Julia package for the analysis of trait evolution along a phylogeny, including phylogenetic networks. It depends on utilities from PhyloNetworks.
See CITATION.bib for the relevant reference(s).
Below is a short list.
For continuous traits, analyses based on the Brownian motion process, with or without transgressive evolution after reticulations:
- 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. SI on dryad including a tutorial for trait evolution and a tutorial for network calibration.
Continuous traits, accounting for within-species variation:
- Benjamin Teo, Jeffrey P. Rose, Paul Bastide & Cécile 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
For a discrete trait (influence of gene flow on the trait, ancestral state reconstruction, rates):
- 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.
Note
Much of this package was formerly part of PhyloNetworks v0.16.4 (and prior). PhyloNetworks v0.17 will be stripped of functions for trait evolution.