DOI: 10.5061/dryad.sf7m0cgbs
title: Data for: Among-species rate variation produces false signals of introgression

description: 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 violated
 as evolutionary divergence increases. To test the limitations of
 introgression detection methods when being applied to old systems, we
 simulated thousands of genomic datasets under a wide range of settings,
 with varying degrees of among-species rate variation and introgression.
 Using these simulated datasets, we showed that some commonly applied
 statistical methods, including the D-statistic and certain tests based on
 sets of local phylogenetic trees, can produce false-positive signals of
 introgression between divergent taxa that have different rates of
 evolution. These misleading signals are caused by the presence of
 homoplasies occurring at different rates in different lineages. To
 distinguish between the patterns caused by rate variation and genuine
 introgression, we developed a new test that is based on the expected
 clustering of introgressed sites along the genome, and implemented this
 test in the program Dsuite. 
description: Genomic datasets have been simulated with msprime, and processed
 with Dsuite, IQ-TREE, SNaQ, and QuIBL.
description: # Among-species rate variation produces false signals of introgression ---
 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 population sizes * **div_time:** divergence of species P1 and P2 in our four-taxon phylogeny, in generations * **rec_rate:** recombination rate of the chromosome * **mut_rate:** mutation rate * **intr_rate:** rate of introgression between species P2 and P3 * **P2_rate:** scale factor indicating the extending or shortening of the branch leading to P2 in order to allow mutation-rate variation * **n_variable_sites_vcf:** number of variable sites per vcf-file * **n_biallelic_sites_vcf:** number of biallelic sites per vcf-file * **n_multiallelic_sites_vcf:** number of multiallelic sites per vcf-file * **n_variable_sites_200bp:** number of variable sites per alignments with a length of 200 bp extracted from the genomic dataset * **n_variable_sites_500bp:** number of variable sites per alignments with a length of 500 bp extracted from the genomic dataset * **n_variable_sites_1000bp:** number of variable sites per alignments with a length of 1000 bp extracted from the genomic dataset * **n_pi_sites_200bp:** number of parsimony-informative sites per alignments with a length of 200 bp extracted from the genomic dataset * **n_pi_sites_500bp:** number of parsimony-informative sites per alignments with a length of 500 bp extracted from the genomic dataset * **n_pi_sites_1000bp:** number of parsimony-informative sites per alignments with a length of 1000 bp extracted from the genomic dataset * **run:** run number, since ten, or fifty (for the main settings), replicate simulations were performed for each possible combination of parameters * **D_stat:** Patterson's *D*-statistic * **p_value:** *p*-values * **f4_ratio:** f4-ratio estimation, a method for estimating ancestry proportions in an admixed population * **sensitive version of the `ABBA'-site clustering:** signals of introgression (given as *p*-values) detected with the “sensitive” version of the new ‘ABBA’-site clustering test * **robust version of the `ABBA'-site clustering:** signals of introgression (given as *p*-values) detected with the “robust” version of the new ‘ABBA’-site clustering test * **BBAA:** number of BBAA sites * **ABBA:** number of ABBA sites * **BABA:** number of BABA sites * **align_length:** lengths of equally spaced windows across the simulated chromosome that were used for extracting variants from (for tree-based introgression-detection methods only) * **n_significant:** number of significant runs * **loglik_dif:** difference in log-likelihood * **topo_ok:** verification whether the inferred topology actually still represents the original topology of the four-taxon phylogeny * **network:** inferred topology * **introgression_rate:** rate of introgression calculated based on the QuIBL results * **mrca_reduction:** difference between the two oldest pairwise mean MRCA ages (dMRCA) * **means_c_genes_length:** mean length of c-genes * **means_tracts_length:** mean length of single-topology tracts * **n_introgressed_tracts:** number of introgressed single-topology tracts * **means_introgressed_tracts_length:** mean length of introgressed single-topology tracts In the following the content of the single nested sheets is specified in more detail: 1. **Dataset statistics:** Here, we present a comprehensive overview of the numbers of variable, biallelic, and multiallelic sites per simulated dataset, as well as the numbers of variable and parsimony-informative sites per alignment lengths of 200, 500, and 1,000 bp. 2. **Dsuite:** Here, both the Dsuite analysis (results obtained after running the script `summarize_dsuite.sh`) and the analysis based on both the “sensitive” and “robust” 'ABBA'-Site Clustering (results obtained after running the script `summarize_abba_clustering.sh`) is summarized and all results obtained are written into a table. 3. **Dtree:** The script `summarize_iqtree.sh` summarizes the *D*<sub>tree</sub> analysis and writes the results into this table. 4. **SNaQ:** The script `summarize_snaq.sh` summarizes the SNaQ analysis and writes the results into this table. 5. **QuIBL:** The script `summarize_quibl.sh` summarizes the QuIBL analysis and writes the results into this table. 6. **MMS17:** The script `summarize_meyer_approach.sh` summarizes the analysis with the method developed by Meyer, Matschiner, and Salzburger (2017) ("MMS17 method") and writes the results into this table. 7. **Moderate ILS:** The script `summarize_abba_clustering.sh` summarizes the analysis based on 'ABBA'-Site Clustering and writes the results for simulations with a moderate level of ILS (obtained after running the script `simulate_data_ils.sh`) into this table. 8. **High ILS:** The script `summarize_abba_clustering.sh` summarizes the analysis based on 'ABBA'-Site Clustering and writes the results for simulations with a moderate level of ILS (obtained after running the script `simulate_data_high_ils.sh`) into this table. 9. **Very high ILS:** The script `summarize_abba_clustering.sh` summarizes the analysis based on 'ABBA'-Site Clustering and writes the results for simulations with a moderate level of ILS (obtained after running the script `simulate_data_very_high_ils.sh`) into this table. 10. **C-genes_tracts_length:** The script `calculate_mean_tracts.sh` analyzes the lengths of c-genes and single-topology tracts and writes the results into this table. Also, the number of introgressed single-topology tracts is listed. Please note, that in some cases there are no single-topology tracts present and therefore the average length of introgressed tracts can be not identified (indicated with "NA" in the column).