Tapestree.jl

Unraveling the evolutionary tapestry:

Tapestree is a Julia package of phylogenetic analyses of diversification, trait and biogeographic dynamics.

Package Features

Tapestree currently holds the following phylogenetic models:

INSANE models using Bayesian Data augmentation (DA)

Diversification (birth-death) models

• "Constant Birth-Death" (CBD): implements a birth-death model of constant speciation rates and extinction rates under a Bayesian data augmentation algorithm, 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

• "Birth-Death Diffusion" (BDD): implements birth-death models where speciation rates follow a geometric Brownian motion with either no extinction, constant extinction, constant turnover, informed extinction or extinction diffusion under a Bayesian data augmentation algorithm, 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

• "Constant Fossilized Birth-Death" (CFBD): implements a birth-death model of constant speciation rates and extinction rates with piece-wise constant temporal changes in fossilization rates under a Bayesian data augmentation algorithm, as described in Quintero, I., Andréoletti, J., Silvestro, D., & Morlon, H. (2025). "The rise, decline and fall of clades". BioRxiv https://doi.org/10.1101/2025.03.20.644316

• "Fossilized Birth-Death Diffusion" (FBDD): implements a fossilized birth-death model where speciation and extinction rates follow separate geometric Brownian motions under a Bayesian data augmentation algorithm, as described in Quintero, I., Andréoletti, J., Silvestro, D., & Morlon, H. (2025). "The rise, decline and fall of clades". BioRxiv https://doi.org/10.1101/2025.03.20.644316

• "Occurrence Birth-Death" (OBD): implements a (fossilized or not) birth-death model of constant speciation rates and extinction rates with piece-wise constant temporal changes in fossilization rates and external occurrences under a Bayesian data augmentation algorithm, as described in Andréoletti J., Quintero, I., Morlon, H. (2025) The Occurrence Birth-Death Diffusion Process: Unraveling Diversification Histories with Fossils and Heterogeneous Rates. bioRxiv https://doi.org/10.1101/2025.08.26.672414

• "Occurrence Birth-Death Diffusion" (OBDD): implements a (fossilized or not) birth-death model where speciation and extinction rates follow separate geometric Brownian motions with piece-wise constant temporal changes in fossilization rates and external occurrences under a Bayesian data augmentation algorithm, as described in Andréoletti J., Quintero, I., Morlon, H. (2025) The Occurrence Birth-Death Diffusion Process: Unraveling Diversification Histories with Fossils and Heterogeneous Rates. bioRxiv https://doi.org/10.1101/2025.08.26.672414

Diffused Brownian motion (DBM) model

• DBM implements a trait evolution model where trait and its underlying rates follow separate geometric Brownian motions under a Bayesian data augmentation algorithm, as described in Quintero, I. (2025). The diffused evolutionary dynamics of morphological novelty. Proceedings of the National Academy of Sciences, U.S.A. 122 (18) e2425573122, https://doi.org/10.1073/pnas.2425573122.

Environmental and State dependent Speciation and Extinction (ESSE) model

• ESSE implements a joint geographic and environmental dependent 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

Trait and Range Interspecific Biogeographic Evolution (TRIBE) model

• TRIBE implements a joint model of trait evolution and biogeographic history shaped by biotic interactions under a Bayesian data augmentation algorithm, 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

Quick Start

• Installation

• Quick runs
• • INSANE models using Bayesian Data augmentation (DA)
  • • Reading a newick tree
    • Diversification (birth-death) models
    • • Constant Birth-Death (CBD):
      • Birth-Death Diffusion (BDD):
      • Constant Fossilized Birth-Death (CFBD):
      • Fossilized Birth-Death Diffusion (FBDD):
      • Occurrence Birth-Death Diffusion (OBDD):
    • Diffused Brownian motion (DBM) model
  • ESSE & TRIBE

Manual

• INSANE
• • Insane Bayesian data augmentation
  • Insane input and structures
  • Insane models
  • Insane plots and utilities
• TRIBE
• • Reference
  • Example
  • Function Documentation
• ESSE
• • Reference
  • Example
  • Function Documentation

Issues

Submit them to Issues