DOI: 10.5061/dryad.fn2z34tz0
title: Data from: The effect of copy number hemiplasy on gene family evolution

description: 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.}
description: 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
description: # 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**.