PhyloTraits

PhyloTraits is a Julia package with core utilities for phylogenetic networks. See the PhyloNetworks package, which PhyloTraits depends on, for background on phylogenetic networks and for how to get help.

References

See them in bibtex format.

Quick links for methods about trait evolution on networks:

• Teo, Rose, Bastide & Ané (2023). Accounting for intraspecific variation in continuous trait evolution on a reticulate phylogeny. Bulletin of the Society of Systematic Biologists, 2(3):1-29. doi: 10.18061/bssb.v2i3.8977
• Karimi, Grover, Gallagher, Wendel, Ané & Baum (2020). Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (Adansonia; Bombacoideae; Malvaceae). Systematic Biology, 69(3):462-478. doi:10.1093/sysbio/syz073.
• Bastide, Solís-Lemus, Kriebel, Sparks, Ané (2018). Phylogenetic Comparative Methods for Phylogenetic Networks with Reticulations. Systematic Biology, 67(5):800–820. doi:10.1093/sysbio/syy033.

Manual

The manual pages contain detailed tutorials on how to use the functions of the package.

• Continuous trait analysis
• • Model and variance matrix
  • Phylogenetic regression
  • Ancestral state reconstruction
  • • From known parameters
    • From estimated parameters
    • Data imputation
    • With known predictors
  • Phylogenetic ANOVA
  • Pagel's Lambda
  • Test of transgressive evolution
  • • References
• Continuous trait simulation
• • Brownian motion
  • shifted Brownian motion
• Discrete trait evolution
• • Reading trait data
  • Substitution models
  • parameter estimation & model fit
  • ancestral state prediction
  • impact of gene flow on the trait
• fitting DNA substitution parameters on a network
• • reading in an alignment
  • substitution models for DNA
  • likelihood of a fixed network
• Discrete trait simulation
• • binary trait example
  • example of DNA simulation

Examples

This section contains example of empirical analyses from the literature.

• Empirical example: Xiphophorus fishes
• • Data loading
  • Ancestral state prediction
  • Phylogenetic signal: Pagel's lambda
  • Phylogenetic regression of sword index versus preference
  • Transgressive evolution

Library

For help on individual functions, see this library.

• public documentation
• • functions & types
  • index
• internal documentation
• • functions & types
  • index