51
|
Coyle AE, Voss ER, Tepolt CK, Carlon DB. Mitochondrial genotype influences the response to cold stress in the European green crab, Carcinus maenas. J Exp Biol 2019; 222:jeb203521. [PMID: 31285243 DOI: 10.1242/jeb.203521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/03/2019] [Indexed: 12/20/2022]
Abstract
Hybrid zones provide natural experiments in recombination within and between genomes that may have strong effects on organismal fitness. On the East Coast of North America, two distinct lineages of the European green crab (Carcinus maenas) have been introduced in the last two centuries. These two lineages with putatively different adaptive properties have hybridized along the coast of the eastern Gulf of Maine, producing new nuclear and mitochondrial combinations that show clinal variation correlated with water temperature. To test the hypothesis that mitochondrial or nuclear genes have effects on thermal tolerance, we first measured the response to cold stress in crabs collected throughout the hybrid zone, then sequenced the mitochondrial CO1 gene and two nuclear single nucleotide polymorphisms (SNPs) representative of nuclear genetic lineage. Mitochondrial haplotype had a strong association with the ability of crabs to right themselves at 4.5°C that was sex specific: haplotypes originally from northern Europe gave male crabs an advantage while there was no haplotype effect on righting in female crabs. By contrast, the two nuclear SNPs that were significant outliers in a comparison between northern and southern C. maenas populations had no effect on righting response at low temperature. These results add C. maenas to the shortlist of ectotherms in which mitochondrial variation has been shown to affect thermal tolerance, and suggest that natural selection is shaping the structure of the hybrid zone across the Gulf of Maine. Our limited genomic sampling does not eliminate the strong possibility that mito-nuclear co-adaptation may play a role in the differences in thermal phenotypes documented here. Linkage between mitochondrial genotype and thermal tolerance suggests a role for local adaptation in promoting the spread of invasive populations of C. maenas around the world.
Collapse
Affiliation(s)
- Aspen E Coyle
- Department of Biology & Schiller Coastal Studies Center, Bowdoin College, Brunswick, ME 04011, USA
| | - Erin R Voss
- Department of Biology & Schiller Coastal Studies Center, Bowdoin College, Brunswick, ME 04011, USA
| | - Carolyn K Tepolt
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - David B Carlon
- Department of Biology & Schiller Coastal Studies Center, Bowdoin College, Brunswick, ME 04011, USA
| |
Collapse
|
52
|
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.
Collapse
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
| |
Collapse
|
53
|
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: 68] [Impact Index Per Article: 13.6] [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.
Collapse
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
| |
Collapse
|
54
|
Nash W, Mohorianu I, Chapman T. Mate choice and gene expression signatures associated with nutritional adaptation in the medfly (Ceratitis capitata). Sci Rep 2019; 9:6704. [PMID: 31040302 PMCID: PMC6491435 DOI: 10.1038/s41598-019-42610-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/25/2019] [Indexed: 11/09/2022] Open
Abstract
Evolutionary responses to nutrition are key to understanding host shifts and the resulting potential for reproductive isolation. Experimental evolution has previously been used to describe the responses of the medfly (Ceratitis capitata) to larval diets with different nutritional properties. Within 30 generations this led to divergence in larval development time, egg to adult survival and adaptation in adult body size. Here we used mRNA-seq to identify differences in gene expression patterns in these same populations, using males from the 60th generation of nutritional selection. We validated differential expression by using qRT-PCR and found that genes linked to metabolism, oxidative phosphorylation and proteolysis were significantly over-represented among the differentially expressed genes. The results provide the first genome-wide survey of the putative mechanisms underpinning evolved responses to nutritional adaptation. In addition, we tested the hypothesis that nutritional adaptation can alter mating patterns. We found evidence for assortative mating by diet at generation 60, but not 90. Hence, the pattern was variable across generations and there was no evidence overall for any isolating mating divergence between the lines. Overall, the results provide insight into the mechanisms underpinning dietary adaptation and extend our knowledge of which traits represent core responses to nutritional selection.
Collapse
Affiliation(s)
- Will Nash
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK. .,School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| |
Collapse
|
55
|
Banguera-Hinestroza E, Ferrada E, Sawall Y, Flot JF. Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments. Genes (Basel) 2019; 10:E324. [PMID: 31035578 PMCID: PMC6562464 DOI: 10.3390/genes10050324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 01/15/2023] Open
Abstract
More than a decade ago, a new mitochondrial Open Reading Frame (mtORF) was discovered in corals of the family Pocilloporidae and has been used since then as an effective barcode for these corals. Recently, mtORF sequencing revealed the existence of two differentiated Stylophora lineages occurring in sympatry along the environmental gradient of the Red Sea (18.5°C to 33.9°C). In the endemic Red Sea lineage RS_LinB, the mtORF and the heat shock protein gene hsp70 uncovered similar phylogeographic patterns strongly correlated with environmental variations. This suggests that the mtORF too might be involved in thermal adaptation. Here, we used computational analyses to explore the features and putative function of this mtORF. In particular, we tested the likelihood that this gene encodes a functional protein and whether it may play a role in adaptation. Analyses of full mitogenomes showed that the mtORF originated in the common ancestor of Madracis and other pocilloporids, and that it encodes a transmembrane protein differing in length and domain architecture among genera. Homology-based annotation and the relative conservation of metal-binding sites revealed traces of an ancient hydrolase catalytic activity. Furthermore, signals of pervasive purifying selection, lack of stop codons in 1830 sequences analyzed, and a codon-usage bias similar to that of other mitochondrial genes indicate that the protein is functional, i.e., not a pseudogene. Other features, such as intrinsically disordered regions, tandem repeats, and signals of positive selection particularly in StylophoraRS_LinB populations, are consistent with a role of the mtORF in adaptive responses to environmental changes.
Collapse
Affiliation(s)
- Eulalia Banguera-Hinestroza
- Evolutionary Biology and Ecology, Université libre de Bruxelles, B-1050 Brussels, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels-(IB)2, 1050 Brussels, Belgium.
| | - Evandro Ferrada
- Center for Genomics and Bioinformatics, Universidad Mayor, Santiago, Chile.
| | - Yvonne Sawall
- Coral Reef Ecology, Bermuda Institute of Ocean Sciences (BIOS), St.George's GE 01, Bermuda.
| | - Jean-François Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles, B-1050 Brussels, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels-(IB)2, 1050 Brussels, Belgium.
| |
Collapse
|
56
|
Hill GE. Reconciling the Mitonuclear Compatibility Species Concept with Rampant Mitochondrial Introgression. Integr Comp Biol 2019; 59:912-924. [DOI: 10.1093/icb/icz019] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
The mitonuclear compatibility species concept defines a species as a population that is genetically isolated from other populations by uniquely coadapted mitochondrial (mt) and nuclear genes. A key prediction of this hypothesis is that the mt genotype of each species will be functionally distinct and that introgression of mt genomes will be prevented by mitonuclear incompatibilities that arise when heterospecific mt and nuclear genes attempt to cofunction to enable aerobic respiration. It has been proposed, therefore, that the observation of rampant introgression of mt genotypes from one species to another constitutes a strong refutation of the mitonuclear speciation. The displacement of a mt genotype from a nuclear background with which it co-evolved to a foreign nuclear background will necessarily lead to fitness loss due to mitonuclear incompatibilities. Here I consider two potential benefits of mt introgression between species that may, in some cases, overcome fitness losses arising from mitonuclear incompatibilities. First, the introgressed mt genotype may be better adapted to the local environment than the native mt genotype such that higher fitness is achieved through improved adaptation via introgression. Second, if the mitochondria of the recipient taxa carry a high mutational load, then introgression of a foreign, less corrupt mt genome may enable the recipient taxa to escape its mutational load and gain a fitness advantage. Under both scenarios, fitness gains from novel mt genotypes could theoretically compensate for the fitness that is lost via mitonuclear incompatibility. I also consider the role of endosymbionts in non-adaptive rampant introgression of mt genomes. I conclude that rampant introgression is not necessarily evidence against the idea of tight mitonuclear coadaptation or the mitonuclear compatibility species concept. Rampant mt introgression will typically lead to erasure of species but in some cases could lead to hybrid speciation.
Collapse
Affiliation(s)
- Geoffrey E Hill
- Department of Biological Sciences, 331 Funchess Hall, Auburn University, Auburn, AL 36849-5414, USA
| |
Collapse
|
57
|
Telschow A, Gadau J, Werren JH, Kobayashi Y. Genetic Incompatibilities Between Mitochondria and Nuclear Genes: Effect on Gene Flow and Speciation. Front Genet 2019; 10:62. [PMID: 30853974 PMCID: PMC6396729 DOI: 10.3389/fgene.2019.00062] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 01/24/2019] [Indexed: 11/13/2022] Open
Abstract
The process of speciation is, according to the biological species concept, the reduction in gene flow between genetically diverging populations. Most of the previous theoretical studies analyzed the effect of nuclear genetic incompatibilities on gene flow. There is, however, an increasing number of empirical examples suggesting that cytoplasmically inherited genetic elements play an important role in speciation. Here, we present a theoretical analysis of mitochondrial driven speciation, in which genetic incompatibilities occur between mitochondrial haplotypes and nuclear alleles. Four population genetic models with mainland-island structure were analyzed that differ with respect to the type of incompatibility and the underlying genetics. Gene flow reduction was measured on selectively neutral alleles of an unlinked locus and quantified by the effective migration rate. Analytical formulae for the different scenarios were derived using the fitness graph method. For the models with haploid genetics, we found that mito-nuclear incompatibilities (MtNI) are as strong as nuclear-nuclear incompatibilities (NNI) in reducing gene flow at the unlinked locus, but only if males and females migrate in equal number. For models with diploid genetics, we found that MtNI reduce gene flow stronger than NNI when incompatibilities are recessive, but weaker when they are dominant. For both haploid and diploid MtNI, we found that gene flow reduction is stronger if females are the migrating sex, but weaker than NNI when males are the migrating sex. These results encourage further examination on the role of mitochondria on genetic divergence and speciation and point toward specific factors (e.g., migrating sex) that could be the focus of an empirical test.
Collapse
Affiliation(s)
- Arndt Telschow
- Institute for Environmental Systems Research, Osnabrück University, Osnabrück, Germany
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity, Westfalian Wilhelms-University, Münster, Germany
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, United States
| | - Yutaka Kobayashi
- School of Economics and Management, Kochi University of Technology, Kami, Japan
| |
Collapse
|
58
|
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
| |
Collapse
|
59
|
Guan DL, Qian ZQ, Ma LB, Bai Y, Xu SQ. Different mitogenomic codon usage patterns between damselflies and dragonflies and nine complete mitogenomes for odonates. Sci Rep 2019; 9:678. [PMID: 30679466 PMCID: PMC6345984 DOI: 10.1038/s41598-018-35760-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/09/2018] [Indexed: 01/08/2023] Open
Abstract
Damselflies and dragonflies, of the order Odonata, have distinct body plans and predatory abilities. Knowledge of their various evolutionary histories will allow for an understanding of the genetic and phenotypic evolution of insects. Mitogenomes are suitable materials to elucidate this, but the mitogenome of only a few odonates have been annotated. Herein, we report the complete mitogenome of nine odonates, including seven dragonflies and two damselflies, and a comprehensive analysis of the codon usage in 31 Odonata mitogenomes with the aim to estimate their evolutionary characteristics. Overall, a weak codon bias exists among odonate mitogenomes, although this favours AT-ending codons. Damselflies have a weaker codon usage bias than dragonflies, and 37 codons have significantly different usages. Both directional mutation and purifying selection shape damselfly and dragonfly mitogenomes. Although inevitable, directional mutation bias plays a minor role, whereas purifying selection pressure is the dominant evolutionary force. A higher selection pressure is observed in dragonflies than in damselflies, but it mainly acts on codon usage patterns rather than amino acid translation. Our findings suggest that dragonflies might have more efficient mitochondrial gene expression levels than damselflies, producing more proteins that support their locomotion and predatory abilities.
Collapse
Affiliation(s)
- De-Long Guan
- College of life science, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Zeng-Qiang Qian
- College of life science, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Li-Bin Ma
- College of life science, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Yi Bai
- School of Life Science, Taizhou University, Taizhou, 317000, P.R. China
| | - Sheng-Quan Xu
- College of life science, Shaanxi Normal University, Xi'an, 710119, P. R. China.
| |
Collapse
|
60
|
Exogenous Factors May Differentially Influence the Selective Costs of mtDNA Mutations. CELLULAR AND MOLECULAR BASIS OF MITOCHONDRIAL INHERITANCE 2019; 231:51-74. [DOI: 10.1007/102_2018_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
61
|
Štorchová H, Stone JD, Sloan DB, Abeyawardana OAJ, Müller K, Walterová J, Pažoutová M. Homologous recombination changes the context of Cytochrome b transcription in the mitochondrial genome of Silene vulgaris KRA. BMC Genomics 2018; 19:874. [PMID: 30514207 PMCID: PMC6280394 DOI: 10.1186/s12864-018-5254-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/15/2018] [Indexed: 01/08/2023] Open
Abstract
Background Silene vulgaris (bladder campion) is a gynodioecious species existing as two genders – male-sterile females and hermaphrodites. Cytoplasmic male sterility (CMS) is generally encoded by mitochondrial genes, which interact with nuclear fertility restorer genes. Mitochondrial genomes of this species vary in DNA sequence, gene order and gene content. Multiple CMS genes are expected to exist in S. vulgaris, but little is known about their molecular identity. Results We assembled the complete mitochondrial genome from the haplotype KRA of S. vulgaris. It consists of five chromosomes, two of which recombine with each other. Two small non-recombining chromosomes exist in linear, supercoiled and relaxed circle forms. We compared the mitochondrial transcriptomes from females and hermaphrodites and confirmed the differentially expressed chimeric gene bobt as the strongest CMS candidate gene in S. vulgaris KRA. The chimeric gene bobt is co-transcribed with the Cytochrome b (cob) gene in some genomic configurations. The co-transcription of a CMS factor with an essential gene may constrain transcription inhibition as a mechanism for fertility restoration because of the need to maintain appropriate production of the necessary protein. Homologous recombination places the gene cob outside the control of bobt, which allows for the suppression of the CMS gene by the fertility restorer genes. We found the loss of three editing sites in the KRA mitochondrial genome and identified four sites with highly distinct editing rates between KRA and another S. vulgaris haplotypes (KOV). Three of these highly differentially edited sites were located in the transport membrane protein B (mttB) gene. They resulted in differences in MttB protein sequences between haplotypes. Conclusions Frequent homologous recombination events that are widespread in plant mitochondrial genomes may change chromosomal configurations and also the control of gene transcription including CMS gene expression. Posttranscriptional processes, e.g. RNA editing shall be evaluated in evolutionary and co-evolutionary studies of mitochondrial genes, because they may change protein composition despite the sequence identity of the respective genes. The investigation of natural populations of wild species such as S. vulgaris are necessary to reveal important aspects of CMS missed in domesticated crops, the traditional focus of the CMS studies. Electronic supplementary material The online version of this article (10.1186/s12864-018-5254-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Helena Štorchová
- Plant Reproduction Laboratory, Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502, Prague, Czech Republic.
| | - James D Stone
- Plant Reproduction Laboratory, Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502, Prague, Czech Republic
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Oushadee A J Abeyawardana
- Plant Reproduction Laboratory, Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502, Prague, Czech Republic
| | - Karel Müller
- Plant Reproduction Laboratory, Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502, Prague, Czech Republic
| | - Jana Walterová
- Plant Reproduction Laboratory, Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502, Prague, Czech Republic
| | - Marie Pažoutová
- Plant Reproduction Laboratory, Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502, Prague, Czech Republic
| |
Collapse
|
62
|
Haddad R, Meter B, Ross JA. The Genetic Architecture of Intra-Species Hybrid Mito-Nuclear Epistasis. Front Genet 2018; 9:481. [PMID: 30505316 PMCID: PMC6250786 DOI: 10.3389/fgene.2018.00481] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 09/28/2018] [Indexed: 01/03/2023] Open
Abstract
Genetic variants that are neutral within, but deleterious between, populations (Dobzhansky-Muller Incompatibilities) are thought to initiate hybrid dysfunction and then to accumulate and complete the speciation process. To identify the types of genetic differences that might initiate speciation, it is useful to study inter-population (intra-species) hybrids that exhibit reduced fitness. In Caenorhabditis briggsae, a close relative of the nematode C. elegans, such minor genetic incompatibilities have been identified. One incompatibility between the mitochondrial and nuclear genomes reduces the fitness of some hybrids. To understand the nuclear genetic architecture of this epistatic interaction, we constructed two sets of recombinant inbred lines by hybridizing two genetically diverse wild populations. In such lines, selection is able to eliminate deleterious combinations of alleles derived from the two parental populations. The genotypes of surviving hybrid lines thus reveal favorable allele combinations at loci experiencing selection. Our genotype data from the resulting lines are consistent with the interpretation that the X alleles participate in epistatic interactions with autosomes and the mitochondrial genome. We evaluate this possibility given predictions that mitochondria-X epistasis should be more prevalent than between mitochondria and autosomes. Our empirical identification of inter-genomic linkage disequilibrium supports the body of literature indicating that the accumulation of mito-nuclear genetic incompatibilities might initiate the speciation process through the generation of less-fit inter-population hybrids.
Collapse
Affiliation(s)
- Rania Haddad
- Department of Biology, California State University, Fresno, Fresno, CA, United States
| | - Brandon Meter
- Department of Biology, California State University, Fresno, Fresno, CA, United States
| | - Joseph A Ross
- Department of Biology, California State University, Fresno, Fresno, CA, United States
| |
Collapse
|
63
|
Abstract
Cytoplasmic components and their interactions with the nuclear genome may mediate patterns of phenotypic expression to form a joint inheritance system. However, proximate mechanisms underpinning these interactions remain elusive. To independently assess nuclear genetic and epigenetic cytoplasmic effects, we created a full-factorial design in which representative cytoplasms and nuclear backgrounds from each of two geographically disjunct populations of Drosophila melanogaster were matched together in all four possible combinations. To capture slowly-accumulating epimutations in addition to immediately occurring ones, these constructed populations were examined one year later. We found the K4 methylation of histone H3, H3K4me3, an epigenetic marker associated with transcription start-sites had diverged across different cytoplasms. The loci concerned mainly related to metabolism, mitochondrial function, and reproduction. We found little overlap (<8%) in sites that varied genetically and epigenetically, suggesting that epigenetic changes have diverged independently from any cis-regulatory sequence changes. These results are the first to show cytoplasm-specific effects on patterns of nuclear histone methylation. Our results highlight that experimental nuclear-cytoplasm mismatch may be used to provide a platform to identify epigenetic candidate loci to study the molecular mechanisms of cyto-nuclear interactions.
Collapse
|
64
|
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]
|
65
|
Bize P, Lowe I, Lehto Hürlimann M, Heckel G. Effects of the Mitochondrial and Nuclear Genomes on Nonshivering Thermogenesis in a Wild Derived Rodent. Integr Comp Biol 2018; 58:532-543. [DOI: 10.1093/icb/icy072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Pierre Bize
- School of Biological Sciences, University of Aberdeen, Zoology Building, AB24 2TZ Aberdeen, UK
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Imogen Lowe
- School of Biological Sciences, University of Aberdeen, Zoology Building, AB24 2TZ Aberdeen, UK
| | - Mikko Lehto Hürlimann
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Gerald Heckel
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Hochschulstrasse 6, CH-3012 Bern, Switzerland
| |
Collapse
|
66
|
Vyskočilová S, Tay WT, van Brunschot S, Seal S, Colvin J. An integrative approach to discovering cryptic species within the Bemisia tabaci whitefly species complex. Sci Rep 2018; 8:10886. [PMID: 30022040 PMCID: PMC6052153 DOI: 10.1038/s41598-018-29305-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/05/2018] [Indexed: 11/26/2022] Open
Abstract
Bemisia tabaci is a cryptic whitefly-species complex that includes some of the most damaging pests and plant-virus vectors of a diverse range of food and fibre crops worldwide. We combine experimental evidence of: (i) differences in reproductive compatibility, (ii) hybrid verification using a specific nuclear DNA marker and hybrid fertility confirmation and (iii) high-throughput sequencing-derived mitogenomes, to show that the "Mediterranean" (MED) B. tabaci comprises at least two distinct biological species; the globally invasive MED from the Mediterranean Basin and the "African silver-leafing" (ASL) from sub-Saharan Africa, which has no associated invasion records. We demonstrate that, contrary to its common name, the "ASL" does not induce squash silver-leafing symptoms and show that species delimitation based on the widely applied 3.5% partial mtCOI gene sequence divergence threshold produces discordant results, depending on the mtCOI region selected. Of the 292 published mtCOI sequences from MED/ASL groups, 158 (54%) are low quality and/or potential pseudogenes. We demonstrate fundamental deficiencies in delimiting cryptic B. tabaci species, based solely on partial sequences of a mitochondrial barcoding gene. We advocate an integrative approach to reveal the true species richness within cryptic species complexes, which is integral to the deployment of effective pest and disease management strategies.
Collapse
Affiliation(s)
- Soňa Vyskočilová
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, United Kingdom.
| | - Wee Tek Tay
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT 2601, Canberra, Australia
| | - Sharon van Brunschot
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, United Kingdom
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Susan Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, United Kingdom
| | - John Colvin
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, United Kingdom
| |
Collapse
|
67
|
Robicheau BM, Chase EE, Hoeh WR, Harris JL, Stewart DT, Breton S. Evaluating the utility of the female-specific mitochondrial f-orf gene for population genetic, phylogeographic and systematic studies in freshwater mussels (Bivalvia: Unionida). PeerJ 2018; 6:e5007. [PMID: 29915706 PMCID: PMC6004104 DOI: 10.7717/peerj.5007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 05/29/2018] [Indexed: 12/19/2022] Open
Abstract
Freshwater mussels (order: Unionida) represent one of the most critically imperilled groups of animals; consequently, there exists a need to establish a variety of molecular markers for population genetics and systematic studies in this group. Recently, two novel mitochondrial protein-coding genes were described in unionoids with doubly uniparental inheritance of mtDNA. These genes are the f-orf in female-transmitted mtDNA and the m-orf in male-transmitted mtDNA. In this study, whole F-type mitochondrial genome sequences of two morphologically similar Lampsilis spp. were compared to identify the most divergent protein-coding regions, including the f-orf gene, and evaluate its utility for population genetic and phylogeographic studies in the subfamily Ambleminae. We also tested whether the f-orf gene is phylogenetically informative at the species level. Our preliminary results indicated that the f-orf gene could represent a viable molecular marker for population- and species-level studies in freshwater mussels.
Collapse
Affiliation(s)
- Brent M Robicheau
- Department of Biology, Acadia University, Wolfville, Canada.,Current affiliation: Department of Biology, Life Science Centre, Dalhousie University, Halifax, Canada
| | - Emily E Chase
- Department of Biology, Acadia University, Wolfville, Canada
| | - Walter R Hoeh
- Department of Biological Sciences, Kent State University, Kent, United States of America
| | - John L Harris
- Department of Biological Sciences, Arkansas State University, Jonesboro, United States of America
| | | | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| |
Collapse
|
68
|
Havird JC, Trapp P, Miller CM, Bazos I, Sloan DB. Causes and Consequences of Rapidly Evolving mtDNA in a Plant Lineage. Genome Biol Evol 2018; 9:323-336. [PMID: 28164243 PMCID: PMC5381668 DOI: 10.1093/gbe/evx010] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2017] [Indexed: 12/23/2022] Open
Abstract
Understanding mechanisms of coevolution between nuclear and mitochondrial (mt) genomes is a defining challenge in eukaryotic genetics. The angiosperm genus Silene is a natural system to investigate the causes and consequences of mt mutation rate variation because closely related species have highly divergent rates. In Silene species with fast-evolving mtDNA, nuclear genes that encode mitochondrially targeted proteins (N-mt genes) are also fast-evolving. This correlation could indicate positive selection to compensate for mt mutations, but might also result from a recent relaxation of selection. To differentiate between these interpretations, we used phylogenetic and population-genetic methods to test for positive and relaxed selection in three classes of N-mt genes (oxidative phosphorylation genes, ribosomal genes, and “RRR” genes involved in mtDNA recombination, replication, and repair). In all three classes, we found that species with fast-evolving mtDNA had: 1) elevated dN/dS, 2) an excess of nonsynonymous divergence relative to levels of intraspecific polymorphism, which is a signature of positive selection, and 3) no clear signals of relaxed selection. “Control” genes exhibited comparatively few signs of positive selection. These results suggest that high mt mutation rates can create selection on N-mt genes and that relaxed selection is an unlikely cause of recent accelerations in the evolution of N-mt genes. Because mt-RRR genes were found to be under positive selection, it is unlikely that elevated mt mutation rates in Silene were caused by inactivation of these mt-RRR genes. Therefore, the causes of extreme increases in angiosperm mt mutation rates remain uncertain.
Collapse
Affiliation(s)
- Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Paul Trapp
- Department of Biology, Colorado State University, Fort Collins, CO
| | | | - Ioannis Bazos
- Department of Ecology and Systematics, National and Kapodistrian University of Athens, Panepistimiopolis, Greece
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO
| |
Collapse
|
69
|
Sharbrough J, Havird JC, Noe GR, Warren JM, Sloan DB. The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes. Genome Biol Evol 2018; 9:1567-1581. [PMID: 28854627 PMCID: PMC5509035 DOI: 10.1093/gbe/evx114] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2017] [Indexed: 12/15/2022] Open
Abstract
Some human populations interbred with Neanderthals and Denisovans, resulting in substantial contributions to modern-human genomes. Therefore, it is now possible to use genomic data to investigate mechanisms that shaped historical gene flow between humans and our closest hominin relatives. More generally, in eukaryotes, mitonuclear interactions have been argued to play a disproportionate role in generating reproductive isolation. There is no evidence of mtDNA introgression into modern human populations, which means that all introgressed nuclear alleles from archaic hominins must function on a modern-human mitochondrial background. Therefore, mitonuclear interactions are also potentially relevant to hominin evolution. We performed a detailed accounting of mtDNA divergence among hominin lineages and used population-genomic data to test the hypothesis that mitonuclear incompatibilities have preferentially restricted the introgression of nuclear genes with mitochondrial functions. We found a small but significant underrepresentation of introgressed Neanderthal alleles at such nuclear loci. Structural analyses of mitochondrial enzyme complexes revealed that these effects are unlikely to be mediated by physically interacting sites in mitochondrial and nuclear gene products. We did not detect any underrepresentation of introgressed Denisovan alleles at mitochondrial-targeted loci, but this may reflect reduced power because locus-specific estimates of Denisovan introgression are more conservative. Overall, we conclude that genes involved in mitochondrial function may have been subject to distinct selection pressures during the history of introgression from archaic hominins but that mitonuclear incompatibilities have had, at most, a small role in shaping genome-wide introgression patterns, perhaps because of limited functional divergence in mtDNA and interacting nuclear genes.
Collapse
Affiliation(s)
- Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Gregory R Noe
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Jessica M Warren
- Department of Biology, Colorado State University, Fort Collins, CO
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO
| |
Collapse
|
70
|
Tobler M, Kelley JL, Plath M, Riesch R. Extreme environments and the origins of biodiversity: Adaptation and speciation in sulphide spring fishes. Mol Ecol 2018; 27:843-859. [DOI: 10.1111/mec.14497] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
| | - Joanna L. Kelley
- School of Biological Sciences Washington State University Pullman WA USA
| | - Martin Plath
- Shaanxi Key Laboratory of Molecular Biology for Agriculture College of Animal Science and Technology Northwest A&F University Yangling Shaanxi China
| | - Rüdiger Riesch
- School of Biological Sciences Centre for Ecology, Evolution and Behaviour Royal Holloway University of London Egham Surrey UK
| |
Collapse
|
71
|
Lamb AM, Gan HM, Greening C, Joseph L, Lee Y, Morán‐Ordóñez A, Sunnucks P, Pavlova A. Climate‐driven mitochondrial selection: A test in Australian songbirds. Mol Ecol 2018; 27:898-918. [DOI: 10.1111/mec.14488] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 11/29/2017] [Accepted: 12/08/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Annika Mae Lamb
- School of Biological Sciences Monash University Melbourne Vic. Australia
| | - Han Ming Gan
- School of Science Monash University Malaysia Bandar Sunway Selangor Malaysia
- Centre for Integrative Ecology School of Life and Environmental Sciences Deakin University Waurn Ponds Vic. Australia
| | - Chris Greening
- School of Biological Sciences Monash University Melbourne Vic. Australia
| | - Leo Joseph
- Australian National Wildlife Collection CSIRO National Research Collections Canberra ACT Australia
| | - Yin Peng Lee
- School of Science Monash University Malaysia Bandar Sunway Selangor Malaysia
| | - Alejandra Morán‐Ordóñez
- InForest Joint Research Unit (CTFC‐CREAF) Forest Science Centre of Catalonia Solsona Catalonia Spain
| | - Paul Sunnucks
- School of Biological Sciences Monash University Melbourne Vic. Australia
| | - Alexandra Pavlova
- School of Biological Sciences Monash University Melbourne Vic. Australia
| |
Collapse
|
72
|
Hill GE. Mitonuclear Mate Choice: A Missing Component of Sexual Selection Theory? Bioessays 2018; 40. [DOI: 10.1002/bies.201700191] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/18/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Geoffrey E. Hill
- Department of Biological Sciences; Auburn University; Auburn Alabama 36849-5414
| |
Collapse
|
73
|
Ramos B, González-Acuña D, Loyola DE, Johnson WE, Parker PG, Massaro M, Dantas GPM, Miranda MD, Vianna JA. Landscape genomics: natural selection drives the evolution of mitogenome in penguins. BMC Genomics 2018; 19:53. [PMID: 29338715 PMCID: PMC5771141 DOI: 10.1186/s12864-017-4424-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 12/28/2017] [Indexed: 12/21/2022] Open
Abstract
Background Mitochondria play a key role in the balance of energy and heat production, and therefore the mitochondrial genome is under natural selection by environmental temperature and food availability, since starvation can generate more efficient coupling of energy production. However, selection over mitochondrial DNA (mtDNA) genes has usually been evaluated at the population level. We sequenced by NGS 12 mitogenomes and with four published genomes, assessed genetic variation in ten penguin species distributed from the equator to Antarctica. Signatures of selection of 13 mitochondrial protein-coding genes were evaluated by comparing among species within and among genera (Spheniscus, Pygoscelis, Eudyptula, Eudyptes and Aptenodytes). The genetic data were correlated with environmental data obtained through remote sensing (sea surface temperature [SST], chlorophyll levels [Chl] and a combination of SST and Chl [COM]) through the distribution of these species. Results We identified the complete mtDNA genomes of several penguin species, including ND6 and 8 tRNAs on the light strand and 12 protein coding genes, 14 tRNAs and two rRNAs positioned on the heavy strand. The highest diversity was found in NADH dehydrogenase genes and the lowest in COX genes. The lowest evolutionary divergence among species was between Humboldt (Spheniscus humboldti) and Galapagos (S. mendiculus) penguins (0.004), while the highest was observed between little penguin (Eudyptula minor) and Adélie penguin (Pygoscelis adeliae) (0.097). We identified a signature of purifying selection (Ka/Ks < 1) across the mitochondrial genome, which is consistent with the hypothesis that purifying selection is constraining mitogenome evolution to maintain Oxidative phosphorylation (OXPHOS) proteins and functionality. Pairwise species maximum-likelihood analyses of selection at codon sites suggest positive selection has occurred on ATP8 (Fixed-Effects Likelihood, FEL) and ND4 (Single Likelihood Ancestral Counting, SLAC) in all penguins. In contrast, COX1 had a signature of strong negative selection. ND4 Ka/Ks ratios were highly correlated with SST (Mantel, p-value: 0.0001; GLM, p-value: 0.00001) and thus may be related to climate adaptation throughout penguin speciation. Conclusions These results identify mtDNA candidate genes under selection which could be involved in broad-scale adaptations of penguins to their environment. Such knowledge may be particularly useful for developing predictive models of how these species may respond to severe climatic changes in the future. Electronic supplementary material The online version of this article (10.1186/s12864-017-4424-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Barbara Ramos
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna, 4860, Santiago, Chile.,Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Republica 252, Santiago, Chile
| | - Daniel González-Acuña
- Departamento de Ciencias Pecuarias, Facultad de Ciencias Veterinarias, Universidad de Concepción, Av. Vicente Méndez 595, 3780000, Chillán, CP, Chile
| | - David E Loyola
- Centro Nacional de Genómica y Bioinformática, Portugal 49, Santiago, Chile.,I+DEA Biotech, Av. Central 3413, Padre Hurtado, Santiago, Chile
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA
| | - Patricia G Parker
- University of Missouri St Louis and Saint Louis Zoo, One University Blvd., St. Louis, MO, 63121-4400, USA
| | - Melanie Massaro
- School of Environmental Sciences and Institute for Land, Water and Society, Charles Sturt University, PO Box 789, Albury, NSW, Australia
| | - Gisele P M Dantas
- Pontifícia Universidade Católica de Minas Gerais, Av. Dom José Gaspar 500, Coração Eucarístico, Belo Horizonte, MG, Brazil
| | - Marcelo D Miranda
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna, 4860, Santiago, Chile
| | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna, 4860, Santiago, Chile. .,Centro de Cambio Global UC, Santiago, Chile.
| |
Collapse
|
74
|
Awadi A. Host species and pathogenicity effects in the evolution of the mitochondrial genomes of Eimeria species (Apicomplexa; Coccidia; Eimeriidae). ACTA ACUST UNITED AC 2017; 24:13. [PMID: 29299440 PMCID: PMC5740889 DOI: 10.1186/s40709-017-0070-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/14/2017] [Indexed: 11/10/2022]
Abstract
Background Mitochondria are fundamental organelles responsible for cellular metabolism and energy production in eukaryotes via the oxidative phosphorylation pathway. Mitochondrial DNA is often used in population and species studies with the assumption of neutral evolution. However, evidence of positive selection in mitochondrial coding genes of various animal species has accumulated suggesting that amino acid changes in mtDNA might be adaptive. The functional and physiological implications of the inferred positively selected sites are usually unknown and are only evaluated based on available structural and functional models. Such studies are absent in unicellular organisms that show several crucial differences to the electron transport chain of animal mitochondria. In the present study, we explored Eimeria mitogenomes for positive selection. We also tested for association between mtDNA polymorphism and environmental variation (i.e. host species), parasite life cycle (i.e. sporulation period), and efficient host cell invasion (i.e. pathogenicity, prepatent period). Findings We used site- and branch-site tests to estimate the extent of purifying and positive selection at each site and each lineage of several Eimeria parasite mitogenomes retrieved from GenBank. We founded sixteen codons in the three mtDNA-encoded proteins to be under positive selection compared to a strong purifying selection. Variation in the ratios of non-synonymous to synonymous changes of the studied parasites was associated with their different host species (F = 13.748; p < 0.001), whereas pathogenicity levels were associated with both synonymous and non-synonymous changes. This association was also confirmed by the multiple regression analysis. Conclusions Our results suggest that host species and pathogenicity are important factors that might shape mitochondrial variation in Eimeria parasites. This supports the important role of mtDNA variations in the evolution and adaptation of these parasites.
Collapse
Affiliation(s)
- Asma Awadi
- UR Génomique des Insectes Ravageurs des Cultures d'intérêt agronomique, Faculty of Sciences of Tunis, University of Tunis El Manar, 2092 Tunis, Tunisia
| |
Collapse
|
75
|
Ostersetzer-Biran O, Lane N, Pomiankowski A, Burton R, Arnqvist G, Filipovska A, Huchon D, Mishmar D. The First Mitochondrial Genomics and Evolution SMBE-Satellite Meeting: A New Scientific Symbiosis. Genome Biol Evol 2017; 9:3054-3058. [PMID: 29106528 PMCID: PMC5714122 DOI: 10.1093/gbe/evx227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/01/2017] [Indexed: 11/12/2022] Open
Abstract
The central role of the mitochondrion for cellular and organismal metabolism is well known, yet its functional role in evolution has rarely been featured in leading international conferences. Moreover, the contribution of mitochondrial genetics to complex disease phenotypes is particularly important, and although major advances have been made in the field of genomics, mitochondrial genomic data have in many cases been overlooked. Accumulating data and new knowledge support a major contribution of this maternally inherited genome, and its interactions with the nucleus, to both major evolutionary processes and diverse disease phenotypes. These advances encouraged us to assemble the first Mitochondrial Genomics and Evolution (MGE) meeting-an SMBE satellite and Israeli Science foundation international conference (Israel, September 2017). Here, we report the content and outcome of the MGE meeting (https://www.mge2017.com/; last accessed November 5, 2017).
Collapse
Affiliation(s)
| | - Nick Lane
- Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | - Andrew Pomiankowski
- Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | - Ron Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego
| | - Göran Arnqvist
- Department of Ecology and Genetics, University of Uppsala, Sweden
| | - Aleksandra Filipovska
- School of Molecular Sciences and The Harry Perkins Institute of Medical Research, The University of Western Australia, Australia
| | - Dorothée Huchon
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel.,The Steinhardt Museum of Natural History and Israel National Center for Biodiversity Studies, Tel Aviv, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| |
Collapse
|
76
|
Forsdyke DR. Base Composition, Speciation, and Why the Mitochondrial Barcode Precisely Classifies. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/s13752-017-0267-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
77
|
Pavlova A, Gan HM, Lee YP, Austin CM, Gilligan DM, Lintermans M, Sunnucks P. Purifying selection and genetic drift shaped Pleistocene evolution of the mitochondrial genome in an endangered Australian freshwater fish. Heredity (Edinb) 2017; 118:466-476. [PMID: 28051058 PMCID: PMC5520527 DOI: 10.1038/hdy.2016.120] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 09/20/2016] [Accepted: 11/02/2016] [Indexed: 11/08/2022] Open
Abstract
Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB). Phylogenetic analysis resolved basin-level clades, supporting incipient speciation previously inferred from differentiation in allozymes, microsatellites and mitochondrial control region. The estimated time of lineage divergence suggested an early- to mid-Pleistocene split between SB and the common ancestor of HNB+MDB, followed by mid-to-late Pleistocene splitting between HNB and MDB. These divergence estimates are more recent than previous ones. Our analyses suggested that evolutionary drivers differed between inland MDB and coastal HNB. In the cooler and more climatically variable MDB, mitogenomes evolved under strong purifying selection, whereas in the warmer and more climatically stable HNB, purifying selection was relaxed. Evidence for relaxed selection in the HNB includes elevated transfer RNA and 16S ribosomal RNA polymorphism, presence of potentially mildly deleterious mutations and a codon (ATP6113) displaying signatures of positive selection (ratio of nonsynonymous to synonymous substitution rates (dN/dS) >1, radical change of an amino-acid property and phylogenetic conservation across the Percichthyidae). In addition, the difference could be because of stronger genetic drift in the smaller and historically more subdivided HNB with low per-population effective population sizes.
Collapse
Affiliation(s)
- A Pavlova
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| | - H M Gan
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
- Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Y P Lee
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
- Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - C M Austin
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
- Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - D M Gilligan
- NSW Department of Primary Industries, Batemans Bay, New South Wales, Australia
| | - M Lintermans
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - P Sunnucks
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, Australia
| |
Collapse
|
78
|
Morales HE, Sunnucks P, Joseph L, Pavlova A. Perpendicular axes of differentiation generated by mitochondrial introgression. Mol Ecol 2017; 26:3241-3255. [DOI: 10.1111/mec.14114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 12/24/2022]
Affiliation(s)
- Hernán E. Morales
- School of Biological Sciences Monash UniversityClayton Campus Melbourne Vic. 3800 Australia
- Centre for Marine Evolutionary Biology Department of Marine Sciences University of GothenburgBox 461 SE 405 30 Göteborg Sweden
| | - Paul Sunnucks
- School of Biological Sciences Monash UniversityClayton Campus Melbourne Vic. 3800 Australia
| | - Leo Joseph
- Australian National Wildlife Collection CSIRO National Research Collections AustraliaGPO Box 1700 Canberra ACT 2601 Australia
| | - Alexandra Pavlova
- School of Biological Sciences Monash UniversityClayton Campus Melbourne Vic. 3800 Australia
| |
Collapse
|
79
|
Skeletal Muscle Nucleo-Mitochondrial Crosstalk in Obesity and Type 2 Diabetes. Int J Mol Sci 2017; 18:ijms18040831. [PMID: 28420087 PMCID: PMC5412415 DOI: 10.3390/ijms18040831] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/01/2017] [Accepted: 04/08/2017] [Indexed: 12/15/2022] Open
Abstract
Skeletal muscle mitochondrial dysfunction, evidenced by incomplete beta oxidation and accumulation of fatty acid intermediates in the form of long and medium chain acylcarnitines, may contribute to ectopic lipid deposition and insulin resistance during high fat diet (HFD)-induced obesity. The present review discusses the roles of anterograde and retrograde communication in nucleo-mitochondrial crosstalk that determines skeletal muscle mitochondrial adaptations, specifically alterations in mitochondrial number and function in relation to obesity and insulin resistance. Special emphasis is placed on the effects of high fat diet (HFD) feeding on expression of nuclear-encoded mitochondrial genes (NEMGs) nuclear receptor factor 1 (NRF-1) and 2 (NRF-2) and peroxisome proliferator receptor gamma coactivator 1 alpha (PGC-1α) in the onset and progression of insulin resistance during obesity and how HFD-induced alterations in NEMG expression affect skeletal muscle mitochondrial adaptations in relation to beta oxidation of fatty acids. Finally, the potential ability of acylcarnitines or fatty acid intermediates resulting from mitochondrial beta oxidation to act as retrograde signals in nucleo-mitochondrial crosstalk is reviewed and discussed.
Collapse
|
80
|
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.
Collapse
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
| |
Collapse
|
81
|
Sunnucks P, Morales HE, Lamb AM, Pavlova A, Greening C. Integrative Approaches for Studying Mitochondrial and Nuclear Genome Co-evolution in Oxidative Phosphorylation. Front Genet 2017; 8:25. [PMID: 28316610 PMCID: PMC5334354 DOI: 10.3389/fgene.2017.00025] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/17/2017] [Indexed: 01/24/2023] Open
Abstract
In animals, interactions among gene products of mitochondrial and nuclear genomes (mitonuclear interactions) are of profound fitness, evolutionary, and ecological significance. Most fundamentally, the oxidative phosphorylation (OXPHOS) complexes responsible for cellular bioenergetics are formed by the direct interactions of 13 mitochondrial-encoded and ∼80 nuclear-encoded protein subunits in most animals. It is expected that organisms will develop genomic architecture that facilitates co-adaptation of these mitonuclear interactions and enhances biochemical efficiency of OXPHOS complexes. In this perspective, we present principles and approaches to understanding the co-evolution of these interactions, with a novel focus on how genomic architecture might facilitate it. We advocate that recent interdisciplinary advances assist in the consolidation of links between genotype and phenotype. For example, advances in genomics allow us to unravel signatures of selection in mitochondrial and nuclear OXPHOS genes at population-relevant scales, while newly published complete atomic-resolution structures of the OXPHOS machinery enable more robust predictions of how these genes interact epistatically and co-evolutionarily. We use three case studies to show how integrative approaches have improved the understanding of mitonuclear interactions in OXPHOS, namely those driving high-altitude adaptation in bar-headed geese, allopatric population divergence in Tigriopus californicus copepods, and the genome architecture of nuclear genes coding for mitochondrial functions in the eastern yellow robin.
Collapse
Affiliation(s)
- Paul Sunnucks
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Hernán E. Morales
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
- Department of Marine Sciences, University of GothenburgGothenburg, Sweden
| | - Annika M. Lamb
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Alexandra Pavlova
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| | - Chris Greening
- School of Biological Sciences, Monash University, ClaytonVIC, Australia
| |
Collapse
|
82
|
MtDNA meta-analysis reveals both phenotype specificity and allele heterogeneity: a model for differential association. Sci Rep 2017; 7:43449. [PMID: 28230165 PMCID: PMC5322532 DOI: 10.1038/srep43449] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/23/2017] [Indexed: 12/13/2022] Open
Abstract
Human mtDNA genetic variants have traditionally been considered markers for ancient population migrations. However, during the past three decades, these variants have been associated with altered susceptibility to various phenotypes, thus supporting their importance for human health. Nevertheless, mtDNA disease association has frequently been supported only in certain populations, due either to population stratification or differential epistatic compensations among populations. To partially overcome these obstacles, we performed meta-analysis of the multiple mtDNA association studies conducted until 2016, encompassing 53,975 patients and 63,323 controls. Our findings support the association of mtDNA haplogroups and recurrent variants with specific phenotypes such as Parkinson’s disease, type 2 diabetes, longevity, and breast cancer. Strikingly, our assessment of mtDNA variants’ involvement with multiple phenotypes revealed significant impact for Caucasian haplogroups H, J, and K. Therefore, ancient mtDNA variants could be divided into those that affect specific phenotypes, versus others with a general impact on phenotype combinations. We suggest that the mtDNA could serve as a model for phenotype specificity versus allele heterogeneity.
Collapse
|
83
|
Abstract
Although genetic transfer between viruses and vertebrate hosts occurs less frequently than gene flow between bacteriophages and prokaryotes, it is extensive and has affected the evolution of both parties. With retroviruses, the integration of proviral DNA into chromosomal DNA can result in the activation of adjacent host gene expression and in the transduction of host transcripts into retroviral genomes as oncogenes. Yet in contrast to lysogenic phage, there is little evidence that viral oncogenes persist in a chain of natural transmission or that retroviral transduction is a significant driver of the horizontal spread of host genes. Conversely, integration of proviruses into the host germ line has generated endogenous retroviral genomes (ERV) in all vertebrate genomes sequenced to date. Some of these genomes retain potential infectivity and upon reactivation may transmit to other host species. During mammalian evolution, sequences of retroviral origin have been repurposed to serve host functions, such as the viral envelope glycoproteins crucial to the development of the placenta. Beyond retroviruses, DNA viruses with complex genomes have acquired numerous genes of host origin which influence replication, pathogenesis and immune evasion, while host species have accumulated germline sequences of both DNA and RNA viruses. A codicil is added on lateral transmission of cancer cells between hosts and on migration of host mitochondria into cancer cells.
Collapse
Affiliation(s)
- Robin A Weiss
- Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT, UK.
| |
Collapse
|
84
|
Jhuang HY, Lee HY, Leu JY. Mitochondrial-nuclear co-evolution leads to hybrid incompatibility through pentatricopeptide repeat proteins. EMBO Rep 2016; 18:87-101. [PMID: 27920033 DOI: 10.15252/embr.201643311] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/09/2016] [Accepted: 10/21/2016] [Indexed: 01/09/2023] Open
Abstract
Mitochondrial-nuclear incompatibility has a major role in reproductive isolation between species. However, the underlying mechanism and driving force of mitochondrial-nuclear incompatibility remain elusive. Here, we report a pentatricopeptide repeat-containing (PPR) protein, Ccm1, and its interacting partner, 15S rRNA, to be involved in hybrid incompatibility between two yeast species, Saccharomyces cerevisiae and Saccharomyces bayanus S. bayanus-Ccm1 has reduced binding affinity for S. cerevisiae-15S rRNA, leading to respiratory defects in hybrid cells. This incompatibility can be rescued by single mutations on several individual PPR motifs, demonstrating the highly evolvable nature of PPR proteins. When we examined other PPR proteins in the closely related Saccharomyces sensu stricto yeasts, about two-thirds of them showed detectable incompatibility. Our results suggest that fast co-evolution between flexible PPR proteins and their mitochondrial RNA substrates may be a common driving force in the development of mitochondrial-nuclear hybrid incompatibility.
Collapse
Affiliation(s)
- Han-Ying Jhuang
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Hsin-Yi Lee
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan.,Molecular and Cell Biology, Taiwan International Graduate Program, Graduate Institute of Life Sciences, National Defense Medical Center and Academia Sinica, Taipei, Taiwan
| | - Jun-Yi Leu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan .,Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
85
|
Tobler M, Passow CN, Greenway R, Kelley JL, Shaw JH. The Evolutionary Ecology of Animals Inhabiting Hydrogen Sulfide–Rich Environments. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032418] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hydrogen sulfide (H2S) is a respiratory toxicant that creates extreme environments tolerated by few organisms. H2S is also produced endogenously by metazoans and plays a role in cell signaling. The mechanisms of H2S toxicity and its physiological functions serve as a basis to discuss the multifarious strategies that allow animals to survive in H2S-rich environments. Despite their toxicity, H2S-rich environments also provide ecological opportunities, and complex selective regimes of covarying abiotic and biotic factors drive trait evolution in organisms inhabiting H2S-rich environments. Furthermore, adaptation to H2S-rich environments can drive speciation, giving rise to biodiversity hot spots with high levels of endemism in deep-sea hydrothermal vents, cold seeps, and freshwater sulfide springs. The diversity of H2S-rich environments and their inhabitants provides ideal systems for comparative studies of the effects of a clear-cut source of selection across vast geographic and phylogenetic scales, ultimately informing our understanding of how environmental stressors affect ecological and evolutionary processes.
Collapse
Affiliation(s)
- Michael Tobler
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | | | - Ryan Greenway
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Jennifer H. Shaw
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma 74078
| |
Collapse
|
86
|
Shipley JR, Campbell P, Searle JB, Pasch B. Asymmetric energetic costs in reciprocal-cross hybrids between carnivorous mice (Onychomys). ACTA ACUST UNITED AC 2016; 219:3803-3809. [PMID: 27688051 DOI: 10.1242/jeb.148890] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 09/25/2016] [Indexed: 01/07/2023]
Abstract
Aerobic respiration is a fundamental physiological trait dependent on coordinated interactions between gene products of the mitochondrial and nuclear genomes. Mitonuclear mismatch in interspecific hybrids may contribute to reproductive isolation by inducing reduced viability (or even complete inviability) due to increased metabolic costs. However, few studies have tested for effects of mitonuclear mismatch on respiration at the whole-organism level. We explored how hybridization affects metabolic rate in closely related species of grasshopper mice (genus Onychomys) to better understand the role of metabolic costs in reproductive isolation. We measured metabolic rate across a range of temperatures to calculate basal metabolic rate (BMR) and cold-induced metabolic rate (MRc) in O. leucogaster, O. torridus and O. arenicola, and in reciprocal F1 hybrids between the latter two species. Within the genus, we found a negative correlation between mass-specific BMR and body mass. Although O. arenicola was smaller than O. torridus, hybrids from both directions of the cross resembled O. arenicola in body mass. In contrast, hybrid BMR was strongly influenced by the direction of the cross: reciprocal F1 hybrids were different from each other but indistinguishable from the maternal species. In addition, MRc was not significantly different between hybrids and either parental species. These patterns indicate that metabolic costs are not increased in Onychomys F1 hybrids and, while exposure of incompatibilities in F2 hybrids cannot be ruled out, suggest that mitonuclear mismatch does not act as a primary barrier to gene flow. Maternal matching of BMR is suggestive of a strong effect of mitochondrial genotype on metabolism in hybrids. Together, our findings provide insight into the metabolic consequences of hybridization, a topic that is understudied in mammals.
Collapse
Affiliation(s)
- J Ryan Shipley
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Polly Campbell
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Bret Pasch
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA .,Bioacoustics Research Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA.,Macaulay Library, Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
87
|
Ross JA, Howe DK, Coleman-Hulbert A, Denver DR, Estes S. Paternal Mitochondrial Transmission in Intra-Species Caenorhabditis briggsae Hybrids. Mol Biol Evol 2016; 33:3158-3160. [PMID: 27613821 PMCID: PMC5100050 DOI: 10.1093/molbev/msw192] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
To study mitochondrial–nuclear genetic interactions in the nematode Caenorhabditis briggsae, our three laboratories independently created 38 intra-species cytoplasmic–nuclear hybrid (cybrid) lines. Although the cross design combines maternal mitotypes with paternal nuclear genotypes, eight lines (21%) unexpectedly contained paternal mitotypes. All eight share in common ancestry of one of two genetically related strains. This unexpected parallel observation of paternal mitochondrial transmission, undesirable given our intent of creating cybrids, provides a serendipitous experimental model and framework to study the molecular and evolutionary basis of uniparental mitochondrial inheritance.
Collapse
Affiliation(s)
- Joseph A Ross
- Department of Biology, California State University, Fresno, CA
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University, Corvallis, OR
| | - Anna Coleman-Hulbert
- Department of Biology, Portland State University, Portland, OR.,Institute of Ecology and Evolution, University of Oregon, Eugene, OR
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR
| | - Suzanne Estes
- Department of Biology, Portland State University, Portland, OR
| |
Collapse
|
88
|
McFarlane SE, Sirkiä PM, Ålund M, Qvarnström A. Hybrid Dysfunction Expressed as Elevated Metabolic Rate in Male Ficedula Flycatchers. PLoS One 2016; 11:e0161547. [PMID: 27583553 PMCID: PMC5008804 DOI: 10.1371/journal.pone.0161547] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 08/08/2016] [Indexed: 02/06/2023] Open
Abstract
Studies of ecological speciation are often biased towards extrinsic sources of selection against hybrids, resulting from intermediate hybrid morphology, but the knowledge of how genetic incompatibilities accumulate over time under natural conditions is limited. Here we focus on a physiological trait, metabolic rate, which is central to life history strategies and thermoregulation but is also likely to be sensitive to mismatched mitonuclear interactions. We measured the resting metabolic rate of male collared, and pied flycatchers as well as of naturally occurring F1 hybrid males, in a recent hybrid zone. We found that hybrid males had a higher rather than intermediate metabolic rate, which is indicative of hybrid physiological dysfunction. Fitness costs associated with elevated metabolic rate are typically environmentally dependent and exaggerated under harsh conditions. By focusing on male hybrid dysfunction in an eco-physiological trait, our results contribute to the general understanding of how combined extrinsic and intrinsic sources of hybrid dysfunction build up under natural conditions.
Collapse
Affiliation(s)
- S. Eryn McFarlane
- Animal Ecology/ Department of Ecology and Genetics, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Päivi M. Sirkiä
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, Helsinki, Finland
- Section of Ecology, Department of Biology, University of Turku, Turku, Finland
| | - Murielle Ålund
- Animal Ecology/ Department of Ecology and Genetics, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Anna Qvarnström
- Animal Ecology/ Department of Ecology and Genetics, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| |
Collapse
|
89
|
Sloan DB, Fields PD, Havird JC. Mitonuclear linkage disequilibrium in human populations. Proc Biol Sci 2016; 282:rspb.2015.1704. [PMID: 26378221 DOI: 10.1098/rspb.2015.1704] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
There is extensive evidence from model systems that disrupting associations between co-adapted mitochondrial and nuclear genotypes can lead to deleterious and even lethal consequences. While it is tempting to extrapolate from these observations and make inferences about the human-health effects of altering mitonuclear associations, the importance of such associations may vary greatly among species, depending on population genetics, demographic history and other factors. Remarkably, despite the extensive study of human population genetics, the statistical associations between nuclear and mitochondrial alleles remain largely uninvestigated. We analysed published population genomic data to test for signatures of historical selection to maintain mitonuclear associations, particularly those involving nuclear genes that encode mitochondrial-localized proteins (N-mt genes). We found that significant mitonuclear linkage disequilibrium (LD) exists throughout the human genome, but these associations were generally weak, which is consistent with the paucity of population genetic structure in humans. Although mitonuclear LD varied among genomic regions (with especially high levels on the X chromosome), N-mt genes were statistically indistinguishable from background levels, suggesting that selection on mitonuclear epistasis has not preferentially maintained associations involving this set of loci at a species-wide level. We discuss these findings in the context of the ongoing debate over mitochondrial replacement therapy.
Collapse
Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Peter D Fields
- Zoological Institute, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland
| | - Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| |
Collapse
|
90
|
Incompatibility between Nuclear and Mitochondrial Genomes Contributes to an Interspecies Reproductive Barrier. Cell Metab 2016; 24:283-94. [PMID: 27425585 PMCID: PMC4981548 DOI: 10.1016/j.cmet.2016.06.012] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 03/29/2016] [Accepted: 06/17/2016] [Indexed: 11/22/2022]
Abstract
Vertebrate cells carry two different genomes, nuclear (nDNA) and mitochondrial (mtDNA), both encoding proteins involved in oxidative phosphorylation. Because of the extensive interactions, adaptive coevolution of the two genomes must occur to ensure normal mitochondrial function. To investigate whether incompatibilities between these two genomes could contribute to interspecies reproductive barriers, we performed reciprocal mtDNA replacement (MR) in zygotes between widely divergent Mus m. domesticus (B6) and conplastic Mus m. musculus (PWD) mice. Transfer of MR1 cybrid embryos (B6nDNA-PWDmtDNA) supported normal development of F1 offspring with reduced male fertility but unaffected reproductive fitness in females. Furthermore, donor PWD mtDNA was faithfully transmitted through the germline into F2 and F3 generations. In contrast, reciprocal MR2 (PWDnDNA-B6mtDNA) produced high embryonic loss and stillborn rates, suggesting an association between mitochondrial function and infertility. These results strongly suggest that functional incompatibility between nuclear and mitochondrial genomes contributes to interspecies reproductive isolation in mammals.
Collapse
|
91
|
Hill GE. Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap. Ecol Evol 2016; 6:5831-42. [PMID: 27547358 PMCID: PMC4983595 DOI: 10.1002/ece3.2338] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial genes are widely used in taxonomy and systematics because high mutation rates lead to rapid sequence divergence and because such changes have long been assumed to be neutral with respect to function. In particular, the nucleotide sequence of the mitochondrial gene cytochrome c oxidase subunit 1 has been established as a highly effective DNA barcode for diagnosing the species boundaries of animals. Rarely considered in discussions of mitochondrial evolution in the context of systematics, speciation, or DNA barcodes, however, is the genomic architecture of the eukaryotes: Mitochondrial and nuclear genes must function in tight coordination to produce the complexes of the electron transport chain and enable cellular respiration. Coadaptation of these interacting gene products is essential for organism function. I extend the hypothesis that mitonuclear interactions are integral to the process of speciation. To maintain mitonuclear coadaptation, nuclear genes, which code for proteins in mitochondria that cofunction with the products of mitochondrial genes, must coevolve with rapidly changing mitochondrial genes. Mitonuclear coevolution in isolated populations leads to speciation because population-specific mitonuclear coadaptations create between-population mitonuclear incompatibilities and hence barriers to gene flow between populations. In addition, selection for adaptive divergence of products of mitochondrial genes, particularly in response to climate or altitude, can lead to rapid fixation of novel mitochondrial genotypes between populations and consequently to disruption in gene flow between populations as the initiating step in animal speciation. By this model, the defining characteristic of a metazoan species is a coadapted mitonuclear genotype that is incompatible with the coadapted mitochondrial and nuclear genotype of any other population.
Collapse
Affiliation(s)
- Geoffrey E. Hill
- Department Biological ScienceAuburn University331 Funchess HallAuburnAlabama36849‐5414
| |
Collapse
|
92
|
Tsai T, St John JC. The role of mitochondrial DNA copy number, variants, and haplotypes in farm animal developmental outcome. Domest Anim Endocrinol 2016; 56 Suppl:S133-46. [PMID: 27345311 DOI: 10.1016/j.domaniend.2016.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 03/11/2016] [Accepted: 03/15/2016] [Indexed: 01/20/2023]
Abstract
The vast majority of cellular energy is generated through the process of oxidative phosphorylation, which takes place in the electron transport chain in the mitochondria. The electron transport chain is encoded by 2 genomes, the chromosomal and the mitochondrial genomes. Mitochondrial DNA is associated with a number of traits, which include tolerance to heat, growth and physical performance, meat and milk quality, and fertility. Mitochondrial genomes can be clustered into groups known as mtDNA haplotypes. Mitochondrial DNA haplotypes are a potential genetic source for manipulating phenotypes in farm animals. The use of assisted reproductive technologies, such as nuclear transfer, allows favorable chromosomal genetic traits to be mixed and matched with sought after mtDNA haplotype traits. As a result super breeds can be generated.
Collapse
Affiliation(s)
- Tesha Tsai
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, Vic, 3168, Australia; Department of Molecular and Translational Science, Monash University, Clayton, Vic, 3168, Australia
| | - Justin C St John
- Centre for Genetic Diseases, Hudson Institute of Medical Research, Clayton, Vic, 3168, Australia; Department of Molecular and Translational Science, Monash University, Clayton, Vic, 3168, Australia.
| |
Collapse
|
93
|
β-Sitosterol increases mitochondrial electron transport by fluidizing mitochondrial membranes and enhances mitochondrial responsiveness to increasing energy demand by the induction of uncoupling in C2C12 myotubes. J Funct Foods 2016. [DOI: 10.1016/j.jff.2016.02.045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
|
94
|
Pereverzeva VV, Primak AA. Genetic diversity of the cytochrome b gene fragment haplotypes in red-backed vole Myodes (Clethrionomys) rutilus Pallas, 1779. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416020095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
95
|
Immonen E, Rönn J, Watson C, Berger D, Arnqvist G. Complex mitonuclear interactions and metabolic costs of mating in male seed beetles. J Evol Biol 2015; 29:360-70. [PMID: 26548644 DOI: 10.1111/jeb.12789] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/03/2015] [Indexed: 02/02/2023]
Abstract
The lack of evolutionary response to selection on mitochondrial genes through males predicts the evolution of nuclear genetic influence on male-specific mitochondrial function, for example by gene duplication and evolution of sex-specific expression of paralogs involved in metabolic pathways. Intergenomic epistasis may therefore be a prevalent feature of the genetic architecture of male-specific organismal function. Here, we assess the role of mitonuclear genetic variation for male metabolic phenotypes [metabolic rate and respiratory quotient (RQ)] associated with ejaculate renewal, in the seed beetle Callosobruchus maculatus, by assaying lines with crossed combinations of distinct mitochondrial haplotypes and nuclear lineages. We found a significant increase in metabolic rate following mating relative to virgin males. Moreover, processes associated with ejaculate renewal showed variation in metabolic rate that was affected by mitonuclear interactions. Mitochondrial haplotype influenced mating-related changes in RQ, but this pattern varied over time. Mitonuclear genotype and the energy spent during ejaculate production affected the weight of the ejaculate, but the strength of this effect varied across mitochondrial haplotypes showing that the genetic architecture of male-specific reproductive function is complex. Our findings unveil hitherto underappreciated metabolic costs of mating and ejaculate renewal, and provide the first empirical demonstration of mitonuclear epistasis on male reproductive metabolic processes.
Collapse
Affiliation(s)
- E Immonen
- Evolutionary Biology Centre, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - J Rönn
- Evolutionary Biology Centre, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - C Watson
- Evolutionary Biology Centre, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - D Berger
- Evolutionary Biology Centre, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - G Arnqvist
- Evolutionary Biology Centre, Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| |
Collapse
|
96
|
Havird JC, Whitehill NS, Snow CD, Sloan DB. Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution. Evolution 2015; 69:3069-81. [PMID: 26514987 DOI: 10.1111/evo.12808] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/09/2015] [Accepted: 10/22/2015] [Indexed: 12/11/2022]
Abstract
Interactions between nuclear and mitochondrial gene products are critical for eukaryotic cell function. Nuclear genes encoding mitochondrial-targeted proteins (N-mt genes) experience elevated rates of evolution, which has often been interpreted as evidence of nuclear compensation in response to elevated mitochondrial mutation rates. However, N-mt genes may be under relaxed functional constraints, which could also explain observed increases in their evolutionary rate. To disentangle these hypotheses, we examined patterns of sequence and structural evolution in nuclear- and mitochondrial-encoded oxidative phosphorylation proteins from species in the angiosperm genus Silene with vastly different mitochondrial mutation rates. We found correlated increases in N-mt gene evolution in species with fast-evolving mitochondrial DNA. Structural modeling revealed an overrepresentation of N-mt substitutions at positions that directly contact mutated residues in mitochondrial-encoded proteins, despite overall patterns of conservative structural evolution. These findings support the hypothesis that selection for compensatory changes in response to mitochondrial mutations contributes to the elevated rate of evolution in N-mt genes. We discuss these results in light of theories implicating mitochondrial mutation rates and mitonuclear coevolution as drivers of speciation and suggest comparative and experimental approaches that could take advantage of heterogeneity in rates of mtDNA evolution across eukaryotes to evaluate such theories.
Collapse
Affiliation(s)
- Justin C Havird
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523.
| | - Nicholas S Whitehill
- Department of Computer Science, Colorado State University, Fort Collins, Colorado, 80523
| | - Christopher D Snow
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, 80523
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523.
| |
Collapse
|
97
|
Bar-Yaacov D, Hadjivasiliou Z, Levin L, Barshad G, Zarivach R, Bouskila A, Mishmar D. Mitochondrial Involvement in Vertebrate Speciation? The Case of Mito-nuclear Genetic Divergence in Chameleons. Genome Biol Evol 2015; 7:3322-36. [PMID: 26590214 PMCID: PMC4700957 DOI: 10.1093/gbe/evv226] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Compatibility between the nuclear (nDNA) and mitochondrial (mtDNA) genomes is important for organismal health. However, its significance for major evolutionary processes such as speciation is unclear, especially in vertebrates. We previously identified a sharp mtDNA-specific sequence divergence between morphologically indistinguishable chameleon populations (Chamaeleo chamaeleon recticrista) across an ancient Israeli marine barrier (Jezreel Valley). Because mtDNA introgression and gender-based dispersal were ruled out, we hypothesized that mtDNA spatial division was maintained by mito-nuclear functional compensation. Here, we studied RNA-seq generated from each of ten chameleons representing the north and south populations and identified candidate nonsynonymous substitutions (NSSs) matching the mtDNA spatial distribution. The most prominent NSS occurred in 14 nDNA-encoded mitochondrial proteins. Increased chameleon sample size (N = 70) confirmed the geographic differentiation in POLRMT, NDUFA5, ACO1, LYRM4, MARS2, and ACAD9. Structural and functionality evaluation of these NSSs revealed high functionality. Mathematical modeling suggested that this mito-nuclear spatial divergence is consistent with hybrid breakdown. We conclude that our presented evidence and mathematical model underline mito-nuclear interactions as a likely role player in incipient speciation in vertebrates.
Collapse
Affiliation(s)
- Dan Bar-Yaacov
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Zena Hadjivasiliou
- Centre for Mathematics, Physics and Engineering in the Life Sciences and Experimental Biology, UCL, London, United Kingdom Department of Genetics, Evolution and Environment, UCL, London, United Kingdom
| | - Liron Levin
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Gilad Barshad
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Amos Bouskila
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| |
Collapse
|
98
|
Chang CC, Rodriguez J, Ross J. Mitochondrial-Nuclear Epistasis Impacts Fitness and Mitochondrial Physiology of Interpopulation Caenorhabditis briggsae Hybrids. G3 (BETHESDA, MD.) 2015; 6:209-19. [PMID: 26585825 PMCID: PMC4704720 DOI: 10.1534/g3.115.022970] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 11/16/2015] [Indexed: 12/18/2022]
Abstract
In order to identify the earliest genetic changes that precipitate species formation, it is useful to study genetic incompatibilities that cause only mild dysfunction when incompatible alleles are combined in an interpopulation hybrid. Such hybridization within the nematode species Caenorhabditis briggsae has been suggested to result in selection against certain combinations of nuclear and mitochondrial alleles, raising the possibility that mitochondrial-nuclear (mitonuclear) epistasis reduces hybrid fitness. To test this hypothesis, cytoplasmic-nuclear hybrids (cybrids) were created to purposefully disrupt any epistatic interactions. Experimental analysis of the cybrids suggests that mitonuclear discord can result in decreased fecundity, increased lipid content, and increased mitochondrial reactive oxygen species levels. Many of these effects were asymmetric with respect to cross direction, as expected if cytoplasmic-nuclear Dobzhansky-Muller incompatibilities exist. One such effect is consistent with the interpretation that disrupting coevolved mitochondrial and nuclear loci impacts mitochondrial function and organismal fitness. These findings enhance efforts to study the genesis, identity, and maintenance of genetic incompatibilities that precipitate the speciation process.
Collapse
Affiliation(s)
- Chih-Chiun Chang
- Department of Biology, California State University, Fresno, California, 93740
| | - Joel Rodriguez
- Department of Biology, California State University, Fresno, California, 93740
| | - Joseph Ross
- Department of Biology, California State University, Fresno, California, 93740
| |
Collapse
|
99
|
Review: can diet influence the selective advantage of mitochondrial DNA haplotypes? Biosci Rep 2015; 35:BSR20150232. [PMID: 26543031 PMCID: PMC4708006 DOI: 10.1042/bsr20150232] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 11/05/2015] [Indexed: 01/12/2023] Open
Abstract
This review explores the potential for changes in dietary macronutrients to differentially influence mitochondrial bioenergetics and thereby the frequency of mtDNA haplotypes in natural populations. Such dietary modification may be seasonal or result from biogeographic or demographic shifts. Mechanistically, mtDNA haplotypes may influence the activity of the electron transport system (ETS), retrograde signalling to the nuclear genome and affect epigenetic modifications. Thus, differential provisioning by macronutrients may lead to selection through changes in the levels of ATP production, modulation of metabolites (including AMP, reactive oxygen species (ROS) and the NAD+/NADH ratio) and potentially complex epigenetic effects. The exquisite complexity of dietary influence on haplotype frequency is further illustrated by the fact that macronutrients may differentially influence the selective advantage of specific mutations in different life-history stages. In Drosophila, complex I mutations may affect larval growth because dietary nutrients are fed through this complex in immaturity. In contrast, the majority of electrons are provided to complex III in adult flies. We conclude the review with a case study that considers specific interactions between diet and complex I of the ETS. Complex I is the first enzyme of the mitochondrial ETS and co-ordinates in the oxidation of NADH and transfer of electrons to ubiquinone. Although the supposition that mtDNA variants may be selected upon by dietary macronutrients could be intuitively consistent to some and counter intuitive to others, it must face a multitude of scientific hurdles before it can be recognized.
Collapse
|
100
|
Sillo F, Garbelotto M, Friedman M, Gonthier P. Comparative Genomics of Sibling Fungal Pathogenic Taxa Identifies Adaptive Evolution without Divergence in Pathogenicity Genes or Genomic Structure. Genome Biol Evol 2015; 7:3190-206. [PMID: 26527650 PMCID: PMC4700942 DOI: 10.1093/gbe/evv209] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2015] [Indexed: 12/27/2022] Open
Abstract
It has been estimated that the sister plant pathogenic fungal species Heterobasidion irregulare and Heterobasidion annosum may have been allopatrically isolated for 34-41 Myr. They are now sympatric due to the introduction of the first species from North America into Italy, where they freely hybridize. We used a comparative genomic approach to 1) confirm that the two species are distinct at the genomic level; 2) determine which gene groups have diverged the most and the least between species; 3) show that their overall genomic structures are similar, as predicted by the viability of hybrids, and identify genomic regions that instead are incongruent; and 4) test the previously formulated hypothesis that genes involved in pathogenicity may be less divergent between the two species than genes involved in saprobic decay and sporulation. Results based on the sequencing of three genomes per species identified a high level of interspecific similarity, but clearly confirmed the status of the two as distinct taxa. Genes involved in pathogenicity were more conserved between species than genes involved in saprobic growth and sporulation, corroborating at the genomic level that invasiveness may be determined by the two latter traits, as documented by field and inoculation studies. Additionally, the majority of genes under positive selection and the majority of genes bearing interspecific structural variations were involved either in transcriptional or in mitochondrial functions. This study provides genomic-level evidence that invasiveness of pathogenic microbes can be attained without the high levels of pathogenicity presumed to exist for pathogens challenging naïve hosts.
Collapse
Affiliation(s)
- Fabiano Sillo
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Matteo Garbelotto
- Department of Environmental Science, Policy and Management, University of California, Berkeley
| | - Maria Friedman
- Department of Environmental Science, Policy and Management, University of California, Berkeley
| | - Paolo Gonthier
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| |
Collapse
|