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.

The type series of Poromitra crassiceps (Pisces, Melamphaidae) with lectotype designation.

The type series of Poromitra crassiceps (Gnther, 1878) was thought to include specimens from four localities in the Atlantic, Pacific, and Southern oceans. Comparison of the extant syntypes with the original description revealed that the specimen from the Pacific Ocean was not included in the original type series; one syntype from the Atlantic Ocean was never incorporated into the collection of the Natural History Museum, London, and is considered lost, and another cannot be identified due to its bad condition. The fourth syntype, from the Southern Ocean and in the best condition, is designated lectotype of this species. Molecular analysis of tissue samples collected by us as well as publically available COI sequences showed that only one species, P. crassiceps, is currently known from the Southern Ocean. Specimens from this ocean named P. atlantica (Norman, 1929) in the literature and in collections are probably misidentifications of P. crassiceps. The validity of P. atlantica needs confirmation from fresh material from the type locality.

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.

Three new species of Australian anthiadine fishes, with comments on the monophyly of Pseudanthias Bleeker (Teleostei: Serranidae).

Three new species of anthiadine species are described from specimens trawled from Australian waters. Pseudanthias paralourgus n. sp. is described from five specimens collected off southeastern Queensland. It resembles P. elongatus (Franz, 1910) from Japan to the South China Sea, but differs in male live coloration. The remaining two species are assigned to the genus Tosana Smith Pope, 1906, which is newly diagnosed to include the two new species and the type species from southern Japan to the South China Sea, T. niwae Smith Pope, 1906. The two new species, T. dampieriensis n. sp. described from three specimens from off Western Australia and T. longipinnis n. sp. described from 42 specimens from off eastern Australia, differ from each other and from T. niwae in various meristic and morphometric details. Pseudanthias paralourgus co-occurs with T. longipinnis. Molecular phylogenetic analysis of mitochondrial COI yielded a tree with the three Tosana species forming the sister group of a clade consisting of P. paralourgus n. sp., P. elongatus and the type species of Pseudanthias Bleeker, 1871, P. pleurotaenia (Bleeker, 1857). Our preliminary phylogenetic analyses suggest that Pseudanthias comprises a polyphyletic assemblage of species that also includes Nemanthias Smith, 1954, Luzonichthys Herre, 1936, Tosanoides Kamohara, 1953, Odontanthias Bleeker, 1873, and Serranocirrhitus Watanabe, 1949, thus highlighting the need for a revised generic classification of species currently assigned to Pseudanthias.

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.].

Review of Australian species of Plectranthias Bleeker and Selenanthias Tanaka (Teleostei: Serranidae: Anthiadinae), with descriptions of four new species.

Australian species of the anthiadine genera Plectranthias and Selenanthias are reviewed. Twenty-two species of Plectranthias and two species of Selenanthias are recorded from Australian waters: Plectranthias sp. 1 from a seamount north of Middleton Reef and Norfolk Ridge, Tasman Sea; P. alleni Randall from off southwest Western Australia; P. azumanus (Jordan Richardson) from off southwest Western Australia; P. bennetti Allen Walsh from Holmes Reef, Coral Sea; P. cruentus Gill Roberts from Lord Howe Island, and possibly off Stradbroke Island, Queensland; P. ferrugineus n. sp. from the North West Shelf and Arafura Sea; P. fourmanoiri Randall from Christmas Island and Holmes Reef, Coral Sea; P. grahami n. sp. from off central New South Wales, Tasman Sea; P. inermis Randall from Christmas Island; P. japonicus (Steindachner) from the Arafura Sea and North West Shelf; P. kamii Randall from the Coral Sea, Lord Howe Island and Christmas Island; P. lasti Randall Hoese from the North West Shelf and off Marion Reef, Queensland; P. longimanus (Weber) from the Timor Sea, Great Barrier Reef, Coral Sea and southern Queensland; P. maculicauda (Regan) from southeastern Australia; P. mcgroutheri n. sp. from the North West Shelf; P. megalophthalmus Fourmanoir Randall from northeast of the Whitsunday Islands, Queensland; P. melanesius Randall from southeastern Queensland and a seamount north of Middleton Reef; P. moretonensis n. sp. from off Stradbroke Island, Queensland; P. nanus Randall from the Cocos (Keeling) Islands, Christmas Island, Great Barrier Reef and Coral Sea; P. retrofasciatus Fourmanoir Randall from the Great Barrier Reef; P. robertsi Randall Hoese from off Queensland, Coral Sea; P. winniensis (Tyler) from the Great Barrier Reef and Coral Sea; Selenanthias analis Tanaka from the North West Shelf and Arafura Sea; and S. barroi (Fourmanoir) from west of Lihou Reef, Coral Sea. Five of the species represent new records for Australia: P. azumanus, P. kamii, P. megalophthalmus, P. melanesius and S. barroi. Previous records of P. megalophthalmus from the North West Shelf are based on misidentified specimens of P. lasti. Records of P. wheeleri from the North West Shelf are based on specimens here identified as P. mcgroutheri n. sp. A record of P. yamakawai Yoshino from Christmas Island is based on a misidentified specimen of P. kamii. Plectranthias retrofasciatus was previously recorded from the Great Barrier Reef as P. pallidus Randall Hoese, here shown to be a junior synonym of P. retrofasciatus. Video-based records of P. kelloggi from the Great Barrier Reef appear to be based on P. retrofasciatus. Identification keys, diagnoses, character summaries, photographs and Australian distribution information are presented for all species. Full descriptions are provided for the new species and for those newly recorded from Australia.

Taxonomy of the genus Dactylanthias Bleeker (Teleostei: Serranidae: Anthiadinae).

The anthiadine genus Dactylanthias is reviewed. Two species, Dactylanthias aplodactylus (Bleeker, 1858) and Dactylanthias baccheti Randall, 2007 are currently recognised, each known only from their holotypes. A specimen of Dactylanthias matching D. baccheti in coloration was recently collected from Nauru in the West Pacific Ocean. It was retained by a recreational fisher and deposited into the CSIRO Australian National Fish Collection, Hobart. Data collected from this specimen and comparison to images of and data from the holotypes of both nominal species indicate that Dactylanthias baccheti Randall, 2007 is a junior synonym of Dactylanthias aplodactylus (Bleeker, 1858). Additional records of specimens from Ambon, Indonesia (type locality of D. apolodactylus) and the Maldives Islands, Indian Ocean are reported. The genus is briefly compared with other anthiadine genera.

Assessing DNA for fish identifications from reference collections: the good, bad and ugly shed light on formalin fixation and sequencing approaches.

Natural history collections are repositories of biodiversity and are potentially used by molecular ecologists for comparative taxonomic, phylogenetic, biogeographic and forensic purposes. Specimens in fish collections are preserved using a combination of methods with many fixed in formalin and then preserved in ethanol for long-term storage. Formalin fixation damages DNA, thereby limiting genetic analyses. In this study, the authors compared the DNA barcoding and identification success for frozen and formalin-fixed tissues obtained from specimens in the CSIRO Australian National Fish Collection. They studied 230 samples from fishes (consisting of >160 fish species). An optimized formalin-fixed, paraffin-embedded DNA extraction method resulted in usable DNA from degraded tissues. Four mini barcoding assays of the mitochondrial DNA (mtDNA) were characterized with Sanger and Illumina amplicon sequencing. In the good quality DNA (without exposure to formalin), up to 88% of the specimens were correctly matched at the species level using the cytochrome oxidase subunit 1 (COI) mini barcodes, whereas up to 58% of the specimens exposed to formalin for less than 8 weeks were correctly identified to species. In contrast, 16S primers provided higher amplification success with formalin-exposed tissues, although the COI gene was more successful for identification. Importantly, the authors found that DNA of a certain size and quality can be amplified and sequenced despite exposure to formalin, and Illumina sequencing provided them with greater power of resolution for taxa identification even when there was little DNA present. Overall, within parameter constraints, this study highlights the possibilities of recovering DNA barcodes for identification from formalin-fixed fish specimens, and the authors provide guidelines for when successful identification could be expected.

Description of a new deep-water species of Heteroclinus (Pisces: Teleostei: Clinidae), from southern Australia.

Heteroclinus argyrospilos, n. sp. is described as a new species from specimens sampled by sled and dredge in 55100 m off South Australia and Western Australia. The species has a strongly compressed body and spatulate orbital tentacle similar to some shallow water species, particularly those of the Heteroclinus heptaeolus complex, which is characterized by having three segmented dorsal-fin rays, with the last two rays widely separate from the first ray. It is distinct from other Australian clinids in having two segmented dorsal-fin rays, well separated from the last dorsal-fin spine and a reduced lateral line on the body. It is known from a greater depth than other members of the genus.

-Redescription and distributional range extension of the Speckled Siphonfish, Siphamia guttulata (Pisces: Apogonidae).

During seabed biodiversity surveys between 2003 and 2005 from the Torres Strait (Papua New Guinea) to the southern Great Barrier Reef (Queensland), hundreds of Siphamia specimens were collected. After Gon Allen's (2012) revision allowed greater interrogation of the Siphamia species present, a re-examination of preserved and frozen Siphamia specimens at the CSIRO Australian National Fish Collection (ANFC) was warranted. The material was re-identified as four commonly collected species (S. cuneiceps, S. roseigaster, S. tubifer, and S. tubulata) and a fifth unidentified species that appeared to key to S. guttulata, previously known only from the type locality. Further detailed investigations including an analysis of meristic, morphometric and COI barcoding data confirmed the identity of S. guttulata from almost the entire length of the Great Barrier Reef, Queensland, from the Torres Strait in the north to the Northumberland Islands Group in the south. This study provides a redescription of Siphamia guttulata and highlights the importance of re-assessing the taxonomic status of museum material after revisionary studies.

Revision of the fish family Euclichthyidae (Pisces: Gadiformes) with the description of two new species from the Western Pacific.

Members of the benthopelagic fish family Euclichthyidae, also known as the Eucla cods, occur on the upper continental slopes off Australasia at 220-1040 m depths. Euclichthyids essentially differ from other gadiform fishes in a combination of two almost contiguous dorsal fins with the second much longer based, a deeply notched anal fin with its anterior portion greatly elevated, jugular pelvic fins consisting of 3 partly united filiform upper rays and 3 free filamentous lower rays, an asymmetrical caudal fin with 5 hypurals fused into two plates, and no chin barbel, or vomerine and palatine tooth patches. Additional characters attributed to the group by other published studies include: no horizontal diaphragm within the posterior chamber of the swim bladder, no swim bladder-auditory capsule connection, presence of a luminous organ, and cranial muscle adductor arcus palatini divided by a strong ligament running from the lateral ethmoid and palatine to the medial face of the hyomandibular. Widely considered to be monotypic since its erection in 1984, the group consists of a single genus and three allopatric species, Euclichthys polynemus McCulloch, 1926 (Western and southern Australia, New Zealand), and two new taxa, E. microdorsalis sp. nov. (northeastern Australia) and E. robertsi sp. nov. (eastern Australia and New Caledonia). Eucla cods are morphologically conservative with both new species superficially resembling the type species, E. polynemus. Euclichthys microdorsalis sp. nov. is the most anatomically and morphologically divergent member of the group in having a shorter first dorsal fin, longer snout, relatively small eye compared to its interorbital width, and fewer caudal-fin rays and primary rakers on the outer gill arch than its congeners. Euclichthys robersti sp. nov. differs from E. polynemus in being smaller with a more slender head, and having a smaller eye, longer anal-fin base and tail, smaller scales, fewer primary rakers on the outer gill arch, more elongate oval otoliths, and usually having a X and/or Y bone in the caudal skeleton (both absent in other Euclichthys). Little is known of their biology but available material suggest that early juveniles remain pelagic in the open ocean with adults benthopelagic near the sea floor. Diagnoses and a key are provided for the three species.

Aphyonid-clade species of Australia (Teleostei, Bythitidae) with four species new to Australian waters and a new species of Barathronus.

During voyages in 2017 off southern and southeastern Australia, the Australian Research Vessel Investigator deployed a series of demersal beam trawls to depths of around 5000 metres. Nineteen specimens of the rarely caught aphyonid-clade of the ophidiiform family Bythitidae, representing five species, were caught. Four of these are new to Australian waters:  Barathronus pacificus Nielsen and Eagle, 1974 known from the northeastern and southwestern Pacific Ocean, Paraphyonus bolini (Nielsen, 1974) known from the western Indian and western Pacific Oceans, Paraphyonus rassi (Nielsen, 1975) known from the Atlantic Ocean and Sciadonus pedicellaris Garman, 1899, known from the northeastern Atlantic and northeastern and southwestern Pacific Oceans. Also included are Aphyonus gelatinosus Günther, 1878 known from all oceans including ten specimens from Australian waters, Barathronus maculatus Shcherbachev, 1976 known from South Africa to the westernmost Pacific including 13 specimens from Australian waters, Sciadonus longiventralis Nielsen, 2018 known from the holotype collected off New South Wales and finally Barathronus algrahami n. sp. known from the holotype caught off South Australia and four paratypes from off Taiwan and northern Philippines. Close examination of specimens collected during recent voyages combined with recent and ongoing studies by the first author and DNA COI barcoding analysis enabled an assessment of the aphyonid-clade species hitherto recorded from Australian waters. An identification key to the eight aphyonid clade species known from Australian waters is provided.

Pseudotrichonotus belos new species, first record of the fish family Pseudotrichonotidae from Australia (Teleostei: Aulopiformes).

Pseudotrichonotus belos new species, described from three specimens trawled in 100-120 m offshore between Exmouth Gulf and Shark Bay, Western Australia, represents the first record of the sand-diving fish family Pseudotrichonotidae from Australian waters. It differs from its two congeners in having a more posteriorly positioned dorsal fin (predorsal length 39.6-41.2 % SL) and fewer dorsal- and anal-fin rays (31-33 and 12, respectively).

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

Fishes are one of the most intensively studied marine taxonomic groups yet cryptic species are still being discovered. An integrated taxonomic approach is used herein to delineate and describe a new cryptic seamoth (genus Pegasus) from what was previously a wide-ranging species. Preliminary mitochondrial DNA barcoding indicated possible speciation in Pegasus volitans specimens collected in surveys of the Torres Strait and Great Barrier Reef off Queensland in Australia. Morphological and meristic investigations found key differences in a number of characters between P. volitans and the new species, P. tetrabelos. Further mt DNA barcoding of both the COI and the slower mutating 16S genes of additional specimens provided strong support for two separate species. Pegasus tetrabelos and P. volitans are sympatric in northern Australia and were frequently caught together in trawls at the same depths.

Three new species of the genus Chlopsis (Anguilliformes: Chlopsidae) from the Indo-Pacific.

Three new species of false moray eels belonging to the genus Chlopsis, family Chlopsidae, are described and illustrated. Chlopsis sagmacollaris, from Western Australia, is characterized by its distinct color pattern with a unique dark saddle on the nape and paler body pigmentation than all other congeners. Chlopsis nanhaiensis, from Taiwan, has a bicolored body with its dorsal-fin origin behind a vertical through posterior margin of gill opening. These characters are shared with C. apterus, C. bicolor, C. bidentatus and C. orientalis sp. nov., but C. nanhaiensis has fewer total vertebrae than other bicolored species (ca. 120 in C. nanhaiensis vs. 125-140 in other four species). Chlopsis orientalis, from Vietnam, is distinguished from all other congeners except C. bicolor by its simple bicolored body, head length (ca. 10% of total length), position of dorsal-fin origin (distinctly behind a vertical through posterior margin of gill opening), and counts of preanal and total vertebrae (35 and 135). Although C. orientalis resembles C. bicolor in meristics and morphometrics, it differs in its pigmentation and possession of stouter intermuscular bones. These new species represent the first records of the genus Chlopsis from the northwestern Pacific Ocean and the eastern Indian Ocean.

The eels of the genus Nettenchelys, with description of a new species from Taiwan (Teleostei: Anguilliformes: Nettastomatidae).

The species of the genus Nettenchelys are summarized. Nine species are recognized on the basis of adult specimens: Nettenchelys dionisi Brito, N. erroriensis Karmovskaya, N. exoria Böhlke & Smith, N. gephyra Castle & Smith, N. inion Smith & Böhlke, N. paxtoni Karmovskaya, N. proxima new species, N. pygmaea Smith & Böhlke, and N. taylori Alcock. Another species, N. bellottii (D'Ancona) is based on a larva. Nettenchelys gephyra is redescribed on the basis of additional specimens from northeastern Taiwan, Indonesia and Australia. Nettenchelys proxima new species is described from a specimen from southwestern Taiwan. Nettenchelys sp. reported by Uyeno & Sasaki (1983) is found to be a specimen of Facciolella. Information on larvae is updated based on new knowledge of the genus.

The deepwater demersal ichthyofauna of the western Coral Sea.

The highly diverse deepwater demersal ichthyofauna of the western Coral Sea was first systematically surveyed in two exploratory voyages in 1985 and 1986, and these fish assemblages have not been investigated at the same level since. Only recently have catch data and specimens, obtained from these first voyages almost 3 decades ago, been rigorously investigated and analysed. Some 393 species of fishes from 125 families were collected during the 1985 voyage which surveyed the northeastern Australian continental margin, and the Saumarez and Queensland Plateaus. A checklist of the species caught is provided. Levels of endemicity of deepwater fishes in the western Coral Sea are very high with about 50% of well-studied groups, such as sharks and rays, confined to this relatively small geographic region. A very high proportion of species caught during this voyage were either undescribed (78 species or 20%) or new Australian records (96 species or 24%) at the time of the survey. Another 68 species (17%) are the subject of further taxonomic investigation or are currently undergoing formal description. The fauna exhibits some intraregional differences in structure. Biogeographically informative fishes such as skates appear to be cryptically partitioned within the region, differing in composition to other Australian regions and those of French territories to the east. Strong depth-related partitioning of the fauna is also evident, and its structure follows zonation patterns observed across the wider Australian region. Given the high level of micro-endemicity and regional uniqueness of the fauna, there is a compelling argument for the existence of a faunal gyre in the Coral Sea.  New gap-filling surveys are needed to better define the structure of this fauna and determine its distribution.