Supplementary material for: PhyloCoalSimulations: A simulator for network multispecies coalescent models, including a new extension for the inheritance of gene flow

Supplementary Material

`supplementarymaterial.pdf` contains an appendix and supplementary figures S1-S6.

Code to reproduce analyses

The code uses Julia and R. Files `Project.toml` and `Manifest.toml` record the Julia packages used and their specific version. To reproduce the environment, activate this folder and run `instantiate` in package mode within Julia.

Fig. 1: node mapping

`figures.jl`: Julia code to simulate a gene tree with degree-2 nodes for mapping of the gene tree into the species network, and to create the first 2 panels of Fig.1, output as `fig_nodemapping*.pdf`

Fig. 2: validation of quartet concordance factors

• `validation_qCF.jl`: Julia code to reproduce the simulations in Fig.2. Running this code will create 3 output files: `qCF_4taxa.csv` for the left network a), and `qCF_case_{1,2}.csv` for the right network b) on 6 taxa. It will also create `net4.pdf` and `net3.pdf`, showing the 4-taxon and 6-taxon networks respectively.
• `validation_qCF.Rmd`: R code to create Fig.2, taking as input the CSV files from above.

Fig. 3: level-2 network

• `fig_level2_network.jl`: Julia code to create Fig.3 showing the level-2 network that was used to validate the distribution of pairwise distances, using either rho=0 or 1 (independent or common inheritance). output: file `fig_level2net.pdf`.
• `ntwk_level_2.tre`: file containing the Newick description of that network, which can be visualized with julia package PhyloPlots.

Figures 4 and supplementary figures: validation of pairwise distances

Figure S2, on a 4-taxon species tree:

• `gtrees_4tax-changing_PhyloNetworks.tre` contains the 10k simulated gene trees.
• `validation_distances.Rmd`: R code to create Fig.S2, taking as input the gene trees in `gtrees_4tax-changing_PhyloNetworks.tre`.

Figure 4 and supplementary figures S3-S5, on a 6-taxon network with 2 reticulations:

• folders `validation_distances_level2net_rho0` and `validation_distances_level2net_rho1`: input files for the figures as compressed `.RData` files:
  • The `samp_big*_d_xy.RData` files contain the pairwise distances from the 100k simulated gene trees between taxa x and y (used for histograms)
  • the `d_*.RData` files contain the pairwise distances drawn from their theoretical distributions, summarized by their frequency in 100,000 small bins (for the theoretical density curve)
  • the `sampleMeans*_dxy.Rdata` files contain the mean (over 100 replicates) of the 1000 ordered distances between taxa x and y (dbar_i in the paper) from 1000 simulated gene trees in each replicate (used for QQ plots).
  • `Dmatrix.Rdata` contains the 6×6 matrix of *minimum* pairwise distances between all pairs of taxa on the network.
• `validation_distances_level2net_figure.R`: R code to create Fig.4 and supplementary figures, for the distances from the 6-taxon level-2 network in Fig.3. Takes as input files in folders above. output: files `fig_pairwisedist_level2net_rho*.pdf`.

Software archive

• `PhyloCoalSimulations-code-1d266fd.zip`: archive of the PhyloCoalSimulations package from GitHub, main branch (for the code), at commit 1d266fd, which is 1 commit ahead of version v0.1.2.
• `PhyloCoalSimulations-documentation-1d266fd.zip`: archive of the PhyloCoalSimulations package's documentation, from the gh-pages branch, at commit 1d266fd.

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: 1902892

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: 2023239

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: 2051760