AreAcila divaricata and Acila mirabilis One Species or Two Distinct Species？ Evidence from COI Mitochondrial DNA

Acila divaricata （Hinds, 1843） and A. mirabilis （Adams and Reeve, 1850） are common benthic bivalves in China. A number of researchers have proposed that the latter species is a junior synonym of the former species. Because of morphological similarities, it is difficult to distinguish these two species based on visual examination only. For better understanding of their taxon-omy, the mitochondrial CO1 gene fragments of five individuals of A. divaricata from the East China Sea and six individuals of A. mirabilis from the Yellow Sea were sequenced in this study. The phylogenetic relationships of the obtained COI sequences, together with nineteen sequences of three species of the genus Nucula, were analyzed. The pairwise intra- and inter-specific distances for the CO1 sequences ranged from 0.002 to 0.017 and from 0.128 to 0.134, respectively, and no overlap was found. Phylogenetically, A. divaricata and A. mirabilis form distinct clades and cluster into a sister to all other Nucula species. The results indicated that A. di-varicata and A. mirabilis are two distinct species. The differences in the morphology and distribution between the two species were briefly discussed.     

A new record of Sebastes koreanus from China based on morphological characters and DNA barcoding

A new record of Sebastes koreanus(Kim and Lee,1994) was documented based on morphological characters and DNA barcoding. Fifty-six S ebastes specimens were collected from the coastal waters of northern China. Samples were identified as S. koreanus based on morphological characters. The coloration and morphometric measurements were consistent with those described from specimens collected in South Korea. In this study,specimens had the following morphological characteristics:light brown body with dark stripes and tiny dark spots,4–5 wide indistinct vertical patterns on the side,2 radial stripes behind and below the eyes,1 large dark blotch on the opercle. Additionally,the following meristic characters were recorded:dorsal fin XIV-13,pectoral fin 16,anal fin III-6–7,pelvic fin I-5,lateral line scales 29–30,and vertebrae 26. The fragment of cytochrome oxidase subunit I(C OI) gene of mitochondrial DNA was sequenced for phylogenetic analysis. The mean genetic distance within the species was 0.3%. Net genetic distances between S. koreanus and other S ebastes species ranged from 3.1% to 7.6%,which was greater than the threshold for species delimitation. The phylogenetic analysis strongly supports the validity of S. koreanus in China at the genetic level. The origion,evolution,patterns of speciation and unique features in genome divergence among primate lineages of this species still need future directions of research.     

A Preliminary Phylogenetic Analysis ofLuidia （Paxillosida： Luidiidae） from Chinese Waters with Cytochrome Oxidase Subunit I （COI） Sequences

Luidia Forbes （Paxillosida： Luidiidae） are common soft bottom sea stars with 49 described species. Because of substan- tial morphological diversity, the taxonomy of the genus is complex and hasn＇t been resolved definitely. In order to resolve general taxonomic issues, and determine species boundaries and phylogenetic relationships within the genus Luidia, the sequences of tyro- chrome oxidase subunit I （COI） gene from 24 specimens of Luidia, belonging to eight taxa in Chinese waters, were studied. Three sequences of two species in genus Luidia from GenBank were used to analyze the phylogenetie relationships. The molecular phy- logeny exhibited three main clades, each with strong bootstrap support： Clade A including Luidia quinaria from the Sea of Japan; Clade B including seven nominal species （L. quinaria von Martens, L. yesoensis Goto, L. ehangi Liu, Liao and Li, L. orientalis Fisher, L. avicularia Fisher, L. longispina Sladen and L. hardwicki Gray） from Chinese waters; and Clade C including L. maculata Miiller ＆ Troschel from Chinese waters. Our molecular phylogeny results support the morphological Quinaria-Group and Alter- nata-Group assigned by D6derlein. Seven nominal species we sampled do not exhibit genetic distances that are large enough to rec- ognize them as separate species. Cryptic species may exist in ＇Luidia quinaria＇ from the Yellow Sea and the Sea of Japan. Meaning- ful morphological characters need further investigation in Luidia.     

DNA barcode assessment of Ceramiales (Rhodophyta) in the intertidal zone of the northwestern Yellow Sea

A total of 142 specimens of Ceramiales(Rhodophyta) were collected each month from October 2011 to November 2012 in the intertidal zone of the northwestern Yellow Sea. These specimens covered 21 species,14 genera,and four families. Cluster analyses show that the specimens had a high diversity for the three DNA markers,namely,partial large subunit r RNA gene(LSU),universal plastid amplicon(UPA),and partial mitochondrial cytochrome c oxidase subunit I gene(COI). No intraspecific divergence was found in our collection for these markers,except for a 1–3 bp divergence in the COI of Ceramium kondoi,Symphyocladia latiuscula,and Neosiphonia japonica. Because short DNA markers were used,the phylogenetic relationships of higher taxonomic levels were hard to evaluate with poor branch support. More than half species of our collection failed to find their matched sequences owing to shortage information of DNA barcodes for macroalgae in Gen Bank or BOLD(Barcode of Life Data) Systems. Three specimens were presumed as H eterosiphonia crispella by cluster analyses on DNA barcodes assisted by morphological identification,which was the first record in the investigated area,implying that it might be a cryptic or invasive species in the coastal area of northwestern Yellow Sea. In the neighbor-joining trees of all three DNA markers,H eterosiphonia japonica converged with D asya spp. and was distant from the other Heterosiphonia spp.,implying that H. japonica had affinities to the genus Dasya. The LSU and UPA markers amplified and sequenced easier than the COI marker across the Ceramiales species,but the COI had a higher ability to discriminate between species.     

Cylindrotheca closterium Is a Species Complex as Was Evidenced by the Variations of rbcL Gene and SSU rDNA

The genus Cylindrotheca consists of a small group of marine diatoms with a few species described. Eleven isolates of diatoms identified as Cylindrotheca closterium morphologically were obtained from Jiaozhou Bay with their nuclear-encoded small-subunit ribosomal RNA （SSU rDNA） and chloroplast-encoded rbcL gene sequences determined in this study. Interestingly, very high sequence divergences of SSU rDNA and rbcL gene were found among these isolates, and numerous nucleotide variation of rbcL gene caused relatively few variation of deduced amino acid sequence. Phylogenetic analyses based on SSU rDNA and rbcL gene, respectively, grouped the isolates into 6 clades. Phylogenetic tree of SSU rDNA placed all the Cylindrotheca isolates together, separating them into two lineages clearly. LineageⅠ was composed of the eleven C. closterium isolates obtained in this study together with another C. closterium isolate, but some clades were not well supported. LineageⅠwas contained two C. closterium isolates and one C. fusiformis isolate. Phylogenetic analysis of rbcL gene also separated the Cylindrotheca isolates into two well-defined lineages. The eleven C. closterium isolates formed a lineage and all clades were supported strongly. Statistical comparisons of SSU rDNA indicated that the average distance within lineageⅠwas significantly higher than that of other microalgae species （P 〈0.01）. These results suggested the existence of cryptic species within C. closterium.     

A New Record of Ponyfish Deveximentum megalolepis(Perciformes: Leiognathidae) in Beibu Gulf of China

A new record ponyfish, Deveximentum megalolepis Mochizuki and Hayashi, 1989, was documented based on its morphological characteristics and DNA barcode. Fifty specimens were collected from Beibu Gulf of China and identified as D. megalolepis by morphological characterization. The coloration, meristic traits, and morphometric measurements were consistent with previously published records. In general, it is a silver-white, laterally compressed and deep bodied ponyfish with 6–9 rows of scales on cheek; scale rows above lateral line 6–8; scale rows below lateral line 14–17. Mitochondrial cytochrome oxidase I subunit(COI) gene fragment was sequenced for phylogenetic analysis. There is no sequence variation of COI gene between the specimens collected in this study. The genetic distances between D. megalolepis and other congeneric species range from 3.6% to 14.0%, which were greater than the threshold for fish species delimitation. The COI sequence analysis also supported the validity of D. megalolepis at genetic level. However, the genetic distance between Chinese and Philippine individuals was about 1.2% and they formed two lineages in gene tree, which may be caused by the geographical distance.     

Molecular Phylogeny ofParapenaeopsis Alcock, 1901（Decapoda： Penaeidae） Based on Chinese Materialsand 16S rDNA and COI Sequence

The phylogenetic relationship among Chinese Parapenaeopsis species was studied by comparing 16S rDNA and CO1gene sequence. The results showed that Parapenaeopsis hardwickii （Miers, 1878） and P cultrirostris Alcock, 1906 identified fromChinese samples were the same species. Parapenaeopsis cornuta （Kishinouye, 1900）, P. incisa Liu and Wang, 1987, and P. sinicaLiu and Wang, 1987 were different species. However, their systematic relationship were closer than those of other species, and theyformed an advanced branch in the phylogenetic trees. Additionally, the systematic position of P. hardwickii （Miers, 1878）, P. hun-gerfordi Alcock, 1905, and P. tenella （Bate, 1888） were not stable in the phylogenetic trees. More genetic markers such as 18S rDNAand 28S rDNA were supposed to be used to confirm the phylogenic relationship of Parapenaeopsis species.     

Phylogenetic analysis of cultivable bacteria isolated from Arctic sea-ice

Phylogenetic analysis based on 16S rDNA of 8 strains of cultivable bacteria isolated from Arctic sea-ice was studied.The results showed that strain BJ1 belonged to genus Planococcus,which was a genus of low mole percent G C gram-positive bacteria;strain BJ6 belonged to genus Burkholderia of β-proteobacteria and the rest 6 strain all belonged to γ-proteobacteria,of which strain BJ8 was a species of Pseudoalteromonas,strain BJ2-BJ5 and BJ7 were members of genus Psychrobacter.Phylogenetic analysis also indicated that bacteria of genus Psychrobacter of the isolates formed a relatively independent phylogenetic cluster in comparison with other bacteria belonged to genus Psychrobacter.     

Molecular identification based on ITS sequences for Kappaphycus and Eucheuma cultivated in China

The systematic classification of the Eucheumatoideae is difficult because of their variable morphology and interpretation of reproductive structures. Kappaphycus and Eucheuma specimens cultivated on the Hainan and Fujian coast of China were introduced from Vietnam, the Philippines and Indonesia. Combined with morphological characteristics, all Kappaphycus and Eucheuma cultivated strains were identified by internal transcribed spacer (ITS) sequences. The phylogenetic tree was constructed using neighbor-joining and maximum likelihood methods. The results indicate that different ITS sequence lengths occurred in the different genera and species. An obvious difference in morphology could be found in the protuberance shape between Kappaphycus and Eucheuma. The protuberance in Eucheuma was thorn-like and in Kappaphycus was wartlike or papillate. Their ITS sequence lengths differed significantly in nucleotide variation rates up to 58.55%-63.90%. All nucleotide variations occurred in the ITS1 and ITS2 regions except for five nucleotide transversions in the 5.8S rDNA region. In addition, the difference was at the branches among congeneric species. Kappaphycus sp. had branches with small buds, while K. alvarezii did not have such a feature. The nucleotide variation rates varied from 7.02% to 7.48% among species; within the same species of the clades it was <1.20%. Eucheumatoideae algae cultivated in China consisted of three clades, K. alvarezii, Kappaphycus sp., and E. denticulatum. The results indicate that ITS sequence analysis was an effective way for identification of interspecies and intraspecies phylogenetic relationships and might provide a clue for molecular identification of algal Eucheumatoideae.     

Virescentia guangxiensis(Batrachospermales,Rhodophyta):a new freshwater red algal species from South China

Virescentia guangxiensis,a new species of Virescentia from Guangxi,South China,is described and illustrated based on morphological observations and phylogenetic analysis.This species was distinguished morphologically from other species by the presence of special expansion cells with a variable shape,obovoid,spherical,pear-shaped,located in the penultimate cells of primary or secondary fascicles,rarely terminal on primary fascicles,as well as by small whorls(250-350-μm wide) and short primary fascicles(5-7 cell stories).Phylogenetic analysis of molecular data from the rbcL and COI-5 P loci supported the separation of the proposed new species from other species in the genus Virescentia.This is the first species of the order Batrachospermales reported in Guangxi and the second species of the genus Virescentia reported in China.This study expands the known species diversity and geographical distribution of fre shwater Rhodophyta in China.     

IMMUNOLOGICAL CROSS REACTIONS BETWEEN P_(700) CHLOROPHYLL PROTEINS ISOLATED FROM TWO MARINE GREEN ALGAE AND ONE HIGHER PLANT

P700 Chi-protein was isolated from a marine green alga Bryopsis corticulans with SDS-resolved thylakoid membranes by SDS-PAGE. After elution from the gel, the recovered protein revealed a 100 KD polypeptide by re-electrophoresis . The same SDS-PAGE procedure was used to isolate P700 Chl-proteins from spinach (Spinacea okracea ) and another marine green alga Codium fragile . Polyclonal antibodies to Bryopsis P700 protein were raised in rabbits. The antibodies were shown to cross-react with P700 Chl-protein and Chl-protein complexes containing P700 protein from B . Corticulans, C. f ragile, and even spinach. Results indicate similarity of the amino acid sequences of the P700 Chl-proteins and the highly conserved structure of the apoproteins of phylogenetically distant species over evolution. The antibodies cross-react with none of the components of PSUU in the species tested , indicating an independent pathway of evolution of photosystem I and photosystem II of later origin.     

Interannual and Seasonal Variability of Winter-Spring Cohort of Neon Flying Squid Abundance in the Northwest Pacific Ocean During 1995–2011

The neon flying squid, Ommastrephes bartramii, is a species of economically important cephalopod in the Northwest Pacific Ocean. Its short lifespan increases the susceptibility of the distribution and abundance to the direct impact of the environmental conditions. Based on the generalized linear model(GLM) and generalized additive model(GAM), the commercial fishery data from the Chinese squid-jigging fleets during 1995 to 2011 were used to examine the interannual and seasonal variability in the abundance of O. bartramii, and to evaluate the influences of variables on the abundance(catch per unit effort, CPUE). The results from GLM suggested that year, month, latitude, sea surface temperature(SST), mixed layer depth(MLD), and the interaction term(SST×MLD) were significant factors. The optimal model based on GAM included all the six significant variables and could explain 42.43% of the variance in nominal CPUE. The importance of the six variables was ranked by decreasing magnitude: year, month, latitude, SST, MLD and SST×MLD. The squid was mainly distributed in the waters between 40?N and 44?N in the Northwest Pacific Ocean. The optimal ranges of SST and MLD were from 14 to 20℃ and from 10 to 30 m, respectively. The squid abundance greatly fluctuated from 1995 to 2011. The CPUE was low during 1995–2002 and high during 2003–2008. Furthermore, the squid abundance was typically high in August. The interannual and seasonal variabilities in the squid abundance were associated with the variations of marine environmental conditions and the life history characteristics of squid.     

Seasonal variation in community structure and body length of dominant copepods around artificial reefs in Xiaoshi Island, China

This study aims to investigate the seasonal variations in copepod community structure and prosome length of dominant species from March 2009 to January 2010 around artificial reefs in Xiaoshi Island,Yellow Sea,Weihai,China.Samples were collected using two types of plankton net(Model I and Model II) for different-sized copepods.The number of taxon was calculated from the data of both the net types,while the copepod abundance was done using the samples from Model II only.Sixteen species of planktonic copepods,including 5 dominant species,were recorded.Results reveal that Oithona similis was the first dominant species from March to June,and was replaced by Paracalanus parvus in September;both dominated the copepod community in January.Acartia hongi was the second dominant species from March to September.Centropages abdominalis was the third dominant species from March to June,and was replaced by O.similis in September and Corycaeus affinis in January.C.affinis was the fourth dominant species in September.Population density of the dominant copepods was compared with that of other similar regions.We found that the dominant species were mostly small copepods(<1 mm) except for adult Centrapages abdominalis.Seasonal variation in prosome length of O.similis,C.abdominalis,and C.affinis,and their copepodites were studied for the first time in China.For P.parvus and A.hongi,seasonal trends in prosome length variation were similar with those in Jiaozhou Bay,Yellow Sea,Qingdao,China,in a similar temperate domain.The results are helpful for future calculation of copepod biomass and production,and for investigation of the relationship between copepods and fish resources.     

A new record of a flathead fish (Teleostei: Platycephalidae) from China based on morphological characters and DNA barcoding

A new record of Platycephalus sp.1 (sensu Nakabo, 2002) was documented based on morphological characters and DNA barcoding. We collected 174 specimens of the genus Platycephalus from Chinese coastal waters of Dongying, Qingdao, Zhoushan, and Beihai. Samples were identified as Platycephalus sp.1 morphologically. The coloration, meristic traits, and morphometric measurements are consistent with previously published records. In brief, it is an orange-brown flathead fish with dark brown spots scattered on head and body, lateral line scales 83 to 99 with one or two spine-bearing anteriormost pored scale, no yellow blotch on the caudal fin. Cytochrome oxidase I subunit (COI) gene fragments were sequenced for phylogenetic analysis. The mean evolutionary distance within the species Platycephalus sp.1 was 0.1%. Net evolutionary distances between Platycephalus sp.1 and other species of Platycephalus ranged from 10.8% to 19.7%, which is much greater than the threshold for species delimitation. The COI sequence analysis strongly supports the validity of Platyceohalus sp.1 at genetic level.     

Diatom distribution as an environmental indicator in surface sediments of the West Philippine Basin

The distribution of diatoms from surface sediments of the West Philippine Basin was analyzed,with 68 species and varieties of diatoms from 26 genera identified.Diatom abundance varied spatially,with the absolute abundance of diatoms ranging from 0 to 3.4×10~4 frustules/g.The seven tropical pelagic diatoms were Alveus marinus,Azpeitia africana,Azpeitia nodulifera,Hemidiscus cuneiformis,Hemidiscus cuneiformis var.ventricosus,Roperia tesselata and Rhizosolenia bergonii.The relative abundance of these species was greater than 20%,and their distribution pattern in the sediments was overlaid by the flow of the Kuroshio Current.Ethmodiscus rex was present at 159 stations,formed the most abundant and dominant species in the diatomaceous ooze,and thus referred to as Ethmodiscus ooze.Ethmodiscus rex was also a major contributor to primary production in the region.A principal component analysis was employed to explain the relationship between samples and variations in diatom species from the WPB.Four diatom assemblages were distinguished,representing different oceanographic conditions;their spatial distributions were closely related with the North Equatorial Current and Kuroshio Current patterns in the region.These diatom assemblages can therefore be useful in deciphering late Quaternary palaeoceanographic reconstructions of the West Philippine Basin.     

Temporal and spatial variation of fish assemblages in Dianshan Lake,Shanghai, China

Using multi-mesh gillnets and trawls, the fish communities in Dianshan Lake at 6 stations from Oct. 2009 to Jul. 2010 were investigated seasonally to reveal the biodiversity and its spatial and temporal distribution patterns. The long-term changes in their structural characteristics were then analyzed to identify the main infl uencing factors and several measures for lake restoration were put forward. Thirty six species, belonging to 9 family and 30 genera, were collected, amongst which, the order Cypriniformes accounted for 61.1% of the total species number. In terms of importance value, Cypriniformes was the predominant group, Coilia nasus the dominant species, while Cyprinus carpio and Rhinogobius giurinus were the subdominant taxa. The community types did not differ among stations, but between seasons. There were no significant differences between seasons and among stations in species diversity, but richness differed both spatially and seasonally. Along with the process of eutrophication and the drastic reduction of the area colonized by macrophytes from 1959 to 2009–2010, the fish diversity declined markedly, and species numbers of herbivores and piscivores declined proportionately more than those of invertivores, omnivores, and planktivores. The decline of potamophilus and river-lake migratory fish was more marked than those of sedentary, river-sea migratory, and estuarine fishes. Eutrophication concomitant with sharp reduction of macrophyte area and overfishing may be the main reasons for the decline in fish diversity in Dianshan Lake.     

Morphological and Phylogenetic Studies of a Copepod Species,Irodes parupenei Ho and Lin (2007), Infecting Parupeneus rubescens in Saudi Arabia

Dammam City is one of the gorgeous coastal areas in the Arabian Gulf of Saudi Arabia.The present study aimed to ex-amine one of the copepod species infecting the rosy goatfish that represents a highly consumed fish species by the local population in the Arabian Gulf.The copepod species isolated from the infected fish specimens belong to the family Taeniacanthidae and was iden-tified as Irodes parupenei Ho and Lin(2007),primarily based on its morphological,morphometric,and ultrastructural characteris-tics,especially the structures of the dorsal cephalic area,segmentation of the first antenna,the absence of the maxilliped claw in the fe-male specimens,and the setation and spinulation of the legs 2-4 for the adult females are of great significance in the taxonomic iden-tification.The 18S rRNA gene sequence was analyzed to ensure the precise identity and exact taxonomic status of the copepod species.The result showed that this copepod species belong to Taenicanthidae and closely related to Irodes sauridi(gb|JF781550.1)in the same taxon.More details on the specificity of the goatfish for Irodes species and identifying these parasitic taxa using molecular analysis are given in the present study.     

Molecular diversity of Enteromorpha from the coast of Yantai: a dual-marker assessment

We collected nine Enteromorpha specimens from the coast of Yantai and evaluated their diversity based on analyses of their ITS （internal transcribed spacer） and 5S rDNA NTS （non-transcribed spacer） sequences. The ITS sequences showed slight nucleotide divergences between Enteromorpha linza and Enteromorpha prolifera. In contrast, multiple highly variable regions were found in the ITS region of Enteromorpha flexuosa. In general, there were more variable sites in the NTS region than in the ITS region in the three species. The variations in 5S rDNA NTS sequences indicated that the molecular diversity of Enteromorpha from the coast of Yantai is very high. However, a phylogenetic tree constructed using 5S rDNA NTS sequence data indicated that genetic differences were not directly related to geographical distribution.     

Morphology and distribution of the marine diatom Azpeitia africana (Janisch ex A. Schmidt) G. Fryxell & T. P. Watkins in the South China Sea

The purpose of the present paper is to study the morphological structure and variability of Azpeitia africana and to determine its geographical distribution in the surface sediments of the South China Sea(SCS). Sediment samples were collected with grabs or box corers in one cruise in 2001 and two cruises in 2007. The sampling stations were located between 3°56.61′–20°59.37′N and 108°30.68′–116°46.70′E,where the water depth ranged from 72 m to 4 238 m. The diatom was observed by phase contrast microscopy and scanning electron microscopy. Microscopical observation showed that A. africana had circular valves with the areolar lines radiating from the eccentric ring. The central rimoportula had an external tube recessed on the edge of a central ring. The marginal rimoportulae were not evenly spaced, and they were positioned more closely together in one quadrant than in the others. Azpeitia africana is the most abundant diatom species in the southern region of the SCS, and accounted for 0.9%–5.6% of all diatom species in the Xisha Islands area. Average cell density of A. africana was 1.1×10~5 valves/g. The percentage abundance of A.africana was low(0%–2.5%) in the northern regions of the SCS and the Sunda Shelf, and it was not detected in the northwestern continental shelf(shallow water area) and northern Kalimantan Island shelf. Our results suggested that A. africana is a typical warm water species and that it could be used as an indicator of the warm Paci?c Ocean water, including the Kuroshio Current, ?owing into the SCS.