This document contains all data and R code required to replicate the analyses in 'Domestication via the commensal pathway in a fish-invertebrate mechanism' as published in Nature Communications. The R Markdown provided includes descriptions of all variables and the code used for the analysis of the following eight datasets: 1. Transects 2. Census of farms 3. Paired choice experiments 4. Predation experiment 1 5. Predation experiment 2 6. Timed observations 7. Farm algae composition 8. Longfin damselfish body condition In addition, the R Markdown also includes descriptions of all variables for two additional datasets: 9. Estimates of mysid swarm density 10. Mysid waste excretion and nutrient availability A PDF version of the R Markdown with all output is also provided. Please see the methods section of the associated manuscript for further information on data collection and analysis procedures. Author contributions to data collection and analysis: RMB, JMC, ZLC, TLS & WEF collected the data; WEF, RMB, JMC, ZLC & AM implemented the analyses. Correspond with: rohan.m.brooker@gmail.com

This research was supported by a National Geographic Research grant to RMB (9860-16). WEF was supported by the Alexander von Humboldt Foundation. We thank the Government of Belize for permission to conduct the study.