A Simple R Package to Find and Visualize Monophyly Issues
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Lecture 2 Phylogenetics of Fishes 1. Phylogenetic Systematics 2
Lecture 2 Phylogenetics of Fishes 1. Phylogenetic systematics 2. General fish evolution 3. Molecular systematics & Genetic approaches Charles Darwin & Alfred Russel Wallace All species are related through common descent 1809 - 1882 1823 - 1913 Willi Hennig (1913 – 1976) • Hennig developed cladistical method to infer relatedness • Goal is to correctly group ancestors and all their descendants Cladistics (a.k.a Phylogenetic Systematics) Fundamental approach • divide characters into two groups • Apomorphies: more recently derived characteristics • Pleisomorhpies: more ancestral, primitive characteristics • Identify Synapomorphies (shared derived characteristics) • group clades by synapomorphies Cladistics (a.k.a Phylogenetic Systematics) eyes Synapomorphy of rockfish, gills bichir, and sharks? jaws bony skeleton swim bladder Bichir Rockfish Sharks Lamprey Hagfish Cladistics (a.k.a Phylogenetic Systematics) eyes Sympleisomorphy of gills rockfish, bichir, and sharks? jaws bony skeleton swim bladder Bichir Rockfish Sharks Lamprey Hagfish Cladistics (a.k.a Phylogenetic Systematics) eyes “Ancestral” and “derived” are gills relative to your focal group jaws bony skeleton swim bladder Bichir Rockfish Sharks Lamprey Hagfish Cladistics (a.k.a Phylogenetic Systematics) Monophyletic (aka clade): all taxa are descended from a common ancestor that is not the ancestor of any other group (every taxa descended from that ancestor is included) examples? Cladistics (a.k.a Phylogenetic Systematics) Paraphyletic: the group does not contain all species descended from the most recent common ancestor of its members examples? Cladistics (a.k.a Phylogenetic Systematics) Polyphyletic: taxa are descended from several ancestors that are also the ancestors of taxa classified into other groups examples? Problems with Traditional Cladistics Homoplasies • traits evolved due to convergence - keel: stabilizes tail at high speeds Problems with Traditional Cladistics Statistically inconsistent • can lend more support for the wrong answer Bernal et al. -
The Behavioral Ecology of the Tibetan Macaque
Fascinating Life Sciences Jin-Hua Li · Lixing Sun Peter M. Kappeler Editors The Behavioral Ecology of the Tibetan Macaque Fascinating Life Sciences This interdisciplinary series brings together the most essential and captivating topics in the life sciences. They range from the plant sciences to zoology, from the microbiome to macrobiome, and from basic biology to biotechnology. The series not only highlights fascinating research; it also discusses major challenges associ- ated with the life sciences and related disciplines and outlines future research directions. Individual volumes provide in-depth information, are richly illustrated with photographs, illustrations, and maps, and feature suggestions for further reading or glossaries where appropriate. Interested researchers in all areas of the life sciences, as well as biology enthu- siasts, will find the series’ interdisciplinary focus and highly readable volumes especially appealing. More information about this series at http://www.springer.com/series/15408 Jin-Hua Li • Lixing Sun • Peter M. Kappeler Editors The Behavioral Ecology of the Tibetan Macaque Editors Jin-Hua Li Lixing Sun School of Resources Department of Biological Sciences, Primate and Environmental Engineering Behavior and Ecology Program Anhui University Central Washington University Hefei, Anhui, China Ellensburg, WA, USA International Collaborative Research Center for Huangshan Biodiversity and Tibetan Macaque Behavioral Ecology Anhui, China School of Life Sciences Hefei Normal University Hefei, Anhui, China Peter M. Kappeler Behavioral Ecology and Sociobiology Unit, German Primate Center Leibniz Institute for Primate Research Göttingen, Germany Department of Anthropology/Sociobiology University of Göttingen Göttingen, Germany ISSN 2509-6745 ISSN 2509-6753 (electronic) Fascinating Life Sciences ISBN 978-3-030-27919-6 ISBN 978-3-030-27920-2 (eBook) https://doi.org/10.1007/978-3-030-27920-2 This book is an open access publication. -
Lições Das Interações Planta – Beija-Flor
UNIVERSIDADE ESTADUAL DE CAMPINAS INSTITUTO DE BIOLOGIA JÉFERSON BUGONI REDES PLANTA-POLINIZADOR NOS TRÓPICOS: LIÇÕES DAS INTERAÇÕES PLANTA – BEIJA-FLOR PLANT-POLLINATOR NETWORKS IN THE TROPICS: LESSONS FROM HUMMINGBIRD-PLANT INTERACTIONS CAMPINAS 2017 JÉFERSON BUGONI REDES PLANTA-POLINIZADOR NOS TRÓPICOS: LIÇÕES DAS INTERAÇÕES PLANTA – BEIJA-FLOR PLANT-POLLINATOR NETWORKS IN THE TROPICS: LESSONS FROM HUMMINGBIRD-PLANT INTERACTIONS Tese apresentada ao Instituto de Biologia da Universidade Estadual de Campinas como parte dos requisitos exigidos para a obtenção do Título de Doutor em Ecologia. Thesis presented to the Institute of Biology of the University of Campinas in partial fulfillment of the requirements for the degree of Doctor in Ecology. ESTE ARQUIVO DIGITAL CORRESPONDE À VERSÃO FINAL DA TESE DEFENDIDA PELO ALUNO JÉFERSON BUGONI E ORIENTADA PELA DRA. MARLIES SAZIMA. Orientadora: MARLIES SAZIMA Co-Orientador: BO DALSGAARD CAMPINAS 2017 Campinas, 17 de fevereiro de 2017. COMISSÃO EXAMINADORA Profa. Dra. Marlies Sazima Prof. Dr. Felipe Wanderley Amorim Prof. Dr. Thomas Michael Lewinsohn Profa. Dra. Marina Wolowski Torres Prof. Dr. Vinícius Lourenço Garcia de Brito Os membros da Comissão Examinadora acima assinaram a Ata de Defesa, que se encontra no processo de vida acadêmica do aluno. DEDICATÓRIA À minha família por me ensinar o amor à natureza e a natureza do amor. Ao povo brasileiro por financiar meus estudos desde sempre, fomentando assim meus sonhos. EPÍGRAFE “Understanding patterns in terms of the processes that produce them is the essence of science […]” Levin, S.A. (1992). The problem of pattern and scale in ecology. Ecology 73:1943–1967. AGRADECIMENTOS Manifestar a gratidão às tantas pessoas que fizeram parte direta ou indiretamente do processo que culmina nesta tese não é tarefa trivial. -
Exclusivity As the Key to Defining a Phylogenetic Species Concept
Biol Philos (2009) 24:473–486 DOI 10.1007/s10539-009-9151-4 When monophyly is not enough: exclusivity as the key to defining a phylogenetic species concept Joel D. Velasco Received: 29 November 2008 / Accepted: 6 January 2009 / Published online: 20 January 2009 Ó Springer Science+Business Media B.V. 2009 Abstract A natural starting place for developing a phylogenetic species concept is to examine monophyletic groups of organisms. Proponents of ‘‘the’’ Phylogenetic Species Concept fall into one of two camps. The first camp denies that species even could be monophyletic and groups organisms using character traits. The second groups organisms using common ancestry and requires that species must be monophyletic. I argue that neither view is entirely correct. While monophyletic groups of organisms exist, they should not be equated with species. Instead, species must meet the more restrictive criterion of being genealogically exclusive groups where the members are more closely related to each other than to anything outside the group. I carefully spell out different versions of what this might mean and arrive at a working definition of exclusivity that forms groups that can function within phylogenetic theory. I conclude by arguing that while a phylogenetic species con- cept must use exclusivity as a grouping criterion, a variety of ranking criteria are consistent with the requirement that species can be placed on phylogenetic trees. Keywords Genealogical exclusivity Á Monophyly Á Phylogenetic species concept Á Phylogeneticsystematics Á Species Introduction The species problem—how to sort organisms into various species—remains a central problem in biological taxonomy. Despite many bitter disagreements about these fundamental units, there is widespread agreement on how to delimit ‘‘higher’’ taxa (those that are more inclusive than species). -
Evaluating the Monophyly and Biogeography of Cryptantha (Boraginaceae)
Systematic Botany (2018), 43(1): pp. 53–76 © Copyright 2018 by the American Society of Plant Taxonomists DOI 10.1600/036364418X696978 Date of publication April 18, 2018 Evaluating the Monophyly and Biogeography of Cryptantha (Boraginaceae) Makenzie E. Mabry1,2 and Michael G. Simpson1 1Department of Biology, San Diego State University, San Diego, California 92182, U. S. A. 2Current address: Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, U. S. A. Authors for correspondence ([email protected]; [email protected]) Abstract—Cryptantha, an herbaceous plant genus of the Boraginaceae, subtribe Amsinckiinae, has an American amphitropical disjunct distri- bution, found in western North America and western South America, but not in the intervening tropics. In a previous study, Cryptantha was found to be polyphyletic and was split into five genera, including a weakly supported, potentially non-monophyletic Cryptantha s. s. In this and subsequent studies of the Amsinckiinae, interrelationships within Cryptantha were generally not strongly supported and sample size was generally low. Here we analyze a greatly increased sampling of Cryptantha taxa using high-throughput, genome skimming data, in which we obtained the complete ribosomal cistron, the nearly complete chloroplast genome, and twenty-three mitochondrial genes. Our analyses have allowed for inference of clades within this complex with strong support. The occurrence of a non-monophyletic Cryptantha is confirmed, with three major clades obtained, termed here the Johnstonella/Albidae clade, the Maritimae clade, and a large Cryptantha core clade, each strongly supported as monophyletic. From these phylogenomic analyses, we assess the classification, character evolution, and phylogeographic history that elucidates the current amphitropical distribution of the group. -
Federal Register/Vol. 78, No. 204/Tuesday, October 22, 2013
62560 Federal Register / Vol. 78, No. 204 / Tuesday, October 22, 2013 / Proposed Rules * * * * * Processing, Attn: FWS–R4–ES–2013– existing regulatory mechanisms; or (E) Dated: September 9, 2013. 0103; Division of Policy and Directives other natural or manmade factors Rachel Jacobson, Management; U.S. Fish and Wildlife affecting its continued existence. Service; 4401 N. Fairfax Drive, MS Principal Deputy Assistant Secretary for Fish We have determined that listing is Wildlife and Parks. 2042–PDM; Arlington, VA 22203. warranted for these species, which are We request that you send comments currently at risk throughout all of their [FR Doc. 2013–24169 Filed 10–3–13; 8:45 am] only by the methods described above. respective ranges due to threats related BILLING CODE 4310–55–C We will post all comments on http:// to: www.regulations.gov. This generally • A. eggersiana—potential future DEPARTMENT OF THE INTERIOR means that we will post any personal development for residential, urban, and information you provide us (see the tourist use; agriculture use; dropping of Fish and Wildlife Service Information Requested section below for debris; competing nonnative plants; more information). fires; predation; and disease cause by 50 CFR Part 17 FOR FURTHER INFORMATION CONTACT: insects (weevils). • [Docket No. FWS–R4–ES–2013–0103; Marelisa Rivera, Deputy Field G. concolor—installation or 4500030113] Supervisor, U.S. Fish and Wildlife expansion of telecommunication towers, Service, Caribbean Ecological Services road improvement, vegetation RIN 1018–AZ10 Field Office, P.O. Box 491, Road 301 management, and small number of ´ individuals and populations. Endangered and Threatened Wildlife Km. 5.1, Boqueron, PR 00622; by • V. -
Number 3, Spring 1998 Director’S Letter
Planning and planting for a better world Friends of the JC Raulston Arboretum Newsletter Number 3, Spring 1998 Director’s Letter Spring greetings from the JC Raulston Arboretum! This garden- ing season is in full swing, and the Arboretum is the place to be. Emergence is the word! Flowers and foliage are emerging every- where. We had a magnificent late winter and early spring. The Cornus mas ‘Spring Glow’ located in the paradise garden was exquisite this year. The bright yellow flowers are bright and persistent, and the Students from a Wake Tech Community College Photography Class find exfoliating bark and attractive habit plenty to photograph on a February day in the Arboretum. make it a winner. It’s no wonder that JC was so excited about this done soon. Make sure you check of themselves than is expected to seedling selection from the field out many of the special gardens in keep things moving forward. I, for nursery. We are looking to propa- the Arboretum. Our volunteer one, am thankful for each and every gate numerous plants this spring in curators are busy planting and one of them. hopes of getting it into the trade. preparing those gardens for The magnolias were looking another season. Many thanks to all Lastly, when you visit the garden I fantastic until we had three days in our volunteers who work so very would challenge you to find the a row of temperatures in the low hard in the garden. It shows! Euscaphis japonicus. We had a twenties. There was plenty of Another reminder — from April to beautiful seven-foot specimen tree damage to open flowers, but the October, on Sunday’s at 2:00 p.m. -
Patterns in Ericaceae: New Phylogenetic Analyses
BS 55 479 Origins and biogeographic patterns in Ericaceae: New insights from recent phylogenetic analyses Kathleen A. Kron and James L. Luteyn Kron, KA. & Luteyn, J.L. 2005. Origins and biogeographic patterns in Ericaceae: New insights from recent phylogenetic analyses. Biol. Skr. 55: 479-500. ISSN 0366-3612. ISBN 87-7304-304-4. Ericaceae are a diverse group of woody plants that span the temperate and tropical regions of the world. Previous workers have suggested that Ericaceae originated in Gondwana, but recent phy logenetic studies do not support this idea. The theory of a Gondwanan origin for the group was based on the concentration of species richness in the Andes, southern Africa, and the southwest Pacific islands (most of which are thought to be of Gondwanan origin). The Andean diversity is comprised primarily of Vaccinieae with more than 800 species occurring in northern South America, Central America, and the Antilles. In the Cape Region of South Africa the genus Erica is highly diverse with over 600 species currently recognized. In the southwest Pacific islands, Vac cinieae and Rhodoreae are very diverse with over 290 species of Rhododendron (sect. Vireya) and approximately 500 species of Vaccinieae (I)imorphanthera, Paphia, Vaccinium). Recent phyloge netic studies have also shown that the Styphelioideae (formerly Epacridaceae) are included within Ericaceae, thus adding a fourth extremely diverse group (approximately 520 species) in areas considered Gondwanan in origin. Phylogenetic studies of the family on a global scale, how ever, have indicated that these highly diverse “Gondwanan” groups are actually derived from within Ericaceae. Both Fitch parsimony character optimization (using MacClade 4.0) and disper- sal-vicariance analysis (DIVA) indicate that Ericaceae is Laurasian in origin. -
ABSTRACTS 117 Systematics Section, BSA / ASPT / IOPB
Systematics Section, BSA / ASPT / IOPB 466 HARDY, CHRISTOPHER R.1,2*, JERROLD I DAVIS1, breeding system. This effectively reproductively isolates the species. ROBERT B. FADEN3, AND DENNIS W. STEVENSON1,2 Previous studies have provided extensive genetic, phylogenetic and 1Bailey Hortorium, Cornell University, Ithaca, NY 14853; 2New York natural selection data which allow for a rare opportunity to now Botanical Garden, Bronx, NY 10458; 3Dept. of Botany, National study and interpret ontogenetic changes as sources of evolutionary Museum of Natural History, Smithsonian Institution, Washington, novelties in floral form. Three populations of M. cardinalis and four DC 20560 populations of M. lewisii (representing both described races) were studied from initiation of floral apex to anthesis using SEM and light Phylogenetics of Cochliostema, Geogenanthus, and microscopy. Allometric analyses were conducted on data derived an undescribed genus (Commelinaceae) using from floral organs. Sympatric populations of the species from morphology and DNA sequence data from 26S, 5S- Yosemite National Park were compared. Calyces of M. lewisii initi- NTS, rbcL, and trnL-F loci ate later than those of M. cardinalis relative to the inner whorls, and sepals are taller and more acute. Relative times of initiation of phylogenetic study was conducted on a group of three small petals, sepals and pistil are similar in both species. Petal shapes dif- genera of neotropical Commelinaceae that exhibit a variety fer between species throughout development. Corolla aperture of unusual floral morphologies and habits. Morphological A shape becomes dorso-ventrally narrow during development of M. characters and DNA sequence data from plastid (rbcL, trnL-F) and lewisii, and laterally narrow in M. -
Epilist 1.0: a Global Checklist of Vascular Epiphytes
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2021 EpiList 1.0: a global checklist of vascular epiphytes Zotz, Gerhard ; Weigelt, Patrick ; Kessler, Michael ; Kreft, Holger ; Taylor, Amanda Abstract: Epiphytes make up roughly 10% of all vascular plant species globally and play important functional roles, especially in tropical forests. However, to date, there is no comprehensive list of vas- cular epiphyte species. Here, we present EpiList 1.0, the first global list of vascular epiphytes based on standardized definitions and taxonomy. We include obligate epiphytes, facultative epiphytes, and hemiepiphytes, as the latter share the vulnerable epiphytic stage as juveniles. Based on 978 references, the checklist includes >31,000 species of 79 plant families. Species names were standardized against World Flora Online for seed plants and against the World Ferns database for lycophytes and ferns. In cases of species missing from these databases, we used other databases (mostly World Checklist of Selected Plant Families). For all species, author names and IDs for World Flora Online entries are provided to facilitate the alignment with other plant databases, and to avoid ambiguities. EpiList 1.0 will be a rich source for synthetic studies in ecology, biogeography, and evolutionary biology as it offers, for the first time, a species‐level overview over all currently known vascular epiphytes. At the same time, the list represents work in progress: species descriptions of epiphytic taxa are ongoing and published life form information in floristic inventories and trait and distribution databases is often incomplete and sometimes evenwrong. -
CURRICULUM VITAE Damon P. Little the New York Botanical Garden
CURRICULUM VITAE Damon P. Little The New York Botanical Garden Bronx, New York 10458-5126 718 817 8521 (office) 718 817 8101 (FAX) [email protected] APPOINTMENTS: 2014–present. Associate Curator of Bioinformatics. Lewis B. and Dorothy Cullman Program for Molecular Systematics. The New York Botanic Garden (Bronx, New York). 2008–present. Doctoral Faculty. The Graduate School and University Center of The City University of New York (New York, New York). 2007–2014. Assistant Curator of Bioinformatics. Lewis B. and Dorothy Cullman Program for Molecular Systematics. The New York Botanic Garden (Bronx, New York). 2007–present. Montgomery Botanical Research Fellow. Montgomery Botanical Center (Coral Gables, Florida). 2004–2007. Postdoctoral Research Associate. Lewis B. and Dorothy Cullman Program for Molecular Systematics. The New York Botanic Garden (Bronx, New York). Supervisor: D. Wm. Stevenson. EDUCATION: 1998–2005. Cornell University (Ithaca, New York). Ph.D. program in systematic botany. Dissertation: Evolution and circumscription of the true cypresses (Cupressaceae: Cupressus and Callitropsis): a combined molecular and morphological approach. Committee: Jeff J. Doyle (representing the plant molecular biology minor), Melissa A. Luckow (representing the plant anatomy minor), Kevin C. Nixon (committee chair, representing plant systematics), Quentin D. Wheeler (representing the comparative zoology minor). 1994–1998. University of Vermont (Burlington, Vermont). Bachelor of Science specializing in botany. PROGRAMMING AND SCRIPTING LANGUAGES: AWK, BASH, C, C++, JavaScript, PERL, R, and SQL. CONTRIBUTED PAPERS—REGULAR PUBLICATIONS: Meyer, R. S., B. D. Whitaker, D. P. Little, S.–B. Wu, E. J. Kennelly, C.–L. Long, and A. Litt. Accepted. Changes in phenolic constituents resulting from the domestication of eggplant. -
Phylogenomic Analyses Support the Monophyly of Excavata and Resolve Relationships Among Eukaryotic ‘‘Supergroups’’
Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic ‘‘supergroups’’ Vladimir Hampla,b,c, Laura Huga, Jessica W. Leigha, Joel B. Dacksd,e, B. Franz Langf, Alastair G. B. Simpsonb, and Andrew J. Rogera,1 aDepartment of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada B3H 1X5; bDepartment of Biology, Dalhousie University, Halifax, NS, Canada B3H 4J1; cDepartment of Parasitology, Faculty of Science, Charles University, 128 44 Prague, Czech Republic; dDepartment of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom; eDepartment of Cell Biology, University of Alberta, Edmonton, AB, Canada T6G 2H7; and fDepartement de Biochimie, Universite´de Montre´al, Montre´al, QC, Canada H3T 1J4 Edited by Jeffrey D. Palmer, Indiana University, Bloomington, IN, and approved January 22, 2009 (received for review August 12, 2008) Nearly all of eukaryotic diversity has been classified into 6 strong support for an incorrect phylogeny (16, 19, 24). Some recent suprakingdom-level groups (supergroups) based on molecular and analyses employ objective data filtering approaches that isolate and morphological/cell-biological evidence; these are Opisthokonta, remove the sites or taxa that contribute most to these systematic Amoebozoa, Archaeplastida, Rhizaria, Chromalveolata, and Exca- errors (19, 24). vata. However, molecular phylogeny has not provided clear evi- The prevailing model of eukaryotic phylogeny posits 6 major dence that either Chromalveolata or Excavata is monophyletic, nor supergroups (25–28): Opisthokonta, Amoebozoa, Archaeplastida, has it resolved the relationships among the supergroups. To Rhizaria, Chromalveolata, and Excavata. With some caveats, solid establish the affinities of Excavata, which contains parasites of molecular phylogenetic evidence supports the monophyly of each of global importance and organisms regarded previously as primitive Rhizaria, Archaeplastida, Opisthokonta, and Amoebozoa (16, 18, eukaryotes, we conducted a phylogenomic analysis of a dataset of 29–34).