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Branch HA, Anstett DN, Angert AL. Phenotypic lags influence rapid evolution throughout a drought cycle. Evolution 2024; 78:1067-1077. [PMID: 38490751 DOI: 10.1093/evolut/qpae037] [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: 07/15/2022] [Revised: 01/24/2024] [Accepted: 03/14/2024] [Indexed: 03/17/2024]
Abstract
Climate anomalies are increasing and posing strong selection, which can lead to rapid evolution. This is occurring on a backdrop of interannual variability that might weaken or even reverse selection. However, the effect of interannual climatic variability on rapid evolution is rarely considered. We study the climatic differences that contribute to rapid evolution throughout a 7-year period, encompassing a severe drought across 12 populations of Mimulus cardinalis (scarlet monkeyflower). Plants were grown in a common greenhouse environment under wet and dry treatments, where specific leaf area and date of flowering were measured. We examine the association between trait values and different climate metrics at different time periods, including the collection year, prior years, and cumulative metrics across sequential years. Of the climatic variables we assessed, we find that anomalies in mean annual precipitation best describe trait differences over our study period. Past climates, of 1-2 years prior, are often related to trait values in a conflicting direction to collection-year climate. Uncovering these complex climatic impacts on evolution is critical to better predict and interpret the impacts of climate change.
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Affiliation(s)
- Haley A Branch
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Daniel N Anstett
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- Plant Resilience Institute, Michigan State University, East Lansing, MI, United States
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
- Department of Entomology, Michigan State University, East Lansing, MI, United States
| | - Amy L Angert
- Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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Kornienko AE, Nizhynska V, Molla Morales A, Pisupati R, Nordborg M. Population-level annotation of lncRNAs in Arabidopsis reveals extensive expression variation associated with transposable element-like silencing. THE PLANT CELL 2023; 36:85-111. [PMID: 37683092 PMCID: PMC10734619 DOI: 10.1093/plcell/koad233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/07/2023] [Accepted: 07/30/2023] [Indexed: 09/10/2023]
Abstract
Long noncoding RNAs (lncRNAs) are understudied and underannotated in plants. In mammals, lncRNA loci are nearly as ubiquitous as protein-coding genes, and their expression is highly variable between individuals of the same species. Using Arabidopsis thaliana as a model, we aimed to elucidate the true scope of lncRNA transcription across plants from different regions and study its natural variation. We used transcriptome deep sequencing data sets spanning hundreds of natural accessions and several developmental stages to create a population-wide annotation of lncRNAs, revealing thousands of previously unannotated lncRNA loci. While lncRNA transcription is ubiquitous in the genome, most loci appear to be actively silenced and their expression is extremely variable between natural accessions. This high expression variability is largely caused by the high variability of repressive chromatin levels at lncRNA loci. High variability was particularly common for intergenic lncRNAs (lincRNAs), where pieces of transposable elements (TEs) present in 50% of these lincRNA loci are associated with increased silencing and variation, and such lncRNAs tend to be targeted by the TE silencing machinery. We created a population-wide lncRNA annotation in Arabidopsis and improve our understanding of plant lncRNA genome biology, raising fundamental questions about what causes transcription and silencing across the genome.
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Affiliation(s)
- Aleksandra E Kornienko
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-gasse 3, Vienna 1030, Austria
| | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-gasse 3, Vienna 1030, Austria
| | - Almudena Molla Morales
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-gasse 3, Vienna 1030, Austria
| | - Rahul Pisupati
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-gasse 3, Vienna 1030, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-gasse 3, Vienna 1030, Austria
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Ruiz-Galea M, Kremer C, Friero E, Hernández I. Tolerant Epitypes of Elicited Holm Oak Somatic Embryos Could Be Revealed by Challenges in Dual Culture with Phytophthora cinnamomi Rands. PLANTS (BASEL, SWITZERLAND) 2023; 12:3056. [PMID: 37687303 PMCID: PMC10489650 DOI: 10.3390/plants12173056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023]
Abstract
Holm oaks (Quercus ilex L.) can suffer severe infection by the oomycete Phytophthora cinnamomi Rands; the production of more tolerant plants is, therefore, required. Embryo formation is a key period in the establishment of epigenetic memory. Somatic embryos from three holm oak genotypes were elicited, either over 3 days or 60 days, with methyl-jasmonate, salicylic acid (SA), β-aminobutyric acid (BABA), or benzothiadiazole (all at 50 μM and 100 μM), or 10% and 30% of a filtered oomycete extract (FILT10 and FILT30) to activate plant immune responses. The number of embryos produced and conversion rate under all conditions were recorded. Some elicited embryos were then exposed to P. cinnamomi in dual culture, and differential mycelial growth and the progression of necrosis were measured. The same was performed with the roots of germinated embryos. Within genotypes, significant differences were seen among the elicitation treatments in terms of both variables. Embryos and roots of 60-day BABA, SA, or FILT10 treatments inhibited mycelium growth. The 3-day BABA (either concentration) and 60-day FILT10 induced the greatest inhibition of necrosis. Mycelium and necrosis inhibition were compared with those of tolerant trees. Both inhibitions might be a defense response maintained after primed embryo germination, thus increasing the likelihood of tolerance to infection.
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Affiliation(s)
- Mar Ruiz-Galea
- Department of Agroenvironmental Research, Instituto Madrileño de Investigación y Desarrollo Rural, Agrario y Alimentario (IMIDRA), Alcalá de Henares, 28805 Madrid, Spain; (C.K.); (E.F.); (I.H.)
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Ran F, Bai X, Li J, Yuan Y, Li C, Li P, Chen H. Cytokinin and Metabolites Affect Rhizome Growth and Development in Kentucky Bluegrass ( Poa pratensis). BIOLOGY 2023; 12:1120. [PMID: 37627004 PMCID: PMC10452147 DOI: 10.3390/biology12081120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Rhizome growth and development is regulated by phytohormone. However, endogenous phytohormones affect rhizome initiation, and sustained growth in perennial grass species remains elusive. In this study, we investigated the morphological characteristics and the content of indole-3-acetic acid (IAA), zeatin (ZT), gibberellic acid (GA3), and abscisic acid (ABA) in the rhizomes of two different Kentucky bluegrass. Using ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS), we performed metabolite analysis of two different rhizomes. In our study, the multi-rhizome Kentucky bluegrass material 'Yuzhong' had an average of 1113 rhizomes, while the few-rhizome material 'Anding' had an average of 347 rhizomes. The diameter of rhizome and length of rhizome internode in 'Yuzhong' were 1.68-fold and 1.33-fold higher than that of the 'Anding', respectively. The rhizome dry weight of 'Yuzhong' was 75.06 g, while the 'Anding' was 20.79 g. 'Yuzhong' had a higher ZT content (5.50 μg·g-1), which is 2.4-fold that of 'Anding' (2.27 μg·g-1). In contrast, the IAA, ABA, and GA3 content of rhizome were markedly higher in 'Anding' than 'Yuzhong'. Correlation analysis revealed significant correlations between ZT and ZT/ABA with the number of rhizomes, diameter of rhizome, and length of rhizome internode, whereas IAA, ABA, GA3, and IAA/ZT were opposite. In the metabolic profiles, we identified 163 differentially expressed metabolites (DEMs) (60 upregulated and 103 downregulated) in positive ion mode and 75 DEMs (36 upregulated and 39 downregulated) in negative ion mode. Histidine metabolism and ABC transporters pathways were the most significantly enriched in the positive and negative ion mode, respectively, both of which are involved in the synthesis and transport of cytokinin. These results indicate that cytokinin is crucial for rhizome development and promotes rhizome germination and growth of Kentucky bluegrass.
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Affiliation(s)
- Fu Ran
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, China; (F.R.)
| | - Xiaoming Bai
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, China; (F.R.)
- Key Laboratory of Grassland Ecosystem, Gansu Agricultural University, Lanzhou 730070, China
| | - Juanxia Li
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, China; (F.R.)
| | - Yajuan Yuan
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, China; (F.R.)
| | - Changning Li
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, China; (F.R.)
| | - Ping Li
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, China; (F.R.)
| | - Hui Chen
- College of Grassland Science, Gansu Agricultural University, Lanzhou 730070, China; (F.R.)
- Key Laboratory of Grassland Ecosystem, Gansu Agricultural University, Lanzhou 730070, China
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Vogt G. Environmental Adaptation of Genetically Uniform Organisms with the Help of Epigenetic Mechanisms-An Insightful Perspective on Ecoepigenetics. EPIGENOMES 2022; 7:1. [PMID: 36648862 PMCID: PMC9844400 DOI: 10.3390/epigenomes7010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022] Open
Abstract
Organisms adapt to different environments by selection of the most suitable phenotypes from the standing genetic variation or by phenotypic plasticity, the ability of single genotypes to produce different phenotypes in different environments. Because of near genetic identity, asexually reproducing populations are particularly suitable for the investigation of the potential and molecular underpinning of the latter alternative in depth. Recent analyses on the whole-genome scale of differently adapted clonal animals and plants demonstrated that epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs are among the molecular pathways supporting phenotypic plasticity and that epigenetic variation is used to stably adapt to different environments. Case studies revealed habitat-specific epigenetic fingerprints that were maintained over subsequent years pointing at the existence of epigenetic ecotypes. Environmentally induced epimutations and corresponding gene expression changes provide an ideal means for fast and directional adaptation to changing or new conditions, because they can synchronously alter phenotypes in many population members. Because microorganisms inclusive of human pathogens also exploit epigenetically mediated phenotypic variation for environmental adaptation, this phenomenon is considered a universal biological principle. The production of different phenotypes from the same DNA sequence in response to environmental cues by epigenetic mechanisms also provides a mechanistic explanation for the "general-purpose genotype hypothesis" and the "genetic paradox of invasions".
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
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