Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Manuscript in preparation

Animal mitochondrial DNA is a small, extrachromosomal genome, typically ~16 kb in size. With few exceptions, all animal mitochondrial genomes contain the same 37 genes: two for rRNAs, 13 for proteins and 22 for tRNAs. The products of these genes, along with RNAs and proteins imported from the cytoplasm, endow mitochondria with their own systems for DNA replication, transcription, mRNA processing and translation of proteins. The study of these genomes as they function in mitochondrial systems—‘mitochondrial genomics’— serves as a model for genome evolution. Furthermore, the comparison of animal mitochondrial gene arrangements has become a very powerful means for inferring ancient evolutionary relationships, since rearrangements appear to be unique, generally rare events that are unlikely to arise independently in separate evolutionary lineages. Complete mitochondrial gene arrangements have been published for 58 chordate species and 29 non-chordate species, and partial arrangements for hundreds of other taxa. This review compares and summarizes these gene arrangements and points out some of the questions that may be addressed by comparing mitochondrial systems.

Animal mitochondrial genomes

Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.

https://science.sciencemag.org/content/sci/346/6210/763.full.pdf

Phylogenomics resolves the timing and pattern of insect evolution

Host switching of human lice to new world monkeys in South America

A new species, Cobleia pudica, is described from the monacanthid fishes Contheschenia grandisquamis, Cantherhines dumerili, Cantherhines pardalis and Pervagor janthinosoma from reef waters around Heron Island, southern Great Barrier Reef, Queensland, Australia. It differs from the only other species in the genus, Cableia trigoni Sogandares-Bernal, 1959 in the more elongate cirrus-sac, longer post-testicular region, smaller prepharynx, the less anterior extent of the vitelline fields and dorsalty subterminal excretory pore. The status of the genus is discussed, but no firm conclusion reached. It is placed, pro tern, in the Acanthocolpidae. The great majority of specimens lack spermatozoa, suggesting that parthenogenesis may occur.

/pdf/cableia-pudica-n-sp-digenea-acanthocolpidae-from-monacanthid-4v50bvm5a4.pdf

Cableia pudica n sp (Digenea:acanthocolpidae) from monacanthid fishes of the Southern Great Barrier Reef, Australia

The morphology of the male genitalia and the internal genital sclerite of the female is described for species of the Heterodoxus octoseriatus group. Homologous sclerites and spines, required for phylogenetic analyses, are identified. Three species, H. closei n. sp., H. hughendensis n. sp. and H. briscoei n. sp., are described and, with the benefit of a new, large series of lice, the other eight species are revised. New data on type-hosts are provided and a number of questions raised by previous workers are addressed.

http://phthiraptera.info/sites/phthiraptera.info/files/40047.pdf

Taxonomic review of the Heterodoxus octoseriatus group (Phthiraptera: Boopiidae) from rock-wallabies with the description of three new species

In the present study, we applied our 'precise annotation' to the mitochondrial (mt) genomes of human, chimpanzee, rhesus macaque and mouse using 5' and 3' end small RNAs. Our new annotations updated previous annotations. In particular, our new annotations led to two important novel findings: (1) the identification of five Conserved Sequence Blocks (CSB1, CSB2, CSB3, LSP and HSP) in the control regions; and (2) the annotation of Transcription Initiation and novel Transcription Termination Sites. Based on these annotations, we proposed a novel model of mt transcription which can account for the mt transcription and its regulation in mammals. According to our model, Transcription Termination Sites function as switches to regulate the production of short, long primary transcripts and uninterrupted transcription, rather than simply terminate the mt transcription. Moreover, the expression levels of mitochondrial transcription termination factors control the proportions of rRNAs, mRNAs and lncRNAs in total mt RNA. Our findings point to the existence of many other, as yet unidentified, Transcription Termination Sites in mammals.

https://www.tandfonline.com/doi/pdf/10.1080/15476286.2019.1709746

Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes leads to insight into mitochondrial transcription in mammals

My goal is to illuminate truth-making by way of illuminating the relation of making. My strategy is not to ask what making is; in the hope of a metaphysical theory about is nature. It's rather to look first to the language of making. The metaphor behind making refers to agency. It would be absurd to suggest that claims about making are claims about agency. It is not absurd, however, to propose that the concept of making somehow emerges from some feature to do with agency. That's the contention to be explored in this paper. The way to do this is through expressivism. Truth-making claims, and making-claims generally, are claims in which we express mental states linked to our manipulation of concepts, like truth. In particular, they express disposition to undertake derivations using inference rules, in which introduction rules have a specific role. I then show how this theory explains our intuitions about truth's asymmetric dependence on being.

/pdf/expressivism-about-making-and-truth-making-49o1o1t4jj.pdf

Stephen C. Barker

Papers

Host switching of human lice to new world monkeys in South America

Cableia pudica n sp (Digenea:acanthocolpidae) from monacanthid fishes of the Southern Great Barrier Reef, Australia

Taxonomic review of the Heterodoxus octoseriatus group (Phthiraptera: Boopiidae) from rock-wallabies with the description of three new species

Precise annotation of human, chimpanzee, rhesus macaque and mouse mitochondrial genomes leads to insight into mitochondrial transcription in mammals

Expressivism about making and truth-making