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Fish are the most diverse and widely distributed vertebrates, yet little is known about the microbial ecology of fishes nor the biological and environmental factors that influence fish microbiota. To identify factors that explain microbial diversity patterns in a geographical subset of marine fish, we analyzed the microbiota (gill tissue, skin mucus, midgut digesta and hindgut digesta) from 101 species of Southern California marine fishes, spanning 22 orders, 55 families and 83 genera, representing ~25% of local marine fish diversity. We compare alpha, beta and gamma diversity while establishing a method to estimate microbial biomass associated with these host surfaces. We show that body site is the strongest driver of microbial diversity while microbial biomass and diversity is lowest in the gill of larger, pelagic fishes. Patterns of phylosymbiosis are observed across the gill, skin and hindgut. In a quantitative synthesis of vertebrate hindguts (569 species), we also show that mammals have the highest gamma diversity when controlling for host species number while fishes have the highest percent of unique microbial taxa. The composite dataset will be useful to vertebrate microbiota researchers and fish biologists interested in microbial ecology, with applications in aquaculture and fisheries management. In this study, the microbiota of multiple body sites from 101 marine fish species from Southern California were sampled and analysed. The authors compared diversity measures while also establishing a method to estimate microbial biomass. Body site is shown to be the strongest driver of microbial diversity and patterns of phylosymbiosis are observed across the gill, skin and hindgut.

A new labrid fish species, Halichoeres sanchezi n. sp., is described from eight specimens collected in the Revillagigedo Archipelago in the tropical eastern Pacific Ocean, off the coast of Mexico. The new species belongs to the Halichoeres melanotis species complex that is found throughout the region, differing by 2.4% in the mtDNA cytochrome c oxidase I sequence from its nearest relative, H. melanotis from Panama, and 2.9% from Halichoeres salmofasciatus from Cocos Island, off Costa Rica. The complex is distinguished from others in the region by having a black spot on the opercular flap and a prominent black area on the caudal fin of males. The juveniles and initial phase of the new species closely resemble those of H. salmofasciatus and Halichoeres malpelo from Malpelo Island of Colombia, differing in having an oblong black spot with a yellow dorsal margin on the mid-dorsal fin of initial-phase adults as well as on juveniles. In contrast, the terminal-phase male color pattern is distinct from other relatives, being vermilion to orangish brown with dark scale outlines, a white patch on the upper abdomen, and a prominent black band covering the posterior caudal peduncle and base of the caudal fin. The new species adds to the list of endemic fish species for the isolated archipelago and is an interesting case of island endemism in the region. The discovery was made during the joint 2022 collecting expedition to the archipelago, which featured a pioneering collaborative approach to an inventory of an island ichthyofauna, specifically including expert underwater photographers systematically documenting specimens in situ , before hand-collection, and then photographed fresh, tissue-sampled, and subsequently vouchered in museum collections.

Pelagic predators are effective biological samplers of midtrophic taxa and are especially useful in deep-sea habitats where relatively mobile taxa frequently avoid observation with conventional methods. We examined specimens sampled from the stomachs of longnose lancetfish, Alepisaurus ferox , to describe the diets and foraging behaviors of three common, but poorly known deep-sea fishes: the hammerjaw ( Omosudis lowii , n = 79, 0.3–92 g), juvenile common fangtooth ( Anoplogaster cornuta , n = 91, 0.6–22 g), and juvenile Al. ferox (n = 138, 0.3–744 g). Diet overlap among the three species was high, with five shared prey families accounting for 63 ± 11% of the total prey mass per species. However, distinct differences in foraging strategies and prey sizes were evident. Resource partitioning was greatest between An. cornuta that specialized on small (mean = 0.13 ± 0.11 g), shallow-living hyperiid amphipods and O. lowii that specialized on large (mean = 0.97 ± 0.45 g), deep-dwelling hatchetfishes. Juvenile Al. ferox foraged on a high diversity of prey from both shallow and deep habitats. We describe the foraging ecologies of three midtrophic fish competitors and demonstrate the potential for biological samplers to improve our understanding of deep-sea food webs.

On September 11, 2022, two megamouth sharks (Megachasma pelagios), estimated at 3.7–4.6 m TL, were observed swimming together near the surface about 39 km off the coast of San Diego, CA, USA. Megamouth sharks are rarely observed pelagic sharks, and the film from this encounter provided new insight into the social behavior of this species. We attempt to put the behavior of these two individuals into the context of past sightings, known megamouth shark biology, and with analogous behavior observed in other shark and pelagic fish species.

Genetic variation is the basis upon which natural selection acts to yield evolutionary change. In a rapidly changing environment, increasing genetic variation should increase evolutionary potential, particularly for small, isolated populations. However, the introduction of new alleles, either through natural or human-mediated processes, may have unpredictable consequences such as outbreeding depression. In this study, we identified a contact zone and limited gene flow between historically separated genetic lineages of American pikas (Ochotona princeps), representing the northern and southern Rocky Mountain subspecies, within Rocky Mountain National Park. The limited spatial extent of gene flow observed may be the result of geographic barriers to dispersal, selection against hybrid individuals, or both. Our fine-scale population genetic analysis suggests gene flow is limited but not completely obstructed by extreme topography such as glacial valleys, as well as streams including the Colorado River. The discovery of two subspecies within this single protected area has implications for monitoring and management, particularly in the light of recent analyses suggesting that the pikas in this park are vulnerable to fragmentation and local extinction under future projected climates. Future research should focus on the fitness consequences of introgression among distinct genetic lineages in this location and elsewhere, as well as within the context of genetic rescue as a conservation and management strategy for a climate sensitive species.

Background The evolutionary relationships within Stomiiformes, a diverse order of deep-sea fishes dominating the mesopelagic and bathypelagic zones, remain contentious due to conflicting morphological and molecular evidence. These fishes, comprising 464 species across four traditionally recognized families (Gonostomatidae, Sternoptychidae, Phosichthyidae, and Stomiidae), exhibit remarkable adaptations such as bioluminescence, ultra-black pigmentation, and extreme jaw morphologies. Their global abundance and ecological significance, including contributions to the biological carbon pump, underscores the need to resolve their phylogeny amid escalating threats from climate change and human activities. Results We conducted the most comprehensive phylogenomic analysis of Stomiiformes to date, integrating 936 nuclear loci from 60 species and an expanded dataset of 135 species with mitochondrial sequences from publicly available repositories such as the Barcode of Life Data Systems (BOLD) database. We used maximum likelihood and coalescent-based approaches to assess family monophyly and relationships, including extensive quality control to address contamination in public databases. Our analyses reveal unstable tree topologies and complex evolutionary histories that challenge traditional classifications, while our quality control analyses identified 29% of BOLD sequences as misidentified or contaminated, emphasizing rigorous curation for deep-sea taxa. Congruent with a recent taxonomic treatment of Stomiiformes, the families Phosichthyidae and Gonostomatidae exhibit polyphyly and paraphyly, respectively, while subfamilies within Stomiidae are extensively non-monophyletic, leading us to recommend their abandonment. We propose the recognition of eight monophyletic families: Vinciguerriidae, Diplophidae, Gonostomatidae, Yarrellidae, Ichthyococcidae, Phosichthyidae, Sternoptychidae, and Stomiidae, supported by robust molecular and morphological evidence. Conclusions This revised classification reflects the morphological and ecological diversity of Stomiiformes, aligning with their evolutionary diversification in the deep sea. Our phylogenomic framework resolves longstanding systematic uncertainties and highlights the power of genome-wide data in tackling taxonomically challenging clades. These findings provide a foundation for understanding deep-sea fish diversification and assessing the potential ecological drivers for their evolutionary diversity.

Gnathophis johnsoni sp. nov. is described on the basis of 15 specimens (138–380 mm TL) from the Emperor–Hawaiian Seamount Chain in the western and central North Pacific. The new species is most similar in morphology to G. bathytopos (Atlantic), G. cinctus (eastern Pacific), and G. smithi (Nazca and Salas-y-Gomez Seamounts in the southeastern Pacific) by the sensory pore configuration and vertebral count, but differs from these species in the following characters in combination: darkly pigmented pectoral fin, dorsal fin with black margin broadened caudally and extended onto the distal half of the caudal fin, relatively long head, jaws, gill slit and caudal fin, and on average a greater preanal distance. Although most of morphometrics overlap between the new species and its closest relatives, multivariate statistical analyses clearly discriminate this species. Molecular analysis shows sister relationships between the new species and G. cinctus, with 1.81% of genetic divergence, which significantly exceeds the differences between the haplotypes belonging to the same species (0.36 and 1.08% of divergence, usually not exceeding 0.9%) and confirms both species as close but distinct. The close relationship of G. johnsoni sp. nov. and G. cinctus represents a rare case of biogeographical relations between western and eastern Pacific demersal fish faunas. Molecular data suggest that some morphologically similar species may represent independently evolved lineages, though the group of Gnathophis possessing elevated lateral-line pores is likely monophyletic.

A new species of grouper, Epinephelus craigi. sp. nov., from the South China Sea is described from 17 specimens (104–250 mm SL). The new species is distinguished from Epinephelus stictus (Randall and Allen 1987) with which it has historically been conflated, based on coloration, meristics, morphology, and genetics. Epinephelus craigi sp. nov. has a unique color pattern of irregular squarish, dark brown blotches interrupting lighter brown bars along the lateral midline of the body, and small dots on the dorsal surface of the body. Additionally, E. craigi sp. nov. has a longer upper jaw, shorter snout length, narrower interorbital width, and shorter caudal peduncle than E. stictus. Both E. stictus and the new species are relatively deep-water species, with the new species occurring to at least 93 m. Epinephelus craigi sp. nov. is known from the South China Sea and E. stictus is known from Western Australia and southern Indonesia, suggesting allopatric and anti-equatorial distributions. DNA sequence divergence data of the mitochondrial COI gene further supports the distinction of E. craigi sp. nov. from E. stictus.

Coral reefs are facing threats from a variety of global change stressors, including ocean warming, acidification, and deoxygenation. It has been hypothesized that growing corals near primary producers such as macroalgae or seagrass may help to ameliorate acidification and deoxygenation stress, however few studies have explored this effect in situ. Here, we investigated differences in coral growth rates across a natural gradient in seawater temperature, pH, and dissolved oxygen (DO) variability in a nearshore seagrass bed on Dongsha Atoll, Taiwan, South China Sea. We observed strong spatial gradients in temperature (5°C), pH (0.29 pH units), and DO (129 μmol O 2 kg -1 ) across the 1-kilometer wide seagrass bed. Similarly, diel variability recorded by an autonomous sensor in the shallow seagrass measured diel ranges in temperature, pH, and DO of up to 2.6°C, 0.55, and 204 μmol O 2 kg -1 , respectively. Skeletal cores collected from 15 massive Porites corals growing in the seagrass bed at 4 sites revealed no significant differences in coral calcification rates between sites along the gradients. However, significant differences in skeletal extension rate and density suggest that the dynamic temperature, pH, and/or DO variability may have influenced these properties. The lack of differences in coral growth between sites may be because favorable calcification conditions during the day (high temperature, pH, and DO) were proportionally balanced by unfavorable conditions during the night (low temperature, pH, and DO). Alternatively, other factors were simply more important in controlling coral calcification and/or corals were acclimated to the prevailing conditions at each site.

The deep-sea environment is associated with a wide range of anatomically specialized morphologies allowing camouflage in this low or no light environment. Specialized ultra-black coloration has been documented in the pelican eel, Eurypharynx pelecanoides, but has not been explored in the other largely deep-sea inhabiting pelagic anguilloid eels. Histological examination of the integument revealed a layer of free melanosomes in the superficial dermis consistent with specialized ultra-black camouflage in the swallower eels Saccopharynx, the bobtail snipe eel Cyema, the sawtooth eels Serrivomer, and the snipe eels Avocettina and Nemichthys. The anatomy in these taxa is consistent with the previously described ultra-black morphology, except that Nemichthys, Avocettina, and Serrivomer have both large amounts of free melanosomes and melanophores. Consideration of this morphology in the context of anguilloid eel evolution in the deep-sea environment suggests repeated independent evolution of ultra-black coloration within the anguilloids, and greater development in the taxa more specifically associated with the bathypelagic habitats and the production of bioluminescence.