Otsuka, Kimio
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A Solution for Universal Classification of Species Based on Genomic
Hindawi Publishing Corporation International Journal of Plant Genomics Volume 2007, Article ID 27894, 8 pages doi:10.1155/2007/27894 Research Article A Solution for Universal Classification of Species Based on Genomic DNA Mariko Kouduka,1 Daisuke Sato,1 Manabu Komori,1 Motohiro Kikuchi,2 Kiyoshi Miyamoto,3 Akinori Kosaku,3 Mohammed Naimuddin,1, 4 Atsushi Matsuoka,5 and Koichi Nishigaki1, 6 1 Department of Functional Materials Science, Saitama University, Saitama, Japan 2 Chitose Salmon Aquarium Chitose, Youth Educational Foundation, Chitose, Hokkaido, Japan 3 Institute of Medical Science, Dokkyo Medical University, Tochigi, Japan 4 Biol. Res. and Functions, National Inst. AIST, Tsukuba, Ibaraki, Japan 5 Department of Geology, Niigata University, Niigata, Japan 6 Rational Evolutionary Design of Advanced Biomolecules, Saitama Small Enterprise Promotion Corporation, SKIP City, Saitama, Japan Received 22 July 2006; Revised 8 October 2006; Accepted 8 October 2006 Recommended by Cheng-Cang Wu Traditionally, organisms have been classified on the basis of their phenotype. Recently, genotype-based classification has become possible through the development of sequencing technology. However, it is still difficult to apply sequencing approaches to the analysis of a large number of species due to the cost and labor. In most biological fields, the analysis of complex systems compris- ing various species has become an important theme, demanding an effective method for handling a vast number of species. In this paper, we have demonstrated, using plants, fish, and insects, that genome profiling, a compact technology for genome analysis, can classify organisms universally. Surprisingly, in all three of the domains of organisms tested, the phylogenetic trees generated from the phenotype topologically matched completely those generated from the genotype. -
Topic Paper Chilterns Beechwoods
. O O o . 0 O . 0 . O Shoping growth in Docorum Appendices for Topic Paper for the Chilterns Beechwoods SAC A summary/overview of available evidence BOROUGH Dacorum Local Plan (2020-2038) Emerging Strategy for Growth COUNCIL November 2020 Appendices Natural England reports 5 Chilterns Beechwoods Special Area of Conservation 6 Appendix 1: Citation for Chilterns Beechwoods Special Area of Conservation (SAC) 7 Appendix 2: Chilterns Beechwoods SAC Features Matrix 9 Appendix 3: European Site Conservation Objectives for Chilterns Beechwoods Special Area of Conservation Site Code: UK0012724 11 Appendix 4: Site Improvement Plan for Chilterns Beechwoods SAC, 2015 13 Ashridge Commons and Woods SSSI 27 Appendix 5: Ashridge Commons and Woods SSSI citation 28 Appendix 6: Condition summary from Natural England’s website for Ashridge Commons and Woods SSSI 31 Appendix 7: Condition Assessment from Natural England’s website for Ashridge Commons and Woods SSSI 33 Appendix 8: Operations likely to damage the special interest features at Ashridge Commons and Woods, SSSI, Hertfordshire/Buckinghamshire 38 Appendix 9: Views About Management: A statement of English Nature’s views about the management of Ashridge Commons and Woods Site of Special Scientific Interest (SSSI), 2003 40 Tring Woodlands SSSI 44 Appendix 10: Tring Woodlands SSSI citation 45 Appendix 11: Condition summary from Natural England’s website for Tring Woodlands SSSI 48 Appendix 12: Condition Assessment from Natural England’s website for Tring Woodlands SSSI 51 Appendix 13: Operations likely to damage the special interest features at Tring Woodlands SSSI 53 Appendix 14: Views About Management: A statement of English Nature’s views about the management of Tring Woodlands Site of Special Scientific Interest (SSSI), 2003. -
Error-Robust Nature of Genome Profiling Applied for Clustering of Species Demonstrated by Computer Simulation
World Academy of Science, Engineering and Technology International Journal of Bioengineering and Life Sciences Vol:1, No:5, 2007 Error-Robust Nature of Genome Profiling Applied for Clustering of Species Demonstrated by Computer Simulation Shamim Ahmed and Koichi Nishigaki factors [4], and the insufficiency in the number of experts [5]. Abstract—Genome profiling (GP), a genotype based technology, Recently, genotype-based approach has become possible which exploits random PCR and temperature gradient gel owing to the development of sequencing technology. electrophoresis, has been successful in identification/classification of organisms. In this technology, spiddos (Species identification dots) However, it is still difficult to apply sequencing approaches to and PaSS (Pattern similarity score) were employed for measuring the the analysis of a large number of species due to logistic closeness (or distance) between genomes. Based on the closeness reason. In most biological fields, the analysis of complex (PaSS), we can buildup phylogenetic trees of the organisms. We systems comprising various species has been an important noticed that the topology of the tree is rather robust against the experimental fluctuation conveyed by spiddos. This fact was theme, demanding an effective method for handling a vast confirmed quantitatively in this study by computer-simulation, number of species. A realistic solution to these problems has providing the limit of the reliability of this highly powerful been to characterize organisms according to the sequence of methodology. As a result, we could demonstrate the effectiveness of their small subunit ribosomal RNA (16S/18S rRNA), an the GP approach for identification/classification of organisms. approach that has been applied to various organisms, initiated Keywords—Fluctuation, Genome profiling (GP), Pattern by Woese and his collaborators [6]~[8]. -
The Associations Between Pteridophytes and Arthropods
FERN GAZ. 12(1) 1979 29 THE ASSOCIATIONS BETWEEN PTERIDOPHYTES AND ARTHROPODS URI GERSON The Hebrew University of Jerusalem, Faculty of Agriculture, Rehovot, Israel. ABSTRACT Insects belonging to 12 orders, as well as mites, millipedes, woodlice and tardigrades have been collected from Pterldophyta. Primitive and modern, as well as general and specialist arthropods feed on pteridophytes. Insects and mites may cause slight to severe damage, all plant parts being susceptible. Several arthropods are pests of commercial Pteridophyta, their control being difficult due to the plants' sensitivity to pesticides. Efforts are currently underway to employ insects for the biological control of bracken and water ferns. Although Pteridophyta are believed to be relatively resistant to arthropods, the evidence is inconclusive; pteridophyte phytoecdysones do not appear to inhibit insect feeders. Other secondary compounds of preridophytes, like prunasine, may have a more important role in protecting bracken from herbivores. Several chemicals capable of adversely affecting insects have been extracted from Pteridophyta. The litter of pteridophytes provides a humid habitat for various parasitic arthropods, like the sheep tick. Ants often abound on pteridophytes (especially in the tropics) and may help in protecting these plants while nesting therein. These and other associations are discussed . lt is tenatively suggested that there might be a difference in the spectrum of arthropods attacking ancient as compared to modern Pteridophyta. The Osmundales, which, in contrast to other ancient pteridophytes, contain large amounts of ·phytoecdysones, are more similar to modern Pteridophyta in regard to their arthropod associates. The need for further comparative studies is advocated, with special emphasis on the tropics. -
Title Host Utilization by a Saw Fly Strongylogaster Osmundae
Host Utilization by a Saw fly Strongylogaster osmundae Title (Hymenoptera : Tenthredinidae) on Osmund Fern Osmunda japonica Author(s) Otsuka, Kimio Memoirs of the Faculty of Science, Kyoto University. Series of Citation biology. New series (2000), 17(1): 11-23 Issue Date 2000-06 URL http://hdl.handle.net/2433/258936 Right Type Departmental Bulletin Paper Textversion publisher Kyoto University Mem. Fac. Sci. Kyoto Univ. (Sen BieL), 17: 11-23, Jun., 2000 Hest Utilizatie" by a Sawfiy Strongylogaster osmuntlae (Hymenoptera: Tellthredinidae) en Osmund Fern Osmundajuponica kMIO OTSUKA Department of Zoology, Faculty of Science, Kyoto University, Sakyo, Kyoto 606, JAPAN (Received May 15, 2000) Abstnict Vo}tinism and host plant utilization of the sawfiy Strengylogaster osmundae were investigated. This species is multivoltine (5 or 6 generations per year) and emerges from late April to July or early August in Kyoto, Japan. Female sawflies deposit eggs on new leaves of the osmund fern, Osmunda iaponica, and the larvae feed on the leaves. The host plant usually develops new leaves from late April to early May (primary shoots), and intact ferns rarely produce new leaves thereafter. SiRce the primary shoots are new and only available to the sawfly until the beginning of June at the latest, only the first and second generations can utilize them. The eggs are laid in clusters, and the larvae feed gregariously and frequently defoliate leaves. It is suggested that egg clumping and defoliation by S. osmundae is a form of host regulation to maintain its multivoltine life history, since the defoliation by the first and secend generations induces corapensatory regrowth of the fern, producing food for the third and subsequent generations. -
Colourful Butterfly Wings: Scale Stacks, Iridescence and Sexual Dichromatism of Pieridae Doekele G
158 entomologische berichten 67(5) 2007 Colourful butterfly wings: scale stacks, iridescence and sexual dichromatism of Pieridae Doekele G. Stavenga Hein L. Leertouwer KEY WORDS Coliadinae, Pierinae, scattering, pterins Entomologische Berichten 67 (5): 158-164 The colour of butterflies is determined by the optical properties of their wing scales. The main scale structures, ridges and crossribs, scatter incident light. The scales of pierid butterflies have usually numerous pigmented beads, which absorb light at short wavelengths and enhance light scattering at long wavelengths. Males of many species of the pierid subfamily Coliadinae have ultraviolet-iridescent wings, because the scale ridges are structured into a multilayer reflector. The iridescence is combined with a yellow or orange-brown colouration, causing the common name of the subfamily, the yellows or sulfurs. In the subfamily Pierinae, iridescent wing tips are encountered in the males of most species of the Colotis-group and some species of the tribe Anthocharidini. The wing tips contain pigments absorbing short-wavelength light, resulting in yellow, orange or red colours. Iridescent wings are not found among the Pierini. The different wing colours can be understood from combinations of wavelength-dependent scattering, absorption and iridescence, which are characteristic for the species and sex. Introduction often complex and as yet poorly understood optical phenomena The colour of a butterfly wing depends on the interaction of encountered in lycaenids and papilionids. The Pieridae have light with the material of the wing and its spatial structure. But- two main subfamilies: Coliadinae and Pierinae. Within Pierinae, terfly wings consist of a wing substrate, upon which stacks of the tribes Pierini and Anthocharidini are distinguished, together light-scattering scales are arranged. -
Beiträge Zur Bayerischen Entomofaunistik 13: 67–207
Beiträge zur bayerischen Entomofaunistik 13:67–207, Bamberg (2014), ISSN 1430-015X Grundlegende Untersuchungen zur vielfältigen Insektenfauna im Tiergarten Nürnberg unter besonderer Betonung der Hymenoptera Auswertung von Malaisefallenfängen in den Jahren 1989 und 1990 von Klaus von der Dunk & Manfred Kraus Inhaltsverzeichnis 1. Einleitung 68 2. Untersuchungsgebiet 68 3. Methodik 69 3.1. Planung 69 3.2. Malaisefallen (MF) im Tiergarten 1989, mit Gelbschalen (GS) und Handfänge 69 3.3. Beschreibung der Fallenstandorte 70 3.4. Malaisefallen, Gelbschalen und Handfänge 1990 71 4. Darstellung der Untersuchungsergebnisse 71 4.1. Die Tabellen 71 4.2. Umfang der Untersuchungen 73 4.3. Grenzen der Interpretation von Fallenfängen 73 5. Untersuchungsergebnisse 74 5.1. Hymenoptera 74 5.1.1. Hymenoptera – Symphyta (Blattwespen) 74 5.1.1.1. Tabelle Symphyta 74 5.1.1.2. Tabellen Leerungstermine der Malaisefallen und Gelbschalen und Blattwespenanzahl 78 5.1.1.3. Symphyta 79 5.1.2. Hymenoptera – Terebrantia 87 5.1.2.1. Tabelle Terebrantia 87 5.1.2.2. Tabelle Ichneumonidae (det. R. Bauer) mit Ergänzungen 91 5.1.2.3. Terebrantia: Evanoidea bis Chalcididae – Ichneumonidae – Braconidae 100 5.1.2.4. Bauer, R.: Ichneumoniden aus den Fängen in Malaisefallen von Dr. M. Kraus im Tiergarten Nürnberg in den Jahren 1989 und 1990 111 5.1.3. Hymenoptera – Apocrita – Aculeata 117 5.1.3.1. Tabellen: Apidae, Formicidae, Chrysididae, Pompilidae, Vespidae, Sphecidae, Mutillidae, Sapygidae, Tiphiidae 117 5.1.3.2. Apidae, Formicidae, Chrysididae, Pompilidae, Vespidae, Sphecidae, Mutillidae, Sapygidae, Tiphiidae 122 5.1.4. Coleoptera 131 5.1.4.1. Tabelle Coleoptera 131 5.1.4.2. -
Hymenoptera: Symphyta): Evidence for Multiple Increases in Sperm Bundle Size
J. HYM. RES. Vol. 10(Z), 2001, pp. 119-125 Spermatodesmata of the Sawflies (Hymenoptera: Symphyta): Evidence for Multiple Increases in Sperm Bundle Size NATHAN SCHIFF, ANTHONY J. FLEMMINC, AND DONALD L. J. QUICKE (NS) U.S. Forest Service, Southern Research Station, Center for Bottomland Hardwoods Research, P.O. Box 227, Stoneville, MS 38776, USA; (AJF) Department of Biology, Imperial College at Silwood Park, Ascot, Berkshire SL5 7PY, U.K.; (DLJQ) Unit of Parasitoid Systematics, Department of Biology, Imperial College at Silwood Park, Ascot, Berkshire SL5 7PY, UK, and Department of Entomology, The Natural History Museum, London SW7 5BD, UK Abstract.-We present the first survey of spermatodesmata (bundles of spermatozoa connected at the head by an extracellular ‘gelatinous’ matrix) across the sawfly superfamilies. Spermatodes- mata occur in all examined taxa within the sawfly grade (Xyelidae-Orussidae inclusive), but are not found in the Apocrita. Using DAPI staining, the numbers of individual sperm per sperma- todesm were calculated and the values obtained are mapped on to the current phylogenetic hy- pothesis. The plesiomorphic spermatodesm in the Hymenoptera, based on that observed in the putatively basal family Xyelidae, contains relatively few sperm, approximately 16. However, in the Tenthredinoidea and in the Siricidae, far larger numbers are found, reaching up to 256 in the Cimbicidae. In many insects, mature sperm released Until now, spermatodesmata have only from testicular follicles are neither free in- been characterised in a few sawflies, al- dividuals nor packaged into variously most entirely as part of ultrastructural in- complex spermatophores, but are ar- vestigations using transmission electron ranged in organised bundles with their microscopy (Quicke et al. -
Science Journals — AAAS
SCIENCE ADVANCES | RESEARCH ARTICLE EVOLUTIONARY BIOLOGY Copyright © 2019 The Authors, some rights reserved; Unprecedented reorganization of holocentric exclusive licensee American Association chromosomes provides insights into the enigma of for the Advancement of Science. No claim to lepidopteran chromosome evolution original U.S. Government Jason Hill1,2*, Pasi Rastas3, Emily A. Hornett4,5,6, Ramprasad Neethiraj1, Nathan Clark7, Works. Distributed 8 1 9,10 under a Creative Nathan Morehouse , Maria de la Paz Celorio-Mancera , Jofre Carnicer Cols , Commons Attribution 11 7,12 1 1 13,14 Heinrich Dircksen , Camille Meslin , Naomi Keehnen , Peter Pruisscher , Kristin Sikkink , NonCommercial 9,10 15 1 1,16 17 Maria Vives , Heiko Vogel , Christer Wiklund , Alyssa Woronik , Carol L. Boggs , License 4.0 (CC BY-NC). Sören Nylin1, Christopher W. Wheat1* Chromosome evolution presents an enigma in the mega-diverse Lepidoptera. Most species exhibit constrained chromosome evolution with nearly identical haploid chromosome counts and chromosome-level gene collinearity among species more than 140 million years divergent. However, a few species possess radically inflated chromo- somal counts due to extensive fission and fusion events. To address this enigma of constraint in the face of an Downloaded from exceptional ability to change, we investigated an unprecedented reorganization of the standard lepidopteran chromosome structure in the green-veined white butterfly (Pieris napi). We find that gene content in P. napi has been extensively rearranged in large collinear blocks, which until now have been masked by a haploid chromosome number close to the lepidopteran average. We observe that ancient chromosome ends have been maintained and collinear blocks are enriched for functionally related genes suggesting both a mechanism and a possible role for selection in determining the boundaries of these genome-wide rearrangements. -
9-3 29 May 2021
Volume 9 Number 3 29 May 2021 The Taxonomic Report OF THE INTERNATIONAL LEPIDOPTERA SURVEY ISSN 2643-4776 (print) / ISSN 2643-4806 (online) Genomics-guided refinement of butterfly taxonomy Jing Zhang2,3, Qian Cong2,4, Jinhui Shen2,3, Paul A. Opler5 and Nick V. Grishin1,2,3* 1Howard Hughes Medical Institute, Departments of 2Biophysics and 3Biochemistry, and 4Eugene McDermott Center for Human Growth & Development, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9050, USA; 5Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523-1177, USA. *Corresponding author: [email protected] ABSTRACT. Continuing with comparative genomic exploration of worldwide butterfly fauna, we use all protein- coding genes as they are retrieved from the whole genome shotgun sequences for phylogeny construction. Analysis of these genome-scale phylogenies projected onto the taxonomic classification and the knowledge about butterfly phenotypes suggests further refinements of butterfly taxonomy that are presented here. As a general rule, we assign most prominent clades of similar genetic differentiation to the same taxonomic rank, and use criteria based on relative population diversification and the extent of gene exchange for species delimitation. As a result, 7 tribes, 4 subtribes, 14 genera, and 9 subgenera are proposed as new, i.e., in subfamily Pierinae Swainson, 1820: Calopierini Grishin, trib. n. (type genus Calopieris Aurivillius, 1898); in subfamily Riodininae Grote, 1895: Callistiumini Grishin, trib. n. (type genus Callistium Stichel, 1911); in subfamily Nymphalinae Rafinesque, 1815: Pycinini Grishin, trib. n. (type genus Pycina Doubleday 1849), Rhinopalpini Grishin, trib. n. (type genus Rhinopalpa C. & R. Felder 1860), Kallimoidini Grishin, trib. -
Invertebrate and Avian Predators As Drivers of Chemical Defensive Strategies in Tenthredinid Sawflies
Boevé et al. BMC Evolutionary Biology 2013, 13:198 http://www.biomedcentral.com/1471-2148/13/198 RESEARCH ARTICLE Open Access Invertebrate and avian predators as drivers of chemical defensive strategies in tenthredinid sawflies Jean-Luc Boevé1*, Stephan M Blank2, Gert Meijer1,3 and Tommi Nyman4,5 Abstract Background: Many insects are chemically defended against predatory vertebrates and invertebrates. Nevertheless, our understanding of the evolution and diversity of insect defenses remains limited, since most studies have focused on visual signaling of defenses against birds, thereby implicitly underestimating the impact of insectivorous insects. In the larvae of sawflies in the family Tenthredinidae (Hymenoptera), which feed on various plants and show diverse lifestyles, two distinct defensive strategies are found: easy bleeding of deterrent hemolymph, and emission of volatiles by ventral glands. Here, we used phylogenetic information to identify phylogenetic correlations among various ecological and defensive traits in order to estimate the relative importance of avian versus invertebrate predation. Results: The mapping of 12 ecological and defensive traits on phylogenetic trees inferred from DNA sequences reveals the discrete distribution of easy bleeding that occurs, among others, in the genus Athalia and the tribe Phymatocerini. By contrast, occurrence of ventral glands is restricted to the monophyletic subfamily Nematinae, which are never easy bleeders. Both strategies are especially effective towards insectivorous insects such as ants, while only Nematinae species are frequently brightly colored and truly gregarious. Among ten tests of phylogenetic correlation between traits, only a few are significant. None of these involves morphological traits enhancing visual signals, but easy bleeding is associated with the absence of defensive body movements and with toxins occurring in the host plant. -
Terrestrial Arthropods of Steel Creek, Buffalo National River, Arkansas. II
Biodiversity Data Journal 4: e8830 doi: 10.3897/BDJ.4.e8830 Data Paper Terrestrial arthropods of Steel Creek, Buffalo National River, Arkansas. II. Sawflies (Insecta: Hymenoptera: "Symphyta") Michael Joseph Skvarla‡,§, David R. Smith |, Danielle M. Fisher§, Ashley P.G. Dowling§ ‡ University of Maryland, University Park, Maryland, United States of America § University of Arkansas, Fayetteville, Arkansas, United States of America | Systematic Entomology Laboratory, Agricultural Research Service, U. S. Department of Agriculture, c/o National Museum of Natural History, Smithsonian Institution, Washington, D.C., United States of America Corresponding author: Michael Joseph Skvarla ([email protected]) Academic editor: Michael Kuhlmann Received: 13 Apr 2016 | Accepted: 03 May 2016 | Published: 09 May 2016 Citation: Skvarla M, Smith D, Fisher D, Dowling A (2016) Terrestrial arthropods of Steel Creek, Buffalo National River, Arkansas. II. Sawflies (Insecta: Hymenoptera: "Symphyta"). Biodiversity Data Journal 4: e8830. doi: 10.38 97/BDJ.4.e8830 Abstract Background This is the second in a series of papers detailing the terrestrial arthropods collected during an intensive survey of a site near Steel Creek campground along the Buffalo National River in Arkansas. The survey was conducted over a period of eight and a half months using twelve trap types – Malaise traps, canopy traps (upper and lower collector), Lindgren multifunnel traps (black, green, and purple), pan traps (blue, purple, red, white, and yellow), and pitfall traps – and Berlese-Tullgren extraction of leaf litter. New information We provide collection records for 47 species of "Symphyta" (Insecta: Hymenoptera), 30 of which are new state records for Arkansas: (Argidae) Sterictiphora serotina; (Cimbicidae) Abia americana; (Diprionidae) Monoctenus fulvus; (Orussidae) Orussus terminalis; © Skvarla M et al.