1
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McDiarmid CS, Hooper DM, Stier A, Griffith SC. Mitonuclear interactions impact aerobic metabolism in hybrids and may explain mitonuclear discordance in young, naturally hybridizing bird lineages. Mol Ecol 2024; 33:e17374. [PMID: 38727686 DOI: 10.1111/mec.17374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/26/2024] [Accepted: 03/20/2024] [Indexed: 06/07/2024]
Abstract
Understanding genetic incompatibilities and genetic introgression between incipient species are major goals in evolutionary biology. Mitochondrial genes evolve rapidly and exist in dense gene networks with coevolved nuclear genes, suggesting that mitochondrial respiration may be particularly susceptible to disruption in hybrid organisms. Mitonuclear interactions have been demonstrated to contribute to hybrid dysfunction between deeply divergent taxa crossed in the laboratory, but there are few empirical examples of mitonuclear interactions between younger lineages that naturally hybridize. Here, we use controlled hybrid crosses and high-resolution respirometry to provide the first experimental evidence in a bird that inter-lineage mitonuclear interactions impact mitochondrial aerobic metabolism. Specifically, respiration capacity of the two mitodiscordant backcrosses (with mismatched mitonuclear combinations) differs from one another, although they do not differ significantly from the parental groups or mitoconcordant backcrosses as we would expect of mitonuclear disruptions. In the wild hybrid zone between these subspecies, the mitochondrial cline centre is shifted west of the nuclear cline centre, which is consistent with the direction of our experimental results. Our results therefore demonstrate asymmetric mitonuclear interactions that impact the capacity of cellular mitochondrial respiration and may help to explain the geographic discordance between mitochondrial and nuclear genomes observed in the wild.
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Affiliation(s)
- Callum S McDiarmid
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Daniel M Hooper
- Institute for Comparative Genomics and Richard Gilder Graduate School, American Museum of Natural History, New York, New York, USA
| | - Antoine Stier
- Department of Biology, University of Turku, Turku, Finland
- Institut Pluridisciplinaire Hubert Curien, UMR7178, Université de Strasbourg, CNRS, Strasbourg, France
| | - Simon C Griffith
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
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2
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Crino OL, Head ML, Jennions MD, Noble DWA. Mitochondrial function and sexual selection: can physiology resolve the 'lek paradox'? J Exp Biol 2024; 227:jeb245569. [PMID: 38206324 DOI: 10.1242/jeb.245569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Across many taxa, males use elaborate ornaments or complex displays to attract potential mates. Such sexually selected traits are thought to signal important aspects of male 'quality'. Female mating preferences based on sexual traits are thought to have evolved because choosy females gain direct benefits that enhance their lifetime reproductive success (e.g. greater access to food) and/or indirect benefits because high-quality males contribute genes that increase offspring fitness. However, it is difficult to explain the persistence of female preferences when males only provide genetic benefits, because female preferences should erode the heritable genetic variation in fitness that sexually selected traits signal. This 'paradox of the lek' has puzzled evolutionary biologists for decades, and inspired many hypotheses to explain how heritable variation in sexually selected traits is maintained. Here, we discuss how factors that affect mitochondrial function can maintain variation in sexually selected traits despite strong female preferences. We discuss how mitochondrial function can influence the expression of sexually selected traits, and we describe empirical studies that link the expression of sexually selected traits to mitochondrial function. We explain how mothers can affect mitochondrial function in their offspring by (a) influencing their developmental environment through maternal effects and (b) choosing a mate to increase the compatibility of mitochondrial and nuclear genes (i.e. the 'mitonuclear compatibility model of sexual selection'). Finally, we discuss how incorporating mitochondrial function into models of sexual selection might help to resolve the paradox of the lek, and we suggest avenues for future research.
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Affiliation(s)
- Ondi L Crino
- School of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - Megan L Head
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - Michael D Jennions
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Centre, 10 Marais Street, Stellenbosch 7600, South Africa
| | - Daniel W A Noble
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
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3
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Reifová R, Ament-Velásquez SL, Bourgeois Y, Coughlan J, Kulmuni J, Lipinska AP, Okude G, Stevison L, Yoshida K, Kitano J. Mechanisms of Intrinsic Postzygotic Isolation: From Traditional Genic and Chromosomal Views to Genomic and Epigenetic Perspectives. Cold Spring Harb Perspect Biol 2023; 15:a041607. [PMID: 37696577 PMCID: PMC10547394 DOI: 10.1101/cshperspect.a041607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Intrinsic postzygotic isolation typically appears as reduced viability or fertility of interspecific hybrids caused by genetic incompatibilities between diverged parental genomes. Dobzhansky-Muller interactions among individual genes, and chromosomal rearrangements causing problems with chromosome synapsis and recombination in meiosis, have both long been considered as major mechanisms behind intrinsic postzygotic isolation. Recent research has, however, suggested that the genetic basis of intrinsic postzygotic isolation can be more complex and involves, for example, overall divergence of the DNA sequence or epigenetic changes. Here, we review the mechanisms of intrinsic postzygotic isolation from genic, chromosomal, genomic, and epigenetic perspectives across diverse taxa. We provide empirical evidence for these mechanisms, discuss their importance in the speciation process, and highlight questions that remain unanswered.
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Affiliation(s)
- Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, 128 00 Prague, Czech Republic
| | | | - Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRD, 34090 Montpellier, France
| | - Jenn Coughlan
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
| | - Jonna Kulmuni
- Institute for Biodiversity and Ecosystem Dynamics, Department of Evolutionary and Population Biology, University of Amsterdam, 1012 Amsterdam, The Netherlands
- Organismal & Evolutionary Biology Research Programme, University of Helsinki, 00100 Helsinki, Finland
| | - Agnieszka P Lipinska
- Department of Algal Development and Evolution, Max Planck Institute for Biology, 72076 Tuebingen, Germany
- CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Genta Okude
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Laurie Stevison
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Kohta Yoshida
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Kitano
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
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4
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Xiong T, Mallet J. On the impermanence of species: The collapse of genetic incompatibilities in hybridizing populations. Evolution 2022; 76:2498-2512. [PMID: 36097352 PMCID: PMC9827863 DOI: 10.1111/evo.14626] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 07/23/2022] [Indexed: 01/22/2023]
Abstract
Species pairs often become genetically incompatible during divergence, which is an important source of reproductive isolation. An idealized picture is often painted where incompatibility alleles accumulate and fix between diverging species. However, recent studies have shown both that incompatibilities can collapse with ongoing hybridization, and that incompatibility loci can be polymorphic within species. This paper suggests some general rules for the behavior of incompatibilities under hybridization. In particular, we argue that redundancy of genetic pathways can strongly affect the dynamics of intrinsic incompatibilities. Since fitness in genetically redundant systems is unaffected by introducing a few foreign alleles, higher redundancy decreases the stability of incompatibilities during hybridization, but also increases tolerance of incompatibility polymorphism within species. We use simulations and theories to show that this principle leads to two types of collapse: in redundant systems, exemplified by classical Dobzhansky-Muller incompatibilities, collapse is continuous and approaches a quasi-neutral polymorphism between broadly sympatric species, often as a result of isolation-by-distance. In nonredundant systems, exemplified by co-evolution among genetic elements, incompatibilities are often stable, but can collapse abruptly with spatial traveling waves. As both types are common, the proposed principle may be useful in understanding the abundance of genetic incompatibilities in natural populations.
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Affiliation(s)
- Tianzhu Xiong
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMA02138USA
| | - James Mallet
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMA02138USA
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5
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Meza‐Lázaro RN, Peña‐Carrillo KI, Poteaux C, Lorenzi MC, Wetterer JK, Zaldívar‐Riverón A. Genome and cuticular hydrocarbon-based species delimitation shed light on potential drivers of speciation in a Neotropical ant species complex. Ecol Evol 2022; 12:e8704. [PMID: 35342602 PMCID: PMC8928884 DOI: 10.1002/ece3.8704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/02/2022] [Accepted: 02/18/2022] [Indexed: 12/03/2022] Open
Abstract
Geographic separation that leads to the evolution of reproductive isolation between populations generally is considered the most common form of speciation. However, speciation may also occur in the absence of geographic barriers due to phenotypic and genotypic factors such as chemical cue divergence, mating signal divergence, and mitonuclear conflict. Here, we performed an integrative study based on two genome-wide techniques (3RAD and ultraconserved elements) coupled with cuticular hydrocarbon (CHC) and mitochondrial (mt) DNA sequence data, to assess the species limits within the Ectatomma ruidum species complex, a widespread and conspicuous group of Neotropical ants for which heteroplasmy (i.e., presence of multiple mtDNA variants in an individual) has been recently discovered in some populations from southeast Mexico. Our analyses indicate the existence of at least five distinct species in this complex: two widely distributed across the Neotropics, and three that are restricted to southeast Mexico and that apparently have high levels of heteroplasmy. We found that species boundaries in the complex did not coincide with geographic barriers. We therefore consider possible roles of alternative drivers that may have promoted the observed patterns of speciation, including mitonuclear incompatibility, CHC differentiation, and colony structure. Our study highlights the importance of simultaneously assessing different sources of evidence to disentangle the species limits of taxa with complicated evolutionary histories.
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Affiliation(s)
- Rubi N. Meza‐Lázaro
- Colección Nacional de InsectosInstituto de BiologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| | - Kenzy I. Peña‐Carrillo
- Laboratoire d’Ethologie Expérimentale et ComparéeUR 4443LEECUniversité Sorbonne Paris NordClémentFrance
- INIFAPCampo Experimental General TeránGeneral TeránMexico
| | - Chantal Poteaux
- Laboratoire d’Ethologie Expérimentale et ComparéeUR 4443LEECUniversité Sorbonne Paris NordClémentFrance
| | - Maria Cristina Lorenzi
- Laboratoire d’Ethologie Expérimentale et ComparéeUR 4443LEECUniversité Sorbonne Paris NordClémentFrance
| | - James K. Wetterer
- Harriet L. Wilkes Honors CollegeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Alejandro Zaldívar‐Riverón
- Colección Nacional de InsectosInstituto de BiologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
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6
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Burton RS. The role of mitonuclear incompatibilities in allopatric speciation. Cell Mol Life Sci 2022; 79:103. [PMID: 35091831 PMCID: PMC11072163 DOI: 10.1007/s00018-021-04059-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 11/03/2022]
Abstract
Aerobic metabolism in eukaryotic cells requires extensive interactions between products of the nuclear and mitochondrial genomes. Rapid evolution of the mitochondrial genome, including fixation of both adaptive and deleterious mutations, creates intrinsic selection pressures favoring nuclear gene mutations that maintain mitochondrial function. As this process occurs independently in allopatry, the resulting divergence between conspecific populations can subsequently be manifest in mitonuclear incompatibilities in inter-population hybrids. Such incompatibilities, mitonuclear versions of Bateson-Dobzhansky-Muller incompatibilities that form the standard model for allopatric speciation, can potentially restrict gene flow between populations, ultimately resulting in varying degrees of reproductive isolation. The potential role of mitonuclear incompatibilities in speciation is further enhanced where mtDNA substitution rates are elevated compared to the nuclear genome and where population structure maintains allopatry for adequate time to evolve multiple mitonuclear incompatibilities. However, the fact that mitochondrial introgression occurs across species boundaries has raised questions regarding the efficacy of mitonuclear incompatibilities in reducing gene flow. Several scenarios now appear to satisfactorily explain this phenomenon, including cases where differences in mtDNA genetic load may drive introgression or where co-introgression of coadapted nuclear genes may support the function of introgressed mtDNA. Although asymmetries in reproductive isolation between taxa are consistent with mitonuclear incompatibilities, interactions between autosomes and sex chromosomes yield similar predictions that are difficult to disentangle. With regard to establishing reproductive isolation while in allopatry, existing studies clearly suggest that mitonuclear incompatibilities can contribute to the evolution of barriers to gene flow. However, there is to date relatively little definitive evidence supporting a primary role for mitonuclear incompatibilities in the speciation process.
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Affiliation(s)
- Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093-0202, USA.
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7
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Esselstyn JA, Achmadi AS, Handika H, Swanson MT, Giarla TC, Rowe KC. Fourteen New, Endemic Species of Shrew (Genus Crocidura) from Sulawesi Reveal a Spectacular Island Radiation. BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY 2021. [DOI: 10.1206/0003-0090.454.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Jacob A. Esselstyn
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA
| | - Anang S. Achmadi
- Museum Zoologicum Bogoriense, Indonesian Institute of Sciences, Cibinong, West Java, Indonesia
| | - Heru Handika
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA
| | - Mark T. Swanson
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA
| | | | - Kevin C. Rowe
- Sciences Department, Museums Victoria, Melbourne, Victoria, Australia
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8
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Zupok A, Kozul D, Schöttler MA, Niehörster J, Garbsch F, Liere K, Fischer A, Zoschke R, Malinova I, Bock R, Greiner S. A photosynthesis operon in the chloroplast genome drives speciation in evening primroses. THE PLANT CELL 2021; 33:2583-2601. [PMID: 34048579 PMCID: PMC8408503 DOI: 10.1093/plcell/koab155] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 05/27/2021] [Indexed: 05/09/2023]
Abstract
Genetic incompatibility between the cytoplasm and the nucleus is thought to be a major factor in species formation, but mechanistic understanding of this process is poor. In evening primroses (Oenothera spp.), a model plant for organelle genetics and population biology, hybrid offspring regularly display chloroplast-nuclear incompatibility. This usually manifests in bleached plants, more rarely in hybrid sterility or embryonic lethality. Hence, most of these incompatibilities affect photosynthetic capability, a trait that is under selection in changing environments. Here we show that light-dependent misregulation of the plastid psbB operon, which encodes core subunits of photosystem II and the cytochrome b6f complex, can lead to hybrid incompatibility, and this ultimately drives speciation. This misregulation causes an impaired light acclimation response in incompatible plants. Moreover, as a result of their different chloroplast genotypes, the parental lines differ in photosynthesis performance upon exposure to different light conditions. Significantly, the incompatible chloroplast genome is naturally found in xeric habitats with high light intensities, whereas the compatible one is limited to mesic habitats. Consequently, our data raise the possibility that the hybridization barrier evolved as a result of adaptation to specific climatic conditions.
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Affiliation(s)
| | | | - Mark Aurel Schöttler
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
| | - Julia Niehörster
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
| | - Frauke Garbsch
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
| | - Karsten Liere
- Institut für Biologie/Molekulare Genetik, Humboldt-Universität zu Berlin, Berlin, D-10115, Germany
| | - Axel Fischer
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
| | - Reimo Zoschke
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
| | - Irina Malinova
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
| | - Ralph Bock
- Department Organelle Biology, Biotechnology and Molecular Ecophysiology, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, D-14476, Germany
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9
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de Melo Teixeira M, Lang BF, Matute DR, Stajich JE, Barker BM. Mitochondrial genomes of the human pathogens Coccidioides immitis and Coccidioides posadasii. G3 (BETHESDA, MD.) 2021; 11:jkab132. [PMID: 33871031 PMCID: PMC8496281 DOI: 10.1093/g3journal/jkab132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/25/2021] [Indexed: 12/25/2022]
Abstract
Fungal mitochondrial genomes encode genes involved in crucial cellular processes, such as oxidative phosphorylation and mitochondrial translation, and the molecule has been used as a molecular marker for population genetics studies. Coccidioides immitis and C. posadasii are endemic fungal pathogens that cause coccidioidomycosis in arid regions across both American continents. To date, approximately 150 Coccidioides isolates have been sequenced to infer patterns of variation in nuclear genomes. However, less attention has been given to the mitochondrial genomes of Coccidioides. In this report, we describe the assembly and annotation of mitochondrial reference genomes for two representative strains of C. posadasii and C. immitis, as well as assess population variation among 77 selected genomes. The sizes of the circular-mapping molecules are 68.2 Kb in C. immitis and 75.1 Kb in C. posadasii. We identify 14 mitochondrial protein-coding genes common to most fungal mitochondria, which are largely syntenic across different populations and species of Coccidioides. Both Coccidioides species are characterized by a large number of group I and II introns, harboring twice the number of elements as compared to closely related Onygenales. The introns contain complete or truncated ORFs with high similarity to homing endonucleases of the LAGLIDADG and GIY-YIG families. Phylogenetic comparisons of mitochondrial and nuclear genomes show extensive phylogenetic discordance suggesting that the evolution of the two types of genetic material is not identical. This work represents the first assessment of mitochondrial genomes among isolates of both species of Coccidioides, and provides a foundation for future functional work.
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Affiliation(s)
- Marcus de Melo Teixeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
- Faculty of Medicine, University of Brasília-DF, Brasília, Federal District 70910-3300, Brazil
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Génomiques, Département de Biochimie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jason E Stajich
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
| | - Bridget M Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
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10
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Smukowski Heil C, Patterson K, Hickey ASM, Alcantara E, Dunham MJ. Transposable Element Mobilization in Interspecific Yeast Hybrids. Genome Biol Evol 2021; 13:6141023. [PMID: 33595639 PMCID: PMC7952228 DOI: 10.1093/gbe/evab033] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
Barbara McClintock first hypothesized that interspecific hybridization could provide a “genomic shock” that leads to the mobilization of transposable elements (TEs). This hypothesis is based on the idea that regulation of TE movement is potentially disrupted in hybrids. However, the handful of studies testing this hypothesis have yielded mixed results. Here, we set out to identify if hybridization can increase transposition rate and facilitate colonization of TEs in Saccharomyces cerevisiae × Saccharomyces uvarum interspecific yeast hybrids. Saccharomyces cerevisiae have a small number of active long terminal repeat retrotransposons (Ty elements), whereas their distant relative S. uvarum have lost the Ty elements active in S. cerevisiae. Although the regulation system of Ty elements is known in S. cerevisiae, it is unclear how Ty elements are regulated in other Saccharomyces species, and what mechanisms contributed to the loss of most classes of Ty elements in S. uvarum. Therefore, we first assessed whether TEs could insert in the S. uvarum sub-genome of a S. cerevisiae × S. uvarum hybrid. We induced transposition to occur in these hybrids and developed a sequencing technique to show that Ty elements insert readily and nonrandomly in the S. uvarum genome. We then used an in vivo reporter construct to directly measure transposition rate in hybrids, demonstrating that hybridization itself does not alter rate of mobilization. However, we surprisingly show that species-specific mitochondrial inheritance can change transposition rate by an order of magnitude. Overall, our results provide evidence that hybridization can potentially facilitate the introduction of TEs across species boundaries and alter transposition via mitochondrial transmission, but that this does not lead to unrestrained proliferation of TEs suggested by the genomic shock theory.
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Affiliation(s)
- Caiti Smukowski Heil
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Kira Patterson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Erica Alcantara
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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11
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Swamy KBS, Schuyler SC, Leu JY. Protein Complexes Form a Basis for Complex Hybrid Incompatibility. Front Genet 2021; 12:609766. [PMID: 33633780 PMCID: PMC7900514 DOI: 10.3389/fgene.2021.609766] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/20/2021] [Indexed: 12/20/2022] Open
Abstract
Proteins are the workhorses of the cell and execute many of their functions by interacting with other proteins forming protein complexes. Multi-protein complexes are an admixture of subunits, change their interaction partners, and modulate their functions and cellular physiology in response to environmental changes. When two species mate, the hybrid offspring are usually inviable or sterile because of large-scale differences in the genetic makeup between the two parents causing incompatible genetic interactions. Such reciprocal-sign epistasis between inter-specific alleles is not limited to incompatible interactions between just one gene pair; and, usually involves multiple genes. Many of these multi-locus incompatibilities show visible defects, only in the presence of all the interactions, making it hard to characterize. Understanding the dynamics of protein-protein interactions (PPIs) leading to multi-protein complexes is better suited to characterize multi-locus incompatibilities, compared to studying them with traditional approaches of genetics and molecular biology. The advances in omics technologies, which includes genomics, transcriptomics, and proteomics can help achieve this end. This is especially relevant when studying non-model organisms. Here, we discuss the recent progress in the understanding of hybrid genetic incompatibility; omics technologies, and how together they have helped in characterizing protein complexes and in turn multi-locus incompatibilities. We also review advances in bioinformatic techniques suitable for this purpose and propose directions for leveraging the knowledge gained from model-organisms to identify genetic incompatibilities in non-model organisms.
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Affiliation(s)
- Krishna B. S. Swamy
- Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Scott C. Schuyler
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Head and Neck Surgery, Department of Otolaryngology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
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12
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Hudon J, Wiebe KL, Stradi R. Disruptions of feather carotenoid pigmentation in a subset of hybrid northern flickers (Colaptes auratus) may be linked to genetic incompatibilities. Comp Biochem Physiol B Biochem Mol Biol 2020; 251:110510. [PMID: 33010421 DOI: 10.1016/j.cbpb.2020.110510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/21/2022]
Abstract
Hybridization can bring in single individuals alleles that were never designed to work together, which can result in unexpected or transgressive phenotypes. The Yellow-shafted (auratus group) and Red-shafted (cafer group) subspecies groups of the Northern Flicker (Colaptes auratus) differ conspicuously in the coloration of their flight feathers, but hybridize freely where their ranges overlap in western North America. The difference in color is largely the result of the Red-shafted form harboring ketolated products at C4(4') of the carotenoids found in the Yellow-shafted form. Characterizing the carotenoid pigments in a series of birds of intermediate color (presumed hybrids) revealed that most accumulated a product of β-cryptoxanthin with a keto group on its hydroxylated ring (3-hydroxy-echinenone), while a few accumulated the product with a keto group on the unhydroxylated ring (3'-hydroxy-echinenone). Surprisingly, the latter group also had feather barbs that were noticeably yellower than the associated rachis, corresponding to a lower level of ketolation at C4(4'). We assessed possible biochemical explanations for the differences by probing the relative carotenoid concentration data in individuals of varying color. The difference between the hybrids could not be explained by the general level of ketolation of carotenoids or a particular selectivity of the 4-ketolase involved. We present a testable genetic explanation that invokes incompatibilities between divergent alleles of the two parental forms at interacting loci. Because the idiosyncrasies affect oxidation, they may be the product of mitonuclear incompatibilities.
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Affiliation(s)
- Jocelyn Hudon
- Royal Alberta Museum, 9810 103A Avenue NW, Edmonton, AB T5J 0G2, Canada.
| | - Karen L Wiebe
- Department of Biology, University of Saskatchewan, Saskatoon, SK S7N 5E2, Canada.
| | - Riccardo Stradi
- DISFARM, Sezione di Chimica Generale e Organica "A. Marchesini", Facoltà di Scienze del Farmaco, Università degli Studi di Milano, Via Venezian, 21, 20133 Milano, Italy
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13
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Abstract
The genus Saccharomyces is an evolutionary paradox. On the one hand, it is composed of at least eight clearly phylogenetically delineated species; these species are reproductively isolated from each other, and hybrids usually cannot complete their sexual life cycles. On the other hand, Saccharomyces species have a long evolutionary history of hybridization, which has phenotypic consequences for adaptation and domestication. A variety of cellular, ecological, and evolutionary mechanisms are responsible for this partial reproductive isolation among Saccharomyces species. These mechanisms have caused the evolution of diverse Saccharomyces species and hybrids, which occupy a variety of wild and domesticated habitats. In this article, we introduce readers to the mechanisms isolating Saccharomyces species, the circumstances in which reproductive isolation mechanisms are effective and ineffective, and the evolutionary consequences of partial reproductive isolation. We discuss both the evolutionary history of the genus Saccharomyces and the human history of taxonomists and biologists struggling with species concepts in this fascinating genus.
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Affiliation(s)
- Jasmine Ono
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6AA, UK; ,
| | - Duncan Greig
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6AA, UK; ,
| | - Primrose J Boynton
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6AA, UK; ,
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14
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An J, Zheng W, Liang J, Xi Q, Chen R, Jia J, Lu X, Jakovlić I. Disrupted architecture and fast evolution of the mitochondrial genome of Argeia pugettensis (Isopoda): implications for speciation and fitness. BMC Genomics 2020; 21:607. [PMID: 32883208 PMCID: PMC7469299 DOI: 10.1186/s12864-020-07021-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/24/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Argeia pugettensis is an isopod species that parasitizes other crustaceans. Its huge native geographic range spans the Pacific from China to California, but molecular data are available only for a handful of specimens from North-American populations. We sequenced and characterised the complete mitogenome of a specimen collected in the Yellow Sea. RESULTS It exhibited a barcode (cox1) similarity level of only 87-89% with North-American populations, which is unusually low for conspecifics. Its mitogenome is among the largest in isopods (≈16.5 Kbp), mostly due to a large duplicated palindromic genomic segment (2 Kbp) comprising three genes. However, it lost a segment comprising three genes, nad4L-trnP-nad6, and many genes exhibited highly divergent sequences in comparison to isopod orthologues, including numerous mutations, deletions and insertions. Phylogenetic and selection analyses corroborated that this is one of the handful of most rapidly evolving available isopod mitogenomes, and that it evolves under highly relaxed selection constraints (as opposed to positive selection). However, its nuclear 18S gene is highly conserved, which suggests that rapid evolution is limited to its mitochondrial genome. The cox1 sequence analysis indicates that elevated mitogenomic evolutionary rates are not shared by North-American conspecifics, which suggests a breakdown of cox1 barcoding in this species. CONCLUSIONS A highly architecturally disrupted mitogenome and decoupling of mitochondrial and nuclear rates would normally be expected to have strong negative impacts on the fitness of the organism, so the existence of this lineage is a puzzling evolutionary question. Additional studies are needed to assess the phylogenetic breadth of this disrupted mitochondrial architecture and its impact on fitness.
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Affiliation(s)
- Jianmei An
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China.
| | - Wanrui Zheng
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Jielong Liang
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Qianqian Xi
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Ruru Chen
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Junli Jia
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Xia Lu
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan, 430075, Hubei, PR China
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15
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Hill GE. Genetic hitchhiking, mitonuclear coadaptation, and the origins of mt DNA barcode gaps. Ecol Evol 2020; 10:9048-9059. [PMID: 32953045 PMCID: PMC7487244 DOI: 10.1002/ece3.6640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 01/02/2023] Open
Abstract
DNA barcoding based on mitochondrial (mt) nucleotide sequences is an enigma. Neutral models of mt evolution predict DNA barcoding cannot work for recently diverged taxa, and yet, mt DNA barcoding accurately delimits species for many bilaterian animals. Meanwhile, mt DNA barcoding often fails for plants and fungi. I propose that because mt gene products must cofunction with nuclear gene products, the evolution of mt genomes is best understood with full consideration of the two environments that impose selective pressure on mt genes: the external environment and the internal genomic environment. Moreover, it is critical to fully consider the potential for adaptive evolution of not just protein products of mt genes but also of mt transfer RNAs and mt ribosomal RNAs. The tight linkage of genes on mt genomes that do not engage in recombination could facilitate selective sweeps whenever there is positive selection on any element in the mt genome, leading to the purging of mt genetic diversity within a population and to the rapid fixation of novel mt DNA sequences. Accordingly, the most important factor determining whether or not mt DNA sequences diagnose species boundaries may be the extent to which the mt chromosomes engage in recombination.
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16
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Piątkowski J, Golik P. Yeast pentatricopeptide protein Dmr1 (Ccm1) binds a repetitive AU-rich motif in the small subunit mitochondrial ribosomal RNA. RNA (NEW YORK, N.Y.) 2020; 26:1268-1282. [PMID: 32467310 PMCID: PMC7430664 DOI: 10.1261/rna.074880.120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
PPR proteins are a diverse family of RNA binding factors found in all Eukaryotic lineages. They perform multiple functions in the expression of organellar genes, mostly on the post-transcriptional level. PPR proteins are also significant determinants of evolutionary nucleo-organellar compatibility. Plant PPR proteins recognize their RNA substrates using a simple modular code. No target sequences recognized by animal or yeast PPR proteins were identified prior to the present study, making it impossible to assess whether this plant PPR code is conserved in other organisms. Dmr1p (Ccm1p, Ygr150cp) is a S. cerevisiae PPR protein essential for mitochondrial gene expression and involved in the stability of 15S ribosomal RNA. We demonstrate that in vitro Dmr1p specifically binds a motif composed of multiple AUA repeats occurring twice in the 15S rRNA sequence as the minimal 14 nt (AUA)4AU or longer (AUA)7 variant. Short RNA fragments containing this motif are protected by Dmr1p from exoribonucleolytic activity in vitro. Presence of the identified motif in mtDNA of different yeast species correlates with the compatibility between their Dmr1p orthologs and S. cerevisiae mtDNA. RNA recognition by Dmr1p is likely based on a rudimentary form of a PPR code specifying U at every third position, and depends on other factors, like RNA structure.
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Affiliation(s)
- Jakub Piątkowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
| | - Paweł Golik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, 02-106, Poland
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
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17
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Vaught RC, Voigt S, Dobler R, Clancy DJ, Reinhardt K, Dowling DK. Interactions between cytoplasmic and nuclear genomes confer sex-specific effects on lifespan in Drosophila melanogaster. J Evol Biol 2020; 33:694-713. [PMID: 32053259 DOI: 10.1111/jeb.13605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 12/19/2022]
Abstract
Genetic variation outside of the cell nucleus can affect the phenotype. The cytoplasm is home to the mitochondria, and in arthropods often hosts intracellular bacteria such as Wolbachia. Although numerous studies have implicated epistatic interactions between cytoplasmic and nuclear genetic variation as mediators of phenotypic expression, two questions remain. Firstly, it remains unclear whether outcomes of cyto-nuclear interactions will manifest differently across the sexes, as might be predicted given that cytoplasmic genomes are screened by natural selection only through females as a consequence of their maternal inheritance. Secondly, the relative contribution of mitochondrial genetic variation to other cytoplasmic sources of variation, such as Wolbachia infection, in shaping phenotypic outcomes of cyto-nuclear interactions remains unknown. Here, we address these questions, creating a fully crossed set of replicated cyto-nuclear populations derived from three geographically distinct populations of Drosophila melanogaster, measuring the lifespan of males and females from each population. We observed that cyto-nuclear interactions shape lifespan and that the outcomes of these interactions differ across the sexes. Yet, we found no evidence that placing the cytoplasms from one population alongside the nuclear background of others (generating putative cyto-nuclear mismatches) leads to decreased lifespan in either sex. Although it was difficult to partition mitochondrial from Wolbachia effects, our results suggest at least some of the cytoplasmic genotypic contribution to lifespan was directly mediated by an effect of sequence variation in the mtDNA. Future work should explore the degree to which cyto-nuclear interactions result in sex differences in the expression of other components of organismal life history.
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Affiliation(s)
- Rebecca C Vaught
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Susanne Voigt
- Faculty of Biology, Applied Zoology, TU Dresden, Dresden, Germany
| | - Ralph Dobler
- Faculty of Biology, Applied Zoology, TU Dresden, Dresden, Germany
| | - David J Clancy
- Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster, UK
| | - Klaus Reinhardt
- Faculty of Biology, Applied Zoology, TU Dresden, Dresden, Germany
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
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18
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Yan Z, Ye G, Werren JH. Evolutionary Rate Correlation between Mitochondrial-Encoded and Mitochondria-Associated Nuclear-Encoded Proteins in Insects. Mol Biol Evol 2019; 36:1022-1036. [PMID: 30785203 DOI: 10.1093/molbev/msz036] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The mitochondrion is a pivotal organelle for energy production, and includes components encoded by both the mitochondrial and nuclear genomes. Functional and evolutionary interactions are expected between the nuclear- and mitochondrial-encoded components. The topic is of broad interest in biology, with implications to genetics, evolution, and medicine. Here, we compare the evolutionary rates of mitochondrial proteins and ribosomal RNAs to rates of mitochondria-associated nuclear-encoded proteins, across the major orders of holometabolous insects. There are significant evolutionary rate correlations (ERCs) between mitochondrial-encoded and mitochondria-associated nuclear-encoded proteins, which are likely driven by different rates of mitochondrial sequence evolution and correlated changes in the interacting nuclear-encoded proteins. The pattern holds after correction for phylogenetic relationships and considering protein conservation levels. Correlations are stronger for both nuclear-encoded OXPHOS proteins that are in contact with mitochondrial OXPHOS proteins and for nuclear-encoded mitochondrial ribosomal amino acids directly contacting the mitochondrial rRNAs. We find that ERC between mitochondrial- and nuclear-encoded proteins is a strong predictor of nuclear-encoded proteins known to interact with mitochondria, and ERC shows promise for identifying new candidate proteins with mitochondrial function. Twenty-three additional candidate nuclear-encoded proteins warrant further study for mitochondrial function based on this approach, including proteins in the minichromosome maintenance helicase complex.
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Affiliation(s)
- Zhichao Yan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,Department of Biology, University of Rochester, Rochester, NY
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY
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19
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Passer AR, Coelho MA, Billmyre RB, Nowrousian M, Mittelbach M, Yurkov AM, Averette AF, Cuomo CA, Sun S, Heitman J. Genetic and Genomic Analyses Reveal Boundaries between Species Closely Related to Cryptococcus Pathogens. mBio 2019; 10:e00764-19. [PMID: 31186317 PMCID: PMC6561019 DOI: 10.1128/mbio.00764-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/08/2019] [Indexed: 12/30/2022] Open
Abstract
Speciation is a central mechanism of biological diversification. While speciation is well studied in plants and animals, in comparison, relatively little is known about speciation in fungi. One fungal model is the Cryptococcus genus, which is best known for the pathogenic Cryptococcus neoformans/Cryptococcus gattii species complex that causes >200,000 new human infections annually. Elucidation of how these species evolved into important human-pathogenic species remains challenging and can be advanced by studying the most closely related nonpathogenic species, Cryptococcus amylolentus and Tsuchiyaea wingfieldii However, these species have only four known isolates, and available data were insufficient to determine species boundaries within this group. By analyzing full-length chromosome assemblies, we reappraised the phylogenetic relationships of the four available strains, confirmed the genetic separation of C. amylolentus and T. wingfieldii (now Cryptococcus wingfieldii), and revealed an additional cryptic species, for which the name Cryptococcus floricola is proposed. The genomes of the three species are ∼6% divergent and exhibit significant chromosomal rearrangements, including inversions and a reciprocal translocation that involved intercentromeric ectopic recombination, which together likely impose significant barriers to genetic exchange. Using genetic crosses, we show that while C. wingfieldii cannot interbreed with any of the other strains, C. floricola can still undergo sexual reproduction with C. amylolentus However, most of the resulting spores were inviable or sterile or showed reduced recombination during meiosis, indicating that intrinsic postzygotic barriers had been established. Our study and genomic data will foster additional studies addressing fungal speciation and transitions between nonpathogenic and pathogenic Cryptococcus lineages.IMPORTANCE The evolutionary drivers of speciation are critical to our understanding of how new pathogens arise from nonpathogenic lineages and adapt to new environments. Here we focus on the Cryptococcus amylolentus species complex, a nonpathogenic fungal lineage closely related to the human-pathogenic Cryptococcus neoformans/Cryptococcus gattii complex. Using genetic and genomic analyses, we reexamined the species boundaries of four available isolates within the C. amylolentus complex and revealed three genetically isolated species. Their genomes are ∼6% divergent and exhibit chromosome rearrangements, including translocations and small-scale inversions. Although two of the species (C. amylolentus and newly described C. floricola) were still able to interbreed, the resulting hybrid progeny were usually inviable or sterile, indicating that barriers to reproduction had already been established. These results advance our understanding of speciation in fungi and highlight the power of genomics in assisting our ability to correctly identify and discriminate fungal species.
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Affiliation(s)
- Andrew Ryan Passer
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Marco A Coelho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Robert Blake Billmyre
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Minou Nowrousian
- Lehrstuhl für Allgemeine und Molekulare Botanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Moritz Mittelbach
- Geobotany, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Andrey M Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anna Floyd Averette
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | | | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
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20
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Hill GE, Havird JC, Sloan DB, Burton RS, Greening C, Dowling DK. Assessing the fitness consequences of mitonuclear interactions in natural populations. Biol Rev Camb Philos Soc 2019; 94:1089-1104. [PMID: 30588726 PMCID: PMC6613652 DOI: 10.1111/brv.12493] [Citation(s) in RCA: 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.
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Affiliation(s)
- Geoffrey E. Hill
- Department of Biological Sciences, Auburn University, United States of America
| | - Justin C. Havird
- Department of Biology, Colorado State University, United States of America
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, United States of America
| | - Ronald S. Burton
- Scripps Institution of Oceanography, University of California, San Diego, United States of America
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Damian K. Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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21
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Hill GE. Reconciling the Mitonuclear Compatibility Species Concept with Rampant Mitochondrial Introgression. Integr Comp Biol 2019; 59:912-924. [DOI: 10.1093/icb/icz019] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Abstract
The mitonuclear compatibility species concept defines a species as a population that is genetically isolated from other populations by uniquely coadapted mitochondrial (mt) and nuclear genes. A key prediction of this hypothesis is that the mt genotype of each species will be functionally distinct and that introgression of mt genomes will be prevented by mitonuclear incompatibilities that arise when heterospecific mt and nuclear genes attempt to cofunction to enable aerobic respiration. It has been proposed, therefore, that the observation of rampant introgression of mt genotypes from one species to another constitutes a strong refutation of the mitonuclear speciation. The displacement of a mt genotype from a nuclear background with which it co-evolved to a foreign nuclear background will necessarily lead to fitness loss due to mitonuclear incompatibilities. Here I consider two potential benefits of mt introgression between species that may, in some cases, overcome fitness losses arising from mitonuclear incompatibilities. First, the introgressed mt genotype may be better adapted to the local environment than the native mt genotype such that higher fitness is achieved through improved adaptation via introgression. Second, if the mitochondria of the recipient taxa carry a high mutational load, then introgression of a foreign, less corrupt mt genome may enable the recipient taxa to escape its mutational load and gain a fitness advantage. Under both scenarios, fitness gains from novel mt genotypes could theoretically compensate for the fitness that is lost via mitonuclear incompatibility. I also consider the role of endosymbionts in non-adaptive rampant introgression of mt genomes. I conclude that rampant introgression is not necessarily evidence against the idea of tight mitonuclear coadaptation or the mitonuclear compatibility species concept. Rampant mt introgression will typically lead to erasure of species but in some cases could lead to hybrid speciation.
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Affiliation(s)
- Geoffrey E Hill
- Department of Biological Sciences, 331 Funchess Hall, Auburn University, Auburn, AL 36849-5414, USA
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22
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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.
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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
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23
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Lima TG, Burton RS, Willett CS. Genomic scans reveal multiple mito‐nuclear incompatibilities in population crosses of the copepod
Tigriopus californicus. Evolution 2019; 73:609-620. [DOI: 10.1111/evo.13690] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 12/20/2018] [Accepted: 01/11/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Thiago G. Lima
- Department of Biology University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599
- Marine Biology Research Division Scripps Institution of Oceanography La Jolla California 92037
| | - Ronald S. Burton
- Marine Biology Research Division Scripps Institution of Oceanography La Jolla California 92037
| | - Christopher S. Willett
- Department of Biology University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599
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24
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Investigating mitonuclear interactions in human admixed populations. Nat Ecol Evol 2019; 3:213-222. [PMID: 30643241 PMCID: PMC6925600 DOI: 10.1038/s41559-018-0766-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/22/2018] [Indexed: 12/13/2022]
Abstract
To function properly, mitochondria utilize products of 37 mitochondrial and >1,000 nuclear genes, which should be compatible with each other. Discordance between mitochondrial and nuclear genetic ancestry could contribute to phenotypic variation in admixed populations. Here, we explored potential mitonuclear incompatibility in six admixed human populations from the Americas: African Americans, African Caribbeans, Colombians, Mexicans, Peruvians and Puerto Ricans. By comparing nuclear versus mitochondrial ancestry in these populations, we first show that mitochondrial DNA (mtDNA) copy number decreases with increasing discordance between nuclear and mtDNA ancestry. The direction of this effect is consistent across mtDNA haplogroups of different geographic origins. This observation indicates suboptimal regulation of mtDNA replication when its components are encoded by nuclear and mtDNA genes with different ancestry. Second, while most populations analysed exhibit no such trend, in African Americans and Puerto Ricans, we find a significant enrichment of ancestry at nuclear-encoded mitochondrial genes towards the source populations contributing the most prevalent mtDNA haplogroups (African and Native American, respectively). This possibly reflects compensatory effects of selection in recovering mitonuclear interactions optimized in the source populations. Our results provide evidence of mitonuclear interactions in human admixed populations and we discuss their implications for human health and disease.
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25
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Baker EP, Peris D, Moriarty RV, Li XC, Fay JC, Hittinger CT. Mitochondrial DNA and temperature tolerance in lager yeasts. SCIENCE ADVANCES 2019; 5:eaav1869. [PMID: 30729163 PMCID: PMC6353617 DOI: 10.1126/sciadv.aav1869] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/03/2019] [Indexed: 06/01/2023]
Abstract
A growing body of research suggests that the mitochondrial genome (mtDNA) is important for temperature adaptation. In the yeast genus Saccharomyces, species have diverged in temperature tolerance, driving their use in high- or low-temperature fermentations. Here, we experimentally test the role of mtDNA in temperature tolerance in synthetic and industrial hybrids (Saccharomyces cerevisiae × Saccharomyces eubayanus or Saccharomyces pastorianus), which cold-brew lager beer. We find that the relative temperature tolerances of hybrids correspond to the parent donating mtDNA, allowing us to modulate lager strain temperature preferences. The strong influence of mitotype on the temperature tolerance of otherwise identical hybrid strains provides support for the mitochondrial climactic adaptation hypothesis in yeasts and demonstrates how mitotype has influenced the world's most commonly fermented beverage.
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Affiliation(s)
- EmilyClare P. Baker
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA
| | - David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Paterna, Valencia, Spain
| | - Ryan V. Moriarty
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
| | - Xueying C. Li
- Molecular Genetics and Genomics Program, Washington University, St. Louis, MO, USA
- Department of Genetics, Washington University, St. Louis, MO, USA
- Center for Genome Sciences and System Biology, Washington University, St. Louis, MO, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Justin C. Fay
- Molecular Genetics and Genomics Program, Washington University, St. Louis, MO, USA
- Department of Genetics, Washington University, St. Louis, MO, USA
- Center for Genome Sciences and System Biology, Washington University, St. Louis, MO, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
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26
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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]
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27
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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.
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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
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28
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Rogers DW, McConnell E, Ono J, Greig D. Spore-autonomous fluorescent protein expression identifies meiotic chromosome mis-segregation as the principal cause of hybrid sterility in yeast. PLoS Biol 2018; 16:e2005066. [PMID: 30419022 PMCID: PMC6258379 DOI: 10.1371/journal.pbio.2005066] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 11/26/2018] [Accepted: 10/29/2018] [Indexed: 11/19/2022] Open
Abstract
Genome-wide sequence divergence between populations can cause hybrid sterility through the action of the anti-recombination system, which rejects crossover repair of double strand breaks between nonidentical sequences. Because crossovers are necessary to ensure proper segregation of homologous chromosomes during meiosis, the reduced recombination rate in hybrids can result in high levels of nondisjunction and therefore low gamete viability. Hybrid sterility in interspecific crosses of Saccharomyces yeasts is known to be associated with such segregation errors, but estimates of the importance of nondisjunction to postzygotic reproductive isolation have been hampered by difficulties in accurately measuring nondisjunction frequencies. Here, we use spore-autonomous fluorescent protein expression to quantify nondisjunction in both interspecific and intraspecific yeast hybrids. We show that segregation is near random in interspecific hybrids. The observed rates of nondisjunction can explain most of the sterility observed in interspecific hybrids through the failure of gametes to inherit at least one copy of each chromosome. Partially impairing the anti-recombination system by preventing expression of the RecQ helicase SGS1 during meiosis cuts nondisjunction frequencies in half. We further show that chromosome loss through nondisjunction can explain nearly all of the sterility observed in hybrids formed between two populations of a single species. The rate of meiotic nondisjunction of each homologous pair was negatively correlated with chromosome size in these intraspecific hybrids. Our results demonstrate that sequence divergence is not only associated with the sterility of hybrids formed between distantly related species but may also be a direct cause of reproductive isolation in incipient species.
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Affiliation(s)
- David W. Rogers
- Experimental Evolution Research Group, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- * E-mail:
| | - Ellen McConnell
- Experimental Evolution Research Group, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jasmine Ono
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Duncan Greig
- Experimental Evolution Research Group, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
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29
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Affiliation(s)
- Jerome H L Hui
- Simon F.S. Li Marine Science Laboratory, Partner State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong.
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30
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Kay KM, Woolhouse S, Smith BA, Pope NS, Rajakaruna N. Sympatric serpentine endemic
Monardella
(Lamiaceae) species maintain habitat differences despite hybridization. Mol Ecol 2018; 27:2302-2316. [DOI: 10.1111/mec.14582] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 02/09/2018] [Accepted: 02/20/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Kathleen M. Kay
- Department of Ecology and Evolutionary Biology University of California Santa Cruz California
| | - Suzie Woolhouse
- Department of Biological Sciences San José State University San José California
| | - Brett A. Smith
- Department of Ecology and Evolutionary Biology University of California Santa Cruz California
| | - Nathaniel S. Pope
- Department of Integrative Biology The University of Texas at Austin Austin Texas
| | - Nishanta Rajakaruna
- Biological Sciences Department California Polytechnic State University San Luis Obispo California
- Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
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31
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Tobler M, Kelley JL, Plath M, Riesch R. Extreme environments and the origins of biodiversity: Adaptation and speciation in sulphide spring fishes. Mol Ecol 2018; 27:843-859. [DOI: 10.1111/mec.14497] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Michael Tobler
- Division of Biology Kansas State University Manhattan KS USA
| | - Joanna L. Kelley
- School of Biological Sciences Washington State University Pullman WA USA
| | - Martin Plath
- Shaanxi Key Laboratory of Molecular Biology for Agriculture College of Animal Science and Technology Northwest A&F University Yangling Shaanxi China
| | - Rüdiger Riesch
- School of Biological Sciences Centre for Ecology, Evolution and Behaviour Royal Holloway University of London Egham Surrey UK
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32
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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
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33
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Giordano L, Sillo F, Garbelotto M, Gonthier P. Mitonuclear interactions may contribute to fitness of fungal hybrids. Sci Rep 2018; 8:1706. [PMID: 29374209 PMCID: PMC5786003 DOI: 10.1038/s41598-018-19922-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 01/05/2018] [Indexed: 12/15/2022] Open
Abstract
Hybridization between species is being recognized as a major force in the rapid adaptive evolution of fungal plant pathogens. The first stages of interspecific hybridization necessarily involve nuclear-mitochondrial chimeras. In their 2001 publication, Olson and Stenlid reported that mitochondria control the virulence of first generation hybrids between the North American fungal pathogen Heterobasidion irregulare and its congeneric H. occidentale. By assessing saprobic ability and gene expression of H. irregulare × H. annosum sensu stricto hybrids and of their parental genotypes, we demonstrate that mitochondria also influence saprobic growth of hybrids. Moreover, gene expression data suggest that fungal fitness is modulated by an intimate interplay between nuclear genes and mitochondrial type, and is dependent on the specific mitonuclear combination.
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Affiliation(s)
- Luana Giordano
- University of Torino, Department of Agricultural, Forest and Food Sciences (DISAFA), Largo Paolo Braccini 2, I-10095, Grugliasco (TO), Italy.,Centre of Competence for the Innovation in the Agro-Environmental Field (AGROINNOVA), University of Torino, Largo Paolo Braccini 2, I-10095, Grugliasco (TO), Italy
| | - Fabiano Sillo
- University of Torino, Department of Agricultural, Forest and Food Sciences (DISAFA), Largo Paolo Braccini 2, I-10095, Grugliasco (TO), Italy.
| | - Matteo Garbelotto
- University of California, Berkeley, Department of Environmental Science, Policy and Management, Forest Pathology and Mycology Laboratory, 54 Mulford Hall, 94720, Berkeley, California, USA
| | - Paolo Gonthier
- University of Torino, Department of Agricultural, Forest and Food Sciences (DISAFA), Largo Paolo Braccini 2, I-10095, Grugliasco (TO), Italy
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34
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Smukowski Heil CS, DeSevo CG, Pai DA, Tucker CM, Hoang ML, Dunham MJ. Loss of Heterozygosity Drives Adaptation in Hybrid Yeast. Mol Biol Evol 2017; 34:1596-1612. [PMID: 28369610 PMCID: PMC5455960 DOI: 10.1093/molbev/msx098] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we examine hybrid genome evolution using experimental evolution of de novo interspecific hybrid yeast Saccharomyces cerevisiae × Saccharomyces uvarum and their parentals. We evolved these strains in nutrient-limited conditions for hundreds of generations and sequenced the resulting cultures identifying numerous point mutations, copy number changes, and loss of heterozygosity (LOH) events, including species-biased amplification of nutrient transporters. We focused on a particularly interesting example, in which we saw repeated LOH at the high-affinity phosphate transporter gene PHO84 in both intra- and interspecific hybrids. Using allele replacement methods, we tested the fitness of different alleles in hybrid and S. cerevisiae strain backgrounds and found that the LOH is indeed the result of selection on one allele over the other in both S. cerevisiae and the hybrids. This is an example where hybrid genome resolution is driven by positive selection on existing heterozygosity and demonstrates that even infrequent outcrossing may have lasting impacts on adaptation.
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Affiliation(s)
| | - Christopher G DeSevo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ
| | - Dave A Pai
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ
| | - Cheryl M Tucker
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ
| | - Margaret L Hoang
- Department of Embryology, Howard Hughes Medical Institute, Carnegie Institution, Baltimore, MD.,Department of Biology, Johns Hopkins University, Baltimore, MD
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, WA
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35
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Dujon BA, Louis EJ. Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina). Genetics 2017; 206:717-750. [PMID: 28592505 PMCID: PMC5499181 DOI: 10.1534/genetics.116.199216] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/03/2017] [Indexed: 12/15/2022] Open
Abstract
Considerable progress in our understanding of yeast genomes and their evolution has been made over the last decade with the sequencing, analysis, and comparisons of numerous species, strains, or isolates of diverse origins. The role played by yeasts in natural environments as well as in artificial manufactures, combined with the importance of some species as model experimental systems sustained this effort. At the same time, their enormous evolutionary diversity (there are yeast species in every subphylum of Dikarya) sparked curiosity but necessitated further efforts to obtain appropriate reference genomes. Today, yeast genomes have been very informative about basic mechanisms of evolution, speciation, hybridization, domestication, as well as about the molecular machineries underlying them. They are also irreplaceable to investigate in detail the complex relationship between genotypes and phenotypes with both theoretical and practical implications. This review examines these questions at two distinct levels offered by the broad evolutionary range of yeasts: inside the best-studied Saccharomyces species complex, and across the entire and diversified subphylum of Saccharomycotina. While obviously revealing evolutionary histories at different scales, data converge to a remarkably coherent picture in which one can estimate the relative importance of intrinsic genome dynamics, including gene birth and loss, vs. horizontal genetic accidents in the making of populations. The facility with which novel yeast genomes can now be studied, combined with the already numerous available reference genomes, offer privileged perspectives to further examine these fundamental biological questions using yeasts both as eukaryotic models and as fungi of practical importance.
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Affiliation(s)
- Bernard A Dujon
- Department Genomes and Genetics, Institut Pasteur, Centre National de la Recherche Scientifique UMR3525, 75724-CEDEX15 Paris, France
- Université Pierre et Marie Curie UFR927, 75005 Paris, France
| | - Edward J Louis
- Centre for Genetic Architecture of Complex Traits, University of Leicester, LE1 7RH, United Kingdom
- Department of Genetics, University of Leicester, LE1 7RH, United Kingdom
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36
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Martin H, Touzet P, Dufay M, Godé C, Schmitt E, Lahiani E, Delph LF, Van Rossum F. Lineages of Silene nutans developed rapid, strong, asymmetric postzygotic reproductive isolation in allopatry. Evolution 2017; 71:1519-1531. [PMID: 28384386 DOI: 10.1111/evo.13245] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 03/18/2017] [Accepted: 03/23/2017] [Indexed: 12/15/2022]
Abstract
Reproductive isolation can rise either as a consequence of genomic divergence in allopatry or as a byproduct of divergent selection in parapatry. To determine whether reproductive isolation in gynodioecious Silene nutans results from allopatric divergence or from ecological adaptation following secondary contact, we investigated the pattern of postzygotic reproductive isolation and hybridization in natural populations using two phylogeographic lineages, western (W1) and eastern (E1). Experimental crosses between the lineages identified strong, asymmetric postzygotic isolation between the W1 and the E1 lineages, independent of geographic overlap. The proportion of ovules fertilized, seeds aborted, and seeds germinated revealed relatively little effect on the fitness of hybrids. In contrast, hybrid mortality was high and asymmetric: while half of the hybrid seedlings with western lineage mothers died, nearly all hybrid seedlings with E1 mothers died. This asymmetric mortality mirrored the proportion of chlorotic seedlings, and is congruent with cytonuclear incompatibility. We found no evidence of hybridization between the lineages in regions of co-occurrence using nuclear and plastid markers. Together, our results are consistent with the hypothesis that strong postzygotic reproductive isolation involving cytonuclear incompatibilities arose in allopatry. We argue that the dynamics of cytonuclear gynodioecy could facilitate the evolution of reproductive isolation.
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Affiliation(s)
- Hélène Martin
- Unité Évolution, Écologie, Paléontologie, UMR CNRS 8198, Université de Lille 1-Sciences et Technologies, F-59655, Villeneuve d'Ascq, France
| | - Pascal Touzet
- Unité Évolution, Écologie, Paléontologie, UMR CNRS 8198, Université de Lille 1-Sciences et Technologies, F-59655, Villeneuve d'Ascq, France
| | - Mathilde Dufay
- Unité Évolution, Écologie, Paléontologie, UMR CNRS 8198, Université de Lille 1-Sciences et Technologies, F-59655, Villeneuve d'Ascq, France
| | - Cécile Godé
- Unité Évolution, Écologie, Paléontologie, UMR CNRS 8198, Université de Lille 1-Sciences et Technologies, F-59655, Villeneuve d'Ascq, France
| | - Eric Schmitt
- Unité Évolution, Écologie, Paléontologie, UMR CNRS 8198, Université de Lille 1-Sciences et Technologies, F-59655, Villeneuve d'Ascq, France
| | - Emna Lahiani
- Unité Évolution, Écologie, Paléontologie, UMR CNRS 8198, Université de Lille 1-Sciences et Technologies, F-59655, Villeneuve d'Ascq, France
| | - Lynda F Delph
- Department of Biology, Indiana University, Bloomington, Indiana, 47405
| | - Fabienne Van Rossum
- Meise Botanic Garden (formerly National Botanic Garden of Belgium), Nieuwelaan 38, BE-1860, Meise, Belgium.,Écologie végétale et Biogéochimie, Université Libre de Bruxelles, CP244, Boulevard du Triomphe, BE-1050, Brussels, Belgium.,Fédération Wallonie-Bruxelles, rue A. Lavallée 1, BE-1080, Brussels, Belgium
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37
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Yeast Population Genomics Goes Wild: The Case of Saccharomyces paradoxus. POPULATION GENOMICS: MICROORGANISMS 2017. [DOI: 10.1007/13836_2017_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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38
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Hénault M, Landry CR. When nuclear-encoded proteins and mitochondrial RNAs do not get along, species split apart. EMBO Rep 2016; 18:8-10. [PMID: 27986790 DOI: 10.15252/embr.201643645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, QC, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes, Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Université Laval, Québec City, QC, Canada
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39
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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.
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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
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40
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Barnard‐Kubow KB, So N, Galloway LF. Cytonuclear incompatibility contributes to the early stages of speciation. Evolution 2016; 70:2752-2766. [DOI: 10.1111/evo.13075] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 09/08/2016] [Accepted: 09/17/2016] [Indexed: 12/20/2022]
Affiliation(s)
| | - Nina So
- Department of Biology University of Virginia Charlottesville Virginia 22904
- Current Address: Doctoral Program in Neurobiology and Behavior Columbia University New York NY 10027
| | - Laura F. Galloway
- Department of Biology University of Virginia Charlottesville Virginia 22904
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41
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Gebiola M, Kelly SE, Hammerstein P, Giorgini M, Hunter MS. “Darwin's corollary” and cytoplasmic incompatibility induced by
Cardinium
may contribute to speciation in
Encarsia
wasps (Hymenoptera: Aphelinidae). Evolution 2016; 70:2447-2458. [DOI: 10.1111/evo.13037] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/04/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Gebiola
- Department of Entomology The University of Arizona Tucson Arizona 85721
- CNR – Istituto per la Protezione Sostenibile delle Piante Portici Italy
| | - Suzanne E. Kelly
- Department of Entomology The University of Arizona Tucson Arizona 85721
| | - Peter Hammerstein
- Institute for Theoretical Biology Humboldt‐Universität zu Berlin Philippstr. 13, Haus 4 10115 Berlin Germany
| | - Massimo Giorgini
- CNR – Istituto per la Protezione Sostenibile delle Piante Portici Italy
| | - Martha S. Hunter
- Department of Entomology The University of Arizona Tucson Arizona 85721
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42
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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.
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Affiliation(s)
- Geoffrey E. Hill
- Department Biological ScienceAuburn University331 Funchess HallAuburnAlabama36849‐5414
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43
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Hou J, Fournier T, Schacherer J. Species-wide survey reveals the various flavors of intraspecific reproductive isolation in yeast. FEMS Yeast Res 2016; 16:fow048. [PMID: 27288348 DOI: 10.1093/femsyr/fow048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2016] [Indexed: 12/13/2022] Open
Abstract
Exploring the origin and extent of reproductive isolation within the same species is valuable to capture early events to the onset of speciation. In multiple genetic models, reproductive isolation was recently observed at the intraspecific scale, indicating that the raw potential for speciation segregates readily within populations, which could be a rule rather than an exception in a broad context. We briefly recapitulate the molecular evidence of intrinsic post-zygotic isolation in major model organisms including Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster and their close relatives. We then focus on recent advances in yeast and review the genetic basis of post-zygotic isolation within and between multiple members of the Saccharomyces genus, especially in Saccharomyces cerevisiae We discuss the role of various mechanisms involved in the onset of reproductive isolation including DNA sequence divergence, chromosomal rearrangement, cytonuclear as well as nuclear-nuclear genetic incompatibilities and provide a comparative view along a continuum of genetic differentiation, which encompasses intraspecific populations, recent delineating nascent species as well as closely related sister species in the same subphylum.
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Affiliation(s)
- Jing Hou
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS UMR 7156, Strasbourg, France
| | - Téo Fournier
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS UMR 7156, Strasbourg, France
| | - Joseph Schacherer
- Department of Genetics, Genomics and Microbiology, University of Strasbourg/CNRS UMR 7156, Strasbourg, France
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44
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Kolondra A, Labedzka-Dmoch K, Wenda JM, Drzewicka K, Golik P. The transcriptome of Candida albicans mitochondria and the evolution of organellar transcription units in yeasts. BMC Genomics 2015; 16:827. [PMID: 26487099 PMCID: PMC4618339 DOI: 10.1186/s12864-015-2078-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 10/13/2015] [Indexed: 02/06/2023] Open
Abstract
Background Yeasts show remarkable variation in the organization of their mitochondrial genomes, yet there is little experimental data on organellar gene expression outside few model species. Candida albicans is interesting as a human pathogen, and as a representative of a clade that is distant from the model yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe. Unlike them, it encodes seven Complex I subunits in its mtDNA. No experimental data regarding organellar expression were available prior to this study. Methods We used high-throughput RNA sequencing and traditional RNA biology techniques to study the mitochondrial transcriptome of C. albicans strains BWP17 and SN148. Results The 14 protein-coding genes, two ribosomal RNA genes, and 24 tRNA genes are expressed as eight primary polycistronic transcription units. We also found transcriptional activity in the noncoding regions, and antisense transcripts that could be a part of a regulatory mechanism. The promoter sequence is a variant of the nonanucleotide identified in other yeast mtDNAs, but some of the active promoters show significant departures from the consensus. The primary transcripts are processed by a tRNA punctuation mechanism into the monocistronic and bicistronic mature RNAs. The steady state levels of various mature transcripts exhibit large differences that are a result of posttranscriptional regulation. Transcriptome analysis allowed to precisely annotate the positions of introns in the RNL (2), COB (2) and COX1 (4) genes, as well as to refine the annotation of tRNAs and rRNAs. Comparative study of the mitochondrial genome organization in various Candida species indicates that they undergo shuffling in blocks usually containing 2–3 genes, and that their arrangement in primary transcripts is not conserved. tRNA genes with their associated promoters, as well as GC-rich sequence elements play an important role in these evolutionary events. Conclusions The main evolutionary force shaping the mitochondrial genomes of yeasts is the frequent recombination, constantly breaking apart and joining genes into novel primary transcription units. The mitochondrial transcription units are constantly rearranged in evolution shaping the features of gene expression, such as the presence of secondary promoter sites that are inactive, or act as “booster” promoters, simplified transcriptional regulation and reliance on posttranscriptional mechanisms. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2078-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam Kolondra
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Karolina Labedzka-Dmoch
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Joanna M Wenda
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Katarzyna Drzewicka
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland.
| | - Pawel Golik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland. .,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland.
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Hunt T. The Microcosm within: An interview with William B. Miller, Jr., on the Extended Hologenome theory of evolution. Commun Integr Biol 2015; 8:e1000711. [PMID: 26478771 PMCID: PMC4594229 DOI: 10.1080/19420889.2014.1000711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/06/2014] [Indexed: 11/25/2022] Open
Abstract
There is a singular unifying reality underlying every biologic interaction on our planet. In immunology, that which does not kill you makes you different. -William B. Miller, Jr. We are experiencing a revolution in our understanding of inner space on a par with our exponentially increasing understanding of outer space. In biology, we are learning that the genetic and epigenetic complexity within organisms is far deeper than suspected. This is a key theme in William B. Miller Jr.'s book, The Microcosm Within: Evolution and Extinction in the Hologenome. We are learning also that a focus on the human genome alone is misleading when it comes to who we really are as biological entities, and in terms of how we and other creatures have evolved. Rather than being defined by the human genome alone, we are instead defined by the “hologenome,” the sum of the human genome and the far larger genetic endowment of the microbiome and symbiotic communities that reside within and around us. Miller is a medical doctor previously in private practice in Pennsylvania and Phoenix, Arizona. This book is his first foray into evolutionary theory. His book could have been titled “The Origin of Variation” because this is his primary focus. He accepts that natural selection plays a role in evolution, but he demotes this mechanism to a less important role than the Modern Synthesis suggests. His main gripe, however, concerns random variation. He argues that random variation is unable to explain the origin and evolution of biological forms that we see in the world around us and in the historical record. Miller suggests that, rather than random variation as the engine of novelty, there is a creative impulse at the heart of cellular life, and even at the level of the genetic aggregate, that generates novelty on a regular basis. I probe this assertion in the interview below. He also highlights the strong role of “exogenous genetic assault” in variation and in his immunological model of evolution.
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Affiliation(s)
- Tam Hunt
- Department of Psychology; Environmental Science & Management; University of California at Santa Barbara ; Santa Barbara, CA USA
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Simple Biophysical Model Predicts Faster Accumulation of Hybrid Incompatibilities in Small Populations Under Stabilizing Selection. Genetics 2015; 201:1525-37. [PMID: 26434721 PMCID: PMC4676520 DOI: 10.1534/genetics.115.181685] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 09/23/2015] [Indexed: 01/07/2023] Open
Abstract
Speciation is fundamental to the process of generating the huge diversity of life on Earth. However, we are yet to have a clear understanding of its molecular-genetic basis. Here, we examine a computational model of reproductive isolation that explicitly incorporates a map from genotype to phenotype based on the biophysics of protein–DNA binding. In particular, we model the binding of a protein transcription factor to a DNA binding site and how their independent coevolution, in a stabilizing fitness landscape, of two allopatric lineages leads to incompatibilities. Complementing our previous coarse-grained theoretical results, our simulations give a new prediction for the monomorphic regime of evolution that smaller populations should develop incompatibilities more quickly. This arises as (1) smaller populations have a greater initial drift load, as there are more sequences that bind poorly than well, so fewer substitutions are needed to reach incompatible regions of phenotype space, and (2) slower divergence when the population size is larger than the inverse of discrete differences in fitness. Further, we find longer sequences develop incompatibilities more quickly at small population sizes, but more slowly at large population sizes. The biophysical model thus represents a robust mechanism of rapid reproductive isolation for small populations and large sequences that does not require peak shifts or positive selection. Finally, we show that the growth of DMIs with time is quadratic for small populations, agreeing with Orr’s model, but nonpower law for large populations, with a form consistent with our previous theoretical results.
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47
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Functional diversity of complex I subunits in Candida albicans mitochondria. Curr Genet 2015; 62:87-95. [PMID: 26373419 DOI: 10.1007/s00294-015-0518-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 08/26/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
Abstract
Our interest in the mitochondria of Candida albicans has progressed to the identification of several proteins that are critical to complex I (CI) activity. We speculated that there should be major functional differences at the protein level between mammalian and fungal mitochondria CI. In our pursuit of this idea, we were helped by published data of CI subunit proteins from a broad diversity of species that included two subunit proteins that are not found in mammals. These subunit proteins have been designated as Nuo1p and Nuo2p (NADH-ubiquinone oxidoreductases). Since functional assignments of both C. albicans proteins were unknown, other than having a putative NADH-oxidoreductase activity, we constructed knock-out strains that could be compared to parental cells. The relevance of our research relates to the critical roles of both proteins in cell biology and pathogenesis and their absence in mammals. These features suggest they may be exploited in antifungal drug discovery. Initially, we characterized Goa1p that apparently regulates CI activity but is not a CI subunit protein. We have used the goa1∆ for comparisons to Nuo1p and Nuo2p. We have demonstrated the critical role of these proteins in maintaining CI activities, virulence, and prolonging life span. More recently, transcriptional profiling of the three mutants and an ndh51∆ (protein is a highly conserved CI subunit) has revealed that there are overlapping yet also different functional assignments that suggest subunit specificity. The differences and similarities of each are described below along with our hypotheses to explain these data. Our conclusion and perspective is that the C. albicans CI subunit proteins are highly conserved except for two that define non-mammalian functions.
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Wolters JF, Chiu K, Fiumera HL. Population structure of mitochondrial genomes in Saccharomyces cerevisiae. BMC Genomics 2015; 16:451. [PMID: 26062918 PMCID: PMC4464245 DOI: 10.1186/s12864-015-1664-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 05/29/2015] [Indexed: 12/13/2022] Open
Abstract
Background Rigorous study of mitochondrial functions and cell biology in the budding yeast, Saccharomyces cerevisiae has advanced our understanding of mitochondrial genetics. This yeast is now a powerful model for population genetics, owing to large genetic diversity and highly structured populations among wild isolates. Comparative mitochondrial genomic analyses between yeast species have revealed broad evolutionary changes in genome organization and architecture. A fine-scale view of recent evolutionary changes within S. cerevisiae has not been possible due to low numbers of complete mitochondrial sequences. Results To address challenges of sequencing AT-rich and repetitive mitochondrial DNAs (mtDNAs), we sequenced two divergent S. cerevisiae mtDNAs using a single-molecule sequencing platform (PacBio RS). Using de novo assemblies, we generated highly accurate complete mtDNA sequences. These mtDNA sequences were compared with 98 additional mtDNA sequences gathered from various published collections. Phylogenies based on mitochondrial coding sequences and intron profiles revealed that intraspecific diversity in mitochondrial genomes generally recapitulated the population structure of nuclear genomes. Analysis of intergenic sequence indicated a recent expansion of mobile elements in certain populations. Additionally, our analyses revealed that certain populations lacked introns previously believed conserved throughout the species, as well as the presence of introns never before reported in S. cerevisiae. Conclusions Our results revealed that the extensive variation in S. cerevisiae mtDNAs is often population specific, thus offering a window into the recent evolutionary processes shaping these genomes. In addition, we offer an effective strategy for sequencing these challenging AT-rich mitochondrial genomes for small scale projects. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1664-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John F Wolters
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA.
| | - Kenneth Chiu
- Computer Science Department, Binghamton University, Binghamton, NY, USA.
| | - Heather L Fiumera
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA.
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Comprehensive survey of condition-specific reproductive isolation reveals genetic incompatibility in yeast. Nat Commun 2015; 6:7214. [PMID: 26008139 PMCID: PMC4445460 DOI: 10.1038/ncomms8214] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 04/17/2015] [Indexed: 12/13/2022] Open
Abstract
Genetic variation within a species could cause negative epistasis leading to reduced hybrid fitness and post-zygotic reproductive isolation. Recent studies in yeasts revealed chromosomal rearrangements as a major mechanism dampening intraspecific hybrid fertility on rich media. Here, by analysing a large number of Saccharomyces cerevisiae crosses on different culture conditions, we show environment-specific genetic incompatibility segregates readily within yeast and contributes to reproductive isolation. Over 24% (117 out of 481) of cases tested show potential epistasis, among which 6.7% (32 out of 481) are severe, with at least 20% of progeny loss on tested conditions. Based on the segregation patterns, we further characterize a two-locus Dobzhansky–Müller incompatibility case leading to offspring respiratory deficiency caused by nonsense mutation in a nuclear-encoding mitochondrial gene and tRNA suppressor. We provide evidence that this precise configuration could be adaptive in fluctuating environments, highlighting the role of ecological selection in the onset of genetic incompatibility and reproductive isolation in yeast. Chromosomal rearrangements may hamper intraspecific hybrid fertility. Here the authors show that environment-specific genetic incompatibility segregates readily within intermating populations and leads to intrinsic reproductive isolation within a yeast species.
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Morales HE, Pavlova A, Joseph L, Sunnucks P. Positive and purifying selection in mitochondrial genomes of a bird with mitonuclear discordance. Mol Ecol 2015; 24:2820-37. [DOI: 10.1111/mec.13203] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Hernán E. Morales
- School of Biological Sciences Monash University; Clayton Campus Melbourne Vic. 3800 Australia
| | - Alexandra Pavlova
- School of Biological Sciences Monash University; Clayton Campus Melbourne Vic. 3800 Australia
| | - Leo Joseph
- Australian National Wildlife Collection; CSIRO National Facilities and Collections; GPO Box 1700 Canberra ACT 2601 Australia
| | - Paul Sunnucks
- School of Biological Sciences Monash University; Clayton Campus Melbourne Vic. 3800 Australia
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