1
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Estes S, Dietz ZP, Katju V, Bergthorsson U. Evolutionary codependency: insights into the mitonuclear interaction landscape from experimental and wild Caenorhabditis nematodes. Curr Opin Genet Dev 2023; 81:102081. [PMID: 37421904 DOI: 10.1016/j.gde.2023.102081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 07/10/2023]
Abstract
Aided by new technologies, the upsurgence of research into mitochondrial genome biology during the past 15 years suggests that we have misunderstood, and perhaps dramatically underestimated, the ongoing biological and evolutionary significance of our long-time symbiotic partner. While we have begun to scratch the surface of several topics, many questions regarding the nature of mutation and selection in the mitochondrial genome, and the nature of its relationship to the nuclear genome, remain unanswered. Although best known for their contributions to studies of developmental and aging biology, Caenorhabditis nematodes are increasingly recognized as excellent model systems to advance understanding in these areas. We review recent discoveries with relevance to mitonuclear coevolution and conflict and offer several fertile areas for future work.
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Affiliation(s)
- Suzanne Estes
- Portland State University, Department of Biology, Portland, OR, USA.
| | - Zachary P Dietz
- Portland State University, Department of Biology, Portland, OR, USA
| | - Vaishali Katju
- Uppsala University, Department of Ecology and Genetics, 752 36 Uppsala, Sweden
| | - Ulfar Bergthorsson
- Uppsala University, Department of Ecology and Genetics, 752 36 Uppsala, Sweden
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2
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Qing X, Peng H, Ma J, Zhang YM, Li H, Peng D, Wang X, Long T. Phylogeography of Chinese cereal cyst nematodes sheds lights on their origin and dispersal. Evol Appl 2022; 15:1236-1248. [PMID: 36051465 PMCID: PMC9423084 DOI: 10.1111/eva.13452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 07/09/2022] [Accepted: 07/15/2022] [Indexed: 11/29/2022] Open
Abstract
Reconstructing the dispersal routes of pathogens can help identify the key drivers of their evolution and provides a basis for disease control. The cereal cyst nematode Heterodera avenae is one of the major nematode pests on cereals that can cause 10%–90% crop yield losses worldwide. Through extensive sampling on wheat and grasses, the Chinese population of H. avenae is widely identified in virtually all wheat growing regions in China, with H1 being the predominant haplotype. The monoculture of wheat in north China might have been the key driver for the prevalence of H1 population, which should date no earlier than the Han Dynasty (202 BCE–220 CE). Molecular phylogenetic and biogeographic analyses of Chinese H. avenae suggest a Pleistocene northwest China origin and an ancestral host of grasses. We assume that the prosperity of Heterodera in this region is a result of their preference for cooler climate and various grass hosts, which only appeared after the uplift of Qinghai‐Tibetan Plateau and aridification of Inner Asia. Nematode samples from the current and historical floodplains show a significant role of the Yellow River in the distribution of Chinese H. avenae. Whereas mechanical harvesters that operate on an inter‐provincial basis suggest the importance in the transmission of this species in eastern China in recent times. This study highlights the role of environmental change, river dynamics, and anthropogenic factors in the origin and long‐distance dissemination of pathogens.
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Affiliation(s)
- Xue Qing
- Department of Plant Pathology Nanjing Agricultural University 210095 Nanjing China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education Nanjing Agricultural University 210095 Nanjing China
| | - Huan Peng
- Institute of Plant Protection Chinese Academy of Agricultural Sciences 100193 Beijing China
| | - Jukui Ma
- Department of Plant Pathology Nanjing Agricultural University 210095 Nanjing China
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai Area Key Laboratory of Biology and Genetic Improvement of Sweet Potato, Ministry of Agriculture, Jiangsu Xuzhou Sweet Potato Research Center, Xuzhou 221131 Jiangsu China
| | - Y. Miles Zhang
- Systematic Entomology Laboratory, USDA‐ARS, c/o National Museum of Natural History 20013 Washington DC USA
| | - Hongmei Li
- Department of Plant Pathology Nanjing Agricultural University 210095 Nanjing China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education Nanjing Agricultural University 210095 Nanjing China
| | - Deliang Peng
- Institute of Plant Protection Chinese Academy of Agricultural Sciences 100193 Beijing China
| | - Xuan Wang
- Department of Plant Pathology Nanjing Agricultural University 210095 Nanjing China
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education Nanjing Agricultural University 210095 Nanjing China
| | - Tengwen Long
- School of Geographical Sciences University of Nottingham Ningbo China, 199 Taikang East Road, Ningbo 315100 China
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3
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Subbotin SA, Roubtsova TV, Bostock RM, Tanha Maafi Z, Chizhov VN. DNA barcoding, phylogeny and phylogeography of the cyst nematode species of the Humuli group from the genus Heterodera (Tylenchida: Heteroderidae). NEMATOLOGY 2022. [DOI: 10.1163/15685411-bja10176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
The Humuli group of the genus Heterodera contains species that parasitise dicotyledons and are characterised by a lemon-shaped cyst having a bifenestrate vulval cone (ambifenestrate for H. fici), long vulval slit and weak underbridge. Presently, the Humuli group includes seven species: H. amaranthusiae, H. fici, H. humuli, H. litoralis, H. ripae, H. turcomanica and H. vallicola. In this study we provided comprehensive phylogenetic analyses of COI and ITS rRNA gene sequences of species from the Humuli group using Bayesian inference, maximum likelihood, and maximum and statistical parsimony. All seven valid species from the Humuli group, one putatively new species belonging to this group and the willow cyst nematode, H. salixophila, sharing a common ancestor with the Humuli group, were analysed. Some 84 COI and 5 ITS rRNA new gene sequences from 37 nematode populations collected from 12 countries were obtained in this study. Our results confirmed that the COI gene is a powerful DNA barcoding marker for identification of populations and species from the Humuli group. Based on the results of phylogeographical analysis and age estimation of clades with a molecular clock approach, it was hypothesised that some species of the Humuli group primarily originated and diversified in Western and Middle Asian regions during the Pleistocene and Holocene periods and then dispersed from this region across the world. Two secondary diversification centres of the Humuli group were likely located in East and Southeast Asia, Russian Far East, and Oceania.
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Affiliation(s)
- Sergei A. Subbotin
- Plant Pest Diagnostic Center, California Department of Food and Agriculture, 3294 Meadowview Road, Sacramento, CA 95832, USA
- Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, 117071 Moscow, Russia
| | - Tatiana V. Roubtsova
- Department of Plant Pathology University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Richard M. Bostock
- Department of Plant Pathology University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Zahra Tanha Maafi
- Iranian Research Institute of Plant Protection, Agricultural Research Education and Extension Organization (AREEO), Tehran, Iran
| | - Vladimir N. Chizhov
- Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, 117071 Moscow, Russia
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4
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Camus MF, Alexander-Lawrie B, Sharbrough J, Hurst GDD. Inheritance through the cytoplasm. Heredity (Edinb) 2022; 129:31-43. [PMID: 35525886 PMCID: PMC9273588 DOI: 10.1038/s41437-022-00540-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/11/2022] Open
Abstract
Most heritable information in eukaryotic cells is encoded in the nuclear genome, with inheritance patterns following classic Mendelian segregation. Genomes residing in the cytoplasm, however, prove to be a peculiar exception to this rule. Cytoplasmic genetic elements are generally maternally inherited, although there are several exceptions where these are paternally, biparentally or doubly-uniparentally inherited. In this review, we examine the diversity and peculiarities of cytoplasmically inherited genomes, and the broad evolutionary consequences that non-Mendelian inheritance brings. We first explore the origins of vertical transmission and uniparental inheritance, before detailing the vast diversity of cytoplasmic inheritance systems across Eukaryota. We then describe the evolution of genomic organisation across lineages, how this process has been shaped by interactions with the nuclear genome and population genetics dynamics. Finally, we discuss how both nuclear and cytoplasmic genomes have evolved to co-inhabit the same host cell via one of the longest symbiotic processes, and all the opportunities for intergenomic conflict that arise due to divergence in inheritance patterns. In sum, we cannot understand the evolution of eukaryotes without understanding hereditary symbiosis.
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Affiliation(s)
- M Florencia Camus
- Department of Genetics, Evolution and Environment, University College London, London, UK.
| | | | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Gregory D D Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, England
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5
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Waneka G, Svendsen JM, Havird JC, Sloan DB. Mitochondrial mutations in Caenorhabditis elegans show signatures of oxidative damage and an AT-bias. Genetics 2021; 219:6346985. [PMID: 34849888 DOI: 10.1093/genetics/iyab116] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/09/2021] [Indexed: 01/25/2023] Open
Abstract
Rapid mutation rates are typical of mitochondrial genomes (mtDNAs) in animals, but it is not clear why. The difficulty of obtaining measurements of mtDNA mutation that are not biased by natural selection has stymied efforts to distinguish between competing hypotheses about the causes of high mtDNA mutation rates. Several studies which have measured mtDNA mutations in nematodes have yielded small datasets with conflicting conclusions about the relative abundance of different substitution classes (i.e., the mutation spectrum). We therefore leveraged Duplex Sequencing, a high-fidelity DNA sequencing technique, to characterize de novo mtDNA mutations in Caenorhabditis elegans. This approach detected nearly an order of magnitude more mtDNA mutations than documented in any previous nematode mutation study. Despite an existing extreme AT bias in the C. elegans mtDNA (75.6% AT), we found that a significant majority of mutations increase genomic AT content. Compared to some prior studies in nematodes and other animals, the mutation spectrum reported here contains an abundance of CG→AT transversions, supporting the hypothesis that oxidative damage may be a driver of mtDNA mutations in nematodes. Furthermore, we found an excess of G→T and C→T changes on the coding DNA strand relative to the template strand, consistent with increased exposure to oxidative damage. Analysis of the distribution of mutations across the mtDNA revealed significant variation among protein-coding genes and as well as among neighboring nucleotides. This high-resolution view of mitochondrial mutations in C. elegans highlights the value of this system for understanding relationships among oxidative damage, replication error, and mtDNA mutation.
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Affiliation(s)
- Gus Waneka
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
| | - Joshua M Svendsen
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
| | - Justin C Havird
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA and
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6
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Lax P, Gonzalez‐Ittig RE, Rondan Dueñas JC, Andrade AJ, Gardenal CN, Franco J, Doucet ME. Decrypting species in the
Nacobbus aberrans
(Nematoda: Pratylenchidae) complex using integrative taxonomy. ZOOL SCR 2021. [DOI: 10.1111/zsc.12494] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Paola Lax
- Instituto de Diversidad y Ecología Animal (CONICET‐UNC) and Centro de Zoología Aplicada, Facultad de Ciencias Exactas, Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
| | - Raúl E. Gonzalez‐Ittig
- Instituto de Diversidad y Ecología Animal (CONICET‐UNC), Facultad de Ciencias Exactas, Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
| | - Juan C. Rondan Dueñas
- Laboratorio de Biología Molecular Pabellón CEPROCOR Santa María de Punilla Córdoba, Argentina
| | - Alberto J. Andrade
- Instituto de Biología de la Altura Universidad Nacional de Jujuy San Salvador de Jujuy Argentina
| | - Cristina N. Gardenal
- Instituto de Diversidad y Ecología Animal (CONICET‐UNC), Facultad de Ciencias Exactas, Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
| | | | - Marcelo E. Doucet
- Instituto de Diversidad y Ecología Animal (CONICET‐UNC) and Centro de Zoología Aplicada, Facultad de Ciencias Exactas, Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
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7
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Nguyen DT, Wu B, Long H, Zhang N, Patterson C, Simpson S, Morris K, Thomas WK, Lynch M, Hao W. Variable Spontaneous Mutation and Loss of Heterozygosity among Heterozygous Genomes in Yeast. Mol Biol Evol 2021; 37:3118-3130. [PMID: 33219379 DOI: 10.1093/molbev/msaa150] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mutation and recombination are the primary sources of genetic variation. To better understand the evolution of genetic variation, it is crucial to comprehensively investigate the processes involving mutation accumulation and recombination. In this study, we performed mutation accumulation experiments on four heterozygous diploid yeast species in the Saccharomycodaceae family to determine spontaneous mutation rates, mutation spectra, and losses of heterozygosity (LOH). We observed substantial variation in mutation rates and mutation spectra. We also observed high LOH rates (1.65-11.07×10-6 events per heterozygous site per cell division). Biases in spontaneous mutation and LOH together with selection ultimately shape the variable genome-wide nucleotide landscape in yeast species.
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Affiliation(s)
- Duong T Nguyen
- Department of Biological Sciences, Wayne State University, Detroit, MI
| | - Baojun Wu
- Department of Biological Sciences, Wayne State University, Detroit, MI
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Nan Zhang
- Department of Biological Sciences, Wayne State University, Detroit, MI
| | | | | | | | | | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI
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8
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Nguyen DT, Wu B, Xiao S, Hao W. Evolution of a Record-Setting AT-Rich Genome: Indel Mutation, Recombination, and Substitution Bias. Genome Biol Evol 2020; 12:2344-2354. [PMID: 32986811 PMCID: PMC7846184 DOI: 10.1093/gbe/evaa202] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2020] [Indexed: 12/16/2022] Open
Abstract
Genome-wide nucleotide composition varies widely among species. Despite extensive research, the source of genome-wide nucleotide composition diversity remains elusive. Yeast mitochondrial genomes (mitogenomes) are highly A + T rich, and they provide a unique opportunity to study the evolution of AT-biased landscape. In this study, we sequenced ten complete mitogenomes of the Saccharomycodes ludwigii yeast with 8% G + C content, the lowest genome-wide %(G + C) in all published genomes to date. The S. ludwigii mitogenomes have high densities of short tandem repeats but severely underrepresented mononucleotide repeats. Comparative population genomics of these record-setting A + T-rich genomes shows dynamic indel mutations and strong mutation bias toward A/T. Indel mutations play a greater role in genomic variation among very closely related strains than nucleotide substitutions. Indels have resulted in presence–absence polymorphism of tRNAArg (ACG) among S. ludwigii mitogenomes. Interestingly, these mitogenomes have undergone recombination, a genetic process that can increase G + C content by GC-biased gene conversion. Finally, the expected equilibrium G + C content under mutation pressure alone is higher than observed G + C content, suggesting existence of mechanisms other than AT-biased mutation operating to increase A/T. Together, our findings shed new lights on mechanisms driving extremely AT-rich genomes.
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Affiliation(s)
- Duong T Nguyen
- Department of Biological Sciences, Wayne State University
| | - Baojun Wu
- Department of Biological Sciences, Wayne State University
| | - Shujie Xiao
- Department of Biological Sciences, Wayne State University
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University
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9
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Wagner JT, Howe DK, Estes S, Denver DR. Mitochondrial DNA Variation and Selfish Propagation Following Experimental Bottlenecking in Two Distantly Related Caenorhabditis briggsae Isolates. Genes (Basel) 2020; 11:genes11010077. [PMID: 31936803 PMCID: PMC7016712 DOI: 10.3390/genes11010077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/11/2022] Open
Abstract
Understanding mitochondrial DNA (mtDNA) evolution and inheritance has broad implications for animal speciation and human disease models. However, few natural models exist that can simultaneously represent mtDNA transmission bias, mutation, and copy number variation. Certain isolates of the nematode Caenorhabditis briggsae harbor large, naturally-occurring mtDNA deletions of several hundred basepairs affecting the NADH dehydrogenase subunit 5 (nduo-5) gene that can be functionally detrimental. These deletion variants can behave as selfish DNA elements under genetic drift conditions, but whether all of these large deletion variants are transmitted in the same preferential manner remains unclear. In addition, the degree to which transgenerational mtDNA evolution profiles are shared between isolates that differ in their propensity to accumulate the nduo-5 deletion is also unclear. We address these knowledge gaps by experimentally bottlenecking two isolates of C. briggsae with different nduo-5 deletion frequencies for up to 50 generations and performing total DNA sequencing to identify mtDNA variation. We observed multiple mutation profile differences and similarities between C. briggsae isolates, a potentially species-specific pattern of copy number dysregulation, and some evidence for genetic hitchhiking in the deletion-bearing isolate. Our results further support C. briggsae as a practical model for characterizing naturally-occurring mtgenome variation and contribute to the understanding of how mtgenome variation persists in animal populations and how it presents in mitochondrial disease states.
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Affiliation(s)
- Josiah T. Wagner
- Cancer Early Detection Advanced Research (CEDAR) Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97201, USA
- Correspondence:
| | - Dana K. Howe
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA; (D.K.H.); (D.R.D.)
| | - Suzanne Estes
- Department of Biology, Portland State University, Portland, OR 97201, USA;
| | - Dee R. Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA; (D.K.H.); (D.R.D.)
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10
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Sullins JA, Coleman-Hulbert AL, Gallegos A, Howe DK, Denver DR, Estes S. Complex Transmission Patterns and Age-Related Dynamics of a Selfish mtDNA Deletion. Integr Comp Biol 2019; 59:983-993. [PMID: 31318034 PMCID: PMC6797909 DOI: 10.1093/icb/icz128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Despite wide-ranging implications of selfish mitochondrial DNA (mtDNA) elements for human disease and topics in evolutionary biology (e.g., speciation), the forces controlling their formation, age-related accumulation, and offspring transmission remain largely unknown. Selfish mtDNA poses a significant challenge to genome integrity, mitochondrial function, and organismal fitness. For instance, numerous human diseases are associated with mtDNA mutations; however, few genetic systems can simultaneously represent pathogenic mitochondrial genome evolution and inheritance. The nematode Caenorhabditis briggsae is one such system. Natural C. briggsae isolates harbor varying levels of a large-scale deletion affecting the mitochondrial nduo-5 gene, termed nad5Δ. A subset of these isolates contains putative compensatory mutations that may reduce the risk of deletion formation. We studied the dynamics of nad5Δ heteroplasmy levels during animal development and transmission from mothers to offspring in genetically diverse C. briggsae natural isolates. Results support previous work demonstrating that nad5Δ is a selfish element and that heteroplasmy levels of this deletion can be quite plastic, exhibiting high degrees of inter-family variability and divergence between generations. The latter is consistent with a mitochondrial bottleneck effect, and contrasts with previous findings from a laboratory-derived model uaDf5 mtDNA deletion in C. elegans. However, we also found evidence for among-isolate differences in the ability to limit nad5Δ accumulation, the pattern of which suggested that forces other than the compensatory mutations are important in protecting individuals and populations from rampant mtDNA deletion expansion over short time scales.
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Affiliation(s)
- Jennifer A Sullins
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | | | - Alexandra Gallegos
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
| | - Suzanne Estes
- Department of Biology, Portland State University, Portland, OR 97201, USA
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11
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Johri P, Marinov GK, Doak TG, Lynch M. Population Genetics of Paramecium Mitochondrial Genomes: Recombination, Mutation Spectrum, and Efficacy of Selection. Genome Biol Evol 2019; 11:1398-1416. [PMID: 30980669 PMCID: PMC6505448 DOI: 10.1093/gbe/evz081] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2019] [Indexed: 12/11/2022] Open
Abstract
The evolution of mitochondrial genomes and their population-genetic environment among unicellular eukaryotes are understudied. Ciliate mitochondrial genomes exhibit a unique combination of characteristics, including a linear organization and the presence of multiple genes with no known function or detectable homologs in other eukaryotes. Here we study the variation of ciliate mitochondrial genomes both within and across 13 highly diverged Paramecium species, including multiple species from the P. aurelia species complex, with four outgroup species: P. caudatum, P. multimicronucleatum, and two strains that may represent novel related species. We observe extraordinary conservation of gene order and protein-coding content in Paramecium mitochondria across species. In contrast, significant differences are observed in tRNA content and copy number, which is highly conserved in species belonging to the P. aurelia complex but variable among and even within the other Paramecium species. There is an increase in GC content from ∼20% to ∼40% on the branch leading to the P. aurelia complex. Patterns of polymorphism in population-genomic data and mutation-accumulation experiments suggest that the increase in GC content is primarily due to changes in the mutation spectra in the P. aurelia species. Finally, we find no evidence of recombination in Paramecium mitochondria and find that the mitochondrial genome appears to experience either similar or stronger efficacy of purifying selection than the nucleus.
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Affiliation(s)
- Parul Johri
- Department of Biology, Indiana University, Bloomington
| | - Georgi K Marinov
- Department of Biology, Indiana University, Bloomington.,Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Thomas G Doak
- Department of Biology, Indiana University, Bloomington.,National Center for Genome Analysis Support, Indiana University, Bloomington
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington.,Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe
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12
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Stegeman GW, Baird SE, Ryu WS, Cutter AD. Genetically Distinct Behavioral Modules Underlie Natural Variation in Thermal Performance Curves. G3 (BETHESDA, MD.) 2019; 9:2135-2151. [PMID: 31048400 PMCID: PMC6643873 DOI: 10.1534/g3.119.400043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/30/2019] [Indexed: 01/01/2023]
Abstract
Thermal reaction norms pervade organismal traits as stereotyped responses to temperature, a fundamental environmental input into sensory and physiological systems. Locomotory behavior represents an especially plastic read-out of animal response, with its dynamic dependence on environmental stimuli presenting a challenge for analysis and for understanding the genomic architecture of heritable variation. Here we characterize behavioral reaction norms as thermal performance curves for the nematode Caenorhabditis briggsae, using a collection of 23 wild isolate genotypes and 153 recombinant inbred lines to quantify the extent of genetic and plastic variation in locomotory behavior to temperature changes. By reducing the dimensionality of the multivariate phenotypic response with a function-valued trait framework, we identified genetically distinct behavioral modules that contribute to the heritable variation in the emergent overall behavioral thermal performance curve. Quantitative trait locus mapping isolated regions on Chromosome II associated with locomotory activity at benign temperatures and Chromosome V loci related to distinct aspects of sensitivity to high temperatures, with each quantitative trait locus explaining up to 28% of trait variation. These findings highlight how behavioral responses to environmental inputs as thermal reaction norms can evolve through independent changes to genetically distinct modular components of such complex phenotypes.
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Affiliation(s)
| | - Scott E Baird
- Department of Biology, Wright State University, Dayton, Ohio, 45435
| | - William S Ryu
- Department of Physics, University of Toronto
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S3B2, Canada
| | - Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto
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13
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Abstract
Mitochondria, a nearly ubiquitous feature of eukaryotes, are derived from an ancient symbiosis. Despite billions of years of cooperative coevolution - in what is arguably the most important mutualism in the history of life - the persistence of mitochondrial genomes also creates conditions for genetic conflict with the nucleus. Because mitochondrial genomes are present in numerous copies per cell, they are subject to both within- and among-organism levels of selection. Accordingly, 'selfish' genotypes that increase their own proliferation can rise to high frequencies even if they decrease organismal fitness. It has been argued that uniparental (often maternal) inheritance of cytoplasmic genomes evolved to curtail such selfish replication by minimizing within-individual variation and, hence, within-individual selection. However, uniparental inheritance creates conditions for cytonuclear conflict over sex determination and sex ratio, as well as conditions for sexual antagonism when mitochondrial variants increase transmission by enhancing maternal fitness but have the side-effect of being harmful to males (i.e., 'mother's curse'). Here, we review recent advances in understanding selfish replication and sexual antagonism in the evolution of mitochondrial genomes and the mechanisms that suppress selfish interactions, drawing parallels and contrasts with other organelles (plastids) and bacterial endosymbionts that arose more recently. Although cytonuclear conflict is widespread across eukaryotes, it can be cryptic due to nuclear suppression, highly variable, and lineage-specific, reflecting the diverse biology of eukaryotes and the varying architectures of their cytoplasmic genomes.
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Affiliation(s)
- Justin C Havird
- Department of Integrative Biology, The University of Texas, Austin, TX 78712, USA.
| | - Evan S Forsythe
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Alissa M Williams
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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14
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Katju V, Bergthorsson U. Old Trade, New Tricks: Insights into the Spontaneous Mutation Process from the Partnering of Classical Mutation Accumulation Experiments with High-Throughput Genomic Approaches. Genome Biol Evol 2019; 11:136-165. [PMID: 30476040 PMCID: PMC6330053 DOI: 10.1093/gbe/evy252] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2018] [Indexed: 12/17/2022] Open
Abstract
Mutations spawn genetic variation which, in turn, fuels evolution. Hence, experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution. Mutation accumulation (MA) experiments have served as a cornerstone for furthering our understanding of spontaneous mutations for four decades. In the pregenomic era, phenotypic measurements of fitness-related traits in MA lines were used to indirectly estimate key mutational parameters, such as the genomic mutation rate, new mutational variance per generation, and the average fitness effect of mutations. Rapidly emerging next-generating sequencing technology has supplanted this phenotype-dependent approach, enabling direct empirical estimates of the mutation rate and a more nuanced understanding of the relative contributions of different classes of mutations to the standing genetic variation. Whole-genome sequencing of MA lines bears immense potential to provide a unified account of the evolutionary process at multiple levels-the genetic basis of variation, and the evolutionary dynamics of mutations under the forces of selection and drift. In this review, we have attempted to synthesize key insights into the spontaneous mutation process that are rapidly emerging from the partnering of classical MA experiments with high-throughput sequencing, with particular emphasis on the spontaneous rates and molecular properties of different mutational classes in nuclear and mitochondrial genomes of diverse taxa, the contribution of mutations to the evolution of gene expression, and the rate and stability of transgenerational epigenetic modifications. Future advances in sequencing technologies will enable greater species representation to further refine our understanding of mutational parameters and their functional consequences.
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Affiliation(s)
- Vaishali Katju
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4458
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4458
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15
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Jorge F, Perera A, Poulin R, Roca V, Carretero MA. Getting there and around: Host range oscillations during colonization of the Canary Islands by the parasitic nematode Spauligodon. Mol Ecol 2018; 27:533-549. [DOI: 10.1111/mec.14458] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/19/2017] [Accepted: 11/20/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Fátima Jorge
- Department of Zoology; University of Otago; Dunedin New Zealand
| | - Ana Perera
- CIBIO Research Centre in Biodiversity and Genetic Resources; InBIO; Universidade do Porto; Vila do Conde Portugal
| | - Robert Poulin
- Department of Zoology; University of Otago; Dunedin New Zealand
| | - Vicente Roca
- Departament de Zoologia; Facultat de Ciències Biològiques; Universitat de València; València Spain
| | - Miguel A. Carretero
- CIBIO Research Centre in Biodiversity and Genetic Resources; InBIO; Universidade do Porto; Vila do Conde Portugal
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16
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Subbotin SA, Toumi F, Elekçioğlu IH, Waeyenberge L, Tanha Maafi Z. DNA barcoding, phylogeny and phylogeography of the cyst nematode species of the Avenae group from the genus Heterodera (Tylenchida: Heteroderidae). NEMATOLOGY 2018. [DOI: 10.1163/15685411-00003170] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Summary
Among the recognised species groups of Heterodera, the Avenae group is one of the largest with a total of 12 species. Ten of them, H. arenaria, H. aucklandica, H. australis, H. avenae, H. filipjevi, H. mani, H. pratensis, H. riparia, H. sturhani and H. ustinovi, are morphologically closely related and represent the H. avenae species complex, and the other two, H. hordecalis and H. latipons, are morphologically more distinct from this complex. In this study we provide comprehensive phylogenetic analyses of several hundred COI and ITS rRNA gene sequences from the Avenae group using Bayesian inference, maximum likelihood and statistical parsimony. Some 220 COI and 11 ITS rRNA new gene sequences from 147 nematode populations collected in 26 countries were obtained in this study. Our study showed that the COI gene is a powerful DNA barcoding marker for identification of populations and species from the Avenae group. A putatively new cyst nematode species related to H. latipons was revealed from the analysis of COI and ITS rRNA gene datasets. COI gene sequences allow distinguishing H. arenaria, H. australis and H. sturhani from each other and other species. Problems of species delimiting of these species are discussed. The results of the analysis showed that COI haplotypes corresponded to certain pathotypes of the cereal cyst nematodes. It is recommended that information on COI haplotypes of studied populations be included in research with these nematodes. Based on the results of phylogeographical analysis and age estimation of clades with a molecular clock approach, it was hypothesised that several species of the Avenae group primarily originated and diversified in the Irano-Anatolian hotspot during the Pleistocene and Holocene periods and then dispersed from this region across the world. Different geographic barriers, centres and times of origin might explain current known distribution patterns for species of the Avenae group. Possible pathways, including a long distance trans-Atlantic dispersal, and secondary centres of diversification are proposed and discussed.
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Affiliation(s)
- Sergei A. Subbotin
- 1Plant Pest Diagnostic Center, California Department of Food and Agriculture, 3294 Meadowview Road, 95832 Sacramento, CA, USA
- 2Center of Parasitology of A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Leninskii Prospect 33, 117071 Moscow, Russia
| | - Fateh Toumi
- 3ILVO, Plant, Crop Protection, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - Ibrahim Halil Elekçioğlu
- 4Çukurova University, Faculty of Agriculture, Plant Protection Department, 01330 Sarıçam, Adana, Turkey
| | - Lieven Waeyenberge
- 3ILVO, Plant, Crop Protection, Burg. Van Gansberghelaan 96, 9820 Merelbeke, Belgium
| | - Zahra Tanha Maafi
- 5Iranian Research Institute of Plant Protection, Agricultural Research Education and Extension Organization (AREEO), Tehran, Iran
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17
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Konrad A, Thompson O, Waterston RH, Moerman DG, Keightley PD, Bergthorsson U, Katju V. Mitochondrial Mutation Rate, Spectrum and Heteroplasmy in Caenorhabditis elegans Spontaneous Mutation Accumulation Lines of Differing Population Size. Mol Biol Evol 2017; 34:1319-1334. [PMID: 28087770 DOI: 10.1093/molbev/msx051] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial genomes of metazoans, given their elevated rates of evolution, have served as pivotal markers for phylogeographic studies and recent phylogenetic events. In order to determine the dynamics of spontaneous mitochondrial mutations in small populations in the absence and presence of selection, we evolved mutation accumulation (MA) lines of Caenorhabditis elegans in parallel over 409 consecutive generations at three varying population sizes of N = 1, 10, and 100 hermaphrodites. The N =1 populations should have a minimal influence of natural selection to provide the spontaneous mutation rate and the expected rate of neutral evolution, whereas larger population sizes should experience increasing intensity of selection. New mutations were identified by Illumina paired-end sequencing of 86 mtDNA genomes across 35 experimental lines and compared with published genomes of natural isolates. The spontaneous mitochondrial mutation rate was estimated at 1.05 × 10-7/site/generation. A strong G/C→A/T mutational bias was observed in both the MA lines and the natural isolates. This suggests that the low G + C content at synonymous sites is the product of mutation bias rather than selection as previously proposed. The mitochondrial effective population size per worm generation was estimated to be 62. Although it was previously concluded that heteroplasmy was rare in C. elegans, the vast majority of mutations in this study were heteroplasmic despite an experimental regime exceeding 400 generations. The frequencies of frameshift and nonsynonymous mutations were negatively correlated with population size, which suggests their deleterious effects on fitness and a potent role for selection in their eradication.
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Affiliation(s)
- Anke Konrad
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Owen Thompson
- Department of Genome Sciences, University of Washington, Seattle, WA
| | | | - Donald G Moerman
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Peter D Keightley
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX
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18
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Guo W, Grewe F, Fan W, Young GJ, Knoop V, Palmer JD, Mower JP. GinkgoandWelwitschiaMitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution. Mol Biol Evol 2016; 33:1448-60. [DOI: 10.1093/molbev/msw024] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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19
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Ness RW, Kraemer SA, Colegrave N, Keightley PD. Direct Estimate of the Spontaneous Mutation Rate Uncovers the Effects of Drift and Recombination in theChlamydomonas reinhardtiiPlastid Genome. Mol Biol Evol 2015; 33:800-8. [DOI: 10.1093/molbev/msv272] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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20
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Chang CC, Rodriguez J, Ross J. Mitochondrial-Nuclear Epistasis Impacts Fitness and Mitochondrial Physiology of Interpopulation Caenorhabditis briggsae Hybrids. G3 (BETHESDA, MD.) 2015; 6:209-19. [PMID: 26585825 PMCID: PMC4704720 DOI: 10.1534/g3.115.022970] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 11/16/2015] [Indexed: 12/18/2022]
Abstract
In order to identify the earliest genetic changes that precipitate species formation, it is useful to study genetic incompatibilities that cause only mild dysfunction when incompatible alleles are combined in an interpopulation hybrid. Such hybridization within the nematode species Caenorhabditis briggsae has been suggested to result in selection against certain combinations of nuclear and mitochondrial alleles, raising the possibility that mitochondrial-nuclear (mitonuclear) epistasis reduces hybrid fitness. To test this hypothesis, cytoplasmic-nuclear hybrids (cybrids) were created to purposefully disrupt any epistatic interactions. Experimental analysis of the cybrids suggests that mitonuclear discord can result in decreased fecundity, increased lipid content, and increased mitochondrial reactive oxygen species levels. Many of these effects were asymmetric with respect to cross direction, as expected if cytoplasmic-nuclear Dobzhansky-Muller incompatibilities exist. One such effect is consistent with the interpretation that disrupting coevolved mitochondrial and nuclear loci impacts mitochondrial function and organismal fitness. These findings enhance efforts to study the genesis, identity, and maintenance of genetic incompatibilities that precipitate the speciation process.
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Affiliation(s)
- Chih-Chiun Chang
- Department of Biology, California State University, Fresno, California, 93740
| | - Joel Rodriguez
- Department of Biology, California State University, Fresno, California, 93740
| | - Joseph Ross
- Department of Biology, California State University, Fresno, California, 93740
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21
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Bundus JD, Alaei R, Cutter AD. Gametic selection, developmental trajectories, and extrinsic heterogeneity in Haldane's rule. Evolution 2015; 69:2005-17. [PMID: 26102479 DOI: 10.1111/evo.12708] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 06/01/2015] [Indexed: 12/31/2022]
Abstract
Deciphering the genetic and developmental causes of the disproportionate rarity, inviability, and sterility of hybrid males, Haldane's rule, is important for understanding the evolution of reproductive isolation between species. Moreover, extrinsic and prezygotic factors can contribute to the magnitude of intrinsic isolation experienced between species with partial reproductive compatibility. Here, we use the nematodes Caenorhabditis briggsae and C. nigoni to quantify the sensitivity of hybrid male viability to extrinsic temperature and developmental timing, and test for a role of mito-nuclear incompatibility as a genetic cause. We demonstrate that hybrid male inviability manifests almost entirely as embryonic, not larval, arrest and is maximal at the lowest rearing temperatures, indicating an intrinsic-by-extrinsic interaction to hybrid inviability. Crosses using mitochondrial substitution strains that have reciprocally introgressed mitochondrial and nuclear genomes show that mito-nuclear incompatibility is not a dominant contributor to postzygotic isolation and does not drive Haldane's rule in this system. Crosses also reveal that competitive superiority of X-bearing sperm provides a novel means by which postmating prezygotic factors exacerbate the rarity of hybrid males. These findings highlight the important roles of gametic, developmental, and extrinsic factors in modulating the manifestation of Haldane's rule.
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Affiliation(s)
- Joanna D Bundus
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Ravin Alaei
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2.
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22
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Phillips WS, Coleman-Hulbert AL, Weiss ES, Howe DK, Ping S, Wernick RI, Estes S, Denver DR. Selfish Mitochondrial DNA Proliferates and Diversifies in Small, but not Large, Experimental Populations of Caenorhabditis briggsae. Genome Biol Evol 2015; 7:2023-37. [PMID: 26108490 PMCID: PMC4524483 DOI: 10.1093/gbe/evv116] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Evolutionary interactions across levels of biological organization contribute to a variety of fundamental processes including genome evolution, reproductive mode transitions, species diversification, and extinction. Evolutionary theory predicts that so-called “selfish” genetic elements will proliferate when the host effective population size (Ne) is small, but direct tests of this prediction remain few. We analyzed the evolutionary dynamics of deletion-containing mitochondrial DNA (ΔmtDNA) molecules, previously characterized as selfish elements, in six different natural strains of the nematode Caenorhabditis briggsae allowed to undergo experimental evolution in a range of population sizes (N = 1, 10, 100, and 1,000) for a maximum of 50 generations. Mitochondrial DNA (mtDNA) was analyzed for replicate lineages at each five-generation time point. Ten different ΔmtDNA molecule types were observed and characterized across generations in the experimental populations. Consistent with predictions from evolutionary theory, lab lines evolved in small-population sizes (e.g., nematode N = 1) were more susceptible to accumulation of high levels of preexisting ΔmtDNA compared with those evolved in larger populations. New ΔmtDNA elements were observed to increase in frequency and persist across time points, but almost exclusively at small population sizes. In some cases, ΔmtDNA levels decreased across generations when population size was large (nematode N = 1,000). Different natural strains of C. briggsae varied in their susceptibilities to ΔmtDNA accumulation, owing in part to preexisting compensatory mtDNA alleles in some strains that prevent deletion formation. This analysis directly demonstrates that the evolutionary trajectories of ΔmtDNA elements depend upon the population-genetic environments and molecular-genetic features of their hosts.
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Affiliation(s)
| | | | - Emily S Weiss
- Department of Integrative Biology, Oregon State University
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University
| | - Sita Ping
- Department of Integrative Biology, Oregon State University
| | | | | | - Dee R Denver
- Department of Integrative Biology, Oregon State University
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23
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Fierst JL, Willis JH, Thomas CG, Wang W, Reynolds RM, Ahearne TE, Cutter AD, Phillips PC. Reproductive Mode and the Evolution of Genome Size and Structure in Caenorhabditis Nematodes. PLoS Genet 2015; 11:e1005323. [PMID: 26114425 PMCID: PMC4482642 DOI: 10.1371/journal.pgen.1005323] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 05/31/2015] [Indexed: 11/18/2022] Open
Abstract
The self-fertile nematode worms Caenorhabditis elegans, C. briggsae, and C. tropicalis evolved independently from outcrossing male-female ancestors and have genomes 20-40% smaller than closely related outcrossing relatives. This pattern of smaller genomes for selfing species and larger genomes for closely related outcrossing species is also seen in plants. We use comparative genomics, including the first high quality genome assembly for an outcrossing member of the genus (C. remanei) to test several hypotheses for the evolution of genome reduction under a change in mating system. Unlike plants, it does not appear that reductions in the number of repetitive elements, such as transposable elements, are an important contributor to the change in genome size. Instead, all functional genomic categories are lost in approximately equal proportions. Theory predicts that self-fertilization should equalize the effective population size, as well as the resulting effects of genetic drift, between the X chromosome and autosomes. Contrary to this, we find that the self-fertile C. briggsae and C. elegans have larger intergenic spaces and larger protein-coding genes on the X chromosome when compared to autosomes, while C. remanei actually has smaller introns on the X chromosome than either self-reproducing species. Rather than being driven by mutational biases and/or genetic drift caused by a reduction in effective population size under self reproduction, changes in genome size in this group of nematodes appear to be caused by genome-wide patterns of gene loss, most likely generated by genomic adaptation to self reproduction per se.
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Affiliation(s)
- Janna L. Fierst
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - John H. Willis
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Cristel G. Thomas
- Department of Ecology and Evolutionary Biology and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Wei Wang
- Department of Ecology and Evolutionary Biology and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Rose M. Reynolds
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Timothy E. Ahearne
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
| | - Asher D. Cutter
- Department of Ecology and Evolutionary Biology and Centre for the Analysis of Genome Evolution and Function, University of Toronto, Ontario, Canada
| | - Patrick C. Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, United States of America
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24
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Opposing forces of A/T-biased mutations and G/C-biased gene conversions shape the genome of the nematode Pristionchus pacificus. Genetics 2014; 196:1145-52. [PMID: 24414549 DOI: 10.1534/genetics.113.159863] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Base substitution mutations are a major source of genetic novelty and mutation accumulation line (MAL) studies revealed a nearly universal AT bias in de novo mutation spectra. While a comparison of de novo mutation spectra with the actual nucleotide composition in the genome suggests the existence of general counterbalancing mechanisms, little is known about the evolutionary and historical details of these opposing forces. Here, we correlate MAL-derived mutation spectra with patterns observed from population resequencing. Variation observed in natural populations has already been subject to evolutionary forces. Distinction between rare and common alleles, the latter of which are close to fixation and of presumably older age, can provide insight into mutational processes and their influence on genome evolution. We provide a genome-wide analysis of de novo mutations in 22 MALs of the nematode Pristionchus pacificus and compare the spectra with natural variants observed in resequencing of 104 natural isolates. MALs show an AT bias of 5.3, one of the highest values observed to date. In contrast, the AT bias in natural variants is much lower. Specifically, rare derived alleles show an AT bias of 2.4, whereas common derived alleles close to fixation show no AT bias at all. These results indicate the existence of a strong opposing force and they suggest that the GC content of the P. pacificus genome is in equilibrium. We discuss GC-biased gene conversion as a potential mechanism acting against AT-biased mutations. This study provides insight into genome evolution by combining MAL studies with natural variation.
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25
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Sommer RJ, McGaughran A. The nematode Pristionchus pacificus as a model system for integrative studies in evolutionary biology. Mol Ecol 2013; 22:2380-93. [PMID: 23530614 DOI: 10.1111/mec.12286] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/30/2013] [Accepted: 01/31/2013] [Indexed: 01/06/2023]
Abstract
Comprehensive studies of evolution have historically been hampered by the division among disciplines. Now, as biology moves towards an '-omics' era, it is more important than ever to tackle the evolution of function and form by considering all those research areas involved in the regulation of phenotypes. Here, we review recent attempts to establish the nematode Pristionchus pacificus as a model organism that allows integrative studies of development and evo-devo, with ecology and population genetics. Originally developed for comparative study with the nematode Caenorhabditis elegans, P. pacificus provided insight into developmental pathways including dauer formation, vulva and gonad development, chemosensation, innate immunity and neurobiology. Its subsequent discovery across a wide geographic distribution in association with scarab beetles enabled its evaluation in a biogeographic context. Development of an evolutionary field station on La Réunion Island, where P. pacificus is present in high abundance across a number of widespread habitat types, allows examination of the microfacets of evolution - processes of natural selection, adaptation and drift among populations can now be examined in this island setting. The combination of laboratory-based functional studies with fieldwork in P. pacificus has the long-term prospective to provide both proximate (mechanistic) and ultimate (evolutionary and ecological) causation and might therefore help to overcome the long-term divide between major areas in biology.
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Affiliation(s)
- Ralf J Sommer
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Tübingen, Germany.
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26
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Hicks KA, Denver DR, Estes S. Natural variation in Caenorhabditis briggsae mitochondrial form and function suggests a novel model of organelle dynamics. Mitochondrion 2012; 13:44-51. [PMID: 23269324 DOI: 10.1016/j.mito.2012.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 12/07/2012] [Accepted: 12/18/2012] [Indexed: 01/28/2023]
Abstract
Mitochondrial functioning and morphology are known to be connected through cycles of organelle fusion and fission that depend upon the mitochondrial membrane potential (ΔΨM); however, we lack an understanding of the features and dynamics of natural mitochondrial populations. Using data from our recent study of univariate mitochondrial phenotypic variation in Caenorhabditis briggsae nematodes, we analyzed patterns of phenotypic correlation for 24 mitochondrial traits. Our findings support a role for ΔΨM in shaping mitochondrial dynamics, but no role for mitochondrial ROS. Further, our study suggests a novel model of mitochondrial population dynamics dependent upon cellular environmental context and with implications for mitochondrial genome integrity.
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Affiliation(s)
- Kiley A Hicks
- Biology Department, Portland State University, 1719 SW 10th Ave., Portland, OR 97201, USA.
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27
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Mitochondrial genome evolution in a single protoploid yeast species. G3-GENES GENOMES GENETICS 2012; 2:1103-11. [PMID: 22973548 PMCID: PMC3429925 DOI: 10.1534/g3.112.003152] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/09/2012] [Indexed: 12/26/2022]
Abstract
Mitochondria are organelles, which play a key role in some essential functions, including respiration, metabolite biosynthesis, ion homeostasis, and apoptosis. The vast numbers of mitochondrial DNA (mtDNA) sequences of various yeast species, which have recently been published, have also helped to elucidate the structural diversity of these genomes. Although a large corpus of data are now available on the diversity of yeast species, little is known so far about the mtDNA diversity in single yeast species. To study the genetic variations occurring in the mtDNA of wild yeast isolates, we performed a genome-wide polymorphism survey on the mtDNA of 18 Lachancea kluyveri (formerly Saccharomyces kluyveri) strains. We determined the complete mt genome sequences of strains isolated from various geographical locations (in North America, Asia, and Europe) and ecological niches (Drosophila, tree exudates, soil). The mt genome of the NCYC 543 reference strain is 51,525 bp long. It contains the same core of genes as Lachancea thermotolerans, the nearest relative to L. kluyveri. To explore the mt genome variations in a single yeast species, we compared the mtDNAs of the 18 isolates. The phylogeny and population structure of L. kluyveri provide clear-cut evidence for the existence of well-defined geographically isolated lineages. Although these genomes are completely syntenic, their size and the intron content were found to vary among the isolates studied. These genomes are highly polymorphic, showing an average diversity of 28.5 SNPs/kb and 6.6 indels/kb. Analysis of the SNP and indel patterns showed the existence of a particularly high overall level of polymorphism in the intergenic regions. The dN/dS ratios obtained are consistent with purifying selection in all these genes, with the noteworthy exception of the VAR1 gene, which gave a very high ratio. These data suggest that the intergenic regions have evolved very fast in yeast mitochondrial genomes.
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28
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Hicks KA, Howe DK, Leung A, Denver DR, Estes S. In vivo quantification reveals extensive natural variation in mitochondrial form and function in Caenorhabditis briggsae. PLoS One 2012; 7:e43837. [PMID: 22952781 PMCID: PMC3429487 DOI: 10.1371/journal.pone.0043837] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 07/30/2012] [Indexed: 12/18/2022] Open
Abstract
We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among-isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential was an excellent predictor of clade membership. We interpret this result in light of recent evidence for local adaptation to temperature in C. briggsae. Analysis of mitochondrial-nuclear hybrid strains provided support for both mtDNA and nuclear genetic variation as drivers of natural mitochondrial phenotype variation. This study demonstrates that multicellular eukaryotic species are capable of extensive natural variation in organellar phenotypes and highlights the potential of integrating evolutionary and cell biology perspectives.
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Affiliation(s)
- Kiley A. Hicks
- Biology Department, Portland State University, Portland, Oregon, United States of America
| | - Dana K. Howe
- Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Aubrey Leung
- Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Dee R. Denver
- Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Suzanne Estes
- Biology Department, Portland State University, Portland, Oregon, United States of America
- * E-mail:
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29
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Selfish little circles: transmission bias and evolution of large deletion-bearing mitochondrial DNA in Caenorhabditis briggsae nematodes. PLoS One 2012; 7:e41433. [PMID: 22859984 PMCID: PMC3409194 DOI: 10.1371/journal.pone.0041433] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 06/25/2012] [Indexed: 01/19/2023] Open
Abstract
Selfish DNA poses a significant challenge to genome stability and organismal fitness in diverse eukaryotic lineages. Although selfish mitochondrial DNA (mtDNA) has known associations with cytoplasmic male sterility in numerous gynodioecious plant species and is manifested as petite mutants in experimental yeast lab populations, examples of selfish mtDNA in animals are less common. We analyzed the inheritance and evolution of mitochondrial DNA bearing large heteroplasmic deletions including nad5 gene sequences (nad5Δ mtDNA), in the nematode Caenorhabditis briggsae. The deletion is widespread in C. briggsae natural populations and is associated with deleterious organismal effects. We studied the inheritance patterns of nad5Δ mtDNA using eight sets of C. briggsae mutation-accumulation (MA) lines, each initiated from a different natural strain progenitor and bottlenecked as single hermaphrodites across generations. We observed a consistent and strong drive toward higher levels of deletion-bearing molecules in the heteroplasmic pool of mtDNA after ten generations of bottlenecking. Our results demonstrate a uniform transmission bias whereby nad5Δ mtDNA accumulates to higher levels relative to intact mtDNA in multiple genetically diverse natural strains of C. briggsae. We calculated an average 1% per-generation transmission bias for deletion-bearing mtDNA relative to intact genomes. Our study, coupled with known deleterious phenotypes associated with high deletion levels, shows that nad5Δ mtDNA are selfish genetic elements that have evolved in natural populations of C. briggsae, offering a powerful new system to study selfish mtDNA dynamics in metazoans.
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Denver DR, Wilhelm LJ, Howe DK, Gafner K, Dolan PC, Baer CF. Variation in base-substitution mutation in experimental and natural lineages of Caenorhabditis nematodes. Genome Biol Evol 2012; 4:513-22. [PMID: 22436997 PMCID: PMC3342874 DOI: 10.1093/gbe/evs028] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Variation among lineages in the mutation process has the potential to impact diverse biological processes ranging from susceptibilities to genetic disease to the mode and tempo of molecular evolution. The combination of high-throughput DNA sequencing (HTS) with mutation-accumulation (MA) experiments has provided a powerful approach to genome-wide mutation analysis, though insights into mutational variation have been limited by the vast evolutionary distances among the few species analyzed. We performed a HTS analysis of MA lines derived from four Caenorhabditis nematode natural genotypes: C. elegans N2 and PB306 and C. briggsae HK104 and PB800. Total mutation rates did not differ among the four sets of MA lines. A mutational bias toward G:C→A:T transitions and G:C→T:A transversions was observed in all four sets of MA lines. Chromosome-specific rates were mostly stable, though there was some evidence for a slightly elevated X chromosome mutation rate in PB306. Rates were homogeneous among functional coding sequence types and across autosomal cores, arms, and tips. Mutation spectra were similar among the four MA line sets but differed significantly when compared with patterns of natural base-substitution polymorphism for 13/14 comparisons performed. Our findings show that base-substitution mutation processes in these closely related animal lineages are mostly stable but differ from natural polymorphism patterns in these two species.
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Affiliation(s)
- Dee R Denver
- Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, OR, USA.
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Xu S, Schaack S, Seyfert A, Choi E, Lynch M, Cristescu ME. High mutation rates in the mitochondrial genomes of Daphnia pulex. Mol Biol Evol 2011; 29:763-9. [PMID: 21998274 DOI: 10.1093/molbev/msr243] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Despite the great utility of mitochondrial DNA (mtDNA) sequence data in population genetics and phylogenetics, key parameters describing the process of mitochondrial mutation (e.g., the rate and spectrum of mutational change) are based on few direct estimates. Furthermore, the variation in the mtDNA mutation process within species or between lineages with contrasting reproductive strategies remains poorly understood. In this study, we directly estimate the mtDNA mutation rate and spectrum using Daphnia pulex mutation-accumulation (MA) lines derived from sexual (cyclically parthenogenetic) and asexual (obligately parthenogenetic) lineages. The nearly complete mitochondrial genome sequences of 82 sexual and 47 asexual MA lines reveal high mtDNA mutation rate of 1.37 × 10(-7) and 1.73 × 10(-7) per nucleotide per generation, respectively. The Daphnia mtDNA mutation rate is among the highest in eukaryotes, and its spectrum is dominated by insertions and deletions (70%), largely due to the presence of mutational hotspots at homopolymeric nucleotide stretches. Maximum likelihood estimates of the Daphnia mitochondrial effective population size reveal that between five and ten copies of mitochondrial genomes are transmitted per female per generation. Comparison between sexual and asexual lineages reveals no statistically different mutation rates and highly similar mutation spectra.
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Affiliation(s)
- Sen Xu
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada.
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Caenorhabditis briggsae recombinant inbred line genotypes reveal inter-strain incompatibility and the evolution of recombination. PLoS Genet 2011; 7:e1002174. [PMID: 21779179 PMCID: PMC3136444 DOI: 10.1371/journal.pgen.1002174] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 05/23/2011] [Indexed: 12/16/2022] Open
Abstract
The nematode Caenorhabditis briggsae is an emerging model organism that allows evolutionary comparisons with C. elegans and exploration of its own unique biological attributes. To produce a high-resolution C. briggsae recombination map, recombinant inbred lines were generated from reciprocal crosses between two strains and genotyped at over 1,000 loci. A second set of recombinant inbred lines involving a third strain was also genotyped at lower resolution. The resulting recombination maps exhibit discrete domains of high and low recombination, as in C. elegans, indicating these are a general feature of Caenorhabditis species. The proportion of a chromosome's physical size occupied by the central, low-recombination domain is highly correlated between species. However, the C. briggsae intra-species comparison reveals striking variation in the distribution of recombination between domains. Hybrid lines made with the more divergent pair of strains also exhibit pervasive marker transmission ratio distortion, evidence of selection acting on hybrid genotypes. The strongest effect, on chromosome III, is explained by a developmental delay phenotype exhibited by some hybrid F2 animals. In addition, on chromosomes IV and V, cross direction-specific biases towards one parental genotype suggest the existence of cytonuclear epistatic interactions. These interactions are discussed in relation to surprising mitochondrial genome polymorphism in C. briggsae, evidence that the two strains diverged in allopatry, the potential for local adaptation, and the evolution of Dobzhansky-Muller incompatibilities. The genetic and genomic resources resulting from this work will support future efforts to understand inter-strain divergence as well as facilitate studies of gene function, natural variation, and the evolution of recombination in Caenorhabditis nematodes.
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Molnar RI, Bartelmes G, Dinkelacker I, Witte H, Sommer RJ. Mutation Rates and Intraspecific Divergence of the Mitochondrial Genome of Pristionchus pacificus. Mol Biol Evol 2011; 28:2317-26. [DOI: 10.1093/molbev/msr057] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Estes S, Coleman-Hulbert AL, Hicks KA, de Haan G, Martha SR, Knapp JB, Smith SW, Stein KC, Denver DR. Natural variation in life history and aging phenotypes is associated with mitochondrial DNA deletion frequency in Caenorhabditis briggsae. BMC Evol Biol 2011; 11:11. [PMID: 21226948 PMCID: PMC3032685 DOI: 10.1186/1471-2148-11-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 01/12/2011] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Mutations that impair mitochondrial functioning are associated with a variety of metabolic and age-related disorders. A barrier to rigorous tests of the role of mitochondrial dysfunction in aging processes has been the lack of model systems with relevant, naturally occurring mitochondrial genetic variation. Toward the goal of developing such a model system, we studied natural variation in life history, metabolic, and aging phenotypes as it relates to levels of a naturally-occurring heteroplasmic mitochondrial ND5 deletion recently discovered to segregate among wild populations of the soil nematode, Caenorhabditis briggsae. The normal product of ND5 is a central component of the mitochondrial electron transport chain and integral to cellular energy metabolism. RESULTS We quantified significant variation among C. briggsae isolates for all phenotypes measured, only some of which was statistically associated with isolate-specific ND5 deletion frequency. We found that fecundity-related traits and pharyngeal pumping rate were strongly inversely related to ND5 deletion level and that C. briggsae isolates with high ND5 deletion levels experienced a tradeoff between early fecundity and lifespan. Conversely, oxidative stress resistance was only weakly associated with ND5 deletion level while ATP content was unrelated to deletion level. Finally, mean levels of reactive oxygen species measured in vivo showed a significant non-linear relationship with ND5 deletion level, a pattern that may be driven by among-isolate variation in antioxidant or other compensatory mechanisms. CONCLUSIONS Our findings suggest that the ND5 deletion may adversely affect fitness and mitochondrial functioning while promoting aging in natural populations, and help to further establish this species as a useful model for explicit tests of hypotheses in aging biology and mitochondrial genetics.
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Affiliation(s)
- Suzanne Estes
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | | | - Kiley A Hicks
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Gene de Haan
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Sarah R Martha
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Jeremiah B Knapp
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Samson W Smith
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Kevin C Stein
- Department of Biology, Portland State University, Portland, OR 97201, USA
| | - Dee R Denver
- Department of Zoology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
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Ho SYW, Lanfear R. Mito-communications. MITOCHONDRIAL DNA 2010; 21:147-148. [PMID: 20958221 DOI: 10.3109/19401736.2010.508091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Affiliation(s)
- Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, Australia
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