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Host repertoire evolution

  • Model files: models/host-repertoire-evolution/flat-root-prior-HRM.tppl and models/host-repertoire-evolution/subroot-HRM.tppl.

  • Example input data: models/host-repertoire-evolution/testdata_flat-root-prior-HRM.json and models/host-repertoire-evolution/testdata_subroot-HRM.json.

  • Brief info: The subroot model considers that there is a branch subtending the root of the symbiont tree, which allows the host gain/loss process to reach stationarity before diversification of the symbiont clade starts. This version of the model is identical to the model implemented in RevBayes. The flat-root-prior model considers that the symbiont tree - and thus the host gain/loss process - starts at the root.

  • Reference: Braga, M. P., Landis, M. J., Nylin, S., Janz, N., & Ronquist, F. (2020). Bayesian inference of ancestral host–parasite interactions under a phylogenetic model of host repertoire evolution. Systematic biology, 69(6), 1149-1162. https://doi.org/10.1093/sysbio/syaa019