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Outline taxonomy


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Outline taxonomy

  1. 1. Course Website: Check weekly for lecture updates, readings, etc. Course Content: Theory & Practice of Systematics Not taxon-specificIntroduction 25 % alpha taxonomyto 75 % phylogeneticsBiosystematics - Lecture 2Introduction to Biological Systematics Lecture 2: Introduction to Biological SystematicsWebsite, Course Outline Outline: The role and value of Systematics Readings (text…, reserve reading room) Taxonomy (! taxonomy) - in decline? Midterm & final exam Describing species Project Identification, Classification “Labs” - Fridays meet in BI 182 Collections, Conservation Beetle exercise Phylogenetics (" taxonomy) Debates (discussions of readings) Phylogeny 5 Questions - bonus Classification (?) Open office hours - make appointment Evolutionary processes / patterns ConservationBiosystematics Godfray (2002)Lecture 1: Introduction to biological systematics (value)Mayr, E.& P. D. Ashlock (1991) Principles of Systematic Zoology, 2nd • alpha taxonomy / phylogeneticsEdition, McGraw-Hill, Inc., NY. pp. 1-8. [PDF] (descriptive taxonomy / phylogenetic tax.)*Godfray, H. C. J. (2002) Challenges for taxonomy. Nature 417: 17-19. - suffering from lack of prestige & resourcesFlowers et al. (2002) Does the decline in systematic biology matter?Chapter 4 of report to the House of Lords (UK). Select Committee onScience & Technology. [webpage] • Solutions?Lecture 2: Value of biosystematics continued; History of taxonomy*Gould, S. J. 2000. Linnaeuss Luck? Natural History. Vol 109 iss.7 : • “web monographs” ?(September): 19-25, 66-76.Mayr, E.& P. D. Ashlock (1991) Principles of Systematic Zoology, 2nd • unitary taxonomy ?Edition, McGraw-Hill, Inc., NY. pp. 9-18. [PDF - see link under lecture 1] 1
  2. 2. Gould - Linnaeus’s Luck ! (alpha) taxonomy “Descriptive” taxonomy “Systematic biology has contracted at - Describing British universities to such an extent that it - Cataloging may be in danger of extinction as a - Classifying sustainable discipline.” - Stamp collecting? - 1992 the Dainton Report on Systematics Hypothetico-deductive taxonomy in the UK - Descriptions based on theory & hypotheses - Seek a ‘natural’ classification! (alpha) taxonomy ! (alpha) taxonomy Demographic trends in alpha taxonomy: “If we found these demographic trends in a newly discovered species of lemur, we would bring specimens into a zoo and start a programme of 1990 survey captive breeding. But if these trends continue among taxonomists and 63% of taxonomists > 46 years old systematists, how soon will it be before we cannot recognize a new species of lemur?” Only 8% < 35 years old Gaston, K. J. and R. M. May. 1992. Taxonomy of taxonomists. Nature 356: 281-28! (alpha) taxonomy ! (alpha) taxonomySystematics training in universities - Results of this decline - - molecular systematics (your text) - systematists who can’t do identifications - phylogenetics - orphaned taxa - rarely any training in alpha taxonomy - fewer people to describe species - knowledge & skills are being lost - lots of new trees, but fewer taxonomic changes 2
  3. 3. “We sit on the brink of ! (alpha) taxonomy a crisis” Solutions - - Modernization - new technology - digitization, web-publication, DNANot enough trained - NSF PEET grantstaxonomists to describeremaining 5-15 million (Partnership for Enhancing Expertisespecies - even if we in Taxonomy)had the money Biosystematics Classification - usage of term Standard: identification character “Activity of grouping entities or phenomena evolution and giving names to the resulting groups” descriptions phylogeny -Wiley (1981) p. 194 collections classification biogeography Classification - usage of term Classification - usage of term Actual usage today: - Not ‘identification’ “Activity of grouping entities or phenomena - Not phylogenetic analysis and giving names to the resulting groups” - often used as such (e.g. “3 schools of classification”) - implications are wrong Phylogenetic analysis - Not a phylogeny - often thought that “tree = classification” Classification - many students misunderstand this 3
  4. 4. Classification - usage of term Example Classification So what is it? Phylum Annelida Class Polychaeta - is an arrangement of names - names for Family Siboglinidae groups (of names…) Class Clitellata Subclass Oligochaeta - Linnaeus prepared classifications Subclass Hirudinea Class Echiura - many modern phylogeneticists do not Phylum Sipuncula -new trees are not new classifications -new classifications can be based on new We’ll do more on classifications and trees later trees howeverTrees Classification Biosystematics - value = Names 1. Provide Classifications for our millions of species Provide natural classifications = reflect evolutionary history = based on sound phylogenetic analyses Natural classifications allow predictionsGiribet et alNature 2001 Biosystematics - value Biosystematics - value Allow prediction of attributes of taxa not yet Bad, “unnatural” classifications studied can be disastrous - medicines (antibiotics, etc.) e.g. Gypsy moth - brought to Boston by a - biological control agents frenchman, Leopold Trouvelot - predict ecological relationships - hoped to start a business in silk - extinct taxa - singing dinosaurs? - chose this moth because of its name at that time: Bombyx dispar - oriental silk moth = Bombyx mori 4
  5. 5. Biosystematics - value Biosystematics - valueMoth was no good for silk (Bad) Taxonomy used for conservation assumed 1 species when there were 2+Was very good at eating native trees Resulted inEscaped & is still a major pest species - possible extinction of a subspecies - near extinction of a second species Current name: Lymantria dispar (extinction of 10 of 40 populations) (different superfamily from Bombyx !) Described in Nature: 347, 177-179 (1990)Biosystematics - value Biosystematics - value2. Infer phylogenies Classified in their own phylum - inform our classifications - to know what a organism “is” requires Only in last few decades have we determined phylogeny they are Arthropods e.g. tongue worms - pentastomids specifically Maxillopod Crustaceans! bizarre parasites of vertebrates - what are they?Biosystematics - value Evolution of Swim Bladders & Lungs3. Understanding evolutionary processes • Both derived from outpocketings of the gut a tree is required to study: • Both structures hold gas - Cospeciation – Swim bladders to adjust buoyancy - Historical biogeography, phylogeography – Lungs for gas exchange - Macroevolutionary patterns explosive radiations • Tetrapods & some fish have lungs extinctions • Many fish have swim bladders - Trait correlations Are warning colors related to the evolution of Which is the came first? gregariousness? Need a tree… - Adaptations 5
  6. 6. Biosystematics - value Biosystematics - valueSound natural classifications or phylogenies Conservation Biology - Biodiversity crisis enable biologists to• intelligently frame their hypotheses• understand the direction of evolutionary change• know which taxa are appropriate for comparative studies Human population Biosystematics - value Biosystematics - valueConservation Biology - Biodiversity crisis Conservation Biology - Biodiversity crisis - Massive habitat destruction Phylogenies help identify unique lineages - ca. 1 species extinction / 20 minutes e.g. “living fossils” - current extinction rates 100 to 1,000 times e.g. a duckbilled platypus greater than “normal” 6
  7. 7. Biosystematics History of TaxonomySystematics "is at the same time the most elementary Father of Biologicaland most inclusive part of biology, most elementary Classificationbecause organisms cannot be discussed or treated ina scientific way until some taxonomy has been Used concept of nested setsachieved, and most inclusive because systematics inits various branches gathers together, utilizes,summarizes, and implements, everything that is Named various taxaknown about organisms, whether morphological,physiological, or ecological.” e.g. Coleoptera “Sheath-wing”Paraphrased from George Gaylord Simpsons book, “Animal Taxonomy” Aristotle Oldest scientific names still in 384-322 B.C. use Phylum Annelida History of Taxonomy Botanical taxonomy developed faster than Class Class Class zoological Polychaeta Clitellata Echiura Subclass Oligochaeta Subclass Hirudinea Plants used for medicines & foods Theophrastes 371-287 B.C. - classified 500 species of plants (e.g. Asparagus) Nested Sets Books on plants (herbals) with illustrations, descriptions & names became common History of Taxonomy History of Taxonomy Herbals copied without improvements Phrase names: throughout the Middle Ages Joseph Pitton de Tournefort - paved the way for Linnaeus Very little progress until the 15th century - Gutenberg’s printing press Key work published in 1700 instituted the genus name Botanists began using phrase names - descriptive names of species e.g. Mentha floribus spicatis, foliis oblongis serratis “mint with flowers in a spike, leaves oblong and Latin, usually < 12 words toothed” 7
  8. 8. History of Taxonomy History of TaxonomyFirst Bioinformatics crisis - too many new The binominal system was actually first species & names, chaos reigned used by Gaspard Bauhin (1623) but never caught onLinnaeus instituted a simpler, more organized system - binominal Linnaeus reintroduced & imposed it on the nomenclature, 1753, [6,000 plants] world - chaos was averted based on binomen - species name Zoological nomenclature began with the composed of two words - as an 10th edition of Linnaeus’s Systema abbreviation for the full phrase names Naturae (1758) - why this edition?(note: not binomial nomenclature)History of Taxonomy You should be able toLinnaeus’s 5 ranks: Describe the decline of alpha taxonomy &Kingdom - Animalia ideas to reverse it Class - Insecta Understand the term Classification (not Order - Coleoptera easy!) Genus - Silpha Species - Silpha vespillo Describe the value of phylogeneticsAll animals in 312 genera Describe the key people & their influence on the development of Systematics 8