Identification of non-native populations and reconstruction of invasion routes in the Redbreast Sunfish Lepomis auritus
Data files
Jan 12, 2024 version files 2.62 MB
Abstract
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.
README: 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.