Polyphyly of the Extinct Family Oviparosiphidae and Its Implications for Inferring Aphid Evolution (Hemiptera, Sternorrhyncha)
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Species Concepts Should Not Conflict with Evolutionary History, but Often Do
ARTICLE IN PRESS Stud. Hist. Phil. Biol. & Biomed. Sci. xxx (2008) xxx–xxx Contents lists available at ScienceDirect Stud. Hist. Phil. Biol. & Biomed. Sci. journal homepage: www.elsevier.com/locate/shpsc Species concepts should not conflict with evolutionary history, but often do Joel D. Velasco Department of Philosophy, University of Wisconsin-Madison, 5185 White Hall, 600 North Park St., Madison, WI 53719, USA Department of Philosophy, Building 90, Stanford University, Stanford, CA 94305, USA article info abstract Keywords: Many phylogenetic systematists have criticized the Biological Species Concept (BSC) because it distorts Biological Species Concept evolutionary history. While defences against this particular criticism have been attempted, I argue that Phylogenetic Species Concept these responses are unsuccessful. In addition, I argue that the source of this problem leads to previously Phylogenetic Trees unappreciated, and deeper, fatal objections. These objections to the BSC also straightforwardly apply to Taxonomy other species concepts that are not defined by genealogical history. What is missing from many previous discussions is the fact that the Tree of Life, which represents phylogenetic history, is independent of our choice of species concept. Some species concepts are consistent with species having unique positions on the Tree while others, including the BSC, are not. Since representing history is of primary importance in evolutionary biology, these problems lead to the conclusion that the BSC, along with many other species concepts, are unacceptable. If species are to be taxa used in phylogenetic inferences, we need a history- based species concept. Ó 2008 Elsevier Ltd. All rights reserved. When citing this paper, please use the full journal title Studies in History and Philosophy of Biological and Biomedical Sciences 1. -
A Phylogenomic Analysis of Turtles ⇑ Nicholas G
Molecular Phylogenetics and Evolution 83 (2015) 250–257 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev A phylogenomic analysis of turtles ⇑ Nicholas G. Crawford a,b,1, James F. Parham c, ,1, Anna B. Sellas a, Brant C. Faircloth d, Travis C. Glenn e, Theodore J. Papenfuss f, James B. Henderson a, Madison H. Hansen a,g, W. Brian Simison a a Center for Comparative Genomics, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA b Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA c John D. Cooper Archaeological and Paleontological Center, Department of Geological Sciences, California State University, Fullerton, CA 92834, USA d Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA e Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA f Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720, USA g Mathematical and Computational Biology Department, Harvey Mudd College, 301 Platt Boulevard, Claremont, CA 9171, USA article info abstract Article history: Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and Received 11 July 2014 prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle Revised 16 October 2014 phylogeny. We sequenced 2381 ultraconserved element (UCE) loci representing a total of 1,718,154 bp of Accepted 28 October 2014 aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and Available online 4 November 2014 an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. -
Congruence of Morphologically-Defined Genera with Molecular Phylogenies
Congruence of morphologically-defined genera with molecular phylogenies David Jablonskia,1 and John A. Finarellib,c aDepartment of Geophysical Sciences, University of Chicago, 5734 South Ellis Avenue, Chicago, IL 60637; bDepartment of Geological Sciences, University of Michigan, 2534 C. C. Little Building, 1100 North University Avenue, Ann Arbor, MI 48109; and cUniversity of Michigan Museum of Paleontology, 1529 Ruthven Museum, 1109 Geddes Road, Ann Arbor, MI 48109 Communicated by James W. Valentine, University of California, Berkeley, CA, March 24, 2009 (received for review December 4, 2008) Morphologically-defined mammalian and molluscan genera (herein ‘‘morphogenera’’) are significantly more likely to be mono- ABCDEHI J GFKLMNOPQRST phyletic relative to molecular phylogenies than random, under 3 different models of expected monophyly rates: Ϸ63% of 425 surveyed morphogenera are monophyletic and 19% are polyphyl- etic, although certain groups appear to be problematic (e.g., nonmarine, unionoid bivalves). Compiled nonmonophyly rates are probably extreme values, because molecular analyses have fo- cused on ‘‘problem’’ taxa, and molecular topologies (treated herein as error-free) contain contradictory groupings across analyses for 10% of molluscan morphogenera and 37% of mammalian mor- phogenera. Both body size and geographic range, 2 key macro- evolutionary and macroecological variables, show significant rank correlations between values for morphogenera and molecularly- defined clades, even when strictly monophyletic morphogenera EVOLUTION are excluded from analyses. Thus, although morphogenera can be imperfect reflections of phylogeny, large-scale statistical treat- ments of diversity dynamics or macroevolutionary variables in time and space are unlikely to be misleading. biogeography ͉ body size ͉ macroecology ͉ macroevolution ͉ systematics Fig. 1. Diagrammatic representations of monophyletic, uniparaphyletic, multiparaphyletic, and polyphyletic morphogenera. -
Hemiptera: Aphididae): New Finding on Ornamental Clematis Spp
Phytoparasitica DOI 10.1007/s12600-014-0417-2 Note: Aphis vitalbae Ferrari, 1872 (Hemiptera: Aphididae): new finding on ornamental Clematis spp. in Poland Roman Hałaj & Barbara Osiadacz Received: 19 March 2014 /Accepted: 29 May 2014 # The Author(s) 2014. This article is published with open access at Springerlink.com Abstract Aphis vitalbae Ferrari is reported from Poland these species concern the central and eastern Palearctic for the first time on ornamental clematis (Clematis spp.). (Hille Ris Lambers 1966; Kumar & Burkhardt 1970; The distribution of this aphid in Europe and its possible Narzikulov & Daniyarova 1990; Pashchenko 1997). So expansion route are presented with a key to identifying far three species of Aphis have been found to infest the aphids infesting Clematis plants in Europe. clematis plants in Europe (Holman 2009), and only two have been reported from Poland (Osiadacz & Hałaj Keywords Climatic changes . Invasiveness forecast . 2010). Besides polyphagous A. fabae, the oligophagous Local populations . Potential pest . Species A. clematidis has been found in some regions of Poland acclimatization . Zoogeography (Osiadacz & Hałaj 2009). The material gathered from Clematis x vitalba L. in Upper Silesia included A. vitalbae [apterae and alate viviparae, Zabrze city, ę ł Ś ą The species of Clematis are infested by 27 aphid species 14.07.2012, leg. M. Kr cia a, Ruda l ska city, 10.09.2012, ł (Blackman & Eastop 2014), of which nine belong to leg. R. Ha aj; apterae males and oviparae, Zabrze city, ę ł the genus Aphis. Three of those species (A. fabae 7.10.2013, leg. M. Kr cia a, Bytom city, 02.11.2013, Scopoli, 1763; A. -
Checklist of Aphidomorpha (Hemiptera: Sternorrhyncha) Known from Slovakia
Folia faunistica Slovaca 18 (3) 2013: 275–300 www.ffs.sk CHECKLIST OF APHIDOMORPHA (HEMIPTERA: STERNORRHYNCHA) KNOWN FROM SLOVAKIA 1,2 3 1 Katarína Goffová & Wacław Wojciechowski 2 Institute of Zoology, Slovak Academy of Sciences, Dúbravská cesta 9, SK–84506 Bratislava, Slovakia [[email protected]] 3 Department of Ecology, Faculty of Natural Sciences, Comenius University, Mlynská dolina, B–2, SK–84215 Bratislava, Slovakia University of Silesia, Faculty of Biology and Environmental Protection, Department of Zoology, Bankova 9, PL–40007 Katowice, Poland [[email protected]] Abstract: This checklist of Aphidomorpha from Slovakia counts 717 species of 10 families and 3 superfamilies (Aphidoidea, Adelgoidea, Phylloxeroidea). This paper presents existing valid names for species found in Slovakia since 1952 untill nowadays. Species were transferred between families due taxonomic changesKey words: from 1977. Aphidomorpha, Aphidoidea, Adelgoidea, Phylloxeroidea, checklist, Slovakia. INTRODUCTION (1984), Blackman (1990), Guldemond (1991), Blackman & Eastop (1994). Knowledge of the diversity of aphids in Slovakia- was summarised by Holman & Pintera (1977). Last checklist of 596 species of Aphidomorpha was Since 1977, entomologists found out new informa- published in 1977 (Holman & Pintera 1977) by tion about aphids, but until nowadays, new check– nomenclature of Mordvilko. Next time, research of list has not been executed. This checklist was pre aphids was stagnating. - pared on the basis of the publications from 1952 till 2009. In the nineteen eighties, on the basis of coopera- tion Department of Zoology – Comenius University- The first faunal records of aphid from Slovakia- in Bratislava and Department of Zoology – Univer were the collections by Horváth (1897) from the sity of Silesia in Katowice, research near Bratisla- Žitný ostrov, but these data weren’t adequate for in va was proceeding. -
Genetic Divergence and Polyphyly in the Octocoral Genus Swiftia [Cnidaria: Octocorallia], Including a Species Impacted by the DWH Oil Spill
diversity Article Genetic Divergence and Polyphyly in the Octocoral Genus Swiftia [Cnidaria: Octocorallia], Including a Species Impacted by the DWH Oil Spill Janessy Frometa 1,2,* , Peter J. Etnoyer 2, Andrea M. Quattrini 3, Santiago Herrera 4 and Thomas W. Greig 2 1 CSS Dynamac, Inc., 10301 Democracy Lane, Suite 300, Fairfax, VA 22030, USA 2 Hollings Marine Laboratory, NOAA National Centers for Coastal Ocean Sciences, National Ocean Service, National Oceanic and Atmospheric Administration, 331 Fort Johnson Rd, Charleston, SC 29412, USA; [email protected] (P.J.E.); [email protected] (T.W.G.) 3 Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th and Constitution Ave NW, Washington, DC 20560, USA; [email protected] 4 Department of Biological Sciences, Lehigh University, 111 Research Dr, Bethlehem, PA 18015, USA; [email protected] * Correspondence: [email protected] Abstract: Mesophotic coral ecosystems (MCEs) are recognized around the world as diverse and ecologically important habitats. In the northern Gulf of Mexico (GoMx), MCEs are rocky reefs with abundant black corals and octocorals, including the species Swiftia exserta. Surveys following the Deepwater Horizon (DWH) oil spill in 2010 revealed significant injury to these and other species, the restoration of which requires an in-depth understanding of the biology, ecology, and genetic diversity of each species. To support a larger population connectivity study of impacted octocorals in the Citation: Frometa, J.; Etnoyer, P.J.; GoMx, this study combined sequences of mtMutS and nuclear 28S rDNA to confirm the identity Quattrini, A.M.; Herrera, S.; Greig, Swiftia T.W. -
Title: Relationships Within Aphidomorpha on the Basis of Thorax Morphology Author: Piotr Węgierek Citation Style: Węgierek
Title: Relationships within Aphidomorpha on the basis of thorax morphology Author: Piotr Węgierek Citation style: Węgierek Piotr. (2002). Relationships within Aphidomorpha on the basis of thorax morphology. Katowice : Wydawnictwo Uniwersytetu Śląskiego P io t r W e g ie r e k Relationships within Aphidomorpha on the basis of thorax morphology Wydawnictwo Uniwersytetu Śląskiego Katowice 2002 Relationships within Aphidomorpha on the basis of thorax morphology Prace Naukowe Uniwersytetu Śląskiego w Katowicach nr 2101 P iotr W egierek Relationships within Aphidomorpha on the basis of thorax morphology Wydawnictwo Uniwersytetu Śląskiego Katowice 2002 Editor of the Series: Biology I w o n a S z a r e jk o Reviewers E l ż b ie t a C ic h o c k a J a n K o t e ja $ £ r 3125 8 3 Executive Editor G r a ż y n a W o j d a ł a Technical Editor B a r b a r a A r e n h ö v e i . Copyright © 2002 by Wydawnictwo Uniwersytetu Śląskiego All rights reserved ISSN 0208-6336 ISBN 83-226-1183-8 Published by Wydawnictwo Uniwersytetu Śląskiego ul. Bankowa 12B, 40-007 Katowice www.wydawnictwo.us.edu.pl e-mail: [email protected] First impression. Edition: 150 + 50 copies. Printed sheets: 6,75. Publishing sheets: 8,0. Passed to the Print ing House in August 2002. Signed for printing and printing finished in October 2002. Price 12 zl Zakład Poligraficzny Marian Wioska ul. 75. Pułku Piechoty 1,41-500 Chorzów Contents A b stra ct............................................................................................................................... -
Phylogenetics
Phylogenetics What is phylogenetics? • Study of branching patterns of descent among lineages • Lineages – Populations – Species – Molecules • Shift between population genetics and phylogenetics is often the species boundary – Distantly related populations also show patterning – Patterning across geography What is phylogenetics? • Goal: Determine and describe the evolutionary relationships among lineages – Order of events – Timing of events • Visualization: Phylogenetic trees – Graph – No cycles Phylogenetic trees • Nodes – Terminal – Internal – Degree • Branches • Topology Phylogenetic trees • Rooted or unrooted – Rooted: Precisely 1 internal node of degree 2 • Node that represents the common ancestor of all taxa – Unrooted: All internal nodes with degree 3+ Stephan Steigele Phylogenetic trees • Rooted or unrooted – Rooted: Precisely 1 internal node of degree 2 • Node that represents the common ancestor of all taxa – Unrooted: All internal nodes with degree 3+ Phylogenetic trees • Rooted or unrooted – Rooted: Precisely 1 internal node of degree 2 • Node that represents the common ancestor of all taxa – Unrooted: All internal nodes with degree 3+ • Binary: all speciation events produce two lineages from one • Cladogram: Topology only • Phylogram: Topology with edge lengths representing time or distance • Ultrametric: Rooted tree with time-based edge lengths (all leaves equidistant from root) Phylogenetic trees • Clade: Group of ancestral and descendant lineages • Monophyly: All of the descendants of a unique common ancestor • Polyphyly: -
Phylogenetic Analysisã
CHAPTER 9 Phylogenetic Analysisà OUTLINE 9.1 Phylogenetics and the Widespread Use 9.4.3 Selection of a Model of Evolution 212 of the Phylogenetic Tree 209 9.4.4 Construction of the Phylogenetic Tree 213 9.4.4.1 Distance-Based (Distance-Matrix) 9.2 Phylogenetic Trees 210 Methods 213 9.2.1 Phylogenetic Trees, Phylograms, 9.4.4.2 Character-Based Methods 213 Cladograms, and Dendrograms 211 9.4.5 Assessment of the Reliability 9.3 Phylogenetic Analysis Tools 211 of a Phylogenetic Tree 215 9.4 Principles of Phylogenetic-Tree Construction 211 9.5 Monophyly, Polyphyly, and Paraphyly 217 9.4.1 Selection of the Appropriate Molecular 9.6 Species Trees Versus Gene Trees 217 Marker 211 9.4.2 Multiple Sequence Alignment 212 References 218 9.1 PHYLOGENETICS AND THE phylogenetic/evolutionary trees is now widespread in WIDESPREAD USE OF THE many areas of study where evolutionary divergence PHYLOGENETIC TREE can be studied and demonstrated; be it pathogens, bio- logical macromolecules, or languages. Phylogeny refers to the evolutionary history of spe- Phylogenetics also provides the basis for compara- cies. Phylogenetics is the study of phylogenies—that tive genomics, which is a more recent term that came is, the study of the evolutionary relationships of spe- into existence in the age of genomics. Comparative cies. Phylogenetic analysis is the means of estimating genomics is the study of the interrelationships of gen- the evolutionary relationships. In molecular phyloge- omes of different species. Comparative genomics helps netic analysis, the sequence of a common gene or pro- identify regions of similarity and differences among tein can be used to assess the evolutionary relationship genomes. -
Agaricales) Reveals Polyphyly of Agaricoid Members
Mycologia, 108(5), 2016, pp. 860–868. DOI: 10.3852/15-370 # 2016 by The Mycological Society of America, Lawrence, KS 66044-8897 Multilocus phylogenetic reconstruction of the Clavariaceae (Agaricales) reveals polyphyly of agaricoid members Joshua M. Birkebak is a single club-shaped (clavarioid) or branched (coral- Slavomír Adamcˇík1,2 loid) basidiome represented by the genera Clavaria L.: Brian P. Looney Fr. (abbreviated Cl.), Clavulinopsis Overeem, Ramariop- P. Brandon Matheny sis (Donk) Corner and Mucronella Fr. Mucronella occu- Department of Ecology and Evolutionary Biology, University pies a well-supported position sister to the remaining of Tennessee, 332 Hesler, Biology Building, Knoxville, groups in the family (Birkebak et al. 2013). Clavulinop- Tennessee 37996-1610 sis and Ramariopsis form a well-supported monophylet- ic group. All agaricoid members of the family (with a differentiated pileus, stipe, and lamellate hymeno- Abstract: The genus Camarophyllopsis contains species phore) are currently classified in the single genus with lamellate (agaricoid) basidiomes in the family Cla- Camarophyllopsis Doty. The genus Hyphodontiella Å. variaceae (Agaricales), a group otherwise dominated Strid produces resupinate morphotypes and, accord- by club-like (clavarioid) or branched (coralloid) ing to Birkebak et al. (2013), is poorly supported as forms. Previous studies have suggested that species the sister group to a clade of Clavicorona-Clavaria- classified in Camarophyllopsis occur in two independent Camarophyllopsis. The genus Clavicorona produces basi- lineages. We reconstructed a multilocus phylogeny of diomes that are inflated upward and have a sterile the Clavaria-Camarophyllopsis-Clavicorona clade in the upper surface but lack lamellar modification of the Clavariaceae using RNA polymerase II second largest hymenophore. -
(Coleoptera: Byrrhoidea), with a Revised Checklist of Species Occurring in Poland
View metadata, citation and similar papers at core.ac.uk brought to you by CORE Title: An annotaded checklist of the Aphids (Hemiptera: Aphidomorpha) of Poland Author: Wacław Wojciechowski, Łukasz Depa, Mariusz Kanturski, Piotr Węgierek, Karina Wieczorek Citation style: Wojciechowski Wacław, Depa Łukasz, Kanturski Mariusz, Węgierek Piotr, Wieczorek Karina. (2015). An annotaded checklist of the Aphids (Hemiptera: Aphidomorpha) of Poland. "Polish Journal of Entomology" (2015, z. 4, s. 383-420), doi 10.1515/pjen-2015-0033 POLISH JOU R NAL OF ENTOM O LOG Y POL SKIE PISMO ENT OMOL OGICZ N E VOL. 84: 383–420 Lublin 30 December 2015 DOI: 10.1515/pjen-2015-0033 An annotated checklist of the Aphids (Hemiptera: Aphidomorpha) of Poland WACŁAW WOJCIECHOWSKI, ŁUKASZ DEPA, MARIUSZ KANTURSKI, PIOTR WEGIEREK, KARINA WIECZOREK Department of Zoology, Faculty of Biology and Environmental Protection, University of Silesia, Bankowa 9, 40-007 Katowice, Poland, e-mails: [email protected], [email protected], [email protected], [email protected], [email protected] ABSTRACT. The paper presents a comprehensive compilation of 764 taxa (species and subspecies), distributed over 167 genera, belonging to 17 subfamilies, three families and three superfamilies of Aphidomorpha recorded to date from Poland. The systematic positions of 19 taxa have been revised in accordance with recent changes in nomenclature. The presence in the Polish aphidofauna of Drepanosiphum oregonensis and Coloradoa huculaki, previously included without any distribution data in checklists of Polish aphids, has been confirmed. One species Sitobion (Sitobion) alopecuri is recognized as being new to Poland. At least 44 species (6% of local fauna of Aphidomorpha) are alien to Poland; among them 11 species collected from plants imported or cultivated in indoor conditions are listed. -
Taxonomy and Classification Goals: Un Ders Tan D Traditi Onal and Hi Erarchi Cal Cl Assifi Cati Ons of Biodiversity, and What Information Classifications May Contain
Taxonomy and classification Goals: Un ders tan d tra ditional and hi erarchi cal cl assifi cati ons of biodiversity, and what information classifications may contain. Readings: 1. Chapter 1. Figure 1-1 from Pough et al. Taxonomy and classification (cont ’d) Some new words This is a cladogram. Each branching that are very poiiint is a nod dEhbhe. Each branch, starti ng important: at the node, is a clade. 9 Cladogram 9 Clade 9 Synapomorphy (Shared, derived character) 9 Monophyly; monophyletic 9 PhlParaphyly; parap hlihyletic 9 Polyphyly; polyphyletic Definitions of cladogram on the Web: A dichotomous phylogenetic tree that branches repeatedly, suggesting the classification of molecules or org anisms based on the time sequence in which evolutionary branches arise. xray.bmc.uu.se/~kenth/bioinfo/glossary.html A tree that depicts inferred historical branching relationships among entities. Unless otherwise stated, the depicted branch lengt hs in a cl ad ogram are arbi trary; onl y th e b ranchi ng ord er is significant. See phylogram. www.bcu.ubc.ca/~otto/EvolDisc/Glossary.html TAKE-HOME MESSAGE: Cladograms tell us about the his tory of the re lati onshi ps of organi sms. K ey word : Hi st ory. Historically, classification of organisms was mainlyypg a bookkeeping task. For this monumental job, Carrolus Linnaeus invented the s ystem of binomial nomenclature that we are all familiar with. (Did you know that his name was Carol Linne? He liidhilatinized his own name th e way h e named speci i!)es!) Merely giving species names and arranging them according to similar groups was acceptable while we thought species were static entities .