Mitochondrial diversity of early-branching metazoa is revealed by the complete mt genome of a haplosclerid demosponge

The first mitochondrial (mt) genomes of demosponges have recently been sequenced and appear to be markedly different from published eumetazoan mt genomes. Here we show that the mt genome of the haplosclerid demosponge Amphimedon queenslandica has features that it shares with both demosponges and eumetazoans. Although the A. queenslandica mt genome has typical demosponge features, including size, long noncoding regions, and bacterialike rRNA genes, it lacks atp9, which is found in the other demosponges sequenced to date. We found strong evidence of a recent transposon-mediated transfer of atp9 to the nuclear genome. In addition, A. queenslandica bears an incomplete tRNA set, unusual amino acid deletion patterns, and a putative control region. Furthermore, the arrangement of mt rRNA genes differs from that of other demosponges. These genes evolve at significantly higher rates than observed in other demosponges, similar to previously observed nuclear rRNA gene rates in other haplosclerid demosponges.     

Origin and evolution of animal life cycles

The ‘origin of larvae’ has been widely discussed over the years, almost invariably with the tacit understanding that larvae are secondary specializations of early stages in a holobenthic life cycle. Considerations of the origin and early radiation of the metazoan phyla have led to the conclusion that the ancestral animal (= metazoan) was a holopelagic organism, and that pelago-benthic life cycles evolved when adult stages of holopelagic ancestors became benthic, thereby changing their life style, including their feeding biology. The literature on the larval development and phylogeny of animal phyla is reviewed in an attempt to infer the ancestral life cycles of the major animal groups. The quite detailed understanding of larval evolution in some echinoderms indicates that ciliary filter-feeding was ancestral within the phylum, and that planktotrophy has been lost in many clades. Similarly, recent studies of the developmental biology of ascidians have demonstrated that a larval structure, such as the tail of the tadpole larva, can easily be lost, viz. through a change in only one gene. Conversely, the evolution of complex structures, such as the ciliary bands of trochophore larvae, must involve numerous genes and numerous adaptations. The following steps of early metazoan evolution have been inferred from the review. The holopelagic ancestor, blastaea, probably consisted mainly of choanocytes, which were the feeding organs of the organism. Sponges may have evolved when blastaea-like organisms settled and became reorganized with the choanocytes in collar chambers. The eumetazoan ancestor was probably the gastraea, as suggested previously by Haeckel. It was holopelagic and digestion of captured particles took place in the archenteron. Cnidarians and ctenophores are living representatives of this type of organization. The cnidarians have become pelago-benthic with the addition of a sessile, adult polyp stage; the pelagic gastraea-like planula larva is retained in almost all major groups, but only anthozoans have feeding larvae. Within the Bilateria, two major lines of evolution can be recognized: Protostomia and Deuterostomia. In protostomes, trochophores or similar types are found in most spiralian phyla; trochophore-like ciliary bands are found in some rotifers, whereas all other aschelminths lack ciliated larvae. It seems probable that the trochophore was the larval type of the ancestral, pelago-benthic spiralian and possible that it was ancestral in all protostomes. Most of the non-chordate deuterostome phyla have ciliary filter-feeding larvae of the dipleurula type, and this strongly indicates that the ancestral deuterostome had this type of larva.     

Old trees, new trees--is there any progress?

The amount of comparative data for phylogenetic analyses is constantly increasing. Data come from different directions such as morphology, molecular genetics, developmental biology and paleontology. With the increasing diversity of data and of analytical tools, the number of competing hypotheses on phylogenetic relationships rises, too. The choice of the phylogenetic tree as a basis for the interpretation of new data is important, because different trees will support different evolutionary interpretations of the data investigated. I argue here that, although many problematic aspects exist, there are several phylogenetic relationships that are supported by the majority of analyses and may be regarded as something like a robust backbone. This accounts, for example, for the monophyly of Metazoa, Bilateria, Deuterostomia, Protostomia (= Gastroneuralia), Gnathifera, Spiralia, Trochozoa and Arthropoda and probably also for the branching order of diploblastic taxa (“Porifera”, Trichoplax adhaerens, Cnidaria and Ctenophora). Along this “backbone”, there are several problematic regions, where either monophyly is questionable and/or where taxa “rotate” in narrow regions of the tree. This is illustrated exemplified by the probable paraphyly of Porifera and the phylogenetic relationships of basal spiralian taxa. Two problems span wider regions of the tree: the position of Arthropoda either as the sister taxon of Annelida (= Articulata) or of Cycloneuralia (= Ecdysozoa) and the position of tentaculate taxa either as sister taxa of Deuterostomia (= Radialia) or within the taxon Spiralia. The backbone makes it possible to develop a basic understanding of the evolution of genes, molecules and structures in metazoan animals.     

Phylogenomic analyses of lophophorates (brachiopods, phoronids and bryozoans) confirm the Lophotrochozoa concept

Based on embryological and morphological evidence, Lophophorata was long considered to be the sister or paraphyletic stem group of Deuterostomia. By contrast, molecular data have consistently indicated that the three lophophorate lineages, Ectoprocta, Brachiopoda and Phoronida, are more closely related to trochozoans (annelids, molluscs and related groups) than to deuterostomes. For this reason, the lophophorate groups and Trochozoa were united to Lophotrochozoa. However, the relationships of the lophophorate lineages within Lophotrochozoa are still largely unresolved. Maximum-likelihood and Bayesian analyses were performed based on a dataset comprising 11,445 amino acid positions derived from 79 ribosomal proteins of 39 metazoan taxa including new sequences obtained from a brachiopod and a phoronid. These analyses show that the three lophophorate lineages are affiliated with trochozoan rather than deuterostome phyla. All hypotheses claiming that they are more closely related to Deuterostomia than to Protostomia can be rejected by topology testing. Monophyly of lophophorates was not recovered but that of Bryozoa including Ectoprocta and Entoprocta and monophyly of Brachiozoa including Brachiopoda and Phoronida were strongly supported. Alternative hypotheses that are refuted include (i) Brachiozoa as the sister group of Mollusca, (ii) ectoprocts as sister to all other Lophotrochozoa including Platyzoa, and (iii) ectoprocts as sister or to all other protostomes except chaetognaths.     

The Interrelationships of the Gastrotricha Using Nuclear Small rRNA Subunit Sequence Data, with an Interpretation Based on Morphology

Gastrotrichs are meiobenthic invertebrates of obscure origin and unclear phylogenetic alliances. Uncertainties also plague the intra-group relationship with major contrasts between the evolutionary scenarios inferred from morphology or molecules. In this study we analysed partial sequences of the 18S rDNA gene of 18 taxa (14 new and 4 published) to test morphological estimates of gastrotrich phylogeny and to verify whether controversial interrelationships from previous molecular data are due to poor sampling. Data were analysed using both maximum parsimony and maximum likelihood. MP topology was then forced to reflect published morphological estimates and the most parsimonious solutions from each constraint analysis was statistically compared against the unconstrained solution. MP analysis yielded a single tree with few nodes well supported by bootstrap resampling. These included the monophyly of the Chaetonotidae and the internal relationships of the members of this family, with Aspidiophorus appearing as the most basal member. The monophyly of the Turbanellidae was also well supported with some suggestion that its sister group might be Mesodasys. Lepidodasyidae was found to be an unnatural taxon with Lepidodasys forming a separated clade but unrelated also to the Thaumastodermatidae. With the exception of genera Lepidodasys and Neodasys, the Macrodasyida appeared to be resolved separately from the Chaetonotida, and Dactylopodola was resolved as the most basal macrodasyid. ML analysis yielded a tree not too dissimilar from MP, although Dactylopodola and Xenodasys were resolved as a clade. Statistics indicate that the output from our MP analysis is compatible with the classical view placing representatives of the two orders within two distinct evolutionary lines. Most of the constrained solutions, except the shortest, corroborate the monophyly of the two orders, whereas all five constrained solutions support also the notion that sees Neodasys as an early divergent clade along the Chaetonotida branch. Thus, results are generally compatible with the hypothesised evolutionary scenario based on morphological data, but are in contrast with previous findings from molecules. Future research should consider using the complete SSU rDNA gene sequence in their analysis and additional genes for deeper resolution.     

The phylogenetic significance of sperm morphology in the Platyhelminthes

The phylogenetic significance of flatworm sperm morphology is discussed against the background of general spermatology. The modified type of spermatozoon of the Nemertodermatida, a group of primitive flatworms, indicates that the Platyhelminthes evolved from forms characterized by the primitive type of metazoan sperm and by the primitive mode of fertilization, implying the release of sperm freely into sea water.The occurrence of aberrant types of spermatozoa in most platyhelminths is obviously a consequence of early evolution of the internal mode of fertilization, which characterizes all true members of this group. It can be concluded, from the ultrastructure of these aberrant spermatozoa that higher metazoans cannot have evolved from seriated flatworms related to the recent Seriata (Proseriata and Tricladida). Even the seemingly primitive Acoela have such aberrant spermatozoa that evolution of higher metazoans from acoels related to the recent Acoela seems highly improbable.The ultrastructure of the spermatozoa of the parasitic groups of flatworms (Monogenea, Digenea, Cestoda) is very similar to that found in the Kalyptorhynchia, a further indication that the parasitic groups are related to the rhabdocoel turbellarians.     

Assembling the lophotrochozoan (=spiralian) tree of life

The advent of numerical methods for analysing phylogenetic relationships, along with the study of morphology and molecular data, has driven our understanding of animal relationships for the past three decades. Within the protostome branch of the animal tree of life, these data have sufficed to establish its two main side branches, the moulting Ecdysozoa and the non-moulting Lophotrochozoa. In this review, I explore our current knowledge of protostome relationships and discuss progress and future perspectives and strategies to increase resolution within the main lophotrochozoan clades. Novel approaches to coding morphological characters are needed by scoring real observations on species selected as terminals. Still, methodological issues, for example, how to deal with inapplicable characters or the coding of absences, may require novel algorithmic developments. Taxon sampling is another key issue, as phyla should include enough species so as to represent their span of anatomical disparity. On the molecular side, phylogenomics is playing an increasingly important role in elucidating animal relationships, but genomic sampling is still fairly limited within the lophotrochozoan protostomes, for which only three phyla are represented in currently available phylogenies. Future work should therefore concentrate on generating novel morphological observations and on producing genomic data for the lophotrochozoan side of the animal tree of life.     

Major discrepancy between phylogenetic hypotheses based on molecular and morphological criteria within the Order Haplosclerida (Phylum Porifera: Class Demospongiae)

Taxonomy within the sponge Order Haplosclerida remains somewhat contentious. Both morphology and biochemistry have been employed to help unravel the relationships of the Order with limited results perhaps because of the small number of reliable characters. We employed phylogenetic analysis of 750 base pairs of the 5′ end of the 28S rRNA gene to study relationships between 20 taxa within the Order. While preliminary (low number of taxa, one gene region) results suggested strong discrepancy to former phylogenies, there was no support for the monophyly of the Order and almost all morphologically defined genera appeared to be polyphyletic.     

The grand game of metazoan phylogeny: rules and strategies

Many cladistic analyses of animal phylogeny have been published by authors arguing that their results are well supported. Comparison of these analyses indicates that there can be as yet no general consensus about the evolution of the animal phyla. We show that the various cladistic studies published to date differ significantly in methods of character selection, character coding, scoring and weighting, ground-pattern reconstructions, and taxa selection. These methodological differences are seldom made explicit, which hinders comparison of different studies and makes it impossible to assess a particular phylogeny outside its own scope. The effects of these methodological differences must be considered before we can hope to reach a morphological reference framework needed for effective comparison and combination with the evidence obtained from molecular and developmental genetic studies.     

Phylogenetic Relationships of Species of the Genus Kluyveromyces van der Walt (Saccharomycetaceae) Deduced from the Partial Sequences of 18S and 26S Ribosomal RNAs

In order to clarify the phylogenetic relationships of the species classified in the genus Kluyveromyces (Saccharomycetaceae), three partial base sequences of 18S and 26S rRNAs of eighteen strains were determined. The regions determined of the strains corresponded to positions 1451 through 1618 (168 bases) of 18S rRNA and to positions 1611 through 1835 (225 bases) and 493 through 622 (130 bases) of a strain (IFO 2376) of Saccharomyces cerevisiae. The analyses of the partial base sequences suggested that the genus Kluyveromyces is phylogenetically heterogeneous, ranging from the strains that are quite close to the strain of S. cerevisiae to the strains that are distinct enough to be classified in genera separate from the genus Saccharomyces. From our sequence data, we concluded that the extent of the genus Kluyveromyces should be restricted to only one species, K. polysporus, the type species of the genus. Kluyveromyces phaffii was also distinct enough to deserve another genus. Kluyveromyces cellobiovorus was not close to any of the strains of Kluyveromyces species examined, and should be excluded from the genus. Most of the strains of the species examined were fairly close to the strain of S. cerevisiae.     

由部分核糖体RNA序列确定的绿僵菌属种系统发育关系

本研究应用特异寡聚核苷酸引物和双脱氧核苷酸终止法测定绿僵菌Metarhizium不同种的部分rRNA序列。这些序列分别选自小亚基(18S)和大亚基(25S)rRNA上的不同区域。校排的不同序列用于计算核苷酸的差异。绿僵菌的系统发育关系采用最大可能性(Maximum-Likelihood)方法分析。所有的分类单元聚类成二个分支。在产生圆柱状瓶形小梗的种中,M.anisopliae var.anisopliae,M.anisopliae var.majus,M.brunneum(NRRL1944),M.guizhouense,M.pingshaense和未知种M.sp.2组成一个密切相关的群组,而M.anisopliae(ACCC 30104)位于这群组之外。在产生棍棒状瓶形小梗的种中,M.album,M.cylindrosporae和M.flavoviride互相独立成支。实验结果不支持Metarhizium只能区分为M.anisopliae和M.flavoviride二个种的分类观点。文中还讨论了经典分类标准的系统发育价值。     

Planktic foraminiferal molecular evolution and their polyphyletic origins from benthic taxa

Phylogenetic analyses based on partial sequences of the small subunit (SSU) ribosomal (r) RNA gene have shown that the planktic and benthic foraminifera form a distinct monophyletic group within the eukaryotes. In order to determine the evolutionary relationships between benthic and planktic foraminifers, representatives of spinose and non-spinose planktic genera have been placed within a molecular SSU rDNA phylogeny containing sequences of the benthic suborders available to date. Our phylogenetic analysis shows that the planktic foraminifers are polyphyletic in origin, not evolving solely from a single ‘globigerinid-like’ lineage in the Mid-Jurassic, but derived from at least two ancestral benthic lines. The benthic ancestor of Neogloboquadrina dutertrei may have entered the plankton later than the Mid-Jurassic, and further investigation of related extant species should provide an indication of the timing of this event. The evolutionary origin of the non-spinose species Globorotalia menardii remains unclear. The divergences of the planktic spinose species generally support recent phylogenies based on the fossil record, which infer a radiation from a globigerinid common ancestor in the Mid- to Late Oligocene. The branching pattern indicates that there are possibly four distinct groups within the main spinose clade, with large evolutionary distances being observed between them. Globigerinoides conglobatus clusters strongly with Globigerinoides ruber and are divergent from Globigerinella siphonifera, Orbulina universa and Globigerinoides sacculifer.Conserved regions of the SSU rRNA gene show sufficient variation to discriminate foraminifers at the species level. Large genetic differences have been observed between the pink and white forms of Gs. ruber and between Ge. siphonifera Type I and II. The two types of Ge. siphonifera cannot be discriminated by traditional palaeontological methods, which has considerable implications for tracing fossil lineages and for the estimation of molecular evolutionary rates based upon the fossil record. The conserved regions show a high degree of sequence identity within a species, providing signature sequences for species identification. The variable regions of the gene may prove informative for population level studies in some species although complete sequence identity was observed in G. sacculifer and O. universa between specimens collected from the Caribbean and Western Pacific.     

A skeleton‐less sponge of Caribbean mangroves: invasive or undescribed?

Recent surveys of sponges occurring on Caribbean mangrove roots demonstrated the presence of a skeleton‐less sponge of the genus Halisarca, very similar in its morphology to the temperate H. dujardinii. This study evaluated the possibility that the mangrove sponge was actually H. dujardinii that had been introduced into the Caribbean mangroves. Detailed histology revealed differences between the mangrove sponge and H. dujardinii in cuticle thickness, and in characteristics of the choanocytes, spherulous, and granular cells. Also, phylogenetic reconstruction and genetic distance estimates based on cytochrome oxidase I gene sequences clearly differentiated the mangrove Halisarca sp. from H. dujardinii. Therefore, we rejected the hypothesis of the invasion of H. dujardinii, recognizing instead the mangrove Halisarca sp. as a new species and naming it H. restingaensis sp. nov. Estimated levels of genetic variation in the ribosomal internal transcribed spacers indicated that populations of H. restingaensis sp. nov. are highly differentiated between Venezuela and Panama (F_st=0.71). This level of population differentiation is consistent with the short larval competence period that is common in members of the genus Halisarca.     

Cryptic diversity of the symbiotic cyanobacterium Synechococcus spongiarum among sponge hosts

Cyanobacteria are common members of sponge-associated bacterial communities and are particularly abundant symbionts of coral reef sponges. The unicellular cyanobacterium Synechococcus spongiarum is the most prevalent photosynthetic symbiont in marine sponges and inhabits taxonomically diverse hosts from tropical and temperate reefs worldwide. Despite the global distribution of S. spongiarum , molecular analyses report low levels of genetic divergence among 16S ribosomal RNA (rRNA) gene sequences from diverse sponge hosts, resulting either from the widespread dispersal ability of these symbionts or the low phylogenetic resolution of a conserved molecular marker. Partial 16S rRNA and entire 16S–23S rRNA internal transcribed spacer (ITS) genes were sequenced from cyanobacteria inhabiting 32 sponges (representing 18 species, six families and four orders) from six geographical regions. ITS phylogenies revealed 12 distinct clades of S. spongiarum that displayed 9% mean sequence divergence among clades and less than 1% sequence divergence within clades. Symbiont clades ranged in specificity from generalists to specialists, with most (10 of 12) clades detected in one or several closely related hosts. Although multiple symbiont clades inhabited some host sponges, symbiont communities appear to be structured by both geography and host phylogeny. In contrast, 16S rRNA sequences were highly conserved, exhibiting less than 1% sequence divergence among symbiont clades. ITS gene sequences displayed much higher variability than 16S rRNA sequences, highlighting the utility of ITS sequences in determining the genetic diversity and host specificity of S. spongiarum populations among reef sponges. The genetic diversity of S. spongiarum revealed by ITS sequences may be correlated with different physiological capabilities and environmental preferences that may generate variable host–symbiont interactions.