Data from: The effect of copy number hemiplasy on gene family evolution
Cite this dataset
Li, Qiuyi; Chan, Yao-Ban; Galtier, Nicolas; Scornavacca, Celine (2024). Data from: The effect of copy number hemiplasy on gene family evolution [Dataset]. Dryad. https://doi.org/10.5061/dryad.fn2z34tz0
Abstract
The evolution of gene families is complex, involving gene-level evolutionary events such as gene duplication, horizontal gene transfer, and gene loss (DTL), and other processes such as incomplete lineage sorting (ILS). Because of this, topological differences often exist between gene trees and species trees. A number of models have been recently developed to explain these discrepancies, the most realistic of which attempt to consider both gene-level events and ILS. When unified in a single model, the interaction between ILS and gene-level events can cause polymorphism in gene copy number, which we refer to as copy number hemiplasy (CNH).
In this paper we extend the Wright-Fisher process to include duplications and losses over several species, and show that the probability of CNH for this process can be significant. We study how well two unified models --- MLMSC (MultiLocus MultiSpecies Coalescent), which models CNH, and DLCoal (Duplication, Loss, and Coalescence), which does not --- approximate the Wright-Fisher process with duplication and loss.
We then study the effect of CNH on gene family evolution by comparing MLMSC and DLCoal. We generate comparable gene trees under both models, showing significant differences in various summary statistics; most importantly, CNH reduces the number of gene copies greatly. If this is not taken into account, the traditional method of estimating duplication rates (by counting the number of gene copies) becomes inaccurate. The simulated gene trees are also used for species tree inference with the summary methods ASTRAL and ASTRAL-Pro, demonstrating that their accuracy, based on CNH-unaware simulations calibrated on real data, may have been overestimated.}
README: Overview
We provide here the simulation scripts and datasets to reproduce the simulation results of the paper The effect of copy number hemiplasy on gene family evolution.
Based on a species tree consisting of 16 fungal genomes, we simulate comparable gene trees under MLMSC-II and SimPhy. The simulated gene trees are compared against various summary statistics including the number of genes, number of species, number of surviving duplications, and balance indices such as Colless index and Sackin index. The simulated gene trees are also used for comparing the performance of the quartet-based species tree inference methods ASTRAL and ASTRAL-Pro under both models.
appendix.pdf
This is a summary of the supplementary materials of the paper The effect of copy number hemiplasy on gene family evolution, including the following topics:
- Supplementary Figures
- Additional WFD Simulations
- Comparisons of Balance Indices
- ASTRAL with Single-labelled Gene Trees
- ASTRAL with Different Number of Input Gene Trees
- ASTRAL with Non-Equal Duplication and Loss Rates
- Simulations on the Primate Tree
data_analysis
This directory stores all simulated data and R scripts for data analysis and plots.
The simulated gene trees are stored in the following directories:
- data_analysis/mlmsc_tree: gene trees simulated using MLMSC-II
- data_analysis/symphy_tree: gene trees simulated using SimPhy
Note that we only keep 1000 gene trees for each set of parameters for demonstration, but 100000 gene trees are used in the original simulation.
The bacis summary statistics of the simulated gene trees (e.g., n_dups, n_genes, n_species) are stored in the following directories:
- data_analysis/mlmsc_summary: bacis summary statistics of the gene trees simulated using MLMSC-II
- data_analysis/symphy_summary: bacis summary statistics of the gene trees simulated using SimPhy
The results of species tree inference are stored in the following directories:
- data_analysis/astral_mlmsc: results of species tree inference using gene trees simulated using MLMSC-II
- data_analysis/astral_symphy: results of species tree inference using gene trees simulated using SimPhy
For more information, please refer to data_analysis/README.md.
mlmsc_bin
This directory contains all the scripts for simulating gene trees using MLMSC-II, and performing species tree inference (by ASTRAL and ASTRAL-Pro) on the simulated gene trees.
To install ASTER/ASTRAL-Pro, do
git clone https://github.com/chaoszhang/ASTER.git
and follow the instructions. The scripts expect the ASTRAL/ASTRAL-Pro binary to be in ./ASTER/bin/astral-pro
When simulating trees, gene trees are stored in mlmsc_bin/output:
- gene_tree.newick: a list of multi-labelled gene trees, each containing of all simulated homologous genes
- random_tree.newick: a list of single-labelled gene trees, each containing only one --randomly-chosen-- gene per species
- summary.txt: summary statistics including the number of surviving duplications (n_d), number of genes (n_genes), and number of species (n_species)
When inferring specie trees, species tree inference results are stored in mlmsc_bin/astral_summary_fungi:
- mlmsc_random.txt: ASTRAL results
- mlmsc_gene.txt: ASTRAL-Pro results
For more information, please refer to mlmsc_bin/README.md.
simphy_bin
This directory is for simulating gene trees using SimPhy, and performing species tree inference (by ASTRAL and ASTRAL-Pro) on the simulated gene tree.
Simulated gene trees are stored in simphy_bin/output:
- gene_tree.newick: a multi-labelled gene tree consisting of all homologous genes
- random_tree.newick: a single-labelled gene tree in which only one gene is randomly selected for each descendant species
- summary.txt: summary statistics including the number of surviving duplications (n_d), number of genes (n_genes), and number of species (n_species)
Species tree inference results are stored in simphy_bin/astral_summary_fungi:
- simphy_random.txt: ASTRAL results
- simphy_gene.txt: ASTRAL-Pro results
For more information, please refer to simphy_bin/README.md.
WFDL_bin
This directory is for simulating the fraction of higher order duplications using the Wright-Fisher model with duplication and loss (WFDL).
For more information, please refer to WFDL_bin/README.md.
Methods
This dataset consists of a variety of summary statistics of the simulated gene trees from the MLMSC-II model and DLCoal model.
The simulation scripts and R code for data analysis are also provided.
The same simulation scripts and dataset can also be found at https://github.com/QiuyiLi/MLMSC-II_simulation_script
Funding
Agence Nationale de la Recherche, Award: ANR-19-CE45-0012