Specific Detection of Pacific Oyster (Crassostrea gigas) Larvae in Plankton Samples Using Nested Polymerase Chain Reaction

Management of sustainable Pacific oyster fisheries would be assisted by an early, rapid, and accurate means of detecting their planktonic larvae. Reported here is an approach, based on polymerase chain reaction (PCR), for the detection of Pacific oyster larvae in plankton samples. Species-specific primers were designed by comparing partial mitochondrial cytochrome oxidase subunit I (COI) sequences from Crassostrea gigas, with other members of the family Ostreidae including those of Crassostrea angulata. Assay specificity was empirically validated through screening DNA samples obtained from several species of oysters. The assay was specific as only C. gigas samples returned PCR-positive results. A nested PCR approach could consistently detect 5 or more D-hinge-stage larvae spiked into a background of about 146 mg of plankton. The assay does not require prior sorting of larvae. We conclude that the assay could be used to screen environmental and ballast water samples, although further specificity testing against local bivalve species is recommended in new locations.     

Mitochondrial and nuclear DNA phylogeography of Crassostrea angulata, the Portuguese oyster endangered in Europe

The respective status of the Portuguese oyster, Crassostrea angulata, and the Pacific oyster, Crassostrea gigas, has long been a matter of controversy. Morphological and physiological similarities, homogeneity of allozyme allelic frequencies between populations of the two taxa and the demonstration of hybridization lead most authors to suggest that they should be regrouped within the same species. The risk of introgression and the present expansion of C. gigas aquaculture in Europe raises the question of the need for preservation of C. angulata in Europe, as only a few populations remain. We studied European and Asian populations of C. gigas and C. angulata using microsatellite and mitochondrial DNA markers to estimate their genetic diversity and differentiation. The analysis of genetic distances and the distribution of allelic and haplotype frequencies revealed significant genetic differences between taxa, showing two clusters: (1) C. gigas French and Japanese populations and (2) C. angulata Portuguese and Taiwanese populations. The Asian origin of the Crassostrea angulata taxa is therefore confirmed. Unlike previous studies based on allozymes, significant nuclear genome differences were noted between C. angulata and C. gigas. Despite the presumed history of the introduction of C. angulata into Southern Europe, these populations did not show any significant reduction of variability compared to Taiwanese populations. Any conservation plans for European C. angulata populations should take its non-native origin into account. They represent a valuable genetic resources for European breeding program.     

A cDNA Microarray for Crassostrea virginica and C. gigas

The eastern oyster, Crassostrea virginica, and the Pacific oyster, C. gigas, are species of global economic significance as well as important components of estuarine ecosystems and models for genetic and environmental studies. To enhance the molecular tools available for oyster research, an international group of collaborators has constructed a 27,496-feature cDNA microarray containing 4460 sequences derived from C. virginica, 2320 from C. gigas, and 16 non-oyster DNAs serving as positive and negative controls. The performance of the array was assessed by gene expression profiling using gill and digestive gland RNA derived from both C. gigas and C. virginica, and digestive gland RNA from C. ariakensis. The utility of the microarray for detection of homologous genes by cross-hybridization between species was also assessed and the correlation between hybridization intensity and sequence homology for selected genes determined. The oyster cDNA microarray is publicly available to the research community on a cost-recovery basis.     

The internal transcribed spacer 2 region of the nuclear ribosomal DNA and the phylogeny of the moss family Hylocomiaceae

Eichhornia azurea is a tristylous species of Pontederiaceae. Moderate self-incompatibility accompanies the floral heteromorphism of this species.Eichhornia azurea is almost exclusively visited by one bee species,Ancyloscelis gigas (Anthophoridae), in South Brazil. This species has an extremely long proboscis covered with recurved hairs. Bees use these hairs to collect pollen from the anthers placed inside the narrow perianth tube ofE. azurea. Analyses of the pollen load ofA. gigas females show that they are flower constant and carry pollen from all three anther levels. The behavior ofA. gigas and its proboscis morphology make this bee species narrowly adapted and an effective pollinator for facilitating legitimate pollination ofE. azurea flowers in southern Brazil.     

The first-stage zoeas of Carpilius convexus (Forskal, 1775) and Carpilius maculatus (Linnaeus, 1758) (Crustacea: Decapoda: Brachyura: Xanthoidea: Carpiliidae): an example of heterochrony

The first-stage zoeas of Carpilius convexus (Forskål,1775) and Carpilius maculatus (Linnaeus, 1758) are describedand fully illustrated. Both these Indo-West Pacific speciesexhibited a unique xanthoidean character for the basis of thesecond maxilliped, which possesses five (arranged 1,1,1,2) setaeinstead of the expected four (arranged 1,1,1,1). A comparisonwith the zoeal stages of Carpilius corallinus (Herbst, 1783)as reported by Laughlin et al. (Laughlin et al., 1983) revealedmarked differences including the possession of carapace lateralspines (v. absent in C. convexus only), the subterminal setationof the distal maxillule endopod segment with two subterminalsetae (versus one subterminal seta in Indo-West Pacific species),the terminal setation of the distal maxillule endopod segmentwith four setae (versus three setae in C. convexus only), twolateral spines on the telson (versus three in Indo-West Pacificspecies) and the number of zoeal stages. The first-stage zoeasof the two Indo-West Pacific species appear to have hatchedin a more advanced state of development than those of C. corallinus,and the expression of a number of characters has been accelerated(early onset). In fact, the zoeal stages of both Indo-West Pacificspecies and carpiliid species appear to be abbreviated becausethe first zoeas are considered to be equivalent to the third-stagezoeas of C. corallinus.     

New record for Halophila decipiens Ostenfeld in Kenya based on morphological and molecular evidence

The seagrass Halophila decipiens Ostenfeld was recorded for the first time in Kenya in 2003. It was growing in subtidal mixed meadows with H. ovalis in protected bays at a depth of 3 m. DNA sequence analysis and morphological characteristics confirmed the identification. It is possible that this species is more widely distributed in the east African region. There was very little sequence differentiation between the Kenyan H. decipiens and the other samples in the Indo-West Pacific, and between this region and the Atlantic Ocean, further validating from an evolutionary perspective recent dispersal of this species.     

Assessment of hidden diversity of crinoids and their symbionts in the Bay of Nhatrang,Vietnam

Crinoid associates represent an abundant and diverse, but poorly explored, component of the hidden biodiversity of coral-reef ecosystems. We studied data from 5 years of collecting in the Bay of Nhatrang (BN), Vietnam, to assess the diversity of crinoids and their symbionts, to compare it with other areas of the Indo-West Pacific, and to elucidate the extent to which the observed diversity of crinoids and their symbionts corresponds to their true diversity. In total, about 2,287 specimens of symbionts belonging to 70 species were found on 203 specimens of crinoids belonging to 33 species. Among the crinoids, the most numerous species were Himerometra robustipinna (36 specimens) and Cenometra bella (29 specimens), among the symbionts the polychaete Paradyte crinoidicola (c. 850 specimens) and the galatheid crustacean Allogalathea elegans (180 specimens). Species accumulation curves suggest that we have sampled most of the crinoid diversity in the BN, whereas the diversity of their symbionts remained undersampled. Estimated species richness of crinoids was higher than previously observed richness, and varied from 39 (estimated by bootstrap) to 46 (jackknife 2). Estimated species richness of symbionts was higher than observed richness, and varied from 71 (bootstrap) to 93 (jackknife 2). We suggest a slight increase in the number of crinoid species to result from more detailed studies of nocturnal species, and an increase in the number of symbiotic species when studies of nocturnal crinoid associates and sibling species among decapods are included. Our study revealed a rather rich crinoid fauna in the bay compared to other areas of the Indo-West Pacific, and the highest species richness of crinoid associates known from anywhere in the World Ocean.     

The Distribution of an Introduced Mollusc and its Role in the Long-term Demise of a Native Confamilial Species

The estuarine mud snail, Batillaria attramentaria, was transported to the Pacific coast of North America with the Pacific oyster, Crassostrea gigas (C. gigas), imported from Japan in the early part of this century, and has proliferated in several bays where the oyster was introduced. Since the arrival of Batillaria there have been declines in populations of its native ecological equivalent, Cerithidea californica. This study documents the distribution of the exotic Batillaria throughout its entire introduced range, concentrating on the few bays in northern California where both snails exist sympatrically. Using dates of initial importation of C. gigas and dates of first documentation of Batillaria within a bay, I established the earliest possible date for the introduction of Batillaria in a particular area. In cases where Cerithidea also was, or had been, present within a bay, I calculated a range of time for either the continued coexistence of the two species or the time until local exclusion of the native. Density measurements of Cerithidea within these bays where the species co-occurred allowed comparison of present Cerithidea numbers to historical accounts. Results indicated that Batillaria is replacing Cerithidea in the northern marshes of California. This replacement of the northernmost Cerithidea populations is not only reducing Cerithidea's overall range, but also eliminating a race recently shown to be a genetically distinct from southern Cerithidea populations. Other studies that have demonstrated superior exploitative competitive ability by Batillaria provide a potential mechanism for this displacement pattern. Regardless, the results presented here indicate that the displacement process is slow, taking on average >50 years to complete. This study illustrates a gradual, but predictable process of exotic replacement of native species, and argues strongly against complacency toward invaders that may currently seem innocuous. This revised version was published online in July 2006 with corrections to the Cover Date.     

Development and characterization of microsatellite markers for a mangrove tree species Sonneratia caseolaris (L.) Engler (Lythraceae sensu lato)

Sonneratia caseolaris is a typical non-viviparous mangrove species and a key component of mangrove community in the Indo-West Pacific region. Here we isolated nine microsatellite simple sequence repeat (SSR) loci from the genome of S. caseolaris. Our isolated loci provided SSR markers with polymorphism of 2–6 alleles per locus. The expected and observed heterozygosities ranged from 0.242 to 0.745 and from 0.083 to 0.417, respectively. Cross-species amplification in S. alba and S. ovata showed that a subset of these markers holds promise for these congeneric species. These polymorphic SSR markers would be useful tools for population genetics studies on S. caseolaris as well as other congeneric species.     

Geographic distribution of the bathypelagic genus paraeuchaeta (Copepoda,Calanoida)

The geographic distribution of the bathypelagic calanoid genus Paraeuchaeta was investigated by examining midwater trawl and plankton net samples collected mostly from depths exceeding 1000 m throughout the world's oceans. Of the 81 species referred to Paraeuchaeta, the geographic ranges of about 50 species could be defined with reasonable certainty. Contrary to early authors, the number of species having a worldwide distribution was surprisingly small (12 species or 15% of the 81 species of the genus) as compared to common species endemic to various geographic regions (34 species or 42% of the total of 81). Almost twice as many species were found in the Indo-Pacific Ocean as in either the Atlantic or the Southern Ocean. Faunistically, the northern Atlantic, mid-Atlantic, northern Pacific, East Pacific, Indo-West Pacific, and Southern Ocean were distinct in terms of endemic species. A number of species were found to be endemic to highly productive areas, where they were usually very abundant. Rare species, on the other hand, were generally found to be widely distributed, although some were too rare for their range to be determined with certainty. To explain these findings, the following hypothesis is proposed: Bathypelagic calanoids endemic to and abundant in eutrophic areas are those adapted to eutrophic conditions of their habitats and therefore cannot expand their ranges into contiguous oligotrophic waters even if the other environmental conditions are favorable. Other species, on the other hand, generally have extensive geographic ranges because of their survival ability in widely expanding oligotrophic conditions and the absence of physicochemical barriers at bathypelagic depths of the world's oceans.     

柔鱼科近缘种茎柔鱼与鸢乌贼营养生态位及相互关系

同域近缘种由于进化选择的压力,会形成不同的行为适应策略。研究同域近缘种生态位格局,有助于理解近缘物种的竞争和共存机制,是深入了解种群动态变化的基础性问题。选取东太平洋赤道海域的柔鱼科头足类近缘种茎柔鱼和鸢乌贼为研究对象,利用生物地球化学示踪物(稳定同位素和脂肪酸)分析两种头足类的营养生态位及相互关系。结果显示,茎柔鱼和鸢乌贼肌肉的部分必需脂肪酸(C18∶2n6、C20∶2n6、C20∶3n3、C20∶4n6和C20∶5n3)含量存在差异,说明二者食物来源不同,但其碳、氮稳定同位素比值无显著差异,可能是因为相同个体大小的茎柔鱼和鸢乌贼营养级相近,且摄食空间相似。这些结果在营养生态位的分析结果中也得到了验证,稳定同位素营养生态位的重叠程度高于脂肪酸营养生态位,表明脂肪酸组成更能体现同域近缘种的食性差异。本研究可加深对头足类进化过程中摄食行为适应机制的理解,并为评估同域近缘种的营养生态位关系提供有益参考。     

A new species,Gazza rhombea, from the Indo-West Pacific, with a redescription ofG. achlamys Jordan & Starks, 1917 (Perciformes: Leiognathidae)

Gazza rhombea sp.nov. is described from 61 type and 81 non-type specimens, 19–176 mm in standard length, collected from the Indo-West Pacific. The species is similar to other congeners in general body appearance, differing from them in having the dorsolateral surface of the body scaled anterior to the dorsal fin origin, but not reaching to a vertical through the tip of the posterior branch of the supratemporal canal (vs. dorsolateral surface of body naked anterior to base of sixth or seventh dorsal fin spine base inG. achlamys; dorsolateral surface of body with scales extending anteriorly beyond tip of posterior branch of supratemporal canal inG. minuta), and having a long narrow anterodorsal extension from the subocular silvery region, in contact with the orbit only proximally (vs. broad anterodorsal extension, with proximal and distal contact with orbit inG. dentex).Gazza rhombea is also distinguishable fromG. achlamys andG. minuta by the morphology of the first dorsal fin pterygiophore, and the neural and hemal spines of the fifth preural centrum. The new species has usually been misidentified asG. achlamys, which is redescribed here, owing to its similarly deep-bodied appearance.     

Two new species of <Emphasis Type="Italic">Kyphosus</Emphasis> (Kyphosidae) and a taxonomic review of <Emphasis Type="Italic">Kyphosus bigibbus</Emphasis> Lacepède from the Indo-Pacific

Two new species of Kyphosus, K. pacificus and K. hawaiiensis, are described and the taxonomy reviewed of K. bigibbus Lacepède, 1801, closely related to the former. These three species are clearly distinguished from other species of Kyphosus in having 12 dorsal-fin soft rays, the anterior part of the dorsal-fin soft-rayed portion not elevated, 11 anal-fin soft rays, and 58–72 (usually more than 59) scales in longitudinal row along the middle body. Kyphosus pacificus is distributed in the Western-Central Pacific, being characterized by a pointed snout and 26–29 gill rakers (mode 27). Kyphosus hawaiiensis is distributed only in the Central Pacific and is characterized by a blunt snout, 23–25 gill rakers (mode 24), 18 pectoral fin soft rays, and the anterior part of the anal-fin soft-rayed portion well elevated. Kyphosus bigibbus is distributed antitropically in the Indo-West Pacific and is characterized by a blunt snout, 21–24 gill rakers (mode 22), 19 pectoral fin soft rays, and the anterior part of the anal-fin soft-rayed portion not elevated. In addition, Pimelepterus fallax Klunzinger, 1884 was found to be a junior synonym of K. bigibbus Lacepède. A lectotype and paralectotypes are designated for the former because the original type series included an example of a second species.     

The Sphyraena obtusata group (Perciformes: Sphyraenidae) with a description of a new species from southern Japan

Sphyraena iburiensis sp. nov. is described, and taxonomic reviews are provided for S. obtusata and S. pinguis. These species, characterized by having 2 gill rakers, are defined as the S. obtusata group. Sphyraena iburiensis, known only from the Pacific coast of southern Japan, is characterized by 8.5–9.5 scales above the lateral line, a single row of scales in the groove along the lower margin of the suborbital region from the posterior tip of the maxilla to below the eye (=suborbital groove) not covered with skin, 2 distinct longitudinal stripes on the lateral surface of the body when fresh (upper stripe usually lost in preserved specimens), the lower stripe reaching the caudal-fin base just below the lateral line. Sphyraena obtusata, distributed in the Indo-West Pacific, is characterized by 5–7.5 scales above the lateral line, a single row of scales in the suborbital groove covered with skin, 2 somewhat indistinct longitudinal stripes on the lateral surface of the body when fresh (upper stripe usually lost in preserved specimens), the lower stripe joining the lateral line midway between the end of the second dorsal-fin base and caudal peduncle and extending to the middle of the caudal-fin base. Sphyraena pinguis, distributed in the Indo-West Pacific, is characterized by 7.5–9.5 scales above the lateral line, a single row of scales in the suborbital groove not covered with skin, and a single longitudinal stripe on the lateral surface of the body joining the lateral line slightly before or just below the end of the second dorsal-fin base and extending to the middle of the caudal-fin base. Seven (S. aureoflammea, S. brachygnathos, S. flavicauda, S. grandisquamis, S. langsar, S. lineata, and S. strenua) and 2 (S. chrysotaenia and S. schlegelii) nominal species are regarded as junior synonyms of S. obtusata and S. pinguis, respectively. In addition, lectotypes are designated for S. flavicauda, S. langsar, S. lineata, and S. obtusata. A key to the three species of the S. obtusata group is provided.     

The Leiognathus splendens complex (Perciformes: Leiognathidae) with the description of a new species, Leiognathus kupanensis Kimura and Peristiwady

Taxonomic analysis of a group of morphologically similar ponyfishes (Perciformes: Leiognathidae) establishes the Leiognathus splendens complex comprising four valid species: L. jonesi James, 1971, widely distributed in the Indo-West Pacific, from Mauritius to Papua New Guinea, north to Hainan I. (China), and south to Brisbane, Australia; L. kupanensis sp. nov., currently known only from Kupang, Timor, Indonesia; L. rapsoni Munro, 1964, currently known only from India, Indonesia, and Papua New Guinea, and L. splendens Cuvier, 1829, widely distributed in the eastern Indian and western Pacific oceans, from India to Papua New Guinea, and from southern Japan to northern Australia. The L. splendens complex can be defined by the following combination of characters: body depth 42–60% of standard length; mouth protruding downward; slender, minute teeth uniserially on jaws; lower margin of orbit above the horizontal through the gape when mouth closed; breast almost completely scaled; lateral line complete, and a dark blotch on top of spinous dorsal fin. Diagnostic characters of the members are as follows: L. jonesi—anterior dorsolateral body surface with a semicircular naked area on nape, and a paler dark blotch on spinous dorsal fin; L. kupanensis—anterior dorsolateral body surface widely naked; L. rapsoni—cheek scaled; L. splendens—anterior dorsolateral body surface completely scaled and a jet black blotch on spinous dorsal fin.     

Diversity,habitats and size-frequency distribution of the gastropod genus Conus at Dahab in the Gulf of Aqaba,Northern Red Sea

Topographically complex subtidal reefs of the Indo-West Pacific region are characterised by a high species richness of cone snails of the genus Conus (up to 36 on some reefs) but low population densities (≤1 individual/m²), whereas Conus assemblages on reef flats usually support fewer species (5–9) and high population densities (up to 5.2 individuals/m²). Subtidal sand areas are known to be least species-rich (1–6 species). Although the diversity of this predatory gastropod genus has been described previously from different areas of the Indo-Pacific, little ecological information is available on Conus in the Northern Red Sea. Therefore, data from five habitat types were obtained along 73 line-transects (245?m²⁾, which yielded ecological data for a total of 175 individuals of 9 species. In accordance with former findings, our results demonstrate that the reef flat was the habitat with the highest observed population densities (6.15 individuals/m²) but low species diversity (H’ = 0.9; 5 species); subtidal reefs, in contrast, were characterised by low densities (0.13 individuals/m²) and a relatively high species diversity (H ‘= 1.5; 6 species). This suggests that Conus diversity and species richness in the Northern Red Sea around Dahab is lower than in other parts of the Indo-West Pacific region. Furthermore, hardand soft substrata were dominated by different Conus species in accordance to the distribution of favourable microhabitat patches, the degree of physical stress and the availability of refuges and prey organisms. The fact that these Conus were predominantly small-bodied vermivores (size range: 6–85?mm; mean shell size: 15?mm; SD = 9?mm) suggests that this size class possesses an advantage over molluscivores and piscivores. Except for subtidal reefs, which showed a highly variable species composition, the studied habitat types around Dahab were characterised by distinct assemblages of Conus.     

Zoogeography and the predator-prey ‘arms race:’ A comparison of eriphia and nerita species from three faunal regions

We measured maximum shell diameters and thicknesses of Nerita funiculata Menke and N. scabricosta Lamarck (Gastropoda: Neritidae), and claw sizes and carapace widths of the predatory crab Eriphia squamata Stimpson (Brachyura: Xanthidae), from the Gulf of California (Eastern Pacific). We also tested the ability of E. squamata to crush Nerita shells of various sizes. We compared this data on predator-prey counteradaptations with previously published data for congeneric species from the Western Atlantic and Indo-West Pacific regions. In relative abilities of the crabs to crush gastropod shells, and of the gastropod shells to resist such crushing, the Eastern Pacific species were stronger than their counterparts in the Western Atlantic, but weaker than their Indo-West Pacific congeners, indicative of an intermediate level of faunal dominance or predator-prey arms race escalation.     

Phylogenetic and morphometric differentiation reveal geographic radiation and pseudo-cryptic speciation in a mangrove crab from the Indo-West Pacific

The presence of boundaries to dispersal has been recently documented for many Indo-West Pacific (IWP) species with planktonic propagules and a widespread distribution. We studied the phylogeography of the mangrove crab Neosarmatium meinerti (Brachyura: Sesarmidae) and the phylogenetic relationship to its presumed sister species N. fourmanoiri in the IWP in order to compare intraspecific with interspecific diversity. Portions of the mitochondrial genes 16S and CoxI were sequenced for 23 specimens of N. meinerti and 5 N. fourmanoiri, while a fragment of the 28S was obtained for a subset of specimens. Genetic data are supplemented by morphometric and based on 37 adult males of N. meinerti and 9 males of N. fourmanoiri.The conserved nuclear 28S reveals the existence of a genetic break between the Indian and Pacific oceans. Otherwise, mitochondrial genes as well as morphometry clearly support the presence of a species complex within N. meinerti composed by four well structured and geographically defined lineages: East African coast; western Indian Ocean islands; South East Asia; and Australia.     

Biases in determining the diet of jumbo squid <Emphasis Type="Italic">Dosidicus gigas</Emphasis> (D’ Orbigny 1835) (Cephalopoda: Ommastrephidae) off southern-central Chile (34°S–40°S)

The diet of jumbo squid (Dosidicus gigas) off southern-central Chile is described to examine potential biases in the determination of their main prey. Specimens were collected from catches using different fishing gear (jigging, trawl and purse-seine), from July 2003 to January 2004, and from December 2005 to October 2006. The stomach contents were analyzed in terms of frequency of occurrence, number, and weight of prey items and the diet composition was analyzed using Detrended Correspondence Analysis. In the industrial purse-seine fleet for jack mackerel (Trachurus murphyi), the dominant prey of D. gigas was T. murphyi. In the industrial mid-trawl fishery for Patagonian grenadier (Macruronus magellanicus), the dominant species in the diet of D. gigas was M. magellanicus. Similarly, Chilean hake (Merluccius gayi) was the main prey in the diet of D. gigas obtained in the industrial trawl fishery for Chilean hake; and, in both artisanal fisheries (purse-seine for small pelagics and jigging), small pelagic fish and D. gigas were the main prey in the stomach contents of D. gigas. Cannibalism in D. gigas varied between different fleets and probably is related to stress behavior during fishing. The Detrended Correspondence Analysis ordination showed that the main prey in the diet of D. gigas is associated with the target species of the respective fishery. Consequently, biases are associated with fishing gear, leading to an overestimate in the occurrence of the target species in the diet. We recommend analyzing samples from jigging taken at the same time and place where the trawl and purse-seine fleets are operating to avoid this problem, and the application of new tools like stable isotope, heavy metal, and fatty acid signature analyses.