First molecular data on the phylum Loricifera: an investigation into the phylogeny of ecdysozoa with emphasis on the positions of Loricifera and Priapulida

Recent progress in molecular techniques has generated a wealth of information for phylogenetic analysis. Among metazoans all but a single phylum have been incorporated into some sort of molecular analysis. However, the minute and rare species of the phylum Loricifera have remained elusive to molecular systematists. Here we report the first molecular sequence data (nearly complete 18S rRNA) for a member of the phylum Loricifera, Pliciloricus sp. from Korea. The new sequence data were analyzed together with 52 other ecdysozoan sequences, with all other phyla represented by three or more sequences. The data set was analyzed using parsimony as an optimality criterion under direct optimization as well as using a Bayesian approach. The parsimony analysis was also accompanied by a sensitivity analysis. The results of both analyses are largely congruent, finding monophyly of each ecdysozoan phylum, except for Priapulida, in which the coelomate Meiopriapulus is separate from a clade of pseudocoelomate priapulids. The data also suggest a relationship of the pseudocoelomate priapulids to kinorhynchs, and a relationship of nematodes to tardigrades. The Bayesian analysis placed the arthropods as the sister group to a clade that includes tardigrades and nematodes. However, these results were shown to be parameter dependent in the sensitivity analysis. The position of Loricifera was extremely unstable to parameter variation, and support for a relationship of loriciferans to any particular ecdysozoan phylum was not found in the data.     

Culturable Bacterial Symbionts Isolated from Two Distinct Sponge Species (Pseudoceratina clavata and Rhabdastrella globostellata) from the Great Barrier Reef Display Similar Phylogenetic Diversity

The diversity of the culturable microbial communities was examined in two sponge species—Pseudoceratina clavata and Rhabdastrella globostellata. Isolates were characterized by 16S rRNA gene sequencing and phylogenetic analysis. The bacterial community structures represented in both sponges were found to be similar at the phylum level by the same four phyla in this study and also at a finer scale at the species level in both Firmicutes and Alphaproteobacteria. The majority of the Alphaproteobacteria isolates were most closely related to isolates from other sponge species including alpha proteobacterium NW001 sp. and alpha proteobacterium MBIC3368. Members of the low %G + C gram-positive (phylum Firmicutes), high %G + C gram-positive (phylum Actinobacteria), and Cytophaga–Flavobacterium–Bacteroides (phylum Bacteroidetes) phyla of domain Bacteria were also represented in both sponges. In terms of culturable organisms, taxonomic diversity of the microbial community in the two sponge species displays similar structure at phylum level. Within phyla, isolates often belonged to the same genus-level monophyletic group. Community structure and taxonomic composition in the two sponge species P. clavata and Rha. globostellata share significant features with those of other sponge species including those from widely separated geographical and climatic regions of the sea.     

CONVERGENT EVOLUTION IN INVERTEBRATES

Resemblance between animal taxa may be due to convergence rather than to recent common ancestry. Constraints on biological materials and adaptation to particular habits or habitats will produce widespread convergence. How may we distinguish the two causes of resemblance? The relationship between convergence and taxonomy is discussed, demonstrating that the choice of taxonomic method will itself determine the extent to which convergence is perceived. In particular, cladistic analysis based on parsimony will tend to minimise and thus conceal convergence: neither the resulting cladogram nor a consistency index derived from it can be used to assess the prevalence of convergence. With any taxonomic system, there can be no substitute for evaluation of the morphological characters used. Complementary use of molecular characters shows promise: we wait further understanding of constraints in genetic evolution and of the possibilities of convergence at this level also. These general principles are illustrated with a range of examples from within and between invertebrate phyla: the phylogeny of Cnidaria and Platyhelminthes cannot be traced with certainty, but where the fossil record allows clear rooting, as for the echinoderms and in particular the echinoids, combination of morphological and molecular methods has made much progress. Sub-groups within a phylum, for example opisthobranch molluscs and the dipteran Phoridae, may show an uncontested phylogeny, and here studies have precisely identified convergence and shown that it may be the commoner cause of resemblance. Adaptation to exacting environments shown by terrestial and freshwater nemertines may also result in a predominance of convergent resemblance. Traditional grouping of phyla breaks down on re-examination of supposedly key characters, such as segmentation, body cavities, germ layers and symmetry, each of which must have had multiple origins: nor are developmental stages (especially not larvae) a reliable guide to relationships. Demarcation of phyla may be difficult, as with arthropods, and location of phyla is even more difficult, due to their early and rapid radiation. Over-simplified definition of characters has bedevilled invertebrate classification and the use of molecular data has not yet resolved the major controversies. The question ‘How common is convergence?’ remains unanswered and may be unanswerable. Our examples indicate that even the minimum detectable levels of convergence are often high, and we conclude that at all levels convergence has been greatly underestimated.     

Phylogeny and biogeography of the "Australian" trichostomes (Ciliophora: Litostomata)

The phylogenetic relationships of members of the ciliate class Litostomatea were determined by a molecular phylogeny using the small subunit of the ribosomal RNA (ssu-rRNA) gene and a morphological phylogeny based on ultrastructural analyses of the group. Molecular analyses consistently supported the monophyly of Trichostomatia, Entodiniomorphida and the "Australian" trichostomes but provided limited support for a monophyletic Vestibuliferida and Haptoria. The results of the morphological analyses depended on the way in which the dataset was treated: "unordered" and "ordered" recovered a monophyletic Trichostomatia, Haptoria and the "Australian" trichostomes but challenged the monophyly of Entodinimorphida and Vestibuliferida; "dollo" recovered a monophyletic Trichostomatia and Entodiniomorphida but at the cost of a greatly longer tree than either "unordered" or "ordered" datasets. The monophyly of each "Australian" trichostome family was supported in all analyses and by both approaches. These results suggest that the trichostome ciliates may have become associated with mammals in Gondwana with the "Australian" trichostome ciliates entering Australia with primitive herbivorous marsupials. Subsequent diversification of the "Australian" families was probably a result of dietary specialization and oral and cortical synapomorphies define each family. We decline at this time to erect a formal taxon name for the "Australian" trichostomes due to the instability of other superfamilial taxa within the Litosomatea and concerns about the stability of tree topology until a better taxon sample of litostome ciliates is available.     

以演化时间为新增指标构建真菌分类系统

随着分子系统发育研究的普及,真菌各分类类群逐渐被修订为单系发生类群,通常结合形态学特征为代表的表型特征("单系+表型特征")对不同的分类等级命名是最为普遍的方法.历史上存在的大量多系名称被逐步修订、补充和完善,各个不同等级类群的分类系统变得更加合理、客观和趋于自然,这是分类学进程中巨大的进步.然而系统发育重建所揭示的单...     

Novelty in phylogeny of gastrotricha: evidence from 18S rRNA gene

Gastrotricha form a phylum which is crucial for defining the origin of pseudocoelomates, in that they share a number of characters with Rotifera and Nematoda but also with acoelomates, and even the evolutionary relationships within the phylum are anything but defined. For this reason the first extensive molecular data on Gastrotricha from the 18S rRNA sequences of both orders have been obtained and analyzed. Sequence analyses show that the phylum Gastrotricha is strictly monophyletic along an evolutionary line quite distinct from that of both Rotifera and Nematoda. A new view of the evolutionary history of the phylum Gastrotricha is put forward, in which Chaetonotida, and not Macrodasyida, are the most primitive forms of the group, contrary to the commonly held view. A polyphyletic origin of aschelminthes is supported, and the misleading term pseudocoelomates should be discarded.     

Sensitivity analysis of different methods of coding taxonomic polymorphism: an example from higher-level bat phylogeny

New information concerning strengths and weaknesses of different methods of coding taxonomic polymorphisms suggests that results of some previous studies may have been unintentionally biased by the methods employed. In this study, we demonstrate that a form of sensitivity analysis can be used to evaluate the effects of different methods of coding taxonomic polymorphisms on the outcome of phylogenetic analyses. Our earlier analysis of higher‐level relationships of bats (Mammalia: Chiroptera) employed superspecific taxa as terminals and scored taxonomic polymorphisms using ambiguity coding. Application of other methods of dealing with polymorphisms (excluding variable characters, inferring ancestral states, majority coding) to the same data yields phylogenetic results that differ somewhat from those originally reported based on ambiguity coding. Monophyly of some clades was supported in all analyses (e.g., Microchiroptera, Rhinopomatoidea, and Nataloidea), while other groups found to be monophyletic in the original study (e.g., neotropical Nataloidea) appeared unresolved or nonmonophyletic when other methods were used to code taxonomic polymorphisms. Several groupings that were apparently refuted in the initial study (e.g., Noctilionoidea including Mystacinidae) were supported in some analyses, reducing some of the apparent incongruence between the trees in our earlier analysis (which were based principally on morphology) and other trees based on molecular data. Perceived support for various groupings (branch support, bootstrap values) were in some cases significantly affected by the methods employed. These results indicate that sensitivity analysis provides a useful tool for evaluating effects of different methods of dealing with taxonomic polymorphism in superspecific terminal taxa. Variation in results obtained with different methods suggests that it is always preferable to sample at the species level when higher‐level taxa exhibit taxonomic polymorphism, thus avoiding methodological biases associated with different methods of dealing with taxonomic polymorphisms during data analysis.     

The Candidate Phylum Poribacteria by Single-Cell Genomics: New Insights into Phylogeny,Cell-Compartmentation,Eukaryote-Like Repeat Proteins,and Other Genomic Features

The candidate phylum Poribacteria is one of the most dominant and widespread members of the microbial communities residing within marine sponges. Cell compartmentalization had been postulated along with their discovery about a decade ago and their phylogenetic association to the Planctomycetes, Verrucomicrobia, Chlamydiae superphylum was proposed soon thereafter. In the present study we revised these features based on genomic data obtained from six poribacterial single cells. We propose that Poribacteria form a distinct monophyletic phylum contiguous to the PVC superphylum together with other candidate phyla. Our genomic analyses supported the possibility of cell compartmentalization in form of bacterial microcompartments. Further analyses of eukaryote-like protein domains stressed the importance of such proteins with features including tetratricopeptide repeats, leucin rich repeats as well as low density lipoproteins receptor repeats, the latter of which are reported here for the first time from a sponge symbiont. Finally, examining the most abundant protein domain family on poribacterial genomes revealed diverse phyH family proteins, some of which may be related to dissolved organic posphorus uptake.     

Cladistic analyses of the animal kingdom

A recently published book on the phylogeny of the animal kingdom, written by the first author, provided a classification based on a 'manual' cladistic analysis at the phylum level. We have extracted a data matrix consisting of 61 characters for 32 phyla from this book and treated it in more formal analyses using three different parsimony programs. Following a posteriori weighting, one cladogram emerged as the most parsimonious explanation of the data. This cladogram is compared to those in recent publications. Congruence is greatest with the phylogeny published by the first author, as the monophyly of 18 of the 21 supraphyletic categories proposed therein are supported in our cladogram. The exceptions are Aschelminthes, Frotornaeozoa and Neorenalia, but the latter group does emerge as a monophyletic taxon in a number of equally parsimonious, equally weighted trees. Comparisons with other recent phytogenies show varying degrees of divergence, especially concerning the monophyly of Spiralia and Aiticulata, both of which are advocated in the present paper. Significant characters of most of the supraphyletic taxa proposed by the first author are discussed. C1996 The Linnean Society of London     

megB1, a novel macroevolutionary genomic marker of the fungal phylum Basidiomycota

Molecular studies on the evolution and systematics of fungi have been established primarily based on the neutral theory by analyzing neutral mutations in some defined segments of housekeeping genes as genetic markers. Such an approach is, however, hardly applicable for analyzing ancient evolutionary radiations. In the present study, we looked for DNA sequences characterizing higher taxa, and discovered a unique macroevolutionary genomic marker, megB1, that specifies the phylum Basidiomycota. megB1 is an approximately 500-bp DNA element, which is defined by terminal sequences and five internal segments conserved throughout the phylum. megB1 resides on the rDNA intergenic spacer 1 (IGS1) from 27 species of 10 Basidiomycota genera examined. While megB1 was not found in IGS1 from the other 92 species of the 27 Basidiomycota genera, several genera representing them carry megB1 in some other genomic regions. No known taxonomic criteria fit into the classification on the basis of whether megB1 resides on rDNA. Neighbor-joining analysis of the megB1 sequence, however, properly assigned species to their respective genera. Thus far, megB1 has not been found in any genomic or genetic databases currently available for other phyla. These results suggest that megB1 may have emerged upon the occurrence of Basidiomycota, and that this phylum evolved thereafter leaving this element conserved throughout their further differentiation. megB1 may be a novel genomic marker useful in the analysis of ancient through the latest evolutionary radiation in Basidiomycota.     

The evolution of the Ecdysozoa

Ecdysozoa is a clade composed of eight phyla: the arthropods, tardigrades and onychophorans that share segmentation and appendages and the nematodes, nematomorphs, priapulids, kinorhynchs and loriciferans, which are worms with an anterior proboscis or introvert. Ecdysozoa contains the vast majority of animal species and there is a great diversity of body plans among both living and fossil members. The monophyly of the clade has been called into question by some workers based on analyses of whole genome datasets. We review the evidence that now conclusively supports the unique origin of these phyla. Relationships within Ecdysozoa are also controversial and we discuss the molecular and morphological evidence for a number of monophyletic groups within this superphylum.     

Comparative aspects of invertebrate neuropeptides

1. We searched for bioactive peptides, most of which were considered to be neuropeptides, in various animals of several phyla. These peptides were compared with each other and with peptides identified by many other investigators. Consequently, we found that structures of neuropeptides are generally conserved in each phylum. 2. We also found some exceptional interesting aspects. First, there are a number of peptide groups whose members are distributed among several phyla. Second, there are many structural similarities between molluscan and annelidan peptides as if molluscs and annelids were the animals in a phylum. Third, certain toxic peptides of invertebrates are closely related to vertebrate neuropeptides. 3. In addition to the above phylogenetic aspects, we found some other interesting aspects. A wide structural variety of members of a peptide group is generally found in invertebrate species. Invertebrate muscles seem to be generally regulated not only by some or several classical non-peptidic neuromediators but also by various peptidic neuromediators. Peptides containing a D-amino acid residue are not rare.     

Evolutionary relationships among basal fungi (Chytridiomycota and Zygomycota): Insights from molecular phylogenetics

Evolutionary relationships of the two basal fungal phyla Chytridiomycota and Zygomycota are reviewed in light of recent molecular phylogenetic investigation based on rDNA (nSSU, nLSU rDNA), entire mitochondrial genomes, and nuclear protein coding gene sequences (e.g., EF-1alpha, RPB1). Accumulated molecular evidence strongly suggests that the two basal fungal phyla are not monophyletic. For example, the chytridiomycete order Blastocladiales appears to be closely related to the zygomycete order Entomophthorales. Within the Zygomycota, a monophyletic clade, consisting of the Dimargaritales, Harpellales, and Kickxellales, which is characterized by a shared unique septal ultrastructure, was identified. Moreover, evidence for the exclusion of zygomycete orders Amoebidiales and Eccrinales from the Fungi, and their placement at the Animal-Fungi boundary has been clearly documented. Microsporidia, a group of amitochondriate organisms currently under intensive study, is not supported as derived within the Fungi, but a fungal affinity cannot be ruled out. Taking these molecular phylogenetic studies into account, we proposed a hypothetical evolutionary framework of basal fungi.     

A molecular approach to arthrotardigrade phylogeny (Heterotardigrada,Tardigrada)

The marine order Arthrotardigrada (class Heterotardigrada, phylum Tardigrada) is known for its conspicuously high morphological diversity and has been traditionally recognized as the most ancestral group within the phylum. Despite its potential importance in understanding the evolution of the phylum, the phylogenetic relationships of Arthrotardigrada have not been clarified. This study conducted molecular phylogenetic analyses of the order encompassing all families except Neoarctidae using nuclear 18S and 28S rRNA fragments. Data from two rare families, Coronarctidae and Renaudarctidae, were included for the first time. The analyses confirmed the monophyly of Heterotardigrada and inferred Coronarctidae as the sister group to all other heterotardigrade taxa. Furthermore, the results support a monophyletic Renaudarctidae + Stygarctidae clade, which has been previously suggested on morphology. Our data indicated that two subfamilies currently placed in Halechiniscidae are only distantly related to this family. We propose that these taxa are each elevated to family level (Styraconyxidae (new rank) and Tanarctidae (new rank)). The morphology of tardigrades is discussed in the context of the inferred phylogeny.     

Molecular phylogenetic evidence that the phylum Haplosporidia has an alveolate ancestry

The phylogenetic position of the phylum Haplosporidia among other protists was investigated with the complete 16S-like rRNA gene sequences from two species in the phylum: Haplosporidium nelsoni, a parasite of oysters, and Minchinia teredinis, a parasite of shipworms. Because the lack of obvious morphological homologies with other protists hampered decisions regarding taxonomic composition for sequence alignment and phylogenetic analysis, the complete sequences for these two haplosporidians were directed as search queries to the blast/ncbi.nlm.nih.gov electronic mail server. The results of this heuristic similarity search provided a basis for constructing a preliminary higher-taxonomic-level analysis comparing the haplosporidians with species from the slime molds, fungi, algae, amoebae, ciliates, dinoflagellates, and apicomplexans. Maximum parsimony yielded equivocal results, whereas transversionally weighted parsimony suggested an affinity with the alveolates (i.e., the ciliates, dinoflagellates, and apicomplexans). Multiple alignment of the two haplosporidian sequences against 17 taxa in a secondary analysis focusing on the alveolates and subsequent parsimony analysis placed the phylum Haplosporidia as a monophyletic group within the Alveolata and as a taxon of equal rank with the other three alveolate phyla. The precise placement within the Alveolata was sensitive to weighting.      

Lophotrochozoan phylogeny assessed with LSU and SSU data: evidence of lophophorate polyphyly

Of the three major bilaterian clades, Lophotrochozoa has the greatest diversity and disparity of body forms and is the least understood in terms of phylogenetic history. Within this clade, small nuclear ribosomal subunit (SSU or 18S) studies have failed to provide resolution and other molecular markers have insufficient taxon sampling. To examine relationships within Lophotrochozoa, we collected and complied complete SSU data and nearly complete (>90%) large nuclear ribosomal subunit (LSU or 28S) data totaling approximately 5kb per taxon, for 36 lophotrochozoans. Results of LSU and combined SSU+LSU likelihood analyses provide topologies more consistent with morphological data than analyses of SSU data alone. Namely, most phyla recognized on morphological grounds are recovered as monophyletic entities when the LSU data is considered (contra SSU data alone). These new data show with significant support that "Lophophorata" (traditionally recognized to include Brachiopoda, Phoronida, and Bryozoa) is not a monophyletic entity. Further, the data suggest that Platyzoa is real and may be derived within lophotrochozans rather than a basal or sister taxon. The recently discovered Cycliophora are allied to entoprocts, consistent with their initial placement based on morphology. Additional evidence for Syndermata (i.e., Rotifera+Acanthocephala) is also found. Although relationships among groups with trochophore-like larvae could not be resolved and nodal support values are generally low, the addition of LSU data is a considerable advance in our understanding of lophotrochozoan phylogeny from the molecular perspective.     

Consistency and variation in kelp holdfast assemblages: Spatial patterns of biodiversity for the major phyla at different taxonomic resolutions

The focus of this study was to measure natural spatial variability in the biodiversity of fauna inhabiting kelp holdfasts in northeastern New Zealand at several spatial scales: from meters up to hundreds of kilometers. We wished to test the hypothesis that multivariate variation and biodiversity would vary significantly at different spatial scales in different ways for the major phyla in the holdfast community (Arthropoda, Annelida, Mollusca and Bryozoa). Biodiversity was considered in terms of richness, total abundance, structural composition (as measured by the Bray-Curtis dissimilarity measure) and taxonomic breadth for each major phylum and for the assemblage as a whole. We also examined the effect of taxonomic resolution on multivariate patterns. Species richness and total abundance increased with increases in holdfast volume. Multivariate variation was greatest at the smallest spatial scale for all phyla, but different phyla showed different patterns of multivariate variation at different spatial scales. Variations among locations at the largest spatial scale were primarily due to differences in the composition and richness of bryozoans and molluscs. Location effects became less and less distinct with decreases in taxonomic resolution. There were very few significant differences in richness or abundance for holdfasts of a given volume, taxonomic breadth did not vary significantly across locations, nor did the proportional abundances of phyla. These consistencies across large spatial scales in the absence of environmental impacts and results from other studies suggest that holdfast communities in New Zealand systems would provide a useful model assemblage against which future impacts may be detected as changes in proportions of component phyla. In addition, high variability detected at small and large scales at the species level, especially for bryozoans and molluscs, suggest that these communities may also provide unique opportunities for studying and understanding sources and functions of marine biodiversity.     

The kingdom Protista and its 45 phyla

Because most recent treatments of the protists ('lower' eukaryotes comprising the kingdom PROTISTA Haeckel, 1866) have been preoccupied with either a 'phylogenetic-tree' approach or a discussion of the impact of possible endosymbiotic origins of major intracellular organelles, the overall systematics of the group, from taxonomic and nomenclatural points of view, has been almost totally neglected. As a result, confusion over contained phyla, their places in a classification scheme, and even their names (and authorships) is growing; the situation could become chaotic. The principal objective of the present paper is to recognize the taxonomic interrelationships among all protist groups; and it includes the specific proposal that some 45 phyla, defined and characterized, be assigned to 18 supraphyletic assemblages within the kingdom PROTISTA (itself redefined and contrasted with the other eukaryotic kingdoms recognized here: ANIMALIA, PLANTAE and FUNGI). Vernacular terms are employed for identification of the 18 assemblages, but defensible formal names are proposed at the level of phylum. None is presented as new: authorship-and-date credits are given to preceding workers on the taxonomy of the many groups involved. By presenting taxonomic characterizations as well as relevant nomenclatural data for each taxon described, a comprehensive scheme of overall higher-level classification within the kingdom emerges that may be considered to serve as a solid base or 'taking-off point' for future discussions. The 18 supraphyletic groups and their phyla (in parentheses and including authorships and dates of their formal names) are as follows: I. The rhizopods (phyla Karyoblastea Margulis, 1974; Amoebozoa Lühe, 1913; Acrasia Van Tieghem, 1880; Eumycetozoa Zopf, 1885; Plasmodiophorea Zopf, 1885; Granuloreticulosa De Saedeleer, 1934; incertae sedis Xenophyophora Schulze, 1904). II. The mastigomycetes (Hypochytridiomycota Sparrow, 1959; Oomycota Winter, 1897; incert. sed. Chytridiomycota Sparrow, 1959). III. The chlorobionts (Chlorophyta Pascher, 1914; Prasinophyta Christensen, 1962; Conjugatophyta Engler, 1892; Charophyta Rabenhorst, 1863; incert. sed. Glaucophyta Bohlin, 1901). IV. The euglenozoa (Euglenophyta Pascher, 1931; Kinetoplastidea Honigberg, 1963; incert. sed. Pseudociliata Corliss & Lipscomb, 1982). V. The rhodophytes (Rhodophyta Rabenhorst, 1863). VI. The cryptomonads (Cryptophyta Pascher, 1914). VII. The choanoflagellates (Choanoflagellata Kent, 1880).(ABSTRACT TRUNCATED AT 400 WORDS)     

Combined large and small subunit ribosomal RNA phylogenies support a basal position of the acoelomorph flatworms

The phylogenetic position of the phylum Platyhelminthes has been re-evaluated in the past decade by analysis of diverse molecular datasets. The consensus is that the Rhabditophora + Catenulida, which includes most of the flatworm taxa, are not primitively simple basal bilaterians but are related to coelomate phyla such as molluscs. The status of two other groups of acoelomate worms, Acoela and Nemertodermatida, is less clear. Although many characteristics unite these two groups, initial molecular phylogenetic studies placed the Nemertodermatida within the Rhabditophora, but placed the Acoela at the base of the Bilateria, distant from other flatworms. This contradiction resulted in scepticism about the basal position of acoels and led to calls for further data. We have sequenced large subunit ribosomal RNA genes from 13 rhabditophorans + catenulids, three acoels and one nemertodermatid, tripling the available data. Our analyses strongly support a basal position of both acoels and nemertodermatids. Alternative hypotheses are significantly less well supported by the data. We conclude that the Nemertodermatida and Acoela are basal bilaterians and, owing to their unique body plan and embryogenesis, should be recognized as a separate phylum, the Acoelomorpha.