Genes, geology and germs: Gut microbiota across a primate hybrid zone are explained by site soil properties, not host species

Laura E. Grieneisen, Marie J.E. Charpentier, Susan C. Alberts, Ran Blekhman, Gideon Bradburd, Jenny Tung, Elizabeth A. Archie

Research output: Contribution to journalArticlepeer-review

15 Scopus citations


Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population differences in host behaviours, environments, genetics and geographical distance. However, which factors are most important remains unknown. Here, we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon populations spanning a natural hybrid zone. Sampling across a hybrid zone allowed us to additionally test whether phylosymbiosis (codiversification between hosts and their microbiota) is detectable in admixed, closely related primates.We found little evidence of genetic effects: none of host genetic ancestry, host genetic relatedness nor genetic distance between host populations were strong predictors of baboon gut microbiota. Instead, gut microbiota were best explained by the baboons' environments, especially the soil's geologic history and exchangeable sodium. Indeed, soil effects were 15 times stronger than those of host-population FST, perhaps because soil predicts which foods are present, or because baboons are terrestrial and consume soil microbes incidentally with their food. Our results support an emerging picture in which environmental variation is the dominant predictor of host-associated microbiomes. We are the first to show that such effects overshadow host species identity among members of the same primate genus.

Original languageEnglish (US)
Article number20190431
JournalProceedings of the Royal Society B: Biological Sciences
Issue number1901
StatePublished - Apr 24 2019

Bibliographical note

Funding Information:
We acknowledge a Marie Curie International Reintegration Grant (proposal 239301), the National Science Foundation and the National Institutes of Aging, including IOS 1053461, DEB 1840223, R21 AG055777, IBN 9985910, IBN 0322613, IBN 0322781, DEB 0846286, DEB 0846532, IOS 0919200 and R21 AG049936. We also thank Duke University, Princeton University, the University of Notre Dame, the Chicago Zoological Society, the Max Planck Institute for Demography, the L. S. B. Leakey Foundation and the National Geographic Society for support over the years.

Publisher Copyright:
© 2019 The Author(s).


  • Papio
  • genetic effects
  • hybrid zone
  • isolation by distance
  • microbiome
  • species sorting


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