Systematics Research Articles

Identifying conserved genomic elements and designing universal bait sets to enrich them

Summary Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non‐model taxa for phylogenetic, phylogeographic and population genetic studies. For example, two available bait sets each allow enrichment of thousands of orthologous loci from >20 000 species (Faircloth et al. Systematic Biology, 61, 717–726, 2012; Molecular Ecology Resources, 15, 489–501, 2015). Unfortunately, few open‐source workflows are available to identify conserved genomic elements shared among divergent taxa and to design enrichment baits targeting these regions. Those that do exist require extensive bioinformatics expertise and significant amounts of time to use. These shortcomings limit the application of targeted enrichment methods to additional organismal groups. Here, I describe a universal workflow for identifying conserved genomic regions in available genomic data and for designing targeted enrichment baits to collect data from these conserved regions. These methods require less expertise, less time and better use commonly available information to identify conserved loci and design baits to capture them. I apply this computational approach to the understudied arthropod groups Arachnida, Coleoptera, Diptera, Hemiptera or Lepidoptera to identify thousands of conserved loci in each group and design target enrichment baits to capture these loci. I then use in silico analyses to demonstrate that targeted enrichment of the conserved loci can be used to reconstruct the accepted relationships among genome sequences from the focal arthropod orders. The software workflow I created allowed me to identify thousands of conserved loci in five diverse arthropod groups and design sequence capture baits to target them. This suite of capture bait designs should enable collection of phylogenomic data from >900 000 arthropod species. Although the examples in this manuscript focus on understudied arthropod groups, the approach I describe is applicable to all organismal groups having some form of pre‐existing genomic information (e.g. other invertebrates, plants, fungi and microbes). Finally, the documentation, design steps, software code and bait sets developed here are available under an open‐source license for restriction‐free testing, use, and additional modification by any research group.

Cohesive Properties of Cu-X and Ni-X (In, Sn) Intermetallics: Ab Initio Systematics, Correlations and “Universality” Features

Fil: Bertoldi, Dalia Surena. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Patagonia Norte. Instituto de Investigacion y Desarrollo en Ingenieria de Procesos, Biotecnologia y Energias Alternativas. Universidad Nacional del Comahue. Instituto de Investigacion y Desarrollo en Ingenieria de Procesos, Biotecnologia y Energias Alternativas; Argentina

Systematics and faunistics of Neotropical Eucosmini, 4: three new genera and their species (Lepidoptera: Tortricidae)

Abstract Three genera (Brasilnotia gen. n., Malinova gen. n., Tiburica gen. n.) and three species (Brasilnotia planaltinana sp. n., Malinova novaelimae sp. n., Tiburica paranae sp. n.) from Brazil are described and illustrated.

Systematic Biology Volume 66, Number 2 March 2017 - Front Cover

Systematic Biology Volume 66, Number 2 March 2017 - Front Cover

Systematic Biology Volume 66, Number 2 March 2017 - Back Cover

Systematic Biology Volume 66, Number 2 March 2017 - Back Cover

Metabonomics and its application in thyroid diseases

As an important branch of systematic biology, metabonomics is an emerging discipline following genomics, proteomics and transcriptomics. It focuses on the quality and quantity changes of the small molecular metabolites in appointed physiological or pathological state, and provides important information for studies of diseases mechanism, clinical early diagnosis and prognosis prediction. Compared with traditional clinical diagnostic method (single index), metabonomics method can more comprehensively analyze metabolites changes in the body. This review introduces the metabonomics and summarizes its application in thyroid diseases. Key words: Thyroid diseases; Metabolomics; Trends

Special Issue: Mathematical and Computational Evolutionary Biology-2015.

This special issue of Systematic Biology contains review articles contributed by keynote speakers at the “Mathematical and Computational EvolutionaryBiology” conference (MCEB; see web sites below), held in 2015. This is the seventh conference in this series, the first being held in Paris in 2003 with keynote addresses from such notables as Joe Felsenstein, Ziheng Yang, and Walter Fitch. Oxford University Press published two books based on the 2003 and 2005 Paris meetings (Gascuel 2005; Gascuel and Steel 2007).

Systematic Biology Volume 66, Number 1 January 2017 - Back Cover

Systematic Biology Volume 66, Number 1 January 2017 - Back Cover

Systematic Biology Volume 66, Number 1 January 2017 - Front Cover

Systematic Biology Volume 66, Number 1 January 2017 - Front Cover

Behaviour and Systematics of New Zealand Plovers

Courtship behaviour and related aspects of reproduction in four endemic and a fifth self-introduced species of plover in New Zealand are described and used to suggest that the monotypic genus Anarhynthus be merged with Charadrius and that Charadrius is also the proper genus for obscurus. The close similarities between patterns of courtship behaviour of bicinctus, obscurus, frontalis and alexandrinus support Bock's (1958) grouping of them together and further indicate that they are a closely related subgroup within the genus Charadrius.

Fungal Systematics and Evolution: FUSE 2

The present study introduces two new genera, 14 new species, five new combinations and 12 interesting host and/or geographical records. A majority of the fungi are Ascomycetes, but the study also includes a Basidiomycete, Xerocomellus fulvus described from Pakistan. Under single name nomenclature Zeuctomorpha arecae is reduced to synonymy under Acroconidiellina arecae (Sympoventuriaceae, Venturiales, Dothideomycetes). Based on morphology and phylogenetic affinities, Wojnowicia dactylidis, W. lonicerae and W. spartii are moved to the genus Wojnowiciella (Phaeosphaeriaceae, Pleosporales, Dothideomycetes) and Zalerion arboricola is now accommodated in Lophium (Mytilinidiaceae, Mytilinidiales, Dothideomycetes). Novel genera include: Alfariacladiella gen. nov. (Stachybotryaceae, Hypocreales, Sordariomycetes) with A. spartii sp. nov. as type species, and Calvolachnella gen. nov. (Chaetosphaeriales, Sordariomycetes) to accommodate Calvolachnella guaviyuensis comb. nov., previously included in Pseudolachnella. Novel species include: Castanediella hyalopenicillata from leaf litter (USA), C. malaysiana on Eucalyptus brassiana (Malaysia) (Xylariales, Sordariomycetes), Morchella pakistanica (Morchellaceae, Pezizales, Pezizomycetes) on loamy soil (Pakistan), Muriphaeosphaeria viburni (Phaeosphaeriaceae, Pleosporales, Dothideomycetes) on twigs of Viburnum lantana (Serbia), Phyllosticta aucubae-japonicae (Phyllostictaceae, Botryosphaeriales, Dothideomycetes) on fruit of Aucuba japonica (Japan), Wojnowiciella leptocarpi (Phaeosphaeriaceae, Pleosporales, Dothideomycetes) on stems of Leptocarpus sp. (Australia), and Xylomelasma shoalensis (Sordariomycetes) on a dead branch (USA). New species from Germany include: Neosetophoma lunariae and Phaeosphaeria lunariae (Phaeosphaeriaceae, Pleosporales, Dothideomycetes) on seeds of Lunaria annua, Patellaria quercus (Patellariaceae, Patellariales, Dothideomycetes) on twigs of Quercus sp., Rhinocladiella coryli on stems of Corylus avellana and Rhinocladiella quercus (Herpotrichiellaceae, Chaetothyriales, Eurotiomycetes) on twigs of Quercus robur. Ramularia eucalypti (Mycosphaerellaceae, Capnodiales, Dothideomycetes) is reported on leaves of Citrus maxima from Italy, Beltrania rhombica (Beltraniaceae, Xylariales, Sordariomycetes) on leaves of Acacia sp. from Malaysia and Myrmecridium spartii (Myrmecridiaceae, Myrmecridiales, Sodariomycetes) on Sarothamnus scoparius from Serbia. New reports from Australia include: Dothiora ceratoniae (Dothideaceae, Dothideales, Dothideomycetes) on leaves of Eucalyptus sp., Readeriella dimorphospora (Teratosphaeriaceae, Capnodiales, Dothideomycetes) on Eucalyptus sp., Vermiculariopsiella dichapetali (Sordariomycetes) on leaves of Grevillea sp. and Acacia glaucoptera, and Verrucoconiothyrium nitidae (Montagnulaceae, Pleosporales, Dothideomycetes), on leaves of Acacia leprosa var. graveolens. New reports from La Reunion (France) include: Botryosphaeria agaves (Botryosphaeriaceae, Botryosphaeriales, Dothideomycetes) on branches of Agave sp., Chrysofolia colombiana (Cryphonectriaceae, Diaporthales, Sordariomycetes) on leaves of Syzygium jambos, Colletotrichum karstii (Glomerellaceae, Glomerellales, Sordariomycetes) on leaves of Acacia heterophylla, Epicoccum sorghinum (Didymellaceae, Pleosporales, Dothideomycetes) on leaves of Paspalum sp. and Helminthosporium velutinum (Massarinaceae, Pleosporales, Dothideomycetes) on branches of Stoebia sp. Finally, an epitype is designated for Tracylla aristata (Sordariomycetes) on Eucalyptus regnans (Australia).

RASAYANA CHIKISTA: ANTIAGENING THERAPY OF AYURVEDA

Ayurveda is the ancient system of Medicine in the world. Ayurved , the science of life deals with every aspect of life . Ayurveda has two aims i.e. pr evention and promotion of health and secondly cure from the disease. Rasayana may be employed for fulfilling both of them i.e. protection and promotion of health and curing the diseases. Rasayana is one of its eight branches being practiced since time immemorial. Rasayana therapy has been described in Ayurved as a systemat ic and scientific medical discipline. Rasayana drugs are those medicines which are capable of imparting superior Rasas and Dhatus to the body and toning up the system of healthy persons. Rasayana aid in increasing natural immunity, enhancing general wellbe ing, improving the functioning of all fundamental organs of the body and keep the signs of early aging at bay. The main purpose of Rasayana therapy is to impede the aging process and to delay the degenerative process in the body. Rasayana is the term given to special herbs, fruits or any other form of medication that are known to promote positive health and longevity. After taking Rasayana we can learn how to maintain a balance between the material and spiritual aspects of life and help others also to under stand it. This will help in establishing the peace, happiness and love.

Assessing similarity: on homology, characters and the need for a semantic approach to non-evolutionary comparative homology.

The problem of homology has been a consistent source of controversy at the heart of systematic biology, as has the step of morphological character analysis in phylogenetics. Based on a clear epistemic framework and a characterization of "characters" as diagnostic evidence units for the recognition of not directly identifiable entities, I discuss the ontological definition and empirical recognition criteria of phylogenetic, developmental and comparative homology, and how these three accounts of homology each contribute to an understanding of the overall phenomenon of homology. I argue that phylogenetic homologies are individuals or historical kinds that require comparative homology for identification. Developmental homologies are natural kinds that ultimately rest on phylogenetic homologies and also require comparative homology for identification. Comparative homologies on the other hand are anatomical structural kinds that are directly identifiable. I discuss pre-Darwinian comparative homology concepts and their problem of invoking non-material forces and involving the a priori assumption of a stable positional reference system. Based on Young's concept of comparative homology, I suggest a procedure for recognizing comparative homologues that lacks these problems and that utilizes a semantic framework. This formal conceptual framework provides the much needed semantic transparency and computer-parsability for documenting, communicating and analysing similarity propositions. It provides an essential methodological framework for generalizing over individual organisms and identifying and demarcating anatomical structural kinds, and it provides the missing link to the logical chain of identifying phylogenetic homology. The approach substantially increases the analytical accessibility of comparative research and thus represents an important contribution to the theoretical and methodological foundation of morphology and comparative biology.

MicroRNAs as biomarkers and regulators of nonalcoholic fatty liver disease.

Nonalcoholic fatty liver disease (NAFLD) is a complicated disease affected by the interaction of environmental and genetic factors; however, the precise pathogenesis of the disease has not been fully determined. There is a need to better understand the pathogenesis of NAFLD and to identify non-invasive diagnostic modalities. Recent advances in systematic biology and epigenetics have improved our understanding of the genotype-phenotype relationships in NAFLD. MicroRNAs (miRNAs) are important regulators of a wide range of biological processes. MiRNAs are extremely stable and protect from RNAase-mediated degradation in body fluids, making them attractive candidate biomarkers for the early detection of the disease and the monitoring of disease progression. In this review, we summarized the current knowledge on miRNAs as potential biomarkers of NAFLD at different stages and for the prognosis of advanced diseases. Furthermore, we discussed the implications of miRNAs that functioning in lipid metabolism and hepatic steatosis as well as in hepatic inflammation and fibrosis with regard to the pathogenesis of NAFLD.

Richard Peter Vari 1949–2016

Richard Peter Vari 1949–2016

Systematic Biology Volume 65, Number 6 November 2016 - Back Cover

Systematic Biology Volume 65, Number 6 November 2016 - Back Cover

Systematic Biology Volume 65, Number 6 November 2016 - Front Cover

Systematic Biology Volume 65, Number 6 November 2016 - Front Cover

Corrigendum.

New PhytologistVolume 212, Issue 3 p. 793-793 CorrigendumFree Access Corrigendum This article corrects the following: Partner choice through concealed floral sugar rewards evolved with the specialization of ant–plant mutualisms Guillaume Chomicki, Yannick M. Staedler, Jürg Schönenberger, Susanne S. Renner, Volume 211Issue 4New Phytologist pages: 1358-1370 First Published online: May 9, 2016 First published: 06 September 2016 https://doi.org/10.1111/nph.14187 Author for correspondence: Guillaume Chomicki Tel: +49 89 17861 285 Email: guillaume.chomicki@gmail.com AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Since its publication, the authors of Chomicki et al. (2016) have drawn to our attention that there is an omission in the Acknowledgements section. Martin Lehmann who performed the GC-MS analyses at the metabolomic service of the University of Munich should have been acknowledged. The correct Acknowledgements section is shown below. We apologize to our readers for this mistake. Acknowledgements We thank Jeremy Aroles for help with fieldwork and for proof-reading of the manuscript, Alivereti Naikatini and Marika Tui-wawa (University of South Pacific, Suva) with whom all collections were made, Benoît Chomicki for help with the editing of Movie S1, Evans Economo for help with ant identification, Andreas Wistuba for cultivated Hydnophytinae samples, Martin Lehmann who performed the GC-MS analyses at the metabolomic service of the University of Munich, Martin Heil and three anonymous reviewers for their comments on the manuscript, and the German Research Foundation (RE 603/20), the Society of Systematic Biologists and the American Association of Plant Taxonomy for funding. Reference Chomicki G, Staedler YM, Schönenberger J, Renner SS. 2016. Partner choice through concealed floral sugar rewards evolved with the specialization of ant–plant mutualisms. New Phytologist 211: 1358– 1370. Volume212, Issue3November 2016Pages 793-793 ReferencesRelatedInformation

Rarefaction and Extrapolation: Making Fair Comparison of Abundance-Sensitive Phylogenetic Diversity among Multiple Assemblages.

Measures of phylogenetic diversity are basic tools in many studies of systematic biology. Faith’s PD (sum of branch lengths of a phylogenetic tree connecting all focal species) is the most widely used phylogenetic measure. Like species richness, Faith’s PD based on sampling data is highly dependent on sample size and sample completeness. The sample-size- and sample-coverage-based integration of rarefaction and extrapolation of Faith’s PD was recently developed to make fair comparison across multiple assemblages. However, species abundances are not considered in Faith’s PD. Based on the framework of Hill numbers, Faith’s PD was generalized to a class of phylogenetic diversity measures that incorporates species abundances. In this article, we develop both theoretical formulae and analytic estimators for seamless rarefaction and extrapolation for this class of abundance-sensitive phylogenetic measures, which includes simple transformations of phylogenetic entropy and of quadratic entropy. This work generalizes the previous rarefaction/extrapolation model of Faith’s PD to incorporate species abundance, and also extends the previous rarefaction/extrapolation model of Hill numbers to include phylogenetic differences among species. Thus a unified approach to assessing and comparing species/taxonomic diversity and phylogenetic diversity can be established. A bootstrap method is suggested for constructing confidence intervals around the phylogenetic diversity, facilitating the comparison of multiple assemblages. Our formulation and estimators can be extended to incidence data collected from multiple sampling units. We also illustrate the formulae and estimators using bacterial sequence data from the human distal esophagus and phyllostomid bat data from three habitats.

Systematic Biology Volume 65, Number 5 September 2016 - Front Cover

Systematic Biology Volume 65, Number 5 September 2016 - Front Cover