bioRxiv preprints

Anderson, J.A., Lea, A.J., Voyles, T.N., Akinyi, M.Y., Nyakundi, R., Ochola, L., Omondi, M., Nyundo, F., Zhang, Y., Campos, F.A., Alberts, S.C., Archie, E.A., and Tung, J. 2021. Distinct gene regulatory signatures of dominance rank and social bond strength in wild baboons. bioRxiv: [Link]

Fogel, A.S., McLean, E.M., Gordon, J.B., Archie, E.A., Tung, J.*, and Alberts, S.C.* 2020. Genetic ancestry predicts male-female affiliation in a natural baboon hybrid zone. bioRxiv: [Link]


Campos, F.A., Archie, E.A., Gesquiere, L.R., Tung, J., Altmann, J., and Alberts, S.C. 2021. Glucocorticoid exposure predicts survival in female baboons. Science Advances 7: eabf6759. [Open Access]

Anderson, J.A.*, Johnston, R.A.*, Lea, A.J., Campos, F.A., Voyles, T.N., Akinyi, M.Y., Alberts, S.C., Archie, E.A., and Tung, J. 2021. High social status males experience accelerated epigenetic aging in wild baboons. eLife 10: e166128 [Open Access]

Gogarten, J.F., Ruhlemann, M., Archie, E.A., Tung, J., Akoua-Koffi, C., Bang, C., Deschner, T., Muyembe-Tamfun, J., Robbins, M.M., Schubert, G., Surbeck, M., Wittig, R.M., Zuberbuhler, K., Baines, J.F., Franke, A., Leendertz, F.H., and Calvignac-Spencer, S. 2021. Primate phageomes are structured by superhost phylogeny and environment. PNAS 118: e2013535118 [Link]

Johnston, R.A., Vuillioud, P., Thorley, J., Kirveslahti, H., Shen, L., Mukherjee, S., Karner, C., Clutton-Brock, T.H., and Tung, J. 2021. Morphological and genomic shifts in mole-rat 'queens' increase fecundity but reduce skeletal integrity. eLife 10: e65760 [Open Access]

Colchero, F., Aburto, J.M., Archie, E.A., Boesch, C., Breuer, T., Campos, F.A., Collins, A., Conde, D.A., Cords, M., Crockford, C., Emery Thompson, M., Fedigan, L.M., Fichtel, C., Groenenberg, M., Hobaiter, C., Kappeler, P.M., Lawler, R.R., Lewis, R.J., Machanda, Z.P., Manguette, M.L., Muller, M., Packer, C., Parnell, R.J., Perry, S., Pusey, A.E., Robbins, M.M., Seyfarth, R.M., Silk, J.B., Staerk, J., Stoinski, T.S., Stokes, E.J., Strier, K.B., Strum, S.C., Tung, J., Vaupel, J.W., Villavicencio, F., Wittig, R.M., Wrangham, R.W., Zuberbühler, K., and Alberts, S.C. 2021. The long lives of primates and the 'invariant rate of ageing' hypothesis. Nature Communications 12: 3666. [Open Access]

Miller, C.M., Snyder-Mackler, N., Nguyen, N., Fashing, P.J., Tung, J., Wroblewski, E.E., Gustison, M.L., and Wilson, M.L. 2021. Extra-group paternity in gelada monkeys (Theropithecus gelada) at Guassa, Ethiopia and a comparison with other primates. Animal Behaviour 177: 277-301. [Link]

Johnston, R.A., Rheinwald, J.G., vonHoldt, B.M., Stahler, D.R., Lowry, W., Tung, J., and Wayne, R.K. 2021. K locus effects in gray wolves: experimental assessment of TLR3 signaling and the gene expression response to canine distemper virus. Journal of Heredity [Link]


Weibel, Chelsea J., Tung, J., Alberts, S.C., and Archie, E.A. 2020. Accelerated reproduction is not an adaptive response to early-life adversity in wild baboons. PNAS 117: 24909-24919. [Open Access]

Anderson, J.A., Vilgalys, T.P., and Tung, J. 2020. Broadening primate genomics: new insights into the ecology and evolution of primate gene regulation. Current Opinion in Genetics & Development 62: 16-22. [Link]

Snyder-Mackler, N., Burger, J.R., Gaydosh, L., Belsky, D., Noppert, G.A., Campos, F.A., Bartolomucci, A., Yang, Y.C., Aiello, A.E., O'Rand, A., Harris, K.M., Shively, C.A., Alberts, S.C., and Tung, J. 2020. Social determinants of health and survival in humans and other animals. Science 368: eaax9553. [Link]

Sanz, J., Maurizio, P.L., Snyder-Mackler, N., Simons, N.D., Voyles, T.P., Kohn, J., Michopoulos, V., Wilson, M.E., Tung, J.*, and Barreiro, L.B.* 2020. Social history and exposure to pathogen signals modulate social status effects on gene regulation in rhesus macaques. PNAS 117: 23317-23322 [Link]


Fan, Y., Vilgalys, T.P., Sun, S., Peng, Q., Tung, J., and Zhou, X. 2019. IMAGE: high-powered detection of genetic effects on DNA methylation using integrated methylation QTL mapping and allele-specific analysis. Genome Biology 20: doi:10.1186/s13059-019-1813-1. [Open Access]

Zipple, M.N., Archie, E.A., Tung, J., Altmann, J., and Alberts, S.C. 2019. Intergenerational effects of early adversity on survival in wild baboons. eLife 8:e47433. [Open Access]. See also the related Insight by Thayer and Sweetman.

Simons, N.D. and Tung, J. 2019. Social status and gene regulation: conservation and context-dependence in primates. Trends in Cognitive Sciences: [Link]

Turan, Z.G., Parvizi, P., Donertas, H.M., Tung, J., Khaitovich, P. and Somel, M. 2019. Molecular footprint of Medawar's mutation accumulation process in mammalian aging. Aging Cell: [Open Access]

Grieneisen, L.E., Charpentier, M.J.E., Alberts, S.C., Blekhman, R., Bradburd, G., Tung, J., and Archie, E.A. 2019. Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species. Proceedings of the Royal Society B 286: 20190431. [Link]

Debray, R., Snyder-Mackler, N., Kohn, J.N., Wilson, M.E., Barreiro, L.B., and Tung, J. 2019. Social affiliation predicts mitochondrial DNA copy number in female rhesus macaques. Biology Letters 15: 20180643. [Link]

Devoto, A.E., Santini, J.M., Olm, M.R., Anantharaman, K., Munk, P., Tung, J., Archie, E.A., Turnbaugh, P.J., Seed, K.D., Blekhman, R., Aarestrup, F.M., Thomas, B.C., and Banfield, J. 2019. Megaphage infect Prevotella and variants are widespread in gut microbiomes. Nature Microbiology: [Open Access]

Rogers, J., Raveendran, M., Harris, R.A., Mailund, T., Leppala, K., Athanasiadis, G., Schierup, M., Cheng, J., Munch, K., Walker, J.A., Konkel, M.K., Jordan, V.E., Steely, C.J., Beckstrom, T.O., Bergey, C., Burrell, A., Schrempf, D., Noll, A., Kothe, M., Kopp, G.H., Liu, Y., Murali, S., Billis, K., Martin, F.J., Muffato, M., Cox, L., Else, J., Disotell, Muzny, D., Phillips-Conroy, J., Aken, B., Eichler, E.E., Marques-Bonet, T., Kosiol, C., Batzer, M.A., Hahn, M.W., Tung, J., Zinner, D., Roos, C., Jolly, C.J., Gibbs, R.A., Worley, K.C., and the Baboon Genome Analysis Consortium. 2019. The comparative genomics and complex population history of Papio baboons. Scientific Advances 5: eaau6947. [Open Access]

Snyder-Mackler, N., Sanz, J., Kohn, J.N., Voyles, T.N., Pique-Regi, R., Wilson, M.E., Barreiro, L.B., and Tung, J. 2019. Social status alters chromatin accessibility and the gene regulatory response to glucocorticoid stimulation in rhesus macaques. Proceedings of the National Academy of Sciences USA: [Open Access]. See also the related Commentary by Hofmann and Friesen.

Vilgalys, T.P., Rogers, J., Jolly, C., the Baboon Genome Analysis Consortium, Mukherjee, S., and Tung, J. 2018. Evolution of DNA methylation in Papio baboons. Molecular Biology & Evolution: 36: 527-540. [Link]


Lea, A.J., Vockley, C.M., Johnston, R.A., Del Carpio, C.A., Barreiro, L.B., Reddy, T.E., and Tung, J. 2018. Genome-wide quantification of the effects of DNA methylation on human gene regulation. eLife 7: e37513. [Open Access]

Lea, A.J., Akinyi, M.Y., Nyakundi, R., Mareri, P., Nyundo, F., Kariuki, T., Alberts, S.C., Archie, E.A., and Tung, J. 2018. Dominance rank-associated immune gene expression is widespread, sex-specific, and a precursor to high social status in wild male baboons. Proceedings of the National Academy of Sciences USA: [Open Access]. See also the related Commentary by Hofmann and Friesen.

Lea, A.J., Tung, J., Archie, E.A., and Alberts, S.C. 2018. Developmental plasticity: bridging research in evolution and human health. Evolution, Medicine, and Public Health 2017: 162-175. [Open Access]


Grieneisen, L., Livermore, J., Alberts, S.C., Tung, J., and Archie, E.A. 2017. Group living and male dispersal predict the core gut microbiome in wild baboons. Integrative and Comparative Biology: doi:10.1093/icb/icx046. [Link]

Tung, J. and Barreiro, L.B. 2017. The contribution of admixture to primate evolution. Current Opinions in Genetics & Development 47: 61-68. [Link]

Wango, T.L., Musiega, D., Mundia, C.N., Altmann, J., Alberts, S.C.*, and Tung, J.* 2017. Climate and land cover analysis suggest no strong ecological barriers to gene flow in a natural baboon hybrid zone. International Journal of Primatology: doi: 10.1007/s10764-017-9989-2. [Link]

Lea, A.J., Vilgalys, T.P., Durst, P.A.P., and Tung, J. 2017. Maximizing ecological and evolutionary insight from bisulfite sequencing data sets. Nature Ecology & Evolution 1: 1074 - 1083. [Link]. [bioRxiv preprint]

Snyder-Mackler, N. and Tung, J. 2017. Vasopressin and the neurogenetics of parental care ("Spotlight" article on Bendesky et al. 2017, Nature). Neuron 95: 9 - 11. (*non-peer reviewed). [Link]

Miller, E.A., Livermore, J.A., Alberts, S.C., Tung, J., and Archie, E.A. 2017. Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons. Microbiome 5: 8. [Open Access]

Sun, S., Hood, M., Scott, L., Peng, Q., Mukherjee, S., Tung, J., and Zhou, X. 2017. Differential expression analysis for RNAseq using Poisson mixed models. Nucleic Acids Research: doi: 10.1093/nar/gkx204 [Open Access]


Snyder-Mackler, N.+, Sanz, J.+, Kohn, J.N., Brinkworth, J.F., Morrow, S., Shaver, A.O., Grenier, J., Pique-Regi, R., Johnson, Z.P., Wilson, M.E., Barreiro, L.B.*, and Tung, J.* 2016. Social status alters immune regulation and response to infection in macaques. Science 354: 1041-1045. [Link]. See also the related Perspective by Robert Sapolsky.

Nédélec, Y., Sanz, J., Baharian, G., Szpiech, Z.A., Pacis, A., Dumaine, A., Grenier, J., Freiman, A., Sams, A.J.,  Hebert, S., Sabourin, A.P., Luca, F., Blekhman, R., Hernandez, R.D., Pique-Regi, R., Tung, J., Yotova, V., and Barreiro, L.B. 2016. Genetic ancestry and natural selection drive population differences in immune responses to infection in humans. Cell 167: 657-669. [Link]

Kohn, J.N., Snyder-Mackler, N., Barreiro, L.B., Johnson, Z.P., Tung, J.*, and Wilson, M.E.* Dominance rank causally affects personality and glucocorticoid regulation in female rhesus macaques. Psychoneuroendocrinology 74: 179-188 [Link]).

Blekhman, R., Tang, K., Archie, E.A., Barreiro, L.B., Johnson, Z.P., Wilson, M.E., Kohn, J., Yuan, M.L., Gesquiere, L., Grieneisen, L.E., and Tung, J. Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data. Scientific Reports 6: 31519 [Open Access]

Wall, J.D., Schlebusch, S.A., Alberts, S.C., Cox, L.A., Snyder-Mackler, N., Nevonen, K., Carbone, L., and Tung, J. 2016. Genome-wide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons. Molecular Ecology 25: 3469-3483. [Link] [Download accepted version]

Snyder-Mackler, N., Majoros, W.H., Yuan, M.L., Shaver, A.O., Gordon, J.B., Kopp, G.H., Schlebusch, S.A., Wall, J.D., Alberts, S.C., Mukherjee, S., Zhou, X., and Tung, J. 2016. Efficient genome-wide sequencing and low coverage pedigree analysis from non-invasively collected samples. Genetics 203: 699-714. [Open Access] [Software available here]

Charruau, P., Johnston, R., Stahler, D.R., Lea, A.J., Snyder-Mackler, N., Smith, D.W., vonHoldt, B., Cole, S.W., Tung, J., and Wayne, R.K. 2016. Pervasive effects of aging on gene expression in wild wolves. Molecular Biology and Evolution 33: 1967-1978. [Link]

Tung, J.*, Archie, E.A.*, Altmann, J., and Alberts, S.C. 2016. Cumulative early adversity predicts longevity in wild baboons. Nature Communications 7: 11181. [Open Access]

Snyder-Mackler, N., Kohn, J.N., Barreiro, L.B., Johnson, Z.P., Wilson, M.E., and Tung, J. 2016. Social status drives social relationships in groups of unrelated female rhesus macaques. Animal Behaviour 111: 207-317. [Link]

Lea, A.J., Altmann, J., Alberts, S.C., and Tung, J. 2016. Resource base influences genome-wide DNA methylation levels in wild baboons (Papio cynocephalus). Molecular Ecology 25: 1681-1696. [Link]


Lea, A.J., Tung, J.*, and Zhou, X.* 2015. A flexible, efficient binomial mixed model for identifying differential DNA methylation in bisulfite sequencing data. PLoS Genetics 11: e1005650. [Open Access] [Software available here]

Pacis, A., Tailleux, L., Morin, A.M., Lambourne, J., MacIsaac, J., Yotova, V., Dumaine, A., Danckaert, A., Luca, F., Grenier, J.C., Hansen, K.D., Gicquel, B., Yu, M., Pai, A., He, C., Tung, J., Pastinen, T., Kobor, M.S., Pique-Regi, R., Gilad, Y., and Barreiro, L.B. 2015. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Research 25: 1801-1811. [Open Access]

Franz, M., McLean, E., Tung, J., Altmann, J., and Alberts, S.C. 2015. Self-organizing dominance hierarchies in a wild primate population. Proceedings of the Royal Society B 282: 20151512. [Link]

Archie, E.A. and Tung, J. 2015. Social behavior and the microbiome. Current Opinions in Behavioral Sciences 6: 28-34. [Open Access]. See the related Insight by Jack Gilbert.

Galbany, J., Tung, J., Altmann, J., Alberts, S.C. 2015. Canine length in wild male baboons: maturation, aging, and social dominance rank. PLoS ONE 10: e0126415. [Open Access]

Tung, J., Barreiro, L.B., Burns, M., Grenier, J.C., Lynch, J., Grieneisen, L., Altmann, J., Alberts, S.C., Blekhman, R., and Archie, E.A. 2015. Social networks predict gut microbiome composition in wild baboons. eLife 4: e05224. [Open Access]

Lea, A.J., Altmann, J., Alberts, S.C.*, and Tung, J.* 2015. Developmental constraints in a wild primate. American Naturalist 185: 809-821. [Link]

Tung, J.*, Zhou, X.*, Alberts, S.C., Stephens, M., and Gilad, Y. 2015. The genetic architecture of gene expression levels in wild baboons. eLife 4: e04729. [Open Access]


Archie, E.A., Tung, J., Clark, M., Altmann, J., and Alberts, S.C. 2014. Social affiliation matters: both same-sex and opposite-sex relationships predict survival in wild female baboons. Proceedings of the Royal Society B. 281: 20141261. [Link]

Tung, J. 2014. Genes revisited: the biodemography of social environmental variation through a functional genomic lens. In: Lane, M. and Weinstein, M., eds. Sociality, Hierarchy, Health: Comparative Biodemography. Washington, DC: The National Academies Press: 39 - 64. [Link]

Snyder-Mackler, N.M., Somel, M., and Tung, J. 2014. Shared signatures of social stress and aging in PBMC gene expression profiles. Aging Cell 13: 954-957 [Open Access]

Gallego Romero, I., Pai., A.A., Tung, J., and Gilad, Y. 2014. RNA-seq: impact of RNA degradation on transcript quantification. BMC Biology 12: 42. [Open Access]


Tung, J. and Gilad, Y. 2013. Social environmental effects on gene regulation. Cellular and Molecular Life Sciences 70: 4323-4339. [Open Access]

Runcie, D.E., Wiedmann, R.T., Archie, E.A., Altmann, J., Wray, G.A., Alberts, S.C., and Tung, J. 2013. Social environment influences the relationship between genotype and gene expression in wild baboons. Philosophical Transactions of the Royal Society B 368: 20120345. [Free full text]

Loisel, D.A. and Tung, J. 2013. Genetic variation in the immune system of old world monkeys: functional and selective effects. In: Brinkworth, J.F. and Pechenkina, E.A., eds. Primates, Pathogens, and Evolution: A Context for Understanding Emerging Disease. New York, NY: Springer: 65 - 90.

Akinyi, M.Y., Tung, J., Jeneby, M., Patel, N.B., Altmann, J., and Alberts, S.C. 2013. Role of grooming in reducing tick load in wild baboons (Papio cynocephalus). Animal Behaviour 85: 559-568. [Free full text]


Harper, K.N., Fyumagwa, R.D., Hoare, R. Wambura, P.N., Coppenhaver, D.H., Sapolsky, R.M., Alberts, S.C., Tung, J., Kilewo, M., Batamuzi, E.K., Leendertz, F.H., Knauf, S., and Armelagos, G.J. 2012. Treponema pallidum infection in the wild baboons of East Africa: distribution and genetic characterization of the strains responsible. PLoS One 7: e50882. [Open Access]

Barreiro, L.B. and Tung, J. 2012. Perspective: Getting under--and through--the skin: ecological genomics of chytridiomycosis infection in frogs. Molecular Ecology 21: 3095-3097. [Free full text]

Tung, J., Barreiro, L.B., Johnson, Z.P., Hansen, K.D., Michopoulous, V., Toufexis, D., Michelini, K.M., Wilson, M.E., and Gilad, Y. 2012. Social environment is associated with gene regulatory variation in the rhesus macaque immune system. Proceedings of the National Academy of Sciences USA 109: 6490-6495 [Open Access]

Tung, J.*, Charpentier, M.J.E.*, Mukherjee, S., Altmann, J., and Alberts, S.C. 2012. Genetic effects on mating success and partner choice in a social mammal. American Naturalist 180: 113-129. [Free full text]

Charpentier, M.J.E.*, Fontaine, M.C.*, Cherel, E., Renoult, J.P., Jenkins, T., Benoit, L., Barthes, N., Alberts, S.C., Tung, J. 2012. Genetic structure in a dynamic baboon hybrid zone corroborates behavioral observations in a hybrid population. Molecular Ecology 21: 715-731. [Free full text]

Babbitt, C.C., Tung, J., Wray, G.A., and Alberts, S.C. 2012. Changes in gene expression associated with reproductive maturation in wild female baboons. Genome Biology and Evolution 4: 102-109.[Free full text]

2007 - 2011

Tung, J., Akinyi, M., Mutura, S., Altmann, J., Wray, G.A.*, and Alberts, S.C.* 2011. Allele specific gene expression in a wild nonhuman primate population. Molecular Ecology 20: 725-739. [Link]

Tung, J., Alberts, S.C.*, and Wray, G.A.* 2010. Evolutionary genetics in wild primates: combining genetic approaches with field studies of natural populations. Trends in Genetics 26: 353-362. [Free full text]

Tung, J. and Wray, G.A. 2009. Evolution of traits deduced from genome comparisons. In: The Encyclopedia of Life Sciences: doi:10.1002/9780470015902.a0021746. [Link]

Tung, J., Fedrigo, O., Haygood, R., Mukherjee, S.*, and Wray, G.A.* 2009. Genomic features that predict allelic imbalance in humans suggest patterns of constraint on gene expression variation. Molecular Biology and Evolution 26: 2047-2059. [Free full text]

Tung, J., Primus, A., Bouley, A.J., Severson, T., Alberts, S.C.*, and Wray, G.A.* 2009. Evolution of a malaria resistance gene in wild primates. Nature 460: 388-392. [Link]

Leonhardt, S.*, Tung, J.*, Camden, J., Leal, M., and Drea, C.M. 2009. Seeing red: behavioral evidence of trichromatic color vision in strepsirrhine primates. Behavioral Ecology 20: 1-12. [Free full text]

Tung, J., Charpentier, M.J.E., Garfield, D.A., Altmann, J., and Alberts, S.C. 2008. Genetic evidence reveals dynamic patterns of hybridization in a wild baboon population. Molecular Ecology 17: 1998-2011. [Link]

Charpentier, M.J.E., Tung, J., Altmann, J., and Alberts, S.C. 2008. Age at maturity in wild baboons: genetic, demographic, and environmental influences. Molecular Ecology 17: 2026-2040. [Link]

Tung, J., Rudolph, J., Altmann, J., and Alberts, S.C. 2007. Parallel effects of genetic variation on ACE activity in baboons and humans. American Journal of Physical Anthropology 134: 1-8. [Link]