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Outline: The role and value of Systematics
Taxonomy (α taxonomy) - in decline? Describing species Identification, Classification Collections, Conservation Phylogenetics (β taxonomy) Phylogeny Classification (?) Evolutionary processes / patterns Conservation
Lecture 1: Introduction to biological systematics (value)
Mayr, E.& P. D. Ashlock (1991) Principles of Systematic Zoology, 2nd Edition, McGraw-Hill, Inc., NY. pp. 1-8. [PDF]
*Godfray, H. C. J. (2002) Challenges for taxonomy. Nature 417: 17-19.
Flowers et al. (2002) Does the decline in systematic biology matter? Chapter 4 of report to the House of Lords (UK). Select Committee on Science & Technology. [webpage]
Lecture 2: Value of biosystematics continued; History of taxonomy
*Gould, S. J. 2000. Linnaeus's Luck? Natural History. Vol 109 iss.7 : (September): 19-25, 66-76.
Mayr, E.& P. D. Ashlock (1991) Principles of Systematic Zoology, 2nd Edition, McGraw-Hill, Inc., NY. pp. 9-18. [PDF - see link under lecture 1]
• alpha taxonomy / phylogenetics (descriptive taxonomy / phylogenetic tax.)
- suffering from lack of prestige & resources
• Solutions?
• “web monographs” ?
• unitary taxonomy ?
Godfray (2002)
“Descriptive” taxonomy - Describing - Cataloging - Classifying - Stamp collecting?
Hypothetico-deductive taxonomy - Descriptions based on theory & hypotheses - Seek a ‘natural’ classification
Gould - Linnaeus’s Luck
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“Systematic biology has contracted at British universities to such an extent that it may be in danger of extinction as a sustainable discipline.”
- 1992 the Dainton Report on Systematics in the UK
α (alpha) taxonomy
Demographic trends in alpha taxonomy:
1990 survey
63% of taxonomists > 46 years old
Only 8% < 35 years old
α (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 captive breeding.
But if these trends continue among taxonomists and systematists, how soon will it be before we cannot
recognize a new species of lemur?”
Gaston, K. J. and R. M. May. 1992. Taxonomy of taxonomists. Nature 356: 281-28
α (alpha) taxonomy
Systematics training in universities -
- molecular systematics (your text)
- phylogenetics
- rarely any training in alpha taxonomy
- knowledge & skills are being lost
α (alpha) taxonomy
Results of this decline -
- systematists who can’t do identifications
- orphaned taxa
- fewer people to describe species
- lots of new trees, but fewer taxonomic changes
α (alpha) taxonomy
Results of this decline -
- systematists who can’t do identifications
- orphaned taxa
- fewer people to describe species
- lots of new trees, but fewer taxonomic changes
“We sit on the brink of a crisis”
Not enough trained taxonomists to describe remaining 5-15 million species - even if we had the money
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Solutions -
- Modernization - new technology
- digitization, web-publication, DNA
- NSF PEET grants (Partnership for Enhancing Expertise in Taxonomy)
α (alpha) taxonomy
descriptions
identification
collections classification
character evolution
phylogeny
biogeography
Systematics
Standard:
“Activity of grouping entities or phenomena and giving names to the resulting groups”
-Wiley (1981) p. 194
Classification - usage of term
Actual usage today:
“Activity of grouping entities or phenomena and giving names to the resulting groups”
Classification - usage of term
Phylogenetic analysis
Classification
- Not ‘identification’
- Not phylogenetic analysis - often used as such (e.g. “3 schools of classification”)
- implications are wrong
- Not a phylogeny - often thought that “tree = classification” - many students misunderstand this
Classification - usage of term
So what is it?
- is an arrangement of names - names for groups (of names…)
- Linnaeus prepared classifications
- many modern phylogeneticists do not - new trees are not new classifications - new classifications can be based on new
trees however
Classification - usage of term
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Phylum Annelida Class Polychaeta Family Siboglinidae Class Clitellata Subclass Oligochaeta Subclass Hirudinea Class Echiura
Phylum Sipuncula
We’ll do more on classifications and trees later
Example Classification Trees Classification
= Names
Giribet et al Nature 2001
1. Provide Classifications for our millions of species
Provide natural classifications = reflect evolutionary history = based on sound phylogenetic analyses
Natural classifications allow predictions
Systematics - value
Allow prediction of attributes of taxa not yet studied
- medicines (antibiotics, etc.) - biological control agents - predict ecological relationships - extinct taxa - singing dinosaurs?
Systematics - value
Bad, “unnatural” classifications can be disastrous
e.g. Gypsy moth - brought to Boston by a frenchman, Leopold Trouvelot - hoped to start a business in silk - chose this moth because of its name at
that time: Bombyx dispar - oriental silk moth = Bombyx mori
Systematics - value
Moth was no good for silk
Was very good at eating native trees
Escaped & is still a major pest species
Current name: Lymantria dispar (different superfamily from Bombyx !)
Systematics - value
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Tuatara - Sphenodon © Frans Lanting 2002
Only surviving genus of an ORDER of Reptiles
(Bad) Taxonomy used for conservation assumed 1 species when there were 2+
Resulted in - possible extinction of a subspecies - near extinction of a second species (extinction of 10 of 40 populations)
Described in Nature: 347, 177-179 (1990)
Systematics - value
2. Infer phylogenies - inform our classifications - to know what a organism “is” requires
phylogeny e.g. tongue worms - pentastomids
bizarre parasites of vertebrates - what are they?
Systematics - value
Classified in their own phylum
Only in last few decades have we determined they are Arthropods specifically Maxillopod Crustaceans!
Systematics - value
3. Understanding evolutionary processes a tree is required to study: - Cospeciation - Historical biogeography, phylogeography - Macroevolutionary patterns explosive radiations extinctions - Trait correlations Are warning colors related to the evolution of
gregariousness? - Adaptations
Systematics - value
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• Both derived from outpocketings of the gut • Both structures hold gas
– Swim bladders to adjust buoyancy – Lungs for gas exchange
• Tetrapods & some fish have lungs • Many fish have swim bladders
Which is the came first? Need a tree…
Evolution of Swim Bladders & Lungs
Sound natural classifications or phylogenies enable biologists to
• intelligently frame their hypotheses
• understand the direction of evolutionary change
• know which taxa are appropriate for comparative studies
Systematics - value
Human population growth (~7 billion currently)
~ 972 million in high income countries
~ 5.4 billion in middle & low income countries
[high income countries use twice the resources of the middle & low income countries]
Mann, M.E., Ammann, C.M., Bradley, R.S., Briffa, K.R., Crowley, T.J., Hughes, M.K., Jones, P.D., Oppenheimer, M., Osborn, T.J., Overpeck, J.T., Rutherford, S., Trenberth, K.E., Wigley, T.M.L., 2003. On Past Temperatures and Anomalous Late 20th Century Warmth. Eos 84, 256-258
Global Warming - ~0.8°C so far; target <2°C (if we burn 565 Gigatons of CO2), but plans are set to burn 2,795 Gigatons...
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Global Warming
Deforestation - habitat destruction >50% of species live in rain forests ~2% of these forests disappear each year e.g. Ghana -1990 and 2005, Ghana lost 25.9%
Relationship between rural population density and remaining closed-canopy forest [(current forest area/estimated original forest area) × 100] for 45 tropical nations in Africa (circles), the Americas (squares) and Asia (diamonds). Adapted with permission from S.J. Wright and H.C. Muller-Landau, The future of tropical forest species, Biotropica 38 (2006), pp. 287–301.
Conservation Biology - Biodiversity crisis
- Massive habitat destruction
- ca. 1 species extinction / 20 minutes (26k/yr) CENTINELAN EXTINCTION = named for Centinela Ridge in Ecuador Gentry & Dodson, 1978, 90 new species endemic to ridge, 8 yrs later destroyed
for a plantation - current extinction rates 100 to 1,000 times
greater than “normal”, Earth’s 6th mass extinction? (Barnosky et al 2011 Nature)
Systematics - value
Conservation Biology - Biodiversity crisis
Phylogenies help identify unique lineages
e.g. “living fossils”
e.g. a duckbilled platypus
Systematics - value
Systematics "is at the same time the most elementary and most inclusive part of biology, most elementary because organisms cannot be discussed or treated in a scientific way until some taxonomy has been achieved, and most inclusive because systematics in its various branches gathers together, utilizes, summarizes, and implements, everything that is known about organisms, whether morphological, physiological, or ecological.”
Paraphrased from George Gaylord Simpson's book, “Animal Taxonomy”
Systematics
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History of Taxonomy
Aristotle
384-322 B.C.
Father of Biological Classification
Used concept of nested sets
Named various taxa e.g. Coleoptera
“Sheath-wing” Oldest scientific names still in
use
Phylum Annelida
Class Polychaeta
Class Clitellata
Class Echiura
Subclass Oligochaeta
Subclass Hirudinea
Nested Sets
History of Taxonomy
Botanical taxonomy developed faster than zoological
Plants used for medicines & foods
Theophrastes 371-287 B.C. - classified 500 species of plants (e.g. Asparagus)
Books on plants (herbals) with illustrations, descriptions & names became common
History of Taxonomy
Herbals copied without improvements throughout the Middle Ages
Very little progress until the 15th century - Gutenberg’s printing press
Botanists began using phrase names - descriptive names of species
Latin, usually < 12 words
History of Taxonomy
Phrase names: Joseph Pitton de Tournefort - paved the
way for Linnaeus
Key work published in 1700 instituted the genus name
e.g. Mentha floribus spicatis, foliis oblongis serratis
“mint with flowers in a spike, leaves oblong and toothed”
History of Taxonomy
First Bioinformatics crisis - too many new species & names, chaos reigned
Linnaeus instituted a simpler, more organized system - binominal nomenclature, 1753, [6,000 plants]
based on binomen - species name composed of two words - as an abbreviation for the full phrase names
(note: not binomial nomenclature)
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History of Taxonomy
The binominal system was actually first used by Gaspard Bauhin (1623) but never caught on
Linnaeus reintroduced & imposed it on the world - chaos was averted
Zoological nomenclature began with the 10th edition of Linnaeus’s Systema Naturae (1758) - why this edition?
History of Taxonomy
Linnaeus’s 5 ranks:
Kingdom - Animalia Class - Insecta Order - Coleoptera Genus - Silpha Species - Silpha vespillo
All animals in 312 genera
Describe the decline of alpha taxonomy & ideas to reverse it
Understand the term Classification (not easy!)
Describe the value of phylogenetics
Describe the key people & their influence on the development of Systematics
You should be able to
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