DOI: 10.5061/dryad.bcc2fqzhx
title: Identification of non-native populations and reconstruction of invasion routes in the Redbreast Sunfish Lepomis auritus

description: Human-mediated introductions of non-native species are expected to
 increase globally and threaten native biodiversity. Lepomis auritus
 (Redbreast Sunfish), a carnivorous freshwater fish native to rivers in
 eastern North America, has been introduced far outside of its native range
 due to its popularity in recreational fisheries. However, poor
 documentation of introductions and lack of thorough ichthyofaunal surveys
 before the mid-20th century have complicated our understanding of the
 establishment and spread of non-native L. auritus over the past 90 years,
 precluding effective management. We conducted phylogenomic analyses using
 ddRAD data from 197 specimens of L. auritus collected throughout the known
 geographic range of the species to reconstruct the introduction history of
 the species. Our protocols allow for the reconstruction of complicated
 introduction routes and reveal that L. auritus in Texas is the result of a
 single-source introduction from the Suwannee River; the population in the
 upper Tennessee River has two sources of introduction from the Savannah
 River and the northeastern rivers that drain into the Atlantic Ocean; and
 the populations in the middle Tennessee River and the Mobile River Basin
 have sources from the upper Tennessee River system and the Apalachicola
 River Basin. Ecological and evolutionary investigations of the non-native
 populations of L. auritus will broaden the understanding of invasion
 dynamics in species of Lepomis and other non-native freshwater fishes in
 North America. Our study provides critical information for the
 conservation of native populations and invasive management of non-native
 populations of L. auritus.
description: # **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.