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Mixed-marker approach suggests maternal philopatry and sex-biased behaviours of narrow sawfish Anoxypristis cuspidata. ENDANGER SPECIES RES 2018. [DOI: 10.3354/esr00912] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Catch composition and aspects of the biology of sharks caught by Thai commercial fisheries in the Andaman Sea. JOURNAL OF FISH BIOLOGY 2018; 92:1487-1504. [PMID: 29635684 DOI: 10.1111/jfb.13605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 02/22/2018] [Indexed: 06/08/2023]
Abstract
Catch composition, landing patterns and biological aspects of sharks caught by commercial fishing fleet operating in the Andaman Sea were recorded from landing sites in Ranong province of Thailand over a period of 1 year. Of the 64 species previously reported in the existing Thailand checklist, only 17 species were recorded in this study. Shark landings from the Andaman Sea appear now to be dominated largely by bamboo sharks Chiloscyllium spp. (Hemiscylliidae), which contribute c. 65% of the total number of sharks recorded. The carcharhinid sharks comprised c. 30·5% to the total catch, while the remaining c. 4·5% of landings comprised sharks from the families Squalidae, Stegostomatidae, Sphyrnidae and Triakidae. The catch composition is remarkably different from the previous landing survey in 2004, in that the current study found noticeable declines in landings of slow-growing, late- maturing and low-fecundity species (especially sphyrnid and carcharhinid species). The absences of many species and changes in life-stage composition suggest that the populations of these groups may be close to collapse. The results from this study emphasize the urgency for additional research and monitoring efforts and also the need for management incentives in order to manage shark fisheries effectively in the Andaman Sea.
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Sawfishes in Papua New Guinea: a preliminary investigation into their status and level of exploitation. ENDANGER SPECIES RES 2017. [DOI: 10.3354/esr00810] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Redescription of the rare and endangered Broadfin Shark Lamiopsis temminckii (Müller & Henle, 1839) (Carcharhiniformes:Carcharhinidae) from the northeastern Arabian Sea. Zootaxa 2016; 4175:155-166. [PMID: 27811779 DOI: 10.11646/zootaxa.4175.2.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Indexed: 11/04/2022]
Abstract
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.
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Life histories of two deep-water Australian endemic elasmobranchs: Argus skate Dipturus polyommata and eastern spotted gummy shark Mustelus walkeri. JOURNAL OF FISH BIOLOGY 2016; 88:1149-1174. [PMID: 26806022 DOI: 10.1111/jfb.12891] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 11/26/2015] [Indexed: 06/05/2023]
Abstract
Two Australian endemic elasmobranchs, the Argus skate Dipturus polyommata and the eastern spotted gummy shark Mustelus walkeri, were collected from the by-catch of a prawn Melicertus plebejus trawl fishery off Queensland. Age and growth parameters were estimated from growth band counts in vertebral sections of 220 D. polyommata and 44 M. walkeri. Dipturus polyommata males and females had an observed maximum age of 10 years and reached maximum sizes of 369 and 371 mm total length (LT ), respectively. Mustelus walkeri lived longer, with the oldest female aged 16 years and measuring 1050 mm stretched total length (LST ), and oldest male aged 9 years and 805 mm LST . Dipturus polyommata grew relatively fast with a von Bertalanffy growth completion parameter of k = 0·208 year(-1) with males reaching maturity at 4·0 years (c. 278 mm LT ) and females at 5·1 years (c. 305 mm LT ). Mustelus walkeri grew more slowly with k = 0·033 year(-1) with males estimated to mature at 7-9 years (670-805 mm LST ) and females at 10-14 years (833-1012 mm LST ). Length at birth inferred from neonate D. polyommata was 89-111 mm LT while for M. walkeri it was estimated to be 273 LST based on the value of L0 from the von Bertalanffy growth model. Both species appeared to have continuous reproductive cycles and low fecundity with an average ovarian fecundity of eight follicles for D. polyommata and a litter size of five to seven pups for M. walkeri. Based on these life-history traits, D. polyommata is more resilient to fishing pressure than M. walkeri.
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Restricted movements and mangrove dependency of the nervous shark Carcharhinus cautus in nearshore coastal waters. JOURNAL OF FISH BIOLOGY 2015; 87:323-341. [PMID: 26179676 DOI: 10.1111/jfb.12724] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 05/10/2015] [Indexed: 06/04/2023]
Abstract
This study used a network of acoustic receivers deployed around a no-take zone in Mangrove Bay, within the Ningaloo Reef Marine Park in Western Australia, to study residency and habitat preference of a small coastal shark, the nervous shark Carcharhinus cautus. Twelve C. cautus were tagged with acoustic tags and monitored for up to 579 days. Based on individuals detected within the receiver array for at least 2 months, C. cautus had small core (50% kernel utilization distribution, KUD) and home ranges (95% KUD) of 0.66 and 3.64 km2, respectively, and showed a strong habitat preference for mangroves, which are only found in the no-take zone. This resulted in C. cautus spending most of their detected time within the no-take zone boundaries (mean = 81.5%), showing that such a protected area could be beneficial to protect this species from extensive fishing pressure and local depletion, where required. Not all C. cautus remained within the acoustic array, however, suggesting that individual variations occur and that not all individuals would benefit from such protection. This study provides important information about the habitat, residency and movements of C. cautus that can be used for management and conservation. The strong affinity and residency of C. cautus within a mangrove-fringing coastline, emphasizes the importance of mangrove habitat to the species and suggests that such preferences can be used to design appropriate no-take zones for this species or others with similar habitat preferences.
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Species composition and aspects of the biology of Orectolobiformes from Indonesian waters. JOURNAL OF FISH BIOLOGY 2015; 86:484-492. [PMID: 25546571 DOI: 10.1111/jfb.12569] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 09/28/2014] [Indexed: 06/04/2023]
Abstract
The biological aspects of members of the order Orectolobiformes exploited in Indonesian waters are given. Seven species belonging to five families were recorded in the catches at various landing sites in southern Indonesia. Of these, Chiloscyllium punctatum was the most abundant species landed, contributing >50% of the number of orectolobiforms recorded. The biological data obtained varied greatly between the species listed. The total length (LT ) at maturity for some species, e.g. C. punctatum and Nebrius ferrugineus, varied from that which has been previously recorded for those species in other regions. This highlights the need for regional-specific biological data for fisheries managers and conservation assessors.
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Age, growth and maturity of the pelagic thresher Alopias pelagicus and the scalloped hammerhead Sphyrna lewini. JOURNAL OF FISH BIOLOGY 2015; 86:333-354. [PMID: 25557431 DOI: 10.1111/jfb.12586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 10/16/2014] [Indexed: 06/04/2023]
Abstract
Indonesia has the greatest reported chondrichthyan catches worldwide, with c.110,000 t caught annually. The pelagic thresher (Alopias pelagicus) and scalloped hammerhead (Sphryna lewini) together comprise about 25% of the total catches of sharks landed in Indonesia. Age and growth parameters were estimated for A. pelagicus and S. lewini from growth-band counts of thin-cut vertebral sections. Alopias pelagicus (n = 158) and S. lewini (n = 157) vertebrae were collected from three Indonesian fish markets over a 5 year period. A multi-model analysis was used to estimate growth parameters for both species. The models of best fit for males and females for A. pelagicus was the three-parameter logistic (L∞ = 3169 mm LT , k = 0·2) and the two-parameter von Bertalanffy models (L∞ = 3281 mm LT , k = 0·12). Age at maturity was calculated to be 10·4 and 13·2 years for males and females, respectively, and these are the oldest estimated for this species. The samples of S. lewini were heavily biased towards females, and the model of best fit for males and females was the three-parameter Gompertz (L∞ = 2598 mm LT , k = 0·15) and the two-parameter Gompertz (L∞ = 2896 mm LT , k= 0·16). Age at maturity was calculated to be 8·9 and 13·2 years for males and females, respectively. Although numerous age and growth studies have previously been undertaken on S. lewini, few studies have been able to obtain adequate samples from all components of the population because adult females, adult males and juveniles often reside in different areas. For the first time, sex bias in this study was towards sexually mature females, which are commonly lacking in previous biological studies on S. lewini. Additionally, some of the oldest aged specimens and highest age at maturity for both species were observed in this study. Both species exhibit slow rates of growth and late age at maturity, highlighting the need for a re-assessment of the relative resilience of these two globally threatened sharks at current high levels of fishing mortality throughout the eastern Indian Ocean.
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Catch composition, reproductive biology and diet of the bramble shark Echinorhinus brucus (Squaliformes: Echinorhinidae) from the south-eastern Arabian Sea. JOURNAL OF FISH BIOLOGY 2013; 83:1112-1127. [PMID: 24580658 DOI: 10.1111/jfb.12201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/14/2013] [Indexed: 06/03/2023]
Abstract
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.
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Biological observations on the bristly catshark Bythaelurus hispidus from deep waters off the south-west coast of India. JOURNAL OF FISH BIOLOGY 2013; 82:1582-1591. [PMID: 23639155 DOI: 10.1111/jfb.12087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 02/01/2013] [Indexed: 06/02/2023]
Abstract
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.
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Aspects of the biology of the pygmy ribbontail catshark Eridacnis radcliffei (Proscylliidae: Carcharhiniformes) from the south-west coast of India. JOURNAL OF FISH BIOLOGY 2012; 81:1138-1144. [PMID: 22880745 DOI: 10.1111/j.1095-8649.2012.03379.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
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.
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The current status of elasmobranchs: biology, fisheries and conservation. JOURNAL OF FISH BIOLOGY 2012; 80:897-900. [PMID: 22497366 DOI: 10.1111/j.1095-8649.2012.03268.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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Biology of the silky shark Carcharhinus falciformis (Carcharhinidae) in the eastern Indian Ocean, including an approach to estimating age when timing of parturition is not well defined. JOURNAL OF FISH BIOLOGY 2012; 80:1320-1341. [PMID: 22497386 DOI: 10.1111/j.1095-8649.2012.03240.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Biological data were recorded for 1265 silky sharks Carcharhinus falciformis collected from fish landing sites in eastern Indonesia. These represented catches taken in most calendar months by gillnetting and longlining in the eastern Indian Ocean and contained individuals ranging from embryos to fully mature adults. The growth zones in centra, which were shown to form annually, were counted in the vertebrae in a sub-sample of 200 fish for ageing purposes. The embryo lengths in the 5 months for which there were such data, and the presence of neonates in virtually all months, however, indicated that birth occurs throughout the year and thus there was no well-defined birth date for ageing individual fish. The approximate birth date of each individual was thus estimated from a combination of the total length (L(T) ) at capture and backcalculated L(T) at the formation of the birth zone and at the first and last growth zones in the vertebral centra, together with the period that had elapsed between the formation of those last two growth zones. The number of eggs or embryos in uteri ranged from two to 14, with a mean of 7·2. The estimated mean L(T) at birth of females (811 mm, range: 799-823 mm) and males (812 mm, range: 794-830 mm), derived from the backcalculations corresponding to the birth zones in the centra, were not significantly different (P > 0·05). The L(T) ranges in the catches of post-natal females (570-2592 mm) and males (553-2289 mm) taken by gillnetting were wider than those of the females (1177-2623 mm) and males (1184-2409 mm) taken by longlining. The oldest female and male were 19 and 20 years-old, respectively. The von Bertalanffy growth curves for the two sexes did not differ significantly. The growth coefficient, k, and the asymptotic length, L(T∞). were 0·066 year⁻¹ and 2994 mm for the curve fitted to the combined data for females and males. The lengths L(T50) and ages A(50) at which C. falciformis attained maturity were 2156 mm and 15 years for females and 2076 mm and 13 years for males. The very high proportion of C. falciformis with lengths <L(T50) in current catches places sustainability of the stock at risk.
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Abstract
Taxonomic clarity is a fundamental requirement as it forms the foundation of all other life sciences. In the last decade, chondrichthyan taxonomy has undergone a scientific renaissance with >180 new species formally described. This effort encompasses c. 15% of the global chondrichthyan fauna, which consists of 1185 currently recognized species. The important role of chondrichthyan taxonomy for conservation management has been highlighted in recent years with new species descriptions or taxonomic resolution of a number of threatened species. These include Australian gulper (genus Centrophorus) and speartooth sharks (genus Glyphis) in coastal waters of Australia and Borneo. Closer examination of other wide-ranging species, for which the taxonomy was thought to be stable, has shown that they consist of species complexes, e.g. manta rays (Manta spp.) and spotted eagle rays (the Aetobatus narinari complex), and highlights the need for critical re-examination of other wide-ranging species. Molecular methods have provided another useful tool to taxonomists and they have proven to assist greatly with identifying cryptic species and species complexes. The limitations of particular molecular methods being used need, however, to be carefully considered and there are some concerns about how these are being integrated with classical taxonomy. The fundamental importance of taxonomic nomenclature to life sciences is often poorly understood but striving for nomenclatural stability is a critical component of taxonomy. Similarly, biological collections are an extremely vital asset to both taxonomists and the broader scientific community. These collections are becoming increasingly important due in part to molecular species identification initiatives such as the Barcode of Life which has resulted in a large number of voucher specimens linked to tissue samples being deposited. Biological collections are also proving to be imperative in biodiversity studies as they contain a 'gold mine' of historical collection information important for assessing changes in faunal assemblages. Resources are typically limited for taxonomic research and the ageing taxonomic community is another issue of concern for the future of taxonomy on this important group. Succession planning and better resource allocation will be essential to ensure that this fundamental discipline is maintained into the future.
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Abstract
The major biogeographic structure and affinities of the Australian chondrichthyan fauna were investigated at both interregional and intraregional scales and comparisons made with adjacent bioregions. Faunal lists were compiled from six geographical regions with species from these regions assigned to distributional classes and broad habitat categories. Australian species were further classified on provincial and bathomic structure following bioregionalization outputs from regional marine planning. About 40% of the world's chondrichthyan fauna occurs in Indo-Australasia (482 species) of which 323 species are found in Australian seas. The tropical Australian component, of which c. 46% of taxa are regional endemics, is most similar to faunas of Indonesia, New Guinea and New Caledonia. The temperate Australian component is most similar to New Zealand and Antarctica with about half of its species endemic. Highest levels of Australian endemism exist in bathomes of the outer continental shelf and upper slope. A relatively high proportion of regional endemism (57% of species) on the slope in the poorly surveyed but species-rich Solanderian unit is probably due to high levels of large-scale habitat complexity in the Coral Sea. The richness of demersal assemblages on the continental shelf and slope appears to be largely related to the spatial complexity of the region and the level of exploration. Much lower diversity off Antarctica is consistent with the pattern in teleosts. The complex chondrichthyan fauna of Australia is confirmed as being amongst the richest of the mega-diverse Indo-West Pacific Ocean. Species-level compositions of regional faunas across Indo-Australasia differ markedly because of moderate to high levels of intraregional speciation. Faunal assemblages in Australian marine provinces and bathomes differ from each other, supporting a broader pattern for fishes that underpins a marine planning framework for the region.
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Squalus formosus, a new species of spurdog shark (Squaliformes: Squalidae), from the western North Pacific Ocean. JOURNAL OF FISH BIOLOGY 2011; 79:954-968. [PMID: 21967583 DOI: 10.1111/j.1095-8649.2011.03068.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A new species of spurdog, Squalus formosus n. sp., from the lower continental shelf and upper continental slope off the coast of Taiwan and southern Japan, is described. It belongs to the 'highfin megalops group', the members of which share a short snout, high dorsal fins, robust dorsal spines, tricuspid denticles and a white posterior caudal margin. Squalus formosus is most similar to Squalus albifrons, a recently described species from eastern Australia, but differs in some morphological characters and fin colouration. Squalus formosus is sympatric with three other species of Squalus in Taiwanese waters, i.e. Squalus brevirostris, Squalus japonicus and Squalus mitsukurii, and can be readily distinguished from these in the following combination of characters: tall and upright first dorsal fin, with a tall and robust spine, short and bluntly pointed snout, white caudal-fin posterior margin and first dorsal fin with a white anterior margin parallel with dorsal spine. This new species was considered by some authors to be conspecific with Squalus blainville from the eastern Atlantic Ocean, but the results of this study reveal that it is probably endemic to Taiwan and southern Japan.
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Abstract
The status of chondrichthyan (sharks, batoids and chimaeras) conservation in the Indo-Australasian region is examined, and issues relevant to the conservation of this fauna at the subregional level [Australia, Indonesia (excluding West Papua), New Guinea (West Papua and Papua New Guinea), New Caledonia and New Zealand] are discussed. According to the 2009 IUCN Red List of Threatened Species, c. 21% of Indo-Australasian chondrichthyans are classified as threatened (critically endangered, endangered and vulnerable) and c. 40% are of conservation concern (threatened and near threatened). The proportion of threatened species is highest in New Guinea (c. 39%) and Indonesia (c. 35%) and least in New Zealand (c. 11%). In New Guinea, three quarters of the species are of conservation concern; in Indonesia, nearly two thirds are of conservation concern. Within the region, the proportion of threatened batoids (c. 29%) is higher than threatened sharks (c. 17%), while there are no threatened chimaeras. Conservation status is discussed at the order (for sharks), suborder (for batoids) and family level. Issues relating to the conservation status of chondrichthyans vary greatly between each subregion, but they mostly relate to targeted or incidental capture in fisheries. A handful of sharks and batoids are protected within Australian waters, while one species is protected in New Zealand. Both Australia and New Zealand have developed National Plans of Action for the Conservation and Management of Sharks (NPOA-Sharks), but these are lacking elsewhere. Development and implementation of NPOA-Sharks are a priority in order to drive the conservation of the regional fauna. Sustainable fisheries management (including by-catch), confronting the challenge of illegal, unreported and unregulated fishing, species protection where appropriate and marine protected areas (MPA) are all likely to prove vital in ensuring the long-term conservation of Indo-Australasian sharks, batoids and chimaeras.
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Aspects of maturation and reproduction in hexanchiform and squaliform sharks. JOURNAL OF FISH BIOLOGY 2010; 76:1362-1378. [PMID: 20537019 DOI: 10.1111/j.1095-8649.2010.02560.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Three species of hexanchiform sharks belonging to two families and 12 species of squaliform sharks belonging to three families were recorded in fish landing site surveys in eastern Indonesia. Of these, the Squalidae were the most abundant species landed, with Squalus hemipinnis, Squalus edmundsi and Squalus montalbani contributing 0.4, 0.4 and 0.5% to the total number of sharks recorded in a 5 year survey of Indonesian fish landing sites. In comparison, the hexanchid Hexanchus griseus contributed the largest percentage to the total shark biomass. For many species, the majority of the catch consisted of immature fishes, which had not yet been able to reproduce. The data presented in this article are the first biological data reported on most of these shark species and are thus vital for fisheries managers and conservation assessors.
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Abstract
Sequence data often have competing signals that are detected by network programs or Lento plots. Such data can be formed by generating sequences on more than one tree, and combining the results, a mixture model. We report that with such mixture models, the estimates of edge (branch) lengths from maximum likelihood (ML) methods that assume a single tree are biased. Based on the observed number of competing signals in real data, such a bias of ML is expected to occur frequently. Because network methods can recover competing signals more accurately, there is a need for ML methods allowing a network. A fundamental problem is that mixture models can have more parameters than can be recovered from the data, so that some mixtures are not, in principle, identifiable. We recommend that network programs be incorporated into best practice analysis, along with ML and Bayesian trees.
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Abstract
It is well known that molecular data "saturates" with increasing sequence divergence (thereby losing phylogenetic information) and that in addition the accumulation of misleading information due to chance similarities or to systematic bias may accompany saturation as well. Exploratory data analysis methods that can quantify the extent of signal loss or convergence for a given data set are scarce. Such methods are needed because genomics delivers very long sequence alignments spanning substantial phylogenetic depth, where site saturation may be compounded by systematic biases or other alternative signals. Here we introduce the Treeness Triangle (TT) graph, in which signals detectable by Hadamard (spectral) analysis are summed into 3 categories--those supporting 1) external and 2) internal branches in the optimal tree, in addition to 3) the residuals (potential internal branches not present in the optimal tree). These 3 values are plotted in a standard ternary coordinate system. The approach is illustrated with simulated and real data sets, the latter from complete chloroplast genomes, where potential problems of paralogy or lateral gene acquisition can be excluded. The TT uncovers the divergence-dependent loss of phylogenetic signal as subsets of chloroplast genomes are investigated that span increasingly deeper evolutionary timescales. The rate of signal loss (or signal retention) varies with the gene and/or the method of analysis.
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Acyl sulfonamide anti-proliferatives. Part 2: Activity of heterocyclic sulfonamide derivatives. Bioorg Med Chem Lett 2005; 15:617-20. [PMID: 15664824 DOI: 10.1016/j.bmcl.2004.11.041] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Revised: 11/12/2004] [Accepted: 11/16/2004] [Indexed: 11/17/2022]
Abstract
The anti-proliferative activity of acylated heterocyclic sulfonamides is described in Vascular Endothelial Growth Factor-dependent Human Umbilical Vascular Endothelial Cells (VEGF-HUVEC) and in HCT116 tumor cells in a soft agar diffusion assay.
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Acyl Sulfonamide Anti-Proliferatives: Benzene Substituent Structure−Activity Relationships for a Novel Class of Antitumor Agents. J Med Chem 2004; 47:5367-80. [PMID: 15481975 DOI: 10.1021/jm030594r] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two closely related diaryl acylsulfonamides were recently reported as potent antitumor agents against a broad spectrum of human tumor xenografts (colon, lung, breast, ovary, and prostate) in nude mice. Especially intriguing was their activity against colorectal cancer xenografts. In this paper, rapid parallel synthesis along with traditional medicinal chemistry techniques were used to quickly delineate the structure-activity relationships of the substitution patterns in both phenyl rings of the acylsufonamide anti-proliferative scaffold. Although the molecular target of the compounds remains unclear, we determined that the vascular endothelial growth factor-dependent human umbilical vein endothelial cells assay in combination with a soft agar disk diffusion assay allowed for optimization of potency in the series. The pharmacokinetic properties and in vivo activity in an HCT116 xenograft model are reported for representative compounds.
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Synthesis of adenosylcobinamide 2-chlorophenyl phosphate, a zwitterionic cobinamide phosphate analog of adenosylcobalamin en route to crystallizable cobinamides. J Inorg Biochem 2002; 91:371-87. [PMID: 12161307 DOI: 10.1016/s0162-0134(02)00402-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The design and implementation of a new, higher yield synthetic method for synthesizing zwitterionic cobinamide phosphates is described. Adenosylcobinamide 2-chlorophenyl phosphate, beta-AdoCbi-PAr -- a 5,6-dimethylbenzimidazole-free adenosylcobalamin analog, where a 2-chlorophenyl group replaces the ribofuranose and 5,6-dimethylbenzimidazole moieties -- is prepared in tens of milligram quantities, quantities sufficient for crystallization and enzyme trials, amounts 100-fold greater than previously available. The use of (31)P NMR spectroscopy to follow reactions directly, the use of control reactions to learn how to reduce reactant water content, and the use of reaction solvents that completely dissolved the corrinoid reactants were crucial for developing this new synthetic route. beta-AdoCbi-PAr was synthesized in 10% overall isolated yield from cyanocobinamide. Cyanocobinamide was converted to cyanocobinamide 2-chlorophenyl phosphate by direct phosphorylation with 2-chlorophenyl phosphodi-(1,2,4-triazolide) in 25% isolated yield and > or = 98% purity. Sodium borohydride reduction of cyanocobinamide 2-chlorophenyl phosphate and reaction with 5'-chloro-5'-deoxy-adenosine produced beta-AdoCbi-PAr in 42% yield and > or = 98% purity. These compounds were characterized by HPLC, (1)H and (31)P NMR, UV-visible spectroscopy, and liquid secondary ionization mass spectroscopy.
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Family-oriented treatment of alcoholism. RHODE ISLAND MEDICAL JOURNAL 1985; 68:123-6. [PMID: 3856911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Clinical pharmacy: how it operates effectively in our hospital. PHARMACY TIMES 1985; 51:34-6, 39-40. [PMID: 10270462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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Nitrofurantoin unmasking peripheral neuropathy in a type 2 diabetic patient. ARCHIVES OF INTERNAL MEDICINE 1984; 144:821. [PMID: 6712378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
It is well documented that patients with preexisting renal dysfunction are at increased risk of having nitrofurantoin-induced peripheral neuropathy develop. A diabetic patient whose condition was controlled by diet alone had peripheral neuropathy develop four days after starting nitrofurantoin therapy for the treatment of a urinary tract infection.
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Direct measurement of the nonlinear refractive-index coefficient gamma at 355 nm in fused silica and in BK-10 glass. OPTICS LETTERS 1984; 9:10-12. [PMID: 19718219 DOI: 10.1364/ol.9.000010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We have measured the nonlinear refractive-index coefficient gamma interferometrically at 355 nm in fused silica and in BK-10, a borosilicate crown glass. These measurements are the first reported direct ultraviolet measurements of the nonlinear index of refraction in any transparent glass. Our results are gamma = (2.5 +/- 1.2) x 10(-16) cm(2)/W and gamma = (1.7 +/- 0.8) x 10(-16) cm(2)/W, respectively, for fused silica and BK-10.
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Abstract
The technique of continuous pump/tube enteric feeding is being utilized with ever increasing frequency and success. Commercially available formulas are being repackaged in 1-liter plastic containers for ease in clinical use. The nutrient solution often hangs at the patient's bedside at room temperature for periods of 8 to 12 hrs and the possibility of significant and serious bacterial growth must be recognized as a potential problem. Though this has never appeared to be a clinical problem in over 15,000 pump/tube feeding days, the bacteriology has not been previously studied. This preliminary study suggests that the major source of nutrient solution contamination relates to the technique of transfer from the commercial can to the clinical liter plastic container and that "hang" times of 8 to 12 hrs at room temperature are quite reasonable if appropriate care is exercised in the transfer process.
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