Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens.

Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g., filets, fish meal); however, DNA reference libraries are incomplete, and public repositories for sequence data contain incorrectly identified sequences. During a nine-year sampling program in the Philippines, a global biodiversity hotspot for marine fishes, we developed a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 2,525 specimens representing 984 species. Specimens were primarily purchased from markets, with additional diversity collected using rotenone or fishing gear. Species identifications were verified based on taxonomic, phenotypic, and genotypic data, and sequences are associated with voucher specimens, live-color photographs, and genetic samples catalogued at Smithsonian Institution, National Museum of Natural History. The Biodiversity of Philippine Marine Fishes dataset is released herein to increase knowledge of species diversity and distributions and to facilitate accurate identification of market fishes.

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.].

Cirripectes matatakaro, a new species of combtooth blenny from the Central Pacific, illuminates the origins of the Hawaiian fish fauna.

Included among the currently recognized 23 species of combtooth blennies of the genus Cirripectes (Blenniiformes: Blenniidae) of the Indo-Pacific are the Hawaiian endemic C. vanderbilti, and the widespread C. variolosus. During the course of a phylogeographic study of these species, a third species was detected, herein described as C. matatakaro. The new species is distinguished primarily by the configuration of the pore structures posterior to the lateral centers of the transverse row of nuchal cirri in addition to 12 meristic characters and nine morphometric characters documented across 72 specimens and ∼4.2% divergence in mtDNA cytochrome oxidase subunit I. The new species is currently known only from the Marquesas, Gambier, Pitcairns, Tuamotus, and Australs in the South Pacific, and the Northern Line Islands and possibly Johnston Atoll south of Hawai'i. Previous researchers speculated that the geographically widespread C. variolosus was included in an unresolved trichotomy with the Hawaiian endemic and other species based on a morphological phylogeny. Our molecular-phylogenetic analysis resolves many of the previously unresolved relationships within the genus and reveals C. matatakaro as the sister lineage to the Hawaiian C. vanderbilti. The restricted geographic distribution of Cirripectes matatakaro combines with its status as sister to C. vanderbilti to indicate a southern pathway of colonization into Hawai'i.

Anthias albofasciatus Fowler and Bean, 1930, a junior synonym of Tosana niwae Smith and Pope, 1906 (Teleostei: Serranidae: Anthiadinae).

Anthias albofasciatus Fowler Bean, known only from the holotype collected east of Hong Kong in the South China Sea, has been considered a valid species of either Anthias or Pseudanthias. The holotype is compared with the holotype of Tosana niwae Smith Pope from Urado Bay, Shikoku, Japan, as well as non-type specimens from the South China Sea and south-eastern Japan, and shown to be conspecific. Anthias albofasciatus is therefore considered a junior subjective synonym of Tosana niwae.

A DNA barcode reference library of French Polynesian shore fishes.

The emergence of DNA barcoding and metabarcoding opened new ways to study biological diversity, however, the completion of DNA barcode libraries is fundamental for such approaches to succeed. This dataset is a DNA barcode reference library (fragment of Cytochrome Oxydase I gene) for 2,190 specimens representing at least 540 species of shore fishes collected over 10 years at 154 sites across the four volcanic archipelagos of French Polynesia; the Austral, Gambier, Marquesas and Society Islands, a 5,000,000 km2 area. At present, 65% of the known shore fish species of these archipelagoes possess a DNA barcode associated with preserved, photographed, tissue sampled and cataloged specimens, and extensive collection locality data. This dataset represents one of the most comprehensive DNA barcoding efforts for a vertebrate fauna to date. Considering the challenges associated with the conservation of coral reef fishes and the difficulties of accurately identifying species using morphological characters, this publicly available library is expected to be helpful for both authorities and academics in various fields.

Evidence of cryptic species in the blenniid Cirripectesalboapicalis species complex, with zoogeographic implications for the South Pacific.

Rapa Nui, commonly known as Easter Island (Chile), is one of the most isolated tropical islands of the Pacific Ocean. The island location of Rapa Nui makes it the easternmost point of the geographic ranges for many western Pacific fish species that are restricted to the subtropical islands south of 20°S latitude. The blenniid fish species Cirripectesalboapicalis has been thought to have one of the most extensive geographic distribution ranges among these southern subtropical fish species, extending from the southern Great Barrier Reef to Rapa Nui. A phylogenetic analysis was conducted to determine the taxonomic status of the species. The results provide genetic evidence that suggests that this formerly South Pacific-wide species comprises at least three cryptic species with allopatric geographic distributions. The analyses reveal the geographic distributions of these clades and their genetic relationships with each other, and with other species within the genus Cirripectes. The processes that culminated in the current geographic distribution of this species complex and the zoogeographic implications of this finding for the South Pacific region are discussed.

Pseudogramma polyacantha complex (Serranidae, tribe Grammistini): DNA barcoding results lead to the discovery of three cryptic species, including two new species from French Polynesia.

The Pseudogramma polyacantha species complex was found to harbor cryptic taxonomic diversity with three similar, but genetically divergent, species previously hidden in the complex. The true Pseudogramma polyacantha occurs from French Polynesia to South Africa and has modally 19 (many with 20) segmented dorsal-fin rays, modally 16 segmented anal-fin rays, a relatively short lateral line, no dermal flap or small tentacle dorsally on eye, and extensive scalation on the interorbital, suborbital and dentary. Pseudogramma brederi (previously synonymized with P. polyacantha) is recognized as a valid species occurring from Hawaii to Mauritius and having modally 21 segmented dorsal-fin rays, modally 17 segmented anal-fin rays, a relatively long lateral line, no dermal flap or small tentacle dorsally on eye, and relatively well-developed scalation on the interorbital, suborbital and dentary. Pseudogramma galzini n. sp. is described as a new species known only from French Polynesia and having modally 22 segmented dorsal-fin rays, modally 17 segmented anal-fin rays, a relatively long lateral line, no dermal flap or small tentacle dorsally on eye, and limited scalation on the interorbital, suborbital and dentary. Pseudogramma paucilepis n. sp. is described as a new species known only from French Polynesia and having 20 segmented dorsal-fin rays, modally 16 segmented anal-fin rays, a relatively long lateral line, no dermal flap or small tentacle dorsally on eye, and relatively reduced scalation on the interorbital, suborbital and dentary. A mtDNA COI analysis including all available Pseudogramma sequences shows well-supported genetic divergence between the two new species and among congeners.

A phase II trial of bevacizumab and everolimus as treatment for patients with refractory, progressive intracranial meningioma.

Meningiomas that progress after standard therapies are challenging with limited effective chemotherapy options. This phase II trial evaluated the efficacy of everolimus plus bevacizumab in patients with recurrent, progressive meningioma after treatment with surgical resection and local radiotherapy when appropriate. Patients with recurrent meningioma (WHO grade I, II, or III) following standard treatments with surgical resection and radiotherapy received bevacizumab (10 mg/kg IV days 1 and 15) and everolimus (10 mg PO daily) each 28 day cycle. Evaluation of response occurred every 2 cycles. The primary endpoint was progression-free survival (PFS). Secondary endpoints included response rate, overall survival and safety. Seventeen patients with a median age of 59 years (29-84) received study treatment. WHO grades at study entry included: I, 5 (29 %); II, 7 (41 %); III, 4 (24 %); unknown, 1 (6 %). Patients received a median of 8 cycles (1-37); all patients are off study treatment. A best response of SD was observed in 15 patients (88 %), and 6 patients had SD for >12 months. Overall median PFS was 22 months (95 % CI 4.5-26.8) and was greater for patients with WHO grade II and III compared to grade I tumors (22.0 months vs 17.5 months). Four patients discontinued treatment due to toxicity (proteinuria, 2; colitis, 1, thrombocytopenia, 1). However, other grade 3 toxicity was uncommon, and no patient had grade 4 toxicity. The combination of everolimus and bevacizumab was well-tolerated, and produced stable disease in 88 % of patients; the median duration of disease stabilization of 10 months (2-29). The median PFS from this prospective trial was similar to previous retrospective reports of bevacizumab in the treatment of recurrent meningioma.

A new fish species of the subfamily Serraninae (Perciformes, Serranidae) from the Philippines.

A new species of serranine fish is described from the Philippine Islands. A single specimen of a new species, Chelidoperca santosi, captured by fishermen working in Palawan waters was discovered in the public fish market in Iloilo City, Panay, Philippines. Two additional specimens of the new species, also from the Philippines, were subsequently discovered in the collections of the Museum Victoria, Australia. The new species is currently known only from the Philippines and is characterized by its distinctive coloration with a row of four small dark spots on the snout (two in front of each eye) and two dark spots on the chin (one on each side of the symphysis of the dentaries), a white anal fin with six large yellow spots separated by broad white interspaces and a narrow yellow distal border, caudal fin with narrow yellow bars and a yellowish distal margin and no dark spots, and a combination of meristic and morphological characters. 

Macropharyngodon pakoko, a new species of wrasse (Teleostei: Labridae) endemic to the Marquesas Islands, French Polynesia.

A new species of wrasse, Macropharyngodon pakoko, is described from the Marquesas Islands, bringing the total number of species of the genus Macropharyngodon to 12. Macropharyngodon pakoko was found at depths from 0-42 m and is endemic to the Marquesas Islands. Macropharyngodon pakoko is similar to M. meleagris, which is widely distributed from the central and western Pacific to Cocos-Keeling in the Indian Ocean, but differs genetically and in several coloration characters: males with irregularly curved black humeral blotch with incomplete iridescent blue border; inverted irregular "U"- shaped band on the cheek; a small black spot at the upper base of the pectoral fin; and background color of the body greenish with faint bluish black spots on each scale. Females lack black pigment on the chest posterior to the ventral attachment of the gill membranes; reddish black blotches on the body are widely spaced, particularly on the head where they are more reddish and half the size of those on body; caudal fin with small, bright yellow spots arranged in narrow vertical bands with pale interspaces; pelvic fins pale with three reddish yellow cross-bands; a small black spot at the upper base of the pectoral fin; and small reddish spots along the base of the anal fin. Juveniles have irregular black blotches on the body, a small black spot instead of an ocellus posteriorly on the dorsal fin and lack large black spots and ocellus on the anal fin. 

Protocol for building a reference standard sequence library for DNA-based seafood identification.

With the recent adoption of a DNA sequencing-based method for the species identification for seafood products by the U.S. Food and Drug Administration (FDA), a library of standard sequences derived from reference specimens with authoritative taxonomic authentication was required. Provided here are details of how the FDA and its collaborators are building this reference standard sequence library that will be used to confirm the accurate labeling of seafood products sold in interstate commerce in the United States. As an example data set from this library, information for 117 fish reference standards, representing 94 species from 43 families in 15 orders, collected over a 4-year period from the Gulf of Mexico, U.S., that are now stored at the Smithsonian Museum Support Center in Suitland, MD, are provided.

Two new fish species of the subfamily Anthiinae (Perciformes, Serranidae) from the Marquesas.

Two new species of anthiine fishes are described from the Marquesas Islands, French Polynesia. Plectranthias flammeus was found at depths from 20-45 m and is characterized by dorsal rays X, 14 or 15, with spines 1-6 bearing fleshy white tabs at their tips, longest fleshy tab on spine 4; 14 unbranched pectoral rays; lateral line incomplete with 16-17 tubed scales; preopercle with 8-10 small spines along posterior margin and 2 antrorse spines on ventral margin; broad, fiery red-orange streak across lower cheek; head and body with irregularly spaced maroon-ringed yellow blotches on a white background; pair of small dark oblong spots (red with black centers in life) on the bases of the middle rays of the caudal fin. Pseudanthias oumati was found on the outer reef slope of Fatu Hiva at a depth of 50-55 m and is characterized by 3rd dorsal spine elongate and tipped with fleshy yellow filament extending beyond tip of spine; lateral-line scales 43; gill rakers 10 + 28; no papillae on posterior edge of orbit; front of upper lip not thickened (male condition unknown); caudal fin lunate; color of female yellow, all fins yellow with narrow magenta margin (except pectoral fin, which lacks magenta); no stripe from snout to pectoral base; small scales located on basal quarter of soft-dorsal fin from segmented rays 1-12; dorsal profile of head slightly concave.

Cryptic diversity in Indo-Pacific coral-reef fishes revealed by DNA-barcoding provides new support to the centre-of-overlap hypothesis.

Diversity in coral reef fishes is not evenly distributed and tends to accumulate in the Indo-Malay-Philippines Archipelago (IMPA). The comprehension of the mechanisms that initiated this pattern is in its infancy despite its importance for the conservation of coral reefs. Considering the IMPA either as an area of overlap or a cradle of marine biodiversity, the hypotheses proposed to account for this pattern rely on extant knowledge about taxonomy and species range distribution. The recent large-scale use of standard molecular data (DNA barcoding), however, has revealed the importance of taking into account cryptic diversity when assessing tropical biodiversity. We DNA barcoded 2276 specimens belonging to 668 coral reef fish species through a collaborative effort conducted concomitantly in both Indian and Pacific oceans to appraise the importance of cryptic diversity in species with an Indo-Pacific distribution range. Of the 141 species sampled on each side of the IMPA, 62 presented no spatial structure whereas 67 exhibited divergent lineages on each side of the IMPA with K2P distances ranging between 1% and 12%, and 12 presented several lineages with K2P distances ranging between 3% and 22%. Thus, from this initial pool of 141 nominal species with Indo-Pacific distribution, 79 dissolved into 165 biological units among which 162 were found in a single ocean. This result is consistent with the view that the IMPA accumulates diversity as a consequence of its geological history, its location on the junction between the two main tropical oceans and the presence of a land bridge during glacial times in the IMPA that fostered allopatric divergence and secondary contacts between the Indian and Pacific oceans.

Biodiversity assessment of the fishes of Saba Bank atoll, Netherlands Antilles.

Biodiversity surveys were conducted on Saba Bank, Netherlands Antilles, to assess ichthyofaunal richness and to compare with published surveys of other Caribbean localities. The primary objective was to estimate the total species richness of the Saba Bank ichthyofauna. A variety of sampling techniques was utilized to survey the fish species of both the visually accessible megafauna and the camouflaged and small-sized species comprising the cryptic ichthyofauna.Based on results presented herein, the number of species known on Saba Bank is increased from 42 previously known species to 270 species. Expected species-accumulation curves demonstrate that the current estimate of species richness of fishes for Saba Bank under represents the actual richness, and our knowledge of the ichthyofauna has not plateaued. The total expected fish-species richness may be somewhere between 320 and 411 species.The Saba Bank ichthyofaunal assemblage is compared to fish assemblages found elsewhere in the Caribbean. Despite the absence of shallow or emergent shore habitats like mangroves, Saba Bank ranks as having the eighth highest ichthyofaunal richness of surveyed localities in the Greater Caribbean. Some degree of habitat heterogeneity was evident. Fore-reef, patch-reef, and lagoonal habitats were sampled. Fish assemblages were significantly different between habitats. Species richness was highest on the fore reef, but 11 species were found only at lagoonal sites.A comprehensive, annotated list of the fishes currently known to occur on Saba Bank, Netherland Antilles, is provided and color photographs of freshly collected specimens are presented for 165 of the listed species of Saba Bank fishes to facilitate identification and taxonomic comparison with similar taxa at other localities. Coloration of some species is shown for the first time. Preliminary analysis indicates that at least six undescribed new species were collected during the survey and these are indicated in the annotated list.

Review of the South American-Antarctic triplefin fish genus Helcogrammoides (Perciformes: Tripterygiidae)

The genus Helcogrammoides comprises three species of small, cryptic shorefishes, H. antarcticus, H. chilensis, and H. cunninghami. All three species inhabit shallow water along exposed rocky coasts. Specimens reported herein extend the known distributions of H. chilensis and H. cunninghami to the vicinity of Lima, Peru, approximately 1600 km north of their previously reported northernmost records in Chile. Helcogrammoides chilensis and H. cunninghami occur sympatrically over most of their ranges in Peru and Chile and are frequently taken together in the same field collections. Lectotypes are designated for H. chilensis and H. cunninghami. Diagnoses and an identification key are provided for the species.