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Preite V, Oplaat C, Biere A, Kirschner J, van der Putten WH, Verhoeven KJF. Increased transgenerational epigenetic variation, but not predictable epigenetic variants, after environmental exposure in two apomictic dandelion lineages. Ecol Evol 2018; 8:3047-3059. [PMID: 29531716 PMCID: PMC5838036 DOI: 10.1002/ece3.3871] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 12/21/2017] [Accepted: 01/01/2018] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is one of the mechanisms underlying epigenetic modifications. DNA methylations can be environmentally induced and such induced modifications can at times be transmitted to successive generations. However, it remains speculative how common such environmentally induced transgenerational DNA methylation changes are and if they persist for more than one offspring generation. We exposed multiple accessions of two different apomictic dandelion lineages of the Taraxacum officinale group (Taraxacum alatum and T. hemicyclum) to drought and salicylic acid (SA) treatment. Using methylation-sensitive amplified fragment length polymorphism markers (MS-AFLPs) we screened anonymous methylation changes at CCGG restriction sites throughout the genome after stress treatments and assessed the heritability of induced changes for two subsequent unexposed offspring generations. Irrespective of the initial stress treatment, a clear buildup of heritable DNA methylation variation was observed across three generations, indicating a considerable background rate of heritable epimutations. Less evidence was detected for environmental effects. Drought stress showed some evidence for accession-specific methylation changes, but only in the exposed generation and not in their offspring. By contrast, SA treatment caused an increased rate of methylation change in offspring of treated plants. These changes were seemingly undirected resulting in increased transgenerational epigenetic variation between offspring individuals, but not in predictable epigenetic variants. While the functional consequences of these MS-AFLP-detected DNA methylation changes remain to be demonstrated, our study shows that (1) stress-induced transgenerational DNA methylation modification in dandelions is genotype and context-specific; and (2) inherited environmental DNA methylation effects are mostly undirected and not targeted to specific loci.
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Affiliation(s)
- Veronica Preite
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Carla Oplaat
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Arjen Biere
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Jan Kirschner
- Institute of Botany of the Czech Academy of SciencesPrůhoniceCzech Republic
| | - Wim H. van der Putten
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Laboratory of NematologyWageningen UniversityWageningenThe Netherlands
| | - Koen J. F. Verhoeven
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
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52
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Lele L, Ning D, Cuiping P, Xiao G, Weihua G. Genetic and epigenetic variations associated with adaptation to heterogeneous habitat conditions in a deciduous shrub. Ecol Evol 2018; 8:2594-2606. [PMID: 29531679 PMCID: PMC5838075 DOI: 10.1002/ece3.3868] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 12/29/2017] [Accepted: 01/02/2018] [Indexed: 12/22/2022] Open
Abstract
Environmentally induced phenotypic plasticity is thought to play an important role in the adaption of plant populations to heterogeneous habitat conditions, and yet the importance of epigenetic variation as a mechanism of adaptive plasticity in natural plant populations still merits further research. In this study, we investigated populations of Vitex negundo var. heterophylla (Chinese chastetree) from adjacent habitat types at seven sampling sites. Using several functional traits, we detected a significant differentiation between habitat types. With amplified fragment length polymorphisms (AFLP) and methylation-sensitive AFLP (MSAP), we found relatively high levels of genetic and epigenetic diversity but very low genetic and epigenetic differences between habitats within sites. Bayesian clustering showed a remarkable habitat-related differentiation and more genetic loci associated with the habitat type than epigenetic, suggesting that the adaptation to the habitat is genetically based. However, we did not find any significant correlation between genetic or epigenetic variation and habitat using simple and partial Mantel tests. Moreover, we found no correlation between genetic and ecologically relevant phenotypic variation and a significant correlation between epigenetic and phenotypic variation. Although we did not find any direct relationship between epigenetic variation and habitat environment, our findings suggest that epigenetic variation may complement genetic variation as a source of functional phenotypic diversity associated with adaptation to the heterogeneous habitat in natural plant populations.
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Affiliation(s)
- Liu Lele
- Institute of Ecology and BiodiversityCollege of Life SciencesShandong UniversityJinanChina
| | - Du Ning
- Institute of Ecology and BiodiversityCollege of Life SciencesShandong UniversityJinanChina
| | - Pei Cuiping
- Institute of Ecology and BiodiversityCollege of Life SciencesShandong UniversityJinanChina
| | - Guo Xiao
- College of Landscape Architecture and ForestryQingdao Agricultural UniversityQingdaoChina
| | - Guo Weihua
- Institute of Ecology and BiodiversityCollege of Life SciencesShandong UniversityJinanChina
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53
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Genomic tools for behavioural ecologists to understand repeatable individual differences in behaviour. Nat Ecol Evol 2018; 2:944-955. [PMID: 29434349 DOI: 10.1038/s41559-017-0411-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 11/10/2017] [Indexed: 12/28/2022]
Abstract
Behaviour is a key interface between an animal's genome and its environment. Repeatable individual differences in behaviour have been extensively documented in animals, but the molecular underpinnings of behavioural variation among individuals within natural populations remain largely unknown. Here, we offer a critical review of when molecular techniques may yield new insights, and we provide specific guidance on how and whether the latest tools available are appropriate given different resources, system and organismal constraints, and experimental designs. Integrating molecular genetic techniques with other strategies to study the proximal causes of behaviour provides opportunities to expand rapidly into new avenues of exploration. Such endeavours will enable us to better understand how repeatable individual differences in behaviour have evolved, how they are expressed and how they can be maintained within natural populations of animals.
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54
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Monteiro F, Frese L, Castro S, Duarte MC, Paulo OS, Loureiro J, Romeiras MM. Genetic and Genomic Tools to Asssist Sugar Beet Improvement: The Value of the Crop Wild Relatives. FRONTIERS IN PLANT SCIENCE 2018; 9:74. [PMID: 29467772 PMCID: PMC5808244 DOI: 10.3389/fpls.2018.00074] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Accepted: 01/15/2018] [Indexed: 05/21/2023]
Abstract
Sugar beet (Beta vulgaris L. ssp. vulgaris) is one of the most important European crops for both food and sugar production. Crop improvement has been developed to enhance productivity, sugar content or other breeder's desirable traits. The introgression of traits from Crop Wild Relatives (CWR) has been done essentially for lessening biotic stresses constraints, namely using Beta and Patellifolia species which exhibit disease resistance characteristics. Several studies have addressed crop-to-wild gene flow, yet, for breeding programs genetic variability associated with agronomically important traits remains unexplored regarding abiotic factors. To accomplish such association from phenotype-to-genotype, screening for wild relatives occurring in habitats where selective pressures are in play (i.e., populations in salt marshes for salinity tolerance; populations subjected to pathogen attacks and likely evolved resistance to pathogens) are the most appropriate streamline to identify causal genetic information. By selecting sugar beet CWR species based on genomic tools, rather than random variations, is a promising but still seldom explored route toward the development of improved crops. In this perspective, a viable streamline for sugar beet improvement is proposed through the use of different genomic tools by recurring to sugar beet CWRs and focusing on agronomic traits associated with abiotic stress tolerance. Overall, identification of genomic and epigenomic landscapes associated to adaptive ecotypes, along with the cytogenetic and habitat characterization of sugar beet CWR, will enable to identify potential hotspots for agrobiodiversity of sugar beet crop improvement toward abiotic stress tolerance.
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Affiliation(s)
- Filipa Monteiro
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Lothar Frese
- Institute for Breeding Research on Agricultural Crops, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants (JKI), Quedlinburg, Germany
| | - Sílvia Castro
- Department of Life Sciences, Centre for Functional Ecology, Universidade de Coimbra, Coimbra, Portugal
| | - Maria C. Duarte
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
| | - Octávio S. Paulo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
| | - João Loureiro
- Department of Life Sciences, Centre for Functional Ecology, Universidade de Coimbra, Coimbra, Portugal
| | - Maria M. Romeiras
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa, Lisboa, Portugal
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
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55
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Weinhold A. Transgenerational stress-adaption: an opportunity for ecological epigenetics. PLANT CELL REPORTS 2018; 37:3-9. [PMID: 29032426 DOI: 10.1007/s00299-017-2216-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/04/2017] [Indexed: 05/14/2023]
Abstract
In the recent years, there has been considerable interest to investigate the adaptive transgenerational plasticity of plants and how a "stress memory" can be transmitted to the following generation. Although, increasing evidence suggests that transgenerational adaptive responses have widespread ecological relevance, the underlying epigenetic processes have rarely been elucidated. On the other hand, model plant species have been deeply investigated in their genome-wide methylation landscape without connecting this to the ecological reality of the plant. What we need is the combination of an ecological understanding which plant species would benefit from transgenerational epigenetic stress-adaption in their natural habitat, combined with a deeper molecular analysis of non-model organisms. Only such interdisciplinary linkage in an ecological epigenetic study could unravel the full potential that epigenetics could play for the transgenerational stress-adaption of plants.
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Affiliation(s)
- Arne Weinhold
- Applied Zoology/Animal Ecology, Dahlem Centre of Plant Sciences (DCPS), Institute of Biology, FU Berlin, Haderslebener Str. 9, 12163, Berlin, Germany.
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56
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Balao F, Paun O, Alonso C. Uncovering the contribution of epigenetics to plant phenotypic variation in Mediterranean ecosystems. PLANT BIOLOGY (STUTTGART, GERMANY) 2018. [PMID: 28637098 DOI: 10.1111/plb.12594] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Epigenetic signals can affect plant phenotype and fitness and be stably inherited across multiple generations. Epigenetic regulation plays a key role in the mechanisms of plant response to the environment, without altering DNA sequence. As plants cannot adapt behaviourally or migrate instantly, such dynamic epigenetic responses may be particularly crucial for survival of plants within changing and challenging environments, such as the Mediterranean-Type Ecosystems (MTEs). These ecosystems suffer recurrent stressful events (warm and dry summers with associated fire regimes) that have selected for plants with similar phenotypic complex traits, resulting in similar vegetation growth forms. However, the potential role of epigenetics in plant adaptation to recurrent stressful environments such as the MTEs has generally been ignored. To understand the full spectrum of adaptive processes in such contexts, it is imperative to prompt study of the causes and consequences of epigenetic variation in natural populations. With this purpose, we review here current knowledge on epigenetic variation in natural populations and the genetic and epigenetic basis of some key traits for plants in the MTEs, namely those traits involved in adaptation to drought, fire and oligotrophic soils. We conclude there is still much to be learned about 'plant epigenetics in the wild' and, thus, we propose future research steps in the study of natural epigenetic variation of key traits in the MTEs at different scales.
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Affiliation(s)
- F Balao
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - O Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - C Alonso
- Estación Biológica de Doñana, CSIC, Sevilla, Spain
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57
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Puy J, Dvořáková H, Carmona CP, de Bello F, Hiiesalu I, Latzel V. Improved demethylation in ecological epigenetic experiments: Testing a simple and harmless foliar demethylation application. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12903] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Javier Puy
- Department of BotanyFaculty of ScienceUniversity of South Bohemia České Budějovice Czech Republic
| | - Hana Dvořáková
- Department of BotanyFaculty of ScienceUniversity of South Bohemia České Budějovice Czech Republic
| | - Carlos P. Carmona
- Department of BotanyFaculty of ScienceUniversity of South Bohemia České Budějovice Czech Republic
- Institute of Ecology and Earth SciencesDepartment of BotanyUniversity of Tartu Tartu Estonia
| | - Francesco de Bello
- Department of BotanyFaculty of ScienceUniversity of South Bohemia České Budějovice Czech Republic
- Institute of BotanyCzech Academy of Science Třeboň Czech Republic
| | - Inga Hiiesalu
- Institute of Ecology and Earth SciencesDepartment of BotanyUniversity of Tartu Tartu Estonia
| | - Vít Latzel
- Institute of BotanyCzech Academy of Sciences Průhonice Czech Republic
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58
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Richards CL, Alonso C, Becker C, Bossdorf O, Bucher E, Colomé-Tatché M, Durka W, Engelhardt J, Gaspar B, Gogol-Döring A, Grosse I, van Gurp TP, Heer K, Kronholm I, Lampei C, Latzel V, Mirouze M, Opgenoorth L, Paun O, Prohaska SJ, Rensing SA, Stadler PF, Trucchi E, Ullrich K, Verhoeven KJF. Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. Ecol Lett 2017; 20:1576-1590. [PMID: 29027325 DOI: 10.1111/ele.12858] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/15/2017] [Accepted: 09/04/2017] [Indexed: 12/15/2022]
Abstract
Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute to a more mechanistic understanding but have limited ecological realism. Understanding the significance of epigenetics for plant ecology requires increased transfer of knowledge and methods from model species research to genomes of evolutionarily divergent species, and examination of responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration among molecular geneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.
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Affiliation(s)
- Christina L Richards
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | | | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology, 1030, Vienna, Austrian Academy of Sciences, Vienna Biocenter (VBC), Austria
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, University of Tübingen, 72076, Tübingen, Germany
| | - Etienne Bucher
- Institut de Recherche en Horticulture et Semences, 49071, Beaucouzé Cedex, France
| | - Maria Colomé-Tatché
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, 9713, Groningen, The Netherlands.,Institute of Computational Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,School of Life Sciences Weihenstephan, Technical University of Munich, 85354, Freising, Germany
| | - Walter Durka
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ, 06120, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Jan Engelhardt
- Institut für Informatik, University of Leipzig, 04107, Leipzig, Germany
| | - Bence Gaspar
- Plant Evolutionary Ecology, University of Tübingen, 72076, Tübingen, Germany
| | - Andreas Gogol-Döring
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.,Institute of Computer Science, University of Halle, 06120, Halle, Germany
| | - Ivo Grosse
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.,Institute of Computer Science, University of Halle, 06120, Halle, Germany
| | - Thomas P van Gurp
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Katrin Heer
- Conservation Biology, Philipps-University of Marburg, 35037, Marburg, Germany
| | - Ilkka Kronholm
- Department of Biological and Environmental Sciences, Center of Excellence in Biological Interactions, University of Jyväskylä, 40014, Jyväskylän yliopisto, Finland
| | - Christian Lampei
- Institute of Plant Breeding, Seed Science and Population Genetics, 70599, Stuttgart, Germany
| | - Vít Latzel
- Institute of Botany, The Czech Academy of Sciences, 25243, Průhonice, Czech Republic
| | - Marie Mirouze
- Institut de Recherche pour le Développement, Laboratoire Génome et Développement des Plantes, 66860, Perpignan, France
| | - Lars Opgenoorth
- Department of Ecology, Philipps-University Marburg, 35037, Marburg, Germany
| | - Ovidiu Paun
- Plant Ecological Genomics, University of Vienna, 1030, Vienna, Austria
| | - Sonja J Prohaska
- Institut für Informatik, University of Leipzig, 04107, Leipzig, Germany.,The Santa Fe Institute, Santa Fe NM, 87501, USA
| | - Stefan A Rensing
- Plant Cell Biology, Philipps-University Marburg, 35037, Marburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, 79098, Freiburg, Germany
| | - Peter F Stadler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany.,Institut für Informatik, University of Leipzig, 04107, Leipzig, Germany.,The Santa Fe Institute, Santa Fe NM, 87501, USA.,Max Planck Institute for Mathematics in the Sciences, 04103, Leipzig, Germany
| | - Emiliano Trucchi
- Plant Ecological Genomics, University of Vienna, 1030, Vienna, Austria
| | - Kristian Ullrich
- Plant Cell Biology, Philipps-University Marburg, 35037, Marburg, Germany
| | - Koen J F Verhoeven
- Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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59
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Assessing SNP genotyping of noninvasively collected wildlife samples using microfluidic arrays. Sci Rep 2017; 7:10768. [PMID: 28883428 PMCID: PMC5589735 DOI: 10.1038/s41598-017-10647-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/11/2017] [Indexed: 11/09/2022] Open
Abstract
Noninvasively collected samples are a common source of DNA in wildlife genetic studies. Currently, single nucleotide polymorphism (SNP) genotyping using microfluidic arrays is emerging as an easy-to-use and cost-effective methodology. Here we assessed the performance of microfluidic SNP arrays in genotyping noninvasive samples from grey wolves, European wildcats and brown bears, and we compared results with traditional microsatellite genotyping. We successfully SNP-genotyped 87%, 80% and 97% of the wolf, cat and bear samples, respectively. Genotype recovery was higher based on SNPs, while both marker types identified the same individuals and provided almost identical estimates of pairwise differentiation. We found that samples for which all SNP loci were scored had no disagreements across the three replicates (except one locus in a wolf sample). Thus, we argue that call rate (amplification success) can be used as a proxy for genotype quality, allowing the reduction of replication effort when call rate is high. Furthermore, we used cycle threshold values of real-time PCR to guide the choice of protocols for SNP amplification. Finally, we provide general guidelines for successful SNP genotyping of degraded DNA using microfluidic technology.
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60
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Riyahi S, Vilatersana R, Schrey AW, Ghorbani Node H, Aliabadian M, Senar JC. Natural epigenetic variation within and among six subspecies of the house sparrow, Passer domesticus. ACTA ACUST UNITED AC 2017; 220:4016-4023. [PMID: 28877923 DOI: 10.1242/jeb.169268] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 09/01/2017] [Indexed: 12/30/2022]
Abstract
Epigenetic modifications can respond rapidly to environmental changes and can shape phenotypic variation in accordance with environmental stimuli. One of the most studied epigenetic marks is DNA methylation. In the present study, we used the methylation-sensitive amplified polymorphism (MSAP) technique to investigate the natural variation in DNA methylation within and among subspecies of the house sparrow, Passer domesticus We focused on five subspecies from the Middle East because they show great variation in many ecological traits and because this region is the probable origin for the house sparrow's commensal relationship with humans. We analysed house sparrows from Spain as an outgroup. The level of variation in DNA methylation was similar among the five house sparrow subspecies from the Middle East despite high phenotypic and environmental variation, but the non-commensal subspecies was differentiated from the other four (commensal) Middle Eastern subspecies. Further, the European subspecies was differentiated from all other subspecies in DNA methylation. Our results indicate that variation in DNA methylation does not strictly follow subspecies designations. We detected a correlation between methylation level and some morphological traits, such as standardized bill length, and we suggest that part of the high morphological variation in the native populations of the house sparrow is influenced by differentially methylated regions in specific loci throughout the genome. We also detected 10 differentially methylated loci among subspecies and three loci that differentiated between commensal or non-commensal status. Therefore, the MSAP technique detected larger scale differences among the European and non-commensal subspecies, but did not detect finer scale differences among the other Middle Eastern subspecies.
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Affiliation(s)
- Sepand Riyahi
- Evolutionary and Behavioural Ecology Research Unit, Natural History Museum of Barcelona, Psg. Picasso s/n, 08003 Barcelona, Spain
| | - Roser Vilatersana
- Botanic Institute of Barcelona (IBB-CSIC-ICUB), Passeig de Migdia s/n, 08038 Barcelona, Spain
| | - Aaron W Schrey
- Department of Biology, Armstrong State University, Savannah, GA 31419, USA
| | - Hassan Ghorbani Node
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177 9489 74, Iran.,Research Department of Zoological Innovations, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177 9489 74, Iran
| | - Mansour Aliabadian
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177 9489 74, Iran.,Research Department of Zoological Innovations, Institute of Applied Zoology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad 9177 9489 74, Iran
| | - Juan Carlos Senar
- Evolutionary and Behavioural Ecology Research Unit, Natural History Museum of Barcelona, Psg. Picasso s/n, 08003 Barcelona, Spain
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61
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Hu J, Barrett RDH. Epigenetics in natural animal populations. J Evol Biol 2017; 30:1612-1632. [PMID: 28597938 DOI: 10.1111/jeb.13130] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 06/01/2017] [Accepted: 06/03/2017] [Indexed: 12/22/2022]
Abstract
Phenotypic plasticity is an important mechanism for populations to buffer themselves from environmental change. While it has long been appreciated that natural populations possess genetic variation in the extent of plasticity, a surge of recent evidence suggests that epigenetic variation could also play an important role in shaping phenotypic responses. Compared with genetic variation, epigenetic variation is more likely to have higher spontaneous rates of mutation and a more sensitive reaction to environmental inputs. In our review, we first provide an overview of recent studies on epigenetically encoded thermal plasticity in animals to illustrate environmentally-mediated epigenetic effects within and across generations. Second, we discuss the role of epigenetic effects during adaptation by exploring population epigenetics in natural animal populations. Finally, we evaluate the evolutionary potential of epigenetic variation depending on its autonomy from genetic variation and its transgenerational stability. Although many of the causal links between epigenetic variation and phenotypic plasticity remain elusive, new data has explored the role of epigenetic variation in facilitating evolution in natural populations. This recent progress in ecological epigenetics will be helpful for generating predictive models of the capacity of organisms to adapt to changing climates.
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Affiliation(s)
- J Hu
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
| | - R D H Barrett
- Redpath Museum and Department of Biology, McGill University, Montreal, QC, Canada
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62
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Robertson M, Schrey A, Shayter A, Moss CJ, Richards C. Genetic and epigenetic variation in Spartina alterniflora following the Deepwater Horizon oil spill. Evol Appl 2017; 10:792-801. [PMID: 29151871 PMCID: PMC5680422 DOI: 10.1111/eva.12482] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/13/2017] [Indexed: 12/13/2022] Open
Abstract
Catastrophic events offer unique opportunities to study rapid population response to stress in natural settings. In concert with genetic variation, epigenetic mechanisms may allow populations to persist through severe environmental challenges. In 2010, the Deepwater Horizon oil spill devastated large portions of the coastline along the Gulf of Mexico. However, the foundational salt marsh grass, Spartina alterniflora, showed high resilience to this strong environmental disturbance. Following the spill, we simultaneously examined the genetic and epigenetic structure of recovering populations of S. alterniflora to oil exposure. We quantified genetic and DNA methylation variation using amplified fragment length polymorphism and methylation sensitive fragment length polymorphism (MS‐AFLP) to test the hypothesis that response to oil exposure in S. alterniflora resulted in genetically and epigenetically based population differentiation. We found high genetic and epigenetic variation within and among sites and found significant genetic differentiation between contaminated and uncontaminated sites, which may reflect nonrandom mortality in response to oil exposure. Additionally, despite a lack of genomewide patterns in DNA methylation between contaminated and uncontaminated sites, we found five MS‐AFLP loci (12% of polymorphic MS‐AFLP loci) that were correlated with oil exposure. Overall, our findings support genetically based differentiation correlated with exposure to the oil spill in this system, but also suggest a potential role for epigenetic mechanisms in population differentiation.
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Affiliation(s)
- Marta Robertson
- Department of Integrative BiologyUniversity of South FloridaTampaFLUSA
| | - Aaron Schrey
- Department of BiologyArmstrong State UniversitySavannahGAUSA
| | - Ashley Shayter
- Rehabilitation InstituteSouthern Illinois UniversityCarbondaleILUSA
| | - Christina J Moss
- Department of Cell BiologyMicrobiology and Molecular BiologyUniversity of South FloridaTampaFLUSA
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63
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Inácio V, Barros PM, Costa A, Roussado C, Gonçalves E, Costa R, Graça J, Oliveira MM, Morais-Cecílio L. Differential DNA Methylation Patterns Are Related to Phellogen Origin and Quality of Quercus suber Cork. PLoS One 2017; 12:e0169018. [PMID: 28045988 PMCID: PMC5207400 DOI: 10.1371/journal.pone.0169018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/09/2016] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is thought to influence Quercus suber cork quality, which is the main constraint for its economic valorisation. However, a deep knowledge of the cytosine methylation patterns disclosing the epigenetic variability of trees with different cork quality types is totally missing. This study investigates the hypothesis that variations in DNA methylation contribute to differences in cork cellular characteristics directly related to original or traumatic phellogen activity. We used MSAPs (Methylation Sensitive Amplified Polymorphism) to assess DNA methylation patterns of cork and leaf tissues of Q. suber adult trees growing in three cork oak stands. The relationship between the detected polymorphisms and the diversity of cork quality traits was explored by a marker-trait analysis focusing on the most relevant quality characteristics. Populations differed widely in cork quality, but only slightly in degree of epigenetic differentiation. Four MSAP markers (1.3% of the total) were significantly associated with the most noteworthy quality traits: wood inclusions (nails) and porosity. This evidence supports the potential role of cytosine methylation in the modulation of differential phellogen activity either involved in localized cell death or in pore production, resulting in different cork qualities. Although, the underlying basis of the methylation polymorphism of loci affecting cork quality traits remain unclear, the disclosure of markers statistically associated with cork quality strengthens the potential role of DNA methylation in the regulation of these traits, namely at the phellogen level.
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Affiliation(s)
- Vera Inácio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Pedro M. Barros
- Genomics of Plant Stress Unit, ITQB NOVA—Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Augusta Costa
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Oeiras, Portugal
- Center for Environmental and Sustainability Research (CENSE), Environmental Sciences and Engineering Department, Faculty of Science and Technology, NOVA University of Lisbon, Caparica, Portugal
| | - Cristóvão Roussado
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Elsa Gonçalves
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Rita Costa
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Oeiras, Portugal
| | - José Graça
- Forest Research Center, Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - M. Margarida Oliveira
- Genomics of Plant Stress Unit, ITQB NOVA—Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- * E-mail: (LM-C); (MMO)
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
- * E-mail: (LM-C); (MMO)
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64
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Verhoeven KJF, vonHoldt BM, Sork VL. Epigenetics in ecology and evolution: what we know and what we need to know. Mol Ecol 2016; 25:1631-8. [DOI: 10.1111/mec.13617] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 03/11/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Koen J. F. Verhoeven
- Terrestrial Ecology Department; Netherlands Institute of Ecology (NIOO-KNAW); Droevendaalsesteeg 10 6708 PB Wageningen the Netherlands
| | | | - Victoria L. Sork
- Ecology & Evolutionary Biology; University of California; Los Angeles CA 90095 USA
- Institute of the Environment and Sustainability; University of California; Los Angeles CA 90095 USA
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65
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Mazzarella AB, Boessenkool S, Østbye K, Vøllestad LA, Trucchi E. Genomic signatures of the plateless phenotype in the threespine stickleback. Ecol Evol 2016; 6:3161-73. [PMID: 27096077 PMCID: PMC4829042 DOI: 10.1002/ece3.2072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/17/2016] [Accepted: 02/22/2016] [Indexed: 12/15/2022] Open
Abstract
Understanding the genetic basis of traits involved in adaptive divergence and speciation is one of the most fundamental objectives in evolutionary biology. Toward that end, we look for signatures of extreme plate loss in the genome of freshwater threespine sticklebacks (Gasterosteus aculeatus). Plateless stickleback have been found in only a few lakes and streams across the world; they represent the far extreme of a phenotypic continuum (plate number) that has been studied for years, although plateless individuals have not yet been the subject of much investigation. We use a dense single nucleotide polymorphism dataset made using RADseq to study fish from three freshwater populations containing plateless and low plated individuals, as well as fish from full plated marine populations. Analyses were performed using FastStructure, sliding windows FST, Bayescan and latent factor mixed models to search for genomic differences between the low plated and plateless phenotypes both within and among the three lakes. At least 18 genomic regions which may contribute to within‐morph plate number variation were detected in our low plated stickleback populations. We see no evidence of a selective sweep between low and plateless fish; rather reduction of plate number within the low plated morph seems to be polygenic.
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Affiliation(s)
- Anna B Mazzarella
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo PO Box 1066 Blindern Norway
| | - Sanne Boessenkool
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo PO Box 1066 Blindern Norway
| | - Kjartan Østbye
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo PO Box 1066 Blindern Norway; Faculty of Applied Ecology and Agricultural Sciences Hedmark University College Campus Evenstad No-2480 Koppang Norway
| | - Leif Asbjørn Vøllestad
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo PO Box 1066 Blindern Norway
| | - Emiliano Trucchi
- Department of Biosciences Centre for Ecological and Evolutionary Synthesis University of Oslo PO Box 1066 Blindern Norway; Department of Botany and Biodiversity Research University of Vienna Rennweg 14A-1030 Vienna Austria
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