The effect of copy number hemiplasy on gene family evolution

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 --- app..., 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, , # 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 Tr...