New insights from nuclear and mitochondrial markers on the genetic diversity and structure of the Indian white shrimp Fenneropenaeus indicus among the marginal seas in the Indian Ocean.

Genetic variation in wild stocks of a major commercial shrimp, Fenneropenaeus indicus, from the marginal seas in the Indian Ocean was analysed using polymorphic microsatellite loci and mitochondrial COI gene. The average observed heterozygosity (Ho = 0.44 ±â€¯0.02) and the expected heterozygosity (He = 0.73 ±â€¯0.01) were high across loci and populations indicating high microsatellite variation. Pairwise FST and Bayesian clustering indicated the occurrence of four genetically distinct stocks out of the eight sampled populations with implications for specific management approaches. Mantel test for isolation by distance proved that genetic differentiation is not related to geographic distance between populations. Mitochondrial COI sequence analysis showed concordant differentiation pattern as well indicated the relevance of COI in population genetics of shrimps. Pairwise ɸST and phylogenetic and Bayesian analyses revealed four distinct clades, as observed with nuclear markers. Divergence time analysis revealed the origin and initial divergence of F. indicus corresponds to late Miocene and divergence to phylogroups in the Pleistocene. BSP analysis presented a long stable population size with a slight decrease in the late Pleistocene and gradually expanded to the current status. The information here will be useful in commercial shrimp breeding and selection programmes and management of natural stocks of Indian white shrimp.

Redescription of Chlorophthalmus corniger, a senior synonym of Chlorophthalmus bicornis (Family: Chlorophthalmidae).

Chlorophthalmus corniger is redescribed on the basis of recently collected specimens. The species is redefined as a species of Chlorophthalmus with the lower jaw terminating in a distinctly projecting horizontal plate with strong, spine-like processes directed forward from the plate's corners; body silvery grey, with numerous minute black spots and traces of broad darker crossbars; base of anterior dorsal fin spines and distal parts of dorsal fins black; adipose fin tiny with numerous black spots; caudal fin black; 3·5 scales above lateral line; three rows of cheek scales; head very large, 34·3-40·1% standard length (LS ); eye large, 29·8-40·8% head length (LH ); pectoral fin long, extending to beyond dorsal fin base, 21·7-26·2% LS . Chlorophthalmus bicornis is a junior synonym of C. corniger based on the examination of the type series of both species. It is confined to the northern half of the Indian Ocean, reliably recorded from Somalia and the Gulf of Aden to southern Java, Indonesia, at depths between 200 and 500 m. A lectotype and three paralectotypes were designated for C. corniger. DNA barcodes for Indian species of Chlorophthalmus were generated.

Rediscovery of Lophiodes triradiatus (Lloyd, 1909), a senior synonym of L. infrabrunneus Smith and Radcliffe (Lophiiformes: Lophiidae).

Examination of the holotype and three recently collected additional specimens from the Indian Ocean has revealed that Lophius triradiatus Lloyd, 1909 (now under Lophiodes)  is a valid species and a senior synonym of Lophiodes infrabrunneus Smith & Radcliffe, 1912 and Lophiodes abdituspinus Ni, Wu & Li, 1990. A detailed description of the additional specimens is provided.

Plectranthias alcocki, a new anthiine fish species (Perciformes: Serranidae) from the Arabian Sea, off southwest India.

A new species of anthiine fish, Plectranthias alcocki n. sp. is described and illustrated based on two specimens, (63.7-72.5 mm SL), recently collected from deep-waters of the Arabian Sea, off Kollam, Kerala, India. The following combination of characters distinguishes it from all other congeners: Dorsal-fin rays X, 15; anal-fin rays III, 7; pectoral-fin rays 14, all unbranched; pelvic-fin rays I, 5; lateral-line complete, the pored lateral-line scales 28; scales above lateral line to origin of dorsal fin 1; scales dorsally on head extending to posterior nostrils; no scales on maxilla or chin; gill rakers 5 + 11 (2 + 7 developed); circumpeduncular scales 10; fourth dorsal spine longest, 2.8 (2.6) in head length (HL), longest dorsal-fin soft ray (second)  2.4 (2.7) in head length; body depth 34.4 (35)% SL; head length 46 (49.8)% SL; orbital length 8.6 in SL; margin of preopercle finely serrate, the serrae 33 (28), ventral edge without antrorse spines; dorsal fin continuous and notched; first anal-fin spine 4.9 (5.6) in HL, second anal-fin spine 2.2 (2.6) in HL; pelvic fins relatively short, 4.0-4.3 in SL; the dorsal fin with a black blotch at base of fourth to eighth spines, one at base of the last three spines, and two at base of soft portion of fin, the dark pigment extending onto adjacent body.

Biological observations on the bristly catshark Bythaelurus hispidus from deep waters off the south-west coast of India.

Biological data are presented for the poorly known bristly catshark Bythaelurus hispidus based on specimens collected from the by-catch of the commercial deep-sea shrimp trawl fishery operating in the Arabian Sea at depths of 200-500 m off the south-west coast of India. One hundred and sixty-two individuals, which ranged from 120 to 366 mm total length (L(T)), were collected for this study. Size-at-maturity (L50) for females and males was estimated at 252 and 235 mm L(T), respectively. The reproductive mode of B. hispidus was aplacental viviparity, which is the rarest reproductive mode within the Scyliorhinidae and is considered to be the most advanced of the three reproductive modes occurring within this family. Dietary analysis of stomach contents revealed B. hispidus feeds on a variety of prey, primarily fishes.

Catch composition, reproductive biology and diet of the bramble shark Echinorhinus brucus (Squaliformes: Echinorhinidae) from the south-eastern Arabian Sea.

Fishery and biological data are presented for the poorly known bramble shark Echinorhinus brucus (Squaliformes: Echinorhinidae), from the deep waters of the south-eastern Arabian Sea. A total of 5318 individuals from by-catch landings of deep-water bottom set longlines, gillnets and shrimp trawl fisheries operating at depths of 200-1200 m were recorded between January 2008 and December 2011 at the Kochi Fisheries Harbour (Kerala). A total of 431 individuals, from 46 to 318 cm total length (L(T)) and 0·8 to 132 kg total mass (M(T)), were examined to determine biological data for this species. The LT at which 50% were mature (L(T)50) for females and males was estimated at 189 and 187 cm LT. Litter size ranged from 10 to 36 and size at birth was between 42 and 46 cm L(T). Dietary analysis of stomach contents revealed E. brucus feeds on a variety of prey including crustaceans (69% index of relative importance, I(RI)), teleosts (25·8% I(RI)), cephalopods (1·7% I(RI)) and elasmobranchs (0·7% I(RI)). This study provides the first detailed biological data for this species and also highlights the extent of the by-catch fishery for this species in Indian waters.

Aspects of the biology of the pygmy ribbontail catshark Eridacnis radcliffei (Proscylliidae: Carcharhiniformes) from the south-west coast of India.

Biological data are presented for the pygmy ribbontail catshark Eridacnis radcliffei based on specimens collected from the by-catch of the commercial deep-sea shrimp trawl fishery operating in the Arabian Sea off the south-west coast of India. A total of 549 individuals, from 101 to 257 mm total length (L(T)) and 2·2 to 56 g, were collected. The L(T) at first maturity (L(T50)) of females and males was estimated at 183 and 170 mm, respectively, and analysis of stomach contents revealed that E. radcliffei feeds primarily on crustaceans.

The taxonomic identity of the monocle bream Scolopsis vosmeri species complex (Perciformes: Nemipteridae), with comments on molecular phylogenetic relationships within the genus Scolopsis.

The monocle bream Scolopsis vosmeri species complex is revised. Three species in the complex are recognized: Scolopsis vosmeri (Bloch, 1792), widespread in the Indo-West Pacific, from the northern Indian Ocean (Pakistan, western India, Sri Lanka, Bay of Bengal, and the Andaman Sea, but not recorded from the Red Sea or Arabian Gulf, east African coast or Madagascar) to western Indonesia and Borneo; S. japonica (Bloch, 1793), restricted to the western Pacific Ocean from western Indonesia and north-western Australia east to the Philippines and north to southern Japan; and S. curite Cuvier, 1815, widespread from the western to the eastern Indian Ocean, including the Red Sea and Arabian Gulf. All three species are similar morphologically, and have been confused taxonomically, but phylogenetic analysis of the COI barcoding region shows they are evolutionarily divergent. The three species are redescribed in detail and characters found to distinguish them. Scolopsis vosmeri is easily distinguished from S. japonica and S. curite in having a white band along the side of the body; having a black spot on most body scales (versus greenish yellow spot in S. japonica and S. curite); in lacking a distinct black spot (sometimes a small and faint spot present) on the upper pectoral-fin base (versus small black wedge-shaped spot present in S. japonica and S. curite); caudal peduncle whitish in live individuals (versus caudal peduncle usually yellowish in S. japonica and S. curite); and pelvic and anal fins crimson to orange-red (versus yellow in S. japonica and S. curite). Scolopsis japonica and S. curite are indistinguishable by color pattern but differ in the degree of spination on the preopercular margin. Neotypes are designated for Scolopsis japonica and S. curite. Nomenclatural problems, including validity of the genus Scolopsis, are discussed. We regard Scolopsis curite Cuvier, 1815 as a valid binomial name and thus the type species of Scolopsis Cuvier, 1814 by subsequent monotypy.

Macromineral and heavy metal profiles of selected deep-sea fish from the Kochi coast of the Arabian Sea, India.

Deep-sea fish from the Arabian Sea in the south western coast of India have been gaining attention as a new edible fish source. Mineral profile of ten selected deep-sea fish from the south west coast of India were assessed for heavy metal and macro mineral content for safety and nutritional quality assessment, respectively. Heavy metal levels were below permissible limits for most of the species studied. But in some species, the levels slightly exceeded the permissible limit of 0.3 mg/kg for Pb, a major heavy metal contaminant in fish, according to the European Union and FSSAI regulations for heavy metals in food. Interestingly, significant content of macro minerals was observed in all the species studied. In conclusion, deep-sea fish were observed to be good source of minerals and were found to be safe for human consumption; except for a couple of species which possess slightly higher Pb content, which may be because of its presence in their habitat.

A new species of white-spotted moray eel, Gymnothorax smithi (Muraenidae: Muraeninae) from deep waters of Arabian Sea, India.

A new species of white-spotted moray eel Gymnothorax smithi sp. nov. is described based on three specimens collected from the southeastern Arabian Sea, India. This is the first deep water report of a moray eel from Indian waters from 200 m depth. This new species is distinguishable from its congeners by the following combination of characters: greyish brown body overlain with white spots of irregular shape, dorsal-fin origin anterior to gill opening, anus positioned slightly behind the mid-point of the body, serrated teeth and a unique vertebral count 3-5 /57/130-132. [Zoobank URL: urn:lsid:zoobank.org:act:9554CE07-E9E7-4B4F-95CD-54F2BB26FF28].

Nemipterus andamanensis, a new nemipterid fish (Perciformes: Nemipteridae) from the Andaman Islands.

A new species of threadfin bream, Nemipterus andamanensis n. sp. from the Andaman Islands is described and figured. N. andamanensis resembles N. marginatus (Valenciennes, 1830) in general body form and colour pattern, but differs from the latter by having four yellow stripes on the head region, upper lobe of caudal fin and filament yellow, and lower lobe of caudal fin pinkish. The mitochondrial cytochrome oxidase C subunit I (COI) gene sequence comparison with close species revealed that Nemipterus andamanensis n. sp. has distinct genetic divergence (8.5%) from Nemipterus marginatus and other species of the genus occurring in the area.

Mitochondrial signatures for identification of grouper species from Indian waters.

Groupers are important commercial fish in many parts of the world. Accurate identification is critical for effective conservation assessment and fisheries management. Genetic barcodes provide a simple and reproducible method for the identification of species even in the absence of taxonomic expertise. The generation of reference barcodes from properly identified specimens is an important first step in this direction. Here, 36 species belonging to the subfamily Epinephelinae (Family: Serranidae) were collected from landings on the west coast of India and Port Blair, Andaman, and partial nucleotide sequence data of the mitochondrial cytochrome C oxidase subunit I (COI) gene was generated. Barcodes for 13 species were developed from Indian waters for the first time. Analysis using the COI gene produced phylogenetic trees in concurrence with other multi-gene studies. Epinephelus fasciatus and E. areolatus were found to be a species complex, as hypothesized in other studies. The DNA barcodes developed in the study can be used for identifying species within Epinehelinae, where taxonomic ambiguity still exists.

DNA barcoding reveals species composition of sharks and rays in the Indian commercial fishery.

DNA barcoding was successfully used for the accurate identification of chondrichthyans in the Indian commercial marine fishery. About 528 specimens of 111 chondrichthyan species and 34 families, collected from the Indian EEZ, were barcoded for a 655 bp region of the mitochondrial gene cytochrome c oxidase subunit 1 (COI). Generally, five specimens per species were barcoded, but numbers ranged from 2 to 13. The average Kimura 2 parameter (K2P) distance separating individuals within species was 0.32%, and the average distance separating species within genera was 6.73%. Ten species were suggested as putative new species requiring formal descriptions. Based on the morphology and molecular support, 11 elasmobranch species were confirmed first records for Indian waters. The present study confirms the ability of DNA barcoding for the accurate identification of sharks, rays, and their products from Indian waters.

Chaunax multilepis sp. nov., a new species of Chaunax (Lophiiformes: Chaunacidae) from the northern Indian Ocean.

A new species of Chaunax is described on the basis of eight type and five non-type specimens. This species belongs to the Chaunax abei species group and can be distinguished from congeners in the group by having a continuous tooth patch on the vomer, not divided into two patches, and four or five neuromasts in the lower preopercular series. It can be further separated by the following combination of characters: large green spots on dorsal surface; simple spinules on dorsal surface; 12 pectoral-fin rays; 13-16 neuromasts in pectoral series; 30-37 neuromasts in lateral-line proper; typically four neuromasts on caudal-fin base; typically 7 neuromasts in mandible; typically 12 gill rakers on second gill arch; gill chamber and buccal cavity pale; and peritoneum black.

DNA sequence information resolves taxonomic ambiguity of the common mud crab species (Genus Scylla) in Indian waters.

For several years, mud crabs of genus Scylla have been misidentified owing to their high morphological plasticity and the absence of distinct morphological diagnostic characters. The taxonomic confusion of genus Scylla de Haan is considered to be a primary constraint to the development of aquaculture. Although genus Scylla was revised using morphological and genetic characteristics, taxonomy of Scylla species occurring in India is still not clear. In this study, partial sequences of two mitochondrial genes, 16S rRNA and CO1 (Cytochrome C oxidase subunit I) in populations of Scylla spp. obtained from eleven locations along the Indian coast were used to differentiate and resolve taxonomical ambiguity of the mud crab species in India. The sequences were compared with previously published sequences of Scylla spp. Both trees generated based on 16S rRNA and CO1 indicated that all S. tranquebarica morphotypes obtained during this study and S. tranquebarica sequences submitted previously from Indian waters reciprocally monophyletic with reference sequence of S. serrata. Both sequence data and morphological characters revealed that the species S. serrata (Forskal) is the most abundant followed by S. olivacea. Further, the 16S rRNA and COI haplotypes of Indian S. tranquebarica obtained in the study significantly differed with the known S. tranquebarica by 6.7% and 10.6% respectively whereas it differed with known S. serrata by 0.0-0.7% only, a difference that was not statistically significant. From these studies it is clear that "S. tranquebarica" commonly reported from India should be S. serrata (Forskal).

Redescription of the rare and endangered Broadfin Shark Lamiopsis temminckii (Müller & Henle, 1839) (Carcharhiniformes:Carcharhinidae) from the northeastern Arabian Sea.

The genus Lamiopsis (Carcharhinidae) was previously considered to be monotypic, containing only the Broadfin Shark Lamiopsis temminckii (Müller & Henle, 1839) widely distributed in the Indo-West Pacific. However, a recent taxonomic study revealed that the Western Central Pacific populations were a separate species and that L. temminckii was restricted to the northern Indian Ocean. In this study, the paucity of data available for the true L. temminckii was highlighted. Recently collected specimens of L. temminckii has allowed for a detailed redescription of this species from the northern Arabian Sea to complement the previous taxonomic work on this genus.

Rebuttal to Koeda et al. (2014) on the Red Sea fishes of the perciform genus Pempheris.

Koeda et al. (2014) published a review of fishes of the genus Pempheris of the Red Sea. They concluded that there are four species: P. adusta Bleeker, P. mangula Cuvier, P. nesogallica Cuvier, and a new species, P. tominagai. We show that the first three species they cite are not present in the Red Sea, as follows. 1) P. adusta is a western Pacific species (type locality Ambon), described only from the holotype, and without a dark border on the anal fin. Koeda et al. (2014) mistakenly apply that name to P. flavicycla which is a widespread Indian Ocean species characterized by a prominent broad black border along the anal fin. Koeda et al. (2014) also redescribe P. adusta, using Indian Ocean specimens of P. flavicycla, despite the coloration difference and a 2.5% difference in the mtDNA sequence (COI) between Indian Ocean and W. Pacific populations. 2) P. mangula is a species from the east coast of India (type locality Visakhapatnam), clearly distinct in both gill-raker counts and a 1.1% sequence divergence in COI from its Red Sea relative P. rhomboidea. Pempheris mangula is not found west of India, and Koeda et al. (2014) mistakenly use DNA from Oman and Madagascar to represent P. mangula, instead of genetic material available from the type locality. 3) Pempheris nesogallica (type locality Mauritius) is unknown from the Red Sea. Koeda et al. (2014) separate P. nesogallica from P. rhomboidea (their "P. mangula") by eye size; we fail to find any difference (and they use their purported eye-size difference to erroneously rename one of the two syntypes of P. nesogallica as "P. mangula"). 4) Their new species P. tominagai is referred to as the Indian Ocean sister species of "P. schwenkii of the Pacific"; however, the type locality of P. schwenkii is the Batu Islands off the SW coast of Sumatra in the Indian Ocean. They mistakenly include specimens of a distant South African species as paratypes of P. tominagai. We have determined that P. tominagai is a valid species endemic to the Red Sea and Gulf of Aden. They misidentify one lot of P. rhomboidea in the collection of the Hebrew University of Jerusalem as their record of P. nesogallica from the Red Sea. They misidentify the specimen in their photograph of Fig. 1B as P. adusta and use it as material for their redescription of the species, but it is now shown to be a paratype of Pempheris bexillon Mooi & Randall, 2014. Additionally, they regard P. malabarica Cuvier as a junior synonym of P. molucca Cuvier, but the name P. molucca is based on a fanciful painting and is unavailable as a nomen dubium. They treat Pempheris russellii Day as a junior synonym of P. mangula; however, it is distinct in having longer pectoral fins, a larger eye, and more gill rakers. Their key to the species of Pempheris of the Red Sea is incorrect. We present a new key and conclude that only three species of Pempheris are presently known from the Red Sea: P. flavicycla, P. rhomboidea, and P. tominagai.