World-wide species distributions in the family Kyphosidae (Teleostei: Perciformes)

New and previously described Acleotrema species (Monogenea, Diplectanidae) parasitizing sea chubs (Centrarchiformes: Kyphosidae) in the Southeastern Pacific Ocean

During a study on the diversity of monogeneans infecting kyphosid fishes off the coast of Puerto Santa Rosa, Lambayeque region, northern Peru, specimens of the Cortez sea chub Kyphosus elegans (Peters) and the brassy chub K. vaigiensis (Quoy & Gaimard) were examined. Five diplectanids, including a new species, were identified: Acleotrema alejandroi sp. nov. from K. vaigiensis; A. diplobulbus (Yamaguti, 1968) from K. vaigiensis; A. nenue (Yamaguti, 1968) Dominques & Boeger, 2007 from both K. vaigiensis and K. elegans; A. oliveri (León-Régagnon, Pérez-Ponce de León & Garcia Prieto, 1997) from K. elegans and K. vaigiensis; A. spiculare (Yamaguti, 1968) from K. vaigiensis. Acleotrema alejandroi sp. nov. is easily differentiated from all congeneric species by its male copulatory organ (MCO), which is J-shaped with a spatulate distal end. The middle portion of MCO is surrounded by a sclerotized sac; and the distal portion of the sac bears an elongated, sclerotized U-shaped process. Acleotrema oliveri is redescribed based on examination of the type specimen (holotype and paratypes) and newly collected specimens. In addition, new morphometric data and whole-mount drawing of A. nenue, A. spiculare and A. diplobulbus are provided. Acleotrema nenuoides (Rakotofiringa, Oliver & Lambert, 1987) is considered a junior synonym of A. nenue. The present finding brings to 13, the number of known species of Acleotrema Johnston & Tiegs, 1922, and represents the first diplectanid species infecting kyphosid fishes from Peru. Furthermore, this study represents the first record of A. spiculare and A. diplobulbus after more than 50 years.

Assembly of Mitochondrial Genomes Using Nanopore Long-Read Technology in Three Sea Chubs (Teleostei: Kyphosidae)

Complete mitochondrial genomes have become markers of choice to explore phylogenetic relationships at multiple taxonomic levels and they are often assembled using whole genome short-read sequencing. Herein, using three species of sea chubs as an example, we explored the accuracy of mitochondrial chromosomes assembled using Oxford Nanopore Technology (ONT) Kit 14 R10.4.1 long reads at different sequencing depths (high, low and very low or genome skimming) by comparing them to 'gold' standard reference mitochondrial genomes assembled using Illumina NovaSeq short reads. In two species of sea chubs, Girella nigricans and Kyphosus azureus, ONT long-read assembled mitochondrial genomes at high sequencing depths (> 25× whole [nuclear] genome) were identical to their respective short-read assembled mitochondrial genomes. Not a single 'homopolymer insertion', 'homopolymer deletion', 'simple substitution', 'single insertion', 'short insertion', 'single deletion' or 'short deletion' were detected in the long-read assembled mitochondrial genomes after aligning each one of them to their short-read counterparts. In turn, in a third species, Medialuna californiensis, a 25× sequencing depth long-read assembled mitochondrial genome was 14 nucleotides longer than its short-read counterpart. The difference in total length between the latter two assemblies was due to the presence of a short motif 14 bp long that was repeated (twice) in the long read but not in the short-read assembly. Read subsampling at a sequencing depth of 1× resulted in the assembly of partial or complete mitochondrial genomes with numerous errors, including, among others, simple indels, and indels at homopolymer regions. At 3× and 5× subsampling, genomes were identical (perfect) or almost identical (quasiperfect, 99.5% over 16,500 bp) to their respective Illumina assemblies. The newly assembled mitochondrial genomes exhibit identical gene composition and organisation compared with cofamilial species and a phylomitogenomic analysis based on translated protein-coding genes suggested that the family Kyphosidae is not monophyletic. The same analysis detected possible cases of misidentification of mitochondrial genomes deposited in GenBank. This study demonstrates that perfect (complete and fully accurate) or quasiperfect (complete but with a single or a very few errors) mitochondrial genomes can be assembled at high (> 25×) and low (3-5×) but not very low (1×, genome skimming) sequencing depths using ONT long reads and the latest ONT chemistries (Kit 14 and R10.4.1 flowcells with SUP basecalling). The newly assembled and annotated mitochondrial genomes can be used as a reference in environmental DNA studies focusing on bioprospecting and biomonitoring of these and other coastal species experiencing environmental insult. Given the small size of the sequencing device and low cost, we argue that ONT technology has the potential to improve access to high-throughput sequencing technologies in low- and moderate-income countries.

The Abrolhos Nominally Herbivorous Coral Reef Fish Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare Have Similarities in Feeding But Species-Specific Microbiomes

Coral reefs rely heavily on reef fish for their health, yet overfishing has resulted in their decline, leading to an increase in fast-growing algae and changes in reef ecosystems, a phenomenon described as the phase-shift. A clearer understanding of the intricate interplay between herbivorous, their food, and their gut microbiomes could enhance reef health. This study examines the gut microbiome and isotopic markers (δ13C and δ15N) of four key nominally herbivorous reef fish species (Acanthurus chirurgus, Kyphosus sp., Scarus trispinosus, and Sparisoma axillare) in the Southwestern Atlantic's Abrolhos Reef systems. Approximately 16.8 million 16S rRNA sequences were produced for the four fish species, with an average of 317,047 ± 57,007 per species. Bacteria such as Proteobacteria, Firmicutes, and Cyanobacteria were prevalent in their microbiomes. These fish show unique microbiomes that result from co-diversification, diet, and restricted movement. Coral-associated bacteria (Endozoicomonas, Rhizobia, and Ruegeria) were found in abundance in the gut contents of the parrotfish species Sc. trispinosus and Sp. axillare. These parrotfishes could aid coral health by disseminating such beneficial bacteria across the reef. Meanwhile, Kyphosus sp. predominantly had Pirellulaceae and Rhodobacteraceae. Four fish species had a diet composed of turf components (filamentous Cyanobacteria) and brown algae (Dictyopteris). They also had similar isotopic niches, suggesting they shared food sources. A significant difference was observed between the isotopic signature of fish muscular gut tissue and gut contents, pointing to the role that host genetics and gut microbes play in differentiating fish tissues.

Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish

Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce genomic information about the microbiota that perform this degradation. This study explores the potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae through in silico study of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) from previously described Kyphosus gut metagenomes and newly sequenced bioreactor enrichments reveals differences in enzymatic capabilities between the major microbial taxa in Kyphosus guts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzyme collections able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from the Bacillota (genus Vallitalea) and Verrucomicrobiota (order Kiritimatiellales) highlight the importance of metabolic contributions from multiple phyla to broaden polysaccharide degradation capabilities. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level among Kyphosus symbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors.IMPORTANCESeaweed has long been considered a promising source of sustainable biomass for bioenergy and aquaculture feed, but scalable industrial methods for decomposing terrestrial compounds can struggle to break down seaweed polysaccharides efficiently due to their unique sulfated structures. Fish of the genus Kyphosus feed on seaweed by leveraging gastrointestinal bacteria to degrade algal polysaccharides into simple sugars. This study reconstructs metagenome-assembled genomes for these gastrointestinal bacteria to enhance our understanding of herbivorous fish digestion and fermentation of algal sugars. Investigations at the gene level identify Kyphosus guts as an untapped source of seaweed-degrading enzymes ripe for further characterization. These discoveries set the stage for future work incorporating marine enzymes and microbial communities in the industrial degradation of algal polysaccharides.

Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish

Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce foundational genomic work on the microbiota that perform this degradation. This study explores the potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae through in silico study of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) reveals differences in enzymatic capabilities between the major microbial taxa in Kyphosus guts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzymes able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from the Bacillota (genus Vallitalea) and Verrucomicrobiota (order Kiritimatiellales) suggest the potential for microbial transfer between marine sediment and Kyphosus digestive tracts. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level among Kyphosus symbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors.

Phylogenomics and body shape morphometrics reveal recent diversification in the goatfishes (Syngnatharia: Mullidae)

Clades of marine fishes exhibit many patterns of diversification, ranging from relatively constant throughout time to rapid changes in the rates of speciation and extinction. The goatfishes (Syngnatharia: Mullidae) are a family of marine, reef associated fishes with a relatively recent origin, distributed globally in tropical and temperate waters. Despite their abundance and economic importance, the goatfishes remain one of the few coral reef families for which the species level relationships have not been examined using genomic techniques. Here we use phylogenomic analysis of ultra-conserved elements (UCE) and exon data to resolve a well-supported, time-calibrated phylogeny for 72 species of goatfishes, supporting a recent crown age of the goatfishes at 21.9 million years ago. We used this framework to test hypotheses about the associations among body shape morphometrics, taxonomy, and phylogeny, as well as to explore relative diversification rates across the phylogeny. Body shape was strongly associated with generic-level taxonomy of goatfishes, with morphometric analyses showing evidence for high phylogenetic signal across all morphotypes. Rates of diversification in this clade reveal a recent sharp increase in lineage accumulation, with 92% of the goatfish species sampled across all clades and major body plans having originated in just the past 5 million years. We suggest that habitat diversity in the early Pliocene oceans and the generalist ecology of goatfishes are key factors in the unusual evolutionary tempo of the family Mullidae.

Substrate degradation pathways, conserved functions and community composition of the hindgut microbiota in the herbivorous marine fish Kyphosus sydneyanus

Symbiotic gut microbiota in the herbivorous marine fish Kyphosus sydneyanus play an important role in digestion by converting refractory algal carbohydrate into short-chain fatty acids. Here we characterised community composition using both 16S rRNA gene amplicon sequencing and shotgun-metagenome sequencing. Sequencing was carried out on lumen and mucosa samples (radial sections) from three axial sections taken from the hindgut of wild-caught fish. Both lumen and mucosa communities displayed distinct distributions along the hindgut, likely an effect of the differing selection pressures within these hindgut locations, as well as considerable variation among individual fish. In contrast, metagenomic sequences displayed a high level of functional similarity between individual fish and gut sections in the relative abundance of genes (based on sequencing depth) that encoded enzymes involved in algal-derived substrate degradation. These results suggest that the host gut environment selects for functional capacity in symbionts rather than taxonomic identity. Functional annotation of the enzymes encoded by the gut microbiota was carried out to infer the metabolic pathways used by the gut microbiota for the degradation of important dietary substrates: mannitol, alginate, laminarin, fucoidan and galactan (e.g. agar and carrageenan). This work provides the first evidence of the genomic potential of K. sydneyanus hindgut microbiota to convert highly refractory algal carbohydrates into metabolically useful short-chain fatty acids.

Molecular phylogenetics reveals the evolutionary history of marine fishes (Actinopterygii) endemic to the subtropical islands of the Southwest Pacific

Remote oceanic islands of the Pacific host elevated levels of actinopterygian (ray-finned fishes) endemism. Characterizing the evolutionary histories of these endemics has provided insight into the generation and maintenance of marine biodiversity in many regions. The subtropical islands of Lord Howe, Norfolk, and Rangitāhua (Kermadec) in the Southwest Pacific are yet to be comprehensively studied. Here, we characterize the spatio-temporal diversification of marine fishes endemic to these Southwest Pacific islands by combining molecular phylogenies and the geographic distribution of species. We built Bayesian ultrametric trees based on open-access and newly generated sequences for five mitochondrial and ten nuclear loci, and using fossil data for time calibration. We present the most comprehensive phylogenies to date for marine ray-finned fish genera, comprising 34 species endemic to the islands, including the first phylogenetic placements for 11 endemics. Overall, our topologies confirm the species status of all endemics, including three undescribed taxa. Our phylogenies highlight the predominant affinity of these endemics with the Australian fish fauna (53%), followed by the East Pacific (15%), and individual cases where the closest sister taxon of our endemic is found in the Northwest Pacific and wider Indo-Pacific. Nonetheless, for a quarter of our focal endemics, their geographic affinity remains unresolved due to sampling gaps within their genera. Our divergence time estimates reveal that the majority of endemic lineages (67.6%) diverged after the emergence of Lord Howe (6.92 Ma), the oldest subtropical island in the Southwest Pacific, suggesting that these islands have promoted diversification. However, divergence ages of some endemics pre-date the emergence of the islands, suggesting they may have originated outside of these islands, or, in some cases, ages may be overestimated due to unsampled taxa. To fully understand the role of the Southwest Pacific subtropical islands as a 'cradle' for diversification, our study advocates for further regional surveys focused on tissue collection for DNA analysis.

Enenterum kyphosi Yamaguti, 1970 and Enenterum petrae n. sp. (Digenea: Enenteridae) from kyphosid fishes (Centrarchiformes: Kyphosidae) collected in marine waters off eastern Australia

Species of the digenean genus Enenterum Linton, 1910 (Lepocreadioidea: Enenteridae) are characterised primarily by their elaborate oral suckers, which are divided into varying numbers of anteriorly directed lobes, and their host-restriction to herbivorous marine fishes of the family Kyphosidae. We describe Enenterum petrae n. sp. from the brassy chub Kyphosus vaigiensis (Quoy & Gaimard) collected off Lizard Island, Great Barrier Reef, Queensland, Australia. Enenterum petrae n. sp. is readily differentiated from congeners by its unique oral sucker morphology, in having a minute pharynx, and the combination of a genital cap and accessory sucker. We also provide the first record of Enenterum kyphosi Yamaguti, 1970 from Australia based on material obtained from the blue sea chub Kyphosus cinerascens (Forsskål) collected off Lizard Island and North Stradbroke Island, Queensland. Morphologically, our specimens of E. kyphosi agree closely with descriptions of this species from Hawaii and South Africa, and despite lack of molecular data from outside of Australian waters, we consider all three reports to represent a single, widespread species. The first ITS2 and COI mtDNA gene sequences for species of Enenterum are provided and molecular phylogenetic analyses of 28S rDNA gene sequences place these species in a strongly-supported clade with the type-species of the genus, Enenterum aureum Linton, 1910. The oral suckers of both E. kyphosi and E. petrae n. sp. can be interpreted as having varying numbers of lobes depending on the particular specimen and how the division between lobes is defined. Scanning electron microscopical images improves understanding of the morphology of the enenterid oral sucker, and permits speculation regarding the evolutionary history leading to its specialisation in this lineage.

An updated, illustrated inventory of the marine fishes of the US Virgin Islands

The US Virgin Islands (USVI) include St. John and St. Thomas on the Puerto Rican Platform (PRP) and St. Croix, isolated by 2000 m deep water 45 km south of that platform. Previous inventories of the marine fishes of these islands include a comprehensive 2014 checklist of the fishes of St. Croix and a list of the fishes of the PRP produced in 2000. The latter list noted the locations of many records of the plateau's fishes, allowing the construction of a combined inventory for St. John and St. Thomas. Those two islands are treated here as a single faunal unit because they are only 3.5 km apart on a shared shallow shelf with various islets and reefs in between. Here we provide updated information on those two USVI (St. Croix and St. John-Thomas) marine fish faunas. The additions to the St. Croix and St. John-Thomas inventories presented here are based on a combination of information from the two sources indicated above, more recent publications dealing with those faunas, a review of location records on various online sources of biogeographic data, and voucher photographs taken of fishes in the field by authors of this paper and other citizen scientists. This assessment increased the known fauna of St. Croix by 7.5% to 585 species. The inventory for St. John-Thomas increased by 39.9% from 401 species on the 2000 PRP list to 561 with the inclusion of records from other sources. On-site mtDNA (COI) barcodes are available for approximately one-third of the species of the St. John-Thomas fauna, but for only one species collected at St. Croix. A set of underwater photographs of 372 species (34 of them representing the sole record of a species) from St. John-Thomas and of 11 shallow-water species added to the St. Croix fauna is included. These represent occurrence vouchers and also are intended to facilitate future work that builds on the present compendium.

Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes

Background

Gut microorganisms aid in the digestion of food by providing exogenous metabolic pathways to break down organic compounds. An integration of longitudinal microbial and chemical data is necessary to illuminate how gut microorganisms supplement the energetic and nutritional requirements of animals. Although mammalian gut systems are well-studied in this capacity, the role of microbes in the breakdown and utilization of recalcitrant marine macroalgae in herbivorous fish is relatively understudied and an emerging priority for bioproduct extraction. Here we use a comprehensive survey of the marine herbivorous fish gut microbial ecosystem via parallel 16S rRNA gene amplicon profiling (microbiota) and untargeted tandem mass spectrometry (metabolomes) to demonstrate consistent transitions among 8 gut subsections across five fish of the genus of Kyphosus.

Results

Integration of microbial phylogenetic and chemical diversity data reveals that microbial communities and metabolomes covaried and differentiated continuously from stomach to hindgut, with the midgut containing multiple distinct and previously uncharacterized microenvironments and a distinct hindgut community dominated by obligate anaerobes. This differentiation was driven primarily by anaerobic gut endosymbionts of the classes Bacteroidia and Clostridia changing in concert with bile acids, small peptides, and phospholipids: bile acid deconjugation associated with early midgut microbiota, small peptide production associated with midgut microbiota, and phospholipid production associated with hindgut microbiota.

Conclusions

The combination of microbial and untargeted metabolomic data at high spatial resolution provides a new view of the diverse fish gut microenvironment and serves as a foundation to understand functional partitioning of microbial activities that contribute to the digestion of complex macroalgae in herbivorous marine fish.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-022-00182-z.

Gorgocephalidae (Digenea: Lepocreadioidea) in the Indo-West Pacific: new species, life-cycle data and perspectives on species delineation over geographic range

The digenetic trematode family Gorgocephalidae comprises just a few species, and the literature devoted to the lineage consists of only a handful of reports. With one exception, all reports have been based on material collected in the Indo-West Pacific, an expansive marine ecoregion stretching from the east coast of Africa to Easter Island, Hawaii and French Polynesia. We collected adult and intramolluscan gorgocephalids from kyphosid fishes and littorinid gastropods from several Australian localities, and from South Africa and French Polynesia. Specimens of Gorgocephalus kyphosi and G. yaaji were collected from, or near, their type-localities, providing new morphological and molecular (COI, ITS2 and 28S) data needed for a revised understanding of species boundaries in the family. Two new species are recognized: Gorgocephalus euryaleae sp. nov. and Gorgocephalus graboides sp. nov. New definitive host records are provided for described species and three new intermediate hosts are identified. These new records are all associated with Kyphosus fishes and littorinid gastropods, reaffirming the restriction of gorgocephalids to these hosts. Most significantly, we provide evidence that G. yaaji is distributed from South Africa to French Polynesia, spanning the breadth of the Indo-West Pacific. Our findings have significant relevance regarding digenean species delineation over geographic range.

Evolutionary origin of the Atlantic Cabo Verde nibbler (Girella stuebeli), a member of a primarily Pacific Ocean family of antitropical herbivorous reef fishes

Nibblers (family Girellidae) are reef fishes that are mostly distributed in the Indo-Pacific, with one exception: Girella stuebeli, which is found in the Cabo Verde Archipelago, in the Atlantic Ocean. We capitalized on this unusual distribution to study the evolutionary history of the girellids, and determine the relationship between G. stuebeli and the remaining nibbler taxa. Based on thousands of genomic markers (RAD sequences), we identified the closest relatives of G. stuebeli as being a clade of three species endemic to the northwestern Pacific, restricted to the Sea of Japan and vicinity. This clade diverged from G. stuebeli approximately 2.2 Mya. Two alternative potential routes of migration may explain this affinity: a western route, from the Tropical Eastern Pacific and the Tropical Western Atlantic, and an eastern route via the Indian Ocean and Southern Africa. The geological history and oceanography of the regions combined with molecular data presented here, suggest that the eastern route of invasion (via the Indian Ocean and Southern Africa) is a more likely scenario.

Natural history footage provides new reef fish biodiversity information for a pristine but rarely visited archipelago

There remain parts of our planet that are seldom visited by humans, let alone scientists. In such locations, crowd-sourced or citizen scientist data can be critical in describing biodiversity and detecting change. Rangitāhua, the Kermadec Islands, are 750 km from the nearest human-habitation. Although our knowledge of this near pristine location has increased with recent biodiversity expeditions, we still lack comprehensive understanding of the marine biodiversity surrounding the islands. In 2015, professional underwater videographers were commissioned to produce a nature documentary focused on Rangitāhua’s reefs. We strategically surveyed the raw documentary video and examined how biodiversity estimates differed from traditional scientific surveys. We uncovered three new fish species records for Rangitāhua, extending the known distribution for each species, two of which are also new records for New Zealand waters. Comparison of documentary video footage with scientific survey methods showed that estimates of reef fish species richness from the documentary video were similar to stationary surveys, but lower than non-stationary surveys. Moreover, all survey methods, including documentary video, captured different fish assemblages, reflecting each method’s particular bias. Overall, we provide a proof-of-concept for how collaborations between scientists and professional natural historians, such as videographers and photographers, can provide valuable biodiversity information.

Annotated checklist of fishes from Monterey Bay National Marine Sanctuary with notes on extralimital species

Monterey Bay National Marine Sanctuary is a federal, marine protected area located off the central coast of California, USA. Understanding biodiversity, and how it is changing, is necessary to effectively manage the sanctuary. The large size of this sanctuary, which contains a variety of habitats and is influenced by several water masses, provides for a diverse fish fauna. The central California coast has a rich history of ichthyological research and surveys, contributing to a unique repository of information on fish diversity. Herein, we provide a checklist of fishes that occur within the sanctuary, including justification for each species. Ancillary record information including name-bearing type specimens, historic species, cold- or warm-water event species, introduced species, and occurrence at Davidson Seamount or Elkhorn Slough are also provided. This represents the first comprehensive annotated checklist of 507 fishes known to occur within the sanctuary. In addition, 18 species are considered to be extralimital. This annotated checklist of fishes can be used by those interested in zoogeography, marine protected areas, ichthyology, regional natural history, and sanctuary management.

An identity crisis in the Indo-Pacific: molecular exploration of the genus Koseiria (Digenea: Enenteridae)

We explore the growing issue of cryptic speciation in the Digenea through study of museum material and newly collected specimens consistent with the enenterid genus Koseiria from five species of the Kyphosidae and Chaetodontoplus meredithi Kuiter (Pomacanthidae) collected in the Indo-Pacific. We use an integrated approach, employing traditional morphometrics, principal components analysis (PCA), and molecular data (ITS2 and 28S rDNA). Our results support recombination of Koseiria allanwilliamsi Bray & Cribb, 2002 as Proenenterum allanwilliamsi (Bray & Cribb, 2002) n. comb. and transfer of Koseiria huxleyi Bray & Cribb, 2001 to a new genus as Enenterageitus huxleyi (Bray & Cribb, 2002) n. comb. Molecular data indicate the presence of four further species consistent with Koseiria, one from Western Australia (sequence data only) and three from eastern Australia. All three eastern Australian species are morphologically consistent with Koseiria xishaensis Gu & Shen, 1983, but distinct from all other previously described species. Although K. xishaensis has been reported from Australia, we conclude that the similarity of the present forms to the original description of K. xishaensis means records of this species from Japan, Palau and Australia are unreliable. Because the eastern Australian forms cannot be reliably ascribed to K. xishaensis, we describe Koseiria argalea n. sp., Koseiria laiphopharophora n. sp., and Koseiria pyknophora n. sp., following application of PCAs and iterative refinement of species concepts and type series. These analyses did not allow convincing identification hypotheses for all specimens examined. In this genus, both morphological and molecular data, together with reliable host identifications, are essential for species recognition, and thus we refrain from attempting to name samples lacking molecular data. The issues presented by these taxa encapsulate those of trematodes in the region as a whole. Many records require dramatically improved supporting data, leading to substantial uncertainly in the identification of this fauna.

A new genus and species of the trematode family Gyliauchenidae Fukui, 1929 from an unexpected, but plausible, host, Kyphosus cornelii (Perciformes: Kyphosidae)

The Enenteridae Yamaguti, 1958 and Gyliauchenidae Fukui, 1929 exhibit an interesting pattern of host partitioning in herbivorous fishes of the Indo-West Pacific. Enenterids are known almost exclusively from fishes of the family Kyphosidae, a group of herbivorous marine fishes common on tropical and temperate reefs. In contrast, gyliauchenids are found in most of the remaining lineages of marine herbivorous fishes, but until the present study, had never been known from kyphosids. Here we report on the first species of gyliauchenid known from a kyphosid. Endochortophagus protoporus gen. nov., sp. nov. was recovered from the Western buffalo bream, Kyphosus cornelii (Whitley, 1944), collected off Western Australia. Kyphosus cornelii also hosts an enenterid, Koseiria allanwilliamsi Bray & Cribb, 2002, and is thus the first fish known in which enenterids and gyliauchenids co-occur. Molecular phylogenetic analyses place the new species close to those of Affecauda Hall & Chambers, 1999 and Flagellotrema Ozaki, 1936, but there is sufficient morphological evidence, combined with the unusual host, to consider it distinct from these genera. We discuss factors which may have contributed to the host partitioning pattern observed between enenterids and gyliauchenids.

Checklist of marine demersal fishes captured by the pair trawl fisheries in Southern (RJ-SC) Brazil

Abstract: Demersal fishery resources are abundant on continental shelves, on the tropical and subtropical coasts, making up a significant part of the marine environment. Marine demersal fishery resources are captured by various fishing methods, often unsustainably, which has led to the depletion of their stocks. In order to inventory the marine demersal ichthyofauna on the Southern Brazilian coast, as well as their conservation status and distribution, this study analyzed the composition and frequency of occurrence of fish captured by pair trawling in 117 fishery fleet landings based in the State of São Paulo between 2005 and 2012. The ichthyofauna consisted of 245 species (81 families, 32 orders and 2 classes). Among the species, 50 species were classified as constant, 38 accessory and 157 accidental. Still, 13.47% of the species were listed as endangered; 35.29% of the Chondrichthyes and 11.85% of the Actinopterygii (15.1% of the total species) belong to the endemic fauna of the Biogeographic Province of Argentina. The richness was directly related to the oceanographic features of the study area, which determined the southern boundary of occurrence of several tropical species and the northern boundary of occurrence for temperate species. This is the region with the highest abundance of fishery resources in Brazil.

Widespread ecomorphological convergence in multiple fish families spanning the marine-freshwater interface

The theoretical definition and quantification of convergence is an increasingly topical focus in evolutionary research, with particular growing interest on study scales spanning deep phylogenetic divergences and broad geographical areas. While much progress has recently been made in understanding the role of convergence in driving terrestrial (e.g. anole lizards) and aquatic (e.g. cichlids) radiations, little is known about its macroevolutionary effects across environmental gradients. This study uses a suite of recently developed comparative approaches integrating diverse aspects of morphology, dietary data, habitat affiliation and phylogeny to assess convergence across several well-known tropical-temperate fish families in the percomorph suborder Terapontoidei, a clade with considerable phenotypic and ecological diversity radiating in both marine and freshwater environments. We demonstrate significant widespread convergence across many lineages occupying equivalent trophic niches, particularly feeding habits such as herbivory and biting of attached prey off hard substrates. These include several examples of convergent morphotypes evolving independently in marine and freshwater clades, separated by deep evolutionary divergences (tens of millions of years). The Terapontoidei present a new example of the macroevolutionary dynamics of morphological and ecological coevolution in relation to habitat and trophic preferences, at a greater phylogenetic and habitat scale than most well-studied adaptive radiations.

Phylogenetic classification of bony fishes

BACKGROUND

Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny ( www.deepfin.org ). We here update the first version of that classification by incorporating the most recent phylogenetic results.

RESULTS

The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified.

CONCLUSIONS

This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees. The classification presented in this study represents, unlike any other, the most up-to-date hypothesis of the Tree of Life of fishes.

Phylogenetic perspectives on reef fish functional traits

Functional traits have been fundamental to the evolution and diversification of entire fish lineages on coral reefs. Yet their relationship with the processes promoting speciation, extinction and the filtering of local species pools remains unclear. We review the current literature exploring the evolution of diet, body size, water column use and geographic range size in reef-associated fishes. Using published and new data, we mapped functional traits on to published phylogenetic trees to uncover evolutionary patterns that have led to the current functional diversity of fishes on coral reefs. When examining reconstructed patterns for diet and feeding mode, we found examples of independent transitions to planktivory across different reef fish families. Such transitions and associated morphological alterations may represent cases in which ecological opportunity for the exploitation of different resources drives speciation and adaptation. In terms of body size, reconstructions showed that both large and small sizes appear multiple times within clades of mid-sized fishes and that extreme body sizes have arisen mostly in the last 10 million years (Myr). The reconstruction of range size revealed many cases of disparate range sizes among sister species. Such range size disparity highlights potential vicariant processes through isolation in peripheral locations. When accounting for peripheral speciation processes in sister pairs, we found a significant relationship between labrid range size and lineage age. The diversity and evolution of traits within lineages is influenced by trait-environment interactions as well as by species and trait-trait interactions, where the presence of a given trait may trigger the development of related traits or behaviours. Our effort to assess the evolution of functional diversity across reef fish clades adds to the burgeoning research focusing on the evolutionary and ecological roles of functional traits. We argue that the combination of a phylogenetic and a functional approach will improve the understanding of the mechanisms of species assembly in extraordinarily rich coral reef communities.

The fishes of Cayo Arcas (Campeche Bank, Gulf of Mexico): an updated checklist

Cayo Arcas is a small, offshore reef complex on the southwest corner of Campeche Bank, Gulf of Mexico. The only published information (from 2000) on the fishes of that reef refers to 37 species. Here additional information is added, some from unpublished observations during the 1980s, as well as author observations made during 2013 and 2016. These bring the checklist of that reef’s fishes up to 162 species. The possible effects of the limited number of fish habitats available at Cayo Arcas on the composition of its fish fauna are discussed. The Indo-Pacific damselfish Neopomacentruscyanomos (Bleeker, 1856) was first recorded in the Atlantic in mid-2013, on shoreline reefs in the southwest corner of the Gulf of Mexico. Recently reviewed underwater photographs show that Neopomacentruscyanomos also was present at Cayo Arcas in mid-2013, 350 km from the first-record site. Hence it evidently had a substantial population in the southwest Gulf of Mexico in 2013, and must have arrived in there long before that year.

Input data for inferring species distributions in Kyphosidae world-wide

Input data files for inferring the relationship among the family Kyphosidae, as presented in (Knudsen and Clements, 2016) [1], is here provided together with resulting topologies, to allow the reader to explore the topologies in detail. The input data files comprise seven nexus-files with sequence alignments of mtDNA and nDNA markers for performing Bayesian analysis. A matrix of recoded character states inferred from the morphology examined in museum specimens representing Dichistiidae, Girellidae, Kyphosidae, Microcanthidae and Scorpididae, is also provided, and can be used for performing a parsimonious analysis to infer the relationship among these perciform families. The nucleotide input data files comprise both multiple and single representatives of the various species to allow for inference of the relationship among the species in Kyphosidae and between the families closely related to Kyphosidae. The '.xml'-files with various constrained relationships among the families potentially closely related to Kyphosidae are also provided to allow the reader to rerun and explore the results from the stepping-stone analysis. The resulting topologies are supplied in newick-file formats together with input data files for Bayesian analysis, together with '.xml'-files. Re-running the input data files in the appropriate software, will enable the reader to examine log-files and tree-files themselves.