Introgression and species delimitation in the longear sunfish Lepomis megalotis (Teleostei: Percomorpha: Centrarchidae)

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, L. megalotis and L. 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 non-sister 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.