Publications

2021

Grieneisen L., Dasari M., Gould T.J., Björk J.R., Grenier J., Yotova V., Jansen D., Gottel N., Gordon J.B., Learn N.H., Gesquiere L.R., Wango T.L., Mututua R.S., Warutere J.K., Siodi L., Gilbert J.A., Barreiro L.B., Alberts S.C., Tung* J., Archie* E.A., Blekhman* R. (2021). Gut microbiome heritability is nearly universal but environmentally contingentScience. 373:181-186.  *these authors contributed equally

[Link to paper] [Zenodo]

Colchero, F. Aburto, J.M., Archie, E.A., Boesch, C. Breuer, T., Campos, F.A., Collins, A. Conde, D.A., Cords, M., Crockford, C. Thompson, M.E., 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.N., 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., Villavicencio, F., Wittig, R.M., Wrangham, R.W., Zuberbühler, K., Vaupel, J.W., Alberts, S.C. (2021). The long lives of primates and the ‘invariant rate of ageing’ hypothesisNature Communications: 12: 3666

[Link to paper] [Dryad]

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

[Link to paper] [Dryad]

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 environmentProceedings of the National Academy of Sciences. 118: e2013535118

[Link to paper] [Zenodo] [Github]

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 baboonseLife. 10: e66128

[Link to paper] [Dryad]

Zeng S., Rosenbaum S., Alberts S.C., Archie E.A., Li F. (2021). Causal Mediation Analysis for Sparse and Irregular Longitudinal DataAnnals of Applied Statistics. 15: 747-767

[Link to paper]

2020

Weibel, C.J., Tung, J.T., 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.

[Link to paper] [Dryad]

Levy*, E.J., Zipple*, M.N. McLean, E., Campos, F.A., Dasari,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. 287: 20201013 *these authors contributed equally

[Link to paper] [Data availability]

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. 375: 20190621

[Link to paper] [Dryad]

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

[Link to paper] [Dryad] [Github]

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

[Link to paper] [Dryad]

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

[Link to paper]

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 populationAmerican Journal of Primatology. 82: e23093

[Link to paper] [Dryad]

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.

[Link to paper]

2019

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

[Link to paper] [Dryad]

McLean, E.M., Archie, E.A., Alberts, S.C. (2019). Lifetime fitness in wild female baboons: trade-offs and individual heterogeneity in qualityAmerican Naturalist. 194: 745-759

[Link to paper] [Dryad]

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 *these authors contributed equally

[Link to paper] [Github] [OSF]

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 speciesProceedings of the Royal Society B. 286: 20190431 

[Link to paper] [Dryad] [Github]

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 baboonsJournal of Animal Ecology. 88: 1029-1043

[Link to paper] [Dryad]

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

[Link to paper] [Dryad]

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

[Link to paper]

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

[Link to paper]

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

[Link to paper] [Github]

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

[Link to paper]

2018

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

[Link to paper]

Habig, B., Doellman, 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

[Link to paper]

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

[Link to paper] [Dryad]

Lea, A.J., Tung, J., Archie, E.A., Alberts, S.C. (2018). Developmental plasticity: Bridging research in evolution and human healthEvolution Medicine and Public Health 2017: 162–175

[Link to paper]

2017

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

[Link to paper] [Dryad]

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

[Link to paper] [Dryad]

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 B 284: 20162561

[Link to paper] [Dryad]

2016

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

[Link to paper]

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

[Link to paper]

Tung*, J., Archie*, E.A., Altmann, J., Alberts, S.C. (2016). Cumulative early adversity predicts longevity in wild baboons. Nature Communications. 7:11181 *these authors contributed equally

[Link to paper] [Dryad]

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

[Link to paper]

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: 1312-25
*these authors contributed equally

[Link to paper]

2015

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

[Link to paper]

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

[Link to paper] [Dryad]

Habig, R., Archie, E.A. (2015). The effect of social status on immune function in males: A meta-analysis. Philosophical Transactions of the Royal Society B. 370: 20140109

[Link to paper]

2014

Archie, E.A., Tung, J., 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 B. 281: 20141261

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

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

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

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

2013

Runcie, D.E., Wiedmann, D.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 B. 368: 20120345

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

2012

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

McLean, E.R., Kinsella, J.M., Chiyo, P.I. Obanda, V., Moss, C.J., and Archie, E.A. (2012) Genetic identification of five Strongyle nematode parasites in wild African elephants (Loxodonta africana). Journal of Wildlife Disease. 48: 707-716

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

2011

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

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

Archie, E.A., Theis, K.R. (2011) Animal behavior meets microbial ecology. Animal Behaviour 82: 425-436

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

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

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.

2010

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

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

Before 2010

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

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

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

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

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

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

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.

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

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

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

the Archie Lab