Comparison of articulate brachiopod nuclear and mitochondrial gene trees leads to a clade-based redefinition of protostomes (Protostomozoa) and deuterostomes (Deuterostomozoa)

Nuclear and mtDNA sequences from selected short-looped terebratuloid (terebratulacean) articulate brachiopods yield congruent and genetically independent phylogenetic reconstructions by parsimony, neighbor-joining and maximum likelihood methods, suggesting that both sources of data are reliable guides to brachiopod species phylogeny. The present-day genealogical relationships and geographical distributions of the tested terebratuloid brachiopods are consistent with a tethyan dispersal and subsequent radiation. Concordance of nuclear and mitochondrial gene phylogenies reinforces previous indications that articulate brachiopods, inarticulate brachiopods, phoronids and ectoprocts cluster with other organisms generally regarded as protostomes. Since ontogeny and morphology in brachiopods, ectoprocts and phoronids depart in important respects from those features supposedly diagnostic of protostomes, this demonstrates that the operational definition of protostomy by the usual ontological characters must be misleading or unreliable. New, molecular, operational definitions are proposed to replace the traditional criteria for the recognition of protostomes and deuterostomes, and the clade-based terms 'Protostomozoa' and 'Deuterostomozoa' are proposed to replace the existing terms 'Protostomia' and 'Deuterostomia'

The Opisthokonta and the Ecdysozoa may be clades: An update on Philip et al. (2005)

To test the monophyly of Opisthokonta (animal-fungal clade) and Ecdysozoa (nematode-arthropod clade), Philip et al [Mol. Biol. Evol. 22: 1175–1184 (2005)] used sequence data from 10 eukaryotic genomes (an alveolate, a plant, two ascomycetous yeasts, a nematode, two dipterans, and three vertebrates). Strict criteria were used to select genes for phylogenetic analyses: single-gene families were identified and from these families, genes capable of recovering the uncontroversial parts of the phylogenetic tree (for example animal and vertebrate monophyly) were selected. Only five single-copy genes were found to be universally distributed across the analyzed taxa and capable of recovering all the uncontroversial parts of the tree. Phylogenetic analyses of those genes gave strong support for plant-animal grouping and the monophyly of Coelomata (vertebrate-arthropod grouping). Because numerous additional genome and EST projects have been completed since 2005, it is now possible to test the results of Philip et al using improved taxon sampling. Here, homologues of those five protein-coding genes (prefoldin 2, Tim22, U6 snRNP-associated protein, MAK16, and autophagocytosis protein) were obtained from sequence databases for additional taxa. Phylogenetic analyses of concatenation of those genes, using improved taxon sampling, recovered monophyly of Opisthokonta and Ecdysozoa, as well as Protostomia and Lophotrochozoa. These results again illustrate the importance of increased taxon sampling as shown in numerous previous studies using other datasets

A new look at the ventral nerve centre of Sagitta: implications for the phylogenetic position of Chaetognatha (arrow worms) and the evolution of the bilaterian nervous system

<p>Abstract</p> <p>Background</p> <p>The Chaetognatha (arrow worms) are a group of marine carnivores whose phylogenetic relationships are still vigorously debated. Molecular studies have as yet failed to come up with a stable hypothesis on their phylogenetic position. In a wide range of metazoans, the nervous system has proven to provide a wealth of characters for analysing phylogenetic relationships (neurophylogeny). Therefore, in the present study we explored the structure of the ventral nerve centre ("ventral ganglion") in <it>Sagitta setosa </it>with a set of histochemical and immunohistochemical markers.</p> <p>Results</p> <p>In specimens that were immunolabeled for acetylated-alpha tubulin the ventral nerve centre appeared to be a condensed continuation of the peripheral intraepidermal nerve plexus. Yet, synapsin immunolocalization showed that the ventral nerve centre is organized into a highly ordered array of ca. 80 serially arranged microcompartments. Immunohistochemistry against RFamide revealed a set of serially arranged individually identifiable neurons in the ventral nerve centre that we charted in detail.</p> <p>Conclusion</p> <p>The new information on the structure of the chaetognath nervous system is compared to previous descriptions of the ventral nerve centre which are critically evaluated. Our findings are discussed with regard to the debate on nervous system organisation in the last common bilaterian ancestor and with regard to the phylogenetic affinities of this Chaetognatha. We suggest to place the Chaetognatha within the Protostomia and argue against hypotheses which propose a deuterostome affinity of Chaetognatha or a sister-group relationship to all other Bilateria.</p

An edit script for taxonomic classifications

BACKGROUND: The NCBI taxonomy provides one of the most powerful ways to navigate sequence data bases but currently users are forced to formulate queries according to a single taxonomic classification. Given that there is not universal agreement on the classification of organisms, providing a single classification places constraints on the questions biologists can ask. However, maintaining multiple classifications is burdensome in the face of a constantly growing NCBI classification. RESULTS: In this paper, we present a solution to the problem of generating modifications of the NCBI taxonomy, based on the computation of an edit script that summarises the differences between two classification trees. Our algorithms find the shortest possible edit script based on the identification of all shared subtrees, and only take time quasi linear in the size of the trees because classification trees have unique node labels. CONCLUSION: These algorithms have been recently implemented, and the software is freely available for download from

Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies

<p>Abstract</p> <p>Background</p> <p>Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, <it>in silico </it>methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP.</p> <p>Results</p> <p>Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters.</p> <p>Conclusion</p> <p>Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and refinement of domain boundaries. Identification of residues that differentiate orthologs and paralogs provided insight into the development and functional consequences of paralogs and forkhead subfamily composition differences among species. Overall we found that after gene duplication of forkhead family members, rapid differentiation and subsequent fixation of amino acid changes through negative selection has occurred.</p

Origin and evolution of plexins, semaphorins, and Met receptor tyrosine kinases

The transition from unicellular to multicellular organisms poses the question as to when genes that regulate cell-cell interactions emerged during evolution. The receptor and ligand pairing of plexins and semaphorins regulates cellular interactions in a wide range of developmental and physiological contexts. We surveyed here genomes of unicellular eukaryotes and of non-bilaterian and bilaterian Metazoa and performed phylogenetic analyses to gain insight into the evolution of plexin and semaphorin families. Remarkably, we detected plexins and semaphorins in unicellular choanoflagellates, indicating their evolutionary origin in a common ancestor of Choanoflagellida and Metazoa. The plexin domain structure is conserved throughout all clades; in contrast, semaphorins are structurally diverse. Choanoflagellate semaphorins are transmembrane proteins with multiple fibronectin type III domains following the N-terminal Sema domain (termed Sema-FN). Other previously not yet described semaphorin classes include semaphorins of Ctenophora with tandem immunoglobulin domains (Sema-IG) and secreted semaphorins of Echinoderamata (Sema-SP, Sema-SI). Our study also identified Met receptor tyrosine kinases (RTKs), which carry a truncated plexin extracellular domain, in several bilaterian clades, indicating evolutionary origin in a common ancestor of Bilateria. In addition, a novel type of Met-like RTK with a complete plexin extracellular domain was detected in Lophotrochozoa and Echinodermata (termed Met-LP RTK). Our findings are consistent with an ancient function of plexins and semaphorins in regulating cytoskeletal dynamics and cell adhesion that predates their role as axon guidance molecules

Systematic errors in phylogenomics with a focus on the major metazoan clade Deuterostomia

Modern-day phylogenomics studies employ large data sets of many genes to resolve evolutionary relationships among many species. A typical phylogenomic workflow consists of certain steps: taxon sampling, orthology inference, marker selection and tree search. All of these steps contain some subjective decisions made by the researcher, posing risks for introducing systematic errors in the final results. In this thesis, I investigate the source and the impact of systematic errors in multiple steps of the phylogenomic workflow, focusing on the major clade Metazoa. First, I create simulated sets of orthologs under different settings for evolutionary rate and rate heterogeneity among sites and use OrthoFinder to infer their (known) orthology relationships. Orthology inference is sensitive to high evolutionary rates and low rate heterogeneity among sites. I show that errors in orthology inference are carried over to downstream analysis such as gene presence/absence phylogenies, gene gains/losses inference and phylostratigraphy. I also introduce a novel computational pipeline which allows us to identify the presence of a hidden break in the 28S ribosomal RNA of a given species. Mapping RNA-seq reads onto the 28S rRNA sequence reveals non-existent coverage of mapped reads near the middle of the 28S rRNA sequence of species that possess the hidden break. I apply this pipeline in hundreds of metazoan and other eukaryotic species and find that the hidden break is a rarely lost protostome feature, with surprising events of convergent evolution outside Metazoa. I finally focus on the major metazoan clade of Deuterostomia; while it has been widely accepted as a monophyletic group for over a century, recent phylogenomic studies addressing known systematic errors have recovered low support for monophyletic Deuterostomia. I examine five recently published metazoan phylogenomic data sets to show that monophyletic Deuterostomia is much less well supported than monophyletic Protostomia. I also create 40 new data sets, with and without fast-evolving taxa, and use them to correlate strong support for monophyletic Deuterostomia with problematic conditions in a phylogenomic analysis

Occurrence of gangliosides in the common squid and pacific octopus among protostomia

AbstractAcidic lipids from tissues of the common squid Todarodes pacificus and the pacific octopus Octopus vulgaris were characterized. Hepatopancreatic tissues of both animals had complex compositions of resorcinol-positive acidic lipids, many of which became reactive with cholera toxin B subunit and anti-GM1 antibody after in situ treatment with sialidase on TLC. One of the major acidic lipids in squid tissue was isolated and examined for its structure. This acidic lipid was identified to be the ganglioside GD1a based upon the susceptibility to sialidases of different substrate specificity, characterization of reaction products, and electrospray ionization-mass spectrometry of the lipid. Hepatopancreatic tissues of squid and octopus also contained acidic lipids that reacted with A2B5, a monoclonal antibody specific to c-series gangliosides. Cerebral ganglia of both animals expressed resorcinol-positive acidic lipids, though their compositional patterns differed from the hepatopancreatic tissues. N-Acetylneuraminic acid was identified as the main species in lipid-bound sialic acid in both tissues. The contents of lipid-bound sialic acid in cerebral ganglia were significantly lower than those of hepatopancreatic tissues in both animals. The present study presents the first evidence for the occurrence of gangliosides in protostomia