Abstract Tropical rivers in Australia and New Guinea (Sahul) provide a rare natural experiment in vertebrate evolution: unlike other continental systems, their freshwater ichthyofaunas are composed almost entirely of marine-derived lineages rather than primary freshwater fishes. This unique biogeographic setting enables replicated tests of why some marine-to-freshwater transitions give rise to extensive adaptive radiations whereas others remain species-poor, and whether these outcomes reflect ecological opportunity or temporally structured paleoenvironmental constraints. Using a densely sampled, time-calibrated phylogenomic framework spanning 2,303 teleost species, we identified a likely range of 27–34 marine-to-freshwater transitions during the Cenozoic, including a pronounced Middle Miocene peak (16–11 Ma). Although ecological opportunity in Sahul rivers enabled repeated colonization in the absence of dominant primary freshwater incumbents, younger freshwater lineages nevertheless diversify faster than older ones, contradicting the expectation that early arrivers should undergo elevated diversification when accessing vacant niche space. Although some colonizations coincide with bursts of speciation consistent with adaptive radiation, many yielded few species despite long residence times. Functional trait analyses likewise revealed no consistent relationship between colonization timing, ecological breadth, or diversification rate, although expanded functional space characterizes previously proposed Sahul adaptive radiations. Comparisons with paleoenvironmental curves indicate that colonization success correlates with sea-level minima and low-oxygen conditions, suggesting that Earth history dynamics modulated when ecological opportunity was accessible. Our results show that although ecological opportunity enabled repeated freshwater invasions into the Sahul region, diversification outcomes are governed by the interaction of paleoenvironmental dynamics and possibly lineage-specific traits, generating stark asymmetries in freshwater radiations. Significance statement Tropical rivers in Australia and New Guinea host one of the most unusual continental freshwater fish assemblages on Earth, composed almost entirely of marine-derived lineages. This system allows asking why some colonizing lineages diversify dramatically while others remain species-poor on a continental scale. Using large-scale phylogenomic and functional trait data, we show that early arrival alone does not predict diversification success. Instead, the lineages that radiate most successfully are those whose arrival coincides with windows of paleoenvironmental opportunity created by sea-level and oxygen fluctuations. These results reveal that the fates of colonizing lineages are shaped not only by ecological opportunity, but also by Earth-history dynamics that govern when, where, and how species can invade and diversify.

The assembly of modern ocean ecosystems was fundamentally affected by the Cretaceous-Palaeogene (K-Pg) mass extinction. Among the casualties of this event were many extinct clades of large pelagic predatory fishes. The extinction of these lineages is thought to have created ecological opportunity that spurred the diversification of living large-bodied (> 2 m) marine predatory fishes such as tunas and mackerels (Scombridae). However, it remains unclear whether a large, endothermic body plan evolved in tunas and mackerels directly after the K-Pg boundary or in a stepwise manner throughout the Cenozoic. Here, we demonstrate that Scombridae, which includes half of living endothermic ray-finned fish species, evolved endothermy and large body sizes long after the initial radiation of the clade at the K-Pg boundary. Our time-calibrated phylogeny also reveals that the origins of endothermy, large body size and increased longevity in true tunas are staggered over evolutionary time. These findings indicate that the evolution of large endothermic scombrids was not triggered by the K-Pg extinction and substantiate the protracted development of the endothermic predatory body plans of tunas and relatives over more than 50 million years of evolutionary history.

The pace of evolutionary diversification varies among groups, between environments, and over geologic timescales. Radiations may be linked to phenotypic innovations and ecological opportunity but for highly diverse groups the factors contributing to accelerated diversification are often less clear. We examine the dynamics and drivers of diversification in gobies, an exceptionally species-rich group with a cosmopolitan distribution in aquatic habitats that exhibits extensive ecological variation coupled with low phenotypic diversity. We establish their evolutionary timescale using a phylogenomic hypothesis of relationships calibrated with multiple fossils and identify a pronounced increase in diversification rate in the clade containing Gobiidae and Oxudercidae. This shift is correlated with both phenotypic and ecological traits; elevated diversification is found among marine lineages and those on reefs as well as in those possessing a fused ventral pelvic disc, a key innovation that facilitates stability on benthic substrates. Our analyses additionally reveal diversification fluctuations at the Eocene-Oligocene transition and in the mid-Miocene, periods of extinction and recovery in global marine habitats. Achieving even near-complete taxon sampling is unlikely in hyperdiverse groups such as gobies, but we show that evolutionary dynamics may still be reliably inferred with less than complete taxon sampling by validating our diversification shift patterns using completely sampled, stochastically resolved trees and confirming the robustness of our rate estimates across congruence classes.

The evolution of new traits can drive species diversification by facilitating the use of new resources, but environmental change may turn these same adaptations into liabilities.Trait loss is also often associated with the origin of new ecologies, but how losses modulate diversification remains unclear. The swim bladder allows ray-finned fishes to regulate their buoyancy and exploit ecosystems throughout the water column, yet this organ has been lost many times among species-rich lineages. Here, we show that timing and ecological context control the macroevolutionary effects of swim bladder loss. Many lineages of fishes lost the swim bladder over the last 66 million years as they specialized for benthic habitats where buoyancy regulation is unnecessary. Swim bladder loss enabled the descendants of these benthic fishes to diversify in the deep sea where extreme pressure makes its inflation untenable, and in the frigid, oxygen-saturated Southern Ocean, where loss of the oxygen delivery mechanisms required for swim bladder inflation carries little physiological cost. Yet, we detect a selective filter associated with swim bladder loss during extreme global warming 56 to 50 million years ago, when its absence limited the capacity of fishes to escape ecological disruptions on the ocean floor. These contrasting patterns explain how the loss of a complex trait promoted major ecological transitions without increasing overall diversification through deep time. As human activity drives rapid global warming, the evolutionary legacies of swim bladder loss may again shape the fate of marine fish diversity.

A rapid drop of sea level at the Eocene-Oligocene transition (EOT; 34-33 Ma) triggered a marine mass extinction event and the turnover of terrestrial fauna, but its influence on the diversification of nearshore marine fish communities is unclear. Goby fishes (Acanthomorpha: Percomorpha: Gobiiformes) provide an ideal system to investigate the hypothesis that ecological opportunity at the EOT triggered the proliferation of coastal marine fishes. However, despite more than 30 years of molecular evolutionary research, divergence time estimates for gobies are widely variable, incomplete with respect to sampling of taxonomic families and sub-familial lineages, and far older than evident by the modest fossil record. Here we use 1,314 ultraconserved element (UCE) sequences sampled from 121 species, including all gobiiform families and sub-familial goby lineages, to infer phylogeny and node ages under species tree and relaxed molecular clock models. Our time-calibrated phylogenomic hypothesis reconciles molecular clock- and fossil-based estimates for gobiiform diversification, dating the origin of Apogonidae and Gobioidei to the uppermost Late Cretaceous, with lower to middle Paleogene divergence of the gobioid backbone and an explosion of goby lineages at the EOT. Our results support a remarkably recent evolutionary origin of goby families and stimulate new questions on the seemingly exceptional diversity of the group.

We present a comprehensive phylogenetic taxonomy of Labridae (wrasses, parrotfishes, hogfishes, and weedwhitings), one of the most species-rich lineages of marine teleost fishes, comprising 676 species distributed across tropical and temperate nearshore habitats worldwide. Using a phylogeny of 415 species inferred using genomic markers as a foundation, we create a synthetic phylogeny of 590 species of Labridae by including an additional 175 species based on mitochondrial DNA gene trees, other phylogenetic studies, and explicit statements of relationships in taxonomic revisions. We establish phylogenetic definitions for Labridae and 12 major rini, Sparisomatini, Xyrichtyinae, Pseudolabrinae, and Julidinae. Our taxonomy places parrotfishes (Scarinae) as a clade within Labridae, aligning with phylogenetic studies conducted over the past two decades. Our synthetic phylogeny highlights that several traditionally recognized genera (e.g., Halichoeres, Coris, Thalassoma), particularly within Julidinae, are polyphyletic. This finding necessitates substantial taxonomic revisions of Labridae including description and elevation of 11 genera, 17 new species synonyms, and more than 150 changes to genus-species combinations. This phylogenetically informed taxonomy provides a framework for understanding character evolution and adaptation in Labridae while preserving nomenclatural stability through the retention of well-established clade names.

The advent of molecular phylogenetics has rapidly transformed the understanding of relationships within Acanthopterygii, the spiny-rayed fishes. Acanthopterygii includes most of the marine fish diversity as well as several lineages in freshwater and contains such iconic groups as tunas, cichlids, seahorses, flatfishes, anglerfishes, and most fishes found on coral reefs. The robust and well-resolved phylogeny resulting from more than two decades of molecular studies includes some highly novel placements as well as unprecedented resolution of the lineages within Percomorpha. In this review, we highlight the patterns of morphology, ecology, biology, and biogeography within and among the major clades of Acanthopterygii using an evolutionary perspective that has been made possible by this emergent phylogenetic consensus. Our aim is to provide a comprehensive summary of each clade’s characteristics, serving as a reorientation for those familiar with previous conceptions of acanthopterygian phylogeny and as an introduction for those new to the biology, evolution, and biogeography of the major acanthopterygian groups.

Classification of the tremendous diversity of ray-finned fishes (Actinopterygii) began with the designation of taxonomic groups on the basis of morphological similarity. Starting in the late 1960s morphological phylogenetics became the basis for the classification of Actinopterygii but failed to resolve many relationships, particularly among lineages within the hyperdiverse Percomorpha. The introduction of molecular phylogenetics led to a dramatic reconfiguration of actinopterygian phylogeny. Refined phylogenetic resolution afforded by molecular studies revealed an uneven diversity among actinopterygian lineages, resulting in a proliferation of redundant group names in Linnean-ranked classifications. Here we provide an unranked phylogenetic classification for actinopterygian fishes based on a summary phylogeny of 830 lineages of ray-finned fishes that includes all currently recognized actinopterygian taxonomic families and 287 fossil taxa. We provide phylogenetic definitions for 90 clade names and review seven previously defined names. For each of the 97 clade names, we review the etymology of the clade name, clade species diversity and constituent lineages, clade diagnostic morphological apomorphies, review synonyms, and provide a discussion of the clade's nomenclatural and systematic history. The new classification is free of redundant group names and includes only one new name among the 97 clade names we review and describe, yielding a comprehensive classification that is based explicitly on the phylogeny of ray-finned fishes that has emerged in the 21st century and rests on the foundation of the previous 200 years of research on the systematics of ray-finned fishes.

Three new records of Bathysciadium pacificum Dall, 1908 from off Oregon and Washington extend the range of the species from Peru by similar to 7,300 km to the temperate northeastern Pacific. The preserved and relaxed animal shows that the mantle extensions are not sensory papillae, but mantle folds forming the periostracum rays on the shell. Examination of radula, mantle, and mantle cavity by scanning electron microscopy (SEM), including environmental SEM (ESEM) of the fluid-preserved animal, adds a novel dimension to the understanding of the anatomy of these rare deep-sea snails. ESEM is a suitable tool for fine morphological investigations of rare natural history specimens. The monotypic genera Bathypelta Moskalev, 1971 and Bonus Moskalev, 1973 are re-synonymized under Bathysciadium Dautzenberg and H. Fischer, 1900. No mineralization of the radula was detected by SEM-Energy Dispersive Spectroscopy (EDS/EDAX) mapping

Eleotridae (sleepers) and five smaller families are the earliest diverging lineages within Gobioidei. Most inhabit freshwaters in and around the Indo-Pacific, but Eleotridae also includes species that have invaded the Neotropics as well as several inland radiations in the freshwaters of Australia, New Zealand, and New Guinea. Previous efforts to infer phylogeny of these families have been based on sets of mitochondrial or nuclear loci and have yielded uncertain resolution of clades within Eleotridae. We expand the taxon sampling of previous studies and use genomic data from nuclear ultraconserved elements (UCEs) to infer phylogeny, then calibrate the hypothesis with recently discovered fossils. Our hypothesis clarifies ambiguously resolved relationships, provides a time scale for divergences, and indicates the core crown Eleotridae diverged over a short period 24.3-26.3 Ma in the late Oligocene. Within Eleotridae, we evaluate diversification dynamics with BAMM and find evidence for an overall slowdown in diversification over the past 35 Ma, but with a sharp increase 3.5 Ma in the genus Mogurnda, a clade of brightly colored species found in the freshwaters of Australia and New Guinea.

We describe two new species in the genus Gobiomorphus, a radiation of fresh and brackish water gudgeons known from Australia and New Zealand. These species are a prominent component of New Zealand's freshwater ichthyofauna and most are widely distributed throughout both the North and South Islands. Two of the inland species, G. breviceps and G. basalis, are composed of disjunct northern and southern populations that are distinguishable with molecular data. We examine individuals from across the ranges of both species, identify morphological differences between them, and describe two new species: Gobiomorphus dinae n. sp. (distinct from G. basalis) and Gobiomorphus mataraerore n. sp. (distinct from G. breviceps). Although the species are similar, they vary in dorsal spine count (G. dinae) and pectoral fin ray count (G. mataraerore). We provide mitochondrial COI sequences for each species pair to facilitate identifications by DNA barcoding. These species represent examples of divergence in allopatry, with diagnostic characters arising over the last 2-5 million years in the G. breviceps/G. mataraerore pair, and fewer than 2 million years in the G. basalis/G. dinae pair. We also designate a lectotype for G. basalis (the paralectotype is G. cotidianus) in order to clarify confusion surrounding the original syntypes.

The rivers of southeastern Australia host a species complex within the carp gudgeon genus Hypseleotris that includes parental species and hemiclonal hybrid lineages. These hemiclones can be difficult to distinguish from their parent taxa, making delineation of species unusually difficult. We approach this historical taxonomic problem by using single nucleotide polymorphism (SNP) genotyping to distinguish individuals of each species and hemiclones, enabling us to quantify the variation among evolutionary lineages and assign names to the species. Hypseleotris klunzingeri remains valid and does not have any hemiclones. We describe Hypseleotris bucephala and Hypseleotris gymnocephala from the Murray-Darling Basin and Hypseleotris acropinna from the Murray-Darling as well as eastern coastal streams north of the Mary River, part of the range attributed to H. galii. We further split H. galii to distinguish a species from the Mary River, Hypseleotris moolooboolaensis. We designate a neotype and redescribe H. galii due to uncertainty about the source and species identity of specimens used in the original description. We reconcile previous taxonomies, provide new common names for parental species, and advocate using the scientific names of both parents when referring to the hemiclone hybrids to avoid confusion with previous common names that did not distinguish parental taxa and hemiclones.

Complete list of specimens examined morphology in this study, listing code numbers for each fish and DNA extraction, type status (holotype/paratype/allotype or non-type examined specimen), SNP analysis (low or medium density), species identification, sex, field code, detailed locality, date collected and collector.

Background Carp gudgeons (genus Hypseleotris ) are a prominent part of the Australian freshwater fish fauna, with species distributed around the western, northern, and eastern reaches of the continent. We infer a calibrated phylogeny of the genus based on nuclear ultraconserved element (UCE) sequences and using Bayesian estimation of divergence times, and use this phylogeny to investigate geographic patterns of diversification with GeoSSE. The southeastern species have hybridized to form hemiclonal lineages, and we also resolve relationships of hemiclones and compare their phylogenetic placement in the UCE phylogeny with a hypothesis based on complete mitochondrial genomes. We then use phased SNPs extracted from the UCE sequences for population structure analysis among the southeastern species and hemiclones. Results Hypseleotris cyprinoides , a widespread euryhaline species known from throughout the Indo-Pacific, is resolved outside the remainder of the species. Two Australian radiations comprise the bulk of Hypseleotris , one primarily in the northwestern coastal rivers and a second inhabiting the southeastern region including the Murray–Darling, Bulloo-Bancannia and Lake Eyre basins, plus coastal rivers east of the Great Dividing Range. Our phylogenetic results reveal cytonuclear discordance between the UCE and mitochondrial hypotheses, place hemiclone hybrids among their parental taxa, and indicate that the genus Kimberleyeleotris is nested within the northwestern Hypseleotris radiation along with three undescribed species. We infer a crown age for Hypseleotris of 17.3 Ma, date the radiation of Australian species at roughly 10.1 Ma, and recover the crown ages of the northwestern (excluding H. compressa ) and southeastern radiations at 5.9 and 7.2 Ma, respectively. Range-dependent diversification analyses using GeoSSE indicate that speciation and extinction rates have been steady between the northwestern and southeastern Australian radiations and between smaller radiations of species in the Kimberley region and the Arnhem Plateau. Analysis of phased SNPs confirms inheritance patterns and reveals high levels of heterozygosity among the hemiclones. Conclusions The northwestern species have restricted ranges and likely speciated in allopatry, while the southeastern species are known from much larger areas, consistent with peripatric speciation or allopatric speciation followed by secondary contact. Species in the northwestern Kimberley region differ in shape from those in the southeast, with the Kimberley species notably more elongate and slender than the stocky southeastern species, likely due to the different topographies and flow regimes of the rivers they inhabit.

Evolutionary transitions between marine and freshwater ecosystems have occurred repeatedly throughout the phylogenetic history of fishes. The theory of ecological opportunity predicts that lineages that colonize species-poor regions will have greater potential for phenotypic diversification than lineages invading species-rich regions. Thus, transitions between marine and freshwaters may promote phenotypic diversification in trans-marine/freshwater fish clades. We used phylogenetic comparative methods to analyze body size data in nine major fish clades that have crossed the marine/freshwater boundary. We explored how habitat transitions, ecological opportunity, and community interactions influenced patterns of phenotypic diversity. Our analyses indicated that transitions between marine and freshwater habitats did not drive body size evolution, and there are few differences in body size between marine and freshwater lineages. We found that body size disparity in freshwater lineages is not correlated with the number of independent transitions to freshwaters. We found a positive correlation between body size disparity and overall species richness of a given area, and a negative correlation between body size disparity and diversity of closely related species. Our results indicate that the diversity of incumbent freshwater species does not restrict phenotypic diversification, but the diversity of closely related taxa can limit body size diversification. Ecological opportunity arising from colonization of novel habitats does not seem to have a major effect in the trajectory of body size evolution in trans-marine/freshwater clades. Moreover, competition with closely related taxa in freshwaters has a greater effect than competition with distantly related incumbent species.

Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and account for more than a quarter of all living vertebrate species. Previous time-calibrated phylogenies and patterns from the fossil record explain this dominance by correlating the origin of major acanthomorph lineages with the Cretaceous–Palaeogene mass extinction. Here we infer a time-calibrated phylogeny using ultraconserved elements that samples 91.4% of all acanthomorph families and investigate patterns of body shape disparity. Our results show that acanthomorph lineages steadily accumulated throughout the Cenozoic and underwent a significant expansion of among-clade morphological disparity several million years after the end-Cretaceous. These acanthomorph lineages radiated into and diversified within distinct regions of morphospace that characterize iconic lineages, including fast-swimming open-ocean predators, laterally compressed reef fishes, bottom-dwelling flatfishes, seahorses and pufferfishes. The evolutionary success of spiny-rayed fishes is the culmination of multiple species-rich and phenotypically disparate lineages independently diversifying across the globe under a wide range of ecological conditions. The authors construct a time-calibrated phylogeny spanning >90% of spiny-rayed fishes to explore patterns of body shape disparity within acanthomorphs. They find a trend of steady accumulation of lineages from the Cenozoic, with an increase in morphological disparity following the Cretaceous–Palaeogene event, facilitating the radiation of diverse morphotypes that characterize acanthomorphs’ widespread ecological success today.

R ICK FEENEY was the Ichthyology Collections Manager at the Natural History Museum of Los Angeles County (LACM) for more than 38 years until his retirement in 2019. He was known for his comprehensive collections management skills as well as his expertise in California fishes and larval fishes of all kinds. During his time at LACM, Rick oversaw the daily management, digital catalog, and loan activity for the Ichthyology collection and frequently for the Herpetology collection as well (Fig. 1). He was an integral part of the Research and Collections staff at LACM, and the Ichthyology collections would not be the same today without his exacting attention to detail, broad knowledge of fishes, and commitment to making the specimens and their data accessible to all. Rick is particularly remembered for his kindness and welcoming support of the many students and researchers who used the LACM Ichthyology collections over the course of his long career. He was beloved at the museum, always jovial and optimistic, and contributed so much to the welcoming and inclusive atmosphere in Ichthyology through the years. Rick died on May 6, 2021 after a long battle with cancer. Rick was born on October 5, 1954 in Burbank, California, the youngest of four children and the only son of Bernard and Virginia Feeney. Rick grew up in the Burbank hills north of Los Angeles, and throughout his life he enjoyed hiking and exploring the nearby Verdugo Mountains. He learned how to catch fish as a child and that love of biology and the outdoors prompted him to study biology at the California Polytechnic State University in San Luis Obispo. He graduated in 1978 and returned to Burbank, where he found a job at St. Joseph Hospital and met Lissette Santos, whom he married in 1979. They had their daughter Pamela in 1983 and settled down in Burbank, surrounded by his extended family. Rick went on to pursue a master’s degree in biology at the University of Southern California (USC), working with Dr. Robert Lavenberg, who was then the Ichthyology Curator at LACM and an adjunct professor at USC. Rick’s association with the LACM collections lasted for more than 40 years, beginning in 1978 when he first took a position sorting and identifying ichthyoplankton through a contract with Southern California Edison, administered initially by Occidental College and then transferred to USC and LACM a few months later. Rick was then hired into a permanent position at LACM as a Curatorial Assistant which later was termed Collections Manager. He completed his thesis entitled ‘‘Early Life History of the Yellowchin Sculpin Icelinus quadriseriatus’’ in 1983 and continued to curate and improve LACM’s ichthyoplankton collections throughout his career. He also remained a lifelong fan of the USC football team and regularly attended games and tailgate parties with Lavenberg and his USC colleagues over the years. In Rick’s years at LACM, he would participate in moving the entire Ichthyology collection (roughly 150,000 lots in those years) twice within the museum (Fig. 2). These moves were grueling but gave Rick a deep familiarity with the Fig. 1. Rick Feeney with a gharial skull model in the LACM Department of Herpetology in 2011. Although Rick’s specialty was ichthyology, he would also serve as Collections Manager in the Department of Herpetology when layoffs or other demands required double duty to keep both departments open to researchers. Photo by Neftali Camacho.

Adaptive radiations are generally thought to occur soon after a lineage invades a region offering high levels of ecological opportunity. However, few adaptive radiations beyond a handful of exceptional examples are known, so a comprehensive understanding of their dynamics is still lacking. Here, we present a novel case of an island species flock of freshwater fishes with a radically different tempo of adaptive history than that found in many popular evolutionary model systems. Using a phylogenomic data set combined with simultaneous Bayesian estimation of divergence times and trait-based speciation and extinction models, we show that the New Zealand Gobiomorphus gudgeons comprise a monophyletic assemblage, but surprisingly, the radiation did not fully occupy freshwater habitats and explosively speciate until more than 10 myr after the lineage invaded the islands. This shift in speciation rate was not accompanied by an acceleration in the rate of morphological evolution in the freshwater crown clade relative to the other species, but is correlated with a reduction in head pores and scales as well as an increase in egg size. Our results challenge the notion that clades always rapidly exploit ecological opportunities in the absence of competing lineages. Instead, we demonstrate that adaptive radiation can experience a slow start before undergoing accelerated diversification and that lineage and phenotypic diversification may be uncoupled in young radiations. [Adaptive radiation; Eleotridae; freshwater; Gobiomorphus; New Zealand.].

Cleaning symbioses are mutualistic relationships where cleaners remove and consume ectoparasites from their clients. Cleaning behavior is rare in fishes and is a highly specialized feeding strategy only observed in around 200 species. Cleaner fishes vary in their degree of specialization, ranging from species that clean as juveniles or facultatively as adults, to nearly obligate or dedicated cleaners. Here, we investigate whether these different levels of trophic specialization correspond with similar changes in feeding morphology. Specifically, we model the evolution of cleaning behavior across the family Gobiidae, which contains the most speciose radiation of dedicated and facultative cleaner fishes. We compared the cranial morphology and dentition of cleaners and non-cleaners across the phylogeny of cleaning gobies and found that facultative cleaners independently evolved four times and have converged on an intermediate morphology relative to that of dedicated cleaners and non-cleaning generalists. This is consistent with their more flexible feeding habits. Cleaner gobies also possess a distinct tooth morphology, which suggests they are adapted for scraping parasites off their clients and show little similarity to other cleaner clades. We propose that evolutionary history and pre-adaptation underlie the morphological and ecological diversification of cleaner fishes.