Identification of non-native populations and reconstruction of invasion routes in the Redbreast Sunfish Lepomis auritus

# **Identification of non-native populations and reconstruction of invasion routes in the Redbreast Sunfish *Lepomis auritus*** Daemin Kim, Jeffrey W. Simmons, and Thomas J. Near ## Description of Data files **SNAPP_divergence_time.xml** Input for the SNAPP divergence time analysis. **SNAPP_divergence_time.nex** Dataset for the SNAPP divergence time analysis. **SNAPP_divergence_time.tre** Time-calibrated species tree inferred from the SNAPP divergence time analysis. **SNMF.ugeno** Dataset for the population structure analysis with a sparse non-negative matrix factorization (snmf) algorithm. **IQTREE_contree.tre** Maximum likelihood phylogeny of concatenated data inferred from the IQTREE analysis. **FSC_Analysis1_MSFS.obs** Multisite frequency spectrum input for the Fastsimcoal2 analysis for Analysis 1. **FSC_Analysis2_MSFS.obs** Multisite frequency spectrum input for the Fastsimcoal2 analysis for Analysis 2. **FSC_Analysis_Combined_MSFS.obs** Multisite frequency spectrum input for the Fastsimcoal2 analysis for the final analysis. **Supplementary Figure S1** (a) Population structure (K=7) for *Lepomis auritus*, inferred from snmf analysis, with specimen labels. (b) Time-calibrated phylogeny for *L. auritus* and the closely related sunfishes, inferred from SNAPP. Light blue bars indicate 95% highest posterior density of divergence-time estimates for the node. A fully annotated phylogeny is available at Dryad. (c) Hierarchical models tested and their parameters used in Fastsimcoal2 analyses for the non-native populations of *L. auritus* in the upper Tennessee River system, the middle Tennessee River system and the Mobile River Basin and their possible source populations. Best-fit model (scenario) for each analysis is highlighted with a red box. For details of the parameter estimates, see Supplementary Table S2. **Supplementary Table S1** List of specimens used in the present study, voucher and tissue catalog numbers, and GPS coordinates of sampling locations. Specimen names correspond to the population structure plot in Supplementary Figure S1 and IQ-TREE phylogeny available at Dryad. Museum and tissue collection catalog abbreviations: MMNS, Mississippi Museum of Natural Science; TCWC, Texas A&M University, Biodiversity Research and Teaching Collections; UF, University of Florida, Florida Museum of Natural History; UT, University of Tennessee Etnier Ichthyological Collection; YPM, Yale Peabody Museum of Natural History; YFTC, Yale Fish Tissue Collection. NA, not available. **Supplementary Table S2** Models tested in the Fastsimcoal2 analysis for the non-native populations of *Lepomis auritus* in the upper Tennessee River system, the middle Tennessee River system and the Mobile River Basin and their possible source populations. Parameter estimates of the highest estimated log-likelihood (MaxEstLhood) for each model are shown. Best-fit model (scenario) for each analysis is highlighted. Population and model parameter abbreviations correspond to those shown in Supplementary Figure S1c. Population abbreviations and ANC are population size parameters. Timing parameters for human-mediated introduction (Tni) and population divergence are in the number of generations, assuming a generation time of four years.