Annexes to the Minabe-Tanabe Ume System
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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. -
State of New York City's Plants 2018
STATE OF NEW YORK CITY’S PLANTS 2018 Daniel Atha & Brian Boom © 2018 The New York Botanical Garden All rights reserved ISBN 978-0-89327-955-4 Center for Conservation Strategy The New York Botanical Garden 2900 Southern Boulevard Bronx, NY 10458 All photos NYBG staff Citation: Atha, D. and B. Boom. 2018. State of New York City’s Plants 2018. Center for Conservation Strategy. The New York Botanical Garden, Bronx, NY. 132 pp. STATE OF NEW YORK CITY’S PLANTS 2018 4 EXECUTIVE SUMMARY 6 INTRODUCTION 10 DOCUMENTING THE CITY’S PLANTS 10 The Flora of New York City 11 Rare Species 14 Focus on Specific Area 16 Botanical Spectacle: Summer Snow 18 CITIZEN SCIENCE 20 THREATS TO THE CITY’S PLANTS 24 NEW YORK STATE PROHIBITED AND REGULATED INVASIVE SPECIES FOUND IN NEW YORK CITY 26 LOOKING AHEAD 27 CONTRIBUTORS AND ACKNOWLEGMENTS 30 LITERATURE CITED 31 APPENDIX Checklist of the Spontaneous Vascular Plants of New York City 32 Ferns and Fern Allies 35 Gymnosperms 36 Nymphaeales and Magnoliids 37 Monocots 67 Dicots 3 EXECUTIVE SUMMARY This report, State of New York City’s Plants 2018, is the first rankings of rare, threatened, endangered, and extinct species of what is envisioned by the Center for Conservation Strategy known from New York City, and based on this compilation of The New York Botanical Garden as annual updates thirteen percent of the City’s flora is imperiled or extinct in New summarizing the status of the spontaneous plant species of the York City. five boroughs of New York City. This year’s report deals with the City’s vascular plants (ferns and fern allies, gymnosperms, We have begun the process of assessing conservation status and flowering plants), but in the future it is planned to phase in at the local level for all species. -
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]. -
1 History of Vitaceae Inferred from Morphology-Based
HISTORY OF VITACEAE INFERRED FROM MORPHOLOGY-BASED PHYLOGENY AND THE FOSSIL RECORD OF SEEDS By IJU CHEN A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2009 1 © 2009 Iju Chen 2 To my parents and my sisters, 2-, 3-, 4-ju 3 ACKNOWLEDGMENTS I thank Dr. Steven Manchester for providing the important fossil information, sharing the beautiful images of the fossils, and reviewing the dissertation. I thank Dr. Walter Judd for providing valuable discussion. I thank Dr. Hongshan Wang, Dr. Dario de Franceschi, Dr. Mary Dettmann, and Dr. Peta Hayes for access to the paleobotanical specimens in museum collections, Dr. Kent Perkins for arranging the herbarium loans, Dr. Suhua Shi for arranging the field trip in China, and Dr. Betsy R. Jackes for lending extant Australian vitaceous seeds and arranging the field trip in Australia. This research is partially supported by National Science Foundation Doctoral Dissertation Improvement Grants award number 0608342. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS ...............................................................................................................4 LIST OF TABLES...........................................................................................................................9 LIST OF FIGURES .......................................................................................................................11 ABSTRACT...................................................................................................................................14 -
Phylogenetic Analysis of Vitaceae Based on Plastid Sequence Data
PHYLOGENETIC ANALYSIS OF VITACEAE BASED ON PLASTID SEQUENCE DATA by PAUL NAUDE Dissertation submitted in fulfilment of the requirements for the degree MAGISTER SCIENTAE in BOTANY in the FACULTY OF SCIENCE at the UNIVERSITY OF JOHANNESBURG SUPERVISOR: DR. M. VAN DER BANK December 2005 I declare that this dissertation has been composed by myself and the work contained within, unless otherwise stated, is my own Paul Naude (December 2005) TABLE OF CONTENTS Table of Contents Abstract iii Index of Figures iv Index of Tables vii Author Abbreviations viii Acknowledgements ix CHAPTER 1 GENERAL INTRODUCTION 1 1.1 Vitaceae 1 1.2 Genera of Vitaceae 6 1.2.1 Vitis 6 1.2.2 Cayratia 7 1.2.3 Cissus 8 1.2.4 Cyphostemma 9 1.2.5 Clematocissus 9 1.2.6 Ampelopsis 10 1.2.7 Ampelocissus 11 1.2.8 Parthenocissus 11 1.2.9 Rhoicissus 12 1.2.10 Tetrastigma 13 1.3 The genus Leea 13 1.4 Previous taxonomic studies on Vitaceae 14 1.5 Main objectives 18 CHAPTER 2 MATERIALS AND METHODS 21 2.1 DNA extraction and purification 21 2.2 Primer trail 21 2.3 PCR amplification 21 2.4 Cycle sequencing 22 2.5 Sequence alignment 22 2.6 Sequencing analysis 23 TABLE OF CONTENTS CHAPTER 3 RESULTS 32 3.1 Results from primer trail 32 3.2 Statistical results 32 3.3 Plastid region results 34 3.3.1 rpL 16 34 3.3.2 accD-psa1 34 3.3.3 rbcL 34 3.3.4 trnL-F 34 3.3.5 Combined data 34 CHAPTER 4 DISCUSSION AND CONCLUSIONS 42 4.1 Molecular evolution 42 4.2 Morphological characters 42 4.3 Previous taxonomic studies 45 4.4 Conclusions 46 CHAPTER 5 REFERENCES 48 APPENDIX STATISTICAL ANALYSIS OF DATA 59 ii ABSTRACT Five plastid regions as source for phylogenetic information were used to investigate the relationships among ten genera of Vitaceae. -
The Mcguire Center for Lepidoptera and Biodiversity
Supplemental Information All specimens used within this study are housed in: the McGuire Center for Lepidoptera and Biodiversity (MGCL) at the Florida Museum of Natural History, Gainesville, USA (FLMNH); the University of Maryland, College Park, USA (UMD); the Muséum national d’Histoire naturelle in Paris, France (MNHN); and the Australian National Insect Collection in Canberra, Australia (ANIC). Methods DNA extraction protocol of dried museum specimens (detailed instructions) Prior to tissue sampling, dried (pinned or papered) specimens were assigned MGCL barcodes, photographed, and their labels digitized. Abdomens were then removed using sterile forceps, cleaned with 100% ethanol between each sample, and the remaining specimens were returned to their respective trays within the MGCL collections. Abdomens were placed in 1.5 mL microcentrifuge tubes with the apex of the abdomen in the conical end of the tube. For larger abdomens, 5 mL microcentrifuge tubes or larger were utilized. A solution of proteinase K (Qiagen Cat #19133) and genomic lysis buffer (OmniPrep Genomic DNA Extraction Kit) in a 1:50 ratio was added to each abdomen containing tube, sufficient to cover the abdomen (typically either 300 µL or 500 µL) - similar to the concept used in Hundsdoerfer & Kitching (1). Ratios of 1:10 and 1:25 were utilized for low quality or rare specimens. Low quality specimens were defined as having little visible tissue inside of the abdomen, mold/fungi growth, or smell of bacterial decay. Samples were incubated overnight (12-18 hours) in a dry air oven at 56°C. Importantly, we also adjusted the ratio depending on the tissue type, i.e., increasing the ratio for particularly large or egg-containing abdomens. -
Faunal Makeup of Macrolepidopterous Moths in Nopporo Forest Park, Hokkaido, Northern Japan, with Some Related Title Notes
Faunal Makeup of Macrolepidopterous Moths in Nopporo Forest Park, Hokkaido, Northern Japan, with Some Related Title Notes Author(s) Sato, Hiroaki; Fukuda, Hiromi Environmental science, Hokkaido : journal of the Graduate School of Environmental Science, Hokkaido University, Citation Sapporo, 8(1), 93-120 Issue Date 1985-07-31 Doc URL http://hdl.handle.net/2115/37177 Type bulletin (article) File Information 8(1)_93-120.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP 93 Environ. Sci., Hokkaiclo 8 (1) 93-v120 I June 1985 Faunal Makeup of Macrolepidopterous Moths in Nopporo Forest Park, Hokkaido, Northern Japan, with Some Related Notes Hiroaki Sato and Hiromi Ful<uda Department of Biosystem Management, Division of Iinvironmental Conservation, Graciuate Schoo! of Environmental Science, Hokkaido University, Sapporo, 060, Japan Abstraet Macrolepidopterous moths were collected in Nopporo Forest Park to disclose the faunal mal<eup. By combining this survey with other from Nopporo, 595 species "rere recorded, compris- ing of roughly 45% of all species discovered in }{{okkaiclo to clate. 'irhe seasonal fiuctuations of a species diversity were bimodal, peal<ing in August and November. The data obtained had a good correlation to both lognormal and logseries clistributions among various species-abundance models. In summer, it was found that specialistic feeders dominated over generalistic feeders. However, in autumn, generalistic feeders clominated, most lil<ely because low temperature shortened hours for seel<ing host plants on which to lay eggs. - Key Words: NopporQ Forest Park, Macrolepidoptera, Species diversity, Species-abundance model, Generalist, Specialist 1. Introduction Nopporo Forest Park, which has an area of approximately 2,OOO ha and is adjacent to the city of Sapporo, contains natural forests representing the temperate and boreal features of vegetation. -
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. -
Diversity of Moth Fauna in the West Bengal State University Campus: a Pictorial Catalogue
International Journal of Zoology Studies International Journal of Zoology Studies ISSN: 2455-7269 Impact Factor: RJIF 5.14 www.zoologyjournals.com Volume 3; Issue 1; January 2018; Page No. 35-38 Diversity of moth fauna in the West Bengal state university campus: A pictorial catalogue Dr. Samir Kumar Saha Assistant Professor, Department of Zoology, West Bengal State University, Berunanpukuria, Malikapur, Kolkata, West Bengal, India Abstract An attempt has been taken to study the diversity of Moth fauna in West Bengal State University (WBSU) campus. A total of 30 genera were recorded under ten families from the study area from November 2017 to December, 2017. The family Erebidae with 12 genera followed by family Crambidae with 9 genera, family Noctuidae with 2 genera, rest of the family Arctiidae, Sphingidae, Pterophoridae, Uraniidae, Geometridae, Scythrididae and Stathmopodidae with 1 genus each were recorded inside campus area. As 30 different genera of moth recorded within a short span of time, it can be presumed to have a good diversity of moth species inside campus area. Keywords: moth, diversity, WBSU, West Bengal, India 1. Introduction Moth fauna. WBSU Campus is located in between 88° 25′ E Lepidoptera is one of the large order of insects that include longitudes and 44°46′ N latitude in the state of West Bengal, butterflies and moths and is probably one of the most suitable India (Fig. 1). groups for most quantitative comparisons between insect Photographs and observations were taken during the day light faunas to be valid, for the many reasons elaborated by hours. Individual images of Moths were photo-documented Holloway [1]. -
The Evolutionary Biology of Herbivorous Insects
GRBQ316-3309G-C01[01-19].qxd 7/17/07 12:07 AM Page 1 Aptara (PPG-Quark) PART I EVOLUTION OF POPULATIONS AND SPECIES GRBQ316-3309G-C01[01-19].qxd 7/17/07 12:07 AM Page 2 Aptara (PPG-Quark) GRBQ316-3309G-C01[01-19].qxd 7/17/07 12:07 AM Page 3 Aptara (PPG-Quark) ONE Chemical Mediation of Host-Plant Specialization: The Papilionid Paradigm MAY R. BERENBAUM AND PAUL P. FEENY Understanding the physiological and behavioral mecha- chemistry throughout the life cycle are central to these nisms underlying host-plant specialization in holo- debates. Almost 60 years ago, Dethier (1948) suggested that metabolous species, which undergo complete development “the first barrier to be overcome in the insect-plant relation- with a pupal stage, presents a particular challenge in that ship is a behavioral one. The insect must sense and discrim- the process of host-plant selection is generally carried out inate before nutritional and toxic factors become opera- by the adult stage, whereas host-plant utilization is more tive.” Thus, Dethier argued for the primacy of adult [AQ2] the province of the larval stage (Thompson 1988a, 1988b). preference, or detection and response to kairomonal cues, Thus, within a species, critical chemical, physical, or visual in host-plant shifts. In contrast, Ehrlich and Raven (1964) cues for host-plant identification may differ over the course reasoned that “after the restriction of certain groups of of the life cycle. An organizing principle for the study of insects to a narrow range of food plants, the formerly repel- host-range evolution is the preference-performance hypoth- lent substances of these plants might . -
ABSTRACT ZHA, CHEN. Evaluating the Dynamics of Anti-Fungal Compounds in Lepidoptera Larvae
ABSTRACT ZHA, CHEN. Evaluating the Dynamics of Anti-Fungal Compounds in Lepidoptera Larvae. (Under the direction of Allen Cohen.) Mold control is one of the most vital issues in insect rearing systems. Mold outbreaks can alter the nutritional value of the diet, do harm to the insects, and even threaten the health of people who work in insectaries. Antifungal agents are widely used in insect diets to suppress the growth of mold; however, the potential detrimental effects of antifungal agents on insects are always a concern. When there is a high level of antifungal agents in artificial diets, the growth, development, survivorship and fecundity of insects are often negatively affected. To study the mechanisms underlying those deleterious effects, nutritional indices were determined for two representative lepidopterans, a butterfly and a moth, Vanessa cardui and Heliothis virescens larvae reared on different concentrations of three widely used antifungal agents: methyl paraben, potassium sorbate and sodium propionate. These antifungal agents were administered in concentrations of 1,000, 5,000, and 10,000 parts per million (ppm). The results show that a high level of antifungal agents in the diets of these insects will suppress nutrient absorption and increase metabolic costs. Relative consumption rates and digestibility increased with increasing antifungal agent concentration, possibly to compensate for the declines in absorption and metabolism. Silk production and frass management by Vanessa cardui larvae were reduced in the presence of the highest level of antifungal agents. Evaluating the Dynamics of Anti-Fungal Compounds in Lepidoptera Larvae by Chen Zha A thesis submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirement for the Degree of Master of Science Entomology Raleigh, North Carolina 2013 APPROVED BY: ________________________ ________________________ Allen C. -
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Advances in Biological Sciences Research (ABSR), volume 4 2nd International Conference on Biomedical and Biological Engineering 2017 (BBE 2017) Ultrastructure and Self-cleaning Function of Moth (Notodontidae) and Butterfly (Lycaenidae) Wings Yan FANG, Gang SUN*, Jing-shi YIN, Wan-xing WANG and Yu-qian WANG School of Life Science, Changchun Normal University, Changchun 130032, China *Corresponding author Keywords: Ultrastructure, Self-cleaning, Wettability, Moth, Butterfly, Biomaterial. Abstract. The microstructure, hydrophobicity, adhesion and chemical composition of the butterfly and moth wing surfaces were investigated by a scanning electron microscope (SEM), a contact angle meter, and a Fourier transform infrared spectrometer (FT-IR). Using ground calcium carbonate (heavy CaCO3 ) as contaminating particle, the self-cleaning performance of the wing surface was evaluated. The wing surfaces, composed of naturally hydrophobic material (chitin, protein, fat, etc.), possess complicated hierarchical micro/nano structures. According to the large contact angle (CA, 148.3~156.2° for butterfly, 150.4~154.7° for moth) and small sliding angle (SA, 1~3° for butterfly, 1~4° for moth), the wing surface is of low adhesion and superhydrophobicity. The removal rate of contaminating particle from the wing surface is averagely 88.0% (butterfly wing) and 87.7% (moth wing). There is a good positive correlation ( R 2 =0.8385 for butterfly, 0.8155 for moth) between particle removal rate and roughness index of the wing surface. The coupling effect of material element and structural element contributes to the outstanding superhydrophobicity and self-cleaning performance of the wing surface. The wings of flying insect can be potentially used as templates for biomimetic preparation of biomedical interfacial material with multi-functions.