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

We consider the evolution of phylogenetic gene trees along phylogenetic species networks, according to the network multispecies coalescent process, and introduce a new network coalescent model with correlated inheritance of gene flow. This model generalizes two traditional versions of the network coalescent: with independent or common inheritance. At each reticulation, multiple lineages of a given locus are inherited from parental populations chosen at random, either independently across lineages, or with positive correlation according to a Dirichlet process. This process may account for locus-specific probabilities of inheritance, for example.
We implemented the simulation of gene trees under these network coalescent models in the Julia package PhyloCoalSimulations, which depends on PhyloNetworks and its powerful network manipulation tools. Input species phylogenies can be read in extended Newick format, either in numbers of generations or in coalescent units. Simulated gene trees can ..., This repository contains code to reproduce the figures and validation studies in: John Fogg, Elizabeth S. Allman, and Cécile Ané (2023). \"PhyloCoalSimulations: A simulator for the network multispecies coalescent, extended with correlated inheritance of gene flow\".
All gene tree simulations used PhyloCoalSimulations, a Julia package available freely and open-source., 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, ...,

我们基于网络多物种溯祖过程，探讨了系统发育基因树沿系统发育物种网络的演化规律，并提出了一类带有基因流相关遗传的新型网络溯祖模型。该模型推广了两类经典的网络溯祖模型：独立遗传模式与共同遗传模式。在每个网状节点处，特定基因座的多条谱系可从随机选择的亲本种群中继承：既可以在谱系间独立选择，也可以依据狄利克雷过程（Dirichlet Process）实现谱系间的正相关遗传。例如，该过程可用于刻画基因座特异性的遗传概率。

我们依托朱莉娅（Julia）编程语言的`PhyloCoalSimulations`包实现了上述网络溯祖模型下的基因树模拟，该包依赖于`PhyloNetworks`及其强大的网络操作工具集。输入的物种系统发育树可通过扩展Newick格式读取，支持以世代数或溯祖单位作为度量单位。模拟得到的基因树可……

本仓库包含用于复现以下论文中的图表与验证研究的代码：John Fogg、Elizabeth S. Allman与Cécile Ané（2023）发表的《PhyloCoalSimulations：一款支持基因流相关遗传扩展的网络多物种溯祖模拟器》。

所有基因树模拟均使用了开源免费的朱莉娅包`PhyloCoalSimulations`。

补充材料
`supplementarymaterial.pdf`包含附录与补充图表S1至S6。

复现分析的代码
本分析代码依托朱莉娅与R语言编写。`Project.toml`与`Manifest.toml`文件记录了所用的朱莉娅包及其具体版本。如需复现运行环境，可激活本文件夹并在朱莉娅的包管理模式中执行`instantiate`命令。

图1：节点映射
`figures.jl`：用于模拟带有二度节点的基因树以实现基因树到物种网络的映射，并生成图1的前两个子图，输出文件为`fig_nodemapping*.pdf`的朱莉娅代码。

图2：四重体一致性因子验证
`validation_qCF.jl`：用于复现图2中模拟实验的朱莉娅代码。运行该代码将生成3个输出文件：针对左侧网络a)的`qCF_4taxa.csv`，以及针对右侧六分类群网络b)的`qCF_case_1.csv`与`qCF_case_2.csv`；同时还将生成`net4.pdf`与`net3.pdf`，分别展示四分类群与六分类群的物种网络。

`validation_qCF.Rmd`：用于生成图2的R语言代码……