Taxonomy of the Gomphoneis Tetrastigmata Species Complex
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Detection of Cryptic Species Xa9846584
DETECTION OF CRYPTIC SPECIES XA9846584 A.F. COCKBURN, T. JENSEN, J.A. SEAWRIGHT United States Department of Agriculture, Agricultural Research Service, Medical and Veterinary Entomology Research Laboratory, Gainesville, Florida, USA Abstract Morphologically similar cryptic species are common in insects. In Anopheles mosquitoes, most morphologically described species are complexes of cryptic species. Cryptic species are of great practical importance for two reasons: first, one or more species of the complex might not be a pest and control efforts directed at the complex as a whole would therefore be partly wasted; and second, genetic (and perhaps biological) control strategies directed against one species of the complex would not affect other species of the complex. At least one SIT effort has failed because the released sterile insects were of a different species and therefore did not mate with the wild insects being targeted. We use a multidisciplinary approach for detection of cryptic species complexes, focusing first on identifying variability in wild populations using RFLPs of mitochondrial and ribosomal RNA genes (mtDNA and rDNA); followed by confirmation using a variety of other techniques. For rapid identification of wild individuals of field collections, we use a DNA dot blot assay. DNA probes can be isolated by differential screening, however we are currently focusing on the sequencing of the rDNA extragenic spacers. These regions are repeated several hundred times per genome in mosquitoes and evolve rapidly. Molecular drive tends to keep the individual genes homogeneous within a species. 1. INTRODUCTION Surprisingly, the problem of cryptic species has not received adequate attention in pest control. Two recent examples of important pests that are cryptic species are the silverleaf whitefly (originally thought to be the sweet potato whitefly), which has caused enormous economic damage in the US in the last few years, and was not described as a separate species until last year [1]; the fall armyworm, which was recently described as two species [2]. -
Local Adaptation Fuels Cryptic Speciation in Terrestrial Annelids’
bioRxiv preprint doi: https://doi.org/10.1101/872309; this version posted December 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Title: ‘Local adaptation fuels cryptic speciation in terrestrial annelids’ Running title: Local adaptation in cryptic terrestrial annelids Daniel Fernández Marchán1,2*, Marta Novo1, Nuria Sánchez1, Jorge Domínguez2, Darío J. Díaz Cosín1, Rosa Fernández3* 1 Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain. 2 Current address: Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Vigo, E-36310, Spain 3 Animal Biodiversity and Evolution Program, Institute of Evolutionary Biology (CSIC- UPF), Passeig Marítim de la Barceloneta, 37-49, 08003 Barcelona, Spain. * Corresponding authors: [email protected], [email protected] Abstract bioRxiv preprint doi: https://doi.org/10.1101/872309; this version posted December 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Uncovering the genetic and evolutionary basis of cryptic speciation is a major focus of evolutionary biology. Next Generation Sequencing (NGS) allows the identification of genome-wide local adaptation signatures, but has rarely been applied to cryptic complexes - particularly in the soil milieu - as is the case with integrative taxonomy. The earthworm genus Carpetania, comprising six previously suggested putative cryptic lineages, is a promising model to study the evolutionary phenomena shaping cryptic speciation in soil-dwelling lineages. Genotyping-By-Sequencing (GBS) was used to provide genome-wide information about genetic variability between seventeen populations, and geometric morphometrics analyses of genital chaetae were performed to investigate unexplored cryptic morphological evolution. -
Receptor-Like Kinases from Arabidopsis Form a Monophyletic Gene Family Related to Animal Receptor Kinases
Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases Shin-Han Shiu and Anthony B. Bleecker* Department of Botany and Laboratory of Genetics, University of Wisconsin, Madison, WI 53706 Edited by Elliot M. Meyerowitz, California Institute of Technology, Pasadena, CA, and approved July 6, 2001 (received for review March 22, 2001) Plant receptor-like kinases (RLKs) are proteins with a predicted tionary relationship between the RTKs and RLKs within the signal sequence, single transmembrane region, and cytoplasmic recognized superfamily of related eukaryotic serine͞threonine͞ kinase domain. Receptor-like kinases belong to a large gene family tyrosine protein kinases (ePKs). An earlier phylogenetic analysis with at least 610 members that represent nearly 2.5% of Arabi- (22), using the six RLK sequences available at the time, indicated dopsis protein coding genes. We have categorized members of this a close relationship between plant sequences and animal RTKs, family into subfamilies based on both the identity of the extracel- although RLKs were placed in the ‘‘other kinase’’ category. A more lular domains and the phylogenetic relationships between the recent analysis using only plant sequences led to the conclusion that kinase domains of subfamily members. Surprisingly, this structur- the 18 RLKs sampled seemed to form a separate family among the ally defined group of genes is monophyletic with respect to kinase various eukaryotic kinases (23). The recent completion of the domains when compared with the other eukaryotic kinase families. Arabidopsis genome sequence (5) provides an opportunity for a In an extended analysis, animal receptor kinases, Raf kinases, plant more comprehensive analysis of the relationships between these RLKs, and animal receptor tyrosine kinases form a well supported classes of receptor kinases. -
Classification of Plants
Classification of Plants Plants are classified in several different ways, and the further away from the garden we get, the more the name indicates a plant's relationship to other plants, and tells us about its place in the plant world rather than in the garden. Usually, only the Family, Genus and species are of concern to the gardener, but we sometimes include subspecies, variety or cultivar to identify a particular plant. Starting from the top, the highest category, plants have traditionally been classified as follows. Each group has the characteristics of the level above it, but has some distinguishing features. The further down the scale you go, the more minor the differences become, until you end up with a classification which applies to only one plant. Written convention indicated with underlined text KINGDOM Plant or animal DIVISION (PHYLLUM) CLASS Angiospermae (Angiosperms) Plants which produce flowers Gymnospermae (Gymnosperms) Plants which don't produce flowers SUBCLASS Dicotyledonae (Dicotyledons, Dicots) Plants with two seed leaves Monocotyledonae (Monocotyledons, Monocots) ‐ Plants with one seed leaf SUPERORDER A group of related Plant Families, classified in the order in which they are thought to have developed their differences from a common ancestor. There are six Superorders in the Dicotyledonae (Magnoliidae, Hamamelidae, Caryophyllidae, Dilleniidae, Rosidae, Asteridae), and four Superorders in the Monocotyledonae (Alismatidae, Commelinidae, Arecidae, Liliidae). The names of the Superorders end in ‐idae ORDER ‐ Each Superorder is further divided into several Orders. The names of the Orders end in ‐ales FAMILY ‐ Each Order is divided into Families. These are plants with many botanical features in common, and is the highest classification normally used. -
The Evolution of Ancestral and Species-Specific Adaptations in Snowfinches at the Qinghai–Tibet Plateau
The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai–Tibet Plateau Yanhua Qua,1,2, Chunhai Chenb,1, Xiumin Chena,1, Yan Haoa,c,1, Huishang Shea,c, Mengxia Wanga,c, Per G. P. Ericsond, Haiyan Lina, Tianlong Caia, Gang Songa, Chenxi Jiaa, Chunyan Chena, Hailin Zhangb, Jiang Lib, Liping Liangb, Tianyu Wub, Jinyang Zhaob, Qiang Gaob, Guojie Zhange,f,g,h, Weiwei Zhaia,g, Chi Zhangb,2, Yong E. Zhanga,c,g,i,2, and Fumin Leia,c,g,2 aKey Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China; bBGI Genomics, BGI-Shenzhen, 518084 Shenzhen, China; cCollege of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China; dDepartment of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden; eBGI-Shenzhen, 518083 Shenzhen, China; fState Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China; gCenter for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China; hSection for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; and iChinese Institute for Brain Research, 102206 Beijing, China Edited by Nils Chr. Stenseth, University of Oslo, Oslo, Norway, and approved February 24, 2021 (received for review June 16, 2020) Species in a shared environment tend to evolve similar adapta- one of the few avian clades that have experienced an “in situ” tions under the influence of their phylogenetic context. Using radiation in extreme high-elevation environments, i.e., higher snowfinches, a monophyletic group of passerine birds (Passer- than 3,500 m above sea level (m a.s.l.) (17, 18). -
A Multidimensional Approach for Detecting Species Patterns in Malagasy Vertebrates
Colloquium A multidimensional approach for detecting species patterns in Malagasy vertebrates Anne D. Yoder*†, Link E. Olson‡§, Carol Hanley*, Kellie L. Heckman*, Rodin Rasoloarison¶, Amy L. Russell*, Julie Ranivo¶ʈ, Voahangy Soarimalala¶ʈ, K. Praveen Karanth*, Achille P. Raselimananaʈ, and Steven M. Goodman§¶ʈ *Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208105, New Haven, CT 06520; ‡University of Alaska Museum of the North, 907 Yukon Drive, Fairbanks, AK 99775; ¶De´partement de Biologie Animale, Universite´d’Antananarivo, BP 906, Antananarivo (101), Madagascar; ʈWWF Madagascar, BP 738, Antananarivo (101), Madagascar; and §Department of Zoology, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605 The biodiversity of Madagascar is extraordinarily distinctive, di- distinctiveness, especially in those cases where reproductive isola- verse, and endangered. It is therefore urgent that steps be taken tion cannot be determined for reasons of geographic separation. to document, describe, interpret, and protect this exceptional Thus, although the BSC by no means provides a universally biota. As a collaborative group of field and laboratory biologists, applicable recipe whereby the working biologist can diagnose a we employ a suite of methodological and analytical tools to species, and thus define its evolutionary significance, the concept investigate the vertebrate portion of Madagascar’s fauna. Given provides a practicable toolkit for embarking upon the enterprise. that species are the fundamental unit of evolution, where micro- As a collaborative group of field and lab biologists, we are and macroevolutionary forces converge to generate biological motivated by an interest in documenting, describing, understanding, diversity, a thorough understanding of species distribution and and preserving the endangered vertebrate biota of Madagascar. -
Species Boundaries and Hybrid Zones of a Recently Diverged Species Complex
Species Boundaries and Hybrid Zones of a Recently Diverged Species Complex Desiree Harpel* and Jeremy L. Marshall Department of Entomology, Kansas State University, Manhattan, KS 66503 Speciation is the biological process of one species splitting into two or more new species, and is the driving force of biodiversity on Earth. When such new species are formed, there are three different ways in which their populations can be distributed relative to each other. They can be sympatric, where species boundaries overlap one another; parapatric, where species boundaries line up along each other’s edges; or allopatric, where the species boundaries do not come in contact with each other. In the Marshall Laboratory, we are interested both in how environmental variables like temperature and moisture influence species distributions (Camp and Marshall 2000; Jensen, Camp, and Marshall 2002; Marshall and Camp 2006; Camp, Huestis, and Marshall 2007) and how closely related species interact at the boundaries of their distributions (Howard et al 2003; Traylor et al. 2008). The combination of these two interests motivated this study. Specifically, we were interested in the Allonemobius socius complex of crickets, which is comprised of four closely related species (i.e., A. socius, A. fasciatus, A. sp. nov. Tex, and A. shalontaki) whose species boundaries are unresolved in the central United States. This complex of crickets has been a model in evolutionary biology, used to study speciation (Howard et al. 2002; Marshall, Arnold, and Howard 2002; Marshall et al. 2011; Marshall and DiRienzo 2012; Marshall 2013), hybrid zones (Howard et al. 2003; Traylor et al. 2008), genetics (Huestis and Marshall 2006a; Britch et al. -
Taxonomy and Classification
Taxonomy and Classification Taxonomy = the science of naming and describing species “Wisdom begins with calling things by their right names” -Chinese Proverb museums contain ~ 2 Billion specimens worldwide about 1.5 M different species of life have been described each year ~ 13,000 new species are described most scientists estimate that there are at least 50 to 100 Million actual species sharing our planet today most will probably remain unknown forever: the most diverse areas of world are the most remote most of the large stuff has been found and described not enough researchers or money to devote to this work Common vs Scientific Name many larger organisms have “common names” but sometimes >1 common name for same organism sometimes same common name used for 2 or more distinctly different organisms eg. daisy eg. moss eg. mouse eg. fern eg. bug Taxonomy and Classification, Ziser Lecture Notes, 2004 1 without a specific (unique) name it’s impossible to communicate about specific organisms What Characteristics are used how do we begin to categorize, classify and name all these organisms there are many ways to classify: form color size chemical structure genetic makeup earliest attempts used general appearance ie anatomy and physiological similarities plants vs animals only largest animals were categorized everything else was “vermes” but algae, protozoa today, much more focus on molecular similarities proteins, DNA, genes History of Classification Aristotle was the first to try to name and classify things based on structural similarities -
Structural Profile of the Pea Or Bean Family
Florida ECS Quick Tips July 2016 Structural Profile of the Pea or Bean Family The Pea Family (Fabaceae) is the third largest family of flowering plants, with approximately 750 genera and over 19,000 known species. (FYI – the Orchid Family is the largest plant family and the Aster Family ranks second in number of species.) I am sure that you are all familiar with the classic pea flower (left). It, much like the human body, is bilaterally symmetrical and can be split from top to bottom into two mirror-image halves. Botanists use the term zygomorphic when referring to a flower shaped like this that has two different sides. Zygomorphic flowers are different than those of a lily, which are radially symmetrical and can be split into more than two identical sections. (These are called actinomorphic flowers.) Pea flowers are made up of five petals that are of different sizes and shapes (and occasionally different colors as well). The diagram at right shows a peanut (Arachis hypogaea) flower (another member of the Pea Family), that identifies the various flower parts. The large, lobed petal at the top is called the banner or standard. Below the banner are a pair of petals called the wings. And, between the wings, two petals are fused together to form the keel, which covers the male and female parts of the flower. Because of the resemblance to a butterfly, pea flowers are called papilionaceous (from Latin: papilion, a butterfly). However, there is group of species in the Pea Family (a subfamily) with flowers like the pride-of-Barbados or peacock flower (Caesalpinia pulcherrima) shown to the left. -
Plant Nomenclature and Taxonomy an Horticultural and Agronomic Perspective
3913 P-01 7/22/02 4:25 PM Page 1 1 Plant Nomenclature and Taxonomy An Horticultural and Agronomic Perspective David M. Spooner* Ronald G. van den Berg U.S. Department of Agriculture Biosystematics Group Agricultural Research Service Department of Plant Sciences Vegetable Crops Research Unit Wageningen University Department of Horticulture PO Box 8010 University of Wisconsin 6700 ED Wageningen 1575 Linden Drive The Netherlands Madison Wisconsin 53706-1590 Willem A. Brandenburg Plant Research International Wilbert L. A. Hetterscheid PO Box 16 VKC/NDS 6700 AA, Wageningen Linnaeuslaan 2a The Netherlands 1431 JV Aalsmeer The Netherlands I. INTRODUCTION A. Taxonomy and Systematics B. Wild and Cultivated Plants II. SPECIES CONCEPTS IN WILD PLANTS A. Morphological Species Concepts B. Interbreeding Species Concepts C. Ecological Species Concepts D. Cladistic Species Concepts E. Eclectic Species Concepts F. Nominalistic Species Concepts *The authors thank Paul Berry, Philip Cantino, Vicki Funk, Charles Heiser, Jules Janick, Thomas Lammers, and Jeffrey Strachan for review of parts or all of our paper. Horticultural Reviews, Volume 28, Edited by Jules Janick ISBN 0-471-21542-2 © 2003 John Wiley & Sons, Inc. 1 3913 P-01 7/22/02 4:25 PM Page 2 2 D. SPOONER, W. HETTERSCHEID, R. VAN DEN BERG, AND W. BRANDENBURG III. CLASSIFICATION PHILOSOPHIES IN WILD AND CULTIVATED PLANTS A. Wild Plants B. Cultivated Plants IV. BRIEF HISTORY OF NOMENCLATURE AND CODES V. FUNDAMENTAL DIFFERENCES IN THE CLASSIFICATION AND NOMENCLATURE OF CULTIVATED AND WILD PLANTS A. Ambiguity of the Term Variety B. Culton Versus Taxon C. Open Versus Closed Classifications VI. A COMPARISON OF THE ICBN AND ICNCP A. -
Characterization of the Sandfly Fever Naples Species Complex and Description of a New Karimabad Species Complex
Journal of General Virology (2014), 95, 292–300 DOI 10.1099/vir.0.056614-0 Short Characterization of the Sandfly fever Naples Communication species complex and description of a new Karimabad species complex (genus Phlebovirus, family Bunyaviridae) Gustavo Palacios,1 Robert B. Tesh,2 Nazir Savji,33 Amelia P. A. Travassos da Rosa,2 Hilda Guzman,2 Ana Valeria Bussetti,3 Aaloki Desai,3 Jason Ladner,1 Maripaz Sanchez-Seco4 and W. Ian Lipkin3 Correspondence 1Center for Genomic Sciences, United States Army Medical Research Institute for Infectious Gustavo Palacios Diseases, Frederick, MD, USA [email protected] 2Center for Biodefense and Emerging Infectious Diseases, Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA 3Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY, USA 4Centro Nacional de Microbiologia, Instituto de Salud ‘Carlos III’, Madrid, Spain Genomic and antigenic characterization of members of the Sandfly fever Naples virus (SFNV) complex reveals the presence of five clades that differ in their geographical distribution. Saint Floris and Gordil viruses, both found in Africa, form one clade; Punique, Granada and Massilia viruses, all isolated in the western Mediterranean, constitute a second; Toscana virus, a third; SFNV isolates from Italy, Cyprus, Egypt and India form a fourth; while Tehran virus and a Serbian isolate Yu 8/76, represent a fifth. Interestingly, this last clade appears not to express the second non-structural protein ORF. Karimabad virus, previously classified as a member of the SFNV complex, and Gabek Forest virus are distinct and form a new species complex (named Karimabad) in the Phlebovirus genus. -
Writing Plant Names
Writing Plant Names 06-09-2020 Nomenclatural Codes and Resources There are two international codes that govern the use and application of plant nomenclature: 1. The International Code of Nomenclature for Algae, Fungi, and Plants, Shenzhen Code, 2018. International Association for Plant Taxonomy. Abbreviation: ICN • Serves the needs of science by setting precise rules for the application of scientific names to taxonomic groups of algae, fungi, and plants • Available online at https://www.iapt-taxon.org/nomen/main.php 2. The International Code of Nomenclature for Cultivated Plants, 9th Edition, 2016. International Association for Horticultural Science. Abbreviation: ICNCP • Serves the applied disciplines of horticulture, agriculture, and forestry by setting rules for the naming of cultivated plants • Available online at https://www.ishs.org/sites/default/files/static/ScriptaHorticulturae_18.pdf These two resources, while authoritative, are very technical and are not easy to read. Two more accessible references are: 1. Plant Names: A guide to botanical nomenclature, 3rd Edition, 2007. Spencer, R., R. Cross, P. Lumley. CABI Publishing. • Hard copy available for reference in the Overlook Pavilion office 2. The Code Decoded, 2nd Edition, 2019. Turland, N. Advanced Books. • Available online at https://ab.pensoft.net/book/38075/list/9/ This document summarizes the rules presented in the above references and, where presentation is a matter of preference rather than hard-and-fast rules (such as with presentation of common names), establishes preferred presentation for the Arboretum at Penn State. Page | 1 Parts of a Name The diagram below illustrates the overall structure of a plant name. Each component, its variations, and its preferred presentation will be addressed in the sections that follow.