Data for: Among-species rate variation produces false signals of introgression

The role of interspecific hybridization has recently seen increasing attention, especially in the context of diversification dynamics. Genomic research has now made it abundantly clear that both hybridization and introgression – the exchange of genetic material through hybridization and backcrossing – are far more common than previously thought. Besides cases of ongoing or recent genetic exchange between taxa, an increasing number of studies report “ancient introgression” – referring to results of hybridization that took place in the distant past. However, it is not clear whether commonly used methods for the detection of introgression are applicable to such old systems, given that most of these methods were originally developed for analyses at the level of populations and recently diverged species, affected by recent or ongoing genetic exchange. In particular, the assumption of constant evolutionary rates, which is implicit in many commonly used approaches, is more likely to be violate..., Genomic datasets have been simulated with msprime, and processed with Dsuite, IQ-TREE, SNaQ, and QuIBL., , # Among-species rate variation produces false signals of introgression

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Supplementary Material for Koppetsch et al. includes Supplementary Notes S1-S4, Supplementary Figures S1-S36, and Supplementary Tables S1-S5.

Supplementary Table 1 is provided in file `Supplementary_Table_1.xlsx`, while all other Supplementary Material is included in file `dstats_supplement.pdf`.

### Supplementary Table 1

This Excel spreadsheet contains nested sheets that correspond to all the summary content that would be obtained after having run the script named `run_all_simulation_data.sh`. All scripts are provided on the GitHub code repository ([https://github.com/thorekop/ABBA-Site-Clustering/blob/main/src/](https://github.com/thorekop/ABBA-Site-Clustering/blob/main/src/)). Please note, that the `run_all_simulation_data.sh` script is not intended to be executed itself.

Abbreviations for the variables and parameters listed in Supplementary Table 1 are defined here:

* **pop_size:** effective populati...