Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa

BACKGROUND: Understanding the phylogenetic relationships among major lineages of multicellular animals (the Metazoa) is a prerequisite for studying the evolution of complex traits such as nervous systems, muscle tissue, or sensory organs. Transcriptome-based phylogenies have dramatically improved our understanding of metazoan relationships in recent years, although several important questions remain. The branching order near the base of the tree, in particular the placement of the poriferan (sponges, phylum Porifera) and ctenophore (comb jellies, phylum Ctenophora) lineages is one outstanding issue. Recent analyses have suggested that the comb jellies are sister to all remaining metazoan phyla including sponges. This finding is surprising because it suggests that neurons and other complex traits, present in ctenophores and eumetazoans but absent in sponges or placozoans, either evolved twice in Metazoa or were independently, secondarily lost in the lineages leading to sponges and placozoans. RESULTS: To address the question of basal metazoan relationships we assembled a novel dataset comprised of 1080 orthologous loci derived from 36 publicly available genomes representing major lineages of animals. From this large dataset we procured an optimized set of partitions with high phylogenetic signal for resolving metazoan relationships. This optimized data set is amenable to the most appropriate and computationally intensive analyses using site-heterogeneous models of sequence evolution. We also employed several strategies to examine the potential for long-branch attraction to bias our inferences. Our analyses strongly support the Ctenophora as the sister lineage to other Metazoa. We find no support for the traditional view uniting the ctenophores and Cnidaria. Our findings are supported by Bayesian comparisons of topological hypotheses and we find no evidence that they are biased by long-branch attraction. CONCLUSIONS: Our study further clarifies relationships among early branching metazoan lineages. Our phylogeny supports the still-controversial position of ctenophores as sister group to all other metazoans. This study also provides a workflow and computational tools for minimizing systematic bias in genome-based phylogenetic analyses. Future studies of metazoan phylogeny will benefit from ongoing efforts to sequence the genomes of additional invertebrate taxa that will continue to inform our view of the relationships among the major lineages of animals. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2146-4) contains supplementary material, which is available to authorized users

Participant Modeling: The Use of a Guided Master in the Modern World of Virtual Reality Exposure Therapy Targeting Fear of Heights

With the percentage of mental health disorders on the rise and the cost for their treatment reaching astounding proportions, research in their treatment has also become quite extensive. Individuals suffering from the effects of their disorder constituting them incapable at various levels to lead a normal life, the need for a more effective treatment has been well established. We have focused on anxiety disorders specifically, which have mainly fear as their common denominator, and using this we decided to look into the role of the clinician in live ET sessions so as to examine whether this role can be replicated in a VRET simulation with similar or better outcomes for the patient, i.e. a more effective treatment. Our hypothesis was tested in an outpatient setting with patients being separated into two groups. We examined whether the presence of a virtual guided master using participant modeling in a virtual environment was as effective or more effective than the Standard ET method. Our VR system is based on the Full Body Immersive Virtual Reality System with Motion Recognition Camera created by Jacob Kritikos. The outcomes were gathered via the Session Rating Scale by Miller which led to the conclusion that participant modeling within a VRET approach can lead to a better treatment quality. © 2021, ICST Institute for Computer Sciences, Social Informatics and Telecommunications Engineering

Correction: Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants.

[This corrects the article DOI: 10.1371/journal.pone.0174701.]

Correction: Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants.

[This corrects the article DOI: 10.1371/journal.pone.0174701.]

Phototransduction and clock gene expression in the troglobiont beetle Ptomaphagus hirtus of Mammoth cave

Obligatory cave species exhibit dramatic trait modifications such as eye reduction, loss of pigmentation and an increase in touch receptors. As molecular studies of cave adaptation have largely concentrated on vertebrate models, it is not yet possible to probe for genetic universalities underlying cave adaptation. We have therefore begun to study the strongly cave-adapted small carrion beetle Ptomaphagus hirtus. For over 100 years, this flightless signature inhabitant of Mammoth Cave, the world's largest known cave system, has been considered blind despite the presence of residual lens structures. By deep sequencing of the adult head transcriptome, we discovered the transcripts of all core members of the phototransduction protein machinery. Combined with the absence of transcripts of select structural photoreceptor and eye pigmentation genes, these data suggest a reduced but functional visual system in P. hirtus. This conclusion was corroborated by a negative phototactic response of P. hirtus in light/dark choice tests. We further detected the expression of the complete circadian clock gene network in P. hirtus, raising the possibility of a role of light sensation in the regulation of oscillating processes. We speculate that P. hirtus is representative of a large number of animal species with highly reduced but persisting visual capacities in the twilight zone of the subterranean realm. These can now be studied on a broad comparative scale given the efficiency of transcript discovery by next-generation sequencing

Comprehensive bioinformatics analysis of <i>Mycoplasma pneumoniae</i> genomes to investigate underlying population structure and type-specific determinants

<div><p><i>Mycoplasma pneumoniae</i> is a significant cause of respiratory illness worldwide. Despite a minimal and highly conserved genome, genetic diversity within the species may impact disease. We performed whole genome sequencing (WGS) analysis of 107 <i>M</i>. <i>pneumoniae</i> isolates, including 67 newly sequenced using the Pacific BioSciences RS II and/or Illumina MiSeq sequencing platforms. Comparative genomic analysis of 107 genomes revealed >3,000 single nucleotide polymorphisms (SNPs) in total, including 520 type-specific SNPs. Population structure analysis supported the existence of six distinct subgroups, three within each type. We developed a predictive model to classify an isolate based on whole genome SNPs called against the reference genome into the identified subtypes, obviating the need for genome assembly. This study is the most comprehensive WGS analysis for <i>M</i>. <i>pneumoniae</i> to date, underscoring the power of combining complementary sequencing technologies to overcome difficult-to-sequence regions and highlighting potential differential genomic signatures in <i>M</i>. <i>pneumoniae</i>.</p></div

Correction: Comprehensive bioinformatics analysis of <i>Mycoplasma pneumoniae</i> genomes to investigate underlying population structure and type-specific determinants

Correction: Comprehensive bioinformatics analysis of <i>Mycoplasma pneumoniae</i> genomes to investigate underlying population structure and type-specific determinant