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

Zeng, S., Rosenbaum, S., Alberts, S.C., Archie, E.A., Li, F. (2021). Causal Mediation Analysis for Sparse and Irregular Longitudinal Data. Annals of Applied Statistics. [link]

Anderson J.A., Johnston R.A., Lea A.J., Campos F.A., Voyles T.A., Akinyi M.Y., Alberts S.C., Archie E.A., Tung J. (2021). High social status males experience accelerated epigenetic aging in wild baboons. eLife. 10:e66128 [link]

Gogarten, J., Rühlemann, M., Archie, E.A., Tung, J., Akoua-Koffi, C., Bang, C., Deschner, T., Muyembe-Tamfun, J.J., Robbins, M.M., Schubert, G., Surbeck, M., Wittig, R.M., Zuberbühler, K., Baines, J.F., Franke, A., Leendertz, F.H., Calvignac-Spencer, S. (2021). Primate phageomes are structured by superhost phylogeny and environment. Proceedings of the National Academy of Sciences. 118: e2013535118 [link]


Weibel, C.J., Tung, J. Alberts, S.C., Archie, E.A. (2020). Accelerated reproduction is not an adaptive response to early-life adversity in wild baboons. Proceedings of the National Academy of Sciences. 117:24909-24919 [pdf]

Campos, F.A., Villavicencio, F., Archie, E.A., Colchero, F., Alberts, S.C. (2020). Social relationships, social status, and survival in wild baboons: A tale of two sexes. Philosophical Transactions of the Royal Society. Proceedings of the Royal Society. 375:20190621.[link]

Levy*, E.J., Zipple*, M.N. McLean, E., Campos, F.A., Dasarig, M., Fogel, A.S., Franz, M. Gesquiere, L.R., Gordon, J.B., Grieneisen, L. Habig, B., Jansen, D.J., Learn, N.H., Weibel, C.J., Altmann, J., Alberts*, S.C., Archie*, E.A. (2020). A comparison of dominance rank metrics reveals multiple competitive landscapes in an animal society. Proceedings of the Royal Society. Proceedings of the Royal Society. 287:20201013 * equal contribution [pdf]

Rosenbaum, S.R., Zeng, S., Campos, F.A., Gesquiere, L., Altmann, J., Alberts, S.C., Li, F. Archie, E.A. (2020). Social bonds do not mediate the relationship between early adversity and adult glucocorticoids in wild baboons. Proceedings of the National Academy of Sciences. 117: 20052–20062 [pdf]

Gesquiere, L.R., Habig, B., Hansen, C., Li, A., Fried, K., Learn, N.H., Alberts, S.C., Graham, A.L., Archie, E.A. (2020). Noninvasive measurement of mucosal immunity in a free-ranging baboon population. American Journal of Primatology. 82: e23093. [pdf].

Levy, E.J., Gesquire, L.R., McLean, E., Franz, M., Warutere, J.K., Sayialel, S.N., Mututua, R.S., Wango, T.L., Oudu, V.K., Altmann, J., Archie, E.A., Alberts, S.C. (2020). Higher dominance rank is associated with lower glucocorticoids in wild female baboons: A rank metric comparison. Hormones and Behavior. 125: 104826 [pdf]

Sarkar, A., Harty, S., Johnson, K.V.-A., Moeller, A.H., Archie, E.A., Schell, L.D., Carmodu, R.N., Clutton-Brock, T.H., Dunbar, R.I.M., Burnet, P.W. (2020). Microbial transmission in animal social networks and the social microbiome. Nature Ecology & Evolution. [link]

Dunn, R.R., Amato, K.R., Archie, E.A., Arandjelovic, M., Crittenden, A.N., Nichols, L.M. (2020). The Internal, External and Extended Microbiomes of Hominins. Frontiers in Ecology and Evolution. 8:25. [pdf].


Grieneisen, L.E., Charpentier, M.J.E., Alberts, S.C., Blekhman, R., Bradburd, G., Tung, J., 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. [pdf].

Akinyi M.Y., Jansen, D., Habig, B., Gesquiere L.R., Alberts, S.C. Archie, E.A. (2019). Costs and drivers of helminth parasite infection in wild female baboons. Journal of Animal Ecology. 88: 1029-1043. [pdf]

Björk, J.R., Dasari, M., Grieneisen, L., Archie, E.A. (2019). Primate microbiomes over time: Longitudinal answers to standing questions in microbiome research. American Journal of Primatology. 2019: e22970. [pdf]

Björk J.B., Díez-Vives C., Astudillo-García C. Archie* E.A., Montoya* J.M. (2019). Vertical transmission of sponge microbiota is inconsistent and unfaithful. Nature Ecology and Evolution. 3: 1172-1183. *equal contribution  [pdf] [data and code]

McLean, E.M., Archie, E.A., Alberts, S.C. (2019). Lifetime Fitness in Wild Female Baboons: Trade-Offs and Individual Heterogeneity in Quality. American Naturalist. [pdf]

Zipple, M.N., Archie, E.A., Tung, J., Altmann, J., Alberts, S.C. (2019). Intergenerational effects of early adversity on survival in wild baboons. eLife. 8:e47433. [pdf] 

Habig, B., Jansen, D., Akinyi, M., Gesquiere, L., Alberts, S.C., Archie, E.A. (2019). Multi-scale predictors of parasite risk in wild male savanna baboons (Papio cynocephalus). Behavioral Ecology and Sociobiology. 73: 134. [pdf].

Obanda, V., Maingi, N., Muchemi, G., Ng’ang’a, C.J., Angelone, S., Archie, E.A. (2019). Infection dynamics of gastrointestinal helminths in sympatric non-human primates, livestock and wild ruminants in Kenya. PLoS One. 14: e0217929. [pdf]

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., Bandield, J.F. (2019). Megaphage infect Prevotella and variants are widespread in gut microbiomes. Nature Microbiology. 4: 693–700. [pdf]

Invited commentaries

Archie, E.A. (2019). Bat microbiomes are socially synchronized. Nature Ecology & Evolution. 3: 18-19. [pdf]


Habig, B., Doellmann, M.M., Woods, K., Olansen, J., Archie, E.A. (2018). Social status and parasitism in male and female vertebrates: a meta-analysis. Scientific Reports. 8: 3629. [open access]. Data and code on Github.

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 gene expression is widespread, sex-specific, and a precursor to high social status in wild male baboons. Proceedings of the National Academy of Sciences. 115: E12163-E12171. [pdf].

Gesquiere, L.R., Altmann, J. Archie, E.A., Alberts, S.C. (2018). Interbirth intervals in wild baboons: Environmental predictors and hormonal correlates. American Journal of Physical Anthropology. 166: 107-126. [pdf] .        

Lea, A.J., Tung, J. Archie, E.A., Alberts, S.C. (2018). Developmental plasticity research in evolution and human health: response to commentaries. Evolution, Medicine, and Public Health, eoy007. [pdf]


Grieneisen, L.G.,  Livermore, J., Alberts, S.C., Tung, J. Archie, E.A. (2017). Group living and male dispersal predict the core gut microbiome in wild baboons. Integrative and Comparative Biology 57: 770-785.   [pdf]

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

Lea, A.J., Tung, J. Archie, E.A., Alberts, S.C. (2017). Developmental plasticity: Bridging research in evolution and human health. Evolution, Medicine, and Public Health 2017: 162–175. [open access]

Zipple, M.N., Grady, J.H., Gordon, J.B., Chow, L.D., Archie, E.A., Altmann, J.A., Alberts, S.C., (2017). Conditional fetal killing by male baboons. Proceedings of the Royal Society 284: 20162561. [pdf]dryadbutton


Miller, E.A., Beasley, D.E., Dunn, R., Archie, E.A. (2016) Lactobacilli dominance and vaginal pH: Why is the human vaginal microbiome Unique? Frontiers in Microbiology 7: 1936. [pdf]

Tung*, J.T., Archie, E.A*., Altmann, J., Alberts, S.C. (2016). Cumulative early life adversity predicts longevity in wild baboons. Nature Communications  7: 11181. [pdf]  dryadbutton *equal contribution

Ezenwa, V.O., Archie, E.A., Craft, M.E., Hawley, D.M., Martin, L.B., Moore, J., White, L. (2016). Host behaviour-parasite feedback: an essential link between animal behaviour and disease ecology. Proceedings of the Royal Society 283:  20153078. [pdf]

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., Tung J. (2016). Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data. Scientific Reports 6:31519. [pdf]

Ren*, T., Grieneisen*, L.E., Alberts, S.C., Archie, E.A., Wu, M. (2016). Development, diet and dynamism: longitudinal and cross-sectional predictors of gut microbial communities in wild baboons.  Environmental Microbiology. 18:1312-1325. [pdf]  

*equal contribution


Archie E.A., Tung J. (2015). Social behavior and the microbiome. Current Opinions in Behavioral Sciences 6: 28-34. [pdf]

Habig, R. and Archie, E.A. (2015). Social status, immune response and parasitism in males: a meta-analysis. Philosophical Transactions of the Royal Society. 370: 20140109. [pdf] dryadbutton

Tung, J., Barriero,L.B., Burns, M., Grenier, J.C., Lynch, J., Grieneisen, L., Altmann, J., Alberts, S.C., Blekhman, R., Archie, E.A. (2015). Social networks predict gut microbiome composition in wild baboons. eLife. 4: e05224. [pdf]dryadbutton*

* highlighted in this eLife Insight by Jack Gilbert. [pdf]


Archie, E.A., Tung, J.T., Clark, M., Altmann, J., 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. 281: 20141261. [pdf] dryadbutton

Archie, E.A., Altmann, J., Alberts, S.C. (2014). Costs of reproduction in a long-lived female primate: injury risk and wound healing. Behavioral Ecology and Sociobiology. 68: 1183-1193. [pdf]dryadbutton

Chiyo, P.I., Grieneisen, L.E., Wittemyer, G., Moss, C.J., Lee, P.C., Douglas-Hamilton, I., Archie, E.A. (2014). The influence of social structure, habitat, and host traits on the transmission of Escherichia coli in wild elephants. PLoS ONE. 9: e93408. [pdf]

Chiyo, P.I., Wilson, J.W., Archie, E.A., Lee, P.C., Moss, C.J., Alberts, S.C. (2014). The influence of forage, protected areas, and mating prospects on grouping patterns in male elephants. Behavioral Ecology. 25: 1494-1504. [pdf]


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

Archie, E.A. (2013) Wound healing in the wild: stress, sociality, and energetic costs affect wound healing in natural populations. Parasite immuology. 35: 374-385. [pdf]


Archie, E.A., Altmann, J., & Alberts, S.C. (2012) Social status predicts wound healing in wild baboons. Proceedings of the National Academy of Sciences. 109: 9017-9022 [pdf]

McLean E.R., Kinsella J.M., Chiyo P., Obanda, V., Moss, C. Archie, E.A. (2012) Genetic identification of five strongyle nematode parasites in wild african elephants (Loxodonta africana). Journal of Wildlife Diseases. 48: 707-716. [pdf]

Archie, E.A. & Chiyo, P.I. (2012) Elephant behaviour and conservation: Social relationships, the effects of poaching, and genetic tools for management. Molecular Ecology 21: 765-778. [pdf]


Archie, E.A. & Theis, T.R. (2011) Animal behaviour meets microbial ecology. Animal Behaviour. 82: 425-436.[pdf]

Archie, E.A., Ezenwa, V.O. (2011) Population genetic structure and history of a generalist parasite infecting multiple sympatric host species. International Journal for Parasitology. 41:89-98. [pdf]

Chiyo, P.I., Archie, E.A., Hollister-Smith, J.A., Lee, P.C., Poole, J.H., Moss, C.J., Alberts, S.C. (2011) Association patterns of African elephants in all-male groups: the role of age and genetic relatedness. Animal Behaviour 81: 1093-1099. [pdf]

Chiyo P.I., Lee P.C., Moss C.J., Archie, E.A., Hollister-Smith, J.A., Alberts, S.C. (2011) No risk, no gain: effects of crop raiding and genetic diversity on body size in male elephants. Behavioral Ecology. 22: 552-558. [pdf]

Chiyo P.I,. Moss C.J., Archie E.A., Hollister-Smith J.A., Alberts S.C. (2011) Using molecular and observational techniques to estimate the number and raiding patterns of crop-raiding elephants. Journal of Applied Ecology. 48: 788-796. [pdf]


Ezenwa, V.O., Hines, A.M., Archie, E.A., Hoberg, E.P., Asmundsson, I.M., Hogg, J.T. (2010) Muellerius capillaris dominates the lungworm community of Bighorn Sheep at the National Bison Range, Montana. Journal of Wildlife Diseases. 46: 988-993.

Archie, E.A., Henry, T. Maldonado, J.E., Moss, C.J. Poole, J.H. Pearson, V.R. Murray, S. Alberts, S.C., Fleischer, R.C. (2010) Major histocompatibility complex variation and evolution at a single expressed DQA locus in two genera of elephants. Immunogenetics. 62: 85-100. [pdf]


Vance, E.R., Archie, E.A., & Moss, C.J. (2009) Social networks in African elephants. Computational and Mathematical Organization Theory. 15: 273-293. [pdf]

Archie, E.A., Luikart, G. & Ezenwa, V.O. (2009) Infecting epidemiology with genetics: a new frontier in disease ecology. Trends in Ecology and Evolution. 24: 21-30. [pdf]


Archie, E.A., Maldonado, J.E., Hollister-Smith, J.A., Poole, J.H., Moss, C.J., Fleischer, R.C. & Alberts, S.C. (2008) Fine-scale population genetic structure in a fission-fusion society. Molecular Ecology. 17: 2666-2679. [pdf]


Archie, E.A., Hollister-Smith, J.A., Poole, J.H., Lee, P.C., Moss, C.J., Maldonado, J.E., Fleischer, R.C., & Alberts, S.C. (2007) Behavioral inbreeding avoidance in wild African elephants. Molecular Ecology. 16: 4138-4148. [pdf]

Hollister-Smith, J.A., Poole, J.H., Archie, E.A., Vance, E.R., Georgiadis, N.J., Moss, C.J., & Alberts, S.C. (2007) Older is better: reproductive success increases with age in wild male African elephants. Animal Behaviour. 74: 287-296. [pdf]

2006 and earlier

Archie, E.A., Moss, C.J., and Alberts, S.C. (2006) The ties that bind: genetic relatedness predicts the fission and fusion of social groups in wild African elephants. Proceedings of the Royal Society B. 273: 513-522. [pdf]

Archie, E.A., Morrison, T.A., Foley, C.A.H., Moss, C.J. & Alberts, S.C. (2006) Dominance rank relationships among wild female African elephants (Loxodonta africana). Animal Behaviour. 71:117-127. [pdf]

Buchan, J.C., Archie, E.A., Van Horn, R.C., Moss, C.J., Alberts, S.C. (2005) Locus effects and sources of error in non-invasive genotyping. Molecular Ecology Notes. 5:680-683. [pdf]

Archie, E.A., Moss, C.J. and Alberts, S.C. (2003) Characterization of tetranucleotide microsatellite loci in the African Savannah Elephant (Loxodonta africana africana). Molecular Ecology Notes. 3:244-246. [pdf]

Archie, E.A. and Digby, L.J. (1999) Juvenile dominance in Eulemur macaco flavifrons: The influence of sex and maternal rank. Folia Primatologica. 70:277-281.

Book chapters

Alberts, S.C., Archie, E.A., Gesquire, L.R., Altmann, J.A., Vaupel, J.W., Christiansen, K. (2014) The male-female health-survival paradox: A comparative perspective on sex differences in aging and mortality.  In: Advances in Biodemography: Cross-Species Comparisons of Social Environments and Social Behaviors, and their Effects on Health and Longevity. (Eds. Weinstein, M., Lane, M.) Washington, DC: National Research Council and National Academies Press. pp. 339-363. [pdf]

Archie, E.A., Fitzpatrick, C.L., Moss, C.J., & Alberts, S.C., (2011) The population genetics of the Amboseli and Kilimanjaro elephants. In: Amboseli Elephants: A long-term perspective on a long-lived mammal (Eds. C.J. Moss, H. Croze). Chicago: University of Chicago Press. [pdf]

Archie, E.A., Moss, C.J., and Alberts, S.C. (2011) Friends and relations: kinship and the nature of female elephant social relationships. In: Amboseli Elephants: A long-term perspective on a long-lived mammal (Eds. C.J. Moss, H. Croze). Chicago: University of Chicago Press. [pdf]

the Archie Lab