A preliminary phylogenetic analysis of Luidia (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 substantial 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 cytochrome 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 phylogenetic relationships. The molecular phylogeny 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. changi 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 Müller & Troschel from Chinese waters. Our molecular phylogeny results support the morphological Quinaria-Group and Alternata-Group assigned by Döderlein. Seven nominal species we sampled do not exhibit genetic distances that are large enough to recognize them as separate species. Cryptic species may exist in’ Luidia quinaria’ from the Yellow Sea and the Sea of Japan. Meaningful morphological characters need further investigation in Luidia.     

Monophyly or polyphyly? Possible conflict between morphological and molecular interpretations of the wellknown genus Zoothamnium(Ciliophora,Peritrichia)

In this paper,we explore possible conflict between morphological and molecular interpretations of phylogenetic relationships within the well-known peritrichous genus Zoothamnium. On the basis of morphological evidence,for a long time this genus has been believed to be a well-defined monophyletic taxon. Nonetheless,Z oothamnium exhibits higher genetic diversity than the gross morphology of its species. Here,we used all available genetic information for the small subunit of ribosomal RNA(SSU r RNA) and internal transcribed spacer region(ITS1-5.8S-ITS2) for this genus to reconstruct phylogenies for four datasets(SSU rRNA,ITS1,ITS2,and ITS1-5.8S-ITS2) and a combined dataset(SSU rRNA+ITS1-5.8SITS2) using different phylogenetic methods and with consideration of the secondary structure of the genes. Confidence in phylogenetic tree selection was assessed with the approximately unbiased test. The molecular results showed both that Zoothamnium is more likely to be polyphyletic,and morphologically similar genera Zoothamnopsis and Myoschiston were always nested among Zoothamnium species. Accordingly,as with some other groups of ciliates,to understand more fully the correct phylogeny of Zoothamnium there remains a need for additional data from both morphological and molecular studies,covering additional Zoothamnium spp. and members of closely related genera(e.g. Zoothamnopsis,Myoschiston,and Epistylis).     

Polyphasic examination on Merismopedia tenuissima CHAB 7021 from Ganjiang River,China revealed the polyphyly of the genus Merismopedia(Cyanobacteria)

Species in the cyanobacterial genus Merismopedia are present in freshwaters at different trophic levels, with some species even as the components of cyanobacterial blooms. However, species diversity in this genus was not fully verified by molecular investigation and polyphasic taxonomic studies. In this study, Merismopedia-like strain tenuissima CHAB 7021 was isolated from Ganjiang River in Jiangxi Province, China, and polyphasic characterization of this strain was performed by morphological observation, ultrastructural examination, chemical detection of pigments and phylogenetic analysis based on 16 S rRNA gene sequences. Morphological identification of the strain was supported by the ultrastructural features, as the tiny species Merismopedia tenuissima Lemmermann. The phylogeny based on 16 S rRNA gene sequences revealed at least three clades formed by the strains of Merismopedia. The three M. tenuissima strains including M. tenuissima CHAB 7021 was gathered in clade III with distant relationship to the clade I formed by the six Merismopedia strains including the type species M. punctata, and such a genetic distance may propose Merismopedia tenuissima to separate from Merismopedia genus. However intermixture relationship in between strains of M. punctate and M. glauca in the phylogenetic tree still complicated the taxonomic status in the genus Merismopedia. The process for taxonomic revision in the Merismopedia genus still await for examination and further information on more strains of type species M. punctata.     

Development of 57 novel polymorphic microsatellite markers in half-smooth tongue sole (Cynoglossus semilaevis)

Half-smooth tongue sole (Cynoglossus semilaevis) is a promising species for aquaculture in China.The wild population of C. semilaevis is under threat from environmental factors. Microsatellite markers are very suitable for assessing genetic diversity. Four microsatellite-enriched libraries of half smooth tongue sole (Cynoglossus semilaevis) were constructed,from which 57 polymorphic microsatellites were isolated and characterized.The polymorphism of these microsatellites was assessed by genotyping in 30 ind...     

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.     

Establishment of Alloptilella splendida gen.et sp.nov.and resurrection of Scytalium veneris(Thomson & Henderson,1906),two sea pens(Cnidaria:Pennatulacea) from seamounts in the tropical Western Pacific

Sea pens are a highly specialized and morphologically distinct group of octocorallians,but many taxa were poorly described and their phylogenetic relationships are still poorly known.We describe two species of sea pens collected from the tropical Western Pacific:Alloptilella splendida gen.et sp.nov.and Scytalium veneris(Thomson Henderson,1906).Alloptilella splendida gen.et sp.nov.accords with the definition of the recently resurrected genus Ptilella Gray,1870 in most characters,but differs from the latter in the arrangement of autozooids and the location of mesozooids.The new species mostly resembles Pennatula naresi K(o|")lliker(1880),but differs by the location of me sozooids and the reddish color of sclerite s surrounding siphonozooids.The generic separation is also well supported by their genetic distances and the molecular phylogenetic trees constructed by the concatenated mtMutS-COI-28 S,where Alloptilella clustered with Scytalium Herklots,1858 and formed a clade with the cluster of Ptilella and Distichoptilum.Scytalium veneris,usually considered as a junior synonym of Scytalium sarsii Herklots,1858,is resurrected by recognizing their distinctive differences.This is the first record of Scytalium veneris outside its type locality,and the phylogenetic analysis indicates that Scytalium is a monophyletic group.Both the families Pennatulidae and Virgulariidae are polyphyletic,and more morphological and molecular data are needed to clarify the phylogenetic positions of pennatulacean families and genera.     

Partial Sequence Analysis of Mitochondrial COI Gene of the Chinese Shrimp, Fenneropenaeus Chinensis

Eight hundred and thirty eight base pair fragment of mitochondrial COI gene of wild and cultured populations (CP1, CP4, CP5 and CP6) of Fenneropenaeus chinensis was amplified and sequenced. The A, T, G and C contents of the sequence were 235bp (28.0% ),.307bp (36.6%), 138bp (16.5%) and 158bp (18.9%), respectively. Furthermore, 556bp fragment of the sequence was used to discuss the phylogenetic relationship among 14 Penaeidae species using Alpheus armillatus as the outgroup. From the molecular phylogenetic tree constructed by neighbor-joining method, we obtained three large shrimp groups: Farfantepenaeus, Litopenaeus and Fenneropenaeus group. The results also indicated that there were a closer genetic relationships between F. aztecus and F. paulensis, L. schmitti and L. setiferus, F. indicus and F. merguiensis, and the genus Farfantepenaeus was closer to Litopenaeus.     

3种江珧同工酶遗传标记

通过对江珧科的栉江珧、旗江珧及二色裂江珧三物种的 5种组织 (消化盲囊、肾组织、外套膜、后闭壳肌和鳃组织 )进行垂直板状聚丙烯酰胺凝胶电泳分离技术 ,研究江珧科的 SOD、EST同工酶酶谱 ,结果表明 ,不同种间的个体其酶谱表型有稳定的差异 ,同属的种间差异小于不同属的种间差异 ,即酶谱的差异程度与形态分类学中的亲缘关系相关。可利用其酶谱表型具有种特异性作为一种蛋白分子标记 ,应用于江珧物种尤其是经济品种的鉴定上     

Morphology and phylogeny of Chrysogorgia pinniformis sp.nov.and C.varians sp.nov.,two golden corals from the Caroline seamounts in the tropical Western Pacific Ocean

Two new species of Chrysogorgia Duchassaing Michelotti,1864 collected from the Caroline seamounts in the tropical Western Pacific Ocean are described.Chrysogorgia pinniformis sp.nov.belongs to Versluys' group C(Squamosae typicae) with only scales in polyp body wall and tentacles.C.pinniformis sp.nov.is characterized by large branches pinnately branched and forming multiple fans with its small branches regularly and quasi-dichotomous branched,and scales and rods present in the polyp mouth area.It is most similar to C.pinnata Cairns,2007 by the pinnate trait,but differs from the latter by its group C pattern(vs.group A,Spiculosae) and having sclerites present in the polyp mouth area(vs.absent).Chrysogorgia varians sp.nov.belongs to the Chrysogorgia group A(Spiculosae) with rods distributed in the polyp body wall and tentacles.It is characterized by warty rods and elongated scales in the tentacles,many warts and ridges on the scales,conspicuously toothed margins at the rounded ends in the pinnules,and small rods with ridge-like warts in the polyp mouth area.This species was frequent and abundant in the Caroline seamounts during our cruises and its morphological variability in growth period was obvious.The phylogenetic analyses based on mtMutS and 28 S rDNA regions supported the assignment of the new species to the genus Chrysogorgia.However,the mtMutS marker showed very limited usefulness for species delimitation and inner relationship inference of Chrysogorgia.In contrast,the 28 S rDNA showed much higher level of genetic variation,and it may be a potential barcode for this genus.In the 28 S rDNA trees,the two new species clustered together.Additionally,compilation of our data showed that 42 of 78(ca.54%) Chrysogorgia species were found in the Indo-West Pacific convergent region,indicating that this area may be a hotspot of deep-water Chrysogorgia species.     

Taxonomic reassessment of Polysiphonia hainanensis(Rhodomelaceae,Rhodophyta) based on molecular and morphological analyses

Polysiphonia hainanensis was previously described from Hainan, China, but DNA sequence had never been provided and its phylogenetic position in Polysiphonieae has not been clear so far. The classification of Polysiphonieae has changed recently based on the molecular analyses and detail morphological anatomy, consequently, the generic assignment of some species must be reassessed. In this study, we analyzed phylogenetic relationships of P. hainanensis and the related taxa in Polysiphonieae and Streblocladieae based on rbcL sequences, with specimens collected from the type locality and the area around. Two genetic types were detected, and formed a clade with Bryocladia thyrsigera with strong bootstrap support, in which the divergence was less than 0.81%. Furthermore, based on morphological analyses, we found characteristics of Chinese specimens, number of pericentral cells, percurrent axis, determinate branchlets, branching pattern, spermatangial axes development, and arrangement of tetrasporangia, etc., were consistent with those of Bryocladia. Combined with morphological and molecular analyses, P. hainanensis was taken a synonymous of B. thyrsigera, and gametophytes of this species were found from China for the first time.     

Sequences and phylogeny analysis of <Emphasis Type="Italic">rbcL</Emphasis> gene in marine chlorophyta

The rbcL gene of Ulva pertusa,Enteromorpha prolifera and Monostroma grevillei was amplified,sequenced and analyzed.By comparing the rbcL sequences with seven other Ulvales species retrieved from GenBank,the sequence divergences and the phyletic evolution were analyzed and the phylogenetic tree was constructed.From the phylogenetic tree,it can be found that U.pertusa,E.prolifera and U.californica group in one branch,while E.compressa,U.rigida and U.fenestrata cluster in another clade.Obviously,unlike the Enteomorpha species,the Ulva species do not gather in one branch.Therefore Ulva and Enteomorpha might be affiliates of one genus.E.compressa and E.intestinalis gathered together,which coincided with the morphological characters.However,the thallus of U.pertusa is thick and with many holes,which is different from E.prolifera in morphology.They cluster together in the phylogenetic tree with a genetic distance of 0.005.The results indicate that Ulva and Enteromorpha are not distinguished strictly.     

Molecular phylogeny of the genus Clibanarius(Decapoda: Anomura: Diogenidae) based on mitochondrial and nuclear DNA sequences

Clibanarius,a genus of hermit crabs,is one of the most diverse genera within Diogenidae.However,studies on the phylogeny within Clibcanarius is very limited.We reconstruct the molecular phylogeny of the genus Clibanarius based on two mitochondrial(16 S rRNA and COI)and two nuclear protein-coding(NaK and PEPCK)genes using a multigene phylogenetic approach.Eleven selected Clibanarius species from the Indo-West Pacific are analyzed and the Bayesian and maximum likelihood analyses produced identical results in topology.Results suggest that C.rutilus and C.infraspinatus are more closely related to each other than to C.snelliusi,and C.striolatus shows a close relationship to C.longitarsus.The close association of C.merguiensis with C.englaucus and C.humilis is strongly supported by the divergence of C.virescens from them.Our phylogenetic results contradict the morphological classification scheme proposed for Clibanarius and indicate that the relative length of dactyls and propodi is not phylogenetically significant in Clibanarius.In addition,we speculate that the morphological characteristic of the median cleft of the telson might be phylogenetically important for Clibanarius.     

A new record of ponyfish <Emphasis Type="Italic">Deveximentum megalolepis</Emphasis> (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.     

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.     

Two new species of the genus Munidopsis Whiteaves,1874(Crustacea:Anomura:Munidopsidae) from the Caroline Ridge,South of the Mariana Trench

The genus Munidopsis has high biodiversity in seamount habitats.In this study,two new Munidopsis species,Munidopsis ahyongi sp.nov.and Munidopsis carolinensis sp.nov.from the Caroline Ridge in the tropical western Pacific Ocean were described.M.ahyongi sp.nov.is very similar to a group of species in the M.serricornis complex,but can be readily distinguished from the related species in having the oblique posterior orbital margins,2 spines on the lateral carapace margin,and a relatively longer rostral median spine.M.carolinensis sp.nov.is different from two related species primarily in having oblique frontal margins,blunt outer orbital angles,straight lateral margins of the rostrum,scale-like rugae on sternites 5-7,and less spinose pereopod 1(chelipeds,P1) merus and carpus.Aside from the morphological comparisons,DNA barcode analysis and phylogenetic analysis based on the cytochrome c oxidase subunit I gene(COI) were employed for the identification of these new species.     

Partial sequence analysis of mitochondrial COI gene of the chinese shrimp, <Emphasis Type="Italic">fenneropenaeus chinensis</Emphasis>

Eight hundred and thirty eight base pair fragment of mitochondrial COI gene of wild and cultured populations (CP1, CP4, CP5 and CP6) of Fenneropenaeus chinensis was amplified and sequenced. The A, T, G and C contents of the sequence were 235 bp (28.0%), 307 bp (36.6%), 138 bp (16.5%) and 158 bp (18.9%), respectively. Furthermore, 556 bp fragment of the sequence was used to discuss the phylogenetic relationship among 14 Penaeidae species using Alpheus armillatus as the outgroup. From the molecular phylogenetic tree constructed by neighbor-joining method, we obtained three large shrimp groups: Farfantepenaeus, Litopenaeus and Fenneropenaeus group. The results also indicated that there were a closer genetic relationships between F. aztecus and F. paulensis, L. schmitti and L. setiferus, F. indicus and F. merguiensis, and the genus Farfantepenaeus was closer to Litopenaeus.     

Taxonomic revision of Gelidium tsengii and Gelidium honghaiwanense sp. nov.(Gelidiales,Rhodophyta) from China based upon molecular and morphological data analyses

The taxonomic relationship of Chinese Gelidium tsengii and Gelidium johnstonii was ambiguous. For almost 20 years they have been regarded as distinct taxa and until 2002 G. johnstonii was considered as a misapplied name of G. tsengii. In this study, herbarium specimens that initially attributed to G. tsengii and fresh G. tsengii specimens were used to address the taxonomic issues. In phylogenetic studies, G. tsengii from Dayawan, China, near the type locality of G. tsengii and G. johnstonii from Sonora, Mexico, the type locality of G. johnstonii, formed a monophyletic group with maximum support in r bc L and COI genes analyses, indicating that they were genetically identical. In morphological studies, G. tsengii was similar to G. johnstonii in branching pattern, inner structures and fructiferous organs. Consequently, we considered that semi-circular outline of G. tsengii could no longer be treated as a discrimating feature. G. johnstonii had priority of publication and according to the International Code of Botanical Nomenclature, G. tsengii was proposed as a synonym of G. johnstonii. Gelidium honghaiwanense sp. nov. was described from Guangdong, China on the basis of morphological and molecular data. For vegetative structures, it was characterized by flattened upright frond, regular two-three times branches pinnate or alternate and clavate ultimate branchlets. For reproductive structures, the tetrasporangial sori were in the apical part of branches and the tetrasporangial branchlets were distichously distributed along second order branches. The present study clarified the relationship between G. tsengii and G. johnstonii from Guangdong and added a new Gelidium species to the Chinese algal flora.