Limb articulation in caridoid crustaceans revisited - new evidence from Euphausiacea (Malacostraca)

The propodial articulation of thoracopods in Malacostraca is revisited. Two major joints at the base of the limb, a thorax-coxa joint and a coxa-basis joint permit promotion-remotion and abduction-adduction, respectively. In representatives of Decapoda, Anaspidacea and Euphausiacea, the coxa forms proximally a dicondylic articulation with the thorax, permitting promotion-remotion, and distally another dicondylic joint with the basis, permitting abduction-adduction. In Lophogastrida and Mysida, the thorax-coxa hinge line is antero-posteriorly oriented, as is the coxa-basis hinge line. Promotion-remotion in Mysida and Lophogastrida is possible because of the presence of an intrabasal joint which is also present in Euphausiacea and Anaspidacea. In Mysida, Lophogastrida and Euphausiacea, the intrabasal joint is only present anteriorly, just distally of the anterior coxa-basis joint between a small, triangular proximal part of the basis and a larger distal part. In Anaspidacea, the intrabasal joint is also present posteriorly and permits abduction-adduction. Homology with the intrabasal joint of the other taxa seems doubtful. Limb articulation in Anaspidacea shows, nevertheless, correspondences with that in Euphausiacea, Lophogastrida and Mysida: the coxa is posteriorly invaginated and has an open ring-like structure very different from the solid coxa in decapods. Despite the high level of structural correspondence between the intrabasal joint in Euphausiacea and that in Lophogastrida and Mysida, their different functional roles make homology implausible. In Lophogastrida and Mysida the intrabasal joint is thought to replace the promotion-remotion movement of the thorax-coxa articulation, which in these taxa permits abduction-adduction only, probably in connection with the evolution of the marsupium. In Euphausiacea, the intrabasal joint might play a role in feeding mechanisms. Neither the feeding basket nor a marsupium can reasonably be suggested for any common ancestor of Euphausiacea and Mysidacea (or Peracarida).     

The evolutionary history of krill inferred from nuclear large subunit rDNA sequence analysis

Early events in the speciation history of krill (Malacostraca: Euphausiacea), an abundant group of extant pelagic crustaceans, were studied with slowly evolving nuclear DNA sequences (large subunit ribosomal DNA, 28S rDNA). Krill have no fossil record, so very little is known about their paleobiology. The timing of past speciation events in krill was estimated by comparing change in their 28S rDNA to change in the 28S rDNA of their close relatives that do have a fossil record. Relationships between krill genera were also studied by phylogenetic analysis of partial 28S rDNA sequences. The analyses estimated the time that the last common ancestor of the krill family Euphausiidae lived to be the lower Cretaceous about 130 million years ago (Mya). Two lineages of krill survived the end Cretaceous extinctions 65 Mya and the modern genera of krill were established before the end of the Palaeogene 23 Mya.     

杉科、柏科的系统发生分析——来自28S rDNA序列分析的证据

对杉科（Taxodiaceae）与柏科（Cupressaceae s.s.）的28S rRNA基因的部分序列（约630 bp）进行PCR扩增、序列测定和系统发生关系分析,用简约法和邻接法构建的系统发生树基本一致。结果表明,杉科与柏科构成一个单系群,支持将杉科、柏科（Sciadopitys除外）合并为一个科——广义柏科（Cupressaceae sensu lato）的观点。在广义柏科中,Taiwania、Athrotaxis分别形成一支系;Metasequoia、Sequoia、Sequoiadendron关系较近,聚成一支系; Taxodium、Glyptostrobus、Cryptomeria聚成一支系;柏科聚成一支系。这一分析结果与叶绿体基因序列的分析结果相吻合,但是由于28S rRNA基因的进化速率较慢,尚不能分辨上述各个支系之间的系统演化关系。 Abstract:DNA sequences from 28S rDNA were used to assess relationships between and within traditional Taxodiaceae and Cupressaceae s.s.The MP tree and NJ tree generally are similar to one another.The results show that Taxodiaceae and Cupressaceae s.s.form a monophyletic conifer lineage excluding Sciadopitys.In the Taxodiaceae-Cupressaceae s.s.monophyletic group,the Taxodiaceae is paraphyletic.Taxodium,Glyptostrobus and Cryptomeria forming a clade(Taxodioideae),in which Glyptostrobus and Taxodium are closely related and sister to Cryptomeria;Sequoia,Sequoiadendron and Metasequoia are closely related to each other,forming another clade (Sequoioideae),in which Sequoia and Sequoiadendron are closely related and sister to Metasequoia;the seven genera of Cupressaceae s.s.are found to be closely related to form a monophyletic lineage (Cupressoideae).These results are basically similar to analyses from chloroplast gene data.But the relationships among Taiwania,Sequoioideae,Taxodioideae,and Cupressoideae remain unclear because of the slow evolution rate of 28S rDNA,which might best be answered by sequencing more rapidly evolving nuclear genes.     

Molecular phylogeny of parasitic Platyhelminthes based on sequences of partial 28S rDNA D1 and mitochondrial cytochrome c oxidase subunit I

The phylogenic relationships existing among 14 parasitic Platyhelminthes in the Republic of Korea were investigated via the use of the partial 28S ribosomal DNA (rDNA) D1 region and the partial mitochondrial cytochrome c oxidase subunit 1 (mCOI) DNA sequences. The nucleotide sequences were analyzed by length, G + C %, nucleotide differences and gaps in order to determine the analyzed phylogenic relationships. The phylogenic patterns of the 28S rDNA D1 and mCOI regions were closely related within the same class and order as analyzed by the PAUP 4.0 program, with the exception of a few species. These findings indicate that the 28S rDNA gene sequence is more highly conserved than are the mCOI gene sequences. The 28S rDNA gene may prove useful in studies of the systematics and population genetic structures of parasitic Platyhelminthes.     

Taxonomic Review of the Orders Mysida and Stygiomysida (Crustacea,Peracarida)

The order Mysida (2 families, 178 genera, 1132 species) contains species across a broad range of habitats, such as subterranean, fresh, brackish, coastal, and surface to deep-sea habitats. The Stygiomysida (2 families, 2 genera, 16 species), however, are found primarily in subterranean waters, but always in waters with a marine influence. The Mysida and Stygiomysida body is divided into three main regions: cephalon, thorax, and abdomen. They are shrimp-like in appearance, containing morphological features earlier referred to as defining a "caridoid facies". The shrimp-like morphology was to some extent diagnostic for the historic Decapod taxon Schizopoda, containing the Nebalia, Mysida, Lophogastrida, and Euphausiacea. In 1904 the concept of Schizopoda was abandoned, and the Mysidacea (Mysida and Lophogastrida) along with Cumacea, Amphipoda, Isopoda, and Tanaidacea were placed in a new taxon, the Peracarida. Later discoveries of groundwater mysids led to the establishment of Stygiomysida, but placement to either Lophogastrida or Mysida remained unclear. The presence of oostegites and absence of podobranchiae, coupled with non-statocyst bearing uropods have been used to classify the Stygiomysida as a primitive Mysida family, comparable to Petalophthalmidae. On the other hand, equally suggestive characters, but for a Lophogastrida affiliation, was suggested for the archaic foregut characters and again, non-statocyst bearing uropods. With the inclusion of DNA sequence data of ribosomal genes, sister group relationships between Stygiomysida, Lophogastrida, and Mictacea within the Peracarida are observed, which supports a classification of the Stygiomysida as a separate order removed from the Mysida.     

Initial results on the molecular phylogeny of the Nudibranchia (Gastropoda, Opisthobranchia) based on 18S rDNA data

This study investigated nudibranch phylogeny on the basis of 18S rDNA sequence data. 18S rDNA sequence data of 19 taxa representing the major living orders and families of the Nudibranchia were analyzed. Representatives of the Cephalaspidea, Anaspidea, Gymnomorpha, Prosobranchia, and Pulmonata were also sequenced and used as outgroups. An additional 28 gastropod sequences taken from GenBank were also included in our analyses. Phylogenetic analyses of these more than 50 gastropod taxa provide strong evidence for support of the monophyly of the Nudibranchia. The monophyly of the Doridoidea, Cladobranchia, and Aeolidoidea within the Nudibranchia are also strongly supported. Phylogenetic utility and information content of the 18S rDNA sequences for Nudibranchia, and Opisthobranchia in general, are examined using the program SplitsTree as well as phylogenetic reconstructions using distance and parsimony approaches. 0Results based on these molecular data are compared with hypotheses about nudibranch phylogeny inferred from morphological data.     

The foregut of the Mysida (Crustacea,Peracarida) and its phylogenetic relevance

The foreguts of the mysids Antarctomysis maxima, A. ohlinii, Hansenomysis antarctica, Heteromysis formosa, Mesopodopsis slabberi, Neomysis integer, Paramysis kessleri, Praunus flexuosus, and Siriella jaltensis were examined by maceration methods, histological techniques, and scanning electron microscopy. Their morphology, their connection with the midgut glands, and probable function are described and summarized. Previous stomach investigations on mysids and the results of the present study are tabulated; a list of foregut characters, common to all Mysida, is presented. The phylogenetic relevance of these characters within the Malacostraca, especially within the Peracarida, is discussed. Most features are inherited from the ground pattern of the Malacostraca or Eumalacostraca. The bulbous cardia with its dorsal fold, the armature of the lateralia, and the construction of the funnel region are apomorphies for the Mysida. The results suggest that characters of mysidan and other peracaridan foreguts might also be useful in the elucidation of the phylogeny of the Mysida and Peracarida, respectively.     

Ribosomal DNA sequence characterization of Maritrema cf. eroliae Yamaguti, 1939 (Digenea: Microphallidae) and its life cycle

The microphallid Maritrema eroliae parasitizes shore birds in marine ecosystems while its larval stages infect mud snails and crustacean hosts. Because it is difficult to morphologically distinguish between larvae of M. eroliae and other microphallids co-occurring in the same habitat, partial nucleotide sequences of the ribosomal DNA (rDNA), including the 28S and 18S in addition to complete sequences of ITS1 and ITS2, were scrutinized. This analysis was used to establish the snail-crab link in the life cycle of M. cf. eroliae . The rDNA 28S, 18S, and ITS sequences of metacercariae from the crab Xantho exaratus and sporocysts from the snail Clypeomorus bifasciata were compared. Sequence alignment demonstrated that the sporocyst and metacercaria may belong to M. eroliae and suggested a new second intermediate host for M. eroliae , the crab X. exaratus . The phylogenetic positions of the larval stages were determined by comparing the 28S, 18S, and ITS sequences with those of other trematodes available in GenBank. The phylogenetic trees confirmed the position of M. cf. eroliae within the Microphallidae and found it to be closely related to Maritrema heardi and Maritrema neomi. The present study represents the first molecular study correlating the larval stages in the life cycle of M. cf. eroliae using partial sequences of 28S and 18S in addition to complete ITS1 and ITS2 sequences. Furthermore, the sequences elucidated the evolutionary relationship of M. cf. eroliae to other microphallids.     

Sequence analysis of 28S ribosomal DNA from the amphibian Xenopus laevis.

We have determined the complete nucleotide sequence of Xenopus laevis 28S rDNA (4110 bp). In order to locate evolutionarily conserved regions within rDNA, we compared the Xenopus 28S sequence to homologous rDNA sequences from yeast, Physarum, and E. coli. Numerous regions of sequence homology are dispersed throughout the entire length of rDNA from all four organisms. These conserved regions have a higher A + T base composition than the remainder of the rDNA. The Xenopus 28S rDNA has nine major areas of sequence inserted when compared to E. coli 23S rDNA. The total base composition of these inserts in Xenopus is 83% G + C, and is generally responsible for the high (66%) G + C content of Xenopus 28S rDNA as a whole. Although the length of the inserted sequences varies, the inserts are found in the same relative positions in yeast 26S, Physarum 26S, and Xenopus 28S rDNAs. In one insert there are 25 bases completely conserved between the various eukaryotes, suggesting that this area is important for eukaryotic ribosomes. The other inserts differ in sequence between species and may or may not play a functional role.     

Molecular Diversity among Communities of Freshwater Microchlorophytes

Current hypotheses on the distribution of freshwater microchlorophytes lead to predictions of low diversity and wide environmental tolerances. Thus, the same few species should be found worldwide in many different habitats. However, these hypotheses are based on a morphospecies concept, which precludes the possibility of numerous cryptic species among these organisms. In this study, we examined the diversity of coccoid green microalgae and chlamydomonads (Chlorophyta) isolated from sites in Minnesota and North Dakota (USA) using techniques of 18S rDNA sequence analysis. Of 93 distinct 18S rDNA sequences identified from among 273 isolates examined by molecular techniques, all but four are new to science. The spatial distribution of organisms represented by these 18S rDNA sequences was not uniform, because some lakes and ponds yielded distinct 18S rDNA types not found at other sites. In addition, organisms generally considered to be cosmopolitan, such as Chlamydomonas reinhardtii and Chlorella vulgaris, were not found. These results challenge predictions of low species number and wide environmental tolerances among these eukaryotic microorganisms.     

Asterotremella gen. nov. albida, an anamorphic tremelloid yeast isolated from the agarics Asterophora lycoperdoides and Asterophora parasitica

Using a genotypic approach (PCR-fingerprinting, DNA/DNA reassociation, partial sequences of the 26S rDNA gene, complete sequences of the 18S rDNA gene, and sequences of the internal transcribed spacers) five tremelloid yeast isolates from the agarics Asterophora lycoperdoides and A. parasitica were shown to be conspecific with Cryptococcus ramirezgomezianus. It was not possible to distinguish the yeast strains from A. lycoperdoides and A. parasitica using sequences from the intergenic spacer (IGS1). Phylogeny based on the 26S (D1/D2-domain), ITS1-5.8S-ITS2 and complete 18S rDNA demonstrated that C. ramirezgomezianus is closely related to several additional Cryptococcus species (C. humicola, C. longus, C. musci, C. pseudolongus) within the Trichosporonales. A new genus, Asterotremella, and a new family, Asterotremellaceae were introduced for Cryptococcus species clustering within the Trichosporonales having a ubiquinone Q-9. Cryptococcus ramirezgomezianus is a synonym of Asterotremella albida.     

Phylogenetic analysis of the Malacostraca (Crustacea)

The Malacostraca comprises about 28 000 species with a broad disparity in morphology, anatomy, embryology, behaviour and ecology. The phylogenetic relationships of the major taxa are still under debate. Is the Leptostraca the sister group of the remaining Malacostraca, or is this taxon more closely related to other Crustacea? Does the Stomatopoda or the Bathynellacea represent the most basal taxon within the remaining taxa? Is the Peracarida monophyletic or are some peracarid taxa more closely related to other ‘caridoid’ taxa? Is the Thermosbaenacea part of the Peracarida or its sister group, and how much support is there for a taxon Amphipoda + Isopoda? To answer these questions a phylogenetic analysis of the Malacostraca combining different phylogenetic approaches was undertaken. In a first step, the monophyly of the Malacostraca including the Leptostraca is shown using the ‘Hennigian approach’. A computer cladistic analysis of the Malacostraca was carried out with NONA and PEE ‐WEE , based on 93 characters from morphology, anatomy and embryology. Nineteen higher malacostracan taxa are included in our analysis. Taxa whose representatives are exclusively fossils were not included. The Leptostraca was used as an operational out‐group. The present analysis supports the basal position of the Stomatopoda. Syncarida and Peracarida (including Thermosbaenacea) are supported as monophyletic, the Eucarida is not. Instead a sister‐group relationship is suggested between Euphausiacea and Peracarida (including Thermosbaenacea), with the Syncarida as the sister group to both taxa. Certain embryonic characters are interpreted as support for the monophyly of the Peracarida (without Thermosbaenacea) because convergences or reversals of these characters seem implausible. Within the Peracarida, the Mysidacea (Lophogastrida + Mysida) represents the sister group to the remaining taxa. A sister‐group relationship between Amphipoda and Isopoda is not supported.     

Phylogenetic relationships within the Mysidae (Crustacea, Peracarida, Mysida) based on nuclear 18S ribosomal RNA sequences

Species of the order Mysida (Crustacea, Peracarida) are shrimp-like animals that occur in vast numbers in coastal regions of the world. The order Mysida comprises 1,053 species and 165 genera. The present study covers 25 species of the well-defined Mysidae, the most speciose family within the order Mysida. 18S rRNA sequence analysis confirms that the subfamily Siriellinae is monophyletic. On the other hand the subfamily Gastrosaccinae is paraphyletic and the subfamily Mysinae, represented in this study by the tribes Mysini and Leptomysini, consistently resolves into three independent clades, and hence is clearly not monophyletic. The tribe Mysini is not monophyletic either, and forms two clades of which one appears to be closely related to the Leptomysini. Our results are concordant with a number of morphological differences urging a taxonomic revision of the Mysidae.     

Evolution and phylogenetic information content of the ribosomal DNA repeat unit in the Blattodea (Insecta)

The organization, structure, and nucleotide variability of the ribosomal repeat unit was compared among families, genera, and species of cockroaches (Insecta:Blattodea). Sequence comparisons and molecular phylogenetic analyses were used to describe rDNA repeat unit variation at differing taxonomic levels. A reverse similar 1200 bp fragment of the 28S rDNA sequence was assessed for its potential utility in reconstructing higher-level phylogenetic relationships in cockroaches. Parsimony and maximum likelihood analyses of these data strongly support the expected pattern of relationships among cockroach groups. The examined 5' end of the 28S rDNA is shown to be an informative marker for larger studies of cockroach phylogeny. Comparative analysis of the nucleotide sequences of the rDNA internal transcribed spacers (ITS1 and ITS2) among closely related species of Blattella and Periplaneta reveals that ITS sequences can vary widely in primary sequence, length, and folding pattern. Secondary structure estimates for the ITS region of Blattella species indicate that variation in this spacer region can also influence the folding pattern of the 5.8S subunit. These results support the idea that ITS sequences play an important role in the stability and function of the rRNA cluster.     

Development of PCR primers specific for the amplification and direct sequencing of gyrB genes from microbacteria, order Actinomycetales

PCR primer sets were developed for the specific amplification and sequence analyses encoding the gyrase subunit B (gyrB) of members of the family Microbacteriaceae, class Actinobacteria. The family contains species highly related by 16S rRNA gene sequence analyses. In order to test if the gene sequence analysis of gyrB is appropriate to discriminate between closely related species, we evaluate the 16S rRNA gene phylogeny of its members. As the published universal primer set for gyrB failed to amplify the responding gene of the majority of the 80 type strains of the family, three new primer sets were identified that generated fragments with a composite sequence length of about 900 nt. However, the amplification of all three fragments was successful only in 25% of the 80 type strains. In this study, the substitution frequencies in genes encoding gyrase and 16S rDNA were compared for 10 strains of nine genera. The frequency of gyrB nucleotide substitution is significantly higher than that of the 16S rDNA, and no linear correlation exists between the similarities of both molecules among members of the Microbacteriaceae. The phylogenetic analyses using the gyrB sequences provide higher resolution than using 16S rDNA sequences and seem able to discriminate between closely related species.     

Species-specificity of DNA trimer densities in chromosomes and their use in the classification of closely related organisms

16S rDNA sequences are conventionally used for classification of organisms. However, the use of these sequences is sometimes not successful, especially for closely related species. For better classification of these organisms, several methods that are genome sequence-based have been developed. Sequence alignment-based methods are tedious and time-consuming, as they need conserved coding sequences to be identified and deduced prior to sequence alignment. Likewise, method that relies on gene function needs genes to be assessed for function similarity. Other alignment-free methods, which are based on particular genome sequence properties, so far have been complex and not species-specific enough for classification of organisms below genus level. The present study found that the ratios of DNA trimer frequencies to chromosomal length were species-specific. Density of a trimer in a chromosomal sequence was defined as the average frequency of the trimer per 1 kbp. The species-specificity of trimer densities in chromosomes of many closely related bacteria was compared in parallel with 16S rDNA sequences in these same bacteria. The results of these comparisons indicate that trimer densities in chromosomes can be used to simply and efficiently classify the organisms below genus level.     

High bacterial diversity in permanently cold marine sediments.

A 16S ribosomal DNA (rDNA) clone library from permanently cold marine sediments was established. Screening 353 clones by dot blot hybridization with group-specific oligonucleotide probes suggested a predominance of sequences related to bacteria of the sulfur cycle (43.4% potential sulfate reducers). Within this fraction, the major cluster (19.0%) was affiliated with Desulfotalea sp. and other closely related psychrophilic sulfate reducers isolated from the same habitat. The cloned sequences showed between 93 and 100% similarity to these bacteria. Two additional groups were frequently encountered: 13% of the clones were related to Desulfuromonas palmitatis, and a second group was affiliated with Myxobacteria spp. and Bdellovibrio spp. Many clones (18.1%) belonged to the gamma subclass of the class Proteobacteria and were closest to symbiotic or free-living sulfur oxidizers. Probe target groups were further characterized by amplified rDNA restriction analysis to determine diversity within the groups and within the clone library. Rarefaction analysis suggested that the total diversity assessed by 16S rDNA analysis was very high in these permanently cold sediments and was only partially revealed by screening of 353 clones.     

Molecular evidence for a uniform microbial community in sponges from different oceans

Sponges (class Porifera) are evolutionarily ancient metazoans that populate the tropical oceans in great abundances but also occur in temperate regions and even in freshwater. Sponges contain large numbers of bacteria that are embedded within the animal matrix. The phylogeny of these bacteria and the evolutionary age of the interaction are virtually unknown. In order to provide insights into the species richness of the microbial community of sponges, we performed a comprehensive diversity survey based on 190 sponge-derived 16S ribosomal DNA (rDNA) sequences. The sponges Aplysina aerophoba and Theonella swinhoei were chosen for construction of the bacterial 16S rDNA library because they are taxonomically distantly related and they populate nonoverlapping geographic regions. In both sponges, a uniform microbial community was discovered whose phylogenetic signature is distinctly different from that of marine plankton or marine sediments. Altogether 14 monophyletic, sponge-specific sequence clusters were identified that belong to at least seven different bacterial divisions. By definition, the sequences of each cluster are more closely related to each other than to a sequence from nonsponge sources. These monophyletic clusters comprise 70% of all publicly available sponge-derived 16S rDNA sequences, reflecting the generality of the observed phenomenon. This shared microbial fraction represents the smallest common denominator of the sponges investigated in this study. Bacteria that are exclusively found in certain host species or that occur only transiently would have been missed. A picture emerges where sponges can be viewed as highly concentrated reservoirs of so far uncultured and elusive marine microorganisms.     

Expansion of the geographic distribution of a novel lineage of epsilon-Proteobacteria to a hydrothermal vent site on the Southern East Pacific Rise

The diversity associated with a microbial mat sample collected from a deep-sea hydrothermal vent on the Southern East Pacific Rise was determined using a molecular phylogenetic approach based on the comparison of sequences from the small subunit ribosomal RNA gene (16S rDNA). The DNA was extracted from the sample and the 16S rDNA was amplified by PCR. Sixteen different phylotypes were identified by restriction fragment length polymorphism analysis; four phylotypes were later identified as putative chimeras. Analysis of the 16S rDNA sequences placed all the phylotypes within the Proteobacteria. The majority of the sequences (98%) were most closely related to a new clade of epsilon-Proteobacteria that were initially identified from an in situ growth chamber deployed on a deep-sea hydrothermal vent on the Mid-Atlantic Ridge in 1995. The similarity between phylotypes identified from Atlantic and Pacific deep-sea hydrothermal vent sites indicates that this new clade of Proteobacteria may be endemic to and widely distributed among deep-sea hydrothermal vents.     

Berkleasmium crunisia sp. nov. and its phylogenetic affinities to the Pleosporales based on 18S and 28S rDNA sequence analyses

Berkleasmium crunisia sp. nov. is described from a decaying rachis of Calamus sp. (Arecaceae) from Khuan Ka Long, Satun Province, Thailand. This Berkleasmium species differs morphologically from other species in possessing subtending cells and larger conidia. The phylogenetic relationship of the genus Berkleasmium among sexual ascomycetes also was examined. Sequence analyses from 18S, 28S and ITS-5.8S rDNA were analyzed phylogenetically under maximum parsimony, Bayesian and neighbor joining criteria. Phylogenies revealed that Berkleasmium is not monophyletic. Berkleasmium micronesicum and B. nigroapicale are related to Westerdykella cylindrica and Sporormia australis, which are members of the family Sporormiaceae (Pleosporales). Other species, including our new taxon, appear to share phylogenetic affinities with other anamorphic fungi, whose classification within the Pleosporales is still obscure. Analyses of 18S, 28S, ITS (+5.8S) rDNA and combined (18S+28S) gene sequences fail to give sufficient phylogenetic resolution within the Pleosporales.