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

Assumptions about the probability distribution of gene tree topologies provides a basis for phylogenetic reconstruction and introgression detection. Initial evidence has suggested that in the presence of purifying selection, population size differences can affect the probability distribution of gene tree topologies. Nevertheless, the impact of this phenomenon on phylogenetic reconstruction and introgression detection remains to be explored. Additionally, a theoretical understanding of this phenomenon remains absent. Here, using the population genetic simulator SLiM, we provide evidence that in the presence of purifying selection, population size differences can cause 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. Additionally, a theoretical analysis is presented to show that the biological..., , , # Population Size Differences Can Lead to Biases in Phylogenetic Inference and Introgression Detection in the Presence of Purifying Selection

[https://doi.org/10.5061/dryad.2z34tmpsz](https://doi.org/10.5061/dryad.2z34tmpsz)

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

## Description of the data and file structure

Figure S1 shows that rescaling will not significantly alter our results. Figure S2 shows the results of changing the population sizes used by Vanderpool et al. (2020). These results aim to show that Vanderpool et al.'s simulations cannot be used to support their claim \"there should be no effect of negative selection on the distribution of tree topologies\". Figure S3 shows the values P(V1|V) under neutral evolution and under purifying selection. These results aim to show that regardless of whether under neutral evolution or under purifying selection, the condition P(V1|V) cannot be sati...,