Identification and phylogenetic inferences on stocks of sharks affected by the fishing industry off the Northern coast of Brazil

The ongoing decline in abundance and diversity of shark stocks, primarily due to uncontrolled fishery exploitation, is a worldwide problem. An additional problem for the development of conservation and management programmes is the identification of species diversity within a given area, given the morphological similarities among shark species, and the typical disembarkation of processed carcasses which are almost impossible to differentiate. The main aim of the present study was to identify those shark species being exploited off northern Brazil, by using the 12S-16S molecular marker. For this, DNA sequences were obtained from 122 specimens collected on the docks and the fish market in Bragança, in the Brazilian state of Pará. We identified at least 11 species. Three-quarters of the specimens collected were either Carcharhinus porosus or Rhizoprionodon sp, while a notable absence was the daggernose shark, Isogomphodon oxyrhyncus, previously one of the most common species in local catches. The study emphasises the value of molecular techniques for the identification of cryptic shark species, and the potential of the 12S-16S marker as a tool for phylogenetic inferences in a study of elasmobranchs.     

应用脂肪酸组成研究热带东太平洋同域中上层鲨鱼营养生态位分化

物种对食物资源利用方式的差异,即营养生态位分化是物种共存的先决条件之一,对种间营养生态位的比较研究有助于了解同域分布物种的共存机制。脂肪酸组成可反映生物较长时间尺度的摄食信息,对探讨物种间营养生态位分化具有重要指示作用。热带东太平洋主要栖息有8种大型中上层鲨鱼,大青鲨(Prionace glauca)、大眼长尾鲨(Alopias superciliosus)、镰状真鲨(Carcharhinus falciformis)、长鳍真鲨(Carcharhinus longimanus)、浅海长尾鲨(Alopias pelagicus)、尖吻鲭鲨(Isurus oxyrinchus)、路氏双髻鲨(Sphyrna lewini)和锤头双髻鲨(Sphyrna zygaena),通过比较其肌肉脂肪酸组成,分析种间食性差异,营养关系及营养生态位分化。结果表明,尖吻鲭鲨营养级相对较高,大青鲨相对较低。3种鼠鲨与5种真鲨存在食性差异或栖息地隔离。浅海长尾鲨与大眼长尾鲨营养生态位重叠程度较高,存在激烈的资源竞争。大青鲨与镰状真鲨生态位宽度较大,表征其对环境的可塑性较强;尖吻鲭鲨和路氏双髻鲨生态位宽度较小,表现为其食性的特化。本研究解释了脂肪酸组成分析在鲨鱼摄食研究中的潜在应用,对分析大洋性鲨鱼的营养生态位分化,资源分配方式及同域共存机制有一定的应用价值。     

An encounter between a pelagic shark and giant cephalopod

An oceanic whitetip shark (Carcharhinus longimanus) was observed off the coast of Kona, Hawaii, with scars caused by the tentacles of a large cephalopod. While the exact species could not be confirmed, candidate species include the giant squid (Architeuthis dux) or species from the genera Thysanoteuthis (flying squids) and Megalocranchia (glass squids). Telemetry shows C. longimanus will dive within the mesopelagic zone and may interact with or even forage for large cephalopods.     

Isotopic enrichment in Rhizoprionodon porosus (Poey, 1861) and Carcharhinus porosus (Ranzani, 1840) embryos

Isotopic values of two Caribbean sharpnose shark Rhizoprionodon porosus litters (Poey, 1861) with two and three embryos and one litter of 11 smalltail shark Carcharhinus porosus embryos showed enriched ¹⁵N and ¹³C compared to their mothers. In R. porosus, embryonic isotope values were 3.06 ± 0.07‰ and 0.69 ± 0.15‰ greater than their mothers' for δ¹⁵N and δ¹³C, respectively, whereas in C. porosus, δ¹⁵N and δ¹³C were 1.79 ± 0.09‰ and 1.31 ± 0.17‰ greater in embryos than their mothers.     

Molecular assessment of the genetic integrity,distinctiveness and phylogeographic context of the Saltwater crocodile (<Emphasis Type="Italic">Crocodylus porosus</Emphasis>) on Palau

The saltwater crocodile (Crocodylus porosus) is the largest and most broadly distributed crocodilian species, and thus is of special conservation and economic interest. Similar to other parts of its range throughout the Indo-Pacific, C. porosus distributed in the Republic of Palau have experienced a severe population decline over the past century primarily due to commercial hunting and eradication campaigns. In addition, several thousand crocodiles of undocumented species and origin were imported into Palau during the 1930’s for commercial farming purposes, potentially polluting the gene pool of the endemic saltwater crocodiles. Analysis of 39 individuals collected throughout the Republic of Palau revealed a single mitochondrial DNA control region haplotype shared by populations sampled in Sulawesi, Borneo and Australia. The mtDNA results, in combination with microsatellite genotypic data at six loci, detected no evidence for inter-specific hybridization between endemic Palauan C. porosus and potentially introduced Crocodylus species. There was no evidence for a genetic bottleneck in the Palauan population, however an excess of rare alleles was identified, indirectly suggesting a recent history of admixture potentially linked to introductions of non-native C. porosus. Following from these findings, Palauan C. porosus should be included in the single ESU previously established for all saltwater crocodiles given the recovery of a fixed, but geographically widespread haplotype. Although Palauan C. porosus exhibited significant genetic differentiation relative to all other sampled populations, it’s delineation as a distinct management unit is precluded at the present time by evidence that the genetic integrity of the population may have been compromised by the introduction of non-native saltwater crocodiles.     

DNA Barcoding of Shark Meats Identify Species Composition and CITES-Listed Species from the Markets in Taiwan

Background

An increasing awareness of the vulnerability of sharks to exploitation by shark finning has contributed to a growing concern about an unsustainable shark fishery. Taiwan’s fleet has the 4th largest shark catch in the world, accounting for almost 6% of the global figures. Revealing the diversity of sharks consumed by Taiwanese is important in designing conservation plans. However, fins make up less than 5% of the total body weight of a shark, and their bodies are sold as filets in the market, making it difficult or impossible to identify species using morphological traits.

Methods

In the present study, we adopted a DNA barcoding technique using a 391-bp fragment of the mitochondrial cytochrome oxidase I (COI) gene to examine the diversity of shark filets and fins collected from markets and restaurants island-wide in Taiwan.

Results

Amongst the 548 tissue samples collected and sequenced, 20 major clusters were apparent by phylogenetic analyses, each of them containing individuals belonging to the same species (most with more than 95% bootstrap values), corresponding to 20 species of sharks. Additionally, Alopias pelagicus, Carcharhinus falciformis, Isurus oxyrinchus, and Prionace glauca consisted of 80% of the samples we collected, indicating that these species might be heavily consumed in Taiwan. Approximately 5% of the tissue samples used in this study were identified as species listed in CITES Appendix II, including two species of Sphyrna, C. longimanus and Carcharodon carcharias.

Conclusion

DNA barcoding provides an alternative method for understanding shark species composition when species-specific data is unavailable. Considering the global population decline, stock assessments of Appendix II species and highly consumed species are needed to accomplish the ultimate goal of shark conservation.     

Analysis of variability in vertebral morphology and growth ring counts in two Carcharhinid sharks

Inter- and intra-regional variations in vertebrae morphology and growth increment counts (band counts) were analyzed for two carcharhinid shark species, Carcharhinus plumbeus (n = 10) and C. limbatus (n = 11). Five sequential vertebrae were removed from the cervical region, above the branchial chamber and posterior to the chondrocrainium, and thoracic region, below the first dorsal fin. Dorsal–ventral height, medial–lateral breadth, and caudal–cranial length were measured for each sampled vertebra. Results indicate no significant difference in vertebral morphology within a sampled region of the vertebral column. However, a significant difference in vertebral morphology was noted between regions for both shark species, with thoracic vertebrae consistently larger than cervical vertebrae. A sub-set of three vertebrae was taken from each sampled region of each shark for sectioning and counting of growth increments. Analyses of growth increment counts by two readers indicated no significant difference in band counts within and between sampled regions.     

Phylogeography and genetic population structure of Caribbean sharpnose shark <Emphasis Type="Italic">Rhizoprionodon porosus</Emphasis>

Sharks of the genus Rhizoprionodon are among the most important predators along the coastal marine ecosystems, and they represent an important economic resource for the small-scale fisheries. To properly manage and conserve exploited shark species, detailed analyses of their population structure are needed. To evaluate the gene flow and levels of the genetic diversity among populations of the Caribbean sharpnose shark R. porosus, we identified the nucleotide sequence based on collections (n = 321 specimens) from 10 different areas, including the Caribbean Sea and several locations along the entire Brazilian coast. The analysis of 802 nucleotides from the mitochondrial DNA control region revealed 53 distinct haplotypes. The majority of these haplotypes were restricted to their collection locales with a significant genetic structure detected among the overall populations (Φ _ST  = 0.237, P < 0.0001). The data suggest a population division with two distinct management units in the western Atlantic. These management units are likely separated by the Equatorial Current. The strong population structure in R. porosus indicates that regional populations, if depleted, will not recover swiftly through immigration.     

New haplotype of the complete mitochondrial genome of <Emphasis Type="Italic">Crocodylus siamensis</Emphasis> and its species-specific DNA markers: distinguishing <Emphasis Type="Italic">C. siamensis</Emphasis> from <Emphasis Type="Italic">C. porosus</Emphasis> in Thailand

Based on molecular phylogeny of available complete mitochondrial DNA (mtDNA) genome sequences reveals that Crocodylus siamensis and C. porosus are closely related species. Yet, the sequence divergence of their mtDNA showed only a few values under conspecific level. In this study, a new haplotype (haplotype2, EF581859) of the complete mtDNA genome of Siamese crocodile (C. siamensis) was determined. The genome organization, which appeared to be highly similar to haplotype1 (DQ353946) mtDNA genome of C. siamensis, was 16,814 bp in length. However, the sequence divergence between the two genomes differed by around 7–10 and 0.7–2.1% for the haplotype1 between C. siamensis and C. porosus (AJ810453). These results were consistent with the phylogenetic relationship among the three genomes, suggesting that C. siamensis haplotype1 mtDNA genome might be the hybrid or the intraspecific variation of C. porosus. On the other hand, our specimen was found to be a true C. siamensis. Simultaneously, the seven species-specific DNA markers designed based on the distinctive site between haplotype2 mtDNA sequences of C. siamensis and haplotype1 mtDNA sequence of C. siamensis–C. porosus were successfully used to distinguish C. siamensis from C. porosus. These effective markers could be used primarily for rapid and accurate species identification in population, ecology and conservation studies.     

First evidence of multiple paternity in the blue shark (Prionace glauca)

Multiple paternity (MP) is defined as the behaviour in which females successfully mate with multiple males leading to offspring from different sires within the same litter. MP seems to be frequent and an evolutionary advantage in elasmobranchs. Here the authors report for the first time the occurrence of MP in the cosmopolitan blue shark Prionace glauca L. The evidence, gathered via microsatellite genotyping of pregnant females and their embryos, suggests that MP is very frequent in this species. Knowledge of MP in P. glauca should help describe more precisely its reproductive biology and contribute to the management of its populations.     

New insights on the trophic ecology of blue (Prionace glauca) and shortfin mako sharks (Isurus oxyrinchus) from the oceanic eastern South Pacific

The blue shark (Prionace glauca) and the shortfin mako shark (Isurus oxyrinchus) are two large and highly migratory sharks distributed in most oceans. Although they are often caught in the south Pacific Ocean long-line fisheries, their trophic ecology is poorly understood. Stable isotopes with Bayesian mixing and dependence concentration models were performed to determine the diet and trophic differences between the two species in the South-eastern Pacific Ocean. According to the mixing models, fishes are the most important prey of these sharks. Dolphin calves and remains were found in the stomachs of both species, which represents a novel finding in trophic ecology of South Pacific sharks. Intra-specific differences were found in P. glauca, but not in specimens of I. oxyrinchus. The two sharks showed a high degree of diet overlap (73%), primarily over mackerel and dolphin carcasses. Our results indicate that blue and shortfin mako sharks have a generalist feeding strategy in the eastern Pacific Ocean, with a strong preference for teleost fishes and also for dolphin carcasses. Therefore, trophic studies are useful to understand energy flow through the food web, and the trophic position of key species.     

Assessing the role of off‐take and source–sink dynamics in the extinction of the amphidromous New Zealand grayling (Prototroctes oxyrhynchus)

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Spiral valve parasites of blue and common thresher sharks as indicators of shark feeding behaviour and ecology

This study documented the parasite faunas of the spiral valves of blue sharks Prionace glauca (L. 1758) and common thresher sharks Alopias vulpinus (Bonnaterre, 1788) caught in the California Current Large Marine Ecosystem (CCLME) north of the Mexican border. The spiral valves of 18 blue and 19 thresher sharks caught in the CCLME from 2009 to 2013 were examined for parasites. Seven parasite taxa were found in blue sharks and nine in threshers. The tetraphyllidean cestode Anthobothrium sp. (78% prevalence) was the most common parasite in blue sharks, and the phyllobothriid cestode Paraorygmatobothrium sp. (90% prevalence) was the most common in threshers. An adult nematode of the genus Piscicapillaria was found in threshers for the first time and may be a new species. Adult individuals of Hysterothylacium sp. were found in both shark species. The adult acanthocephalan Rhadinorhynchus cololabis and remains of the parasitic copepod Pennella sp. – both parasites of Pacific saury, Cololabis saira – were found in the intestines of threshers, indicating recent feeding on saury. This study paves the way for a more comprehensive examination, including more samples and a wider variety of shark species, to provide a greater understanding of shark feeding behaviour and possibly provide information on shark population biology.     

Diet,trophic interactions and possible ecological role of commercial sharks and batoids in northern Peruvian waters

The Peruvian sea represents one of the most productive ocean ecosystems and possesses one of the largest elasmobranch fisheries in the Pacific Ocean. Ecosystem-based management of these fisheries will require information on the trophic ecology of elasmobranchs. This study aimed to understand the diet, trophic interactions and the role of nine commercial elasmobranch species in northern Peru through the analysis of stomach contents. A total of 865 non-empty stomachs were analysed. Off northern Peru, elasmobranchs function as upper-trophic-level species consuming 78 prey items, predominantly teleosts and cephalopods. Two distinctive trophic assemblages were identified: (a) sharks (smooth hammerhead shark Sphyrna zygaena, thresher shark Alopias spp. and blue shark Prionace glauca) that feed mainly on cephalopods in the pelagic ecosystem; and (b) sharks and batoids (Chilean eagle ray Myliobatis chilensis, humpback smooth-hound Mustelus whitneyi, spotted houndshark Triakis maculata, Pacific guitarfish Pseudobatos planiceps, copper shark Carcharhinus brachyurus and school shark Galeorhinus galeus) that feed mainly on teleosts and invertebrates in the benthonic and pelagic coastal ecosystem. This study reveals for the first time the diet of T. maculata and the importance of elasmobranchs as predators of abundant and commercial species (i.e., jumbo squid Dosidicus gigas and Peruvian anchovy Engraulis ringens). The results of this study can assist in the design of an ecosystem-based management for the northern Peruvian sea and the conservation of these highly exploited, threatened or poorly understood group of predators in one of the most productive marine ecosystems.     

A Novel Mini-DNA Barcoding Assay to Identify Processed Fins from Internationally Protected Shark Species

There is a growing need to identify shark products in trade, in part due to the recent listing of five commercially important species on the Appendices of the Convention on International Trade in Endangered Species (CITES; porbeagle, Lamna nasus, oceanic whitetip, Carcharhinus longimanus scalloped hammerhead, Sphyrna lewini, smooth hammerhead, S. zygaena and great hammerhead S. mokarran) in addition to three species listed in the early part of this century (whale, Rhincodon typus, basking, Cetorhinus maximus, and white, Carcharodon carcharias). Shark fins are traded internationally to supply the Asian dried seafood market, in which they are used to make the luxury dish shark fin soup. Shark fins usually enter international trade with their skin still intact and can be identified using morphological characters or standard DNA-barcoding approaches. Once they reach Asia and are traded in this region the skin is removed and they are treated with chemicals that eliminate many key diagnostic characters and degrade their DNA (“processed fins”). Here, we present a validated mini-barcode assay based on partial sequences of the cytochrome oxidase I gene that can reliably identify the processed fins of seven of the eight CITES listed shark species. We also demonstrate that the assay can even frequently identify the species or genus of origin of shark fin soup (31 out of 50 samples).     

Distribution patterns and predation risk of the coexisting cladocerans Bythotrephes longimanus and Leptodora kindtii in a large lake – Lake Constance

The distributions of the coexisting, planktonic, predatory cladocerans Bythotrephes longimanus and Leptodora kindtii were studied at four different stations (Langenargen-Arbon, Fischbach-Uttwil, Bregenzer Bucht and Zeller See) of a great lake, Lake Constance. The stations Langenargen-Arbon and Fischbach-Uttwil are deep (>200 m) with a high density of the coregonid fish Coregonus lavaretus, the stations Bregenzer Bucht and Zeller See are shallow (<60 m) with lower densities of coregonid fish. B. longimanus was present in the pelagic zone from mid May to November at all stations. L. kindtii generally appeared slightly later in the year than B. longimanus. Peak abundances of B. longimanus with more than 5000 ind. m^–2 (Langenargen-Arbon) appeared in late spring. During summer, when predation pressure by fish is high, abundance of B. longimanus decreased gradually. In contrast, L. kindtii displayed maximum abundances with more than 18 000 ind. m^–2 (Zeller See) in summer. During the summer months, B. longimanus lived in greater depths than L. kindtii. Differences of vertical distribution between both species were most pronounced at the deep stations (Langenargen-Arbon, Fischbach-Uttwil). Analysis of stomachs of the planktivorous fish Coregonus lavaretus showed that B. longimanus was preferred by C. lavaretus over all other prey; Ivlev's selectivity index was 0.97–0.99. Due to this high positive selection for B. longimanus by coregonids, it is surprising that the cladoceran could maintain its existence since the first recordings in 1877. Spatial refuge or indigestible resting eggs may be the underlying mechanism for this phenomenon.     

First record of a bicephalic embryo of smalltail shark Carcharhinus porosus

This study reports the first bicephalic embryo of smalltail shark Carcharhinus porosus, which was removed from a pregnant female in coastal waters of the tropical eastern Pacific Ocean. The observation suggested that although the individual's body was well formed, the malformation of the head would have affected it survival.     

Characterization of the pelagic shark‐fin trade in north‐central Chile by genetic identification and trader surveys

Shark fins have become a highly valued commodity with the major Asian fin‐trade centres supplied from global sources, including Chile. With growing concerns about the resilience of shark populations to heavy fishing pressure, there is a need for better information on shark landings to aid management efforts. In the widespread absence of shark landing records especially by species, monitoring the fin trade has been proposed as a way to assess species exploitation levels. Here, the first species assessment of the Chilean shark‐fin trade was provided. The goals of this study were to (1) determine the species composition and relative species proportion of sharks utilized in the fin trade, (2) determine the relationship between fin trader market names and species and (3) assess trader accuracy in identifying shark fin species based on fin photographs. Fins were analysed from two different fin drying facilities (n = 654) (secaderos) and two fin‐storage warehouses (n = 251). In contrast to official government landing records that only document four species in the landings, molecular species identification of the fins demonstrated that at least 10 pelagic shark species are present in the north‐central Chilean shark fin trade: Alopias superciliosus, Alopias vulpinus, Carcharhinus obscurus, Galeorhinus galeus, Isurus oxyrinchus, Isurus paucus, Lamna nasus, Prionace glauca, Sphyrna lewini, Sphyrna zygaena. The species composition of the fins from the secaderos was P. glauca (83·9%), I. oxyrinchus (13·6%), L. nasus (1·7%) and A. superciliosus (0·2%). There was generally good agreement between market names and single shark species for the trade categories ‘Azulejo’, ‘Tiburon’, ‘Tintorera’, ‘Cola de zorro’ and ‘Martillo’. In contrast, the market category ‘Carcharhinus’ consisted of a mixture of at least five species. The molecular results also identified two species (S. lewini and I. paucus) not previously recorded in Chilean waters. The fin identification survey given to nine regional traders demonstrated that they were highly accurate in recognizing pictures of fins from P. glauca and I. oxyrinchus. The overall strong concordance between market categories and fins from single species and the trader accuracy in survey fin identification suggests that monitoring the Chilean fin trade by market names will provide a reasonably accurate picture of the volume of sharks landed by species.     

Survival and growth of hatchling Crocodylus porosus in saltwater without access to fresh drinking water

Summary It has been suggested that C. porosus select nest sites which provide a source of freshwater for hatchlings during the dry season. From a mark-recapture study, we conclude that hatchling C. porosus can survive and grow in hyperosmotic saltwater without drinking freshwater. Hence, the siting of nests is unlikely to be the consequence of a requirement by hatchlings for freshwater. Considered along with other information, our observations imply that hatchling C. porosus have functional salt glands.     

Cytometric determination of genome size and base composition of tree species of three genera of Casuarinaceae

The genome size and base composition of diploid plant species from three genera of the Casuarinaceae family were determined by flow cytometry. Casuarina glauca Sieb. ex Spring. and Gymnostoma deplancheana (Miq.) L. Johnson showed a small genome with 2C = 0.70 pg, 58.6% AT, 40.5% GC for the first species and 2C = 0.75 pg, 58.7% AT, 40.5% GC for the second. Allocasuarina verticillata (Lam.) L. Johnson had a larger genome: 2C = 1.90 pg, 59.3% AT, 41.1% GC. One haploid genome of C. glauca is therefore about 340×10⁶ base pairs. In leaves, roots or bark of these three species, polysomaty was virtually absent: a maximum frequency of 4C nuclei of only 0.08 was found in bark of C. glauca. The genome sizes of C. glauca and G. deplancheana are among the smallest described for higher plants. Small genome size, diploidy and the absence of polysomaty are advantageous traits for facilitating molecular approaches to improvement of these actinorhizal plants and developing the study of their symbiotic interactions with Frankia. Received: 20 December 1997 / Revision received: 13 March 1998 / Accepted: 30 March 1998