DOCSLIB.ORG

Title of Dissertation Goes Here in All Caps

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Title of Dissertation Goes Here in All Caps TOWARD STRUCTURAL AND FUNCTIONAL PREDICTIONS FROM BIOLOGICAL SEQUENCES APPROVED BY SUPERVISORY COMMITTEE Nick V. Grishin, Ph.D.: Advisor Zbyszek Otwinowski, Ph.D.: Committee Chair Philip J. Thomas, Ph.D. Daniel Rosenbaum, Ph.D. DEDICATION To those who care TOWARD STRUCTURAL AND FUNCTIONAL PREDICTIONS FROM BIOLOGICAL SEQUENCES by WENLIN LI DISSERTATION Presented to the Faculty of the Graduate School of Biomedical Sciences The University of Texas Southwestern Medical Center at Dallas In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY The University of Texas Southwestern Medical Center at Dallas Dallas, Texas May, 2018 Copyright by Wenlin Li, 2018 All Rights Reserved TOWARD STRUCTURAL AND FUNCTIONAL PREDICTIONS FROM BIOLOGICAL SEQUENCES Publication No. Wenlin Li, Ph.D. The University of Texas Southwestern Medical Center at Dallas, 2018 Supervising Professor: Nick V. Grishin, Ph.D. Biological sequences, including DNA and protein sequences, are believed to encode sufficient information to determine the structure and function of biological molecules, which in turn decide the phenotypic traits of animals. Deciphering the biological sequences is an important and multiscale problem that connecting the information flow from genotypes to phenotypes. Current advances in next-generation sequence technology provided tons of sequencing data, demanding innovations in computational algorithm for better interpretation. I developed computational methodologies to understand the biological sequences in various v levels. In the primary sequence level, I analyzed the evolutionary information encoded in protein families and predicted the function (and active sites) of the proteins. To aid my sequence analysis, I developed a set of computational methodologies and deployed them as public web-servers. In the protein structure level, I studied the plasticity of the 3D structures, as well as demonstrated its effect on the uncertainty of computational scoring algorithms. In the organism level, I innovated the computational methodology to assemble and analyze complete genomes of butterflies and discovered convergence evolution in butterfly wing patterns. In conclusion, I advanced the knowledge of biological sequences in multi-layers by computational approaches. ACKNOWLEDGEMENTS I am so grateful to have Dr. Nick Grishin as my mentor. Nick showed very strong support, which is far more than what I can imagine, for both my research and my personal development. He encouraged and inspired me to become a better man. He was always so patient and tolerant when I made mistakes, and walked me through those dark days. I felt so lucky to be able to do researches based on my personal interests and participated in multiple projects. He is more like the sincerest friend who always be there to have my back. I also thank my committee members, Drs. Phillip Thomas, Denial Rosenbaum, and Zbyszek Otwinowski for kind supports. You guys are so good that I always received more than what I expected. I also thank Dr. Dominika Borek for her patience to explain the naïve problems I asked in great details. Great thanks to everyone in the Grishin lab, particularly Lisa Kinch, Jimin Pei, Qian Cong, Jeremy Semeiks, Bong-Hyun Kim, Jinhui Shen, Jing Zhang and Ming Tang, for their friendship, collaboration, help with many questions, and being a wonderful team of colleagues. I especially acknowledged Dr. Qian Cong, who is the model of successful graduate student I am running after and the closest colleague helping me a lot, Drs. Lisa Kinch and Jimin Pei, who selflessly offer me help in both scientific topics and everyday life. Thanks to everybody in UT Southwestern Medical Center, and particularly, people located in ND10, for maintaining such an open, friendly, and inspiring working environment. Finally, I am grateful to my parents, Zongchi Li and ShuiLi Li, for their constant support and complete trust on my choices in life. Special thanks to my wife, Dr. Fang Zhang, who listens to my words in my sleepless night and embraces me with warm arms. TABLE OF CONTENTS TABLE OF CONTENTS ....................................................................................................... viii PRIOR PUBLICATIONS ......................................................................................................... 1 CHAPTER 1 GENERAL INTRODUCTION .......................................................................... 3 CHAPTER 2 SEQ2REF: A WEB SERVER TO FACILITATE FUNCTIONAL INTERPRETATION............................................................................................................... 11 CHAPTER 3 PCLUST: PROTEIN NETWORK VISUALIZATION HIGHLIGHTING EXPERIMENTAL DATA ...................................................................................................... 29 CHAPTER 4 THE ABC TRANSPORTERS IN CANDIDATUS LIBERIBACTER ASIATICUS ............................................................................................................................ 36 CHAPTER 5 CONSERVED EVOLUTIONARY UNITS IN THE HEME‐COPPER OXIDASE SUPERFAMILY REVEALED BY NOVEL HOMOLOGOUS PROTEIN FAMILIES .............................................................................................................................. 82 CHAPTER 6 ESTIMATION OF UNCERTAINTIES IN THE GLOBAL DISTANCE TEST (GDT_TS) FOR CASP MODELS ........................................................................................ 124 CHAPTER 7 CHSEQ: A DATABASE OF CHAMELEON SEQUENCES ...................... 152 CHAPTER 8 ASSESSMENT OF CASP11 CONTACT‐ASSISTED PREDICTIONS .... 188 CHAPTER 9 GENOMES OF 250 SKIPPER BUTTERFLIES REVEAL RAMPANT CONVERGENCE IN WING PATTERNS .......................................................................... 234 viii PRIOR PUBLICATIONS 1. Li W, Cong Q, Pei J, Kinch LN, Grishin N V. The ABC transporters in Candidatus Liberibacter asiaticus. Proteins Struct Funct Bioinforma 2012;80(11):2614–2628. 2. Cong Q, Kinch LN, Pei J, Shi S, Grishin VN, Li W, Grishin N V. An automatic method for CASP9 free modeling structure prediction assessment. Bioinformatics 2011;27(24):3371–3378. 3. Li W, Kinch LN, Grishin N V. Pclust: protein network visualization highlighting experimental data. Bioinformatics 2013;29(20):2647–2648. 4. Li W, Kinch LN, Karplus PA, Grishin N V. ChSeq: a database of chameleon sequences. Protein Sci 2015;24(7):1075–1086. 5. Pei J*, Li W*, Kinch LN, Grishin N V. Conserved evolutionary units in the heme- copper oxidase superfamily revealed by novel homologous protein families. Protein Sci 2014;23(9):1220–1234. 6. Li W, Schaeffer RD, Otwinowski Z, Grishin N V. Estimation of uncertainties in the global distance test (GDT_TS) for CASP Models. PLoS One 2016;11(5):e0154786. 7. Ji R, Cong Q, Li W, Grishin N V. M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci. Bioinformatics 2013;29(22):2953– 2954. 8. Kinch LN, Li W, Monastyrskyy B, Kryshtafovych A, Grishin N V. Evaluation of free modeling targets in CASP11 and ROLL. Proteins Struct Funct Bioinforma 2016;84(S1):51–66. 1 9. Cong Q, Shen J, Li W, Borek D, Otwinowski Z, Grishin N V. The first complete genomes of Metalmarks and the classification of butterfly families. Genomics 2017. 10. Kinch LN*, Li W*, Monastyrskyy B, Kryshtafovych A, Grishin N V. Assessment of CASP11 Contact-Assisted Predictions. Proteins 2016. 11. Kinch LN, Li W, Schaeffer RD, Dunbrack RL, Monastyrskyy B, Kryshtafovych A, Grishin N V. CASP 11 Target Classification. Proteins 2016. 12. Li W, Cong Q, Kinch LN, Grishin N V. Seq2Ref: a web server to facilitate functional interpretation. BMC Bioinformatics 2013;14(1):30. * Authors contributed equally CHAPTER 1 GENERAL INTRODUCTION Biological sequences, including DNA and protein sequences, are believed to encode all the information needed to determine the phenotype of an organism. Understanding what nature says in such biological words and how the words define the molecular function has drawn board attention in biological sciences. Recent advances in the next-generation sequencing technology generated avalanche of sequencing data and motivated biologists to use computational methods to decipher the sequence information. Achievements have been made in different levels, including predicting protein tertiary structures, predicting the functional site of a protein, and understanding the gene determinants for morphological traits, but yet far from satisfactory. I decoded the information in the biological sequences, both protein and DNA, for structural and functional prediction using computational approaches. To better process the biological sequences, I innovated computational data mining methodologies, which were applied on protein sequences to bring medical insights from evolutionary perspectives. I also studied the conformation ambiguity in the protein structures and was invited to assess the performance of the 11st Critical Assessment of Structure Prediction experiment, the community-wide blind test to evaluate advances in structure prediction. Using the butterfly as the model system for evolution studies, I revolutionized the next- generation sequencing analysis algorithms and discovered the butterfly wing pattern divergence. 3 The size of the protein sequence database has been exponentially increasing due to advances in genome sequencing. However, experimentally characterized proteins only constitute a small portion of the database, such that the majority of sequences have been annotated by computational approaches. Current automatic annotation pipelines
Load more

Recommended publications
  • Butterflies (Lepidoptera: Papilionoidea) in a Coastal Plain Area in the State of Paraná, Brazil
    62 TROP. LEPID. RES., 26(2): 62-67, 2016 LEVISKI ET AL.: Butterflies in Paraná Butterflies (Lepidoptera: Papilionoidea) in a coastal plain area in the state of Paraná, Brazil Gabriela Lourenço Leviski¹*, Luziany Queiroz-Santos¹, Ricardo Russo Siewert¹, Lucy Mila Garcia Salik¹, Mirna Martins Casagrande¹ and Olaf Hermann Hendrik Mielke¹ ¹ Laboratório de Estudos de Lepidoptera Neotropical, Departamento de Zoologia, Universidade Federal do Paraná, Caixa Postal 19.020, 81.531-980, Curitiba, Paraná, Brazil Corresponding author: E-mail: [email protected]٭ Abstract: The coastal plain environments of southern Brazil are neglected and poorly represented in Conservation Units. In view of the importance of sampling these areas, the present study conducted the first butterfly inventory of a coastal area in the state of Paraná. Samples were taken in the Floresta Estadual do Palmito, from February 2014 through January 2015, using insect nets and traps for fruit-feeding butterfly species. A total of 200 species were recorded, in the families Hesperiidae (77), Nymphalidae (73), Riodinidae (20), Lycaenidae (19), Pieridae (7) and Papilionidae (4). Particularly notable records included the rare and vulnerable Pseudotinea hemis (Schaus, 1927), representing the lowest elevation record for this species, and Temenis huebneri korallion Fruhstorfer, 1912, a new record for Paraná. These results reinforce the need to direct sampling efforts to poorly inventoried areas, to increase knowledge of the distribution and occurrence patterns of butterflies in Brazil. Key words: Atlantic Forest, Biodiversity, conservation, inventory, species richness. INTRODUCTION the importance of inventories to knowledge of the fauna and its conservation, the present study inventoried the species of Faunal inventories are important for providing knowledge butterflies of the Floresta Estadual do Palmito.
    [Show full text]
  • Phylogenetic Relationships of Subfamilies and Circumscription of Tribes in the Family Hesperiidae (Lepidoptera: Hesperioidea)
    Cladistics Cladistics 24 (2008) 642–676 10.1111/j.1096-0031.2008.00218.x Phylogenetic relationships of subfamilies and circumscription of tribes in the family Hesperiidae (Lepidoptera: Hesperioidea) Andrew D. Warrena,b,*, Joshua R. Ogawac and Andrew V. Z. Browerc aMcGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, SW 34th Street and Hull Road, PO Box 112710, Gainesville, FL 32611-2710, USA; bMuseo de Zoologı´a, Departamento de Biologı´a Evolutiva, Facultad de Ciencias, Universidad Nacional Auto´noma de Me´xico, Apdo. Postal 70-399, Me´xico DF 04510, Me´xico; cDepartment of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA Accepted 10 January 2008 Abstract A comprehensive tribal-level classification for the worldÕs subfamilies of Hesperiidae, the skipper butterflies, is proposed for the first time. Phylogenetic relationships between tribes and subfamilies are inferred using DNA sequence data from three gene regions (cytochrome oxidase subunit I-subunit II, elongation factor-1a and wingless). Monophyly of the family is strongly supported, as are some of the traditionally recognized subfamilies, with the following relationships: (Coeliadinae + (‘‘Pyrginae’’ + (Heteropteri- nae + (Trapezitinae + Hesperiinae)))). The subfamily Pyrginae of contemporary authors was recovered as a paraphyletic grade of taxa. The formerly recognized subfamily Pyrrhopyginae, although monophyletic, is downgraded to a tribe of the ‘‘Pyrginae’’. The former subfamily Megathyminae is an infra-tribal group of the Hesperiinae. The Australian endemic Euschemon rafflesia is a hesperiid, possibly related to ‘‘Pyrginae’’ (Eudamini). Most of the traditionally recognized groups and subgroups of genera currently employed to partition the subfamilies of the Hesperiidae are not monophyletic.
    [Show full text]
  • Out of the Orient: Post-Tethyan Transoceanic and Trans-Arabian Routes
    Systematic Entomology Page 2 of 55 1 1 Out of the Orient: Post-Tethyan transoceanic and trans-Arabian routes 2 fostered the spread of Baorini skippers in the Afrotropics 3 4 Running title: Historical biogeography of Baorini skippers 5 6 Authors: Emmanuel F.A. Toussaint1,2*, Roger Vila3, Masaya Yago4, Hideyuki Chiba5, Andrew 7 D. Warren2, Kwaku Aduse-Poku6,7, Caroline Storer2, Kelly M. Dexter2, Kiyoshi Maruyama8, 8 David J. Lohman6,9,10, Akito Y. Kawahara2 9 10 Affiliations: 11 1 Natural History Museum of Geneva, CP 6434, CH 1211 Geneva 6, Switzerland 12 2 Florida Museum of Natural History, University of Florida, Gainesville, Florida, 32611, U.S.A. 13 3 Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta, 37, 08003 14 Barcelona, Spain 15 4 The University Museum, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan 16 5 B. P. Bishop Museum, 1525 Bernice Street, Honolulu, Hawaii, 96817-0916 U.S.A. 17 6 Biology Department, City College of New York, City University of New York, 160 Convent 18 Avenue, NY 10031, U.S.A. 19 7 Biology Department, University of Richmond, Richmond, Virginia, 23173, USA 20 8 9-7-106 Minami-Ôsawa 5 chome, Hachiôji-shi, Tokyo 192-0364, Japan 21 9 Ph.D. Program in Biology, Graduate Center, City University of New York, 365 Fifth Ave., New 22 York, NY 10016, U.S.A. 23 10 Entomology Section, National Museum of the Philippines, Manila 1000, Philippines 24 25 *To whom correspondence should be addressed: E-mail: [email protected] Page 3 of 55 Systematic Entomology 2 26 27 ABSTRACT 28 The origin of taxa presenting a disjunct distribution between Africa and Asia has puzzled 29 biogeographers for centuries.
    [Show full text]
  • Extreme Diversity of Tropical Parasitoid Wasps Exposed by Iterative Integration of Natural History, DNA Barcoding, Morphology, and Collections
    Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections M. Alex Smith*†, Josephine J. Rodriguez‡, James B. Whitfield‡, Andrew R. Deans§, Daniel H. Janzen†¶, Winnie Hallwachs¶, and Paul D. N. Hebert* *The Biodiversity Institute of Ontario, University of Guelph, Guelph Ontario, N1G 2W1 Canada; ‡Department of Entomology, 320 Morrill Hall, University of Illinois, 505 S. Goodwin Avenue, Urbana, IL 61801; §Department of Entomology, North Carolina State University, Campus Box 7613, 2301 Gardner Hall, Raleigh, NC 27695-7613; and ¶Department of Biology, University of Pennsylvania, Philadelphia, PA 19104-6018 Contributed by Daniel H. Janzen, May 31, 2008 (sent for review April 18, 2008) We DNA barcoded 2,597 parasitoid wasps belonging to 6 microgas- A detailed recognition of species in parasitoid communities is trine braconid genera reared from parapatric tropical dry forest, cloud necessary because of the pivotal role parasitoids play in food web forest, and rain forest in Area de Conservacio´ n Guanacaste (ACG) in structure and dynamics. While generalizations about the effects of northwestern Costa Rica and combined these data with records of parasitoids on community diversity are complex (7), a common- caterpillar hosts and morphological analyses. We asked whether place predictor of the impact of a parasitoid species on local host barcoding and morphology discover the same provisional species and dynamics is whether the parasitoid is a generalist or specialist. A whether the biological entities revealed by our analysis are congruent generalist, especially a mobile one, is viewed as stabilizing food webs with wasp host specificity. Morphological analysis revealed 171 (see ref.
    [Show full text]
  • Orange Fringes, Crenulate Hindwings and Genomic DNA Identify a New Species of Jonaspyge from Honduras (Hesperiidae: Pyrrhopyginae)
    48 TROP. LEPID. RES., 31(1): 48-52, 2021 GALLARDO & GRISHIN: New species of Jonaspyge Orange fringes, crenulate hindwings and genomic DNA identify a new species of Jonaspyge from Honduras (Hesperiidae: Pyrrhopyginae) Robert J. Gallardo1 and Nick V. Grishin2 1. La Unión Suyapa, Las Vegas, Santa Barbará, Honduras; email: [email protected] 2. Howard Hughes Medical Institute and Departments of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, USA 75390-9050; email: [email protected] Date of issue online: 2 July 2021 Zoobank Registered: urn:lsid:zoobank.org:pub:99BE7151-F6C8-4546-8669-A4E4206028B7 Electronic copies (ISSN 2575-9256) in PDF format at: http://journals.fcla.edu/troplep; https://zenodo.org; archived by the Institutional Repository at the University of Florida (IR@UF), http://ufdc.ufl.edu/ufir;DOI : 10.5281/zenodo.4966725 © The author(s). This is an open access article distributed under the Creative Commons license CC BY-NC 4.0 (https://creativecommons.org/ licenses/by-nc/4.0/). Abstract: Jonaspyge elizabethae n. sp. is described from southwestern Honduras. It is similar to the other two Jonaspyge O. Mielke, 2002 species in having metallic dark-blue wings with purple sheen, crenulate hindwing outer margin, and black body with orange palpi and an orange abdomen tip. It is diagnosed by bright-orange (instead of white) fringes and dark (instead of orange) cheeks. Genomic sequence analysis of Jonaspyge reveals that it is a close relative of Jonaspyge jonas (C. Felder & R. Felder, 1859) and Jonaspyge tzotzili (H. Freeman, 1969), differing from them by 5.3% in the COI DNA barcode.
    [Show full text]
  • (Lepidoptera). Zootaxa 3198: 1-28
    INSECTA MUNDI A Journal of World Insect Systematics 0327 Thorax and abdomen morphology of some Neotropical Hesperiidae (Lepidoptera) Eduardo Carneiro, Olaf H. H. Mielke, Mirna M. Casagrande Laboratório de Estudos de Lepidoptera Neotropical Departamento de Zoologia, UFPR Caixa Postal 19020, 81531-980 Curitiba, Paraná, Brasil Date of Issue: October 25, 2013 CENTER FOR SYSTEMATIC ENTOMOLOGY, INC., Gainesville, FL Eduardo Carneiro, Olaf H. H. Mielke, and Mirna M. Casagrande Thorax and abdomen morphology of some Neotropical Hesperiidae (Lepidoptera) Insecta Mundi 0327: 1-47 ZooBank Registered: urn:lsid:zoobank.org: pub:074AC2A8-83D9-4B8A-9F1B-7860E1AFF172IM Published in 2013 by Center for Systematic Entomology, Inc. P. O. Box 141874 Gainesville, FL 32614-1874 USA http://www.centerforsystematicentomology.org/ Insecta Mundi is a journal primarily devoted to insect systematics, but articles can be published on any non- marine arthropod. Topics considered for publication include systematics, taxonomy, nomenclature, checklists, faunal works, and natural history. Insecta Mundi will not consider works in the applied sciences (i.e. medical entomology, pest control research, etc.), and no longer publishes book reviews or editorials. Insecta Mundi pub- lishes original research or discoveries in an inexpensive and timely manner, distributing them free via open access on the internet on the date of publication. Insecta Mundi is referenced or abstracted by several sources including the Zoological Record, CAB Abstracts, etc. Insecta Mundi is published irregularly throughout the year, with completed manuscripts assigned an indi- vidual number. Manuscripts must be peer reviewed prior to submission, after which they are reviewed by the editorial board to ensure quality. One author of each submitted manuscript must be a current member of the Center for Systematic Entomology.
    [Show full text]
  • Ten Genes and Two Topologies: an Exploration of Higher Relationships in Skipper Butterflies (Hesperiidae)
    Ten genes and two topologies: an exploration of higher relationships in skipper butterflies (Hesperiidae) Ranjit Kumar Sahoo1, Andrew D. Warren2, Niklas Wahlberg3,4, Andrew V. Z. Brower5, Vladimir A. Lukhtanov6,7 and Ullasa Kodandaramaiah1 1 School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala, India 2 McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, UF Cultural Plaza, Gainesville, FL, USA 3 Department of Biology, Lund University, Lund, Sweden 4 Department of Biology, University of Turku, Turku, Finland 5 Evolution and Ecology Group, Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA 6 Department of Insect Systematics, Zoological Institute of Russian Academy of Sciences, St. Petersburg, Russia 7 Department of Entomology, St. Petersburg State University, St. Petersburg, Russia ABSTRACT Despite multiple attempts to infer the higher-level phylogenetic relationships of skipper butterflies (Family Hesperiidae), uncertainties in the deep clade relationships persist. The most recent phylogenetic analysis included fewer than 30% of known genera and data from three gene markers. Here we reconstruct the higher-level relationships with a rich sampling of ten nuclear and mitochondrial markers (7,726 bp) from 270 genera and find two distinct but equally plausible topologies among subfamilies at the base of the tree. In one set of analyses, the nuclear markers suggest two contrasting topologies, one of which is supported by the mitochondrial dataset. However, another set of analyses suggests mito-nuclear conflict as the reason for topological incongruence. Neither topology is strongly supported, and we conclude that there is insufficient phylogenetic evidence in the Submitted 24 May 2016 Accepted 4 October 2016 molecular dataset to resolve these relationships.
    [Show full text]
  • Oviposition Selection in Montane Habitats, Biological Conservation
    Biological Conservation 143 (2010) 862–872 Contents lists available at ScienceDirect Biological Conservation journal homepage: www.elsevier.com/locate/biocon Oviposition selection by a rare grass skipper Polites mardon in montane habitats: Advancing ecological understanding to develop conservation strategies Loni J. Beyer, Cheryl B. Schultz * Washington State University Vancouver, 14204 NE Salmon Creek Ave, Vancouver, WA 98686, USA article info abstract Article history: The Grass skipper subfamily (Hesperiinae) includes many at risk species across the globe. Conservation Received 31 March 2009 efforts for these skippers are hindered by insufficient information about their basic biology. Mardon skip- Received in revised form 3 November 2009 per (Polites mardon) is declining throughout its range. We surveyed mardon oviposition across nine study Accepted 25 December 2009 meadows in the Gifford Pinchot National Forest of Washington State. We conducted habitat surveys with Available online 21 January 2010 respect to oviposition (n = 269) and random (n = 270) locations, recording data on over 50 variables. Mar- don oviposited on 23 different graminoid species, yet are selective for specific graminoids within mead- Keywords: ows. Most frequent ovipositions across meadows occurred on Festuca idahoensis and Poa pratensis Butterfly (accounting for 112 of 269 total oviposition observations). Discriminant Function Analyses revealed that Graminoids Habitat preference mardon habitat was too variable to detect oviposition selection across study meadows, yet there was 2 Host selection strong selection occurring within meadows (r ranging from 0.82 to 0.99). Variables important to within Life history meadow selection were graminoid cover, height, and community; oviposition plant structure (leaf den- Management sity, height, area); insolation factors (tree abundance and canopy shading); and litter layer factors (cover Meadow and depth).
    [Show full text]
  • Book Reviews, New Publica- Tions, Metamorphosis, Announcements
    ________________________________________________________________________________________ Volume 57, Number 4 Winter 2015 www.lepsoc.org ________________________________________________________________________________________ Inside: Butterflies of Bolivia Are there caterpillars on butterfly wings? A citizen science call for action Ghost moths of the world website A conservation concern from the 1870’s Fruit-feeding Nymphali- dae in a west Mexican neotropical garden Fender’s Blue Butterfly conservation and re- covery Membership Updates, Marketplace, Book Reviews, New Publica- tions, Metamorphosis, Announcements ... ... and more! ________________________________________________________________________________________ ________________________________________________________ Contents ________________________________________________________www.lepsoc.org Species diversity and temporal distribution in a community of fruit- ____________________________________ feeding Nymphalidae in a west Mexican neotropical garden Volume 57, Number 4 Gerald E. Einem and William Adkins. ............................................... 163 Winter 2015 Windows for butterfly nets The Lepidopterists’ Society is a non-profit ed- J. Alan Wagar. ................................................................................... 173 ucational and scientific organization. The ob- Announcements: .......................................................................................... 174 ject of the Society, which was formed in May Zone Coordinator Needed; Season Summary
    [Show full text]
  • The Butterflies (Lepidoptera, Papilionoidea) of Tobago, West
    INSECTA MUNDI A Journal of World Insect Systematics 0539 The butterfl ies (Lepidoptera, Papilionoidea) of Tobago, West Indies: An updated and annotated checklist Matthew J.W. Cock CABI, Bakeham Lane Egham, Surrey, TW20 9TY United Kingdom Date of Issue: April 28, 2017 CENTER FOR SYSTEMATIC ENTOMOLOGY, INC., Gainesville, FL Matthew J.W. Cock The butterfl ies (Lepidoptera, Papilionoidea) of Tobago, West Indies: An updated and annotated checklist Insecta Mundi 0539: 1–38 ZooBank Registered: urn:lsid:zoobank.org:pub:B96122B2-6325-4D7F-A260-961BB086A2C5 Published in 2017 by Center for Systematic Entomology, Inc. P. O. Box 141874 Gainesville, FL 32614-1874 USA http://centerforsystematicentomology.org/ Insecta Mundi is a journal primarily devoted to insect systematics, but articles can be published on any non-marine arthropod. Topics considered for publication include systematics, taxonomy, nomenclature, checklists, faunal works, and natural history. Insecta Mundi will not consider works in the applied sciences (i.e. medical entomology, pest control research, etc.), and no longer publishes book reviews or editorials. Insecta Mundi publishes original research or discoveries in an inexpensive and timely manner, distributing them free via open access on the internet on the date of publication. Insecta Mundi is referenced or abstracted by several sources including the Zoological Record, CAB Ab- stracts, etc. Insecta Mundi is published irregularly throughout the year, with completed manuscripts assigned an individual number. Manuscripts must be peer reviewed prior to submission, after which they are reviewed by the editorial board to ensure quality. One author of each submitted manuscript must be a current member of the Center for Systematic Entomology.
    [Show full text]
  • I =- I - 1-----• 47 Red-Spotted Purple 1 __ 2] -=- ~2 3 ! ~Oy --
    .- A B c 0 E South Total 1 --~.-----=-- _ _S_PE_C_l_ES____ -+- __..North ±-Central -i------- -- 23 7/14/2001 -t- I -- I 4 5 Swallowtails -- -------·- -- 6 Black Swallowta-il - -- ------1--- - -4 -·-- 27 11T 42 7 Eastern Tiger Swallowtail _____.,_; -· - -- 5 7 --- 31 1;4 -·· ·--- 5 : $plcebush Swa_n_owt- ail ___ +:---=:2:===-·-----+--·- 10 Whites -f- _.._ ___ 11 Cabbage W_h_ite_ __________ I 156 _ 90 97 343 12 ,---~-- - 13 Sulphurs ----------- -- ·- 14 CloudedSulphur -- -- I 9 - 10 42 15 Orange Sulphur ·--·. -36 9 115 ~t-1 -- I 16 -- - ~:-_ ----.-----I -l 2 3 5 r- ... I --- - .. -·--- 1 1 26 28 2 4 1-· I I ---·-- 31 Brush-foots - Heliconians/Frltiiiaries ].[ Great ~angled Fritillary_ -_-+-_- =_1 _8__ _ --·~ ~~ Meadow Fritillary___ ___ ·-;E 1 Ts True Brush-to~ - - -- I 36 Pearl Cres~ent - - _ - 1~5 _ _ 86 , 77 37 Baltimore Checkerspot 1 1 Ts OLiestion Mark-- i - 11: 2· -- 3 -·-:rs 39 Eastern Comma -- -- 1 - 2~· 6 - 4 35 40 Mourning Cloak -- I~ - 2 2 1 5 41 Milberfs Tortoiseshell _ ~ -= 12 . ·- ~ 1 r 18 42 American Lady 11 -- 11 _ - 8 30 43 Painted Lady ·-- - 5 2 7 Ts44~ Red- Admiral----- -- -· - 1210 - 394- 103.....~ 1767 ~ ~dmlrals and ReiiiiVOs _ I =- I - 1-----• 47 Red-spotted Purple 1 __ 2] -=- ~2 3 ! ~oy -- - . - . - ·:·=--- ~ I---~ 1---==·_-3..... 50 Satyrs , ;~ ~~=:~r~=~a-rly_-e_v_e ·_ --~ l - r ---_-1-+l; ____=---_- :1+,!--~~---_-_-1 -:~· 53 Appalachian Brown -, _ ~ Little Wood satv-r- -· . .. A B C D E ;~ Common Wood-nymph 2~ -- ~~- 127 181 57 Monarch -----1-- -- + 1- -j- 58 MOilarc_h____ -·1-·- 15j - ~1- 16 1 -- 4 2 ~~ Skippers - S readwing_! r:= ,-- ~ -=r- r - =- 61 Silver-spotted Skipper _____,_ ·- 4 ::::::::_ _!_._ __ _1 1 ---~--- ~- 62 Common Checkered Skipper 1 5 5 ~! Common Sootywin9 ~:.===.+= F-- ~~ _ 2 65 Skippers - Grass Skippers I - t ·-- .
    [Show full text]
  • Running Head 1 the AGE of BUTTERFLIES REVISITED
    bioRxiv preprint doi: https://doi.org/10.1101/259184; this version posted February 2, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Running head 2 THE AGE OF BUTTERFLIES REVISITED (AND TESTED) 3 Title 4 The Trials and Tribulations of Priors and Posteriors in Bayesian Timing of 5 Divergence Analyses: the Age of Butterflies Revisited. 6 7 Authors 8 NICOLAS CHAZOT1*, NIKLAS WAHLBERG1, ANDRÉ VICTOR LUCCI FREITAS2, 9 CHARLES MITTER3, CONRAD LABANDEIRA3,4, JAE-CHEON SOHN5, RANJIT KUMAR 10 SAHOO6, NOEMY SERAPHIM7, RIENK DE JONG8, MARIA HEIKKILÄ9 11 Affiliations 12 1Department of Biology, Lunds Universitet, Sölvegatan 37, 223 62, Lund, Sweden. 13 2Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de 14 Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Caixa postal 6109, 15 Barão Geraldo 13083-970, Campinas, SP, Brazil. 16 3Department of Entomology, University of Maryland, College Park, MD 20742, U.S.A. 17 4Department of Paleobiology, National Museum of Natural History, Smithsonian 18 Institution, Washington, DC 20013, USA; Department of Entomology and BEES 19 Program, University of Maryland, College Park, MD 20741; and Key Lab of Insect 20 Evolution and Environmental Change, School of Life Sciences, Capital Normal 21 University, Beijing 100048, bioRxiv preprint doi: https://doi.org/10.1101/259184; this version posted February 2, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]