Hierarchical Heuristic Species Delimitation under the Multispecies Coalescent Model with Migration.

The multispecies coalescent (MSC) model accommodates genealogical fluctuations across the genome and provides a natural framework for comparative analysis of genomic sequence data from closely related species to infer the history of species divergence and gene flow. Given a set of populations, hypotheses of species delimitation (and species phylogeny) may be formulated as instances of MSC models (e.g., MSC for one species versus MSC for two species) and compared using Bayesian model selection. This approach, implemented in the program bpp, has been found to be prone to over-splitting. Alternatively heuristic criteria based on population parameters (such as popula- tion split times, population sizes, and migration rates) estimated from genomic data may be used to delimit species. Here we develop hierarchical merge and split algorithms for heuristic species delimitation based on the genealogical divergence index (𝑔𝑑𝑖) and implement them in a python pipeline called hhsd. We characterize the behavior of the 𝑔𝑑𝑖 under a few simple scenarios of gene flow. We apply the new approaches to a dataset simulated under a model of isolation by distance as well as three empirical datasets. Our tests suggest that the new approaches produced sensible results and were less prone to over-splitting. We discuss possible strategies for accommodating paraphyletic species in the hierarchical algorithm, as well as the challenges of species delimitation based on heuristic criteria.

New northerly limit for the sharptail mola in the northeast Atlantic: first sighting of Masturus lanceolatus in the northeast Irish Sea.

The ocean sunfishes are currently represented by five species within three genera: Mola mola (Linnaeus, 1758), Mola alexandrini (Ranzani, 1839), Mola tecta (Nyegaard, Sawai, Gemmell, Gillum, Loneragan, Yamanoue & Stewart, 2017) (Sawai et al., 2018), Masturus lanceolatus (Lienard, 1840), and Ranzania laevis (Pennant, 1776). Growing conservation concerns have led to an ongoing re-examination of their classification status on the International Union for the Conservation of Nature Red Lists, a process requiring the latest data to best support their conservation management on a global scale. Here we report the first sighting of Masturus lanceolatus in the northeast Irish Sea, representing a new northerly range limit for this species in the northeast Atlantic. The species is more commonly reported in tropical seas, and in the Western Atlantic they occur from North Carolina in the United States to southeast Brazil. This sighting increases the most northerly range limit by 2610 km, providing additional insight into the ecology and potentially changing distribution of this generally considered tropical megafaunal species.

First long-term trajectory of an ocean sunfish (Mola mola L.) from the northwestern Mediterranean.

The ocean sunfish is a large fish for which many aspects of its ecology and biology are still poorly known. Electronic tagging was used to provide the first information on the movements of an ocean sunfish from the northwestern Mediterranean. The sunfish moved towards the Gibraltar strait over the year and displayed substantial movements in the water column. The potential of the tagging technique employed for studying its behavior and long-term migratory dynamics, and assessing the post-release survival of ocean sunfish is highlighted.

Evolutionary divergence in phenotypic plasticity shapes brain size variation between coexisting sunfish ecotypes.

Mechanisms that generate brain size variation and the consequences of such variation on ecological performance are poorly understood in most natural animal populations. We use a reciprocal-transplant common garden experiment and foraging performance trials to test for brain size plasticity and the functional consequences of brain size variation in Pumpkinseed sunfish (Lepomis gibbosus) ecotypes that have diverged between nearshore littoral and offshore pelagic lake habitats. Different age-classes of wild-caught juveniles from both habitats were exposed for 6 months to treatments that mimicked littoral and pelagic foraging. Plastic responses in oral jaw size suggested that treatments mimicked natural habitat-specific foraging conditions. Plastic brain size responses to foraging manipulations differed between ecotypes, as only pelagic sourced fish showed brain size plasticity. Only pelagic juveniles under 1 year-old expressed this plastic response, suggesting that plastic brain size responses decline with age and so may be irreversible. Finally, larger brain size was associated with enhanced foraging performance on live benthic but not pelagic prey, providing the first experimental evidence of a relationship between brain size and prey-specific foraging performance in fishes. The recent post-glacial origin of these ecotypes suggests that brain size plasticity can rapidly evolve and diverge in fish under contrasting ecological conditions.

Stress response gene family expansions correlate with invasive potential in teleost fish.

The bluegill sunfish Lepomis macrochirus and the closely related redear sunfish Lepomis microlophus have important ecological and recreational value and are widely used for research and aquaculture. While both species have been introduced outside of their native ranges, only the bluegill is considered invasive. Here, we report de novo transcriptome assemblies for these fish as a resource for sunfish biology. Comparative analyses of the transcriptomes revealed an unexpected, bluegill-specific expansion in the HSP70 and HSP90 molecular chaperone gene families. These expansions were not unique to the bluegill as expansions in HSP70s and HSP90s were identified in the genomes of other teleost fish using the NCBI RefSeq database. To determine whether gene family expansions are specific for thermal stress responses, GST and SOD gene families that are associated with oxidative stress responses were also analyzed. Species-specific expansions were also observed for these gene families in distinct fish species. Validating our approach, previously described expansions in the MHC gene family were also identified. Intriguingly, the number of HSP70 paralogs was positively correlated with thermotolerance range for each species, suggesting that these expansions can impact organismal physiology. Furthermore, fish that are considered invasive contained a higher average number of HSP70 paralogs than non-invasive fish. Invasive fish also had higher average numbers of HSP90, MHC and GST paralogs, but not SOD paralogs. Taken together, we propose that expansions in key cellular stress response gene families represent novel genetic signatures that correlate with invasive potential.

Seasonal changes in mitochondrial bioenergetics and physiological performance of the bluegill sunfish, Lepomis macrochirus, from a shallow, Midwest river.

As global temperature shifts due to anthropogenic impacts, seasonal temperatures in shallow aquatic ecosystems are expected to increase. Previous studies on freshwater fishes that experience significant temperature changes during the annual seasons found pronounced physiological restructuring not observed in animals inhabiting more thermally stable environments. Studies evaluating mitochondrial bioenergetics in fish are often performed on animals acclimated to constant temperatures in the laboratory. However, natural habitats are much more complex. Fishes may experience substantial daily and seasonal variation in temperature, energy requirements and resource availability, which are impossible to emulate on acclimation studies. Our study explores the effects of these more complex natural environments on whole-organism thermal tolerance and mitochondrial bioenergetics in bluegill sunfish (Lepomis macrochirus), a native fish to the temperate zone of North America. Compensatory mechanisms and variations in physiological thresholds were observed in specimens acclimatized to the fall season compared to specimens acclimatized to spring and summer seasons. Somatic indices, such as relative weights and hepatosomatic indices, showed significant differences across seasons and critical thermal maxima significantly decreased in the cold acclimatized specimens. Liver mitochondria from L. macrochirus also showed significantly higher uncoupled proton conductance, cytochrome c oxidase (COX) activity, and reduced respiratory control ratios in individuals sampled in the colder season. These findings suggest that mechanisms regulating proton conductance and COX activity modulate mitochondrial function across seasons to sustain physiological fitness in ectotherms inhabiting shallow, inland aquatic habitats.

Interspecific and intraspecific comparisons reveal the importance of evolutionary context in sunfish brain form divergence.

Habitats can select for specialized phenotypic characteristics in animals. However, the consistency of evolutionary responses to particular environmental conditions remains difficult to predict. One trait of great ecological importance is brain form, which is expected to vary between habitats that differ in their cognitive requirements. Here, we compared divergence in brain form and oral jaw size across a common littoral-pelagic ecological axis in two sunfishes at both the intraspecific and interspecific levels. Brain form differed between habitats at every level of comparison; however, divergence was inconsistent, despite consistent differences in oral jaw size. Pumpkinseed and bluegill species differed in cerebellum, optic tectum and olfactory bulb size. These differences are consistent with a historical ecological divergence because they did not manifest between littoral and pelagic ecotypes within either species, suggesting constraints on changes to these regions over short evolutionary time scales. There were also differences in brain form between conspecific ecotypes, but they were inconsistent between species. Littoral pumpkinseed had larger brains than their pelagic counterpart, and littoral bluegill had smaller telencephalons than their pelagic counterpart. Inconsistent brain form divergence between conspecific ecotypes of pumpkinseed and bluegill sharing a common littoral-pelagic habitat axis suggests that contemporary ecological conditions and historic evolutionary context interact to influence evolutionary changes in brain form in fishes.

A foraging ocean sunfish and the 'nearest neighbor' problem.

A predator that preys on randomly-distributed stationary energetically-equivalent small prey will probably choose its next prey to be the nearest one. But what if no prey is found within the detection range of the predator? It is hypothesized that in this case the predator will move along an arbitrary chosen direction until a prey is detected, and turn towards it. In a stochastic environment this strategy leads to a certain distribution function of distances that the predator moves between consequent prey catches. It is shown that when the detection range of the predator exceeds the average distance between prey, this distribution function becomes the nearest neighbor distribution function, whereas; wherew when the detection range is small as compared with the average distance between prey, it becomes the exponential distribution, as the distribution of distances between neighbors on a line. In the first case, the average distance between catches becomes roughly half the average distance between prey; in the second case, it becomes inversely proportional to the square of the detection range. Ocean sunfish preys on practically stationary jellyfish at depth of more than a hundred meters, in dim light. Plausibly, it can detect jellyfish only at close quarters, and hence its detection range is probably small as compared with the average distance between prey. Analysis of the tracking data from seven animals over a few days yielded many thousands of swimming segments separating consequent prey catches. Indeed, lengths of these segments were shown to have the exponential distribution. This finding not only supports the initial hypothesis of this study, but also reveals the fragility of the energetic balance of this animal. A two-fold decrease in the detection range (e.g. due to a decreased visibility) is expected to increase the average distance it moves between catches four-fold, and hence decrease its specific energy intake (the number of jellyfishes per distance moved) by the same rate.

Isolating the effects of ontogenetic niche shift on brain size development using pumpkinseed sunfish ecotypes.

A functional relationship between relative brain size and cognitive performance has been hypothesized. However, the influence of ontogenetic niche shifts on cognitive performance is not well understood. Increases in body size can affect niche use but distinguishing nonecologically relevant brain development from effects associated with ecology is difficult. If survival is enhanced by functional changes in ecocognitive performance over ontogeny, then brain size development should track ontogenetic shifts in ecology. We control for nonecologically relevant brain size development by comparing brain growth between two ecotypes of Pumpkinseed sunfish whose ecologies diverge over ontogeny from a shared juvenile niche. Brain size differs between ecotypes from their birth year onwards even though their foraging ecology appears to diverge at age 3. This finding suggests that the eco-cognitive requirements of adult niches shape early life brain growth more than the requirements of juvenile ecology.

First report of megalocytivirus (iridoviridae) in cultured bluegill sunfish, Lepomis macrochirus, in China.

The bluegill sunfish, Lepomis macrochirus, is an important aquacultural and recreational species in southern China because of its excellent taste, rapid growth rate, and good looks. At present, few pathogens are known to affect the bluegill sunfish. However, an iridovirus-like disease recently caused heavy losses to the bluegill sunfish aquaculture industry in Guangdong, China. We report that a virus, designated BSMIV-SD-20171020, was isolated from diseased bluegill sunfish in China. The isolate was efficiently propagated in a Chinese perch brain (CPB) cell line. The cytopathic effect was observed, the MCP gene PCR amplified, and the virus observed with electron microscopy. Its viral titer in CPB cells reached 104.13 TCID50 mL-1. The mortality rate was 100% when bluegill sunfish were challenged with BSMIV-SD-20171020 at a dose of 103.13 TCID50/fish. A histopathological examination revealed basophilic hypertrophied cells in the intestine, liver, and spleen. A nucleotide sequence alignment and phylogenetic analysis of the major capsid protein revealed that isolate BSMIV-SD-20171020 is the species Infectious spleen and kidney necrosis virus (ISKNV), in the genus Megalocytivirus.

Drag coefficient estimates from coasting bluegill sunfish Lepomis macrochirus.

The drag coefficient bluegill sunfish Lepomis macrochirus was estimated from coasting deceleration as (mean ± SD) 0.0154 ± 0.0070 at a Reynolds number of 41,000 ± 14,000. This was within the coasting range in other species and lower than values obtained from dead drag measurements in this species and others. Low momentum losses during coasting may allow its use during intermittent propulsion to modulate power output or maximize energy economy.

Intraspecific brain size variation between coexisting sunfish ecotypes.

Variation in spatial complexity and foraging requirements between habitats can impose different cognitive demands on animals that may influence brain size. However, the relationship between ecologically related cognitive performance and brain size is not well established. We test whether variation in relative brain size and brain region size is associated with habitat use within a population of pumpkinseed sunfish composed of different ecotypes that inhabit either the structurally complex shoreline littoral habitat or simpler open-water pelagic habitat. Sunfish using the littoral habitat have on average 8.3% larger brains than those using the pelagic habitat. We found little difference in the proportional sizes of five brain regions between ecotypes. The results suggest that cognitive demands on sunfish may be reduced in the pelagic habitat given no habitat-specific differences in body condition. They also suggest that either a short divergence time or physiological processes may constrain changes to concerted, global modifications of brain size between sunfish ecotypes.

The locomotor system of the ocean sunfish Mola mola (L.): role of gelatinous exoskeleton, horizontal septum, muscles and tendons.

Adult ocean sunfish are the heaviest living teleosts. They have no axial musculature or caudal fin. Propulsion is by unpaired dorsal and anal fins; a pseudocaudal fin ('clavus') acts as a rudder. Despite common perception, young sunfish are active predators that swim quickly, beating their vertical fins in unison to generate lift-based propulsion and attain cruising speeds similar to salmon and marlin. Here we show that the thick subcutaneous layer (or 'capsule'), already known to provide positive buoyancy, is also crucial to locomotion. It provides two compartments, one for dorsal fin musculature and one for anal fin muscles, separated by a thick, fibrous, elastic horizontal septum that is bound to the capsule itself, the roof of the skull and the dorsal surface of the short vertebral column. The compartments are braced sagittally by bony haemal and neural spines. Both fins are powered by white muscles distributed laterally and red muscles located medially. The anal fin muscles are mostly aligned dorso-ventrally and have origins on the septum and haemal spines. Dorsal fin muscles vary in orientation; many have origins on the capsule above the skull and run near-horizontally and some bipennate muscles have origins on both capsule and septum. Such bipennate muscle arrangements have not been described previously in fishes. Fin muscles have hinged tendons that pass through capsular channels and radial cartilages to insertions on fin rays. The capsule is gelatinous (89.8% water) with a collagen and elastin meshwork. Greasy in texture, calculations indicate capsular buoyancy is partly provided by lipid. Capsule, septum and tendons provide elastic structures likely to enhance muscle action and support fast cruising.

A comparison of fish pesticide metabolic pathways with those of the rat and goat.

Ecological risk assessments are often limited in their ability to consider metabolic transformations for fish species due to a lack of data. When these types of evaluations are attempted they are often based on parent chemical only, or by assuming similarity to available mammalian metabolic pathways. The metabolism maps for five pesticides (fluazinam, halauxifen-methyl, kresoxim-methyl, mandestrobin, and tolclofos-methyl) were compared across three species. A rapid and transparent process, utilizing a database of systematically collected information for rat, goat, and fish (bluegill or rainbow trout), and using data evaluation tools in the previously described metabolism pathway software system MetaPath, is presented. The approach demonstrates how comparisons of metabolic maps across species are aided by considering the sample matrix in which metabolites were quantified for each species, differences in analytical methods used to identify metabolites in each study, and the relative amounts of metabolites quantified. By incorporating these considerations, more extensive rat and goat metabolism maps were found to be useful predictors of the more limited metabolism of the five pesticides in fish.

Graphene oxide induces cytotoxicity and oxidative stress in bluegill sunfish cells.

Graphene oxide (GO) is considered a promising material for biological application due to its unique properties. However, the potential toxicity of GO to aquatic organism particularly bluegill sun fish cells (BF-2) is unexplored or remains poorly understood. GO-induced cytotoxicity and oxidative stress in BF-2 cells were assessed using a battery of biomarkers. Two different biological assays (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide and neutral red uptake were used to evaluate the cytotoxicity of GO on BF-2 cells. It was found that GO induced dose- and time-dependent cytotoxicity on BF-2 cells. BF-2 cells exposed to lower concentration of GO (40 µg ml-1 ) for 24 induced morphological changes when compared to their respective controls. As evidence for oxidative stress lipid peroxidation, superoxide dismutase, catalase, reactive oxygen species and 8-hydroxy-2'-deoxyguanosine levels were increased and glutathione levels were found to decline in BF-2 cells after treatment with GO. Our findings demonstrate that GO when exposed to BF-2 fish cells cause oxidative stress.

Development of a vortex generator to perturb fish locomotion.

Knowledge about the stiffness of fish fins, and whether stiffness is modulated during swimming, is important for understanding the mechanics of a fin's force production. However, the mechanical properties of fins have not been studied during natural swimming, in part because of a lack of instrumentation. To remedy this, a vortex generator was developed that produces traveling vortices of adjustable strength which can be used to perturb the fins of swimming fish. Experiments were conducted to understand how the generator's settings affected the resulting vortex rings. A variety of vortices (14-32 mm diameter traveling at 371-2155 mm s-1) were produced that elicited adequate responses from the fish fins to help us to understand the fin's mechanical properties at various swimming speeds (0-350 mm s-1).

Phylogeny and morphology of Ovipleistophora diplostomuri n. sp. (Microsporidia) with a unique dual-host tropism for bluegill sunfish and the digenean parasite Posthodiplostomum minimum (Strigeatida).

Microsporidia are diverse opportunistic parasites abundant in aquatic organisms with some species hyperparasitic in digenean parasites. In the current study, we describe a unique microsporidian parasite, Ovipleistophora diplostomuri n. sp. that has a tropism for both the bluegill sunfish Lepomis macrochirus, and its digenean parasite Posthodiplostomum minimum. Though the microsporidium first infects a fish, the subsequent infection causes hypertrophy of the metacercarial wall and degeneration of the P. minimum metacercariae within the fish tissue. Genetic analysis placed this species within Ovipleistophora and ultrastructural characteristics were consistent with the genus, including the presence of dimorphic spores within sporophorous vesicles. Meronts did not have a surface coat of dense material, which has been previously reported for the genus. This is the first Ovipleistophora species described that does not have a tropism for ovary. Genetics demonstrated that O. diplostomuri n. sp. groups closely within fish microsporidia and not other species known to be hyperparasitic in digeneans, suggesting that it evolved from fish-infecting microsporidians and developed a secondary tropism for a common and widespread digenean parasite. The high genetic identity to Ovipleistophora species demonstrates the close relationship of this unique microsporidian with other microsporidia that infect ovary.

A bacterium with close genetic identity to Pseudomonas mandelii associated with spring fish kills in wild bluegill Lepomis macrochirus Rafinesque and pumpkinseed sunfish Lepomis gibbosus (Linnaeus).

Pseudomonas fluorescens are known bacterial pathogens in fish. The P. fluorescens group contains at least nine different bacterial species, although species from fish have rarely been differentiated. Two isolated fish kills affecting wild bluegills, Lepomis macrochirus Rafinesque, and pumpkinseed sunfish, Lepomis gibbosus (Linnaeus), occurred in the spring of 2015 during cool water temperatures (12.5°C-15.5°C). Disease signs included severe bacteraemia with rare gross external signs. Pure bacterial cultures isolated from kidneys of all affected fish were identified as P. fluorescens using the API 20NE system, while no bacteria were isolated from asymptomatic fish. To further identify the species of bacterium within the P. fluorescens complex, genetic analysis of the 16S rRNA, rpoD and gyrB genes was conducted. DNA sequences of bacterial isolates from both mortality events were identical and had close identity (≥99.7%) to Pseudomonas mandelii. Although likely widespread in the aquatic environment, this is the first report of a bacterium closely resembling P. mandelii infecting and causing disease in fish. The bacterium grew at temperatures between 5°C and 30°C, but not at 37°C. It is possible that infections in fish were a result of immunosuppression associated with spring conditions combined with the psychrotrophic nature of the bacterium.

New and historical records of the ocean sunfish Mola mola in Icelandic waters.

The ocean sunfish Mola mola is considered to be globally distributed in both temperate and tropical waters, but there are many gaps in the knowledge of this species' distribution. A total of 31 records of M. mola from Icelandic waters, dating from 1845 to 2014, are presented and georeferenced. An increase in the number of records at the beginning of this century and particularly in 2012, is suggested to be a consequence of both an increase in ocean temperature on the Icelandic shelf and changes in large scale temperature variations in the North Atlantic Ocean.

First confirmed record of Mola sp. A in the western Mediterranean Sea: morphological, molecular and parasitological findings.

Recent molecular and morphological studies suggest the existence of at least three species of Mola (Mola spp. A, B and C). Currently, only Mola mola and Mola ramsayi are formally accepted and species A, B or C have not been assigned to these thus far. In this study, a large ocean sunfish in the western Mediterranean Sea was analysed molecularly and morphologically, identified as Mola sp. A and a detailed account of the specimen's parasite load is reported.