between ornamental coloration and performance invoked the need for color displays to be costly, but evidence for such hypothesized costs is equivocal. An alternative explanation for the condition-dependence of carotenoid-based coloration, the Shared-Pathway Hypothesis, was developed in response. This hypothesis proposes that red ketocarotenoid-based coloration is tied to core cellular processes involving a shared pathway with mitochondrial energy metabolism, making the concentration of carotenoids an index of mitochondrial function. Since the presentation of this hypothesis, empirical tests of the mechanisms proposed therein have been conducted in many species. In this manuscript, we review the Shared-Pathway Hypothesis and the growing number of studies that have investigated a connection between carotenoid-based coloration and mitochondrial function. We also discuss future strategies for assessing the Shared-Pathway Hypothesis to more effectively disentangle evidence that may simultaneously support evidence of carotenoid-resource tradeoffs.
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Affiliation(s)
- Matthew J Powers
- Department of Biological Sciences, Auburn University, Auburn, AL 36849 USA
| | - Geoffrey E Hill
- Department of Biological Sciences, Auburn University, Auburn, AL 36849 USA
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18
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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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19
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Hirase S, Tezuka A, Nagano AJ, Sato M, Hosoya S, Kikuchi K, Iwasaki W. Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population. Evolution 2021; 75:176-194. [PMID: 33165944 PMCID: PMC7898790 DOI: 10.1111/evo.14120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 08/14/2020] [Accepted: 09/30/2020] [Indexed: 12/28/2022]
Abstract
Hybridization between divergent lineages generates new allelic combinations. One mechanism that can hinder the formation of hybrid populations is mitonuclear incompatibility, that is, dysfunctional interactions between proteins encoded in the nuclear and mitochondrial genomes (mitogenomes) of diverged lineages. Theoretically, selective pressure due to mitonuclear incompatibility can affect genotypes in a hybrid population in which nuclear genomes and mitogenomes from divergent lineages admix. To directly and thoroughly observe this key process, we de novo sequenced the 747-Mb genome of the coastal goby, Chaenogobius annularis, and investigated its integrative genomic phylogeographics using RNA-sequencing, RAD-sequencing, genome resequencing, whole mitogenome sequencing, amplicon sequencing, and small RNA-sequencing. Chaenogobius annularis populations have been geographically separated into Pacific Ocean (PO) and Sea of Japan (SJ) lineages by past isolation events around the Japanese archipelago. Despite the divergence history and potential mitonuclear incompatibility between these lineages, the mitogenomes of the PO and SJ lineages have coexisted for generations in a hybrid population on the Sanriku Coast. Our analyses revealed accumulation of nonsynonymous substitutions in the PO-lineage mitogenomes, including two convergent substitutions, as well as signals of mitochondrial lineage-specific selection on mitochondria-related nuclear genes. Finally, our data implied that a microRNA gene was involved in resolving mitonuclear incompatibility. Our integrative genomic phylogeographic approach revealed that mitonuclear incompatibility can affect genome evolution in a natural hybrid population.
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Affiliation(s)
- Shotaro Hirase
- Department of Biological SciencesGraduate School of ScienceThe University of TokyoBunkyo‐kuTokyo113‐0032Japan
- Fisheries LaboratoryGraduate School of Agricultural and Life SciencesThe University of TokyoHamamatsuShizuoka431‐0214Japan
| | - Ayumi Tezuka
- Faculty of AgricultureRyukoku UniversityOtsuShiga520–2194Japan
| | | | - Mana Sato
- Fisheries LaboratoryGraduate School of Agricultural and Life SciencesThe University of TokyoHamamatsuShizuoka431‐0214Japan
| | - Sho Hosoya
- Fisheries LaboratoryGraduate School of Agricultural and Life SciencesThe University of TokyoHamamatsuShizuoka431‐0214Japan
| | - Kiyoshi Kikuchi
- Fisheries LaboratoryGraduate School of Agricultural and Life SciencesThe University of TokyoHamamatsuShizuoka431‐0214Japan
| | - Wataru Iwasaki
- Department of Biological SciencesGraduate School of ScienceThe University of TokyoBunkyo‐kuTokyo113‐0032Japan
- Atmosphere and Ocean Research InstituteThe University of TokyoKashiwaChiba277–8564Japan
- Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoKashiwaChiba277–8561Japan
- Institute for Quantitative BiosciencesThe University of TokyoBunkyo‐kuTokyo113‐0032Japan
- Collaborative Research Institute for Innovative MicrobiologyThe University of TokyoBunkyo‐kuTokyo113‐0032Japan
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20
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Lechuga-Vieco AV, Justo-Méndez R, Enríquez JA. Not all mitochondrial DNAs are made equal and the nucleus knows it. IUBMB Life 2020; 73:511-529. [PMID: 33369015 PMCID: PMC7985871 DOI: 10.1002/iub.2434] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/06/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022]
Abstract
The oxidative phosphorylation (OXPHOS) system is the only structure in animal cells with components encoded by two genomes, maternally transmitted mitochondrial DNA (mtDNA), and biparentally transmitted nuclear DNA (nDNA). MtDNA‐encoded genes have to physically assemble with their counterparts encoded in the nucleus to build together the functional respiratory complexes. Therefore, structural and functional matching requirements between the protein subunits of these molecular complexes are rigorous. The crosstalk between nDNA and mtDNA needs to overcome some challenges, as the nuclear‐encoded factors have to be imported into the mitochondria in a correct quantity and match the high number of organelles and genomes per mitochondria that encode and synthesize their own components locally. The cell is able to sense the mito‐nuclear match through changes in the activity of the OXPHOS system, modulation of the mitochondrial biogenesis, or reactive oxygen species production. This implies that a complex signaling cascade should optimize OXPHOS performance to the cellular‐specific requirements, which will depend on cell type, environmental conditions, and life stage. Therefore, the mitochondria would function as a cellular metabolic information hub integrating critical information that would feedback the nucleus for it to respond accordingly. Here, we review the current understanding of the complex interaction between mtDNA and nDNA.
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Affiliation(s)
- Ana Victoria Lechuga-Vieco
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.,MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Raquel Justo-Méndez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
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21
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Nguyen THM, Sondhi S, Ziesel A, Paliwal S, Fiumera HL. Mitochondrial-nuclear coadaptation revealed through mtDNA replacements in Saccharomyces cerevisiae. BMC Evol Biol 2020; 20:128. [PMID: 32977769 PMCID: PMC7517635 DOI: 10.1186/s12862-020-01685-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/07/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondrial function requires numerous genetic interactions between mitochondrial- and nuclear- encoded genes. While selection for optimal mitonuclear interactions should result in coevolution between both genomes, evidence for mitonuclear coadaptation is challenging to document. Genetic models where mitonuclear interactions can be explored are needed. RESULTS We systematically exchanged mtDNAs between 15 Saccharomyces cerevisiae isolates from a variety of ecological niches to create 225 unique mitochondrial-nuclear genotypes. Analysis of phenotypic profiles confirmed that environmentally-sensitive interactions between mitochondrial and nuclear genotype contributed to growth differences. Exchanges of mtDNAs between strains of the same or different clades were just as likely to demonstrate mitonuclear epistasis although epistatic effect sizes increased with genetic distances. Strains with their original mtDNAs were more fit than strains with synthetic mitonuclear combinations when grown in media that resembled isolation habitats. CONCLUSIONS This study shows that natural variation in mitonuclear interactions contributes to fitness landscapes. Multiple examples of coadapted mitochondrial-nuclear genotypes suggest that selection for mitonuclear interactions may play a role in helping yeasts adapt to novel environments and promote coevolution.
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Affiliation(s)
- Tuc H M Nguyen
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
| | - Sargunvir Sondhi
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
| | - Andrew Ziesel
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
| | - Swati Paliwal
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Rajasthan, India
| | - Heather L Fiumera
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA.
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22
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Salminen TS, Vale PF. Drosophila as a Model System to Investigate the Effects of Mitochondrial Variation on Innate Immunity. Front Immunol 2020; 11:521. [PMID: 32269576 PMCID: PMC7109263 DOI: 10.3389/fimmu.2020.00521] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 03/06/2020] [Indexed: 12/14/2022] Open
Abstract
Understanding why the response to infection varies between individuals remains one of the major challenges in immunology and infection biology. A substantial proportion of this heterogeneity can be explained by individual genetic differences which result in variable immune responses, and there are many examples of polymorphisms in nuclear-encoded genes that alter immunocompetence. However, how immunity is affected by genetic polymorphism in an additional genome, inherited maternally inside mitochondria (mtDNA), has been relatively understudied. Mitochondria are increasingly recognized as important mediators of innate immune responses, not only because they are the main source of energy required for costly immune responses, but also because by-products of mitochondrial metabolism, such as reactive oxygen species (ROS), may have direct microbicidal action. Yet, it is currently unclear how naturally occurring variation in mtDNA contributes to heterogeneity in infection outcomes. In this review article, we describe potential sources of variation in mitochondrial function that may arise due to mutations in vital nuclear and mitochondrial components of energy production or due to a disruption in mito-nuclear crosstalk. We then highlight how these changes in mitochondrial function can impact immune responses, focusing on their effects on ATP- and ROS-generating pathways, as well as immune signaling. Finally, we outline how being a powerful and genetically tractable model of infection, immunity and mitochondrial genetics makes the fruit fly Drosophila melanogaster ideally suited to dissect mitochondrial effects on innate immune responses to infection.
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Affiliation(s)
- Tiina S. Salminen
- School of Biological Sciences, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, United Kingdom
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Pedro F. Vale
- School of Biological Sciences, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, United Kingdom
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23
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Strong selective effects of mitochondrial DNA on the nuclear genome. Proc Natl Acad Sci U S A 2020; 117:6616-6621. [PMID: 32156736 DOI: 10.1073/pnas.1910141117] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Oxidative phosphorylation, the primary source of cellular energy in eukaryotes, requires gene products encoded in both the nuclear and mitochondrial genomes. As a result, functional integration between the genomes is essential for efficient adenosine triphosphate (ATP) generation. Although within populations this integration is presumably maintained by coevolution, the importance of mitonuclear coevolution in key biological processes such as speciation and mitochondrial disease has been questioned. In this study, we crossed populations of the intertidal copepod Tigriopus californicus to disrupt putatively coevolved mitonuclear genotypes in reciprocal F2 hybrids. We utilized interindividual variation in developmental rate among these hybrids as a proxy for fitness to assess the strength of selection imposed on the nuclear genome by alternate mitochondrial genotypes. Developmental rate varied among hybrid individuals, and in vitro ATP synthesis rates of mitochondria isolated from high-fitness hybrids were approximately two-fold greater than those of mitochondria isolated from low-fitness individuals. We then used Pool-seq to compare nuclear allele frequencies for high- or low-fitness hybrids. Significant biases for maternal alleles were detected on 5 (of 12) chromosomes in high-fitness individuals of both reciprocal crosses, whereas maternal biases were largely absent in low-fitness individuals. Therefore, the most fit hybrids were those with nuclear alleles that matched their mitochondrial genotype on these chromosomes, suggesting that mitonuclear effects underlie individual-level variation in developmental rate and that intergenomic compatibility is critical for high fitness. We conclude that mitonuclear interactions can have profound impacts on both physiological performance and the evolutionary trajectory of the nuclear genome.
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24
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Wong ELY, Nevado B, Osborne OG, Papadopulos AST, Bridle JR, Hiscock SJ, Filatov DA. Strong divergent selection at multiple loci in two closely related species of ragworts adapted to high and low elevations on Mount Etna. Mol Ecol 2019; 29:394-412. [PMID: 31793091 DOI: 10.1111/mec.15319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/28/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022]
Abstract
Recently diverged species present particularly informative systems for studying speciation and maintenance of genetic divergence in the face of gene flow. We investigated speciation in two closely related Senecio species, S. aethnensis and S. chrysanthemifolius, which grow at high and low elevations, respectively, on Mount Etna, Sicily and form a hybrid zone at intermediate elevations. We used a newly generated genome-wide single nucleotide polymorphism (SNP) dataset from 192 individuals collected over 18 localities along an elevational gradient to reconstruct the likely history of speciation, identify highly differentiated SNPs, and estimate the strength of divergent selection. We found that speciation in this system involved heterogeneous and bidirectional gene flow along the genome, and species experienced marked population size changes in the past. Furthermore, we identified highly-differentiated SNPs between the species, some of which are located in genes potentially involved in ecological differences between species (such as photosynthesis and UV response). We analysed the shape of these SNPs' allele frequency clines along the elevational gradient. These clines show significantly variable coincidence and concordance, indicative of the presence of multifarious selective forces. Selection against hybrids is estimated to be very strong (0.16-0.78) and one of the highest reported in literature. The combination of strong cumulative selection across the genome and previously identified intrinsic incompatibilities probably work together to maintain the genetic and phenotypic differentiation between these species - pointing to the importance of considering both intrinsic and extrinsic factors when studying divergence and speciation.
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Affiliation(s)
- Edgar L Y Wong
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Owen G Osborne
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | | - Jon R Bridle
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Simon J Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, UK
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25
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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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26
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Rand DM, Mossman JA. Mitonuclear conflict and cooperation govern the integration of genotypes, phenotypes and environments. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190188. [PMID: 31787039 PMCID: PMC6939372 DOI: 10.1098/rstb.2019.0188] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The mitonuclear genome is the most successful co-evolved mutualism in the history of life on Earth. The cross-talk between the mitochondrial and nuclear genomes has been shaped by conflict and cooperation for more than 1.5 billion years, yet this system has adapted to countless genomic reorganizations by each partner, and done so under changing environments that have placed dramatic biochemical and physiological pressures on evolving lineages. From putative anaerobic origins, mitochondria emerged as the defining aerobic organelle. During this transition, the two genomes resolved rules for sex determination and transmission that made uniparental inheritance the dominant, but not a universal pattern. Mitochondria are much more than energy-producing organelles and play crucial roles in nutrient and stress signalling that can alter how nuclear genes are expressed as phenotypes. All of these interactions are examples of genotype-by-environment (GxE) interactions, gene-by-gene (GxG) interactions (epistasis) or more generally context-dependent effects on the link between genotype and phenotype. We provide evidence from our own studies in Drosophila, and from those of other systems, that mitonuclear interactions—either conflicting or cooperative—are common features of GxE and GxG. We argue that mitonuclear interactions are an important model for how to better understand the pervasive context-dependent effects underlying the architecture of complex phenotypes. Future research in this area should focus on the quantitative genetic concept of effect size to place mitochondrial links to phenotype in a proper context. This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.
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Affiliation(s)
- David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI, USA
| | - Jim A Mossman
- Department of Ecology and Evolutionary Biology, Brown University, 80 Waterman Street, Box G, Providence, RI, USA
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27
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Havird JC, Noe GR, Link L, Torres A, Logan DC, Sloan DB, Chicco AJ. Do angiosperms with highly divergent mitochondrial genomes have altered mitochondrial function? Mitochondrion 2019; 49:1-11. [PMID: 31229574 PMCID: PMC6885534 DOI: 10.1016/j.mito.2019.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 06/07/2019] [Accepted: 06/17/2019] [Indexed: 02/06/2023]
Abstract
Angiosperm mitochondrial (mt) genes are generally slow-evolving, but multiple lineages have undergone dramatic accelerations in rates of nucleotide substitution and extreme changes in mt genome structure. While molecular evolution in these lineages has been investigated, very little is known about their mt function. Some studies have suggested altered respiration in individual taxa, although there are several reasons why mt variation might be neutral in others. Here, we develop a new protocol to characterize respiration in isolated plant mitochondria and apply it to species of Silene with mt genomes that are rapidly evolving, highly fragmented, and exceptionally large (~11 Mbp). This protocol, complemented with traditional measures of plant fitness, cytochrome c oxidase activity assays, and fluorescence microscopy, was also used to characterize inter- and intraspecific variation in mt function. Contributions of the individual "classic" OXPHOS complexes, the alternative oxidase, and external NADH dehydrogenases to overall mt respiratory flux were found to be similar to previously studied angiosperms with more typical mt genomes. Some differences in mt function could be explained by inter- and intraspecific variation. This study suggests that Silene species with peculiar mt genomes still show relatively normal mt respiration. This may be due to strong purifying selection on mt variants, coevolutionary responses in the nucleus, or a combination of both. Future experiments should explore such questions using a comparative framework and investigating other lineages with unusual mitogenomes.
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Affiliation(s)
- Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO, USA; Department of Integrative Biology, The University of Texas, Austin, TX, USA.
| | - Gregory R Noe
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Luke Link
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Amber Torres
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - David C Logan
- IRHS, INRA, Université d'Angers, AGROCAMPUS-Ouest, SFR 4207 QUASAV, 49071 Beaucouzé cedex, France
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - Adam J Chicco
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, USA.
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28
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Shtolz N, Mishmar D. The Mitochondrial Genome–on Selective Constraints and Signatures at the Organism, Cell, and Single Mitochondrion Levels. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00342] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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29
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Forsythe ES, Sharbrough J, Havird JC, Warren JM, Sloan DB. CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis. Genome Biol Evol 2019; 11:2194-2202. [PMID: 31282937 PMCID: PMC6685490 DOI: 10.1093/gbe/evz144] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2019] [Indexed: 12/11/2022] Open
Abstract
The function and evolution of eukaryotic cells depend upon direct molecular interactions between gene products encoded in nuclear and cytoplasmic genomes. Understanding how these cytonuclear interactions drive molecular evolution and generate genetic incompatibilities between isolated populations and species is of central importance to eukaryotic biology. Plants are an outstanding system to investigate such effects because of their two different genomic compartments present in the cytoplasm (mitochondria and plastids) and the extensive resources detailing subcellular targeting of nuclear-encoded proteins. However, the field lacks a consistent classification scheme for mitochondrial- and plastid-targeted proteins based on their molecular interactions with cytoplasmic genomes and gene products, which hinders efforts to standardize and compare results across studies. Here, we take advantage of detailed knowledge about the model angiosperm Arabidopsis thaliana to provide a curated database of plant cytonuclear interactions at the molecular level. CyMIRA (Cytonuclear Molecular Interactions Reference for Arabidopsis) is available at http://cymira.colostate.edu/ and https://github.com/dbsloan/cymira and will serve as a resource to aid researchers in partitioning evolutionary genomic data into functional gene classes based on organelle targeting and direct molecular interaction with cytoplasmic genomes and gene products. It includes 11 categories (and 27 subcategories) of different cytonuclear complexes and types of molecular interactions, and it reports residue-level information for cytonuclear contact sites. We hope that this framework will make it easier to standardize, interpret, and compare studies testing the functional and evolutionary consequences of cytonuclear interactions.
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Affiliation(s)
| | | | - Justin C Havird
- Department of Integrative Biology, University of Texas, Austin
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30
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Dobelmann J, Alexander A, Baty JW, Gemmell NJ, Gruber MAM, Quinn O, Wenseleers T, Lester PJ. The association between mitochondrial genetic variation and reduced colony fitness in an invasive wasp. Mol Ecol 2019; 28:3324-3338. [PMID: 31233636 DOI: 10.1111/mec.15159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 05/27/2019] [Accepted: 05/31/2019] [Indexed: 12/13/2022]
Abstract
Despite the mitochondrion's long-recognized role in energy production, mitochondrial DNA (mtDNA) variation commonly found in natural populations was assumed to be effectively neutral. However, variation in mtDNA has now been increasingly linked to phenotypic variation in life history traits and fitness. We examined whether the relative fitness in native and invasive common wasp (Vespula vulgaris) populations in Belgium and New Zealand (NZ), respectively, can be linked to mtDNA variation. Social wasp colonies in NZ were smaller with comparatively fewer queen cells, indicating a reduced relative fitness in the invaded range. Interestingly, queen cells in this population were significantly larger leading to larger queen offspring. By sequencing 1,872 bp of the mitochondrial genome, we determined mitochondrial haplotypes and detected reduced genetic diversity in NZ. Three common haplotypes in NZ frequently produced many queens, whereas the four rare haplotypes produced significantly fewer or no queens. The entire mitochondrial genome for each of these haplotypes was sequenced to identify polymorphisms associated with fitness reduction. We found 16 variable sites; however, no nonsynonymous mutation that was clearly causing impaired mitochondrial function was detected. We discuss how detected variants may alter secondary structures, gene expression or mito-nuclear interactions, or could be associated with nuclear-encoded variation. Whatever the ultimate mechanism, we show reduced fitness and mtDNA variation in an invasive wasp population as well as specific mtDNA variants associated with fitness variation within this population. Ours is one of only a few studies that confirm fitness impacts of mtDNA variation in wild nonmodel populations.
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Affiliation(s)
- Jana Dobelmann
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Alana Alexander
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - James W Baty
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Monica A M Gruber
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Oliver Quinn
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Tom Wenseleers
- Department of Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Philip J Lester
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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31
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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: 74] [Impact Index Per Article: 14.8] [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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32
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Harada AE, Healy TM, Burton RS. Variation in Thermal Tolerance and Its Relationship to Mitochondrial Function Across Populations of Tigriopus californicus. Front Physiol 2019; 10:213. [PMID: 30930787 PMCID: PMC6429002 DOI: 10.3389/fphys.2019.00213] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/19/2019] [Indexed: 12/22/2022] Open
Abstract
Variation in thermal tolerance plays a key role in determining the biogeographic distribution of organisms. Consequently, identifying the mechanistic basis for thermal tolerance is necessary for understanding not only current species range limits but also the capacity for range limits to shift in response to climate change. Although variation in mitochondrial function likely contributes to variation in thermal tolerance, the extent to which mitochondrial function underlies local thermal adaptation is not fully understood. In the current study, we examine variation in thermal tolerance and mitochondrial function among three populations of the intertidal copepod Tigriopus californicus found across a latitudinal thermal gradient along the coast of California, USA. We tested (1) acute thermal tolerance using survivorship and knockdown assays, (2) chronic thermal tolerance using survivorship of nauplii and developmental rate, and (3) mitochondrial performance at a range of temperatures using ATP synthesis fueled by complexes I, II, and I&II, as well as respiration of permeabilized fibers. We find evidence for latitudinal thermal adaptation: the southernmost San Diego population outperforms the northernmost Santa Cruz in measures of survivorship, knockdown temperature, and ATP synthesis rates during acute thermal exposures. However, under a chronic thermal regime, survivorship and developmental rate are more similar in the southernmost and northernmost population than in the mid-range population (Abalone Cove). Though this pattern is unexpected, it aligns well with population-specific rates of ATP synthesis at these chronic temperatures. Combined with the tight correlation of ATP synthesis decline and knockdown temperature, these data suggest a role for mitochondria in setting thermal range limits and indicate that divergence in mitochondrial function is likely a component of adaptation across latitudinal thermal gradients.
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Affiliation(s)
- Alice E Harada
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Timothy M Healy
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
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33
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Matos I, Machado MP, Schartl M, Coelho MM. Allele-specific expression variation at different ploidy levels in Squalius alburnoides. Sci Rep 2019; 9:3688. [PMID: 30842567 PMCID: PMC6403402 DOI: 10.1038/s41598-019-40210-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/07/2019] [Indexed: 11/09/2022] Open
Abstract
Allopolyploid plants are long known to be subject to a homoeolog expression bias of varying degree. The same phenomenon was only much later suspected to occur also in animals based on studies of single selected genes in an allopolyploid vertebrate, the Iberian fish Squalius alburnoides. Consequently, this species became a good model for understanding the evolution of gene expression regulation in polyploid vertebrates. Here, we analyzed for the first time genome-wide allele-specific expression data from diploid and triploid hybrids of S. alburnoides and compared homoeolog expression profiles of adult livers and of juveniles. Co-expression of alleles from both parental genomic types was observed for the majority of genes, but with marked homoeolog expression bias, suggesting homoeolog specific reshaping of expression level patterns in hybrids. Complete silencing of one allele was also observed irrespective of ploidy level, but not transcriptome wide as previously speculated. Instead, it was found only in a restricted number of genes, particularly ones with functions related to mitochondria and ribosomes. This leads us to hypothesize that allelic silencing may be a way to overcome intergenomic gene expression interaction conflicts, and that homoeolog expression bias may be an important mechanism in the achievement of sustainable genomic interactions, mandatory to the success of allopolyploid systems, as in S. alburnoides.
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Affiliation(s)
- Isa Matos
- Faculdade de Ciências, cE3c- Centro de Ecologia, Evolução e Alterações Ambientais, Departamento de Biologia Animal, Universidade de Lisboa Campo Grande, 1749-016, Lisboa, Portugal.,University of Würzburg, Biozentrum, Physiological Chemistry, Am Hubland, Würzburg, Germany
| | - Miguel P Machado
- Faculdade de Ciências, cE3c- Centro de Ecologia, Evolução e Alterações Ambientais, Departamento de Biologia Animal, Universidade de Lisboa Campo Grande, 1749-016, Lisboa, Portugal.,University of Würzburg, Biozentrum, Physiological Chemistry, Am Hubland, Würzburg, Germany.,Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Manfred Schartl
- University of Würzburg, Biozentrum, Physiological Chemistry, Am Hubland, Würzburg, Germany. .,Comprehensive Cancer Center, University Clinic Würzburg, Josef Schneider Straße 6, 97074, Würzburg, Germany. .,Hagler Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, USA.
| | - Maria Manuela Coelho
- Faculdade de Ciências, cE3c- Centro de Ecologia, Evolução e Alterações Ambientais, Departamento de Biologia Animal, Universidade de Lisboa Campo Grande, 1749-016, Lisboa, Portugal
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34
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Dobler R, Dowling DK, Morrow EH, Reinhardt K. A systematic review and meta-analysis reveals pervasive effects of germline mitochondrial replacement on components of health. Hum Reprod Update 2019; 24:519-534. [PMID: 29757366 DOI: 10.1093/humupd/dmy018] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 05/03/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Mitochondrial replacement, a form of nuclear transfer, has been proposed as a germline therapy to prevent the transmission of mitochondrial diseases. Mitochondrial replacement therapy has been licensed for clinical application in the UK, and already carried out in other countries, but little is known about negative or unintended effects on the health of offspring born using this technique. OBJECTIVE AND RATIONALE Studies in invertebrate models have used techniques that achieve mitochondrial replacement to create offspring with novel combinations of mitochondrial and nuclear genotype. These have demonstrated that the creation of novel mitochondrial-nuclear interactions can lead to alterations in offspring characteristics, such as development rates, fertility and longevity. However, it is currently unclear whether such interactions could similarly affect the outcomes of vertebrate biomedical studies, which have sought to assess the efficacy of the replacement therapy. SEARCH METHODS This systematic review addresses whether the effects of mitochondrial replacement on offspring characteristics differ in magnitude between biological (conducted on invertebrate models, with an ecological or evolutionary focus) and biomedical studies (conducted on vertebrate models, with a clinical focus). Studies were selected based on a key-word search in 'Web of Science', complemented by backward searches of reviews on the topic of mitochondrial-nuclear (mito-nuclear) interactions. In total, 43 of the resulting 116 publications identified in the search contained reliable data to estimate effect sizes of mitochondrial replacement. We found no evidence of publication bias when examining effect-size estimates across sample sizes. OUTCOMES Mitochondrial replacement consistently altered the phenotype, with significant effects at several levels of organismal performance and health, including gene expression, anatomy, metabolism and life-history. Biomedical and biological studies, while differing in the methods used to achieve mitochondrial replacement, showed only marginally significant differences in effect-size estimates (-0.233 [CI: -0.495 to -0.011]), with larger effect-size estimates in biomedical studies (0.697 [CI: 0.450-0.956]) than biological studies (0.462 [CI: 0.287-0.688]). Humans showed stronger effects than other species. Effects of mitochondrial replacement were also stronger in species with a higher basal metabolic rate. Based on our results, we conducted the first formal risk analysis of mitochondrial replacement, and conservatively estimate negative effects in at least one in every 130 resulting offspring born to the therapy. WIDER IMPLICATIONS Our findings suggest that mitochondrial replacement may routinely affect offspring characteristics across a wide array of animal species, and that such effects are likely to extend to humans. Studies in invertebrate models have confirmed mito-nuclear interactions as the underpinning cause of organismal effects following mitochondrial replacement. This therefore suggests that mito-nuclear interactions are also likely to be contributing to effects seen in biomedical studies, on vertebrate models, whose effect sizes exceeded those of biological studies. Our results advocate the use of safeguards that could offset any negative effects (defining any unintended effect as being negative) mediated by mito-nuclear interactions following mitochondrial replacement in humans, such as mitochondrial genetic matching between donor and recipient. Our results also suggest that further research into the molecular nature of mito-nuclear interactions would be beneficial in refining the clinical application of mitochondrial replacement, and in establishing what degree of variation between donor and patient mitochondrial DNA haplotypes is acceptable to ensure 'haplotype matching'.
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Affiliation(s)
- Ralph Dobler
- Applied Zoology, Technische Universität Dresden, Zellescher Weg 20b, Dresden, Germany
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Vic., Australia
| | - Edward H Morrow
- Evolution, Behaviour and Environment Group, School of Life Sciences, University of Sussex, Brighton, UK
| | - Klaus Reinhardt
- Applied Zoology, Technische Universität Dresden, Zellescher Weg 20b, Dresden, Germany
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35
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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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36
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Foley HB, Sun PY, Ramirez R, So BK, Venkataraman YR, Nixon EN, Davies KJA, Edmands S. Sex-specific stress tolerance, proteolysis, and lifespan in the invertebrate Tigriopus californicus. Exp Gerontol 2019; 119:146-156. [PMID: 30738921 DOI: 10.1016/j.exger.2019.02.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/04/2019] [Accepted: 02/06/2019] [Indexed: 11/30/2022]
Abstract
Because stress tolerance and longevity are mechanistically and phenotypically linked, the sex with higher acute stress tolerance might be expected to also live longer. On the other hand, the association between stress tolerance and lifespan may be complicated by tradeoffs between acute tolerance and long-term survival. Here we use the copepod Tigriopus californicus to test for sex differences in stress resistance, proteolytic activity and longevity. Unlike many model organisms, this species does not have sex chromosomes. However, substantial sex differences were still observed. Females were found to have superior tolerance to a range of acute stressors (high temperature, high salinity, low salinity, copper and bisphenol A (BPA)) across a variety of treatments including different populations, pure vs. hybrid crosses, and different shading environments. Upregulation of proteolytic capacity - one molecular mechanism for responding to acute stress - was also found to be sexually dimorphic. In the combined stress treatment of chronic copper exposure followed by acute heat exposure, proteolytic capacity was suppressed for males. Females, however, maintained a robust proteolytic stress response. While females consistently showed greater tolerance to short-term stress, lifespan was largely equivalent between the two sexes under both benign conditions and mild thermal stress. Our findings indicate that short-term stress tolerance does not predict long-term survival under relatively mild conditions.
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Affiliation(s)
- Helen B Foley
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA 90089, USA
| | - Patrick Y Sun
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA 90089, USA; Leonard Davis School of Gerontology of the Ethel Percy Andrus Gerontology Center, University of Southern California, Los Angeles, CA 90089, USA
| | - Rocio Ramirez
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA 90089, USA
| | - Brandon K So
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA 90089, USA
| | - Yaamini R Venkataraman
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA 90089, USA
| | - Emily N Nixon
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA 90089, USA
| | - Kelvin J A Davies
- Leonard Davis School of Gerontology of the Ethel Percy Andrus Gerontology Center, University of Southern California, Los Angeles, CA 90089, USA; Molecular & Computational Biology Division, Department of Biological Sciences, College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Biochemistry and Molecular Medicine, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA 90089, USA
| | - Suzanne Edmands
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA 90089, USA.
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37
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Sex and Mitonuclear Adaptation in Experimental Caenorhabditis elegans Populations. Genetics 2019; 211:1045-1058. [PMID: 30670540 DOI: 10.1534/genetics.119.301935] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/17/2019] [Indexed: 01/10/2023] Open
Abstract
To reveal phenotypic and functional genomic patterns of mitonuclear adaptation, a laboratory adaptation study with Caenorhabditis elegans nematodes was conducted in which independently evolving lines were initiated from a low-fitness mitochondrial electron transport chain (ETC) mutant, gas-1 Following 60 generations of evolution in large population sizes with competition for food resources, two distinct classes of lines representing different degrees of adaptive response emerged: a low-fitness class that exhibited minimal or no improvement compared to the gas-1 mutant ancestor, and a high-fitness class containing lines that exhibited partial recovery of wild-type fitness. Many lines that achieved higher reproductive and competitive fitness levels were also noted to evolve high frequencies of males during the experiment, consistent with adaptation in these lines having been facilitated by outcrossing. Whole-genome sequencing and analysis revealed an enrichment of mutations in loci that occur in a gas-1-centric region of the C. elegans interactome and could be classified into a small number of functional genomic categories. A highly nonrandom pattern of mitochondrial DNA mutation was observed within high-fitness gas-1 lines, with parallel fixations of nonsynonymous base substitutions within genes encoding NADH dehydrogenase subunits I and VI. These mitochondrial gene products reside within ETC complex I alongside the nuclear-encoded GAS-1 protein, suggesting that rapid adaptation of select gas-1 recovery lines was driven by fixation of compensatory mitochondrial mutations.
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38
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Investigating mitonuclear interactions in human admixed populations. Nat Ecol Evol 2019; 3:213-222. [PMID: 30643241 PMCID: PMC6925600 DOI: 10.1038/s41559-018-0766-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/22/2018] [Indexed: 12/13/2022]
Abstract
To function properly, mitochondria utilize products of 37 mitochondrial and >1,000 nuclear genes, which should be compatible with each other. Discordance between mitochondrial and nuclear genetic ancestry could contribute to phenotypic variation in admixed populations. Here, we explored potential mitonuclear incompatibility in six admixed human populations from the Americas: African Americans, African Caribbeans, Colombians, Mexicans, Peruvians and Puerto Ricans. By comparing nuclear versus mitochondrial ancestry in these populations, we first show that mitochondrial DNA (mtDNA) copy number decreases with increasing discordance between nuclear and mtDNA ancestry. The direction of this effect is consistent across mtDNA haplogroups of different geographic origins. This observation indicates suboptimal regulation of mtDNA replication when its components are encoded by nuclear and mtDNA genes with different ancestry. Second, while most populations analysed exhibit no such trend, in African Americans and Puerto Ricans, we find a significant enrichment of ancestry at nuclear-encoded mitochondrial genes towards the source populations contributing the most prevalent mtDNA haplogroups (African and Native American, respectively). This possibly reflects compensatory effects of selection in recovering mitonuclear interactions optimized in the source populations. Our results provide evidence of mitonuclear interactions in human admixed populations and we discuss their implications for human health and disease.
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39
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Giannoulis T, Plageras D, Stamatis C, Chatzivagia E, Tsipourlianos A, Birtsas P, Billinis C, Suchentrunk F, Mamuris Z. Islands and hybrid zones: combining the knowledge from "Natural Laboratories" to explain phylogeographic patterns of the European brown hare. BMC Evol Biol 2019; 19:17. [PMID: 30630408 PMCID: PMC6329171 DOI: 10.1186/s12862-019-1354-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 01/02/2019] [Indexed: 12/30/2022] Open
Abstract
Background The aim of the study was to use hybrid populations as well as island populations of the European brown hare (Lepus europaeus) to explore the effect of evolutionary events, such as the post-deglaciation translocations, spontaneous and human-mediated, local adaptation and the genetic drift in the shaping of the phylogeographic patterns of the species. For this purpose, we used molecular markers, both nuclear and mitochondrial, that are indicative for local adaptation as well as neutral markers to elucidate the patterns of population differentiation based on geographic isolation and the clade of origin. To broaden our analysis, we included data from our previous studies concerning mainland populations, to explore the genetic differentiation in the base of the geographic origin (mainland/island) of the populations. Results Our results suggest that local adaptation shapes the differentiation in both genomes, favoring specific alleles in nuclear genes (e.g. DQA) or haplotypes in mtDNA (e.g. Control Region, CR). mtDNA variation was found to be in a higher level and was able to give a phylogeographic signal for the populations. Furthermore, the degree of variation was influenced not only by the geographic origin, but also by the clade of origin, since specific island populations of Anatolian origin showed a greater degree of variation compared to specific mainland populations of the European clade. Concerning the hybrid population, we confirmed the existence of both clades in the territory and we provided a possible explanation for the lack of introgression between the clades. Conclusion Our results indicate that the Quaternary’s climatic oscillations played a major role in the shaping of the phylogeographic patterns of the species, by isolating populations in the distinct refugia, where they adapted and differentiate in allopatry, leading to genome incompatibilities observed nowadays. Electronic supplementary material The online version of this article (10.1186/s12862-019-1354-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Themistoklis Giannoulis
- Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, Larissa, Greece
| | - Dimitrios Plageras
- Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, Larissa, Greece
| | - Costas Stamatis
- Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, Larissa, Greece
| | - Eleni Chatzivagia
- Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, Larissa, Greece
| | - Andreas Tsipourlianos
- Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, Larissa, Greece
| | - Periklis Birtsas
- Department of Forestry and Natural Environment Administration, TEI of Thessaly, Larissa, Greece
| | | | - Franz Suchentrunk
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, University of Thessaly, Viopolis, Mezourlo, Larissa, Greece.
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40
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Zascavage RR, Planz JV. Admixture Effects on Coevolved Metabolic Systems. Front Genet 2019; 9:634. [PMID: 30619461 PMCID: PMC6299042 DOI: 10.3389/fgene.2018.00634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/27/2018] [Indexed: 11/13/2022] Open
Abstract
Oxidative phosphorylation (OXPHOS) is the primary energy generating system in eukaryotic organisms. The complexes within the OXPHOS pathway are of mixed genomic origin. Although most subunit-coding genes are located within the nuclear genome, several genes are coded for in the mitochondrial genome. There is strong evidence to support coadaptation between the two genomes in these OXPHOS gene regions in order to create tight protein interactions necessary for a functional energetics system. In this study, we begin to assess the physiological impact of separating coevolved protein motifs that make up the highly conserved energy production pathway, as we hypothesize that divergent matings will significantly diminish the protein interactions and therefore hinder efficient OXPHOS activity We measured mitochondrial activity in high energy-demanding tissues from six strains of Mus musculus with varying degrees of mixed ancestral background. Mice with divergent mitochondrial and nuclear backgrounds consistently yielded lower mitochondrial activity. Bioinformatic analysis of common single nucleotide variants across the nuclear and mitochondrial genomes failed to identify any non-synonymous variants that could account for the energetic differences, suggesting that interpopulational mating between ancestrally distinct groups influences energy production efficiency.
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Affiliation(s)
- Roxanne R Zascavage
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, United States.,Department of Criminology and Criminal Justice, University of Texas at Arlington, Arlington, TX, United States
| | - John V Planz
- Department of Microbiology, Immunology and Genetics, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX, United States
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41
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Sloan DB, Warren JM, Williams AM, Wu Z, Abdel-Ghany SE, Chicco AJ, Havird JC. Cytonuclear integration and co-evolution. Nat Rev Genet 2018; 19:635-648. [PMID: 30018367 PMCID: PMC6469396 DOI: 10.1038/s41576-018-0035-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The partitioning of genetic material between the nucleus and cytoplasmic (mitochondrial and plastid) genomes within eukaryotic cells necessitates coordinated integration between these genomic compartments, with important evolutionary and biomedical implications. Classic questions persist about the pervasive reduction of cytoplasmic genomes via a combination of gene loss, transfer and functional replacement - and yet why they are almost always retained in some minimal form. One striking consequence of cytonuclear integration is the existence of 'chimeric' enzyme complexes composed of subunits encoded in two different genomes. Advances in structural biology and comparative genomics are yielding important insights into the evolution of such complexes, including correlated sequence changes and recruitment of novel subunits. Thus, chimeric cytonuclear complexes provide a powerful window into the mechanisms of molecular co-evolution.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
| | - Jessica M Warren
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Alissa M Williams
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Adam J Chicco
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO, USA
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42
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Haenel GJ, Del Gaizo Moore V. Functional Divergence of Mitochondria and Coevolution of Genomes: Cool Mitochondria in Hot Lizards. Physiol Biochem Zool 2018; 91:1068-1081. [DOI: 10.1086/699918] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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43
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Barreto FS, Watson ET, Lima TG, Willett CS, Edmands S, Li W, Burton RS. Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus. Nat Ecol Evol 2018; 2:1250-1257. [DOI: 10.1038/s41559-018-0588-1] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Accepted: 05/21/2018] [Indexed: 12/19/2022]
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44
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Angers B, Chapdelaine V, Deremiens L, Vergilino R, Leung C, Doucet SL, Glémet H, Angers A. Gene flow prevents mitonuclear co-adaptation: A comparative portrait of sympatric wild types and cybrids in the fish Chrosomus eos. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 27:77-84. [PMID: 29986214 DOI: 10.1016/j.cbd.2018.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 11/26/2022]
Abstract
Allospecific mtDNA can occasionally be beneficial for the fitness of populations. It is, however, difficult to assess the effect of mtDNA in natural conditions due to genetic and/or environmental interactions. In the fish Chrosomus eos, the transfer of C. neogaeus mitochondria occurs in a single generation and results in natural cybrids. For a few lakes in Quebec, C. eos can harbor either a C. eos mtDNA (wild types) or a C. neogaeus mtDNA (cybrids). Moreover, mtDNA of cybrids originated either from Mississippian or Atlantic glacial refuges. Such diversity provides a useful system for in situ assessment of allospecific mtDNA effects. We determined genetic, epigenetic and transcriptomic variation as well as mitochondrial enzymatic activity (complex IV) changes among wild types and cybrids either in sympatry or allopatry. Wild types and cybrids did not segregate spatially within a lake. Moreover, no significant genetic differentiation was detected among wild types and cybrids indicating sustained gene flow. Mitochondrial complex IV activity was higher for cybrids in both sympatry and allopatry while no difference was detected among cybrid haplotypes. Epigenetic and transcriptomic analyses revealed only subtle differences between sympatric wild types and cybrids compared to differences between sites. Altogether, these results indicate a limited influence of allospecific mtDNA in nuclear gene expression when controlling for genetic and environmental effects. The absence of a reproductive barrier between wild types and cybrids results in random association of either C. eos or C. neogaeus mtDNA with C. eos nDNA at each generation, and prevents mitonuclear co-adaptation in sympatry.
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Affiliation(s)
- Bernard Angers
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada.
| | - Vincent Chapdelaine
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Léo Deremiens
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Roland Vergilino
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Christelle Leung
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Simon-Luc Doucet
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
| | - Hélène Glémet
- Department of environmental sciences, Université du Québec à Trois-Rivières, C.P. 500, Trois-Rivières, Québec G9A 5H7, Canada
| | - Annie Angers
- Department of biological sciences, Université de Montréal, C.P. 6128, Succ. Centre-Ville, Montréal, Québec H3C 3J7, Canada
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45
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Sharbrough J, Cruise JL, Beetch M, Enright NM, Neiman M. Genetic Variation for Mitochondrial Function in the New Zealand Freshwater Snail Potamopyrgus antipodarum. J Hered 2018; 108:759-768. [PMID: 28460111 DOI: 10.1093/jhered/esx041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/26/2017] [Indexed: 02/04/2023] Open
Abstract
The proteins responsible for mitochondrial function are encoded by 2 different genomes with distinct inheritance regimes, rendering rigorous inference of genotype-phenotype connections intractable for all but a few model systems. Asexual organisms provide a powerful means to address these challenges because offspring produced without recombination inherit both nuclear and mitochondrial genomes from a single parent. As such, these offspring inherit mitonuclear genotypes that are identical to the mitonuclear genotypes of their parents and siblings but different from those of other asexual lineages. Here, we compared mitochondrial function across distinct asexual lineages of Potamopyrgus antipodarum, a New Zealand freshwater snail model for understanding the evolutionary consequences of asexuality. Our analyses revealed substantial phenotypic variation across asexual lineages at 3 levels of biological organization: mitogenomic, organellar, and organismal. These data demonstrate that different asexual lineages have different mitochondrial function phenotypes, likely reflecting heritable variation (i.e., the raw material for evolution) for mitochondrial function in P. antipodarum. The discovery of this variation combined with the methods developed here sets the stage to use P. antipodarum to study central evolutionary questions involving mitochondrial function, including whether mitochondrial mutation accumulation influences the maintenance of sexual reproduction in natural populations.
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Affiliation(s)
- Joel Sharbrough
- Department of Biology, University of Iowa, Iowa City, IA.,Department of Biology, Colorado State University, Fort Collins, CO
| | | | - Megan Beetch
- Department of Biology, University of Iowa, Iowa City, IA.,Department of Biology, University of St. Thomas, Saint Paul, MN
| | | | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA
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46
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Comparative biochemistry of cytochrome c oxidase in animals. Comp Biochem Physiol B Biochem Mol Biol 2017; 224:170-184. [PMID: 29180239 DOI: 10.1016/j.cbpb.2017.11.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022]
Abstract
Cytochrome c oxidase (COX), the terminal enzyme of the electron transport system, is central to aerobic metabolism of animals. Many aspects of its structure and function are highly conserved, yet, paradoxically, it is also an important model for studying the evolution of the metabolic phenotype. In this review, part of a special issue honouring Peter Hochachka, we consider the biology of COX from the perspective of comparative and evolutionary biochemistry. The approach is to consider what is known about the enzyme in the context of conventional biochemistry, but focus on how evolutionary researchers have used this background to explore the role of the enzyme in biochemical adaptation of animals. In synthesizing the conventional and evolutionary biochemistry, we hope to identify synergies and future research opportunities. COX represents a rare opportunity for researchers to design studies that span the breadth of biology: molecular genetics, protein biochemistry, enzymology, metabolic physiology, organismal performance, evolutionary biology, and phylogeography.
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47
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Du SNN, Khajali F, Dawson NJ, Scott GR. Hybridization increases mitochondrial production of reactive oxygen species in sunfish. Evolution 2017; 71:1643-1652. [PMID: 28444733 DOI: 10.1111/evo.13254] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/11/2017] [Indexed: 02/06/2023]
Abstract
Mitochondrial dysfunction and oxidative stress have been suggested to be possible mechanisms underlying hybrid breakdown, as a result of mito-nuclear incompatibilities in respiratory complexes of the electron transport system. However, it remains unclear whether hybridization increases the production of reactive oxygen species (ROS) by mitochondria. We used high-resolution respirometry and fluorometry on isolated liver mitochondria to examine mitochondrial physiology and ROS emission in naturally occurring hybrids of pumpkinseed (Lepomis gibbosus) and bluegill (L. macrochirus). ROS emission was greater in hybrids than in both parent species when respiration was supported by complex I (but not complex II) substrates, and was associated with increases in lipid peroxidation. However, respiratory capacities for oxidative phosphorylation, phosphorylation efficiency, and O2 kinetics in hybrids were intermediate between those in parental species. Flux control ratios of capacities for electron transport (measured in uncoupled mitochondria) relative to oxidative phosphorylation suggested that the limiting influence of the phosphorylation system is reduced in hybrids. This likely helped offset impairments in electron transport capacity and complex III activity, but contributed to augmenting ROS production. Therefore, hybridization can increase mitochondrial ROS production, in support of previous suggestions that mitochondrial dysfunction can induce oxidative stress and thus contribute to hybrid breakdown.
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Affiliation(s)
- Sherry N N Du
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Fariborz Khajali
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada.,Department of Animal Science, Shahrekord University, Shahrekord, Iran
| | - Neal J Dawson
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada.,Department of Biology, University of Miami, Coral Gables, Florida, 33146
| | - Graham R Scott
- Department of Biology, McMaster University, Hamilton, ON, L8S 4K1, Canada
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48
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Mitochondrial genotype modulates mtDNA copy number and organismal phenotype in Drosophila. Mitochondrion 2017; 34:75-83. [DOI: 10.1016/j.mito.2017.02.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 11/28/2016] [Accepted: 02/01/2017] [Indexed: 11/21/2022]
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49
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Schield DR, Adams RH, Card DC, Perry BW, Pasquesi GM, Jezkova T, Portik DM, Andrew AL, Spencer CL, Sanchez EE, Fujita MK, Mackessy SP, Castoe TA. Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes. Ecol Evol 2017; 7:3951-3966. [PMID: 28616190 PMCID: PMC5468163 DOI: 10.1002/ece3.2996] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 03/21/2017] [Indexed: 01/03/2023] Open
Abstract
Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake (Crotalus atrox) to determine whether genomic regions under selection in allopatry also contribute to reproductive isolation during introgression. We used thousands of nuclear loci to study genomic differentiation between two lineages that have experienced recent secondary contact following isolation, and incorporated sampling from a zone of secondary contact to identify loci that are resistant to gene flow in hybrids. Comparisons of patterns of divergence and introgression revealed a positive relationship between allelic differentiation and resistance to introgression across the genome, and greater‐than‐expected overlap between genes linked to lineage‐specific divergence and loci that resist introgression. Genes linked to putatively selected markers were related to prominent aspects of rattlesnake biology that differ between populations of Western Diamondback rattlesnakes (i.e., venom and reproductive phenotypes). We also found evidence for selection against introgression of genes that may contribute to cytonuclear incompatibility, consistent with previously observed biased patterns of nuclear and mitochondrial alleles suggestive of partial reproductive isolation due to cytonuclear incompatibilities. Our results provide a genome‐scale perspective on the relationships between divergence and introgression in secondary contact that is relevant for understanding the roles of selection in maintaining partial isolation of lineages, causing admixing lineages to not completely homogenize.
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Affiliation(s)
- Drew R Schield
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Richard H Adams
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Daren C Card
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Blair W Perry
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Giulia M Pasquesi
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Tereza Jezkova
- Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ USA
| | - Daniel M Portik
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Audra L Andrew
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Carol L Spencer
- Museum of Vertebrate Zoology University of California Berkeley CA USA
| | - Elda E Sanchez
- National Natural Toxins Research Center and Department of Chemistry Texas A&M University Kingsville Kingsville TX USA
| | - Matthew K Fujita
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Stephen P Mackessy
- School of Biological Sciences University of Northern Colorado Greeley CO USA
| | - Todd A Castoe
- Department of Biology The University of Texas at Arlington Arlington TX USA
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50
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Sloan DB, Havird JC, Sharbrough J. The on-again, off-again relationship between mitochondrial genomes and species boundaries. Mol Ecol 2017; 26:2212-2236. [PMID: 27997046 PMCID: PMC6534505 DOI: 10.1111/mec.13959] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 11/16/2016] [Accepted: 11/18/2016] [Indexed: 12/12/2022]
Abstract
The study of reproductive isolation and species barriers frequently focuses on mitochondrial genomes and has produced two alternative and almost diametrically opposed narratives. On one hand, mtDNA may be at the forefront of speciation events, with co-evolved mitonuclear interactions responsible for some of the earliest genetic incompatibilities arising among isolated populations. On the other hand, there are numerous cases of introgression of mtDNA across species boundaries even when nuclear gene flow is restricted. We argue that these seemingly contradictory patterns can result from a single underlying cause. Specifically, the accumulation of deleterious mutations in mtDNA creates a problem with two alternative evolutionary solutions. In some cases, compensatory or epistatic changes in the nuclear genome may ameliorate the effects of mitochondrial mutations, thereby establishing coadapted mitonuclear genotypes within populations and forming the basis of reproductive incompatibilities between populations. Alternatively, populations with high mitochondrial mutation loads may be rescued by replacement with a more fit, foreign mitochondrial haplotype. Coupled with many nonadaptive mechanisms of introgression that can preferentially affect cytoplasmic genomes, this form of adaptive introgression may contribute to the widespread discordance between mitochondrial and nuclear genealogies. Here, we review recent advances related to mitochondrial introgression and mitonuclear incompatibilities, including the potential for cointrogression of mtDNA and interacting nuclear genes. We also address an emerging controversy over the classic assumption that selection on mitochondrial genomes is inefficient and discuss the mechanisms that lead lineages down alternative evolutionary paths in response to mitochondrial mutation accumulation.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
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