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 Materials, and the scripts that produce the results described in the paper.

## Description of the data and file structure

Supplementary Materials contain Supplementary Figures and more detailed explanations of our conclusions presented in the main text.

A part of raw data can be found in file \"raw_data.zip\", which include the reconstructed gene trees used to generate the Figures 2 and 4, the reconstructed phylogenetic trees used to generate the Figure 3, and the Dsuite results used to generate the Figure 4. The SLiM simulation results are not incluced in \"raw_data.zip\" because they are too large.

In \"raw_data.zip\", files with suffix \".treefile\" in folder \"iqtree_trees_four_species_1000bp_nucleotide_u=2.4e-6\" are the reconst..., , **Changes after Feb 6, 2024:** 

* File \"analyze_Vanderpool_et_al.py\" has been added, and the results generated by this script (Figure S1) has been added.
* More population size combinations have been added in \"analyze_1000bp_nucleotide.py\", which generated the results presented in Figure 9.
* The previous Figure S2 has been moved to the main text and therefore is no longer contained in supplementary data. Additionally, because the new Figure S1 has been added, the previous Figure S1 becomes Figure S2.

**Changes after Nov 1, 2024:** 

* Files \"analyze_1bp_biallelic_large_pop.py\" and \"sim_three_species_1bp_biallelic_large_pop\" have been added. These scripts implement simulations to show that rescaling does not alter our results (new Figure S1).
* Because the new Figure S1 has been added, the previous Figures S1 and S2 becomes Figures S2 and S3 respectively.
* The original SLiM recipe used for biallelic simulations has been added (original_biallelic_recipe.pdf)
* Some cote...