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Ian J Kitching, Rodolphe Rougerie, Andreas Zwick, Chris A Hamilton, Ryan A St Laurent, Stefan Naumann, Liliana Ballesteros Mejia, Akito Y Kawahara
Background: Bombycoidea is an ecologically diverse and speciose superfamily of Lepidoptera. The superfamily includes many model organisms, but the taxonomy and classification of the superfamily has remained largely in disarray. Here we present a global checklist of Bombycoidea. Following Zwick (2008) and Zwick et al. (2011), ten families are recognized: Anthelidae, Apatelodidae, Bombycidae, Brahmaeidae, Carthaeidae, Endromidae, Eupterotidae, Phiditiidae, Saturniidae and Sphingidae. The former families Lemoniidae and Mirinidae are included within Brahmaeidae and Endromidae respectively...
2018: Biodiversity Data Journal
Hoang Thi Binh, Nguyen Van Ngoc, Shuichiro Tagane, Hironori Toyama, Keiko Mase, Chika Mitsuyuki, Joeri Sergej Strijk, Yoshihisa Suyama, Tetsukazu Yahara
The taxonomy of Quercus langbianensis and its relatives in Vietnam and Cambodia have been revised based on evidence obtained from field observations, morphological comparison of herbarium specimens and molecular analyses using both classic and next generation DNA markers. Based on Bayesian inference using rbc L, mat K and ITS regions and Neighbour-joining tree using genome-wide sequences amplified with multiplexed inter-simple sequence repeat (ISSR) primers (MIG-seq), the authors recognised ten species in the complex in Vietnam and Cambodia, three of which are newly described in this paper: Q...
2018: PhytoKeys
Camille Moreau, Christopher Mah, Antonio Agüera, Nadia Améziane, David Barnes, Guillaume Crokaert, Marc Eléaume, Huw Griffiths, Charlène Guillaumot, Lenaïg G Hemery, Anna Jażdżewska, Quentin Jossart, Vladimir Laptikhovsky, Katrin Linse, Kate Neill, Chester Sands, Thomas Saucède, Stefano Schiaparelli, Jacek Siciński, Noémie Vasset, Bruno Danis
The present dataset is a compilation of georeferenced occurrences of asteroids (Echinodermata: Asteroidea) in the Southern Ocean. Occurrence data south of 45°S latitude were mined from various sources together with information regarding the taxonomy, the sampling source and sampling sites when available. Records from 1872 to 2016 were thoroughly checked to ensure the quality of a dataset that reaches a total of 13,840 occurrences from 4,580 unique sampling events. Information regarding the reproductive strategy (brooders vs...
2018: ZooKeys
Thorsten Assmann, Estève Boutaud, Jörn Buse, Jörg Gebert, Claudia Drees, Ariel-Leib-Leonid Friedman, Fares Khoury, Tamar Marcus, Eylon Orbach, Ittai Renan, Constantin Schmidt, Pascale Zumstein
The tiger beetles of the southern Levant (Egypt: Sinai, Israel, Jordan) and adjacent regions of the neighboring countries Lebanon, Syria, Iraq, Saudi Arabia and Egypt are reviewed in terms of species taxonomy, ecological and distributional traits and conservation biology. An illustrated dichotomous identification key from the species of this region is provided. Based on the classical identification key, we developed a digital identification application for smartphones and tablets. The species status of Calomera aulicoides (J...
2018: ZooKeys
Rendong Yang, Jamie L Van Etten, Scott M Dehm
BACKGROUND: Insertions and deletions (indels) are a major class of genomic variation associated with human disease. Indels are primarily detected from DNA sequencing (DNA-seq) data but their transcriptional consequences remain unexplored due to challenges in discriminating medium-sized and large indels from splicing events in RNA-seq data. RESULTS: Here, we developed transIndel, a splice-aware algorithm that parses the chimeric alignments predicted by a short read aligner and reconstructs the mid-sized insertions and large deletions based on the linear alignments of split reads from DNA-seq or RNA-seq data...
April 19, 2018: BMC Genomics
Gaurav Vaidya, Denis Lepage, Robert Guralnick
While studies of taxonomy usually focus on species description, there is also a taxonomic correction process that retests and updates existing species circumscriptions on the basis of new evidence. These corrections may themselves be subsequently retested and recorrected. We studied this correction process by using the Check-List of North and Middle American Birds, a well-known taxonomic checklist that spans 130 years. We identified 142 lumps and 95 splits across sixty-three versions of the Check-List and found that while lumping rates have markedly decreased since the 1970s, splitting rates are accelerating...
2018: PloS One
Aline Menin, Rafael Torchelsen, Luciana Nedel
Using virtual environments (VEs) is a safer and cost-effective alternative to executing dangerous tasks, such as training firefighters and industrial operators. Immersive virtual reality (VR) combined with game aspects have the potential to improve the user experience in the VE by increasing realism, engagement, and motivation. This article investigates the impact of VR technology on 46 immersive gamified simulations with serious purposes and classifies it towards a taxonomy. Our findings suggest that immersive VR improves simulation outcomes, such as increasing learning gain and knowledge retention and improving clinical outcomes for rehabilitation...
March 2018: IEEE Computer Graphics and Applications
Lei Xu, Lianggen Wang, Jiajia Ning, Hong Li, Yingying Ji, Feiyan Du
Ostracods (Crustacea, Ostracoda) are small bivalved crustaceans, contributing over 200 described species to the marine zooplankton community. They are widely distributed and are relatively abundant components of the mesozooplankton, playing an important role in the transport of organic matter to deep layers. However, identification of ostracods based on micro-morphological characters is extremely difficult and time-consuming. Previous fragmentary taxonomic studies of ostracods in the South China Sea (SCA), were based solely on morphology...
April 19, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Carlos Prieto, Rayner Nuñez, Axel Hausmann
In this work, we used mtDNA data as a tool to delimit species and we compared the resulting molecular operational taxonomic units (barcode index number, BIN) with morphology-based identifications in the Colombian species of Rhamma Johnson, 1992 exploring the usefulness of DNA barcodes for taxonomy, species identification and delimitation. We obtained cytochrome oxidase I (COI) sequences for 134 morphologically identified specimens, representing 12 species of Rhamma from Colombia. Ten of these species have not been previously barcoded...
April 19, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Bruno F Melo, Beatriz F Dorini, Fausto Foresti, Claudio Oliveira
Evidence that migration prevents population structure among Neotropical characiform fishes has been reported recently but the effects upon species diversification remain unclear. Migratory species of Prochilodus have complex species boundaries and intrincate taxonomy representing a good model to address such questions. Here, we analyzed 147 specimens through barcode sequences covering all species of Prochilodus across a broad geographic area of South America. Species delimitation and population genetic methods revealed very little genetic divergence among mitochondrial lineages suggesting that extensive gene flow resulted likely from the highly migratory behavior, natural hybridization or recent radiation prevent accumulation of genetic disparity among lineages...
2018: Frontiers in Genetics
Matthew R Moore, Ronald D Cave, Marc A Branham
Cyclocephaline scarab beetles represent the second largest tribe of the subfamily Dynastinae, and the group includes the most speciose genus of dynastines, Cyclocephala . The period following publication of Sebő Endrődi's The Dynastinae of the World has seen a huge increase in research interest on cyclocephalines, and much of this research has not been synthesized. The objective of this catalog and bibliography is to compile an exhaustive list of taxa in Cyclocephalini. This paper provides an updated foundation for understanding the taxonomy and classification of 14 genera and over 500 species in the tribe...
2018: ZooKeys
Kôji Sasakawa, Hirotarô Itô
Trephionus Bates, 1883, a Japanese endemic genus in the subtribe Synuchina (Coleoptera, Carabidae, Sphodrini), is revised taxonomically based mainly on the shape of the endophallus, a membranous inner sac everted from the aedeagus of the male genitalia. Three known species from central Honshu, T. kinoshitai Habu, 1954; T. shibataianus Habu, 1978; and T. babai Habu, 1978, are re-defined based on this genital character, and five new species are described from the region: T. cylindriphallus Sasakawa, sp . n ., T...
2018: ZooKeys
Xuezhong Zhou, Lei Lei, Jun Liu, Arda Halu, Yingying Zhang, Bing Li, Zhili Guo, Guangming Liu, Changkai Sun, Joseph Loscalzo, Amitabh Sharma, Zhong Wang
The International Classification of Diseases (ICD) relies on clinical features and lags behind the current understanding of the molecular specificity of disease pathobiology, necessitating approaches that incorporate growing biomedical data for classifying diseases to meet the needs of precision medicine. Our analysis revealed that the heterogeneous molecular diversity of disease chapters and the blurred boundary between disease categories in ICD should be further investigated. Here, we propose a new classification of diseases (NCD) by developing an algorithm that predicts the additional categories of a disease by integrating multiple networks consisting of disease phenotypes and their molecular profiles...
April 6, 2018: EBioMedicine
Tanja M Schuster, Sabrina D Setaro, Josquin F G Tibbits, Erin L Batty, Rachael M Fowler, Todd G B McLay, Stephen Wilcox, Peter K Ades, Michael J Bayly
Previous molecular phylogenetic analyses have resolved the Australian bloodwood eucalypt genus Corymbia (~100 species) as either monophyletic or paraphyletic with respect to Angophora (9-10 species). Here we assess relationships of Corymbia and Angophora using a large dataset of chloroplast DNA sequences (121,016 base pairs; from 90 accessions representing 55 Corymbia and 8 Angophora species, plus 33 accessions of related genera), skimmed from high throughput sequencing of genomic DNA, and compare results with new analyses of nuclear ITS sequences (119 accessions) from previous studies...
2018: PloS One
Isaure Scavezzoni, Valentin Fischer
Modern marine turtles (chelonioids) are the remnants of an ancient radiation that roots in the Cretaceous. The oldest members of that radiation are first recorded from the Early Cretaceous and a series of species are known from the Albian-Cenomanian interval, many of which have been allocated to the widespread but poorly defined genus Rhinochelys , possibly concealing the diversity and the evolution of early marine turtles. In order to better understand the radiation of chelonioids, we redescribe the holotype and assess the taxonomy of Rhinochelys amaberti Moret (1935) (UJF-ID...
2018: PeerJ
Ricardo J Eloy Alves, Bui Quang Minh, Tim Urich, Arndt von Haeseler, Christa Schleper
Ammonia-oxidising archaea (AOA) are ubiquitous and abundant in nature and play a major role in nitrogen cycling. AOA have been studied intensively based on the amoA gene (encoding ammonia monooxygenase subunit A), making it the most sequenced functional marker gene. Here, based on extensive phylogenetic and meta-data analyses of 33,378 curated archaeal amoA sequences, we define a highly resolved taxonomy and uncover global environmental patterns that challenge many earlier generalisations. Particularly, we show: (i) the global frequency of AOA is extremely uneven, with few clades dominating AOA diversity in most ecosystems; (ii) characterised AOA do not represent most predominant clades in nature, including soils and oceans; (iii) the functional role of the most prevalent environmental AOA clade remains unclear; and (iv) AOA harbour molecular signatures that possibly reflect phenotypic traits...
April 17, 2018: Nature Communications
Helen Pineo, Ketevan Glonti, Harry Rutter, Nici Zimmermann, Paul Wilkinson, Michael Davies
Urban health indicator (UHI) tools provide evidence about the health impacts of the physical urban environment which can be used in built environment policy and decision-making. Where UHI tools provide data at the neighborhood (and lower) scale they can provide valuable information about health inequalities and environmental deprivation. This review performs a census of UHI tools and explores their nature and characteristics (including how they represent, simplify or address complex systems) to increase understanding of their potential use by municipal built environment policy and decision-makers...
April 16, 2018: Journal of Urban Health: Bulletin of the New York Academy of Medicine
Nelson J Aranguren-Riaño, Cástor Guisande, Jonathan B Shurin, Natalie T Jones, Aldo Barreiro, Santiago R Duque
Variation in resource use among species determines their potential for competition and co-existence, as well as their impact on ecosystem processes. Planktonic crustaceans consume a range of micro-organisms that vary among habitats and species, but these differences in resource consumption are difficult to characterize due to the small size of the organisms. Consumers acquire amino acids from their diet, and the composition of tissues reflects both the use of different resources and their assimilation in proteins...
April 16, 2018: Oecologia
Rafael R de la Haba, Paulina Corral, Cristina Sánchez-Porro, Carmen Infante-Domínguez, Andrea M Makkay, Mohammad A Amoozegar, Antonio Ventosa, R Thane Papke
To gain a better understanding of how divergence occurs, and how taxonomy can benefit from studying natural populations, we isolated and examined 25 closely related Halorubrum strains obtained from different hypersaline communities and compared them to validly named species and other reference strains using five taxonomic study approaches: phylogenetic analysis using the 16S rRNA gene and multilocus sequencing analysis (MLSA), polar lipid profiles (PLP), average nucleotide identity (ANI) and DNA-DNA hybridization (DDH)...
2018: Frontiers in Microbiology
Stilianos Louca, Martin F Polz, Florent Mazel, Michaeline B N Albright, Julie A Huber, Mary I O'Connor, Martin Ackermann, Aria S Hahn, Diane S Srivastava, Sean A Crowe, Michael Doebeli, Laura Wegener Parfrey
Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms...
April 16, 2018: Nature Ecology & Evolution
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