1
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Schmutz A, Schöb C. Coadaptation of coexisting plants enhances productivity in an agricultural system. Proc Natl Acad Sci U S A 2024; 121:e2305517121. [PMID: 38621135 PMCID: PMC11047107 DOI: 10.1073/pnas.2305517121] [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: 04/05/2023] [Accepted: 03/12/2024] [Indexed: 04/17/2024] Open
Abstract
Growing crops in more diverse crop systems (i.e., intercropping) is one way to produce food more sustainably. Even though intercropping, compared to average monocultures, is generally more productive, the full yield potential of intercropping might not yet have been achieved as modern crop cultivars are bred to be grown in monoculture. Breeding plants for more familiarity in mixtures, i.e., plants that are adapted to more diverse communities (i.e., adaptation) or even to coexist with each other (i.e., coadaptation) might have the potential to sustainably enhance productivity. In this study, the productivity benefits of familiarity through evolutionary adaptation and coevolutionary coadaptation were disentangled in a crop system through an extensive common garden experiment. Furthermore, evolutionary and coevolutionary effects on species-level and community-level productivity were linked to corresponding changes in functional traits. We found evidence for higher productivity and trait convergence with increasing familiarity with the plant communities. Furthermore, our results provide evidence for the coevolution of plants in mixtures leading to higher productivity of coadapted species. However, with the functional traits measured in our study, we could not fully explain the productivity benefits found upon coevolution. Our study investigated coevolution among randomly interacting plants and was able to demonstrate that coadaptation through coevolution of coexisting species in mixtures occurs and promotes ecosystem functioning (i.e., higher productivity). This result is particularly relevant for the diversification of agricultural and forest ecosystems, demonstrating the added value of artificially selecting plants for the communities they are familiar with.
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Affiliation(s)
- Anja Schmutz
- Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zürich, 8092Zurich, Switzerland
| | - Christian Schöb
- Department of Environmental Systems Science, Institute of Agricultural Sciences, ETH Zürich, 8092Zurich, Switzerland
- Área Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933Móstoles, Madrid, Spain
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2
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Schiestl FP. Is experimental evolution relevant for botanical research? AMERICAN JOURNAL OF BOTANY 2024; 111:e16296. [PMID: 38384109 DOI: 10.1002/ajb2.16296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Affiliation(s)
- Florian P Schiestl
- Department Systematic and Evolutionary Botany, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
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3
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Bogan SN, Yi SV. Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations. Genome Biol Evol 2024; 16:evae022. [PMID: 38324384 PMCID: PMC10899001 DOI: 10.1093/gbe/evae022] [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: 07/13/2023] [Revised: 01/09/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024] Open
Abstract
There is great interest in exploring epigenetic modifications as drivers of adaptive organismal responses to environmental change. Extending this hypothesis to populations, epigenetically driven plasticity could influence phenotypic changes across environments. The canonical model posits that epigenetic modifications alter gene regulation and subsequently impact phenotypes. We first discuss origins of epigenetic variation in nature, which may arise from genetic variation, spontaneous epimutations, epigenetic drift, or variation in epigenetic capacitors. We then review and synthesize literature addressing three facets of the aforementioned model: (i) causal effects of epigenetic modifications on phenotypic plasticity at the organismal level, (ii) divergence of epigenetic patterns in natural populations distributed across environmental gradients, and (iii) the relationship between environmentally induced epigenetic changes and gene expression at the molecular level. We focus on DNA methylation, the most extensively studied epigenetic modification. We find support for environmentally associated epigenetic structure in populations and selection on stable epigenetic variants, and that inhibition of epigenetic enzymes frequently bears causal effects on plasticity. However, there are pervasive confounding issues in the literature. Effects of chromatin-modifying enzymes on phenotype may be independent of epigenetic marks, alternatively resulting from functions and protein interactions extrinsic of epigenetics. Associations between environmentally induced changes in DNA methylation and expression are strong in plants and mammals but notably absent in invertebrates and nonmammalian vertebrates. Given these challenges, we describe emerging approaches to better investigate how epigenetic modifications affect gene regulation, phenotypic plasticity, and divergence among populations.
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Affiliation(s)
- Samuel N Bogan
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Soojin V Yi
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
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4
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Waterton J, Mazer SJ, Cleland EE. When the neighborhood matters: contextual selection on seedling traits in native and non-native California grasses. Evolution 2023; 77:2039-2055. [PMID: 37393951 DOI: 10.1093/evolut/qpad119] [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: 11/04/2019] [Revised: 06/13/2023] [Accepted: 06/30/2023] [Indexed: 07/04/2023]
Abstract
Plants interact extensively with their neighbors, but the evolutionary consequences of variation in neighbor identity are not well understood. Seedling traits are likely to experience selection that depends on the identity of neighbors because they influence competitive outcomes. To explore this, we evaluated selection on seed mass and emergence time in two California grasses, the native perennial Stipa pulchra, and the non-native annual Bromus diandrus, in the field with six other native and non-native neighbor grasses in single- and mixed-species treatments. We also quantified characteristics of each neighbor treatment to further investigate factors influencing their effects on fitness and phenotypic selection. Selection favored larger seeds in both focal species and this was largely independent of neighbor identity. Selection generally favored earlier emergence in both focal species, but neighbor identity influenced the strength and direction of selection on emergence time in S. pulchra, but not B. diandrus. Greater light interception, higher soil moisture, and greater productivity of neighbors were associated with more intense selection for earlier emergence and larger seeds. Our findings suggest that changes in plant community composition can alter patterns of selection in seedling traits, and that these effects can be associated with measurable characteristics of the community.
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Affiliation(s)
- Joseph Waterton
- Ecology, Behavior and Evolution Section, University of California San Diego, La Jolla, CA, United States
| | - Susan J Mazer
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA, United States
| | - Elsa E Cleland
- Ecology, Behavior and Evolution Section, University of California San Diego, La Jolla, CA, United States
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5
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Blanchet S, Fargeot L, Raffard A. Phylogenetically-conserved candidate genes unify biodiversity-ecosystem function relationships and eco-evolutionary dynamics across biological scales. Mol Ecol 2023; 32:4467-4481. [PMID: 37296539 DOI: 10.1111/mec.17043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
The intra- and interspecific facets of biodiversity have traditionally been analysed separately, limiting our understanding of how evolution has shaped biodiversity, how biodiversity (as a whole) alters ecological dynamics and hence eco-evolutionary feedbacks at the community scale. Here, we propose using candidate genes phylogenetically-conserved across species and sustaining functional traits as an inclusive biodiversity unit transcending the intra- and interspecific boundaries. This framework merges knowledge from functional genomics and functional ecology, and we first provide guidelines and a concrete example for identifying phylogenetically-conserved candidate genes (PCCGs) within communities and for measuring biodiversity from PCCGs. We then explain how biodiversity measured at PCCGs can be linked to ecosystem functions, which unifies recent observations that both intra- and interspecific biodiversity are important for ecosystem functions. We then highlight the eco-evolutionary processes shaping PCCG diversity patterns and argue that their respective role can be inferred from concepts derived from population genetics. Finally, we explain how PCCGs may shift the field of eco-evolutionary dynamics from a focal-species approach to a more realistic focal-community approach. This framework provides a novel perspective to investigate the global ecosystem consequences of diversity loss across biological scales, and how these ecological changes further alter biodiversity evolution.
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Affiliation(s)
- Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Station d'Écologie Théorique et Expérimentale du CNRS à Moulis, UAR2029, Moulis, France
| | - Laura Fargeot
- Centre National de la Recherche Scientifique (CNRS), Station d'Écologie Théorique et Expérimentale du CNRS à Moulis, UAR2029, Moulis, France
| | - Allan Raffard
- Univ. Savoie Mont Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
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6
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Ibañez VN, van Antro M, Peña-Ponton C, Milanovic-Ivanovic S, Wagemaker CAM, Gawehns F, Verhoeven KJF. Environmental and genealogical effects on DNA methylation in a widespread apomictic dandelion lineage. J Evol Biol 2023; 36:663-674. [PMID: 36810811 DOI: 10.1111/jeb.14162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/08/2022] [Accepted: 01/05/2023] [Indexed: 02/24/2023]
Abstract
DNA methylation in plant genomes occurs in different sequences and genomic contexts that have very different properties. DNA methylation that occurs in CG (mCG) sequence context shows transgenerational stability and high epimutation rate, and can thus provide genealogical information at short time scales. However, due to meta-stability and because mCG variants may arise due to other factors than epimutation, such as environmental stress exposure, it is not clear how well mCG captures genealogical information at micro-evolutionary time scales. Here, we analysed DNA methylation variation between accessions from a geographically widespread, apomictic common dandelion (Taraxacum officinale) lineage when grown experimentally under different light conditions. Using a reduced-representation bisulphite sequencing approach, we show that the light treatment induced differentially methylated cytosines (DMCs) in all sequence contexts, with a bias towards transposable elements. Accession differences were associated mainly with DMCs in CG context. Hierarchical clustering of samples based on total mCG profiles revealed a perfect clustering of samples by accession identity, irrespective of light conditions. Using microsatellite information as a benchmark of genetic divergence within the clonal lineage, we show that genetic divergence between accessions correlates strongly with overall mCG profiles. However, our results suggest that environmental effects that do occur in CG context may produce a heritable signal that partly dilutes the genealogical signal. Our study shows that methylation information in plants can be used to reconstruct micro-evolutionary genealogy, providing a useful tool in systems that lack genetic variation such as clonal and vegetatively propagated plants.
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Affiliation(s)
- Verónica Noé Ibañez
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, Université Paris Diderot, Gif sur Yvette, France.,Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Morgane van Antro
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Cristian Peña-Ponton
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Slavica Milanovic-Ivanovic
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | | | - Fleur Gawehns
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, the Netherlands
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7
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Zhang L, Cappelli SL, Huang M, Liu X, Xiao Y, Cardou F, Rong Y, Zhou S. Intraspecific trait variability mediates the effect of nitrogen addition and warming on aboveground productivity. OIKOS 2023. [DOI: 10.1111/oik.09559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Li Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Shanghai Inst. of Eco-Chongming (SIEC), and School of Life Sciences, Fudan Univ. Shanghai PR China
- Co‐Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Inst., Nanjing Forestry Univ. Nanjing PR China
| | - Seraina Lisa Cappelli
- Department of Evolutionary Biology and Environmental Studies, Univ. of Zürich Zürich
| | - Mengjiao Huang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Coastal Ecosystems Research Station of the Yangtze River Estuary, Shanghai Inst. of Eco-Chongming (SIEC), and School of Life Sciences, Fudan Univ. Shanghai PR China
| | - Xiang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro‐ecosystems, College of Ecology, Lanzhou Univ. Lanzhou PR China
| | - Yao Xiao
- State Key Laboratory of Herbage Improvement and Grassland Agro‐ecosystems, College of Ecology, Lanzhou Univ. Lanzhou PR China
| | - Françoise Cardou
- Biological Sciences Dept, Univ. of Toronto Scarborough Toronto ON Canada
| | - Yizhong Rong
- School of Resources and Environment, Anhui Agricultural Univ. Hefei PR China
| | - Shurong Zhou
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan Univ. Haikou PR China
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8
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Brown KE, Koenig D. On the hidden temporal dynamics of plant adaptation. CURRENT OPINION IN PLANT BIOLOGY 2022; 70:102298. [PMID: 36126489 DOI: 10.1016/j.pbi.2022.102298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 07/28/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Adaptation to a wide range of environments is a major driver of plant diversity. It is now possible to catalog millions of potential adaptive genomic differences segregating between environments within a plant species in a single experiment. Understanding which of these changes contributes to adaptive phenotypic divergence between plant populations is a major goal of evolutionary biologists and crop breeders. In this review, we briefly highlight the approaches frequently used to understand the genetic basis of adaptive phenotypes in plants, and we discuss some of the limitations of these methods. We propose that direct observation of the process of adaptation using multigenerational studies and whole genome sequencing is a crucial missing component of recent studies of plant adaptation because it complements several shortcomings of sampling-based techniques.
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Affiliation(s)
- Keely E Brown
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.
| | - Daniel Koenig
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA; Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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9
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Evolution of plasticity prevents postinvasion extinction of a native forb. Proc Natl Acad Sci U S A 2022; 119:e2118866119. [PMID: 35914140 PMCID: PMC9371648 DOI: 10.1073/pnas.2118866119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Exotic plant invaders pose a serious threat to native plants. However, despite showing inferior competitive ability and decreased performance, native species often subsist in invaded communities. The decline of native populations is hypothesized to be halted and eventually reversed if adaptive evolutionary changes can keep up with the environmental stress induced by invaders, that is, when population extinction is prevented by evolutionary rescue (ER). Nevertheless, evidence for the role of ER in postinvasion persistence of native flora remains scarce. Here, I explored the population density of a native forb, Veronica chamaedrys, and evaluated the changes in the shade-responsive traits of its populations distributed along the invasion chronosequence of an exotic transformer, Heracleum mantegazzianum, which was replicated in five areas. I found a U-shaped population trajectory that paralleled the evolution of plasticity to shade. Whereas V. chamaedrys genotypes from intact, more open sites exhibited a shade-tolerance strategy (pronounced leaf area/mass ratio), reduced light availability at the invaded sites selected for a shade-avoidance strategy (greater internode elongation). Field experiments subsequently confirmed that the shifts in shade-response strategies were adaptive and secured postinvasion population persistence, as indicated by further modeling. Alternative ecological mechanisms (habitat improvement or arrival of immigrants) were less likely explanations than ER for the observed population rebound, although the contribution of maternal effects cannot be dismissed. These results suggest that V. chamaedrys survived because of adaptive evolutionary changes operating on the same timescale as the invasion-induced stress, but the generality of ER for postinvasion persistence of native plants remains unknown.
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10
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De Kort H, Toivainen T, Van Nieuwerburgh F, Andrés J, Hytönen TP, Honnay O. Signatures of polygenic adaptation align with genome-wide methylation patterns in wild strawberry plants. THE NEW PHYTOLOGIST 2022; 235:1501-1514. [PMID: 35575945 DOI: 10.1111/nph.18225] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Epigenetic inheritance can drive adaptive evolution independently of DNA sequence variation. However, to what extent epigenetic variation represents an autonomous evolutionary force remains largely elusive. Through gene ontology and comparative analyses of genomic and epigenomic variation of wild strawberry plants raised in distinct drought settings, we characterised genome-wide covariation between single nucleotide polymorphisms (SNPs) and differentially methylated cytosines (DMCs). Covariation between SNPs and DMCs was independent of genomic proximity, but instead associated with fitness-related processes such as stress responses, genome regulation and reproduction. We expected this functional SNP-DMC covariation to be driven by adaptive evolution canalising SNP and DMC variation, but instead observed significantly lower covariation with DMCs for adaptive rather than for neutral SNPs. Drought-induced DMCs frequently co-varied with tens of SNPs, suggesting high genomic redundancy as a broad potential basis for polygenic adaptation of gene expression. Our findings suggest that stress-responsive DMCs initially co-vary with many SNPs under increased environmental stress, and that natural selection acting upon several of these SNPs subsequently reduces standing covariation with stress-responsive DMCs. Our study supports DNA methylation profiles that represent complex quantitative traits rather than autonomous evolutionary forces. We provide a conceptual framework for polygenic regulation and adaptation shaping genome-wide methylation patterns in plants.
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Affiliation(s)
- Hanne De Kort
- Plant Conservation and Population Biology, University of Leuven, Kasteelpark Arenberg 31-2435, BE-3001, Leuven, Belgium
| | - Tuomas Toivainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Latokartanonkaari 7, 00790, Helsinki, Finland
| | | | - Javier Andrés
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Latokartanonkaari 7, 00790, Helsinki, Finland
| | - Timo P Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Latokartanonkaari 7, 00790, Helsinki, Finland
| | - Olivier Honnay
- Plant Conservation and Population Biology, University of Leuven, Kasteelpark Arenberg 31-2435, BE-3001, Leuven, Belgium
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11
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Drought-exposure history increases complementarity between plant species in response to a subsequent drought. Nat Commun 2022; 13:3217. [PMID: 35680926 PMCID: PMC9184649 DOI: 10.1038/s41467-022-30954-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 05/18/2022] [Indexed: 01/10/2023] Open
Abstract
Growing threats from extreme climatic events and biodiversity loss have raised concerns about their interactive consequences for ecosystem functioning. Evidence suggests biodiversity can buffer ecosystem functioning during such climatic events. However, whether exposure to extreme climatic events will strengthen the biodiversity-dependent buffering effects for future generations remains elusive. We assess such transgenerational effects by exposing experimental grassland communities to eight recurrent summer droughts versus ambient conditions in the field. Seed offspring of 12 species are then subjected to a subsequent drought event in the glasshouse, grown individually, in monocultures or in 2-species mixtures. Comparing productivity between mixtures and monocultures, drought-selected plants show greater between-species complementarity than ambient-selected plants when recovering from the subsequent drought, causing stronger biodiversity effects on productivity and better recovery of drought-selected mixtures after the drought. These findings suggest exposure to recurrent climatic events can improve ecosystem responses to future events through transgenerational reinforcement of species complementarity. Using experimental communities of grassland species, this study shows that drought-exposure history can accelerate recovery from subsequent drought through increased niche complementarity between species. This transgenerational effect may enhance the sustainability of biodiversity and ecosystem functioning in a future with more frequent droughts.
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12
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Mounger JM, van Riemsdijk I, Boquete MT, Wagemaker CAM, Fatma S, Robertson MH, Voors SA, Oberstaller J, Gawehns F, Hanley TC, Grosse I, Verhoeven KJF, Sotka EE, Gehring CA, Hughes AR, Lewis DB, Schmid MW, Richards CL. Genetic and Epigenetic Differentiation Across Intertidal Gradients in the Foundation Plant Spartina alterniflora. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.868826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ecological genomics approaches have informed us about the structure of genetic diversity in natural populations that might underlie patterns in trait variation. However, we still know surprisingly little about the mechanisms that permit organisms to adapt to variable environmental conditions. The salt marsh foundation plant Spartina alterniflora exhibits a dramatic range in phenotype that is associated with a pronounced intertidal environmental gradient across a narrow spatial scale. Both genetic and non-genetic molecular mechanisms might underlie this phenotypic variation. To investigate both, we used epigenotyping-by-sequencing (epiGBS) to evaluate the make-up of natural populations across the intertidal environmental gradient. Based on recent findings, we expected that both DNA sequence and DNA methylation diversity would be explained by source population and habitat within populations. However, we predicted that epigenetic variation might be more strongly associated with habitat since similar epigenetic modifications could be rapidly elicited across different genetic backgrounds by similar environmental conditions. Overall, with PERMANOVA we found that population of origin explained a significant amount of the genetic (8.6%) and epigenetic (3.2%) variance. In addition, we found that a small but significant amount of genetic and epigenetic variance (<1%) was explained by habitat within populations. The interaction of population and habitat explained an additional 2.9% of the genetic variance and 1.4% of the epigenetic variance. By examining genetic and epigenetic variation within the same fragments (variation in close-cis), we found that population explained epigenetic variation in 9.2% of 8,960 tested loci, even after accounting for differences in the DNA sequence of the fragment. Habitat alone explained very little (<0.1%) of the variation in these close-cis comparisons, but the interaction of population and habitat explained 2.1% of the epigenetic variation in these loci. Using multiple matrix regression with randomization (MMRR) we found that phenotypic differences in natural populations were correlated with epigenetic and environmental differences even when accounting for genetic differences. Our results support the contention that sequence variation explains most of the variation in DNA methylation, but we have provided evidence that DNA methylation distinctly contributes to plant responses in natural populations.
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13
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Dietrich P, Schumacher J, Eisenhauer N, Roscher C. Eco-evolutionary dynamics modulate plant responses to global change depending on plant diversity and species identity. eLife 2022; 11:74054. [PMID: 35353037 PMCID: PMC9110027 DOI: 10.7554/elife.74054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/29/2022] [Indexed: 11/30/2022] Open
Abstract
Global change has dramatic impacts on grassland diversity. However, little is known about how fast species can adapt to diversity loss and how this affects their responses to global change. Here, we performed a common garden experiment testing whether plant responses to global change are influenced by their selection history and the conditioning history of soil at different plant diversity levels. Using seeds of four grass species and soil samples from a 14-year-old biodiversity experiment, we grew the offspring of the plants either in their own soil or in soil of a different community, and exposed them either to drought, increased nitrogen input, or a combination of both. Under nitrogen addition, offspring of plants selected at high diversity produced more biomass than those selected at low diversity, while drought neutralized differences in biomass production. Moreover, under the influence of global change drivers, soil history, and to a lesser extent plant history, had species-specific effects on trait expression. Our results show that plant diversity modulates plant-soil interactions and growth strategies of plants, which in turn affects plant eco-evolutionary pathways. How this change affects species' response to global change and whether this can cause a feedback loop should be investigated in more detail in future studies. Over the last hundred years, human activities including burning of fossil fuels, clearing of forests, and fertilizer use have caused environmental changes that have resulted in many species of plants, animals and other forms of life becoming extinct. Loss of plant species can change the local environment by, for example, altering the availability of nutrients and local communities of microbes in the soil. This may, in turn, cause remaining plant species to develop differently: they may take up fewer resources or become more prone to pathogens, both of which may alter their physical appearance. However, little is known about whether this happens and, if so, how rapidly such changes occur. Since 2002, researchers in Germany have been running a long-term project known as the Jena Experiment to study how plants behave when they grow in communities with different numbers of other plant species. For the experiment, various species of grass and other plants commonly found in grasslands were grown together in different combinations. Some plots contained many species (referred to as “high diversity”) and others contained only a few (“low diversity”). Here, Dietrich et al. collected seeds from four grasses grown for 12 years in Jena Experiment plots with two or six plant species. The seeds were then transferred to pots and grown in a greenhouse using soil either from the plot where the seeds originated or from another plot with a different diversity level. To simulate human-made changes in the environment, the team added nitrogen fertilizer or decreased how much they watered some of the plants. The greenhouse experiment showed that after receiving nitrogen fertilizer, the seeds from the high diversity Jena Experiment plots grew into larger plants than the seeds from the low diversity plots. But there was no difference in size when the plants were watered less. Moreover, both fertilizer and watering treatment had different effects on the plants’ physical appearance (root and leaf architecture) depending on the soil in which they were growing in. The findings of Dietrich et al. suggest that plants may respond differently to changes in their environment based on their origins and the soil they are growing in. This study provides the first indication that species loss could accelerate a further loss of species due to changes in how the plants develop and the communities of organisms living in the soil.
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Affiliation(s)
- Peter Dietrich
- Department of Physiological Diversity, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jens Schumacher
- Institute of Mathematics, Friedrich Schiller University Jena, Jena, Germany
| | - Nico Eisenhauer
- Experimental Interaction Ecology, German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig,, Leipzig, Germany
| | - Christiane Roscher
- Department of Physiological Diversity, Helmholtz Centre for Environmental Research, Leipzig, Germany
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14
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Gawehns F, Postuma M, Van Antro M, Nunn A, Sepers B, Fatma S, van Gurp TP, Wagemaker NCAM, Mateman AC, Milanovic-Ivanovic S, Grosse I, van Oers K, Vergeer P, Verhoeven KJF. epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing. Mol Ecol Resour 2022; 22:2087-2104. [PMID: 35178872 PMCID: PMC9311447 DOI: 10.1111/1755-0998.13597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 02/04/2022] [Accepted: 02/09/2022] [Indexed: 11/28/2022]
Abstract
Several reduced‐representation bisulfite sequencing methods have been developed in recent years to determine cytosine methylation de novo in nonmodel species. Here, we present epiGBS2, a laboratory protocol based on epiGBS with a revised and user‐friendly bioinformatics pipeline for a wide range of species with or without a reference genome. epiGBS2 is cost‐ and time‐efficient and the computational workflow is designed in a user‐friendly and reproducible manner. The library protocol allows a flexible choice of restriction enzymes and a double digest. The bioinformatics pipeline was integrated in the snakemake workflow management system, which makes the pipeline easy to execute and modular, and parameter settings for important computational steps flexible. We implemented bismark for alignment and methylation analysis and we preprocessed alignment files by double masking to enable single nucleotide polymorphism calling with freebayes (epifreebayes). The performance of several critical steps in epiGBS2 was evaluated against baseline data sets from Arabidopsis thaliana and great tit (Parus major), which confirmed its overall good performance. We provide a detailed description of the laboratory protocol and an extensive manual of the bioinformatics pipeline, which is publicly accessible on github (https://github.com/nioo‐knaw/epiGBS2) and zenodo (https://doi.org/10.5281/zenodo.4764652).
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Affiliation(s)
- Fleur Gawehns
- Netherlands Institute of Ecology (NIOO-KNAW), Bioinformatics Unit, Wageningen, the Netherlands
| | - Maarten Postuma
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, the Netherlands.,Wageningen University & Research (WUR), Plant Ecology and Nature Conservation Group, Wageningen, the Netherlands
| | - Morgane Van Antro
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, the Netherlands
| | - Adam Nunn
- ecSeq Bioinformatics GmbH, Leipzig, Germany.,Universität Leipzig, Institut für Informatik, Leipzig, Germany
| | - Bernice Sepers
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Animal Ecology, Wageningen, the Netherlands.,Wageningen University & Research (WUR), Behavioural Ecology Group, Wageningen, the Netherlands
| | - Samar Fatma
- Martin Luther University Halle-Wittenberg, Institute of Computer Science, Halle, Germany
| | - Thomas P van Gurp
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, the Netherlands
| | | | - A Christa Mateman
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Animal Ecology, Wageningen, the Netherlands
| | - Slavica Milanovic-Ivanovic
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, the Netherlands
| | - Ivo Grosse
- Martin Luther University Halle-Wittenberg, Institute of Computer Science, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Kees van Oers
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Animal Ecology, Wageningen, the Netherlands.,Wageningen University & Research (WUR), Behavioural Ecology Group, Wageningen, the Netherlands
| | - Philippine Vergeer
- Wageningen University & Research (WUR), Plant Ecology and Nature Conservation Group, Wageningen, the Netherlands
| | - Koen J F Verhoeven
- Netherlands Institute of Ecology (NIOO-KNAW), Department of Terrestrial Ecology, Wageningen, the Netherlands
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15
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Mounger J, Boquete MT, Schmid MW, Granado R, Robertson MH, Voors SA, Langanke KL, Alvarez M, Wagemaker CAM, Schrey AW, Fox GA, Lewis DB, Lira CF, Richards CL. Inheritance of DNA methylation differences in the mangrove Rhizophora mangle. Evol Dev 2021; 23:351-374. [PMID: 34382741 DOI: 10.1111/ede.12388] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 05/15/2021] [Accepted: 07/02/2021] [Indexed: 12/11/2022]
Abstract
The capacity to respond to environmental challenges ultimately relies on phenotypic variation which manifests from complex interactions of genetic and nongenetic mechanisms through development. While we know something about genetic variation and structure of many species of conservation importance, we know very little about the nongenetic contributions to variation. Rhizophora mangle is a foundation species that occurs in coastal estuarine habitats throughout the neotropics where it provides critical ecosystem functions and is potentially threatened by anthropogenic environmental changes. Several studies have documented landscape-level patterns of genetic variation in this species, but we know virtually nothing about the inheritance of nongenetic variation. To assess one type of nongenetic variation, we examined the patterns of DNA sequence and DNA methylation in maternal plants and offspring from natural populations of R. mangle from the Gulf Coast of Florida. We used a reduced representation bisulfite sequencing approach (epi-genotyping by sequencing; epiGBS) to address the following questions: (a) What are the levels of genetic and epigenetic diversity in natural populations of R. mangle? (b) How are genetic and epigenetic variation structured within and among populations? (c) How faithfully is epigenetic variation inherited? We found low genetic diversity but high epigenetic diversity from natural populations of maternal plants in the field. In addition, a large portion (up to ~25%) of epigenetic differences among offspring grown in common garden was explained by maternal family. Therefore, epigenetic variation could be an important source of response to challenging environments in the genetically depauperate populations of this foundation species.
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Affiliation(s)
- Jeannie Mounger
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - M Teresa Boquete
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA.,Department of Evolutionary Ecology, CSIC, Estación Biológica de Doñana, Sevilla, Spain
| | | | - Renan Granado
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA.,Diretoria de Pesquisas, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro/RJ, Brazil
| | - Marta H Robertson
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Sandy A Voors
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Kristen L Langanke
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Mariano Alvarez
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA.,Avalo, Durham, NC, USA
| | | | - Aaron W Schrey
- Department of Biology, Georgia Southern University, Armstrong Campus, Savannah, Georgia, USA
| | - Gordon A Fox
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - David B Lewis
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA
| | - Catarina Fonseca Lira
- Diretoria de Pesquisas, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro/RJ, Brazil
| | - Christina L Richards
- Department of Integrative Biology, University of South Florida, Tampa, Florida, USA.,Plant Evolutionary Ecology, University of Tübingen, Institute of Evolution & Ecology, Tübingen, Germany
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16
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Dietrich P, Eisenhauer N, Otto P, Roscher C. Plant history and soil history jointly influence the selection environment for plant species in a long-term grassland biodiversity experiment. Ecol Evol 2021; 11:8156-8169. [PMID: 34188877 PMCID: PMC8216899 DOI: 10.1002/ece3.7647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/09/2021] [Accepted: 04/17/2021] [Indexed: 11/08/2022] Open
Abstract
Long-term biodiversity experiments have shown increasing strengths of biodiversity effects on plant productivity over time. However, little is known about rapid evolutionary processes in response to plant community diversity, which could contribute to explaining the strengthening positive relationship. To address this issue, we performed a transplant experiment with offspring of seeds collected from four grass species in a 14-year-old biodiversity experiment (Jena Experiment). We used two- and six-species communities and removed the vegetation of the study plots to exclude plant-plant interactions. In a reciprocal design, we transplanted five "home" phytometers (same origin and actual environment), five "away-same" phytometers (same species richness of origin and actual environment, but different plant composition), and five "away-different" phytometers (different species richness of origin and actual environment) of the same species in the study plots. In the establishment year, plants transplanted in home soil produced more shoots than plants in away soil indicating that plant populations at low and high diversity developed differently over time depending on their associated soil community and/or conditions. In the second year, offspring of individuals selected at high diversity generally had a higher performance (biomass production and fitness) than offspring of individuals selected at low diversity, regardless of the transplant environment. This suggests that plants at low and high diversity showed rapid evolutionary responses measurable in their phenotype. Our findings provide first empirical evidence that loss of productivity at low diversity is not only caused by changes in abiotic and biotic conditions but also that plants respond to this by a change in their micro-evolution. Thus, we conclude that eco-evolutionary feedbacks of plants at low and high diversity are critical to fully understand why the positive influence of diversity on plant productivity is strengthening through time.
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Affiliation(s)
- Peter Dietrich
- Department of Physiological DiversityUFZHelmholtz Centre for Environmental ResearchLeipzigGermany
- German Centre of Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Nico Eisenhauer
- German Centre of Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Department of Experimental Interaction EcologyInstitute of BiologyLeipzig UniversityLeipzigGermany
| | - Peter Otto
- Institute of BiologyHerbarium Universitatis Lipsiensis (LZ)Leipzig UniversityLeipzigGermany
| | - Christiane Roscher
- Department of Physiological DiversityUFZHelmholtz Centre for Environmental ResearchLeipzigGermany
- German Centre of Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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17
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McNew SM, Boquete MT, Espinoza‐Ulloa S, Andres JA, Wagemaker NCAM, Knutie SA, Richards CL, Clayton DH. Epigenetic effects of parasites and pesticides on captive and wild nestling birds. Ecol Evol 2021; 11:7713-7729. [PMID: 34188846 PMCID: PMC8216931 DOI: 10.1002/ece3.7606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022] Open
Abstract
Anthropogenic changes to the environment challenge animal populations to adapt to new conditions and unique threats. While the study of adaptation has focused on genetic variation, epigenetic mechanisms may also be important. DNA methylation is sensitive to environmental stressors, such as parasites and pesticides, which may affect gene expression and phenotype. We studied the effects of an invasive ectoparasite, Philornis downsi, on DNA methylation of Galápagos mockingbirds (Mimus parvulus). We used the insecticide permethrin to manipulate P. downsi presence in nests of free-living mockingbirds and tested for effects of parasitism on nestling mockingbirds using epiGBS, a reduced-representation bisulfite sequencing (RRBS) approach. To distinguish the confounding effects of insecticide exposure, we conducted a matching experiment exposing captive nestling zebra finches (Taeniopygia guttata) to permethrin. We used zebra finches because they were the closest model organism to mockingbirds that we could breed in controlled conditions. We identified a limited number of differentially methylated cytosines (DMCs) in parasitized versus nonparasitized mockingbirds, but the number was not more than expected by chance. In contrast, we saw clear effects of permethrin on methylation in captive zebra finches. DMCs in zebra finches paralleled documented effects of permethrin exposure on vertebrate cellular signaling and endocrine function. Our results from captive birds indicate a role for epigenetic processes in mediating sublethal nontarget effects of pyrethroid exposure in vertebrates. Environmental conditions in the field were more variable than the laboratory, which may have made effects of both parasitism and permethrin harder to detect in mockingbirds. RRBS approaches such as epiGBS may be a cost-effective way to characterize genome-wide methylation profiles. However, our results indicate that ecological epigenetic studies in natural populations should consider the number of cytosines interrogated and the depth of sequencing in order to have adequate power to detect small and variable effects.
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Affiliation(s)
- Sabrina M. McNew
- School of Biological SciencesUniversity of UtahSalt Lake CityUTUSA
- Cornell Lab of OrnithologyCornell UniversityIthacaNYUSA
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
| | - M. Teresa Boquete
- Department of Integrative BiologyUniversity of South FloridaTampaFLUSA
- Department of Evolutionary EcologyEstación Biológica de DoñanaCSICSevillaSpain
| | - Sebastian Espinoza‐Ulloa
- Department of BiologyUniversity of SaskatchewanSaskatoonSKCanada
- Facultad de MedicinaPontifica Universidad Católica del EcuadorQuitoEcuador
| | - Jose A. Andres
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
- Department of BiologyUniversity of SaskatchewanSaskatoonSKCanada
| | | | - Sarah A. Knutie
- School of Biological SciencesUniversity of UtahSalt Lake CityUTUSA
- Department of Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsCTUSA
- Institute for Systems GenomicsUniversity of ConnecticutStorrsCTUSA
| | | | - Dale H. Clayton
- School of Biological SciencesUniversity of UtahSalt Lake CityUTUSA
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18
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Puy J, de Bello F, Dvořáková H, Medina NG, Latzel V, Carmona CP. Competition-induced transgenerational plasticity influences competitive interactions and leaf decomposition of offspring. THE NEW PHYTOLOGIST 2021; 229:3497-3507. [PMID: 33111354 DOI: 10.1111/nph.17037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Phenotypic plasticity, within and across generations (transgenerational plasticity), allows organisms and their progeny to adapt to the environment without modification of the underlying DNA. Recent findings suggest that epigenetic modifications are important mediators of such plasticity. However, empirical studies have, so far, mainly focused on plasticity in response to abiotic factors, overlooking the response to competition. We tested for within-generation and transgenerational phenotypic plasticity triggered by plant-plant competition intensity, and we tested whether it was mediated via DNA methylation, using the perennial, apomictic herb Taraxacum brevicorniculatum in four coordinated experiments. We then tested the consequences of transgenerational plasticity affecting competitive interactions of the offspring and ecosystem processes, such as decomposition. We found that, by promoting differences in DNA methylation, offspring of plants under stronger competition developed faster and presented more resource-conservative phenotypes. Further, these adjustments associated with less degradable leaves, which have the potential to reduce nutrient turnover and might, in turn, favour plants with more conservative traits. Greater parental competition enhanced competitive abilities of the offspring, by triggering adaptive phenotypic plasticity, and decreased offspring leaf decomposability. Our results suggest that competition-induced transgenerational effects could promote rapid adaptations and species coexistence and feed back on biodiversity assembly and nutrient cycling.
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Affiliation(s)
- Javier Puy
- Department of Botany, Faculty of Sciences, University of South Bohemia, České Budějovice, 37005, Czech Republic
- Zoology, School of Natural Sciences, Trinity College Dublin, Dublin 2, D02 PN40, Ireland
| | - Francesco de Bello
- Department of Botany, Faculty of Sciences, University of South Bohemia, České Budějovice, 37005, Czech Republic
- Centro de Investigaciones sobre Desertificación, Valencia, 46113, Spain
| | - Hana Dvořáková
- Department of Botany, Faculty of Sciences, University of South Bohemia, České Budějovice, 37005, Czech Republic
| | - Nagore G Medina
- Department of Botany, Faculty of Sciences, University of South Bohemia, České Budějovice, 37005, Czech Republic
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, 28049, Spain
| | - Vit Latzel
- Institute of Botany, Czech Academy of Sciences, Průhonice, 25243, Czech Republic
| | - Carlos P Carmona
- Institute of Ecology and Earth Sciences, Department of Botany, University of Tartu, Tartu, 51005, Estonia
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19
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van Moorsel SJ. Born with a silver spoon: dandelion parents' life experiences affect the lives and afterlives of their offspring. THE NEW PHYTOLOGIST 2021; 229:3044-3047. [PMID: 33617004 DOI: 10.1111/nph.17186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Sofia J van Moorsel
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
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20
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Eckert S, Herden J, Stift M, Joshi J, van Kleunen M. Manipulation of cytosine methylation does not remove latitudinal clines in two invasive goldenrod species in Central Europe. Mol Ecol 2020; 30:222-236. [PMID: 33150604 DOI: 10.1111/mec.15722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/03/2020] [Accepted: 10/23/2020] [Indexed: 12/23/2022]
Abstract
Invasive species frequently differentiate phenotypically in novel environments within a few generations, often even with limited genetic variation. For the invasive plants Solidago canadensis and S. gigantea, we tested whether such differentiation might have occurred through heritable epigenetic changes in cytosine methylation. In a 2-year common-garden experiment, we grew plants from seeds collected along a latitudinal gradient in their non-native Central European range to test for trait differentiation and whether differentiation disappeared when seeds were treated with the demethylation agent zebularine. Microsatellite markers revealed no population structure along the latitudinal gradient in S. canadensis, but three genetic clusters in S. gigantea. Solidago canadensis showed latitudinal clines in flowering phenology and growth. In S. gigantea, the number of clonal offspring decreased with latitude. Although zebularine had a significant effect on early growth, probably through effects on cytosine methylation, latitudinal clines remained (or even got stronger) in plants raised from seeds treated with zebularine. Thus, our experiment provides no evidence that epigenetic mechanisms by selective cytosine methylation contribute to the observed phenotypic differentiation in invasive goldenrods in Central Europe.
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Affiliation(s)
- Silvia Eckert
- Biodiversity Research/Systematic Botany, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jasmin Herden
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Marc Stift
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Jasmin Joshi
- Biodiversity Research/Systematic Botany, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,Institute for Landscape and Open Space, Eastern Switzerland University of Applied Sciences, Rapperswil, Switzerland.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Mark van Kleunen
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany.,Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
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21
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van Moorsel SJ, Hahl T, Petchey OL, Ebeling A, Eisenhauer N, Schmid B, Wagg C. Co-occurrence history increases ecosystem stability and resilience in experimental plant communities. Ecology 2020; 102:e03205. [PMID: 32979225 DOI: 10.1002/ecy.3205] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/03/2020] [Accepted: 08/17/2020] [Indexed: 01/29/2023]
Abstract
Understanding factors that maintain ecosystem stability is critical in the face of environmental change. Experiments simulating species loss from grassland have shown that losing biodiversity decreases ecosystem stability. However, as the originally sown experimental communities with reduced biodiversity develop, plant evolutionary processes or the assembly of interacting soil organisms may allow ecosystems to increase stability over time. We explored such effects in a long-term grassland biodiversity experiment with plant communities with either a history of co-occurrence (selected communities) or no such history (naïve communities) over a 4-yr period in which a major flood disturbance occurred. Comparing communities of identical species composition, we found that selected communities had temporally more stable biomass than naïve communities, especially at low species richness. Furthermore, selected communities showed greater biomass recovery after flooding, resulting in more stable post-flood productivity. In contrast to a previous study, the positive diversity-stability relationship was maintained after the flooding. Our results were consistent across three soil treatments simulating the presence or absence of co-selected microbial communities. We suggest that prolonged exposure of plant populations to a particular community context and abiotic site conditions can increase ecosystem temporal stability and resilience due to short-term evolution. A history of co-occurrence can in part compensate for species loss, as can high plant diversity in part compensate for the missing opportunity of such adaptive adjustments.
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Affiliation(s)
- Sofia J van Moorsel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland.,Department of Biology, McGill University, 1205 Dr Penfield Avenue, Montreal, Quebec, H3A 1B1, Canada
| | - Terhi Hahl
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | - Owen L Petchey
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | - Anne Ebeling
- Institute of Ecology and Evolution, University of Jena, Dornburger Strasse 159, Jena, 07743, Germany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany.,Institute of Biology, Leipzig University, Deutscher Platz 5e, Leipzig, 04103, Germany
| | - Bernhard Schmid
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland.,Department of Geography, University of Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | - Cameron Wagg
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland.,Agriculture and Agri-Food Canada, 850 Lincoln Road, Fredericton, New Brunswick, E3B 4Z7, Canada
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22
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Iriart V, Baucom RS, Ashman TL. Herbicides as anthropogenic drivers of eco-evo feedbacks in plant communities at the agro-ecological interface. Mol Ecol 2020; 30:5406-5421. [PMID: 32542840 DOI: 10.1111/mec.15510] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 04/27/2020] [Accepted: 05/29/2020] [Indexed: 12/16/2022]
Abstract
Herbicides act as human-mediated novel selective agents and community disruptors, yet their full effects on eco-evolutionary dynamics in natural communities have only begun to be appreciated. Here, we synthesize how herbicide exposures can result in dramatic phenotypic and compositional shifts within communities at the agro-ecological interface and how these in turn affect species interactions and drive plant (and plant-associates') evolution in ways that can feedback to continue to affect the ecology and ecosystem functions of these assemblages. We advocate a holistic approach to understanding these dynamics that includes plastic changes and plant community transformations and also extends beyond this single trophic level targeted by herbicides to the effects on nontarget plant-associated organisms and their potential to evolve, thereby embracing the complexity of these real-world systems. We make explicit recommendations for future research to achieve this goal and specifically address impacts of ecology on evolution, evolution on ecology and their feedbacks so that we can gain a more predictive view of the fates of herbicide-impacted communities.
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Affiliation(s)
- Veronica Iriart
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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23
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Werner O, Prudencio ÁS, de la Cruz-Martínez E, Nieto-Lugilde M, Martínez-Gómez P, Ros RM. A Cost Reduced Variant of Epi-Genotyping by Sequencing for Studying DNA Methylation in Non-model Organisms. FRONTIERS IN PLANT SCIENCE 2020; 11:694. [PMID: 32547585 PMCID: PMC7270828 DOI: 10.3389/fpls.2020.00694] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 05/01/2020] [Indexed: 05/27/2023]
Abstract
Reference-free reduced representation bisulfite sequencing uses enzymatic digestion for reducing genome complexity and allows detection of markers to study DNA methylation of a high number of individuals in natural populations of non-model organisms. Current methods like epiGBS enquire the use of a higher number of methylated DNA oligos with a significant cost (especially for small labs and first pilot studies). In this paper, we present a modification of this epiGBS protocol that requires the use of only one hemimethylated P2 (common) adapter, which is combined with unmethylated barcoded adapters. The unmethylated cytosines of one chain of the barcoded adapter are replaced by methylated cytosines using nick translation with methylated cytosines in dNTP solution. The basic version of our technique uses only one restriction enzyme, and as a result, genomic fragments are integrated into two orientations with respect to the adapter sequences. Comparing the sequences of two chain orientations makes it possible to reconstruct the original sequence before bisulfite treatment with the help of standard software and newly developed software written in C and described here. We provide a proof of concept via data obtained from almond (Prunus dulcis). Example data and a detailed description of the complete software pipeline starting from the raw reads up until the final differentially methylated cytosines are given in Supplementary Material making this technique accessible to non-expert computer users. The adapter design showed in this paper should allow the use of a two restriction enzyme approach with minor changes in software parameters.
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Affiliation(s)
- Olaf Werner
- Laboratory of Molecular Systematics, Phylogeography and Conservation in Bryophytes, Department of Plant Biology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Ángela S. Prudencio
- Laboratory of Fruit Tree Breeding, Department of Plant Breeding, CEBAS-CSIC, Murcia, Spain
| | - Elena de la Cruz-Martínez
- Laboratory of Molecular Systematics, Phylogeography and Conservation in Bryophytes, Department of Plant Biology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Marta Nieto-Lugilde
- Laboratory of Molecular Systematics, Phylogeography and Conservation in Bryophytes, Department of Plant Biology, Faculty of Biology, University of Murcia, Murcia, Spain
| | - Pedro Martínez-Gómez
- Laboratory of Fruit Tree Breeding, Department of Plant Breeding, CEBAS-CSIC, Murcia, Spain
| | - Rosa M. Ros
- Laboratory of Molecular Systematics, Phylogeography and Conservation in Bryophytes, Department of Plant Biology, Faculty of Biology, University of Murcia, Murcia, Spain
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24
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Boquete MT, Wagemaker NCAM, Vergeer P, Mounger J, Richards CL. Epigenetic Approaches in Non-Model Plants. Methods Mol Biol 2020; 2093:203-215. [PMID: 32088898 DOI: 10.1007/978-1-0716-0179-2_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Reduced representation bisulfite sequencing is an emerging methodology for evolutionary and ecological genomics and epigenomics research because it provides a cost-effective, high-resolution tool for exploration and comparative analysis of DNA methylation and genetic variation. Here we describe how digestion of genomic plant DNA with restriction enzymes, subsequent bisulfite conversion of unmethylated cytosines, and final DNA sequencing allow for the examination of genome-wide genetic and epigenetic variation in plants without the need for a reference genome. We explain how the use of several combinations of barcoded adapters for the creation of highly multiplexed libraries allows the inclusion of up to 144 different samples/individuals in only one sequencing lane.
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Affiliation(s)
- M Teresa Boquete
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Niels C A M Wagemaker
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Philippine Vergeer
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
- Plant Ecology and Nature Conservation Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Jeannie Mounger
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
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Hahl T, Moorsel SJ, Schmid MW, Zuppinger‐Dingley D, Schmid B, Wagg C. Plant responses to diversity‐driven selection and associated rhizosphere microbial communities. Funct Ecol 2020. [DOI: 10.1111/1365-2435.13511] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Terhi Hahl
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zurich Switzerland
| | - Sofia J. Moorsel
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zurich Switzerland
- Department of Biology McGill University Montreal QC Canada
| | - Marc W. Schmid
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zurich Switzerland
- MWSchmid GmbH Zurich Switzerland
| | - Debra Zuppinger‐Dingley
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zurich Switzerland
| | - Bernhard Schmid
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zurich Switzerland
- Department of Geography University of Zürich Zurich Switzerland
- Institute of Ecology College of Urban and Environmental Sciences Peking University Beijing China
| | - Cameron Wagg
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zurich Switzerland
- Fredericton Research and Development Centre Agriculture and Agri‐Food Canada Fredericton NB Canada
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