1
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Taff CC, McNew SM, Campagna L, Vitousek MN. Corticosterone exposure is associated with long-term changes in DNA methylation, physiology and breeding decisions in a wild bird. Mol Ecol 2024; 33:e17456. [PMID: 38953311 DOI: 10.1111/mec.17456] [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: 07/31/2023] [Revised: 06/07/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
When facing challenges, vertebrates activate a hormonal stress response that can dramatically alter behaviour and physiology. Although this response can be costly, conceptual models suggest that it can also recalibrate the stress response system, priming more effective responses to future challenges. Little is known about whether this process occurs in wild animals, particularly in adulthood, and if so, how information about prior experience with stressors is encoded. One potential mechanism is hormonally mediated changes in DNA methylation. We simulated the spikes in corticosterone that accompany a stress response using non-invasive dosing in tree swallows (Tachycineta bicolor) and monitored the phenotypic effects 1 year later. In a subset of individuals, we characterized DNA methylation using reduced representation bisulfite sequencing shortly after treatment and a year later. The year after treatment, experimental females had stronger negative feedback and initiated breeding earlier-traits that are associated with stress resilience and reproductive performance in our population-and higher baseline corticosterone. We also found that natural variation in corticosterone predicted patterns of DNA methylation. Finally, corticosterone treatment influenced methylation on short (1-2 weeks) and long (1 year) time scales; however, these changes did not have clear links to functional regulation of the stress response. Taken together, our results are consistent with corticosterone-induced priming of future stress resilience and support DNA methylation as a potential mechanism, but more work is needed to demonstrate functional consequences. Uncovering the mechanisms linking experience with the response to future challenges has implications for understanding the drivers of stress resilience.
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Affiliation(s)
- Conor C Taff
- Department of Ecology & Evolutionary Biology and Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
- Department of Biology, Colby College, Waterville, Maine, USA
| | - Sabrina M McNew
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Leonardo Campagna
- Department of Ecology & Evolutionary Biology and Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
| | - Maren N Vitousek
- Department of Ecology & Evolutionary Biology and Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
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2
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Vullioud C, Benhaiem S, Meneghini D, Szyf M, Shao Y, Hofer H, East ML, Fickel J, Weyrich A. Epigenetic signatures of social status in wild female spotted hyenas (Crocuta crocuta). Commun Biol 2024; 7:313. [PMID: 38548860 PMCID: PMC10978994 DOI: 10.1038/s42003-024-05926-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 02/16/2024] [Indexed: 04/01/2024] Open
Abstract
In mammalian societies, dominance hierarchies translate into inequalities in health, reproductive performance and survival. DNA methylation is thought to mediate the effects of social status on gene expression and phenotypic outcomes, yet a study of social status-specific DNA methylation profiles in different age classes in a wild social mammal is missing. We tested for social status signatures in DNA methylation profiles in wild female spotted hyenas (Crocuta crocuta), cubs and adults, using non-invasively collected gut epithelium samples. In spotted hyena clans, female social status influences access to resources, foraging behavior, health, reproductive performance and survival. We identified 149 differentially methylated regions between 42 high- and low-ranking female spotted hyenas (cubs and adults). Differentially methylated genes were associated with energy conversion, immune function, glutamate receptor signalling and ion transport. Our results provide evidence that socio-environmental inequalities are reflected at the molecular level in cubs and adults in a wild social mammal.
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Affiliation(s)
- Colin Vullioud
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Sarah Benhaiem
- Department of Ecological Dynamics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Dorina Meneghini
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | | | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Heribert Hofer
- Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Marion L East
- Department of Ecological Dynamics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Jörns Fickel
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- University of Potsdam, Potsdam, Germany
| | - Alexandra Weyrich
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
- Universität Leipzig, Leipzig, Germany.
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3
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Anderson JA, Lin D, Lea AJ, Johnston RA, Voyles T, Akinyi MY, Archie EA, Alberts SC, Tung J. DNA methylation signatures of early-life adversity are exposure-dependent in wild baboons. Proc Natl Acad Sci U S A 2024; 121:e2309469121. [PMID: 38442181 PMCID: PMC10945818 DOI: 10.1073/pnas.2309469121] [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: 06/06/2023] [Accepted: 12/13/2023] [Indexed: 03/07/2024] Open
Abstract
The early-life environment can profoundly shape the trajectory of an animal's life, even years or decades later. One mechanism proposed to contribute to these early-life effects is DNA methylation. However, the frequency and functional importance of DNA methylation in shaping early-life effects on adult outcomes is poorly understood, especially in natural populations. Here, we integrate prospectively collected data on fitness-associated variation in the early environment with DNA methylation estimates at 477,270 CpG sites in 256 wild baboons. We find highly heterogeneous relationships between the early-life environment and DNA methylation in adulthood: aspects of the environment linked to resource limitation (e.g., low-quality habitat, early-life drought) are associated with many more CpG sites than other types of environmental stressors (e.g., low maternal social status). Sites associated with early resource limitation are enriched in gene bodies and putative enhancers, suggesting they are functionally relevant. Indeed, by deploying a baboon-specific, massively parallel reporter assay, we show that a subset of windows containing these sites are capable of regulatory activity, and that, for 88% of early drought-associated sites in these regulatory windows, enhancer activity is DNA methylation-dependent. Together, our results support the idea that DNA methylation patterns contain a persistent signature of the early-life environment. However, they also indicate that not all environmental exposures leave an equivalent mark and suggest that socioenvironmental variation at the time of sampling is more likely to be functionally important. Thus, multiple mechanisms must converge to explain early-life effects on fitness-related traits.
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Affiliation(s)
- Jordan A. Anderson
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
| | - Dana Lin
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
| | - Amanda J. Lea
- Canadian Institute for Advanced Research, Child & Brain Development Program, Toronto, ONM5G 1M1, Canada
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37235
| | | | - Tawni Voyles
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
| | - Mercy Y. Akinyi
- Institute of Primate Research, National Museums of Kenya, Nairobi00502, Kenya
| | - Elizabeth A. Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN46556
| | - Susan C. Alberts
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
- Department of Biology, Duke University, Durham, NC27708
- Duke Population Research Institute, Duke University, Durham, NC27708
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, NC27708
- Canadian Institute for Advanced Research, Child & Brain Development Program, Toronto, ONM5G 1M1, Canada
- Department of Biology, Duke University, Durham, NC27708
- Duke Population Research Institute, Duke University, Durham, NC27708
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig04103, Germany
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4
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Sepers B, Verhoeven KJF, van Oers K. Early developmental carry-over effects on exploratory behaviour and DNA methylation in wild great tits ( Parus major). Evol Appl 2024; 17:e13664. [PMID: 38487391 PMCID: PMC10937296 DOI: 10.1111/eva.13664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/21/2023] [Accepted: 01/31/2024] [Indexed: 03/17/2024] Open
Abstract
Adverse, postnatal conditions experienced during development are known to induce lingering effects on morphology, behaviour, reproduction and survival. Despite the importance of early developmental stress for shaping the adult phenotype, it is largely unknown which molecular mechanisms allow for the induction and maintenance of such phenotypic effects once the early environmental conditions are released. Here we aimed to investigate whether lasting early developmental phenotypic changes are associated with post-developmental DNA methylation changes. We used a cross-foster and brood size experiment in great tit (Parus major) nestlings, which induced post-fledging effects on biometric measures and exploratory behaviour, a validated personality trait. We investigated whether these post-fledging effects are associated with DNA methylation levels of CpG sites in erythrocyte DNA. Individuals raised in enlarged broods caught up on their developmental delay after reaching independence and became more explorative as days since fledging passed, while the exploratory scores of individuals that were raised in reduced broods remained stable. Although we previously found that brood enlargement hardly affected the pre-fledging methylation levels, we found 420 CpG sites that were differentially methylated between fledged individuals that were raised in small versus large sized broods. A considerable number of the affected CpG sites were located in or near genes involved in metabolism, growth, behaviour and cognition. Since the biological functions of these genes line up with the observed post-fledging phenotypic effects of brood size, our results suggest that DNA methylation provides organisms the opportunity to modulate their condition once the environmental conditions allow it. In conclusion, this study shows that nutritional stress imposed by enlarged brood size during early development associates with variation in DNA methylation later in life. We propose that treatment-associated DNA methylation differences may arise in relation to pre- or post-fledging phenotypic changes, rather than that they are directly induced by the environment during early development.
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Affiliation(s)
- Bernice Sepers
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Behavioural Ecology GroupWageningen University & Research (WUR)WageningenThe Netherlands
- Department of Animal BehaviourBielefeld UniversityBielefeldGermany
| | - Koen J. F. Verhoeven
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Kees van Oers
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Behavioural Ecology GroupWageningen University & Research (WUR)WageningenThe Netherlands
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5
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Laine VN, Sepers B, Lindner M, Gawehns F, Ruuskanen S, van Oers K. An ecologist's guide for studying DNA methylation variation in wild vertebrates. Mol Ecol Resour 2023; 23:1488-1508. [PMID: 35466564 DOI: 10.1111/1755-0998.13624] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 03/29/2022] [Accepted: 04/13/2022] [Indexed: 11/30/2022]
Abstract
The field of molecular biology is advancing fast with new powerful technologies, sequencing methods and analysis software being developed constantly. Commonly used tools originally developed for research on humans and model species are now regularly used in ecological and evolutionary research. There is also a growing interest in the causes and consequences of epigenetic variation in natural populations. Studying ecological epigenetics is currently challenging, especially for vertebrate systems, because of the required technical expertise, complications with analyses and interpretation, and limitations in acquiring sufficiently high sample sizes. Importantly, neglecting the limitations of the experimental setup, technology and analyses may affect the reliability and reproducibility, and the extent to which unbiased conclusions can be drawn from these studies. Here, we provide a practical guide for researchers aiming to study DNA methylation variation in wild vertebrates. We review the technical aspects of epigenetic research, concentrating on DNA methylation using bisulfite sequencing, discuss the limitations and possible pitfalls, and how to overcome them through rigid and reproducible data analysis. This review provides a solid foundation for the proper design of epigenetic studies, a clear roadmap on the best practices for correct data analysis and a realistic view on the limitations for studying ecological epigenetics in vertebrates. This review will help researchers studying the ecological and evolutionary implications of epigenetic variation in wild populations.
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Affiliation(s)
- Veronika N Laine
- Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Bernice Sepers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, The Netherlands
| | - Melanie Lindner
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Fleur Gawehns
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Suvi Ruuskanen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Department of Biology, University of Turku, Finland
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Behavioural Ecology Group, Wageningen University & Research (WUR), Wageningen, The Netherlands
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6
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Patterson SK, Petersen RM, Brent LJN, Snyder-Mackler N, Lea AJ, Higham JP. Natural Animal Populations as Model Systems for Understanding Early Life Adversity Effects on Aging. Integr Comp Biol 2023; 63:681-692. [PMID: 37279895 PMCID: PMC10503476 DOI: 10.1093/icb/icad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/25/2023] [Accepted: 05/30/2023] [Indexed: 06/08/2023] Open
Abstract
Adverse experiences in early life are associated with aging-related disease risk and mortality across many species. In humans, confounding factors, as well as the difficulty of directly measuring experiences and outcomes from birth till death, make it challenging to identify how early life adversity impacts aging and health. These challenges can be mitigated, in part, through the study of non-human animals, which are exposed to parallel forms of adversity and can age similarly to humans. Furthermore, studying the links between early life adversity and aging in natural populations of non-human animals provides an excellent opportunity to better understand the social and ecological pressures that shaped the evolution of early life sensitivities. Here, we highlight ongoing and future research directions that we believe will most effectively contribute to our understanding of the evolution of early life sensitivities and their repercussions.
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Affiliation(s)
- Sam K Patterson
- Department of Anthropology, New York University, New York City, 10003, USA
| | - Rachel M Petersen
- Department of Biological Science, Vanderbilt University, Nashville, 37232, USA
| | - Lauren J N Brent
- Department of Psychology, University of Exeter, Exeter, EX4 4QG, United Kingdom
| | - Noah Snyder-Mackler
- School of Life Sciences, Center for Evolution and Medicine, and School of Human Evolution and Social Change, Arizona State University, Tempe, 85281, USA
| | - Amanda J Lea
- Department of Biological Science, Vanderbilt University, Nashville, 37232, USA
- Child and Brain Development Program, Canadian Institute for Advanced Study, Toronto, M5G 1M1, Canada
| | - James P Higham
- Department of Anthropology, New York University, New York City, 10003, USA
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7
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Dettmer AM, Chusyd DE. Early life adversities and lifelong health outcomes: A review of the literature on large, social, long-lived nonhuman mammals. Neurosci Biobehav Rev 2023; 152:105297. [PMID: 37391110 PMCID: PMC10529948 DOI: 10.1016/j.neubiorev.2023.105297] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023]
Abstract
Social nonhuman animals are powerful models for studying underlying factors related to lifelong health outcomes following early life adversities (ELAs). ELAs can be linked to lifelong health outcomes depending on the species, system, sensitive developmental periods, and biological pathways. This review focuses on the literature surrounding ELAs and lifelong health outcomes in large, social, relatively long-lived nonhuman mammals including nonhuman primates, canids, hyenas, elephants, ungulates, and cetaceans. These mammals, like humans but unlike the most-studied rodent models, have longer life histories, complex social structures, larger brains, and comparable stress and reproductive physiology. Collectively, these features make them compelling models for comparative aging research. We review studies of caregiver, social, and ecological ELAs, often in tandem, in these mammals. We consider experimental and observational studies and what each has contributed to our knowledge of health across the lifespan. We demonstrate the continued and expanded need for comparative research to inform about the social determinants of health and aging in both humans and nonhuman animals.
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Affiliation(s)
- Amanda M Dettmer
- Yale Child Study Center, Yale School of Medicine, 230 S. Frontage Rd., New Haven, CT, USA.
| | - Daniella E Chusyd
- Department of Environmental and Occupational Health, Indiana University Bloomington, 1025 E. 7th St., Bloomington, IN, USA; Department of Health and Wellness Design, Indiana University Bloomington, 1025 E. 7th St., Bloomington, IN, USA
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8
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Strauss ED. Demographic turnover can be a leading driver of hierarchy dynamics, and social inheritance modifies its effects. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220308. [PMID: 37381857 PMCID: PMC10291429 DOI: 10.1098/rstb.2022.0308] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/10/2023] [Indexed: 06/30/2023] Open
Abstract
Individuals and societies are linked through a feedback loop of mutual influence. Demographic turnover shapes group composition and structure by adding and removing individuals, and social inheritance shapes social structure through the transmission of social traits from parents to offspring. Here I examine how these drivers of social structure feedback to influence individual outcomes. I explore these society-to-individual effects in systems with social inheritance of hierarchy position, as occur in many primates and spotted hyenas. Applying Markov chain models to empirical and simulated data reveals how demography and social inheritance interact to strongly shape individual hierarchy positions. In hyena societies, demographic processes-not status seeking-account for the majority of hierarchy dynamics and cause an on-average lifetime decline in social hierarchy position. Simulated societies clarify how social inheritance alters demographic effects-demographic processes cause hierarchy position to regress to the mean, but the addition of social inheritance modifies this pattern. Notably, the combination of social inheritance and rank-related reproductive success causes individuals to decline in rank over their lifespans, as seen in the hyena data. Further analyses explore how 'queens' escape this pattern of decline, and how variation in social inheritance generates variability in reproductive inequality. This article is part of the theme issue 'Evolutionary ecology of inequality'.
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Affiliation(s)
- Eli D. Strauss
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, Konstanz, Baden-Württemberg, 78464, Germany
- Ecology of Animal Societies Department, Max Planck Institute of Animal Behavior, Radolfzell, Baden-Württemberg, 78315, Germany
- Collective Behavior Department, Max Planck Institute of Animal Behavior, Radolfzell, Baden-Württemberg, 78315, Germany
- Integrative Biology Department, Michigan State University, East Lansing, Michigan, 48824, USA
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9
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Anderson JA, Lin D, Lea AJ, Johnston RA, Voyles T, Akinyi MY, Archie EA, Alberts SC, Tung J. DNA methylation signatures of early life adversity are exposure-dependent in wild baboons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.542485. [PMID: 37333311 PMCID: PMC10274726 DOI: 10.1101/2023.06.05.542485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The early life environment can profoundly shape the trajectory of an animal's life, even years or decades later. One mechanism proposed to contribute to these early life effects is DNA methylation. However, the frequency and functional importance of DNA methylation in shaping early life effects on adult outcomes is poorly understood, especially in natural populations. Here, we integrate prospectively collected data on fitness-associated variation in the early environment with DNA methylation estimates at 477,270 CpG sites in 256 wild baboons. We find highly heterogeneous relationships between the early life environment and DNA methylation in adulthood: aspects of the environment linked to resource limitation (e.g., low-quality habitat, early life drought) are associated with many more CpG sites than other types of environmental stressors (e.g., low maternal social status). Sites associated with early resource limitation are enriched in gene bodies and putative enhancers, suggesting they are functionally relevant. Indeed, by deploying a baboon-specific, massively parallel reporter assay, we show that a subset of windows containing these sites are capable of regulatory activity, and that, for 88% of early drought-associated sites in these regulatory windows, enhancer activity is DNA methylation-dependent. Together, our results support the idea that DNA methylation patterns contain a persistent signature of the early life environment. However, they also indicate that not all environmental exposures leave an equivalent mark and suggest that socioenvironmental variation at the time of sampling is more likely to be functionally important. Thus, multiple mechanisms must converge to explain early life effects on fitness-related traits.
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Affiliation(s)
- Jordan A Anderson
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina 27708, USA
| | - Dana Lin
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina 27708, USA
| | - Amanda J Lea
- Canadian Institute for Advanced Research, Toronto, Canada M5G 1M1, Canada
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, 37235, USA
| | - Rachel A Johnston
- Zoo New England, Stoneham, Massachusetts, 02180
- Broad Institute, Cambridge, Massachusetts, 02142
| | - Tawni Voyles
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina 27708, USA
| | - Mercy Y Akinyi
- Institute of Primate Research, National Museums of Kenya, Nairobi 00502, Kenya
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Susan C Alberts
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina 27708, USA
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
- Duke Population Research Institute, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina 27708, USA
- Canadian Institute for Advanced Research, Toronto, Canada M5G 1M1, Canada
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
- Duke Population Research Institute, Duke University, Durham, NC 27708, USA
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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10
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Bock SL, Smaga CR, McCoy JA, Parrott BB. Genome-wide DNA methylation patterns harbour signatures of hatchling sex and past incubation temperature in a species with environmental sex determination. Mol Ecol 2022; 31:5487-5505. [PMID: 35997618 PMCID: PMC9826120 DOI: 10.1111/mec.16670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 01/11/2023]
Abstract
Conservation of thermally sensitive species depends on monitoring organismal and population-level responses to environmental change in real time. Epigenetic processes are increasingly recognized as key integrators of environmental conditions into developmentally plastic responses, and attendant epigenomic data sets hold potential for revealing cryptic phenotypes relevant to conservation efforts. Here, we demonstrate the utility of genome-wide DNA methylation (DNAm) patterns in the face of climate change for a group of especially vulnerable species, those with temperature-dependent sex determination (TSD). Due to their reliance on thermal cues during development to determine sexual fate, contemporary shifts in temperature are predicted to skew offspring sex ratios and ultimately destabilize sensitive populations. Using reduced-representation bisulphite sequencing, we profiled the DNA methylome in blood cells of hatchling American alligators (Alligator mississippiensis), a TSD species lacking reliable markers of sexual dimorphism in early life stages. We identified 120 sex-associated differentially methylated cytosines (DMCs; FDR < 0.1) in hatchlings incubated under a range of temperatures, as well as 707 unique temperature-associated DMCs. We further developed DNAm-based models capable of predicting hatchling sex with 100% accuracy (in 20 training samples and four test samples) and past incubation temperature with a mean absolute error of 1.2°C (in four test samples) based on the methylation status of 20 and 24 loci, respectively. Though largely independent of epigenomic patterning occurring in the embryonic gonad during TSD, DNAm patterns in blood cells may serve as nonlethal markers of hatchling sex and past incubation conditions in conservation applications. These findings also raise intriguing questions regarding tissue-specific epigenomic patterning in the context of developmental plasticity.
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Affiliation(s)
- Samantha L. Bock
- Eugene P. Odum School of EcologyUniversity of GeorgiaAthensGeorgiaUSA
- Savannah River Ecology LaboratoryAikenSouth CarolinaUSA
| | - Christopher R. Smaga
- Eugene P. Odum School of EcologyUniversity of GeorgiaAthensGeorgiaUSA
- Savannah River Ecology LaboratoryAikenSouth CarolinaUSA
| | - Jessica A. McCoy
- Department of BiologyCollege of CharlestonCharlestonSouth CarolinaUSA
| | - Benjamin B. Parrott
- Eugene P. Odum School of EcologyUniversity of GeorgiaAthensGeorgiaUSA
- Savannah River Ecology LaboratoryAikenSouth CarolinaUSA
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11
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Wanner N, Larsen PA, McLain A, Faulk C. The mitochondrial genome and Epigenome of the Golden lion Tamarin from fecal DNA using Nanopore adaptive sequencing. BMC Genomics 2021; 22:726. [PMID: 34620074 PMCID: PMC8499546 DOI: 10.1186/s12864-021-08046-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/29/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The golden lion tamarin (Leontopithecus rosalia) is an endangered Platyrrhine primate endemic to the Atlantic coastal forests of Brazil. Despite ongoing conservation efforts, genetic data on this species remains scarce. Complicating factors include limitations on sample collection and a lack of high-quality reference sequences. Here, we used nanopore adaptive sampling to resequence the L. rosalia mitogenome from feces, a sample which can be collected non-invasively. RESULTS Adaptive sampling doubled the fraction of both host-derived and mitochondrial sequences compared to sequencing without enrichment. 258x coverage of the L. rosalia mitogenome was achieved in a single flow cell by targeting the unfinished genome of the distantly related emperor tamarin (Saguinus imperator) and the mitogenome of the closely related black lion tamarin (Leontopithecus chrysopygus). The L. rosalia mitogenome has a length of 16,597 bp, sharing 99.68% sequence identity with the L. chrysopygus mitogenome. A total of 38 SNPs between them were identified, with the majority being found in the non-coding D-loop region. DNA methylation and hydroxymethylation were directly detected using a neural network model applied to the raw signal from the MinION sequencer. In contrast to prior reports, DNA methylation was negligible in mitochondria in both CpG and non-CpG contexts. Surprisingly, a quarter of the 642 CpG sites exhibited DNA hydroxymethylation greater than 1% and 44 sites were above 5%, with concentration in the 3' side of several coding regions. CONCLUSIONS Overall, we report a robust new mitogenome assembly for L. rosalia and direct detection of cytosine base modifications in all contexts.
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Affiliation(s)
- Nicole Wanner
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, 1988 Fitch Ave., Saint Paul, MN 55108 USA
| | - Peter A. Larsen
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN USA
| | - Adam McLain
- Department of Biology and Chemistry, College of Arts and Sciences, SUNY Polytechnic Institute, Utica, NY USA
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, 1988 Fitch Ave., Saint Paul, MN 55108 USA
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Laubach ZM, Greenberg JR, Turner JW, Montgomery TM, Pioon MO, Sawdy MA, Smale L, Cavalcante RG, Padmanabhan KR, Lalancette C, vonHoldt B, Faulk CD, Dolinoy DC, Holekamp KE, Perng W. Early-life social experience affects offspring DNA methylation and later life stress phenotype. Nat Commun 2021; 12:4398. [PMID: 34285226 PMCID: PMC8292380 DOI: 10.1038/s41467-021-24583-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 06/24/2021] [Indexed: 02/06/2023] Open
Abstract
Studies in rodents and captive primates suggest that the early-life social environment affects future phenotype, potentially through alterations to DNA methylation. Little is known of these associations in wild animals. In a wild population of spotted hyenas, we test the hypothesis that maternal care during the first year of life and social connectedness during two periods of early development leads to differences in DNA methylation and fecal glucocorticoid metabolites (fGCMs) later in life. Here we report that although maternal care and social connectedness during the den-dependent life stage are not associated with fGCMs, greater social connectedness during the subadult den-independent life stage is associated with lower adult fGCMs. Additionally, more maternal care and social connectedness after den independence correspond with higher global (%CCGG) DNA methylation. We also note differential DNA methylation near 5 genes involved in inflammation, immune response, and aging that may link maternal care with stress phenotype.
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Affiliation(s)
- Zachary M Laubach
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA.
- BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya.
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA.
| | - Julia R Greenberg
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
| | - Julie W Turner
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
- BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
| | - Tracy M Montgomery
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
- Max Planck Institute of Animal Behavior, Department for the Ecology of Animal Societies, Konstanz, Germany
| | - Malit O Pioon
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
| | - Maggie A Sawdy
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
| | - Laura Smale
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Department of Psychology, Michigan State University, East Lansing, MI, USA
| | | | | | | | - Bridgett vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | - Dana C Dolinoy
- Epigenomics Core, University of Michigan, Ann Arbor, MI, USA
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kay E Holekamp
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
- Program in Ecology, Evolution, and Behavior, Michigan State University, East Lansing, USA MI, USA
- BEACON, NSF Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
- Mara Hyena Project, Masai Mara National Reserve, Narok, Kenya
| | - Wei Perng
- Department of Epidemiology and Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Denver, Aurora, CO, USA
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Watson H, Powell D, Salmón P, Jacobs A, Isaksson C. Urbanization is associated with modifications in DNA methylation in a small passerine bird. Evol Appl 2021; 14:85-98. [PMID: 33519958 PMCID: PMC7819559 DOI: 10.1111/eva.13160] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022] Open
Abstract
Urbanization represents a fierce driver of phenotypic change, yet the molecular mechanisms underlying observed phenotypic patterns are poorly understood. Epigenetic changes are expected to facilitate more rapid adaption to changing or novel environments, such as our towns and cities, compared with slow changes in gene sequence. A comparison of liver and blood tissue from great tits Parus major originating from an urban and a forest site demonstrated that urbanization is associated with variation in genome-wide patterns of DNA methylation. Combining reduced representation bisulphite sequencing with transcriptome data, we revealed habitat differences in DNA methylation patterns that suggest a regulated and coordinated response to the urban environment. In the liver, genomic sites that were differentially methylated between urban- and forest-dwelling birds were over-represented in regulatory regions of the genome and more likely to occur in expressed genes. DNA methylation levels were also inversely correlated with gene expression at transcription start sites. Furthermore, differentially methylated CpG sites, in liver, were over-represented in pathways involved in (i) steroid biosynthesis, (ii) superoxide metabolism, (iii) secondary alcohol metabolism, (iv) chylomicron remodelling, (v) cholesterol transport, (vi) reactive oxygen species (ROS) metabolic process and (vii) epithelial cell proliferation. This corresponds with earlier studies identifying diet and exposure to ROS as two of the main drivers of divergence between organisms in urban and nonurban environments. Conversely, in blood, sites that were differentially methylated between urban- and forest-dwelling birds were under-represented in regulatory regions, more likely to occur in nonexpressed genes and not over-represented in specific biological pathways. It remains to be determined whether diverging patterns of DNA methylation represent adaptive evolutionary responses and whether the conclusions can be more widely attributed to urbanization.
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Affiliation(s)
- Hannah Watson
- Evolutionary Ecology, Biology DepartmentLund UniversityLundSweden
| | - Daniel Powell
- Evolutionary Ecology, Biology DepartmentLund UniversityLundSweden
- Global Change Ecology, School of Science, Technology and EngineeringUniversity of the Sunshine CoastSippy DownsQLDAustralia
| | - Pablo Salmón
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
- Department of Natural ResourcesCornell UniversityIthacaNYUSA
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14
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Guerrero TP, Fickel J, Benhaiem S, Weyrich A. Epigenomics and gene regulation in mammalian social systems. Curr Zool 2020; 66:307-319. [PMID: 32440291 PMCID: PMC7233906 DOI: 10.1093/cz/zoaa005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 02/12/2020] [Indexed: 12/19/2022] Open
Abstract
Social epigenomics is a new field of research that studies how the social environment shapes the epigenome and how in turn the epigenome modulates behavior. We focus on describing known gene-environment interactions (GEIs) and epigenetic mechanisms in different mammalian social systems. To illustrate how epigenetic mechanisms integrate GEIs, we highlight examples where epigenetic mechanisms are associated with social behaviors and with their maintenance through neuroendocrine, locomotor, and metabolic responses. We discuss future research trajectories and open questions for the emerging field of social epigenomics in nonmodel and naturally occurring social systems. Finally, we outline the technological advances that aid the study of epigenetic mechanisms in the establishment of GEIs and vice versa.
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Affiliation(s)
- Tania P Guerrero
- Department Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
- Faculty of Environment and Natural Resources, Albert Ludwig University of Freiburg, Tennenbacher Str. 4, Freiburg, D-79085, Germany
| | - Jörns Fickel
- Department Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam, 14476, Germany
| | - Sarah Benhaiem
- Department Ecological Dynamics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
| | - Alexandra Weyrich
- Department Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str. 17, Berlin, D-10315, Germany
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15
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Poullet M, Orlando L. Assessing DNA Sequence Alignment Methods for Characterizing Ancient Genomes and Methylomes. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00105] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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16
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Strauss ED, Shizuka D, Holekamp KE. Juvenile rank acquisition is associated with fitness independent of adult rank. Proc Biol Sci 2020; 287:20192969. [PMID: 32126950 DOI: 10.1098/rspb.2019.2969] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Social rank is a significant determinant of fitness in a variety of species. The importance of social rank suggests that the process by which juveniles come to establish their position in the social hierarchy is a critical component of development. Here, we use the highly predictable process of rank acquisition in spotted hyenas to study the consequences of variation in rank acquisition in early life. In spotted hyenas, rank is 'inherited' through a learning process called 'maternal rank inheritance.' This pattern is very consistent: approximately 80% of juveniles acquire the exact rank expected under the rules of maternal rank inheritance. The predictable nature of rank acquisition in these societies allows the process of rank acquisition to be studied independently from the ultimate rank that each juvenile attains. In this study, we use Elo-deviance scores, a novel application of the Elo-rating method, to calculate each juvenile's deviation from the expected pattern of maternal rank inheritance during development. Despite variability in rank acquisition among juveniles, most of these juveniles come to attain the exact rank expected of them according to the rules of maternal rank inheritance. Nevertheless, we find that transient variation in rank acquisition in early life is associated with long-term fitness consequences for these individuals: juveniles 'underperforming' their expected ranks show reduced survival and lower lifetime reproductive success than better-performing peers, and this relationship is independent of both maternal rank and rank achieved in adulthood. We also find that multiple sources of early life adversity have cumulative, but not compounding, effects on fitness. Future work is needed to determine if variation in rank acquisition directly affects fitness, or if some other variable, such as maternal investment or juvenile condition, causes variation in both of these outcomes.
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Affiliation(s)
- Eli D Strauss
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA.,School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Daizaburo Shizuka
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Kay E Holekamp
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, USA
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