References
Anderson, T.R., 2008. Biology of the ubiquitous house sparrow: from genes to populations . Oxford University Press.
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(1), p.e2772.
Deniz, Ö., Frost, J.M. and Branco, M.R., 2019. Regulation of transposable elements by DNA modifications. Nature Reviews Genetics 20: 417-431.
Grinnell, J., 1919. The English sparrow has arrived in Death Valley: An experiment in nature. American Naturalist 53: 468–472.
Hanson, H.E., Zolik, J.E., and Martin L,B., 2020a. ”House Sparrow (Passer domesticus Linnaeus, 1758).” In Invasive Birds: Global trends and impacts , pp. 85-96. Wallingford UK: CABI, 2020.
Hanson, H.E., Kilvitis, H.J., Schrey, A.W., Maddox, J.D., Martin, L.B.,2020b . Epigenetic potential in native and introduced populations of house sparrows (Passer domesticus ). Integrative and Comparative Biology icaa060, doi.org/10.1093/icb/icaa060
Hanson, H.E., Wanga, C., Schrey, A.W., Liebl, A.L., Jianga, R.H.Y., Martin, L.B., 2022. Epigenetic potential and DNA methylation in an ongoing house sparrow (Passer domesticus ) range expansion. American Naturalist 200: 662-674.
Kilvitis, H., Alvarez, M., Foust, C., Richards, C.L., Robertson, M., and Schrey, A.. 2014. Ecological epigenetics. In  “Ecological and Evolutionary Genomics”. Edited by Landry, C. and N. Aubin-Horth.
Kilvitis, H.J., Schrey, A.W., Ragsdale, A.K., Berrio, A., Phelps, S., and Martin, L.B., 2019. DNA methylation predicts immune gene expression in introduced house sparrows (Passer domesticus ). Journal of Avian Biology 50. https://doi.org/10.1111/jav.01965
Laine, V.N., Verschuuren, M., van Oers, K., Espín, S., Sánchez-Virosta, P., Eeva, T. and Ruuskanen, S., 2021. Does arsenic contamination affect DNA methylation patterns in a wild bird population? An experimental approach. Environmental Science & Technology 55: 8947-8954.
Lauer, M.E., Kodak, H., Albayrak, T., Lima, M., Ray, D., Simpson, E., Tevs, D., Sheldon, E., Martin, L., and Schrey, A.W., 2024 . Introduced house sparrows (Passer domesticus ) have greater variation in DNA methylation than native house sparrows. Journal of Heredity 115:11-8. p.esad067.
Li, H., and Durbin, R., 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25: 1754-1760.
Li, H., and Durbin, R., 2010. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatic 26: 589-595.
Liao, Y., Smyth, G. K., and Shi, W., 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30: 923-930.
Liebl, A., Schrey, A., Richards, C., and Martin, L., 2013. Patterns of DNA methylation throughout a range expansion of an introduced songbird. Integrative and Comparative Biology 53: 351-358.
Liebl, A.L., Schrey, A., Andrews, S.C., Sheldon, E., and Griffith, S.C., 2015. Invasion genetics: lessons from a ubiquitous bird, the house sparrow (Passer domesticus ). Current Zoology 61: 465–476.
Liebl, A.L., Wesner, J.S., Russell, A.F., and Schrey, A.W., 2021. Methylation patterns at fledgling predict dispersal in a cooperative breeding bird. PLOS One https://doi.org/10.1371/journal.pone.0252227
Lima, M., Macedo, R., Martins, T., Schrey, A., Martin, L., and Bensch, S., 2012. Genetic and morphometric divergence of an invasive bird: the introduced house sparrow (Passer domesticus ) in Brazil. PLoS ONE 7(12): e53332. doi:10.1371/journal.pone.0053332.
Lindner, M., Laine, V.N., Verhagen, I., Viitaniemi, H.M., Visser, M.E., van Oers, K. and Husby, A., 2021a. Rapid changes in DNA methylation associated with the initiation of reproduction in a small songbird. Molecular Ecology 30:3645-3659.
Lindner, M., Verhagen, I., Viitaniemi, H.M., Laine, V.N., Visser, M.E., Husby, A. and van Oers, K., 2021b. Temporal changes in DNA methylation and RNA expression in a small song bird: within-and between-tissue comparisons. BMC Genomics 22: 1-16.
Lundregan, S.L., Mäkinen, H., Buer, A., Holand, H., Jensen, H. and Husby, A., 2022. Infection by a helminth parasite is associated with changes in DNA methylation in the house sparrow. Ecology and Evolution 12(11), p.e9539.
Martin, L., Coon, C., Liebl, A., and Schrey, A., 2014. Surveillance for microbes and range expansion in house sparrows. Proceedings of the Royal Society B 281: 20132690.
McCain, K.M., Mansilla, G., Sheldon, E.L., Zimmer, C., Schrey, A.W., Rowe, M., Dor, R., Kohl, K., Soraker, J., Jensen, H., Mathot, K., Vu, T., Phoung, H.T., Jimeno, B., Buchanan, K., Thiam, M., Briskie, J., Martin, L.B., 2025. Microbial surveillance verses cytokine responsiveness in native and non-native house sparrows Biology Letters 21: 2024031.
McNew, S.M., Taff, C.C. and Vitousek, M.N., 2024. Manipulation of a social signal affects DNA methylation of a stress-related gene in a free-living bird. Journal of Experimental Biology 227(15), p.jeb246819.
Mäkinen, H., van Oers, K., Eeva, T., Laine, V.N. and Ruuskanen, S., 2019. The effect of experimental lead pollution on DNA methylation in a wild bird population. bioRxiv 851998.
O’Dea, R.E., Noble, D.W., Johnson, S.L., Hesselson, D., and Nakagawa, S., 2016. The role of non-genetic inheritance in evolutionary rescue: epigenetic buffering, heritable bet hedging and epigenetic traps. Environmental Epigenetics 2(1), dvv014.
Ray, D., Sheldon, E., Zimmer, C., Martin, L.B., and Schrey, A., 2024. Screening H3 histone acetylation in a wild bird, the house sparrow (Passer domesticus ) IOB 2024 Feb 27:obae004
Rice, W. R., 1989. Analyzing tables of statistical tests. Evolution, 43(1), 223-225.
Robinson, M.D., McCarthy, D.J., and Smyth, G.K., 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
Rubenstein, D.R., Skolnik, H., Berrio, A., Champagne, F.A., Phelps, S. and Solomon, J., 2016. Sex‐specific fitness effects of unpredictable early life conditions are associated with DNA methylation in the avian glucocorticoid receptor. Molecular Ecology 25: 1714-1728.
Schield, D.R., Walsh, M.R., Card, D.C., Andrew, A.L., Adams, R.H., and Castoe, T.A., 2016. Epi RAD seq: scalable analysis of genomewide patterns of methylation using next‐generation sequencing. Methods in Ecology and Evolution 7: 60-69.
Schrey, A., Grispo, M., Awad, M., Cook, M., McCoy, E., Mushinsky, H., Albayrak, T., Bensch, S., Butler, L., Fokidis, H., Jensen, H., Imboma, T., Kessler-Rios, M., Marzal, A., Stewart, I., Westerdahl, H., Westneat, D., Zehtindjiev, P., and Martin, L., 2011. Broad-scale latitudinal patterns of genetic diversity among native European and introduced house sparrow (Passer domesticus ) populations. Molecular Ecology 20: 1133-1143.
Schrey, A., Coon, C., Grispo, M., Awad, M., McCoy, E., Mushinsky, H., Richards, C., and Martin, L., 2012. Epigenetic variation may compensate for decreased genetic variation with introductions: a case study using house sparrows (Passer domesticus ) on two continents. Genetics Research International.Volume 2012 Article ID 979751.
Schrey, A., Alvarez, M., Foust, C.M., Kilvitis, H.J., Lee, J.D., Liebl, A.L., Martin, L.B., Richards, C.L., and Robertson, M., 2013. Ecological Epigenetics: beyond MS-AFLP. Integrative and Comparative Biology 53: 340-350.
Sepers, B., Mateman, A.C., Gawehns, F., Verhoeven, K.J. and van Oers, K., 2023. Developmental stress does not induce genome‐wide DNA methylation changes in wild great tit (Parus major ) nestlings. Molecular Ecology 32: 3960-3974.
Sepers, B., Verhoeven, K.J. and van Oers, K., 2024. Early developmental carry‐over effects on exploratory behaviour and DNA methylation in wild great tits (Parus major ). Evolutionary Applications 17(3), p.e13664.
Sheldon, E., Ragsdale, A.K., Schrey, A.W., and Griffith, S., 2018a. Epigenetic and genetic variation among three separate introductions of the house sparrow (Passer domesticus ) into Australia. Royal Society Open Science 5: 172185.
Sheldon, E., Schrey, A.W., Ragsdale, A.K., Griffith, S., 2018b. Brood size influences genome-wide DNA methylation levels in wild zebra finches (Taeniopygia guttata). Auk.135: 1113-1122.
Sheldon, E., Schrey, A., and Griffith, S.. 2020. Dynamic changes in DNA methylation during postnatal development in zebra finches (Taeniopygia guttata ) exposed to different temperature. Journal Avian Biology 51 doi.org/10.1111/jav.02294
Sheldon, E.L., Ton, R., Boner, W., Monaghan, P., Raveh, S., Schrey, A.W., and Griffith, S., 2022. Associations between DNA methylation and telomere length during early life: insight from wild zebra finches (Taeniopygia guttata ). Molecular Ecology 31: 6261-6272.
Sheldon, E., Zimmer, C., Hanson, H., Koussayer, B., Schrey, A., Reese, D., Wigley, P., Wedley, A.L., and Martin, L.B., 2023. High epigenetic potential protects songbirds against pathogenic Salmonella enterica infection. Journal of Experimental Biology jeb-245475.
Siller, S.J. and Rubenstein, D.R., 2019. A tissue comparison of DNA methylation of the glucocorticoid receptor gene (Nr3c1) in European starlings. Integrative and Comparative Biology 59: 264-272.
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: 17291.
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.
Taff, C.C., Campagna, L. and Vitousek, M.N., 2019. Genome‐wide variation in DNA methylation is associated with stress resilience and plumage brightness in a wild bird. Molecular Ecology 28: 3722-3737.
Taff, C.C., McNew, S.M., Campagna, L. and Vitousek, M.N., 2024. Corticosterone exposure is associated with long‐term changes in DNA methylation, physiology and breeding decisions in a wild bird. Molecular Ecology 33(15), p.e17456.
Viitaniemi, H.M., Verhagen, I., Visser, M.E., Honkela, A., Van Oers, K. and Husby, A., 2019. Seasonal variation in genome-wide DNA methylation patterns and the onset of seasonal timing of reproduction in great tits. Genome Biology and Evolution 11L 970-983.
Watson, H., Powell, D., Salmón, P., Jacobs, A. and Isaksson, C., 2021. Urbanization is associated with modifications in DNA methylation in a small passerine bird. Evolutionary Applications 14: 85-98.