Introgression and Species Delimitation in the Longear Sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)

Abstract

Introgression and hybridization are major impediments to genomic-based species delimitation because many implementations of the multispecies coalescent framework assume no gene flow among species. The sunfish genus Lepomis, one of the world’s most popular groups of freshwater sport fish, has a complicated taxonomic history. The results of ddRAD phylogenomic analyses do not provide support for the current taxonomy that recognizes two species, Lepomis megalotis and Lepomis peltastes, in the L. megalotis complex. Instead, evidence from phylogenomics and phenotype warrants recognizing six relatively ancient evolutionary lineages in the complex. The introgressed and hybridizing populations in the L. megalotis complex are localized and appear to be the result of secondary contact or rare hybridization events between nonsister species. Segregating admixed populations from our multispecies coalescent analyses identifies six species with moderate to high genealogical divergence, whereas including admixed populations drives all but one lineage below the species threshold of genealogical divergence. Segregation of admixed individuals also helps reveal phenotypic distinctiveness among the six species in morphological traits used by ichthyologists to discover and delimit species over the last two centuries. Our protocols allow for the identification and accommodation of hybridization and introgression in species delimitation. Genomic-based species delimitation validated with multiple lines of evidence provides a path towards the discovery of new biodiversity and resolving long-standing taxonomic problems.[ddRAD; genealogical divergence index; hybridization; integrative species delimitation; phylogeny; secondary contact; systematics; taxonomy.]

Phylogenomics and species delimitation of the economically important Black Basses (Micropterus)

“…S3 a,b) indicate that historical introgression from Alabama Bass and Guadalupe Bass may result in the paraphyly of Spotted Bass by resolving introgressed populations outside of a clade containing non-introgressed Spotted Bass plus Guadalupe Bass or as early diverging lineages of the Guadalupe Bass clade. This pattern is consistent with observations from the Longear Sunfish complex (e.g., Lepomis megalotis ), where introgressed populations are resolved as early diverging or pectinate branches along stem lineages in phylogenetic analyses of concatenated datasets 12 .…”

“…The preparation of ddRAD libraries followed protocols outlined in Peterson et al 44 , using PstI / MspI restriction enzymes. The details of genomic DNA extraction, ddRAD library preparation, and sequencing are described in Kim et al 12 . The demultiplexed reads were analyzed with ipyrad v.0.9.68 45 , using default setting with the following exceptions: ‘denovo’ for assembly method, ‘ddrad’ for datatype, ‘TGCAG, CCG’ for restriction overhang, and 0.96 for clustering threshold 46 .…”

“…The best-fit sequence substitution model (TVM + F + R7) was determined using ModelFinder 48 implemented in IQ-TREE based on the Bayesian information criterion (BIC). During the IQ-TREE analysis, trees were rooted with the Suwannee Bass ( M. notius ), following its placement in the centrarchid species tree inferred from the dataset of 16 Sanger-sequenced nuclear loci and in preliminary concatenated ddRAD loci phylogenies of Micropterus and its sister lineage Lepomis 12 , 49 . We assessed topological support with 1000 ultrafast bootstrap replications 50 .…”

“…Contemporary genomics and analytical methods complement traditional morphology-based species delimitation of fishes (e.g., Ref. 12 ). The application of genomics to species delimitation facilitates the resolution of genetic population structure and the discovery of distinct evolutionary lineages 13 .…”

Genomic divergence, local adaptation, and complex demographic history may inform management of a popular sportfish species complex

“…While minor cluster membership of 0 ≤ q ≤ 0.05 for an individual may indicate historical introgression, we retained individuals in this range for phylogenomic comparison to avoid excessively limiting sample sizes. Other studies have resolved lineage divergence using individuals with minor ancestry of 0 ≤ q ≤ 0.25 (Kim et al, 2021 ). Hybrids of Smallmouth Bass or Neosho Bass with Spotted Bass were removed from downstream analyses.…”