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Venney CJ, Anastasiadi D, Wellenreuther M, Bernatchez L. The Evolutionary Complexities of DNA Methylation in Animals: From Plasticity to Genetic Evolution. Genome Biol Evol 2023; 15:evad216. [PMID: 38015807 PMCID: PMC10701099 DOI: 10.1093/gbe/evad216] [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: 08/21/2023] [Revised: 10/22/2023] [Accepted: 11/22/2023] [Indexed: 11/30/2023] Open
Abstract
The importance of DNA methylation in plastic responses to environmental change and evolutionary dynamics is increasingly recognized. Here, we provide a Perspective piece on the diverse roles of DNA methylation on broad evolutionary timescales, including (i) short-term transient acclimation, (ii) stable phenotypic evolution, and (iii) genomic evolution. We show that epigenetic responses vary along a continuum, ranging from short-term acclimatory responses in variable environments within a generation to long-term modifications in populations and species. DNA methylation thus unlocks additional potential for organisms to rapidly acclimate to their environment over short timeframes. If these changes affect fitness, they can circumvent the need for adaptive changes at the genome level. However, methylation has a complex reciprocal relationship with genetic variation as it can be genetically controlled, yet it can also induce point mutations and contribute to genomic evolution. When habitats remain constant over many generations, or populations are separated across habitats, initially plastic phenotypes can become hardwired through epigenetically facilitated mutagenesis. It remains unclear under what circumstances plasticity contributes to evolutionary outcomes, and when plastic changes will become permanently encoded into genotype. We highlight how studies investigating the evolution of epigenetic plasticity need to carefully consider how plasticity in methylation state could evolve among different evolutionary scenarios, the possible phenotypic outcomes, its effects on genomic evolution, and the proximate energetic and ultimate fitness costs of methylation. We argue that accumulating evidence suggests that DNA methylation can contribute toward evolution on various timescales, spanning a continuum from acclimatory plasticity to genomic evolution.
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Affiliation(s)
- Clare J Venney
- Institut de Biologie Intégrative des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, QC, Canada
| | - Dafni Anastasiadi
- The New Zealand Institute for Plant and Food Research Ltd, Nelson Research Centre, Nelson, New Zealand
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd, Nelson Research Centre, Nelson, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Louis Bernatchez
- Institut de Biologie Intégrative des Systèmes (IBIS), Département de Biologie, Université Laval, Québec, QC, Canada
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2
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The regulation mechanisms and the Lamarckian inheritance property of DNA methylation in animals. Mamm Genome 2021; 32:135-152. [PMID: 33860357 DOI: 10.1007/s00335-021-09870-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/05/2021] [Indexed: 12/19/2022]
Abstract
DNA methylation is a stable and heritable epigenetic mechanism, of which the main functions are stabilizing the transcription of genes and promoting genetic conservation. In animals, the direct molecular inducers of DNA methylation mainly include histone covalent modification and non-coding RNA, whereas the fundamental regulators of DNA methylation are genetic and environmental factors. As is well known, competition is present everywhere in life systems, and will finally strike a balance that is optimal for the animal's survival and reproduction. The same goes for the regulation of DNA methylation. Genetic and environmental factors, respectively, are responsible for the programmed and plasticity changes of DNA methylation, and keen competition exists between genetically influenced procedural remodeling and environmentally influenced plastic alteration. In this process, genetic and environmental factors collaboratively decide the methylation patterns of corresponding loci. DNA methylation alterations induced by environmental factors can be transgenerationally inherited, and exhibit the characteristic of Lamarckian inheritance. Further research on regulatory mechanisms and the environmental plasticity of DNA methylation will provide strong support for understanding the biological function and evolutionary effects of DNA methylation.
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Anderson JA, Johnston RA, Lea AJ, Campos FA, Voyles TN, Akinyi MY, Alberts SC, Archie EA, Tung J. High social status males experience accelerated epigenetic aging in wild baboons. eLife 2021; 10:e66128. [PMID: 33821798 PMCID: PMC8087445 DOI: 10.7554/elife.66128] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/18/2021] [Indexed: 12/14/2022] Open
Abstract
Aging, for virtually all life, is inescapable. However, within populations, biological aging rates vary. Understanding sources of variation in this process is central to understanding the biodemography of natural populations. We constructed a DNA methylation-based age predictor for an intensively studied wild baboon population in Kenya. Consistent with findings in humans, the resulting 'epigenetic clock' closely tracks chronological age, but individuals are predicted to be somewhat older or younger than their known ages. Surprisingly, these deviations are not explained by the strongest predictors of lifespan in this population, early adversity and social integration. Instead, they are best predicted by male dominance rank: high-ranking males are predicted to be older than their true ages, and epigenetic age tracks changes in rank over time. Our results argue that achieving high rank for male baboons - the best predictor of reproductive success - imposes costs consistent with a 'live fast, die young' life-history strategy.
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Affiliation(s)
- Jordan A Anderson
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | - Rachel A Johnston
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | - Amanda J Lea
- Department of Biology, Duke UniversityDurhamUnited States
- Lewis-Sigler Institute for Integrative Genomics, Carl Icahn Laboratory, Princeton UniversityPrincetonUnited States
- Department of Ecology and Evolution, Princeton UniversityPrincetonUnited States
| | - Fernando A Campos
- Department of Biology, Duke UniversityDurhamUnited States
- Department of Anthropology, University of Texas at San AntonioSan AntonioUnited States
| | - Tawni N Voyles
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | - Mercy Y Akinyi
- Institute of Primate Research, National Museums of KenyaNairobiKenya
| | - Susan C Alberts
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Department of Biology, Duke UniversityDurhamUnited States
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Department of Biology, Duke UniversityDurhamUnited States
- Duke Population Research Institute, Duke UniversityDurhamUnited States
- Canadian Institute for Advanced ResearchTorontoCanada
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Housman G, Gilad Y. Prime time for primate functional genomics. Curr Opin Genet Dev 2020; 62:1-7. [PMID: 32544775 DOI: 10.1016/j.gde.2020.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/14/2022]
Abstract
Functional genomics research is continually improving our understanding of genotype-phenotype relationships in humans, and comparative genomics perspectives can provide additional insight into the evolutionary histories of such relationships. To specifically identify conservation or species-specific divergence in humans, we must look to our closest extant evolutionary relatives. Primate functional genomics research has been steadily advancing and expanding, in spite of several limitations and challenges that this field faces. New technologies and cheaper sequencing provide a unique opportunity to enhance and expand primate comparative studies, and we outline possible paths going forward. The potential human-specific insights that can be gained from primate functional genomics research are substantial, and we propose that now is a prime time to expand such endeavors.
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Affiliation(s)
- Genevieve Housman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, 5841 S. Maryland Ave., N417, MC6091, Chicago, IL 60637 USA.
| | - Yoav Gilad
- Section of Genetic Medicine, Department of Medicine, University of Chicago, 5841 S. Maryland Ave., N417, MC6091, Chicago, IL 60637 USA; Department of Human Genetics, University of Chicago, Cummings Life Science Center, 928 E. 58th St., Chicago, IL 60637 USA
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Anderson JA, Vilgalys TP, Tung J. Broadening primate genomics: new insights into the ecology and evolution of primate gene regulation. Curr Opin Genet Dev 2020; 62:16-22. [PMID: 32569794 PMCID: PMC7483836 DOI: 10.1016/j.gde.2020.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/17/2022]
Abstract
Comparative analyses have played a key role in understanding how gene regulatory evolution contributes to primate phenotypic diversity. Recently, these studies have expanded to include a wider range of species, within-population as well as interspecific analyses, and research on wild as well as captive individuals. This expansion provides context for understanding genetic and environmental effects on gene regulation in humans, including the importance of the pathogen and social environments. Although taxonomic representation remains biased, inclusion of more species has also begun to reveal the evolutionary processes that explain whether and when gene regulation is conserved. Together, this work highlights how studies in other primates contribute to understanding evolution in our own lineage, and we conclude by identifying promising avenues for future work.
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Affiliation(s)
- Jordan A Anderson
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Tauras P Vilgalys
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA; Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA; Department of Biology, Duke University, Durham, NC 27708, USA; Institute of Primate Research, National Museums of Kenya, Nairobi 00502, Kenya; Duke Population Research Institute, Duke University, Durham, NC 27708, USA.
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Housman G, Quillen EE, Stone AC. Intraspecific and interspecific investigations of skeletal DNA methylation and femur morphology in primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:34-49. [PMID: 32170728 DOI: 10.1002/ajpa.24041] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Epigenetic mechanisms influence the development and maintenance of complex phenotypes and may also contribute to the evolution of species-specific phenotypes. With respect to skeletal traits, little is known about the gene regulation underlying these hard tissues or how tissue-specific patterns are associated with bone morphology or vary among species. To begin exploring these topics, this study evaluates one epigenetic mechanism, DNA methylation, in skeletal tissues from five nonhuman primate species which display anatomical and locomotor differences representative of their phylogenetic groups. MATERIALS AND METHODS First, we test whether intraspecific variation in skeletal DNA methylation is associated with intraspecific variation in femur morphology. Second, we identify interspecific differences in DNA methylation and assess whether these lineage-specific patterns may have contributed to species-specific morphologies. Specifically, we use the Illumina Infinium MethylationEPIC BeadChip to identify DNA methylation patterns in femur trabecular bone from baboons (n = 28), macaques (n = 10), vervets (n = 10), chimpanzees (n = 4), and marmosets (n = 6). RESULTS Significant differentially methylated positions (DMPs) were associated with a subset of morphological variants, but these likely have small biological effects and may be confounded by other variables associated with morphological variation. Conversely, several species-specific DMPs were identified, and these are found in genes enriched for functions associated with complex skeletal traits. DISCUSSION Overall, these findings reveal that while intraspecific epigenetic variation is not readily associated with skeletal morphology differences, some interspecific epigenetic differences in skeletal tissues exist and may contribute to evolutionarily distinct phenotypes. This work forms a foundation for future explorations of gene regulation and skeletal trait evolution in primates.
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Affiliation(s)
- Genevieve Housman
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - Ellen E Quillen
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
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7
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Fischer J, Higham JP, Alberts SC, Barrett L, Beehner JC, Bergman TJ, Carter AJ, Collins A, Elton S, Fagot J, Ferreira da Silva MJ, Hammerschmidt K, Henzi P, Jolly CJ, Knauf S, Kopp GH, Rogers J, Roos C, Ross C, Seyfarth RM, Silk J, Snyder-Mackler N, Staedele V, Swedell L, Wilson ML, Zinner D. Insights into the evolution of social systems and species from baboon studies. eLife 2019; 8:e50989. [PMID: 31711570 PMCID: PMC6850771 DOI: 10.7554/elife.50989] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/16/2019] [Indexed: 01/03/2023] Open
Abstract
Baboons, members of the genus Papio, comprise six closely related species distributed throughout sub-Saharan Africa and southwest Arabia. The species exhibit more ecological flexibility and a wider range of social systems than many other primates. This article summarizes our current knowledge of the natural history of baboons and highlights directions for future research. We suggest that baboons can serve as a valuable model for complex evolutionary processes, such as speciation and hybridization. The evolution of baboons has been heavily shaped by climatic changes and population expansion and fragmentation in the African savanna environment, similar to the processes that acted during human evolution. With accumulating long-term data, and new data from previously understudied species, baboons are ideally suited for investigating the links between sociality, health, longevity and reproductive success. To achieve these aims, we propose a closer integration of studies at the proximate level, including functional genomics, with behavioral and ecological studies.
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Affiliation(s)
- Julia Fischer
- Cognitive Ethology LaboratoryGerman Primate Center, Leibniz-Institute for Primate ResearchGöttingenGermany
- Department of Primate CognitionGeorg-August-University of GöttingenGöttingenGermany
- Leibniz ScienceCampus for Primate CognitionGöttingenGermany
| | - James P Higham
- Department of AnthropologyNew York UniversityNew YorkUnited States
| | - Susan C Alberts
- Department of BiologyDuke UniversityDurhamUnited States
- Department of Evolutionary AnthropologyDuke UniversityDurhamUnited States
- Institute of Primate ResearchNairobiKenya
| | - Louise Barrett
- Department of PsychologyUniversity of LethbridgeLethbridgeCanada
- Applied Behavioural Ecology and Ecosystems Research UnitUniversity of South AfricaPretoriaSouth Africa
| | - Jacinta C Beehner
- Department of PsychologyUniversity of MichiganAnn ArborUnited States
- Department of AnthropologyUniversity of MichiganAnn ArborUnited States
| | - Thore J Bergman
- Department of PsychologyUniversity of MichiganAnn ArborUnited States
- Department of AnthropologyUniversity of MichiganAnn ArborUnited States
| | - Alecia J Carter
- Institut des Sciences de l’Evolution de MontpellierMontpellierFrance
- Université de Montpellier, CNRS, IRD, EPHEMontpellierFrance
| | - Anthony Collins
- Gombe Stream Research CentreJane Goodall InstituteKigomaUnited Republic of Tanzania
| | - Sarah Elton
- Department of AnthropologyDurham UniversityDurhamUnited Kingdom
| | - Joël Fagot
- Aix Marseille UniversitéMarseilleFrance
- Centre National de la Recherche ScientifiqueMontpellierFrance
| | - Maria Joana Ferreira da Silva
- Organisms and Environment Division, School of BiosciencesCardiff UniversityCardiffUnited Kingdom
- Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoPortoPortugal
- Centro de Administração e Políticas Públicas, School of Social and PoliticalSciencesUniversity of LisbonLisbonPortugal
| | - Kurt Hammerschmidt
- Cognitive Ethology LaboratoryGerman Primate Center, Leibniz-Institute for Primate ResearchGöttingenGermany
| | - Peter Henzi
- Applied Behavioural Ecology and Ecosystems Research UnitUniversity of South AfricaPretoriaSouth Africa
| | - Clifford J Jolly
- Department of AnthropologyNew York UniversityNew YorkUnited States
- New York Consortium in Evolutionary PrimatologyNew YorkUnited States
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Infection Biology UnitGerman Primate Center, Leibniz-Institute for Primate ResearchGöttingenGermany
- Division of Microbiology and Animal HygieneGeorg-August-UniversityGöttingenGermany
| | - Gisela H Kopp
- ZukunftskollegUniversity of KonstanzKonstanzGermany
- Department of BiologyUniversity of KonstanzKonstanzGermany
- Centre for the Advanced Study of Collective BehaviourUniversity of KonstanzKonstanzGermany
- Department of MigrationMax Planck Institute for Animal BehaviourKonstanzGermany
| | - Jeffrey Rogers
- Human Genome Sequencing CenterHoustonUnited States
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - Christian Roos
- Gene Bank of PrimatesGerman Primate Center, Leibniz-Institute for Primate ResearchGöttingenGermany
- Primate Genetics LaboratoryGerman Primate Center, Leibniz-Institute for Primate ResearchGöttingenGermany
| | - Caroline Ross
- Department of Life SciencesRoehampton UniversityLondonUnited Kingdom
| | - Robert M Seyfarth
- Department of PsychologyUniversity of PennsylvaniaPhiladelphiaUnited States
| | - Joan Silk
- School of Human Evolution and Social ChangeArizona State UniversityTempeUnited States
- Institute for Human OriginsArizona State UniversityTempeUnited States
| | - Noah Snyder-Mackler
- Department of PsychologyUniversity of WashingtonSeattleUnited States
- Center for Studies in Demography and EcologyUniversity of WashingtonSeattleUnited States
- National Primate Research CenteUniversity of WashingtonSeattleUnited States
| | - Veronika Staedele
- Department of BiologyDuke UniversityDurhamUnited States
- Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Larissa Swedell
- New York Consortium in Evolutionary PrimatologyNew YorkUnited States
- Department of AnthropologyQueens College, City University of New YorkNew YorkUnited States
- Department of ArchaeologyUniversity of Cape TownCape TownSouth Africa
| | - Michael L Wilson
- Department of AnthropologyUniversity of MinnesotaMinneapolisUnited States
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaMinneapolisUnited States
- Institute on the EnvironmentUniversity of MinnesotaSaint PaulUnited States
| | - Dietmar Zinner
- Cognitive Ethology LaboratoryGerman Primate Center, Leibniz-Institute for Primate ResearchGöttingenGermany
- Leibniz ScienceCampus for Primate CognitionGöttingenGermany
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