Population size differences can lead to biases in phylogenetic inference and introgression detection in the presence of purifying selection

Phylogenetic reconstruction and introgression detection rely on an assumption about the probability distribution of gene tree topologies. Recently, evidence has emerged that population size differences can affect the probability distribution of gene tree topologies in the presence of purifying selection. Here, using the population genetic simulator SLiM, we provide evidence that in the presence of purifying selection, population size differences can lead to biases in phylogenetic inference. We also provide evidence that in the presence of purifying selection, population size differences can cause statistics used for introgression detection to exhibit patterns resembling those caused by introgression. In addition, we present a theoretical analysis showing that the occurrence of population size–dependent gene tree distributions is an inherent consequence of purifying selection. Our work underscores the importance of considering the potential confounding effect of purifying selection on ph..., , , # Population Size Differences Can Lead to Biases in Phylogenetic Inference and Introgression Detection in the Presence of Purifying Selection

This dataset includes Supplementary Materials and Methods, Supplementary Figures, and the scripts that produce the results described in the paper.

## Description of the data and file structure

Supplementary Materials and Methods describes the simulation used to examine the value of P(V1|V) and the simulation used to examine the replicability of the results of He et al. (2020).

In Supplementary Figures, the results produced by the simulations described in Supplementary Materials and Methods are shown.

A part of raw data can be found in file \"raw_data.zip\", which include the reconstructed gene trees involved in the generation of Figure 3 and Figure 5, the reconstructed phylogenetic trees involved in the generation of Figure 4, and the Dsuite results involved in the generation of Figure 5. The SLiM simulation results are not incluced in \"raw_...