A new classification of viviparous brotulas (Bythitidae) - with family status for Dinematichthyidae - based on molecular, morphological and fossil data

Novel neurocranial fenestrae and expansions in Monomitopus and Selachophidium (Teleostei: Ophidiidae), with comments on the morphology, taxonomy, and evolution of the genera

The Ophidiidae is a group of more than 300 species of fishes characterized by elongated, snake-like bodies and continuous dorsal, anal, and caudal fins. While describing a new species in the genus Monomitopus, we discovered a bilaterally paired fenestra on the dorsomedial surface of the neurocranium. We surveyed the distribution of this fenestra across species of Monomitopus and previously hypothesized allies in the genera Dannevigia, Dicrolene, Homostolus, Neobythites, and Selachophidium, finding variation in its presence and size. We also found a prominent bilaterally paired lateral fenestra and a posterior expansion of the exoccipital in the neurocrania of M. americanus and S. guentheri, with soft tissue connecting the back of the neurocranium to the first epineural and pectoral girdle in S. guentheri. In this study, we describe the distribution of and variation in these features. We integrate morphological characters and DNA data to generate a phylogeny of Monomitopus and allies to understand their relationships and trace the evolutionary history of these novel features. Our results call the monophyly of Monomitopus into question. The presence of the lateral neurocranial fenestra and posterior expansion of the exoccipital support the reclassification of M. americanus as a species of Selachophidium.

Second world record for Barathronus roulei Nielsen, 2019 (Ophidiiformes, Bythitidae), from the Porcupine Bank (Northeast Atlantic)

Barathronus is a genus of blind cusk eels comprising 11 valid species. In this paper, we report the second specimen ever documented of Barathronus roulei (Bythitidae) obtained from the Porcupine Bank by R.V. Vizconde de Eza using a bottom trawl at a depth of 1349 m. Morphological description and illustrations, including a radiograph, are provided. In addition, three new sequences corresponding to three different genes, cytochrome c oxidase subunit I (COI)-DNA barcoding, 16S ribosomal RNA (16S), and recombination activating protein 1 (RAG1), have been added to the molecular repositories, representing the first sequences for the species.

The complete mitochondrial genome of the Mexican blind brotula Typhlias pearsei (Ophidiiformes: Dinematichthydae): an endemic and troglomorphic cavefish from the Yucatán Peninsula karst aquifer

In this study we report the first complete and annotated mitochondrial genome of the Mexican blind brotula, Typhlias pearsei, a troglobitic cavefish endemic to the Yucatán peninsula karst aquifer in southeastern Mexico. Genomic sequencing was accomplished via next generation sequencing (NGS). The resulting mitogenome is 16,813 bp long and, as in most vertebrates, consists of a total of 37 genes (13 PCGs, 2 rRNAs, 22 tRNAs) and two non-coding regions (control region and origin of the light strand replication). Other than a rearrangement in the position of two tRNAs (shuffling between tRNA-Ile and tRNA-Gln), the mitogenome of T. pearsei exhibits a genomic composition and organization similar to that of most teleost mitogenomes. Besides offering this valuable genomic resource for future studies, the resulting mitogenome was used in a comparative context to test the current higher-level taxonomy of ophidiiform fishes and to examine the phylogenetic position of T. pearsei among viviparous brotulas. Our phylogenetic results confirm those from the most comprehensive molecular phylogenetic study of the group.

Checklist of marine and estuarine fishes from the AlaskaYukon Border, Beaufort Sea, to Cabo San Lucas, Mexico

This paper is a checklist of the fishes that have been documented, through both published and unpublished sources, in marine and estuarine waters, and out 200 miles, from the United States-Canadian border on the Beaufort Sea to Cabo San Lucas, Mexico. A minimum of 241 families and 1,644 species are known within this range, including both native and nonnative species. For each of these species, we include maximum size, geographic and depth ranges, whether it is native or nonnative, as well as a brief mention of any taxonomic issues.

A new species of viviparous brotula genus Pseudogilbia (Ophidiiformes: Dinematichthyidae) from Brazilian reefs, with an updated diagnosis of the genus

In this study, a new species of Pseudogilbia Møller, Schwarzhans & Nielsen 2004 is described based on two male specimens (40-44 mm L_S ) from shallow reefs of Bahia, Brazil. Pseudogilbia australis sp. nov. is distinguished from its only congener, Pseudogilbia sanblasensis Møller, Schwarzhans & Nielsen 2004 from Caribbean Panama, by having: two lower preopercular pores (vs. one); dorsal-fin rays 65-67 (vs. 69); anal-fin rays 51-53 (vs. 56); pectoral-fin rays 18 (vs. 20); caudal vertebrae 27-28 (vs. 30); pectoral-fin length 15.0%-15.9% L_S (vs. 14.3); pelvic-fin length 13.5% L_S (vs. 16.4) and a different morphology of the male copulatory organ. Pseudogilbia australis sp. nov. is the only dinematichthyid so far recorded in the South Atlantic. An updated diagnosis for the genus is also provided.

Contrasting Gene Decay in Subterranean Vertebrates: Insights from Cavefishes and Fossorial Mammals

Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the decay of genes involved in vision, circadian clock, and pigmentation in cavefishes. The analysis of the genomes of two Cuban species belonging to the genus Lucifuga provided evidence for the largest loss of eye-specific genes and nonvisual opsin genes reported so far in cavefishes. Comparisons with a recently evolved cave population of Astyanax mexicanus and three species belonging to the Chinese tetraploid genus Sinocyclocheilus revealed the combined effects of the level of eye regression, time, and genome ploidy on eye-specific gene pseudogenization. The limited extent of gene decay in all these cavefishes and the very small number of loss-of-function mutations per pseudogene suggest that their eye degeneration may not be very ancient, ranging from early to late Pleistocene. This is in sharp contrast with the identification of several vision genes carrying many loss-of-function mutations in ancient fossorial mammals, further suggesting that blind fishes cannot thrive more than a few million years in cave ecosystems.

The marine fishes of St Eustatius Island, northeastern Caribbean: an annotated, photographic catalog

Sint Eustatius (Statia) is a 21 km² island situated in the northeastern Caribbean Sea. The most recent published sources of information on that island's marine fish fauna is in two non-governmental organization reports from 2015-17 related to the formation of a marine reserve. The species-list in the 2017 report was based on field research in 2013-15 using SCUBA diving surveys, shallow "baited underwater video surveys" (BRUVs), and data from fishery surveys and scientific collections over the preceding century. That checklist comprised 304 species of shallow (mostly) and deep-water fishes. In 2017 the Smithsonian Deep Reef Observation Project surveyed deep-reef fishes at Statia using the crewed submersible Curasub. That effort recorded 120 species, including 59 new occurrences records. In March-May 2020, two experienced citizen scientists completed 62 SCUBA dives there and recorded 244 shallow species, 40 of them new records for Statia. The 2017-2020 research effort increased the number of species known from the island by 33.6% to 406. Here we present an updated catalog of that marine fish fauna, including voucher photographs of 280 species recorded there in 2017 and 2020. The Statia reef-fish fauna likely is incompletely documented as it has few small, shallow, cryptobenthic species, which are a major component of the regional fauna. A lack of targeted sampling is probably the major factor explaining that deficit, although a limited range of benthic marine habitats may also be contributing.

A new species of the cave-fish genus Lucifuga (Ophidiiformes, Bythitidae), from eastern Cuba

Recently, a barcoding study and a molecular phylogenetic analysis of the Cuban species of the cave-fish genus Lucifuga Poey, 1858 revealed the existence of different evolutionary lineages that were previously unknown or passed unnoticed by morphological scrutiny (i.e., cryptic candidate species). In the present study, Lucifugagibarensis is described as a new species restricted to anchialine caves in the northeastern karst region of the main island. The species was earlier described as a variety of Lucifugadentata, but since the name was introduced as a variety after 1960, it is deemed to be infrasubspecific and unavailable according to the International Code of Zoological Nomenclature Art. 15.2. The new species differs from L.dentata by pigmented eyes vs. eyes absent and lack of palatine teeth vs. present. Lucifugagibarensis seems to be most similar to the Bahamian species L.lucayana by showing pigmented eyes, 13 or 14 precaudal vertebrae and ten caudal fin rays. However, differs from it by a larger size of the pigmented eye (1.1–1.9 vs. 0.9–1.0% SL) and number of posterior lateral line neuromasts (30–33 vs. 34–35).

Zygoparity in Characidae - the first case of internal fertilization in the teleost cohort Otomorpha

Abstract Most teleosts are externally fertilizing, with internal fertilization occurring as a relatively rare event. Until now, Euteleosteomorpha is the only teleost cohort known to undergo internal fertilization. In the teleost cohort Otomorpha, it has been recorded the presence of sperm in the ovaries of some species of Characiformes and Siluriformes, but no fertilized eggs have been found so far in the female reproductive tract. It has been presumed that oocytes can be released into the water with associated spermatozoa and only there becomes fertilized, and the term insemination has been used to characterize the strategy adopted by these fish. Here, we present the discovery of the first case of internal fertilization in the teleost cohort Otomorpha, in Compsura heterura (Characiformes: Characidae). In the course of spawning, the eggs form the perivitelline space and the animal and vegetative poles within the ovaries, evidencing oocyte fertilization. The newly spawned eggs then continue to form the animal and vegetative poles and increase the perivitelline space. These eggs are in the zygotic stage. These data indicate that fertilized eggs are only retained for a short period, providing evidence that C. heterura is a zygoparous fish.

Distribution, composition and functions of gelatinous tissues in deep-sea fishes

Many deep-sea fishes have a gelatinous layer, or subdermal extracellular matrix, below the skin or around the spine. We document the distribution of gelatinous tissues across fish families (approx. 200 species in ten orders), then review and investigate their composition and function. Gelatinous tissues from nine species were analysed for water content (96.53 ± 1.78% s.d.), ionic composition, osmolality, protein (0.39 ± 0.23%), lipid (0.69 ± 0.56%) and carbohydrate (0.61 ± 0.28%). Results suggest that gelatinous tissues are mostly extracellular fluid, which may allow animals to grow inexpensively. Further, almost all gelatinous tissues floated in cold seawater, thus their lower density than seawater may contribute to buoyancy in some species. We also propose a new hypothesis: gelatinous tissues, which are inexpensive to grow, may sometimes be a method to increase swimming efficiency by fairing the transition from trunk to tail. Such a layer is particularly prominent in hadal snailfishes (Liparidae); therefore, a robotic snailfish model was designed and constructed to analyse the influence of gelatinous tissues on locomotory performance. The model swam faster with a watery layer, representing gelatinous tissue, around the tail than without. Results suggest that the tissues may, in addition to providing buoyancy and low-cost growth, aid deep-sea fish locomotion.

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.

Evolutionary affinities of the unfathomable Parabrotulidae: Molecular data indicate placement of Parabrotula within the family Bythitidae, Ophidiiformes

Fishes are widely diverse in shape and body size and can quite rapidly undergo these changes. Consequently, some relationships are not clearly resolved with morphological analyses. In the case of fishes of small body size, informative characteristics can be absent due to simplification of body structures. The Parabrotulidae, a small family of diminutive body size consisting of two genera and three species has most recently been classified as either a perciform within the suborder Zoarcoidei or an ophidiiform. Classification of parabrotulids as ophidiiforms has become predominant; however the Parabrotulidae has not yet been investigated in a molecular phylogenetic framework. We examine molecular data from ten genetic loci to more specifically place the Parabrotulidae within the fish tree of life. In a hypothesis testing framework, the Parabrotulidae as a zoarcoid taxon is rejected. Previous identity with zoarcoids due to the one fin ray for each vertebra being present, a characteristic for the Zoarcidae, appears to be an example of convergence. Our results indicate that parabrotulids are viviparous ophidiiforms within the family Bythitidae.

New species of Plagioporus Stafford, 1904 (Digenea: Opecoelidae) from California, with an amendment of the genus and a phylogeny of freshwater plagioporines of the Holarctic

Plagioporus hageli n. sp. is described from the intestine of Oncorhynchus mykiss (Walbaum) collected from the River Yuba, California, USA. Of the accepted, nominal species of Plagioporus Stafford, 1904 from the Nearctic, the new species is morphologically similar to three intestinal species from the western USA parasitising diadromous fishes, including Plagioporus shawi (McIntosh, 1939), Plagioporus kolipinskii Tracey, Choudhury, Cheng & Ghosh, 2009 and Plagioporus siliculus Sinitsin, 1931, and is also similar to Plagioporus serotinus Stafford, 1904 from catostomids from eastern Canada. Plagioporus hageli n. sp. is distinguished from the former three species in lacking a dorsal vitelline field and from the latter species in having a consistent interruption in the distribution of the vitellarium at the level of the ventral sucker. The new species is also morphologically similar to an unnamed species of Plagioporus and a species misidentified as 'Plagioporus angusticolle' that were collected from California, but it is easily distinguished from both in its shorter body length. To estimate the placement of the new species within Plagioporus and within the Opecoelidae Ozaki, 1925, we conducted a Bayesian inference (BI) analysis of partial 28S rDNA sequence data that included sequences from Plagioporus hageli n. sp., five other species of Plagioporus, three species of Neoplagioporus Shimazu, 1990, including the type-species, Neoplagioporus zacconis (Yamaguti, 1934), two species of Urorchis Ozaki, 1927 (including the type-species, Urorchis goro Ozaki, 1927) and sequences of 42 opecoelid species obtained from GenBank. Our phylogenetic analysis revealed (i) plagioporines parasitising freshwater hosts form a monophyletic group; (ii) Plagiocirrus loboides Curran, Overstreet & Tkach, 2007 nested within the rest of the members of Plagioporus; (iii) the new species was closer to Plagiocirrus loboides than to Plagioporus shawi, the other salmonid parasite included in our analysis; (iv) P. shawi was the poorly supported sister to its congeners; (v) Neoplagioporus elongatus (Goto & Ozaki, 1930) Shimazu, 1990 was closer to the two species of Urorchis than to the other two species of Neoplagioporus; and (vi) the paraphyly of the Plagioporinae Manter, 1947 was reinforced. Based on 28S rDNA sequence data and our BI analysis, we propose Plagioporus loboides (Curran, Overstreet & Tkach, 2007) n. comb., and amend Plagioporus accordingly. This analysis represents the first phylogenetic study of the opecoelids that estimates the interrelationships of the Plagioporinae that includes a member of Plagioporus.

Molecular, morphological and fossil input data for inferring relationship among viviparous brotulas (Bythitidae) - Resulting in a family status change for Dinematichthyidae

This article comprise the data related to the research article (Møller et al., 2016) [1], and makes it possible to explore and reproduce the topologies that allowed [1] to infer the relationship between the families Bythitidae and Dinematichthyidae. The supplementary data holds nexus-input files for the Bayesian analysis and the '.xml'-input files - with and without nucleotide data - that are used in the fossil-calibrated phylogenetic analysis with a relaxed clock model. The resulting topologies are provided as '.new'-files together with a characters matrix file for traits to trace across the inferred phylogenies.

A new classification of viviparous brotulas (Bythitidae) - with family status for Dinematichthyidae - based on molecular, morphological and fossil data

The order Ophidiiformes is a large but not very well known group of fishes, unique among teleosts for showing high diversity in both deep sea and shallow reef habitats. The current classification includes more than 500 species, 115 genera and four families, based primarily on mode of reproduction: viviparous Aphyonidae and Bythitidae vs oviparous Carapidae and Ophidiidae. Since 2004 we revised the bythitid tribe Dinematichthyini, described more than 100 new species and noticed that this group has unique morphological characters, perhaps supporting a higher level of classification than the current status. Here we study the viviparous families phylogenetically with partial mitochondrial (nd4, 16s) and nuclear (Rag1) DNA sequences (2194bp). We use a fossil calibration of otolith-based taxa to calibrate the age of the clade comprising bythitid and dinematicththyid representatives, together with fossil calibrations adopted from previous phylogenetic studies. The separation of the order into two major lineages, the viviparous Bythitoidei and the oviparous Ophidioidei is confirmed. At the familial level, however, a new classification is presented for the viviparous clades, placing Aphyonidae as a derived, pedomorphic member of Bythitidae (new diagnosis provided, 33 genera and 118 species). The current subfamily Brosmophycinae is considered polyphyletic and we propose family status for Dinematichthyidae (25 genera, 114 species), supported by unique, morphological synapomorphic characters in the male copulatory apparatus. Previous use of the caudal fin separation or fusion with vertical fins is ambiguous. Age estimates based on calibrated molecular phylogeny agrees with fossil data, giving an origin within the Cretaceous (between 84 and 104mya) for a common ancestor to Ophidiiformes.