Phylogeny and time scale of diversification in the fossil-rich sunfishes and black basses (Teleostei: Percomorpha: Centrarchidae)

Robust Sensory Traits Across Light Habitats: Visual Signals but Not Receptors Vary in Centrarchids Inhabiting Distinct Photic Environments

Visual communication in fish is often shaped by their light environment, which influences both sensory (e.g., eye size, opsin gene expression) and signalling traits (e.g., body reflectance). This study explores the phenotypic variation in the visual communication traits of six species of centrarchids (Centrarchidae) inhabiting two contrasting light environments. We measured morphological, molecular and signalling traits to determine their variation across photic conditions. Our findings reveal significant interspecific variation in sensory traits but no consistent phenotypic variation between light environments. Centrarchids showed robust visual systems with green-sensitive rh2 and red-sensitive lws opsin genes representing the main chromatic channels, with their expression remaining largely unaffected between distinct light habitats. We also found significant molecular evolution in the visual opsin genes, although these changes were not associated with environmental conditions. However, body reflectance displayed species-specific responses to environmental conditions, suggesting that signalling traits may be more flexible than sensory traits. Overall, our results challenge the generality of the current paradigm in visual ecology, which portrays visual systems in fish as highly tunable owing to photic conditions. Our study highlights the potential evolutionary or developmental constraints on centrarchid visual systems and their implications for adaptability to various habitats and novel environmental threats.

A new species of Myxobolus (Cnidaria: Myxosporea: Myxobolidae) from the gills of the green sunfish, Lepomis cyanellus (Perciformes: Centrarchidae), from the Ouachita River Drainage of Western Arkansas

Forty-two species of myxozoans, including 31 species of Myxobolus Bütschli, 1882, have been described from centrarchid fishes. One species, the green sunfish (Lepomis cyanellus), has been reported to host at least three species of Myxobolus. Between March 2023 and June 2024, 42 L. cyanellus were collected from watersheds in Montgomery and Polk counties, Arkansas, and their gills, gallbladders, urinary bladders, fins, integument, other major organs, and musculature were examined for myxozoans. Two (5%) L. cyanellus from Polk County were found to harbor a new species of Myxobolus infecting the gill lamellae. A qualitative and quantitative morphological description was based on formalin-fixed preserved plasmodia and myxospores. Plasmodia of Myxobolus polkensis n. sp. are 133 µm long × 123 µm wide, and myxospores are 19.8 µm long × 6.5 µm wide, with two narrowly pyriform unequal polar capsules, one usually longer (9.2 µm) than the other (8.5 µm). Molecular data consisted of a 2,025 base pair sequence of the partial small subunit rRNA gene (SSU). Variably sized, polysporic plasmodia were randomly distributed throughout the gill lamellae in intralamellar locations. Large plasmodia displaced adjacent lamellae inducing mild epithelial proliferation but minimal inflammatory changes. Phylogenetic analysis revealed that M. polkensis n. sp. is a member of a clade of myxozoan species that predominately infect centrarchids from North America. This is the fourth report of a Myxobolus from L. cyanellus but the first report of a species infecting the gill lamellae. This article was registered in the Official Register of Zoological Nomenclature (ZooBank) as urn:lsid:zoobank.org:pub:E9BA08E0-0A7E-487B-80AE-C5C723DBB661.

Intraspecific variation in feeding and locomotor kinematics during prey capture in redbreast sunfish (Lepomis auritus)

Biomechanics research often revolves around understanding traits impacting suction feeding performance in fishes, using freshwater ray-finned sunfishes (Family Centrarchidae) as models. However, simultaneous feeding and locomotion kinematics during prey capture are not recorded for many species and there is less information on how these kinematics vary within a species and within individuals. To (1) add to existing data on the prey capture kinematics of centrarchids, (2) assess variation in a species both within and across individuals, and (3) compare morphology and prey capture kinematics of well-sampled centrarchids, we filmed five redbreast sunfish (Lepomis auritus) at 500 fps-1 approaching and striking non-evasive prey. Redbreast approach prey at ~30 cm s-1 and use approximately 70% of their maximum gape size. Traits related to feeding are more repeatable than traits related to locomotion. However, the Accuracy Index (AI) was consistent across individuals (AI = 0.76 ± 0.07). Functionally, redbreast sunfish are more similar to bluegill sunfish but morphologically they fall in the intermediate morphospace alongside green sunfish when compared with other centrarchids. These data show that whole organism outcomes (AI) are similar despite variation present both within and across individuals and demonstrate the importance of considering both interspecific and intraspecific differences in the functional diversity of ecologically and evolutionarily important behaviors such as prey capture.

A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus)

North American sunfishes (Family Centrarchidae) are among the most popular sportfish throughout the United States and Canada. Despite the popularity of sunfishes, their ecological importance, and their extensive stocking and aquacultural history, few molecular studies have examined the evolutionary relationships and species boundaries among members of this group, many of which are known to hybridize. Here, we describe a chromosome-scale genome assembly representing Bluegill (Lepomis macrochirus), one of the most widespread centrarchid species. By combining long-read, Oxford Nanopore sequencing data with short-insert, whole-genome and HiC sequence reads, we produced an assembly (Lm_LA_1.1) having a total length of 889 Mb including 1,841 scaffolds and having a scaffold N50 of 36 Mb, L50 of 12, N90 of 29 Mb, and L90 of 22. We detected 99% (eukaryota_odb10) and 98% (actinopterygii_odb10) universal single-copy orthologs (BUSCOs), and ab initio gene prediction performed using this new assembly identified a set of 17,233 genes that were supported by external (OrthoDB v10) data. This new assembly provides an important addition to the growing set of assemblies already available for spiny-rayed fishes (Acanthomorpha), and it will serve as a resource for future studies that focus on the complex evolutionary history of centrarchids.

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

The Neosho Bass (Micropterus velox), a former subspecies of the keystone top-predator and globally popular Smallmouth Bass (M. dolomieu), is endemic and narrowly restricted to small, clear streams of the Arkansas River Basin in the Central Interior Highlands (CIH) ecoregion, USA. Previous studies have detected some morphological, genetic, and genomic differentiation between the Neosho and Smallmouth Basses; however, the extent of neutral and adaptive divergence and patterns of intraspecific diversity are poorly understood. Furthermore, lineage diversification has likely been impacted by gene flow in some Neosho populations, which may be due to a combination of natural biogeographic processes and anthropogenic introductions. We assessed: (1) lineage divergence, (2) local directional selection (adaptive divergence), and (3) demographic history among Smallmouth Bass populations in the CIH using population genomic analyses of 50,828 single-nucleotide polymorphisms (SNPs) obtained through ddRAD-seq. Neosho and Smallmouth Bass formed monophyletic clades with 100% bootstrap support. We identified two major lineages within each species. We discovered six Neosho Bass populations (two nonadmixed and four admixed) and three nonadmixed Smallmouth Bass populations. We detected 29 SNPs putatively under directional selection in the Neosho range, suggesting populations may be locally adapted. Two populations were admixed via recent asymmetric secondary contact, perhaps after anthropogenic introduction. Two other populations were likely admixed via combinations of ancient and recent processes. These species comprise independently evolving lineages, some having experienced historical and natural admixture. These results may be critical for management of Neosho Bass as a distinct species and may aid in the conservation of other species with complex biogeographic histories.

AZYGIID PARASITES OF NORTH AMERICAN ENDEMIC PLEUROCERIDS AND CENTRARCHIDS: REVISION OF LEUCERUTHRUS MARSHALL AND GILBERT, 1905 (DIGENEA: AZYGIIDAE), DESCRIPTION OF TWO NEW SPECIES, AND PHYLOGENETIC ANALYSIS

We revise monotypic LeuceruthrusMarshall and Gilbert, 1905 (Azygiidae Lühe, 1909) by emending its generic diagnosis, redescribing its type species (Leuceruthrus micropteriMarshall and Gilbert, 1905), reassigning 2 species (Leuceruthrus stephanocauda [Faust, 1921] n. comb., Leuceruthrus ocalana [Smith, 1935] n. comb.), describing 2 new congeners (Leuceruthrus ksepkai n. sp. and Leuceruthrus blaisei n. sp.), and providing a phylogenetic analysis based on the internal transcribed spacer 2 (ITS2). Leuceruthrus is unique by having oblique preovarian testes, a vitellarium that does not extend anteriad into the forebody, and a uterus that is intercecal and between the ovary and ventral sucker. We describe the cercaria of Leuceruthrus cf. stephanocauda from cercariae shed from Elimia cf. carinifera and Elimia cf. modesta from Big Canoe Creek, Alabama. Leuceruthrus ksepkai n. sp. is described from cercariae shed from rasp elimia, Elimia floridensis (Reeve, 1860) from Holmes Creek, Florida, and Elimia sp. 1 from the Chocktawhatchee River, Florida. It differs from its congeners by the combination of having broadly rounded furcae with slight marginal pigmentation in live cercariae, no spines on the tail stem, distinct anterior and posterior ridges that flank the tail stem portion accommodating the withdrawn distome, minute protuberances occupying the lateral margin of the tail stem for its entire length, and protuberances that encircle the anterior third of the posterior tail stem (immediately posterior to the tail stem portion containing the withdrawn distome). Leuceruthrus blaisei n. sp. infects Elimia sp. and is the only known congener having proportionally small furcae (>tail stem maximum width) with a nipple-like distal projection and numerous minute projections on the tail stem surface. Our phylogenetic analysis included all of our new sequences plus all publicly available ITS2 sequences for Leuceruthrus spp. and Proteromera spp., and supported the monophyly of Leuceruthrus. It recovered L. ksepkai and L. cf. ksepkai in a polytomy, and Leuceruthrus blaisei as monophyletic (identical sequences), with L. micropteri and L. cf. stephanocauda recovered as sister taxa. The present study comprises the first systematic treatment of Leuceruthrus in over a century, the first description of a new species of Leuceruthrus in 117 yr, and the first taxonomic characterization of a species of Leuceruthrus from the Mobile River Basin. It also increases the number of accepted congeners from 1 to 5 and provides new host records (E. cf. carinifera and E. floridensis) for Leuceruthrus spp.

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

Informed management and conservation efforts are vital to sustainable recreational fishing and biodiversity conservation. Because the taxonomic rank of species is important in conservation and management strategies, success of these efforts depends on accurate species delimitation. The Black Basses (Micropterus) are an iconic lineage of freshwater fishes that include some of the world’s most popular species for recreational fishing and world's most invasive species. Despite their popularity, previous studies to delimit species and lineages in Micropterus suffer from insufficient geographic coverage and uninformative molecular markers. Our phylogenomic analyses of ddRAD data result in the delimitation of 19 species of Micropterus, which includes 14 described species, the undescribed but well-known Altamaha, Bartram’s, and Choctaw basses, and two additional undescribed species currently classified as Smallmouth Bass (M. dolomieu). We provide a revised delimitation of species in the Largemouth Bass complex that necessitates a change in scientific nomenclature: Micropterus salmoides is retained for the Florida Bass and Micropterus nigricans is elevated from synonymy for the Largemouth Bass. The new understanding of diversity, distribution, and systematics of Black Basses will serve as important basis for the management and conservation of this charismatic and economically important clade of fishes.

Integrating ecological and molecular data to investigate species maintenance and interspecific hybridization between the redbreast sunfish (Lepomis auritus) and the pumpkinseed sunfish (L. gibbosus)

True sunfishes (genus Lepomis) of North America are renowned for hybridization, although hybrids often comprise of only a fraction of the sunfish population in natural systems. Species boundaries may be maintained through premating mechanisms (e.g., ethological and habitat isolation), which may be facilitated by the promiscuous sunfish mating system; primarily, singular males guard nests which multiple females visit. Natural hybridization occurs between redbreast (L. auritus (Linnaeus, 1758)) and pumpkinseed (L. gibbosus (Linnaeus, 1758)) sunfishes, but there is no published research into its extent and causes. In this study, we assessed the relationship of ecological variables to the prevalence of hybridization in a sunfish population in a freshwater lake. Nests of both species were evaluated for differences in substrate, date, water depth, temperature, and dissolved oxygen. Sequencing of one fragment of nuclear DNA (calmodulin intron 4) and one fragment of mitochondrial DNA (12S) was employed on adult males and eight offspring from each nest to determine genetic identity and hybridization direction. Nonparametric tests found a significant difference in substrate between species’ nests (p < 0.01), warranting further investigation into nest substrate as a mechanism for species maintenance. Furthermore, we observed asymmetrical hybridization with the less abundant species (redbreast sunfish) disproportionately affected.

Complex introgression among three diverged largemouth bass lineages

Hybrid zones between diverged lineages offer a unique opportunity to study evolutionary processes related to speciation. Natural and anthropogenic hybridization in the black basses (Micropterus spp.) is well documented, including an extensive intergrade zone between the widespread northern Largemouth Bass (M. salmoides) and the Florida Bass (M. floridanus). Phenotypic surveys have identified an estuarine population of Largemouth Bass (M. salmoides) in the Mobile-Tensaw Delta, with larger relative weight and smaller adult size compared to inland populations, suggesting a potential third lineage of largemouth bass. To determine the evolutionary relationships among these Mobile Delta bass populations, M. salmoides and M. floridanus, putative pure and intergrade populations of all three groups were sampled across the eastern United States. Phylogenetic analyses of 8582 nuclear SNPs derived from genotype-by-sequencing and the ND2 mitochondrial gene determined that Delta bass populations stem from a recently diverged lineage of Largemouth Bass. Using a novel quantitative pipeline, a panel of 73 diagnostic SNPs was developed for the three lineages, evaluated for accuracy, and then used to screen 881 samples from 52 sites for genetic integrity and hybridization on the Agena MassARRAY platform. These results strongly support a redrawing of native ranges for both the intergrade zone and M. floridanus, which has significant implications for current fisheries management. Furthermore, Delta bass ancestry was shown to contribute significantly to the previously described intergrade zone between northern Largemouth Bass and Florida Bass, suggesting a more complex pattern of secondary contact and introgression among these diverged Micropterus lineages.

Holosteans contextualize the role of the teleost genome duplication in promoting the rise of evolutionary novelties in the ray-finned fish innate immune system

Over 99% of ray-finned fishes (Actinopterygii) are teleosts, a clade that comprises half of all living vertebrate species that have diversified across virtually all fresh and saltwater ecosystems. This ecological breadth raises the question of how the immunogenetic diversity required to persist under heterogeneous pathogen pressures evolved. The teleost genome duplication (TGD) has been hypothesized as the evolutionary event that provided the substrate for rapid genomic evolution and innovation. However, studies of putative teleost-specific innate immune receptors have been largely limited to comparisons either among teleosts or between teleosts and distantly related vertebrate clades such as tetrapods. Here we describe and characterize the receptor diversity of two clustered innate immune gene families in the teleost sister lineage: Holostei (bowfin and gars). Using genomic and transcriptomic data, we provide a detailed investigation of the phylogenetic history and conserved synteny of gene clusters encoding diverse immunoglobulin domain-containing proteins (DICPs) and novel immune-type receptors (NITRs). These data demonstrate an ancient linkage of DICPs to the major histocompatibility complex (MHC) and reveal an evolutionary origin of NITR variable-joining (VJ) exons that predate the TGD by at least 50 million years. Further characterizing the receptor diversity of Holostean DICPs and NITRs illuminates a sequence diversity that rivals the diversity of these innate immune receptor families in many teleosts. Taken together, our findings provide important historical context for the evolution of these gene families that challenge prevailing expectations concerning the consequences of the TGD during actinopterygiian evolution.

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.