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.

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.

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.].

Morphology of the unique egg cases of hornsharks (Heterodontiformes: Heterodontidae).

Many of the egg cases of oviparous chondrichthyans remain unknown and undescribed in the literature. Egg cases can be a useful taxonomic character for species distinction and can be a valuable indicator of a species distribution in the field. In this study, the egg cases for 9 of the 10 nominal species of Heterodontus are described and compared, and the terminology and methodology for studying them are standardized. Heterodontus egg cases are distinct and easily identifiable from other oviparous egg cases by having a unique corkscrew shape formed by a pair of lateral keels spiraling along its length. Heterodontus egg cases range between 7.5 and 14.5 cm in egg case length, 3.7 and 5.8 cm in egg case width at midportion, and have 0.75-4 complete rotations. Morphometric measurements of egg cases from the nine species were subjected to multivariate analysis, with unique characters enabling distinction between them. Egg cases can be separated into three morphotypes: the "wide keels lacking tendrils" group, the "narrow keels with tendrils" group, and the "wide keels with tendrils" group. The egg case of Heterodontus ramalheira remains unknown.

Reallocation of the magnificent catshark Proscyllium magnificum Last & Vongpanich, 2004 to the genus Ctenacis Compagno, 1973 (Carcharhiniformes: Proscylliidae).

The magnificent catshark Proscyllium magnificum was described in 2004 based off five specimens collected in the Andaman Sea off Myanmar. It was originally allocated to the genus Proscyllium, but recent molecular analyses suggested it was more closely related to the harlequin catshark Ctenacis fehlmanni from the western Indian Ocean. This study incorporated meristics and external and internal morphology, together with molecular data to reclassify the magnificent catshark as Ctenacis magnificum and provides revised diagnoses for the genera Ctenacis and Proscyllium. Ctenacis consists of two allopatric Indian Ocean species, while Proscyllium is monotypic genus confined to the northwest Pacific. The revised Ctenacis can be distinguished from Proscyllium in having a broader and longer head (head length 21%-23% vs. 16%-18% of total length), distance between pectoral and pelvic bases shorter than head length (vs. greater than head length), more teeth (upper jaw with 80-86 vs. 46-62 tooth files), and a complex colour pattern of dark reddish-brown blotches and saddles (vs. colour pattern of small black spots). A revised key to the genera of proscylliids and species of Ctenacis is provided.

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.

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.

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.

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.].

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].

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.

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.

Refining mortality estimates in shark demographic analyses: a Bayesian inverse matrix approach.

Leslie matrix models are an important analysis tool in conservation biology that are applied to a diversity of taxa. The standard approach estimates the finite rate of population growth (λ) from a set of vital rates. In some instances, an estimate of λ is available, but the vital rates are poorly understood and can be solved for using an inverse matrix approach. However, these approaches are rarely attempted due to prerequisites of information on the structure of age or stage classes. This study addressed this issue by using a combination of Monte Carlo simulations and the sample-importance-resampling (SIR) algorithm to solve the inverse matrix problem without data on population structure. This approach was applied to the grey reef shark (Carcharhinus amblyrhynchos) from the Great Barrier Reef (GBR) in Australia to determine the demography of this population. Additionally, these outputs were applied to another heavily fished population from Papua New Guinea (PNG) that requires estimates of λ for fisheries management. The SIR analysis determined that natural mortality (M) and total mortality (Z) based on indirect methods have previously been overestimated for C. amblyrhynchos, leading to an underestimated λ. Updated distributions of Z and λ were produced for the GBR population and corrected obvious error in the demographic parameters for the PNG population. This approach provides opportunity for the inverse matrix approach to be applied more broadly to situations where information on population structure is lacking.

DNA capture reveals transoceanic gene flow in endangered river sharks.

For over a hundred years, the "river sharks" of the genus Glyphis were only known from the type specimens of species that had been collected in the 19th century. They were widely considered extinct until populations of Glyphis-like sharks were rediscovered in remote regions of Borneo and Northern Australia at the end of the 20th century. However, the genetic affinities between the newly discovered Glyphis-like populations and the poorly preserved, original museum-type specimens have never been established. Here, we present the first (to our knowledge) fully resolved, complete phylogeny of Glyphis that includes both archival-type specimens and modern material. We used a sensitive DNA hybridization capture method to obtain complete mitochondrial genomes from all of our samples and show that three of the five described river shark species are probably conspecific and widely distributed in Southeast Asia. Furthermore we show that there has been recent gene flow between locations that are separated by large oceanic expanses. Our data strongly suggest marine dispersal in these species, overturning the widely held notion that river sharks are restricted to freshwater. It seems that species in the genus Glyphis are euryhaline with an ecology similar to the bull shark, in which adult individuals live in the ocean while the young grow up in river habitats with reduced predation pressure. Finally, we discovered a previously unidentified species within the genus Glyphis that is deeply divergent from all other lineages, underscoring the current lack of knowledge about the biodiversity and ecology of these mysterious sharks.

A new goatfish of the genus Upeneus (Mullidae) from Lombok, Indonesia and first verified record of U. asymmetricus for the Indian Ocean.

Upeneus lombok n. sp. is described from two specimens collected off Lombok, Indonesia, at depths of 54-76 m, and one subadult specimen from the local fish market at Tanjung Luar, Lombok. Four specimens of U. asymmetricus were collected at the same fish market representing the first record of the species since its description from two Philippine Islands in 1954. These two species are compared in detail and with five congeneric species that all share a 7-spined dorsal fin and a high gill-raker count. Upeneus lombok n. sp. differs from all other congeners in having a short snout (snout length 9.0-9.6% SL) combined with a low anal fin (anal-fin height 12-13% SL in adults, 15% in single subadult). The newly recorded U. asymmetricus specimens differ from their types only slightly and all eight specimens together differ from all congeneric species in the combination of 7 dorsal spines, 12-14 pectoral fin rays, 26-28 total gill rakers, short pectoral fins (pectoral-fin length 18-21% SL) and short jaws (upper jaw length 8.7-11% SL). In both species the caudal-fin colour patterns of fresh fish are of diagnostic significance, the only exception being a close similarity between Upeneus lombok n.sp., U. saiab, and U. seychellensis. Additional comparisons with 14 Upeneus species which overlap in distribution or occur in nearby areas are also made. Needs for further taxonomic exploration of the Indonesian-Philippine region and for enhanced attention to the economic and ecological importance of Upeneus species are discussed.

Redescription of Paragaleus tengi (Chen, 1963) (Carcharhiniformes: Hemigaleidae) and first record of Paragaleus randalli Compagno, Krupp & Carpenter, 1996 from the western North Pacific.

Paragaleus tengi was previously considered to be the only member of this genus occurring in the Western Pacific, with Paragaleus randalli occurring in the Indian Ocean and allopatric in distribution. Recent molecular and morphological studies showed that P. randalli also occurs in the Western Pacific with records from Thailand, Malaysia and Indonesia previously mostly incorrectly attributed to P. tengi. This paper provides a redescription of P. tengi and confirms the presence of P. randalli from off Taiwan in the western North Pacific. These two species are morphologically very similar in appearance but differ in meristics, dentition, some coloration attributes and minor morphological characters. The conservation status of these two species needs to be reassessed based on this new information.

Notes on shark and ray types at the South China Sea Fisheries Research Institute (SCSFRI) in Guangzhou, China.

Most of the shark and ray type material at the South China Sea Fisheries Research Institute (SCSFRI) in Guangzhou, China was examined during a museum visit by the senior author in 2009. The status of the shark and ray species described from the South China Sea in the 1980s and deposited in this collection is discussed. Squalus acutirostris is considered a junior synonym of Squalus mitsukurii from the western North Pacific. Centrophorus ferrugineus is considered a junior synonym of Centrophorus squamosus. Centroscymnus macrops is confirmed as a junior synonym of Centroscymnus coelolepis. Scymnodon niger is confirmed as a junior synonym of Zameus squamulosus. Isistius labialis is considered a synonym of Isistius brasiliensis. Halaelurus immaculatus is confirmed as a valid species of the genus Bythaelurus. Urolophus marmoratus is considered a junior synonym of the widespread Plesiobatis daviesi. Springeria nanhaiensis is a questionable synonym of Sinobatis borneensis, following previous researchers. Springeria stenosoma is considered as questionably valid but with further investigation into generic placement required. The validity of species with SCSFRI type specimens not examined in this study are also briefly discussed.

Two new stingrays (Chondrichthyes: Dasyatidae) from the eastern Indonesian Archipelago.

Two new stingrays, Dasyatis longicauda sp. nov. and Himanturajavaensis sp. nov., are described from material collected in the eastern Indonesian Archipelago. These species, which are both relatively small stingrays (both probably smaller than 40 cm DW), have been confused with closest relatives in the region. Dasyatis longicauda sp. nov., known from West Papua, differs from its congener, the Australian endemic D. fluviorum, in having a slightly lower vertebral count, lower pectoral-radial count, a longer tail, larger and less numerous thorns along the mid-disc and tail, as well as a different CO1 Barcode. Himantura javaensis sp. nov., known only from southern Java (near Cilacap), belongs to a complex of small whiprays which also includes another Indonesian species, H. walga. Apart from major differences in squamation and a different CO1 Barcode, Himantura javaensis is more brownish in coloration, has more vertebrae, a longer tail, smaller eye and orbit, more posteriorly positioned sting, shorter adult claspers, shorter pelvic fin, and differs in various measurements around the head.