PhyloNetworks: analysis for phylogenetic networks

Overview

PhyloNetworks is a Julia package with utilities to:

• read / write phylogenetic trees and networks, in (extended) Newick format. Networks are considered explicit: nodes represent ancestral species. They can be rooted or unrooted.
• manipulate networks: re-root, prune taxa, remove hybrid edges, extract the major tree from a network, extract displayed networks / trees
• compare networks / trees with dissimilarity measures (Robinson-Foulds distance on trees)
• summarize samples of bootstrap networks (or trees) with edge and node support
• estimate species networks from multilocus data (see below)
• phylogenetic comparative methods for continuous trait evolution on species networks / trees
• plot networks (and trees), via the companion package PhyloPlots

To get help, check

• the latest documentation
• the wiki for a step-by-step tutorial (July 2018) with background on networks
• the google group for common questions. Join the group to post/email your questions, or to receive information on new versions, bugs fixed, etc.

If you use the package, please cite (bibtex format here)

• Claudia Solís-Lemus, Paul Bastide and Cécile Ané (2017). PhyloNetworks: a package for phylogenetic networks. Molecular Biology and Evolution 34(12):3292–3298. doi:10.1093/molbev/msx235

Maximum pseudolikelihood estimation of species network: SNaQ

SNaQ implements the statistical inference method in Solís-Lemus and Ané (2016). The procedure involves a numerical optimization of branch lengths and inheritance probabilities and a heuristic search in the space of phylogenetic networks.

If you use SNaQ, please cite

• Claudia Solís-Lemus and Cécile Ané (2016). Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting. PLoS Genet 12(3):e1005896. doi:10.1371/journal.pgen.1005896

Phylogenetic comparative methods for trait evolution

For continuous traits, study 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 (2022). Accounting for intraspecific variation in continuous trait evolution on a reticulate phylogeny. bioRxiv

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.