An Investigation of a Cluster S Mycobacteriophage Genome, Corazon, Genes 4-16: Location and Function

Mycobacteriophages are a type of virus particle that specifically attack mycobacteria. This attribute can be exploited to fight antibiotic resistance mycobacteria. As of February 2019, only 14 Cluster S types (a specific group of mycobacteriophage) have been completely sequenced and published in the Actinobacteriophage Database. The purpose of this investigation is to establish the presence, location, and function of genes within the genome of a novel bacteriophage, Corazon and add to this database. Corazon, isolated from a soil sample collected in Lafayette, Indiana, is a member of Cluster S and belongs to the Siphoviridae morphotype. It has 109 genes and a 64kbp genome size. The genome was analyzed with the program DNA Master and a variety of sources such as NCBI BLAST, HHPred, and Phamerator to determine the location and function of genes within the auto-annotated range of genes 4-16. Within the investigated range, only one gene was assigned a function (MazG-like nucleotide pyrophosphohydrolase, which interacts with an essential GTPase in bacteria). The other 13 genes were annotated as genes with no known function. The investigation of significant gaps in the genome resulted in an additional gene (14.5) being added. Contributing to the global understanding of bacteriophages is of interest since the phage-bacteria model has expanded scientists’ capabilities of studying evolution and exploring novel medical applications. Publishing these annotations will allow generations of researchers to compare their results to this member of Cluster S and potentially identify a new candidate for phage-mediated transduction, phage therapy, or other application

DNA Barcoding for Community Ecology - How to Tackle a Hyperdiverse, Mostly Undescribed Melanesian Fauna

Trigonopterus weevils are widely distributed throughout Melanesia and hyperdiverse in New Guinea. They are a dominant feature in natural forests, with narrow altitudinal zonation. Their use in community ecology has been precluded by the "taxonomic impediment". We sampled >6,500 specimens from seven areas across New Guinea; 1,002 specimens assigned to 270 morphospecies were DNA sequenced. Objective clustering of a refined dataset (excluding nine cryptic species) at 3% threshold revealed 324 genetic clusters (DNA group count relative to number of morphospecies = 20.0% overestimation of species diversity, or 120.0% agreement) and 85.6% taxonomic accuracy (the proportion of DNA groups that "perfectly" agree with morphology-based species hypotheses). Agreement and accuracy were best at an 8% threshold. GMYC analysis revealed 328 entities (21.5% overestimation) with 227 perfect GMYC entities (84.1% taxonomic accuracy). Both methods outperform the parataxonomist (19% underestimation; 31.6% taxonomic accuracy). The number of species found in more than one sampling area was highest in the Eastern Highlands and Huon (Sørensen similarity index 0.07, 4 shared species); ⅓ of all areas had no species overlap. Success rates of DNA barcoding methods were lowest when species showed a pronounced geographical structure. In general, Trigonopterus show high α and β-diversity across New Guinea. DNA barcoding is an excellent tool for biodiversity surveys but success rates might drop when closer localities are included. Hyperdiverse Trigonopterus are a useful taxon for evaluating forest remnants in Melanesia, allowing finer-grained analyses than would be possible with vertebrate taxa commonly used to date. Our protocol should help establish other groups of hyperdiverse fauna as target taxa for community ecology. Sequencing delivers objective data on taxa of incredible diversity but mostly without a solid taxonomic foundation and should help pave the road for the eventual formal naming of new species

Anisomeriini diving beetles—an Atlantic–Pacific Island disjunction on Tristan da Cunha and Robinson Crusoe Island, Juan Fernández?

Anisomeriini diving beetles contain only two enigmatic species, representing a remarkable disjunction between the Pacific Juan Fernández Islands (Anisomeria bistriata) and the South Atlantic Tristan da Cunha Archipelago (Senilites tristanicola). They belong to the Colymbetinae, which contain 140 species worldwide. Here we aim to reconstruct the evolutionary history of the Anisomerinii and use > 9000 bp DNA sequence data from 13 fragments of 12 loci for a comprehensive sampling of Colymbetinae species. Analyses under different optimization criteria converge on very similar topologies, and show unambiguously that Anisomeria bistriata and Senilites tristanicola belong to the Neotropical Rhantus signatus species group, a comparatively recent clade within Colymbetinae. Anisomeriini therefore are synonomized with Colymbetini and both species are transferred to Rhantus accordingly, resulting in secondary homonymy of Rhantus bistriatus (Brullé, 1835) with Rhantus bistriatus (Bergsträsser, 1778). We propose the replacement name Rhantus selkirki Jäch, Balke & Michat nom. nov. for the Juan Fernández species. Presence of these species on remote islands is therefore not relictary, but the result of more recent range expansions out of mainland South America. Finally, we suggest that Carabdytini should be synonymized with Colymbetini. Our study underpins the Hennigian principle that a natural classification can be derived only from the search for shared apomorphies between species, not from differences.Fil: Moriniére, Jérome. Zoological State Collection; AlemaniaFil: Michat, Mariano Cruz. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Biodiversidad y Biología Experimental y Aplicada. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Biodiversidad y Biología Experimental y Aplicada; ArgentinaFil: Jäch, Manfred A.. Naturhistorisches Museum Wien; AustriaFil: Bergsten, Johannes. Swedish Museum of Natural History; SueciaFil: Hendrich, Lars. Zoological State Collection; AlemaniaFil: Balke, Michael. Ludwig Maximilians Universitat; Alemani