Zoology: War of the Worms

The phylogenetic affinities of Xenacoelomorpha - the phylum comprising Xenoturbella bocki and acoelomorph worms - are debated. Two recent studies conclude they represent the earliest branching bilaterally symmetrical animals, but additional tests may be needed to confirm this notion

Topology-dependent asymmetry in systematic errors affects phylogenetic placement of Ctenophora and Xenacoelomorpha

The evolutionary relationships of two animal phyla, Ctenophora and Xenacoelomorpha, have proved highly contentious. Ctenophora have been proposed as the most distant relatives of all other animals (Ctenophora-first rather than the traditional Porifera-first). Xenacoelomorpha may be primitively simple relatives of all other bilaterally symmetrical animals (Nephrozoa) or simplified relatives of echinoderms and hemichordates (Xenambulacraria). In both cases, one of the alternative topologies must be a result of errors in tree reconstruction. Here, using empirical data and simulations, we show that the Ctenophora-first and Nephrozoa topologies (but not Porifera-first and Ambulacraria topologies) are strongly supported by analyses affected by systematic errors. Accommodating this finding suggests that empirical studies supporting Ctenophora-first and Nephrozoa trees are likely to be explained by systematic error. This would imply that the alternative Porifera-first and Xenambulacraria topologies, which are supported by analyses designed to minimize systematic error, are the most credible current alternatives

Systematic errors in phylogenetic trees

The effort to reconstruct the tree of life was revolutionized by the use of sequences of proteins and nucleic acids. Phylogenetic trees are now routinely inferred using hundreds of thousands of amino acid or nucleotide characters. It thus seems surprising that many aspects of the tree of life are still controversial; conflicting results between large scale phylogenomic studies show that errors remain common despite large datasets. These errors often result from systematic biases in the way sequences evolve. While the resulting systematic errors are well understood, it requires careful efforts to reduce their effects

Orthonectids Are Highly Degenerate Annelid Worms

The animal groups of Orthonectida and Dicyemida are tiny, extremely simple, vermiform endoparasites of various marine animals and have been linked in the Mesozoa (Figure 1). The Orthonectida (Figures 1A and 1B) have a few hundred cells, including a nervous system of just ten cells, and the Dicyemida (Figure 1C) are even simpler, with ∼40 cells. They are classic “Problematica”—the name Mesozoa suggests an evolutionary position intermediate between Protozoa and Metazoa (animals) and implies that their simplicity is a primitive state, but molecular data have shown they are members of Lophotrochozoa within Bilateria, which means that they derive from a more complex ancestor. Their precise affinities remain uncertain, however, and it is disputed whether they even constitute a clade. Ascertaining their affinities is complicated by the very fast evolution observed in their genes, potentially leading to the common systematic error of long-branch attraction (LBA). Here, we use mitochondrial and nuclear gene sequence data and show that both dicyemids and orthonectids are members of the Lophotrochozoa. Carefully addressing the effects of unequal rates of evolution, we show that the Mesozoa is polyphyletic. While the precise position of dicyemids remains unresolved within Lophotrochozoa, we identify orthonectids as members of the phylum Annelida. This result reveals one of the most extreme cases of body-plan simplification in the animal kingdom; our finding makes sense of an annelid-like cuticle in orthonectids and suggests that the circular muscle cells repeated along their body may be segmental in origin

Systematic errors in orthology inference and their effects on evolutionary analyses

Summary The availability of complete sets of genes from many organisms makes it possible to identify genes unique to (or lost from) certain clades. This information is used to reconstruct phylogenetic trees; identify genes involved in the evolution of clade specific novelties; and for phylostratigraphy—identifying ages of genes in a given species. These investigations rely on accurately predicted orthologs. Here we use simulation to produce sets of orthologs that experience no gains or losses. We show that errors in identifying orthologs increase with higher rates of evolution. We use the predicted sets of orthologs, with errors, to reconstruct phylogenetic trees; to count gains and losses; and for phylostratigraphy. Our simulated data, containing information only from errors in orthology prediction, closely recapitulate findings from empirical data. We suggest published downstream analyses must be informed to a large extent by errors in orthology prediction that mimic expected patterns of gene evolution

CeLaVi: an interactive cell lineage visualization tool

Recent innovations in genetics and imaging are providing the means to reconstruct cell lineages, either by tracking cell divisions using live microscopy, or by deducing the history of cells using molecular recorders. A cell lineage on its own, however, is simply a description of cell divisions as branching events. A major goal of current research is to integrate this description of cell relationships with information about the spatial distribution and identities of the cells those divisions produce. Visualizing, interpreting and exploring these complex data in an intuitive manner requires the development of new tools. Here we present CeLaVi, a web-based visualization tool that allows users to navigate and interact with a representation of cell lineages, whilst simultaneously visualizing the spatial distribution, identities and properties of cells. CeLaVi's principal functions include the ability to explore and manipulate the cell lineage tree; to visualise the spatial distribution of cell clones at different depths of the tree; to colour cells in the 3D viewer based on lineage relationships; to visualise various cell qualities on the 3D viewer (e.g. gene expression, cell type) and to annotate selected cells/clones. All these capabilities are demonstrated with four different example data sets. CeLaVi is available at http://www.celavi.pro

Is it possible to reconstruct an accurate cell lineage using CRISPR recorders?

Cell lineages provide the framework for understanding how multicellular organisms are built and how cell fates are decided during development. Describing cell lineages in most organisms is challenging, given the number of cells involved; even a fruit fly larva has ~50,000 cells and a small mammal has more than 1 billion cells. Recently, the idea of using CRISPR to induce mutations during development as heritable markers for lineage reconstruction has been proposed and trialled by several groups. While an attractive idea, its practical value depends on the accuracy of the cell lineages that can be generated by this method. Here, we use computer simulations to estimate the performance of this approach under different conditions. Our simulations incorporate empirical data on CRISPR-induced mutation frequencies in Drosophila. We show significant impacts from multiple biological and technical parameters - variable cell division rates, skewed mutational outcomes, target dropouts and different mutation sequencing strategies. Our approach reveals the limitations of recently published CRISPR recorders, and indicates how future implementations can be optimised to produce accurate cell lineages

Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers

In some eukaryotes, a ‘hidden break’ has been described in which the 28S ribosomal RNA molecule is cleaved into two subparts. The break is common in protostome animals (arthropods, molluscs, annelids etc.) but a break has also been reported in some vertebrates and non-metazoan eukaryotes. We present a new computational approach to determine the presence of the hidden break in 28S rRNAs using mapping of RNA-Seq data. We find a homologous break is present across protostomes although has been lost in a small number of taxa. We show that rare breaks in vertebrate 28S rRNAs are not homologous to the protostome break. A break is found in just 4 out of 331 species of non-animal eukaryotes studied and three of these are located in the same position as the protostome break suggesting a striking instance of convergent evolution. RNA Integrity Numbers (RIN) rely on intact 28s rRNA and will be consistently underestimated in the great majority of animal species with a break

Evaluation of the role of information technology in the effectiveness of internal audit (Case study Melli Bank of Iran branches in Sistan and Baluchistan province (

Today, the importance of information technology and communications has been clearly specified to increase the speed and accuracy of the various activities of organizations and the relationship between its various components together, and thus increase their effectiveness. The purpose of this research is to investigate the role of information technology in increasing the effectiveness of the internal audit. The statistical population of the study consisted of 120 heads of banks and employees of different parts of internal audit of Iran Melli Bank Branches in Sistan and Baluchestan province. Of these, 92 samples were selected as research samples according to the sample size formula. The method of sampling in this research is Krjusi Morgan method. Then the questionnaire has been distributed among them and then collected. The research questionnaire contains 30 questions based on the research hypotheses. To assess the validity of the questionnaire, content validity was used and the Cronbach's alpha method was used to calculate the validity coefficient of the measure in this research

The mitochondrial genomes of the acoelomorph worms Paratomella rubra, Isodiametra pulchra and Archaphanostoma ylvae

Acoels are small, ubiquitous - but understudied - marine worms with a very simple body plan. Their internal phylogeny is still not fully resolved, and the position of their proposed phylum Xenacoelomorpha remains debated. Here we describe mitochondrial genome sequences from the acoels Paratomella rubra and Isodiametra pulchra, and the complete mitochondrial genome of the acoel Archaphanostoma ylvae. The P. rubra and A. ylvae sequences are typical for metazoans in size and gene content. The larger I. pulchra  mitochondrial genome contains both ribosomal genes, 21 tRNAs, but only 11 protein-coding genes. We find evidence suggesting a duplicated sequence in the I. pulchra mitochondrial genome. The P. rubra, I. pulchra and A. ylvae mitochondria have a unique genome organisation in comparison to other metazoan mitochondrial genomes. We found a large degree of protein-coding gene and tRNA overlap with little non-coding sequence in the compact P. rubra genome. Conversely, the A. ylvae and I. pulchra genomes have many long non-coding sequences between genes, likely driving genome size expansion in the latter. Phylogenetic trees inferred from mitochondrial genes retrieve Xenacoelomorpha as an early branching taxon in the deuterostomes. Sequence divergence analysis between P. rubra sampled in England and Spain indicates cryptic diversity