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Helanterä H, Uller T. Different perspectives on non-genetic inheritance illustrate the versatile utility of the Price equation in evolutionary biology. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190366. [PMID: 32146886 DOI: 10.1098/rstb.2019.0366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The diversity of genetic and non-genetic processes that make offspring resemble their parents are increasingly well understood. In addition to genetic inheritance, parent-offspring similarity is affected by epigenetic, behavioural and cultural mechanisms that collectively can be referred to as non-genetic inheritance. Given the generality of the Price equation as a description of evolutionary change, is it not surprising that the Price equation has been adopted to model the evolutionary implications of non-genetic inheritance. In this paper, we briefly introduce the heredity perspectives on which those models rely, discuss the extent to which these perspectives make different assumptions and place different emphases on the roles of heredity and development in evolution, and the types of empirical research programmes they motivate. The existence of multiple perspectives and explanatory aims highlight, on the one hand, the versatility of the Price equation and, on the other hand, the importance of understanding how heredity and development can be conceptualized in evolutionary studies. This article is part of the theme issue 'Fifty years of the Price equation'.
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Affiliation(s)
- Heikki Helanterä
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, 90014 Oulu, Finland
| | - Tobias Uller
- Department of Biology, Lund University, Sölvegatan 37, 22362 Lund, Sweden
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2
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Sarkies P. Molecular mechanisms of epigenetic inheritance: Possible evolutionary implications. Semin Cell Dev Biol 2020; 97:106-115. [PMID: 31228598 PMCID: PMC6945114 DOI: 10.1016/j.semcdb.2019.06.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/04/2019] [Accepted: 06/18/2019] [Indexed: 12/30/2022]
Abstract
Recently interest in multi-generational epigenetic phenomena have been fuelled by highly reproducible intergenerational and transgenerational inheritance paradigms in several model organisms. Such paradigms are essential in order to begin to use genetics to unpick the mechanistic bases of how epigenetic information may be transmitted between generations; indeed great strides have been made towards understanding these mechanisms. Far less well understood is the relationship between epigenetic inheritance, ecology and evolution. In this review I focus on potential connections between laboratory studies of transgenerational epigenetic inheritance phenomena and evolutionary processes that occur in natural populations. In the first section, I consider whether transgenerational epigenetic inheritance might provide an advantage to organisms over the short term in adapting to their environment. Second, I consider whether epigenetic changes can contribute to the evolution of species by contributing to stable phenotypic variation within a population. Finally I discuss whether epigenetic changes could influence evolution by either directly or indirectly promoting DNA sequence changes that could impact phenotypic divergence. Additionally, I will discuss how epigenetic changes could influence the evolution of human cancer and thus be directly relevant for the development of this disease.
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Affiliation(s)
- Peter Sarkies
- MRC London Institute of Medical Sciences, Du Cane Road, London, W120NN, United Kingdom; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London, W120NN, United Kingdom.
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3
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Mothersill C, Abend M, Bréchignac F, Copplestone D, Geras'kin S, Goodman J, Horemans N, Jeggo P, McBride W, Mousseau TA, O'Hare A, Papineni RVL, Powathil G, Schofield PN, Seymour C, Sutcliffe J, Austin B. The tubercular badger and the uncertain curve:- The need for a multiple stressor approach in environmental radiation protection. ENVIRONMENTAL RESEARCH 2019; 168:130-140. [PMID: 30296640 DOI: 10.1016/j.envres.2018.09.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/23/2018] [Accepted: 09/24/2018] [Indexed: 06/08/2023]
Abstract
This article presents the results of a workshop held in Stirling, Scotland in June 2018, called to examine critically the effects of low-dose ionising radiation on the ecosphere. The meeting brought together participants from the fields of low- and high-dose radiobiology and those working in radioecology to discuss the effects that low doses of radiation have on non-human biota. In particular, the shape of the low-dose response relationship and the extent to which the effects of low-dose and chronic exposure may be predicted from high dose rate exposures were discussed. It was concluded that high dose effects were not predictive of low dose effects. It followed that the tools presently available were deemed insufficient to reliably predict risk of low dose exposures in ecosystems. The workshop participants agreed on three major recommendations for a path forward. First, as treating radiation as a single or unique stressor was considered insufficient, the development of a multidisciplinary approach is suggested to address key concerns about multiple stressors in the ecosphere. Second, agreed definitions are needed to deal with the multiplicity of factors determining outcome to low dose exposures as a term can have different meanings in different disciplines. Third, appropriate tools need to be developed to deal with the different time, space and organisation level scales. These recommendations permit a more accurate picture of prospective risks.
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Affiliation(s)
- Carmel Mothersill
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1.
| | - Michael Abend
- Bundeswehr Institute of Radiobiology, Neuherbergstrasse 11, 80937 Munich, Germany.
| | - Francois Bréchignac
- Institute for Radioprotection and Nuclear Safety (IRSN) & International Union of Radioecology, Centre du Cadarache, Bldg 229, St Paul-lez-Durance, France.
| | - David Copplestone
- Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK.
| | - Stanislav Geras'kin
- Russian Institute of Radiology & Agroecology, Kievskoe shosse, 109km, Obninsk 249020, Russia.
| | - Jessica Goodman
- Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK.
| | - Nele Horemans
- Belgian Nuclear Research Centre SCK CEN, Biosphere Impact Studies, Boeretang 200, B-2400 Mol, Belgium.
| | - Penny Jeggo
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK.
| | - William McBride
- University of California Los Angeles, David Geffen School of Medicine, Department of Radiation Oncology, 10833 Le Conte Avenue, Los Angeles, CA 90095, USA.
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
| | - Anthony O'Hare
- Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK.
| | - Rao V L Papineni
- Department of Surgery, University of Kansas Medical Center - KUMC (Adjunct), and PACT & Health, Branford, CT, USA.
| | - Gibin Powathil
- Department of Mathematics, College of Science, Swansea University, Singleton Park, Swansea, Wales SA2 8PP, UK.
| | - Paul N Schofield
- Dept of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
| | - Colin Seymour
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1.
| | - Jill Sutcliffe
- Low Level Radiation and Health Conference, Ingrams Farm Fittleworth Road, Wisborough Green RH14 0JA, West Sussex, UK.
| | - Brian Austin
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, Scotland, UK.
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Mothersill C, Abend M, Bréchignac F, Iliakis G, Impens N, Kadhim M, Møller AP, Oughton D, Powathil G, Saenen E, Seymour C, Sutcliffe J, Tang FR, Schofield PN. When a duck is not a duck; a new interdisciplinary synthesis for environmental radiation protection. ENVIRONMENTAL RESEARCH 2018; 162:318-324. [PMID: 29407763 DOI: 10.1016/j.envres.2018.01.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/18/2018] [Accepted: 01/19/2018] [Indexed: 06/07/2023]
Abstract
This consensus paper presents the results of a workshop held in Essen, Germany in September 2017, called to examine critically the current approach to radiological environmental protection. The meeting brought together participants from the field of low dose radiobiology and those working in radioecology. Both groups have a common aim of identifying radiation exposures and protecting populations and individuals from harmful effects of ionising radiation exposure, but rarely work closely together. A key question in radiobiology is to understand mechanisms triggered by low doses or dose rates, leading to adverse outcomes of individuals while in radioecology a key objective is to recognise when harm is occurring at the level of the ecosystem. The discussion provided a total of six strategic recommendations which would help to address these questions.
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Affiliation(s)
- Carmel Mothersill
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1.
| | - Michael Abend
- Bundeswehr Institute of Radiobiology, Neuherbergstr. 11, 80937 Munich, Germany.
| | - François Bréchignac
- Institute for Radioprotection and Nuclear Safety (IRSN) & International Union of Radioecology (IUR), Centre du Cadarache, Bldg 229, St Paul-lez-Durance, France.
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen, Medical School, Hufeland Str. 55, 45122 Essen, Germany.
| | - Nathalie Impens
- Institute of Environment, Health and Safety, Biosphere Impact Studies, SCK•CEN, Boeretang 200, 2400 Mol, Belgium.
| | - Munira Kadhim
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
| | - Anders Pape Møller
- Ecologie Systématique Evolution, Equipe Diversité, Ecologie et Evolution Microbiennes Université Paris-Sud, CNRS, and AgroParisTech, Université Paris-Saclay, F-91405 Orsay Cedex, France.
| | - Deborah Oughton
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Campus Ås, Universitetstunet 3, 1432 Ås, Norway.
| | - Gibin Powathil
- Department of Mathematics, College of Science, Swansea University, Singleton Park, Swansea Wales SA2 8PP, UK.
| | - Eline Saenen
- Institute of Environment, Health and Safety, Biosphere Impact Studies, SCK•CEN, Boeretang 200, 2400 Mol, Belgium.
| | - Colin Seymour
- Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1.
| | - Jill Sutcliffe
- Low Level Radiation and Health Group, Ingrams Farm Fittleworth Road, Wisborough Green RH14 0JA, West Sussex, UK.
| | - Fen-Ru Tang
- National University of Singapore, Radiobiology Research Laboratory, Singapore Nuclear, Research and Safety Initiative, Singapore.
| | - Paul N Schofield
- Dept of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
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Villota-Salazar NA, Mendoza-Mendoza A, González-Prieto JM. Epigenetics: from the past to the present. FRONTIERS IN LIFE SCIENCE 2016. [DOI: 10.1080/21553769.2016.1249033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Affiliation(s)
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), F-75005 Paris, France;
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8
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Sharma A. Transgenerational epigenetic inheritance: resolving uncertainty and evolving biology. Biomol Concepts 2016; 6:87-103. [PMID: 25898397 DOI: 10.1515/bmc-2015-0005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/04/2015] [Indexed: 12/21/2022] Open
Abstract
Transgenerational epigenetic inheritance in animals has increasingly been reported in recent years. Controversies, however, surround this unconventional mode of heredity, especially in mammals, for several reasons. First, its existence itself has been questioned due to perceived insufficiency of available evidence. Second, it potentially implies transfer of hereditary information from soma to germline, against the established principle in biology. Third, it inherently requires survival of epigenetic memory across reprogramming, posing another fundamental challenge in biology. Fourth, evolutionary significance of epigenetic inheritance has also been under debate. This article pointwise addresses all these concerns on the basis of recent empirical, theoretical and conceptual advances. 1) Described here in detail are the key experimental findings demonstrating the occurrence of germline epigenetic inheritance in mammals. 2) Newly emerging evidence supporting soma to germline communication in transgenerational inheritance in mammals, and a role of exosome and extracellular microRNA in this transmission, is thoroughly discussed. 3) The plausibility of epigenetic information propagation across reprogramming is highlighted. 4) Analyses supporting evolutionary significance of epigenetic inheritance are briefly mentioned. Finally, an integrative model of 'evolutionary transgenerational systems biology' is proposed to provide a framework to guide future advancements in epigenetic inheritance.
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O’Dea RE, Noble DWA, Johnson SL, Hesselson D, Nakagawa S. The role of non-genetic inheritance in evolutionary rescue: epigenetic buffering, heritable bet hedging and epigenetic traps. ENVIRONMENTAL EPIGENETICS 2016; 2:dvv014. [PMID: 29492283 PMCID: PMC5804513 DOI: 10.1093/eep/dvv014] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 11/30/2015] [Accepted: 12/09/2015] [Indexed: 05/17/2023]
Abstract
Rapid environmental change is predicted to compromise population survival, and the resulting strong selective pressure can erode genetic variation, making evolutionary rescue unlikely. Non-genetic inheritance may provide a solution to this problem and help explain the current lack of fit between purely genetic evolutionary models and empirical data. We hypothesize that epigenetic modifications can facilitate evolutionary rescue through 'epigenetic buffering'. By facilitating the inheritance of novel phenotypic variants that are generated by environmental change-a strategy we call 'heritable bet hedging'-epigenetic modifications could maintain and increase the evolutionary potential of a population. This process may facilitate genetic adaptation by preserving existing genetic variation, releasing cryptic genetic variation and/or facilitating mutations in functional loci. Although we show that examples of non-genetic inheritance are often maladaptive in the short term, accounting for phenotypic variance and non-adaptive plasticity may reveal important evolutionary implications over longer time scales. We also discuss the possibility that maladaptive epigenetic responses may be due to 'epigenetic traps', whereby evolutionarily novel factors (e.g. endocrine disruptors) hack into the existing epigenetic machinery. We stress that more ecologically relevant work on transgenerational epigenetic inheritance is required. Researchers conducting studies on transgenerational environmental effects should report measures of phenotypic variance, so that the possibility of both bet hedging and heritable bet hedging can be assessed. Future empirical and theoretical work is required to assess the relative importance of genetic and epigenetic variation, and their interaction, for evolutionary rescue.
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Affiliation(s)
- Rose E. O’Dea
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel W. A. Noble
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sheri L. Johnson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Daniel Hesselson
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, UNSW, Australia, Sydney, NSW, Australia
| | - Shinichi Nakagawa
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
- Department of Zoology, University of Otago, Dunedin, New Zealand
- Diabetes and Metabolism Division, Garvan Institute of Medical Research, Sydney, NSW, Australia
- *Correspondence address. School of BEES, UNSW, Sydney, NSW 2052, Australia, Tel:
+61-2-9385-8084
; Fax:
+61-2-9385-9138
; E-mail:
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Springer NM, McGinnis KM. Paramutation in evolution, population genetics and breeding. Semin Cell Dev Biol 2015; 44:33-8. [PMID: 26325077 DOI: 10.1016/j.semcdb.2015.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 08/18/2015] [Indexed: 11/19/2022]
Abstract
Paramutation is a fascinating phenomenon in which directed allelic interactions result in heritable changes in the state of an allele. Paramutation has been carefully characterized at a handful of loci but the prevalence of paramutable/paramutagenic alleles is not well characterized within genomes or populations. In order to consider the role of paramutation in evolutionary processes and plant breeding, we focused on several questions. First, what causes certain alleles to become subject to paramutation? While paramutation clearly involves epigenetic regulation it is also true that only certain alleles defined by genetic sequences are able to participate in paramutation. Second, what is the prevalence of paramutation? There are only a handful of well-documented examples of paramutation. However, there is growing evidence that many loci may undergo changes in chromatin state or expression that are similar to changes observed as a result of paramutation. Third, how will paramutation events be inherited in natural or artificial populations? Many factors, including stability of epigenetic state, mating style and ploidy, may influence the prevalence of paramutation states within populations. Developing a clear understanding of the mechanisms and frequency of paramutation in crop plant genomes will facilitate new opportunities in genetic manipulation, and will also enhance plant breeding programs and our understanding of genome evolution.
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Affiliation(s)
- Nathan M Springer
- Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.
| | - Karen M McGinnis
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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Pilu R. Paramutation phenomena in plants. Semin Cell Dev Biol 2015; 44:2-10. [DOI: 10.1016/j.semcdb.2015.08.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 08/26/2015] [Indexed: 02/05/2023]
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English S, Pen I, Shea N, Uller T. The information value of non-genetic inheritance in plants and animals. PLoS One 2015; 10:e0116996. [PMID: 25603120 PMCID: PMC4300080 DOI: 10.1371/journal.pone.0116996] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 12/18/2014] [Indexed: 11/18/2022] Open
Abstract
Parents influence the development of their offspring in many ways beyond the transmission of DNA. This includes transfer of epigenetic states, nutrients, antibodies and hormones, and behavioural interactions after birth. While the evolutionary consequences of such non-genetic inheritance are increasingly well understood, less is known about how inheritance mechanisms evolve. Here, we present a simple but versatile model to explore the adaptive evolution of non-genetic inheritance. Our model is based on a switch mechanism that produces alternative phenotypes in response to different inputs, including genes and non-genetic factors transmitted from parents and the environment experienced during development. This framework shows how genetic and non-genetic inheritance mechanisms and environmental conditions can act as cues by carrying correlational information about future selective conditions. Differential use of these cues is manifested as different degrees of genetic, parental or environmental morph determination. We use this framework to evaluate the conditions favouring non-genetic inheritance, as opposed to genetic determination of phenotype or within-generation plasticity, by applying it to two putative examples of adaptive non-genetic inheritance: maternal effects on seed germination in plants and transgenerational phase shift in desert locusts. Our simulation models show how the adaptive value of non-genetic inheritance depends on its mechanism, the pace of environmental change, and life history characteristics.
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Affiliation(s)
- Sinead English
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Ido Pen
- Theoretical Biology Group, Centre for Ecological and Evolutionary Studies, University of Groningen, Groningen, The Netherlands
| | - Nicholas Shea
- Department of Philosophy, King’s College London, London, United Kingdom
| | - Tobias Uller
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Biology, Lund University, Lund, Sweden
- * E-mail:
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Skinner MK, Gurerrero-Bosagna C, Haque MM, Nilsson EE, Koop JAH, Knutie SA, Clayton DH. Epigenetics and the evolution of Darwin's Finches. Genome Biol Evol 2014; 6:1972-89. [PMID: 25062919 PMCID: PMC4159007 DOI: 10.1093/gbe/evu158] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The prevailing theory for the molecular basis of evolution involves genetic mutations that ultimately generate the heritable phenotypic variation on which natural selection acts. However, epigenetic transgenerational inheritance of phenotypic variation may also play an important role in evolutionary change. A growing number of studies have demonstrated the presence of epigenetic inheritance in a variety of different organisms that can persist for hundreds of generations. The possibility that epigenetic changes can accumulate over longer periods of evolutionary time has seldom been tested empirically. This study was designed to compare epigenetic changes among several closely related species of Darwin's finches, a well-known example of adaptive radiation. Erythrocyte DNA was obtained from five species of sympatric Darwin's finches that vary in phylogenetic relatedness. Genome-wide alterations in genetic mutations using copy number variation (CNV) were compared with epigenetic alterations associated with differential DNA methylation regions (epimutations). Epimutations were more common than genetic CNV mutations among the five species; furthermore, the number of epimutations increased monotonically with phylogenetic distance. Interestingly, the number of genetic CNV mutations did not consistently increase with phylogenetic distance. The number, chromosomal locations, regional clustering, and lack of overlap of epimutations and genetic mutations suggest that epigenetic changes are distinct and that they correlate with the evolutionary history of Darwin's finches. The potential functional significance of the epimutations was explored by comparing their locations on the genome to the location of evolutionarily important genes and cellular pathways in birds. Specific epimutations were associated with genes related to the bone morphogenic protein, toll receptor, and melanogenesis signaling pathways. Species-specific epimutations were significantly overrepresented in these pathways. As environmental factors are known to result in heritable changes in the epigenome, it is possible that epigenetic changes contribute to the molecular basis of the evolution of Darwin's finches.
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Affiliation(s)
- Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University
| | - Carlos Gurerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State UniversityPresent address: Department of Physics, Biology and Chemistry (IFM), Linköping University, Sweden
| | - M Muksitul Haque
- Center for Reproductive Biology, School of Biological Sciences, Washington State University
| | - Eric E Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University
| | - Jennifer A H Koop
- Department of Biology, University of UtahPresent address: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ
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