References:
AGRELIUS, T. C., ALTMAN, J. and DUDYCHA, J. L. 2023. The maternal effects of dietary restriction on Dnmt expression and reproduction in two clones of Daphnia pulex. -Heredity, 130 : 73-81.ALVARADO, S., MAK, T., LIU, S., STOREY, K. B. and SZYF, M. 2015. Dynamic changes in global and gene-specific DNA methylation during hibernation in adult thirteen-lined ground squirrels, Ictidomys tridecemlineatus. -The Journal of experimental biology, 218 : 1787-1795.BALL, P. 2023. How Life Works: A User’s Guide to the New Biology. How Life Works. University of Chicago Press.BARTON, K. and BARTON, M. K. 2015. Package ‘mumin’. -Version, 1 : 439.BATES, D. 2014. Fitting linear mixed-effects models using lme4. -arXiv preprint arXiv:1406.5823 .BOGAN, S. N. and YI, S. V. 2024. Potential role of DNA methylation as a driver of plastic responses to the environment across cells, organisms, and populations. -Genome biology and evolution, 16 : evae022.CARDOSO-JúNIOR, C. A. M., EYER, M., DAINAT, B., HARTFELDER, K. and DIETEMANN, V. 2018. Social context influences the expression of DNA methyltransferase genes in the honeybee. -Scientific reports, 8 : 11076.CHEN, Y., NI, P., FU, R., MURPHY, K. J., WYETH, R. C., BISHOP, C. D., HUANG, X., LI, S. and ZHAN, A. 2024. (Epi) genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions. -Ecological Applications, 34 : e2772.CHOWN, S. L. and MCGEOCH, M. A. 2023. Functional trait variation along animal invasion pathways. -Annual Review of Ecology, Evolution, and Systematics, 54 : 151-170.COLWELL, R. K. 1974. Predictability, constancy, and contingency of periodic phenomena. -Ecology, 55 : 1148-1153.COYLE, C. S., TOLLA, E. and STEVENSON, T. J. 2020. Rhythmic epigenetics in neuroendocrine and immune systems. -Developmental Neuroendocrinology : 295-314.DAVIDSON, A. M., JENNIONS, M. and NICOTRA, A. B. 2011. Do invasive species show higher phenotypic plasticity than native species and, if so, is it adaptive? A meta‚Äêanalysis. -Ecology Letters, 14 : 419-431.DU, Y., WANG, X., ASHRAF, S., TU, W., XI, Y., CUI, R., CHEN, S., YU, J., HAN, L. and GU, S. 2024. Climate match is key to predict range expansion of the world’s worst invasive terrestrial vertebrates. -Global Change Biology, 30 : e17137.DUCATEZ, S., SAYOL, F., SOL, D. and LEFEBVRE, L. 2018. Are urban vertebrates city specialists, artificial habitat exploiters, or environmental generalists? -Integrative and Comparative Biology, 58 : 929-938.DUPONT, L., THIERRY, M., ZINGER, L., LEGRAND, D. and JACOB, S. 2024. Beyond reaction norms: the temporal dynamics of phenotypic plasticity. -Trends in Ecology & Evolution, 39 : 41-51.ECKER, S., PANCALDI, V., VALENCIA, A., BECK, S. and PAUL, D. S. 2018. Epigenetic and transcriptional variability shape phenotypic plasticity. -Bioessays, 40 : 1700148.FAN, G., MARTINOWICH, K., CHIN, M. H., HE, F., FOUSE, S. D., HUTNICK, L., HATTORI, D., GE, W., SHEN, Y. and WU, H. 2005. DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling.FENG, J., ZHOU, Y., CAMPBELL, S. L., LE, T., LI, E., SWEATT, J. D., SILVA, A. J. and FAN, G. 2010. Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. -Nature neuroscience, 13 : 423-430.FISHMAN, B. and TAUBER, E. 2024. Epigenetics and seasonal timing in animals: a concise review. -Journal of Comparative Physiology A, 210 : 565-574.FRISTON, K. 2010. The free-energy principle: a unified brain theory? -Nature reviews neuroscience, 11 : 127-138.FU, R., HUANG, X. and ZHAN, A. 2021. Identification of DNA (de) methylation-related genes and their transcriptional response to environmental challenges in an invasive model ascidian. -Gene, 768 : 145331.GELMAN, A., YU-SUNG, S., YAJIMA, M., HILL, J., PITTAU, M. G., KERMAN, J., ZHENG, T. and DORIE, V. 2007. arm: Data analysis using regression and multilevel/hierarchical models.HADFIELD, J. D. 2010. MCMC Methods for Multi-Response Generalized Linear Mixed Models: The MCMCglmm R Package. -Journal of Statistical Software, 33 : 1-22.HANSON, H. E., KOUSSAYER, B., KILVITIS, H. J., SCHREY, A. W., MADDOX, J. D. and MARTIN, L. B. 2020a. Epigenetic potential in native and introduced populations of house sparrows (Passer domesticus). -Integrative and Comparative Biology, 60 : 1458-1468.HANSON, H. E. and LIEBL, A. L. 2022. The mutagenic consequences of DNA methylation within and across generations. -Epigenomes, 6 : 33.HANSON, H. E., MATHEWS, N. S., HAUBER, M. E. and MARTIN, L. B. 2020b. The house sparrow in the service of basic and applied biology. -Elife, 9 : e52803.HANSON, H. E., WANG, C. Q., SCHREY, A. W., LIEBL, A. L., RAVINET, M., JIANG, R. H. Y. and MARTIN, L. B. 2022. Epigenetic Potential and DNA Methylation in an Ongoing House Sparrow (Passer domesticus) Range Expansion. -American Naturalist .HARRIS, I., JONES, P., OSBORN, T. and LISTER, D. 2014. Updated high-resolution grids of monthly climatic observations-the CRU TS3. 10 Dataset. -International journal of climatology, 34 : 623-642.HAU, M. 2001. Timing of breeding in variable environments: Tropical birds as model systems. -Hormones and Behavior, 40 : 281-290.HONG, J. Y. and MEDZHITOV, R. 2023. On developmental programming of the immune system. -Trends in Immunology .HOUSLAY, T. M. and WILSON, A. J. 2017. Avoiding the misuse of BLUP in behavioural ecology. -Behavioral Ecology, 28 : 948-952.HUSBY, A. 2022a. Wild epigenetics: insights from epigenetic studies on natural populations. -Proceedings of the Royal Society B-Biological Sciences, 289 .HUSBY, A. 2022b. Wild epigenetics: insights from epigenetic studies on natural populations. -Proceedings of the Royal Society B, 289 : 20211633.JESCHKE, J. M. and STRAYER, D. L. 2006. Determinants of vertebrate invasion success in Europe and North America. -Global Change Biology, 12 : 1608-1619.JIANG, M., FELZER, B. S., NIELSEN, U. N. and MEDLYN, B. E. 2017. Biome‐specific climatic space defined by temperature and precipitation predictability. -Global ecology and biogeography, 26 : 1270-1282.KILVITIS, H. J., ARDIA, D. R., THIAM, M. and MARTIN, L. B. 2018. Corticosterone is correlated to mediators of neural plasticity and epigenetic potential in the hippocampus of Senegalese house sparrows (Passer domesticus). -General and Comparative Endocrinology, 269 : 177-183.KILVITIS, H. J., HANSON, H., SCHREY, A. W. and MARTIN, L. B. 2017. Epigenetic Potential as a Mechanism of Phenotypic Plasticity in Vertebrate Range Expansions. -Integrative and comparative biology, 57 : 385-395.KIRCHHOFF, M., PARR, T., PALACIOS, E., FRISTON, K. and KIVERSTEIN, J. 2018. The Markov blankets of life: autonomy, active inference and the free energy principle. -Journal of The royal society interface, 15 : 20170792.LAINE, V. N., SEPERS, B., LINDNER, M., GAWEHNS, F., RUUSKANEN, S. and VAN OERS, K. 2023. An ecologist’s guide for studying DNA methylation variation in wild vertebrates. -Molecular Ecology Resources, 23 : 1488-1508.LAW, J. A. and JACOBSEN, S. E. 2010. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. -Nature Reviews Genetics, 11 : 204-220.LEE, P. P., FITZPATRICK, D. R., BEARD, C., JESSUP, H. K., LEHAR, S., MAKAR, K. W., PéREZ-MELGOSA, M., SWEETSER, M. T., SCHLISSEL, M. S. and NGUYEN, S. 2001. A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival. -Immunity, 15 : 763-774.LIEBL, A. L. and MARTIN, L. B. 2012. Exploratory behaviour and stressor hyper-responsiveness facilitate range expansion of an introduced songbird. -Proceedings of the Royal Society B, 279 : 4375-4381.LIEBL, A. L. and MARTIN, L. B. 2014. Living on the edge: range edge birds consume novel foods sooner than established ones. -Behavioral Ecology, 25 : 1089-1096.LIEBL, A. L., SCHREY, A. W., RICHARDS, C. L. and MARTIN, L. B. 2013. Patterns of DNA methylation throughout a range expansion of an introduced songbird. -Integrative and Comparative Biology, 53 : 351-358.LOUGHLAND, I., LITTLE, A. and SEEBACHER, F. 2021. DNA methyltransferase 3a mediates developmental thermal plasticity. -Bmc Biology, 19 : 1-11.LUO, J., YU, Y., CHANG, S., TIAN, F., ZHANG, H. and SONG, J. 2012. DNA methylation fluctuation induced by virus infection differs between MD-resistant and-susceptible chickens. -Frontiers in genetics, 3 : 20.LYKO, F., FORET, S., KUCHARSKI, R., WOLF, S., FALCKENHAYN, C. and MALESZKA, R. 2010. The honey bee epigenomes: differential methylation of brain DNA in queens and workers. -PLoS biology, 8 : e1000506.LYNCH, E. W., COYLE, C. S., LORGEN, M., CAMPBELL, E. M., BOWMAN, A. S. and STEVENSON, T. J. 2016. Cyclical DNA methyltransferase 3a expression is a seasonal and estrus timer in reproductive tissues. -Endocrinology, 157 : 2469-2478.MARIN, P., GENITONI, J., BARLOY, D., MAURY, S., GIBERT, P., GHALAMBOR, C. K. and VIEIRA, C. 2019. Biological Invasion: The Influence of the Hidden Side of the (Epi) Genome. -Functional Ecology .MARIN, P., GENITONI, J., BARLOY, D., MAURY, S., GIBERT, P., GHALAMBOR, C. K. and VIEIRA, C. 2020. Biological invasion: The influence of the hidden side of the (epi) genome. -Functional Ecology, 34 : 385-400.MARTIN, L. B., KILVITIS, H. J., THIAM, M. and ARDIA, D. R. 2017. Corticosterone regulation in house sparrows invading Senegal. -General and Comparative Endocrinology, 250 : 15-20.MCCAW, B. A., STEVENSON, T. J. and LANCASTER, L. T. 2020. Epigenetic responses to temperature and climate. -Integrative and Comparative Biology, 60 : 1469-1480.MISHRA, I., SHARMA, A., PRABHAT, A., BATRA, T., MALIK, I. and KUMAR, V. 2020. Changes in DNA methylation and histone modification gene expression in response to daily food times in zebra finches: Epigenetic implications. -The Journal of experimental biology : jeb. 217422.MITCHELL, K. J. 2023. Free agents: how evolution gave us free will.MOUNGER, J., AINOUCHE, M. L., BOSSDORF, O., CAVé-RADET, A., LI, B., PAREPA, M., SALMON, A., YANG, J. and RICHARDS, C. L. 2021. Epigenetics and the success of invasive plants. -Philosophical Transactions of the Royal Society B, 376 : 20200117.NAKAGAWA, S. and SCHIELZETH, H. 2010. Repeatability for Gaussian and non‐Gaussian data: a practical guide for biologists. -Biological Reviews, 85 : 935-956.NGUYEN, N. D., MATSUURA, T., KATO, Y. and WATANABE, H. 2021. DNMT3. 1 controls trade-offs between growth, reproduction, and life span under starved conditions in Daphnia magna. -Scientific reports, 11 : 7326.NOGUCHI, H., KIMURA, A., MURAO, N., MATSUDA, T., NAMIHIRA, M. and NAKASHIMA, K. 2015. Expression of DNMT1 in neural stem/precursor cells is critical for survival of newly generated neurons in the adult hippocampus. -Neuroscience research, 95 : 1-11.POLAINA, E., SOULTAN, A., PäRT, T. and RECIO, M. R. 2021. The future of invasive terrestrial vertebrates in Europe under climate and land-use change. -Environmental Research Letters, 16 : 044004.RASMUSSEN, K. D., JIA, G., JOHANSEN, J. V., PEDERSEN, M. T., RAPIN, N., BAGGER, F. O., PORSE, B. T., BERNARD, O. A., CHRISTENSEN, J. and HELIN, K. 2015. Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis. -Genes & development, 29 : 910-922.RAVINET, M., ELGVIN, T. O., TRIER, C., ALIABADIAN, M., GAVRILOV, A. and SæTRE, G.-P. 2018. Signatures of human-commensalism in the house sparrow genome. -Proceedings of the Royal Society B: Biological Sciences, 285 : 20181246.REGEV, A., LAMB, M. J. and JABLONKA, E. 1998. The role of DNA methylation in invertebrates: developmental regulation or genome defense? -Molecular Biology and Evolution, 15 : 880-891.ROBERTSON, K. D. and WOLFFE, A. P. 2000. DNA methylation in health and disease. -Nature reviews genetics, 1 : 11-19.SEPERS, B., CHEN, R. S., MEMELINK, M., VERHOEVEN, K. J. and VAN OERS, K. 2023. Variation in DNA methylation in avian nestlings is largely determined by genetic effects. -Molecular Biology and Evolution, 40 : msad086.SEPERS, B., VAN DEN HEUVEL, K., LINDNER, M., VIITANIEMI, H., HUSBY, A. and VAN OERS, K. 2019. Avian ecological epigenetics: pitfalls and promises. -Journal of Ornithology, 160 : 1183-1203.SHARMA, A., SINGH, D., MALIK, S., GUPTA, N. J., RANI, S. and KUMAR, V. 2018. Difference in control between spring and autumn migration in birds: insight from seasonal changes in hypothalamic gene expression in captive buntings. -Proceedings of the Royal Society B, 285 : 20181531.SHELDON, E., SCHREY, A., ANDREW, S., RAGSDALE, A. and GRIFFITH, S. 2018. Epigenetic and genetic variation among three separate introductions of the house sparrow (Passer domesticus) into Australia. -Royal Society open science, 5 : 172185.SHELDON, E. L., SCHREY, A. W., HURLEY, L. L. and GRIFFITH, S. C. 2020. Dynamic changes in DNA methylation during postnatal development in zebra finches Taeniopygia guttata exposed to different temperatures. -Journal of Avian Biology, 51 .SILLER WILKS, S. J., HEIDINGER, B. J., WESTNEAT, D. F., SOLOMON, J. and RUBENSTEIN, D. R. 2024. The impact of parental and developmental stress on DNA methylation in the avian hypothalamic–pituitary–adrenal axis. -Molecular Ecology, 33 : e17291.SNELL-ROOD, E. C., KOBIELA, M. E., SIKKINK, K. L. and SHEPHARD, A. M. 2018. Mechanisms of plastic rescue in novel environments. -Annual Review of Ecology, Evolution, and Systematics, 49 : 331-354.STEVENSON, T. J. 2017. Circannual and circadian rhythms of hypothalamic DNA methyltransferase and histone deacetylase expression in male Siberian hamsters (Phodopus sungorus). -General and Comparative Endocrinology, 243 : 130-137.STEVENSON, T. J. 2018. Epigenetic regulation of biological rhythms: an evolutionary ancient molecular timer. -Trends in Genetics, 34 : 90-100.SUAREZ-ALVAREZ, B., RODRIGUEZ, R. M., FRAGA, M. F. and LóPEZ-LARREA, C. 2012. DNA methylation: a promising landscape for immune system-related diseases. -Trends in Genetics, 28 : 506-514.SUN, D., LAYMAN, T. S., JEONG, H., CHATTERJEE, P., GROGAN, K., MERRITT, J. R., MANEY, D. L. and YI, S. V. 2021. Genome‐wide variation in DNA methylation linked to developmental stage and chromosomal suppression of recombination in white‐throated sparrows. -Molecular Ecology, 30 : 3453-3467.TALEB, N. N. 2014. Antifragile: Things that gain from disorder , Random House Trade Paperbacks.USUI, T., LERNER, D., ECKERT, I., ANGERT, A. L., GARROWAY, C. J., HARGREAVES, A., LANCASTER, L. T., LESSARD, J.-P., RIVA, F. and SCHMIDT, C. 2023. The evolution of plasticity at geographic range edges. -Trends in Ecology & Evolution, 38 : 831-842.VOGT, G. 2017a. Evolution of epigenetic mechanisms in animals and their role in speciation. Handbook of Epigenetics. Elsevier, pp. 409-426.VOGT, G. 2017b. Facilitation of environmental adaptation and evolution by epigenetic phenotype variation: insights from clonal, invasive, polyploid, and domesticated animals. -Environmental epigenetics, 3 .VOGT, G. 2021. Epigenetic variation in animal populations: sources, extent, phenotypic implications, and ecological and evolutionary relevance. -Journal of Biosciences, 46 : 24.WADE, M. J. and SULTAN, S. E. 2023. Niche construction and the environmental term of the price equation: How natural selection changes when organisms alter their environments. -Evolution & Development, 25 : 451-469.WANG, L., OZARK, P. A., SMITH, E. R., ZHAO, Z., MARSHALL, S. A., RENDLEMAN, E. J., PIUNTI, A., RYAN, C., WHELAN, A. L. and HELMIN, K. A. 2018. TET2 coactivates gene expression through demethylation of enhancers. -Science advances, 4 : eaau6986.WATSON, R. A. and SZATHMáRY, E. 2016. How can evolution learn? -Trends in ecology & evolution, 31 : 147-157.WILKS, S. J. S., WESTNEAT, D. F., HEIDINGER, B. J., SOLOMON, J. and RUBENSTEIN, D. R. 2023. Epigenetic modification of the hypothalamic–pituitary–adrenal (HPA) axis during development in the house sparrow (Passer domesticus). -General and Comparative Endocrinology, 341 : 114336.WU, S. C. and ZHANG, Y. 2010. Active DNA demethylation: many roads lead to Rome. -Nature reviews Molecular cell biology, 11 : 607-620.ZHANG, Y., WENDTE, J. M., JI, L. and SCHMITZ, R. J. 2020. Natural variation in DNA methylation homeostasis and the emergence of epialleles. -Proceedings of the National Academy of Sciences, 117 : 4874-4884.