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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. -
The Genome Sequence of the Ringlet, Aphantopus Hyperantus
Edinburgh Research Explorer The genome sequence of the ringlet, Aphantopus hyperantus Linnaeus 1758 Citation for published version: Mead, D, Saccheri, I, Yung, CJ, Lohse, K, Lohse, C, Ashmole, P, Smith, M, Corton, C, Oliver, K, Skelton, J, Betteridge, E, Quail, MA, Dolucan, J, McCarthy, SA, Howe, K, Wood, J, Torrance, J, Tracey, A, Whiteford, S, Challis, R, Durbin, R & Blaxter, M 2021, 'The genome sequence of the ringlet, Aphantopus hyperantus Linnaeus 1758', Wellcome Open Research, vol. 6, no. 165. https://doi.org/10.12688/wellcomeopenres.16983.1 Digital Object Identifier (DOI): 10.12688/wellcomeopenres.16983.1 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Wellcome Open Research General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 06. Oct. 2021 Wellcome Open Research 2021, 6:165 Last updated: 29 JUN 2021 DATA NOTE The genome sequence of the ringlet, Aphantopus hyperantus Linnaeus 1758 [version 1; peer review: awaiting peer review] Dan Mead 1,2, Ilik Saccheri3, Carl J. -
Phylogenetic Relationships and Historical Biogeography of Tribes and Genera in the Subfamily Nymphalinae (Lepidoptera: Nymphalidae)
Blackwell Science, LtdOxford, UKBIJBiological Journal of the Linnean Society 0024-4066The Linnean Society of London, 2005? 2005 862 227251 Original Article PHYLOGENY OF NYMPHALINAE N. WAHLBERG ET AL Biological Journal of the Linnean Society, 2005, 86, 227–251. With 5 figures . Phylogenetic relationships and historical biogeography of tribes and genera in the subfamily Nymphalinae (Lepidoptera: Nymphalidae) NIKLAS WAHLBERG1*, ANDREW V. Z. BROWER2 and SÖREN NYLIN1 1Department of Zoology, Stockholm University, S-106 91 Stockholm, Sweden 2Department of Zoology, Oregon State University, Corvallis, Oregon 97331–2907, USA Received 10 January 2004; accepted for publication 12 November 2004 We infer for the first time the phylogenetic relationships of genera and tribes in the ecologically and evolutionarily well-studied subfamily Nymphalinae using DNA sequence data from three genes: 1450 bp of cytochrome oxidase subunit I (COI) (in the mitochondrial genome), 1077 bp of elongation factor 1-alpha (EF1-a) and 400–403 bp of wing- less (both in the nuclear genome). We explore the influence of each gene region on the support given to each node of the most parsimonious tree derived from a combined analysis of all three genes using Partitioned Bremer Support. We also explore the influence of assuming equal weights for all characters in the combined analysis by investigating the stability of clades to different transition/transversion weighting schemes. We find many strongly supported and stable clades in the Nymphalinae. We are also able to identify ‘rogue’ -
Bulletin Biological Assessment Boletín RAP Evaluación Biológica
Rapid Assessment Program Programa de Evaluación Rápida Evaluación Biológica Rápida de Chawi Grande, Comunidad Huaylipaya, Zongo, La Paz, Bolivia RAP Bulletin A Rapid Biological Assessment of of Biological Chawi Grande, Comunidad Huaylipaya, Assessment Zongo, La Paz, Bolivia Boletín RAP de Evaluación Editores/Editors Biológica Claudia F. Cortez F., Trond H. Larsen, Eduardo Forno y Juan Carlos Ledezma 70 Conservación Internacional Museo Nacional de Historia Natural Gobierno Autónomo Municipal de La Paz Rapid Assessment Program Programa de Evaluación Rápida Evaluación Biológica Rápida de Chawi Grande, Comunidad Huaylipaya, Zongo, La Paz, Bolivia RAP Bulletin A Rapid Biological Assessment of of Biological Chawi Grande, Comunidad Huaylipaya, Assessment Zongo, La Paz, Bolivia Boletín RAP de Evaluación Editores/Editors Biológica Claudia F. Cortez F., Trond H. Larsen, Eduardo Forno y Juan Carlos Ledezma 70 Conservación Internacional Museo Nacional de Historia Natural Gobierno Autónomo Municipal de La Paz The RAP Bulletin of Biological Assessment is published by: Conservation International 2011 Crystal Drive, Suite 500 Arlington, VA USA 22202 Tel: +1 703-341-2400 www.conservation.org Cover Photos: Trond H. Larsen (Chironius scurrulus). Editors: Claudia F. Cortez F., Trond H. Larsen, Eduardo Forno y Juan Carlos Ledezma Design: Jaime Fernando Mercado Murillo Map: Juan Carlos Ledezma y Veronica Castillo ISBN 978-1-948495-00-4 ©2018 Conservation International All rights reserved. Conservation International is a private, non-proft organization exempt from federal income tax under section 501c(3) of the Internal Revenue Code. The designations of geographical entities in this publication, and the presentation of the material, do not imply the expression of any opinion whatsoever on the part of Conservation International or its supporting organizations concerning the legal status of any country, territory, or area, or of its authorities, or concerning the delimitation of its frontiers or boundaries. -
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 Genus Acraea (Lepidoptera : Nymphalidae) - Peter Hendry
The genus Acraea (Lepidoptera : Nymphalidae) - Peter Hendry With the recent migration to Australia of the Tawny Coster (Acraea terpsicore (Linnaeus, 1758)), (see Creature Feature this issue), I thought it might be timely to take a look at the genus worldwide. It must be noted that due to a misidentification A. terpsicore had long been known as A. violae and many references in the literature and on the web refer to it as A. violae. As with much of the Lepidoptera the genus is in a state of flux, and has long been split into the subgenera Acraea (Acraea) and Acraea (Actinote). The genus is placed in the tribe Acraeini and until Harvey (1991) placed it in the subfamily Heliconiinae it was listed in the subfamily Acraeinae. Recent molecular work has made changes and a current listing of the tribe Acraeini, by Niklas Wahlberg, is available at http://www.nymphalidae.net/Classification/Acraeini.htm. It shows members of the old subgenus Acraea (Actinote) being placed in the genus Actinote, and the old subgenus Acraea (Acraea) becoming the genus Acraea with a subgenus Acraea (Bematistes). It also lists several Acraea as unplaced. This may further change as some believe the subgenus Acraea (Bematistes) will move to the genus Bematistes. The genus is primarily Afrotropical with only four species occurring outside this region, these being, Acraea andromacha (Fig. 1) A. meyeri (Fig. 10) A. moluccana and A. terpsicore. A fifth species the Yellow Coster Acraea (Actinote) issoria is now referred to the genus Actinote. Like many of the Nymphalidae the larvae feed on plants which contain cyanogens making the larvae and adults poisonous to predators. -
Check-List of the Butterflies of the Kakamega Forest Nature Reserve in Western Kenya (Lepidoptera: Hesperioidea, Papilionoidea)
Nachr. entomol. Ver. Apollo, N. F. 25 (4): 161–174 (2004) 161 Check-list of the butterflies of the Kakamega Forest Nature Reserve in western Kenya (Lepidoptera: Hesperioidea, Papilionoidea) Lars Kühne, Steve C. Collins and Wanja Kinuthia1 Lars Kühne, Museum für Naturkunde der Humboldt-Universität zu Berlin, Invalidenstraße 43, D-10115 Berlin, Germany; email: [email protected] Steve C. Collins, African Butterfly Research Institute, P.O. Box 14308, Nairobi, Kenya Dr. Wanja Kinuthia, Department of Invertebrate Zoology, National Museums of Kenya, P.O. Box 40658, Nairobi, Kenya Abstract: All species of butterflies recorded from the Kaka- list it was clear that thorough investigation of scientific mega Forest N.R. in western Kenya are listed for the first collections can produce a very sound list of the occur- time. The check-list is based mainly on the collection of ring species in a relatively short time. The information A.B.R.I. (African Butterfly Research Institute, Nairobi). Furthermore records from the collection of the National density is frequently underestimated and collection data Museum of Kenya (Nairobi), the BIOTA-project and from offers a description of species diversity within a local literature were included in this list. In total 491 species or area, in particular with reference to rapid measurement 55 % of approximately 900 Kenyan species could be veri- of biodiversity (Trueman & Cranston 1997, Danks 1998, fied for the area. 31 species were not recorded before from Trojan 2000). Kenyan territory, 9 of them were described as new since the appearance of the book by Larsen (1996). The kind of list being produced here represents an information source for the total species diversity of the Checkliste der Tagfalter des Kakamega-Waldschutzge- Kakamega forest. -
With Descriptions of Nine New Species
European Journal of Taxonomy 551: 1–67 ISSN 2118-9773 https://doi.org/10.5852/ejt.2019.551 www.europeanjournaloftaxonomy.eu 2019 · Nakahara S. et al. This work is licensed under a Creative Commons Attribution License (CC BY 4.0). Monograph urn:lsid:zoobank.org:pub:C3C851C3-0F12-412C-A15B-56F0F263CD00 Revision of the poorly known Neotropical butterfly genus Zischkaia Forster, 1964 (Lepidoptera, Nymphalidae, Satyrinae), with descriptions of nine new species Shinichi NAKAHARA 1,*, Thamara ZACCA 2, Fernando M.S. DIAS 3, Diego R. DOLIBAINA 4, Lei XIAO 5, Marianne ESPELAND 6, Mirna M. CASAGRANDE 7, Olaf H.H. MIELKE 8, Gerardo LAMAS 9, Blanca HUERTAS 10, Kaylin KLECKNER 11 & Keith R. WILLMOTT 12 1,5,11,12 McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, USA. 1,11 Department of Entomology and Nematology, University of Florida, Gainesville, Florida 32611, USA. 2 Departamento de Biologia Animal and Museu de Zoologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil. 3,4,7,8 Laboratório de Estudos de Lepidoptera Neotropical, Departamento de Zoologia, Universidade Federal do Paraná, Curitiba, Paraná, Brazil. 6 Arthropoda Department, Zoological Research Museum Alexander Koenig, Adenauer Allee 160, 53113 Bonn, Germany. 1,9 Departamento de Entomología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru. 10 Life Sciences Department, Natural History Museum, London, UK. * Corresponding author: [email protected] -
A Time-Calibrated Phylogeny of the Butterfly Tribe Melitaeini
UC Davis UC Davis Previously Published Works Title A time-calibrated phylogeny of the butterfly tribe Melitaeini. Permalink https://escholarship.org/uc/item/1h20r22z Journal Molecular phylogenetics and evolution, 79(1) ISSN 1055-7903 Authors Long, Elizabeth C Thomson, Robert C Shapiro, Arthur M Publication Date 2014-10-01 DOI 10.1016/j.ympev.2014.06.010 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Molecular Phylogenetics and Evolution 79 (2014) 69–81 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev A time-calibrated phylogeny of the butterfly tribe Melitaeini ⇑ Elizabeth C. Long a, , Robert C. Thomson b, Arthur M. Shapiro a a Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, CA 95616, USA b Department of Biology, University of Hawaii at Manoa, Honolulu, HI 96822, USA article info abstract Article history: The butterfly tribe Melitaeini [Nymphalidae] contains numerous species that have been the subjects of a Received 10 March 2014 wide range of biological studies. Despite numerous taxonomic revisions, many of the evolutionary Revised 22 May 2014 relationships within the tribe remain unresolved. Utilizing mitochondrial and nuclear gene regions, we Accepted 11 June 2014 produced a time-calibrated phylogenetic hypothesis for 222 exemplars comprising at least 178 different Available online 18 June 2014 species and 21 of the 22 described genera, making this the most complete phylogeny of the tribe to date. Our results suggest that four well-supported clades corresponding to the subtribes Euphydryina, Keywords: Chlosynina, Melitaeina, and Phyciodina exist within the tribe. -
The Radiation of Satyrini Butterflies (Nymphalidae: Satyrinae): A
Zoological Journal of the Linnean Society, 2011, 161, 64–87. With 8 figures The radiation of Satyrini butterflies (Nymphalidae: Satyrinae): a challenge for phylogenetic methods CARLOS PEÑA1,2*, SÖREN NYLIN1 and NIKLAS WAHLBERG1,3 1Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden 2Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Apartado 14-0434, Lima-14, Peru 3Laboratory of Genetics, Department of Biology, University of Turku, 20014 Turku, Finland Received 24 February 2009; accepted for publication 1 September 2009 We have inferred the most comprehensive phylogenetic hypothesis to date of butterflies in the tribe Satyrini. In order to obtain a hypothesis of relationships, we used maximum parsimony and model-based methods with 4435 bp of DNA sequences from mitochondrial and nuclear genes for 179 taxa (130 genera and eight out-groups). We estimated dates of origin and diversification for major clades, and performed a biogeographic analysis using a dispersal–vicariance framework, in order to infer a scenario of the biogeographical history of the group. We found long-branch taxa that affected the accuracy of all three methods. Moreover, different methods produced incongruent phylogenies. We found that Satyrini appeared around 42 Mya in either the Neotropical or the Eastern Palaearctic, Oriental, and/or Indo-Australian regions, and underwent a quick radiation between 32 and 24 Mya, during which time most of its component subtribes originated. Several factors might have been important for the diversification of Satyrini: the ability to feed on grasses; early habitat shift into open, non-forest habitats; and geographic bridges, which permitted dispersal over marine barriers, enabling the geographic expansions of ancestors to new environ- ments that provided opportunities for geographic differentiation, and diversification. -
John Oscar Stireman III Curriculum Vitae
John Oscar Stireman III Curriculum Vitae Professor Department of Biological Sciences 3640 Colonel Glen Hwy 235A BH, Wright State University Dayton, OH 45435 [email protected] 937-775-3192 Academic Experience____________________________________________________ Professor, Biological Sciences, Wright State University; 2014 - present Associate Professor, Biological Sciences, Wright State University; 2009 - 2014 Assistant professor, Biological Sciences, Wright State University; 2005 – 2009 Research Associate, Museo Ecuatoriano de Ciencias Naturales, Sección Invertebrados, Ecuador, 2014 – present Doctoral Evaluation Committee, Environmental and Evolutionary Biology PhD program, Dipartimento di Biologia Ambientale, Universitá di Roma (2017-present). Postdoctoral fellow: Host race formation and population phylogeography of insect herbivores and their parasitoids. Advisor: John Nason; Iowa State University; 8/02-7/05 Postdoctoral fellow: Parasitoid-host and plant-insect ecological interactions. Advisor: Lee Dyer; Tulane University; 5/01-8/02. PhD. Ecology and Evolutionary Biology, University of Arizona: The ecology and evolution of tachinid-host associations. Advisor: Nancy A. Moran, 4/2001. BS, biology, University of Utah (evolution and ecology emphasis), 5/1993 Scholarships, Fellowships, and Grants_______________________________________ National Science Foundation/FAPSEP (Brazil): Collaborative Research: Dimensions US- Biota Sao Paulo: Chemically mediated multi-trophic interaction diversity across tropical gradients (M. Kato, L. Dyer et al.). WSU portion: $266,000, 11/25/2014. National Science Foundation REU (Research Experience for Undergraduates): Supplement to DEB: Collaborative research: The Phylogeny and Evolution of World Tachinidae (Diptera). $7,300, 5/1/2014. National Science Foundation MRI: Acquisition of Ion Torrent Personal Genome Machine to establish high-throughput sequencing capability for ecological and environmental biology (with PIs O. Paliy, S. Baird, J. Peters, D. Cipollini). $123,300, 8/1/2013. -
Peru Conservation Recorded Wildlife at Taricaya
Peru Conservation Recorded Wildlife at Taricaya Butterflies (Mariposas) in Taricaya Reserve, Madre de Dios CLASS: Insecta ORDER: Lepidoptera 1. Familia Nymphalidae Subfamilia Apaturinae Doxocopa kallina (Staudinger, 1886). Doxocopa laure (Drury, 1776). Doxocopa lavinia (Butler, 1886). Doxocopa linda (C. Felder & R. Felder, 1860). Doxocopa pavon (Latreille, 1809). Subfamilia Nymphalinae Tribu Coeini Baetus aelius (Stoll, 1780). Baetus deucaliom (C. Felder & R. Felder, 1860). Baetus japetus (Staudinger, 1885). Colobura annulata (Willmot, Constantino & J. Hall, 2001). Colobura dirce (Linnaeus, 1758). Historis acheronta (Fabricius, 1775). Historis odius (Fabricius, 1775). Smyrna blomfilda (Fabricius, 1781). Tigridia acesta (Linnaeus, 1758). Tribu Kallimini Anartia jatrophae (Linnaeus, 1763). Junonia everate (Cramer, 1779). Junonia genoveva (Cramer, 1780). Metamorpha elissa (Hübner, 1818). Siproeta stelenes (Linnaeus, 1758). Tribu Melitaeini Eresia clio (Linnaeus, 1758). Eresia eunice (Hübner, 1807). Eresia nauplios (Linnaeus, 1758). Tegosa claudina (Escholtz, 1821). Tegosa fragilis (H. W. Bates, 1864). Tribu Nymphalini Hypanarthia lethe (Fabricius, 1793). Tribu Acraeini Actinote pellenea (Hübner, 1821). Subfamilia Charaxinae Tribu Preponini Agrias amydon (Hewitson, 1854). Agrias claudina (Godart, 1824). Archaeoprepona amphimacus (Fabricius, 1775). Archaeoprepona demophon (Linnaeus, 1758). Archaeoprepona meander (Cramer, 1775). Prepona dexamenus (Hopffer, 1874). Prepona laertes (Hübner, 1811). Prepona pheridamas (Cramer, 1777). Prepona pylene