First observation of a skate egg case nursery in the Ross Sea.

Areas of importance to Southern Ocean skates are poorly defined. Here, we identify a deepwater skate egg case nursery in a discrete location at ~460 m depth off Cape Adare in the Southern Ocean. This is the first confirmed observation of a skate nursery area in the Ross Sea and only the second observation for the Southern Ocean. The morphology and size of the egg cases were consistent with the genus Bathyraja and most likely belong to the Bathyraja sp. (cf. eatonii). The nursery occurs within the "no take" General Protection Zone of the Ross Sea region marine protected area, where commercial fishing is prohibited.

Sharks checking in to the sponge hotel: First internal use of sponges of the genus Agelas and family Irciniidae by banded sand catsharks Atelomycterus fasciatus.

Trawl surveys within and surrounding two northwestern Australian marine parks revealed banded sand catsharks Atelomycterus fasciatus (family Atelomycteridae) taking refuge within large sponges of the family Irciniidae (Demospongiae: Dictyoceratida) and the genus Agelas (Demospongiae: Agelasida: Agelasidae). Five sponges contained a total of 57 A. fasciatus, comprising both sexes and both immature and mature individuals ranging from 102 to 390 mm total length (TL). In the same surveys, only five A. fasciatus were captured unassociated with sponges, suggesting that sponges are an important microhabitat for A. fasciatus and may provide a daytime refuge from predators. A southerly range extension is also reported for this species.

Elemental analysis of vertebrae discerns diadromous movements of threatened non-marine elasmobranchs.

River sharks (Glyphis spp.) and some sawfishes (Pristidae) inhabit riverine environments, although their long-term habitat use patterns are poorly known. We investigated the diadromous movements of the northern river shark (Glyphis garricki), speartooth shark (Glyphis glyphis), narrow sawfish (Anoxypristis cuspidata), and largetooth sawfish (Pristis pristis) using in situ laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) on vertebrae to recover elemental ratios over each individual's lifetime. We also measured elemental ratios for the bull shark (Carcharhinus leucas) and a range of inshore and offshore stenohaline marine species to assist in interpretation of results. Barium (Ba) was found to be an effective indicator of freshwater use, whereas lithium (Li) and strontium (Sr) were effective indicators of marine water use. The relationships between Ba and Li and Ba and Sr were negatively correlated, whereas the relationship between Li and Sr was positively correlated. Both river shark species had elemental signatures indicative of prolonged use of upper-estuarine environments, whereas adults appear to mainly use lower-estuarine environments rather than marine environments. Decreases in Li:Ba and Sr:Ba at the end of the prenatal growth zone of P. pristis samples indicated that parturition likely occurs in fresh water. There was limited evidence of prolonged riverine habitat use for A. cuspidata. The results of this study support elemental-environment relationships observed in teleost otoliths and indicate that in situ LA-ICP-MS elemental characterization is applicable to a wide range of elasmobranch species as a discriminator for use and movement across salinity gradients. A greater understanding of processes that lead to element incorporation in vertebrae, and relative concentrations in vertebrae with respect to the ambient environment, will improve the applicability of elemental analysis to understand movements across the life history of elasmobranchs into the future.

A median fin derived from the lateral plate mesoderm and the origin of paired fins.

The development of paired appendages was a key innovation during evolution and facilitated the aquatic to terrestrial transition of vertebrates. Largely derived from the lateral plate mesoderm (LPM), one hypothesis for the evolution of paired fins invokes derivation from unpaired median fins via a pair of lateral fin folds located between pectoral and pelvic fin territories1. Whilst unpaired and paired fins exhibit similar structural and molecular characteristics, no definitive evidence exists for paired lateral fin folds in larvae or adults of any extant or extinct species. As unpaired fin core components are regarded as exclusively derived from paraxial mesoderm, any transition presumes both co-option of a fin developmental programme to the LPM and bilateral duplication2. Here, we identify that the larval zebrafish unpaired pre-anal fin fold (PAFF) is derived from the LPM and thus may represent a developmental intermediate between median and paired fins. We trace the contribution of LPM to the PAFF in both cyclostomes and gnathostomes, supporting the notion that this is an ancient trait of vertebrates. Finally, we observe that the PAFF can be bifurcated by increasing bone morphogenetic protein signalling, generating LPM-derived paired fin folds. Our work provides evidence that lateral fin folds may have existed as embryonic anlage for elaboration to paired fins.

What came first, the shark or the egg? Discovery of a new species of deepwater shark by investigation of egg case morphology.

Apristurus ovicorrugatus, a new species of deepwater catshark, is described from northwestern Australia. Unique egg cases belonging to an unknown species of Apristurus prompted a more detailed investigation of Apristurus specimens off northwestern Australia. One specimen previously identified as A. sinensis collected off Dampier Archipelago was found gravid with a single egg case. Removal of this egg case confirmed that this species was responsible for producing the unique egg cases previously recorded. The egg cases of this species have strong T-shaped longitudinal ridges on the dorsal and ventral surfaces which are unique in the genus Apristurus. The ridges most closely resemble those present in Bythaelurus canescens from South America, but are larger and always T-shaped. The holotype is closest morphologically to A. sinensis but differs in having a medium brown buccal cavity (vs. jet black), ridged egg cases (vs. smooth egg cases), fewer intestinal spiral valve turns and larger pectoral fins. The holotype is also similar, and closest on a molecular level, to A. nakayai with which it shares a unique synapomorphic character, the white shiny iris (apomorphic within the genus). A late-term embryo removed from an egg case superficially resembled the holotype except in having two parallel rows of enlarged dermal denticles on the dorsolateral predorsal surface. Recent nomenclatural changes to the genera Apristurus and Pentanchus are discussed and challenged. This study highlights the important contribution that egg case morphology has on oviparous elasmobranch taxonomy.

Concordance and Discordance in the Phylogenomics of the Wrasses and Parrotfishes (Teleostei: Labridae).

Phylogenomic analysis of large genome-wide sequence data sets can resolve phylogenetic tree topologies for large species groups, help test the accuracy of and improve resolution for earlier multi-locus studies and reveal the level of agreement or concordance within partitions of the genome for various tree topologies. Here we used a target-capture approach to sequence 1088 single-copy exons for more than 200 labrid fishes together with more than 100 outgroup taxa to generate a new data-rich phylogeny for the family Labridae. Our time-calibrated phylogenetic analysis of exon-capture data pushes the root node age of the family Labridae back into the Cretaceous to about 79 Ma years ago. The monotypic Centrogenys vaigiensis, and the order Uranoscopiformes (stargazers) are identified as the sister lineages of Labridae. The phylogenetic relationships among major labrid subfamilies and within these clades were largely congruent with prior analyses of select mitochondrial and nuclear datasets. However, the position of the tribe Cirrhilabrini (fairy and flame wrasses) showed discordance, resolving either as the sister to a crown julidine clade or alternatively sister to a group formed by the labrines, cheilines and scarines. Exploration of this pattern using multiple approaches leads to slightly higher support for this latter hypothesis, highlighting the importance of genome-level data sets for resolving short internodes at key phylogenetic positions in a large, economically important groups of coral reef fishes. More broadly, we demonstrate how accounting for sources of biological variability from incomplete lineage sorting and exploring systematic error at conflicting nodes can aid in evaluating alternative phylogenetic hypotheses. [coral reefs; divergence time estimation; exon-capture; fossil calibration; incomplete lineage sorting.].

Revision of the genus Centrophorus (Squaliformes: Centrophoridae): Part 3Redescription of Centrophorus uyato (Rafinesque) with a discussion of its complicated nomenclatural history.

Centrophorus uyato (Rafinesque, 1810) has a complicated nomenclatural history which has led to multiple scientific names being ascribed to this species. In the Mediterranean Sea, and elsewhere in its range, this species was previously referred to as C. granulosus (Bloch Schneider, 1801). The first paper in this revision series clarified that C. granulosus refers to a much larger species of gulper shark which attains at least 1.7 m length and is absent from the Mediterranean Sea. Further complicating the nomenclature of this species is the fact that the original description clearly refers to a Squalus species, and not a Centrophorus species. In this third part of the revision of the genus Centrophorus, this problematic species is redescribed. A detailed synonymy is provided and it is confirmed that C. machiquensis, C. bragancae and C. zeehaani are junior synonyms of this species. To preserve nomenclatural stability within the genus, the name Centrophorus uyato is retained for this species with a neotype from close to the original type locality off Italy being designated. Intraspecific variation within Centrophorus uyato is also discussed, particularly relating to denticle morphology and body morphology.

Beach showers as sources of contamination for sunscreen pollution in marine protected areas and areas of intensive beach tourism in Hawaii, USA.

In 2019, sands in nearby runoff streams from public beach showers were sampled on three islands in the State of Hawaii and tested for over 18 different petrochemical UV filters. Beach sands that are directly in the plume discharge of beach showers on three of the islands of Hawaii (Maui, Oahu, Hawai'i) were found to be contaminated with a wide array of petrochemical-based UV-filters that are found in sunscreens. Sands from beach showers across all three islands had a mean concentration of 5619 ng/g of oxybenzone with the highest concentration of 34,518 ng/g of oxybenzone at a beach shower in the Waikiki area of Honolulu. Octocrylene was detected at a majority of the beach shower locations, with a mean concentration of 296.3 ng/g across 13 sampling sites with the highest concentration of 1075 ng/g at the beach shower in Waikiki. Avobenzone, octinoxate, 4-methylbenzylidene camphor and benzophenone-2 were detected, as well as breakdown products of oxybenzone, including benzophenone-1, 2,2'-dihydroxy-4-methoxybenzophenone, and 4-hydroxybenzophenone. Dioxybenzone (DHMB) presented the highest concentration in water (75.4 ng/mL), whereas octocrylene was detected in all water samples. Some of these same target analytes were detected in water samples on coral reefs that are adjacent to the beach showers. Risk assessments for both sand and water samples at a majority of the sampling sites had a Risk Quotient > 1, indicating that these chemicals could pose a serious threat to beach zones and coral reef habitats. There are almost a dozen mitigation options that could be employed to quickly reduce contaminant loads associated with discharges from these beach showers, like those currently being employed (post-study sampling and analysis) in the State of Hawaii, including banning the use of sunscreens using petrochemical-based UV filters or educating tourists before they arrive on the beach.

The impact of paleoclimatic changes on body size evolution in marine fishes.

Body size is an important species trait, correlating with life span, fecundity, and other ecological factors. Over Earth's geological history, climate shifts have occurred, potentially shaping body size evolution in many clades. General rules attempting to summarize body size evolution include Bergmann's rule, which states that species reach larger sizes in cooler environments and smaller sizes in warmer environments, and Cope's rule, which poses that lineages tend to increase in size over evolutionary time. Tetraodontiform fishes (including pufferfishes, boxfishes, and ocean sunfishes) provide an extraordinary clade to test these rules in ectotherms owing to their exemplary fossil record and the great disparity in body size observed among extant and fossil species. We examined Bergmann's and Cope's rules in this group by combining phylogenomic data (1,103 exon loci from 185 extant species) with 210 anatomical characters coded from both fossil and extant species. We aggregated data layers on paleoclimate and body size from the species examined, and inferred a set of time-calibrated phylogenies using tip-dating approaches for downstream comparative analyses of body size evolution by implementing models that incorporate paleoclimatic information. We found strong support for a temperature-driven model in which increasing body size over time is correlated with decreasing oceanic temperatures. On average, extant tetraodontiforms are two to three times larger than their fossil counterparts, which otherwise evolved during periods of warmer ocean temperatures. These results provide strong support for both Bergmann's and Cope's rules, trends that are less studied in marine fishes compared to terrestrial vertebrates and marine invertebrates.

Further description of the Kerguelen sandpaper skate Bathyraja irrasa (Rajiformes: Arhynchobatidae) based on additional specimens, including egg cases and embryos.

Adult specimens, additional juvenile specimens, egg cases and embryos were used to provide a more detailed anatomical description of the Kerguelen sandpaper skate Bathyraja irrasa, a species of skate endemic to the Kerguelen Plateau and listed as Vulnerable by the IUCN Red List of Threatened Species. The morphological and meristic data reveal a relatively high level of intraspecific variation, mostly related to size. Egg cases are described for the first time and were shown to vary in colour and fouling depending on the length of time spent in the marine environment. Embryos removed from egg cases represent all stages of embryonic development in this species and include the largest embryo recorded for this species, i.e., 230 mm total length (LT ), which increases the range of size at hatching of B. irrasa to 178-230 mm LT . A number of morphometric and meristic characters varied ontogenetically in B. irrasa, in particular relative tail length, number of tail thorns in the median row and the size of orbits. This study highlights the importance of describing intraspecific variation in species and the importance of egg cases to taxonomic and biological research on oviparous species.

Market surveys and social media provide confirmation of the endangered giant freshwater whipray Urogymnus polylepis in Myanmar.

The giant freshwater whipray Urogymnus polylepis is a threatened species that is vulnerable to riverine and coastal marine pressures. Despite its threatened status, the range of U. polylepis is still being determined. In this study, photographic evidence of U. polylepis in Myanmar was provided through market surveys (2017-2018) and social media (Sharks and Rays of Rakhine Facebook page, 2021). Urogymnus polylepis is exposed to fisheries and habitat degradation pressures in Myanmar; therefore, conservation management is likely needed to ensure populations persist into the future.

Integrated Taxonomy Revealed Genetic Differences in Morphologically Similar and Non-Sympatric Scoliodon macrorhynchos and S. laticaudus.

Previous examination of the mitochondrial NADH2 gene and morphological characteristics led to the resurrection of Scoliodon macrorhynchos as a second valid species in the genus, in addition to S. laticaudus. This study applied an integrated taxonomic approach to revisit the classification of the genus Scoliodon based on new materials from the Malaysian Peninsula, Malaysian Borneo and Eastern Bay of Bengal. Mitochondrial DNA data suggested the possibility of three species of Scoliodon in the Indo-West Pacific, while the nuclear DNA data showed partially concordant results with a monophyletic clade of S. macrorhynchos and paraphyletic clades of S. laticaudus and S. cf. laticaudus from the Malacca Strait. Morphological, meristic and dental characteristics overlapped between the three putative species. Collective molecular and morphological evidence suggested that the differences that exist among the non-sympatric species of Scoliodon are consistent with isolation by distance, and Scoliodon macrorhynchos remains as a valid species, while S. cf. laticaudus is assigned as S. laticaudus. The Malacca Strait acts as a spatial delineator in separating the Pacific S. macrorhynchos (including South China Sea) from the Northern Indian Ocean S. laticaudus. Future taxonomic work should focus on clarifying the taxonomic status of Scoliodon from the Indonesian waters.

New records of elasmobranchs in the Bay of Bengal, Bangladesh: further taxonomic research is essential.

To evaluate the species diversity and strengthen the taxonomic identification of elasmobranchs in the Bay of Bengal, Bangladesh, a study was conducted in the southeast coastal region between January 2016 and March 2018. Using morphological and genetic identification techniques, this study presents 22 species from the region. Thirteen of these are new records. The new records consist of eight species from the family Dasyatidae, and one each from Mobulidae, Rhinobatidae, Narcinidae, Hemiscylliidae and Triakidae. Furthermore, four occurrences are first verified reports, and five are potential new records requiring further taxonomic investigation.

Raja mauritaniensis: a replacement name for Raja africana Capapé, 1977 (Rajiformes: Rajidae), a junior homonym of Raja africana Bloch amp; Schneider, 1801 (Myliobatiformes: Dasyatidae).

Raja africana Capapé, 1977 is a primary junior synonym of Raja africana Bloch Schneider, 1801 and therefore permanently invalid (International Code of Zoological Nomenclature, article 57.2) and must be replaced. Raja africana Bloch Schneider, 1801 was first described by Bloch Schneider (1801: 367), based on a specimen from Guinea, West Africa (eastern Atlantic Ocean). The unique holotype is extant in the Zoologisches Museum of the Humboldt University, Berlin (ZMB 7837, a partial dry skin). The species was treated as valid as Urogymnus africanus (Bloch Schneider 1801) by Compagno Roberts (1984: 285), but later synonymized with Urogymnus asperrimus (Bloch Schneider 1801) in the subfamily Urogymninae of the family Dasyatidae (Myliobatiformes) by Compagno (1986: 141), Capapé Desoutter (1990: 63) and Séret (2016: 1418). It is widespread in the eastern Atlantic, Red Sea and IndoWest Pacific.

Correction: Integrated Taxonomy Reveals Hidden Diversity in Northern Australian Fishes: A New Species of Seamoth (Genus Pegasus).

[This corrects the article DOI: 10.1371/journal.pone.0149415.].

Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences.

The charismatic trumpetfishes, goatfishes, dragonets, flying gurnards, seahorses, and pipefishes encompass a recently defined yet extraordinarily diverse clade of percomorph fishes-the series Syngnatharia. This group is widely distributed in tropical and warm-temperate regions, with a great proportion of its extant diversity occurring in the Indo-Pacific. Because most syngnatharians feature long-range dispersal capabilities, tracing their biogeographic origins is challenging. Here, we applied an integrative phylogenomic approach to elucidate the evolutionary biogeography of syngnatharians. We built upon a recently published phylogenomic study that examined ultraconserved elements by adding 62 species (total 169 species) and one family (Draconettidae), to cover ca. 25% of the species diversity and all 10 families in the group. We inferred a set of time-calibrated trees and conducted ancestral range estimations. We also examined the sensitivity of these analyses to phylogenetic uncertainty (estimated from multiple genomic subsets), area delimitation, and biogeographic models that include or exclude the jump-dispersal parameter ($j)$. Of the three factors examined, we found that the $j$ parameter has the strongest effect in ancestral range estimates, followed by number of areas defined, and tree topology and divergence times. After accounting for these uncertainties, our results reveal that syngnatharians originated in the ancient Tethys Sea ca. 87 Ma (84-94 Ma; Late Cretaceous) and subsequently occupied the Indo-Pacific. Throughout syngnatharian history, multiple independent lineages colonized the eastern Pacific (6-8 times) and the Atlantic (6-14 times) from their center of origin, with most events taking place following an east-to-west route prior to the closure of the Tethys Seaway ca. 12-18 Ma. Ultimately, our study highlights the importance of accounting for different factors generating uncertainty in macroevolutionary and biogeographic inferences.[Historical biogeography; jump-dispersal parameter; macroevolutionary uncertainty; marine fishes; syngnathiformes; ultraconserved elements].

Testing the Utility of Alternative Metrics of Branch Support to Address the Ancient Evolutionary Radiation of Tunas, Stromateoids, and Allies (Teleostei: Pelagiaria).

The use of high-throughput sequencing technologies to produce genome-scale data sets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these data sets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to quantify gene-tree discordance. We applied multiple branch-support metrics to a study of an ancient group of marine fishes (Teleostei: Pelagiaria) whose interfamilial relationships have proven difficult to resolve due to a rapid accumulation of lineages very early in its history. We analyzed hundreds of loci including published ultraconserved elements and newly generated exonic data along with their flanking regions to represent all 16 extant families for more than 150 out of 284 valid species in the group. Branch support was typically lower at inter- than intra-familial relationships regardless of the type of marker used. Several nodes that were highly supported with bootstrap had a very low site and gene-tree concordance, revealing underlying conflict. Despite this conflict, we were able to identify four consistent interfamilial clades, each comprised of two or three families. Combining exons with their flanking regions also produced increased branch lengths at the deep branches of the pelagiarian tree. Our results demonstrate the limitations of employing current metrics of branch support and species-tree estimation when assessing the confidence of ancient evolutionary radiations and emphasize the necessity to embrace alternative measurements to explore phylogenetic uncertainty and discordance in phylogenomic data sets.[Concatenation; exons; introns; phylogenomics; species-tree methods; target capture.].

Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics.

Exon markers have a long history of use in phylogenetics of ray-finned fishes, the most diverse clade of vertebrates with more than 35,000 species. As the number of published genomes increases, it has become easier to test exons and other genetic markers for signals of ancient duplication events and filter out paralogues that can mislead phylogenetic analysis. We present seven new probe sets for current target-capture phylogenomic protocols that capture 1,104 exons explicitly filtered for paralogues using gene trees. These seven probe sets span the diversity of teleost fishes, including four sets that target five hyperdiverse percomorph clades which together comprise ca. 17,000 species (Carangaria, Ovalentaria, Eupercaria, and Syngnatharia + Pelagiaria combined). We additionally included probes to capture legacy nuclear exons and mitochondrial markers that have been commonly used in fish phylogenetics (despite some exons being flagged for paralogues) to facilitate integration of old and new molecular phylogenetic matrices. We tested these probes experimentally for 56 fish species (eight species per probe set) and merged new exon-capture sequence data into an existing data matrix of 1,104 exons and 300 ray-finned fish species. We provide an optimized bioinformatics pipeline to assemble exon capture data from raw reads to alignments for downstream analysis. We show that legacy loci with known paralogues are at risk of assembling duplicated sequences with target-capture, but we also assembled many useful orthologous sequences that can be integrated with many PCR-generated matrices. These probe sets are a valuable resource for advancing fish phylogenomics because targeted exons can easily be extracted from increasingly available whole genome and transcriptome data sets, and also may be integrated with existing PCR-based exon and mitochondrial data.

Shape-preserving erosion controlled by the graded microarchitecture of shark tooth enameloid.

The teeth of all vertebrates predominantly comprise the same materials, but their lifespans vary widely: in stark contrast to mammals, shark teeth are functional only for weeks, rather than decades, making lifelong durability largely irrelevant. However, their diets are diverse and often mechanically demanding, and as such, their teeth should maintain a functional morphology, even in the face of extremely high and potentially damaging contact stresses. Here, we reconcile the dilemma between the need for an operative tooth geometry and the unavoidable damage inherent to feeding on hard foods, demonstrating that the tooth cusps of Port Jackson sharks, hard-shelled prey specialists, possess unusual microarchitecture that controls tooth erosion in a way that maintains functional cusp shape. The graded architecture in the enameloid provokes a location-specific damage response, combining chipping of outer enameloid and smooth wear of inner enameloid to preserve an efficient shape for grasping hard prey. Our discovery provides experimental support for the dominant theory that multi-layered tooth enameloid facilitated evolutionary diversification of shark ecologies.

Description of the egg cases and juvenile colouration in two catsharks of the genus Atelomycterus (Carcharhiniformes: Scyliorhinidae).

Descriptions of egg cases and hatchlings of the Bali catshark Atelomycterus baliensis and the Australian marbled catshark Atelomycterus macleayi are provided. Comparisons are made with two of their congeners, banded sand catshark Atelomycterus fasciatus and coral catshark Atelomycterus marmoratus. The Atelomycterus egg cases have the same general morphology, i.e., elongate with anterior and posterior waists, a depressed and truncate anterior end sometimes with attachment fibres, a medially tapered posterior end with two horns sometimes terminating in short, tightly curled tendrils and four respiratory fissures (one at each left corner on opposing sides). Morphometric measurements taken of the egg cases of the four species differed significantly when subjected to multivariate analysis, with unique characters enabling distinction between them. The morphological characters that best distinguished the Atelomycterus species from each other were anterior border width, posterior waist width and posterior case width. Thus, egg case morphology could be used to distinguish the egg cases of the four Atelomycterus species examined, consistent with other studies on scyliorhinid and pentanchid egg cases. Colouration of A. baliensis and A. macleayi juveniles was similar to that of other Atelomycterus juveniles in being pale with a series of dark-brown distinct dorsal saddles along the body, blotches and sometimes with a low number of small dark spots.