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Tapestree.jl

Unraveling the evolutionary tapestry: Tapestree is a Julia package of phylogenetic analyses of diversification, trait and biogeographic dynamics.

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See the Documentation for examples and manual.

References

For the BDD model:

  1. "Birth-Death Diffusion" (BDD): which implements speciation rates following a geometric Brownian motion with no extinction, constant extinction, constant turnover or extinction diffusion as described in Quintero, I., Lartillot, N., & Morlon, H. (2024). "Imbalanced speciation pulses sustain the radiation of mammals". Science, 384 (6699) 1007-1012 https://doi.org/10.1126/science.adj2793

For the ESSE model:

  1. "Environmental and State dependent Speciation and Extinction" (ESSE): which implements a joint geographic and environmental model of diversification as described in Quintero, I., Landis, M. J., Jetz, W., & Morlon, H. (2022). The build-up of the present-day tropical diversity of tetrapods. Proceedings of the National Academy of Sciences, 2023. 120 (20) e2220672120. https://doi.org/10.1073/pnas.2220672120

For the TRIBE model:

  1. "Trait and Range Interspecific Biogeographic Evolution" (TRIBE): which implements a joint model of trait evolution and biogeographic history as described in Quintero, I., & Landis, M. J. (2020). Interdependent phenotypic and biogeographic evolution driven by biotic interactions. Systematic biology, 69 (4), 739-755. https://doi.org/10.1093/sysbio/syz082