Week 1, Wednesday

Taxonomy
Origin of the term Term invented by Candolle in 1813. He combined 2 latin words: taxis (arrangement/orientation) and nomos (laws) Naming Random names were given to things. Relationships between entities only came about 150 years ago Things are grouped now Aristotle to pre Darwin Discrete units, or essences, grouped some organisms of the same essence. Then people grouped the essence groupings (this was post Aristotle) Effort to identify everything out there 16th century: botanists and zoologists were really attached to medicine. Botanists were really herbalists for medicine. Describing plants for their herbal properties. Zoology wasnt about taxonomy. It was about anatomy and physiology. Late 16th century to 18th century, just taxonomy Darwin to post Darwin After his book, phylogeny and evolutionary concepts added to field Added concepts of divergence, evolutionary pathways, and causes/mechanisms of those changes George Gaylord Simpson: defined systematics as the study of diversity Taxonomy and systematics werent studied together Systematics relationships studies in colleges Taxonomy describing species was done in museums. Burden was that they had to name everything that came in

Mayr: taxonomy fell from favor in the 1870s. anti-taxonomy biases: 1. Emerging fields in biology and young scientists wanted to be on the cutting edge like genetics and physiology. Taxonomy seemed like an old boring field. 2. Taxonomists had a bad reputation that they earned Ex: Fowler: more money than brains. He described males and females as different species. Described the juveniles and adults as different species. He basically defined lots of different species when they werent different Lots of sloppy scientists like fowler. Overdescribers Rules about synonoyms. There are species that have been described more than once. Only one legit name. but have to figure it out Ex: freshwater fish of Vietnam. There were same species that were separated by salt water and land, but described them as different species. But didnt know that the water rose and they all used to be the same species. Dutch, French, and English all made the same mistake Splitters: recognize trivial differences and made a bunch of names that didnt need to be there Lumper: makes a lot of species one species Very first name described is the legit name! Non-taxonomic scientists were getting annoyed bc the names kept getting changed. But eventually there would be stability when all the earliest names were discovered Taxonomy is viewed as a descriptive science and is ranked low. Experimental science is better. But now ppl are accepting of different approaches But it is a legit science bc youre recognizing a unit in nature. It takes brains

History of theories of classification

Began with the studies of local faunas and floras Used to list everything in a territory. Inform the public of what was in a place Linnaeus (Carl von Linne) only we call him Linnaeus, a latinization of his name Invented the system we call binomial nomenclature, a two name system He predicted there were 35000 species, bc he though every jungle had the same type of species, but wrong. Acutally millions He was a creationist. But it had units Huxley: species concepts

1970: complete reexamination of the field of systematics: 3 types Entered the computer age, numerical aspects added to the field Biochemical and molecular techiniques An empirical approach followed; its basis on degree of similarity Darwin Population systematics Post-modern synthesis developments (according to Mayr, 1969) Ernst Mayr (1969) Described in his book Pre-darwinian and post darwiniam theories of classification Pre-darwinian: look at the handout to get the descriptions of each. Essentialism (Aristotle to Linnaeus): highly philosophical Nominalism: tangent, didnt catch on Empiricism : what it was until 40 years ago. If you study something enough, then youre the expert Post-darwinian: 3 schools of systematics Cladistics (phylogenetics) Evolutionary systematics. What he was promoting Phenetics (Mayr thought it was just evolutionary systematics with computers) Stages Alpha: level: IDENTIFICATION trying to find limits of units. Describe species. Recognizing units and naming them. Beta: CLASSIFICATION relationships among the species Gamma: POPULATION GENETICIST go back to unit, study the species in great detail esp geography and gene flow Done in order from alpha to beta to gamma

Week 1 Discussion

Review of Lecture
Taxon/taxa: group. Ex: primates Genera: plural for genus. Group of genera is a taxa. Each genus is a group. Classification: practice of doing taxonomy Systematics: study of historical, evolutionary, and genetic relationships Taxonomy: naming Taxonomy and systematics are topics. Classification is actually doing them Aristotle first taxonomist. Was typological, focused on essences Difference between pre-Darwinian taxonomy and post-Darwinian taxonomy: before was essences, after was more rigorous and evolutionary (Darwin presented the evolutionary system)

Papers
Origins of Taxonomy Linnaen binomial nomenclature is dated Folk taxonomy: there are natural groupings. Driving force: useful things had more names. The biggest group was genera, and it would be something like medicinal plants or poisonous plants Nothing useful communicated in Linnaen nomenclature, so its kind of useless bc no one knows latin Back then when there were less species, it was probably more useful. Now there are 10 million species Linnaeus was a fold taxonomist bc he only named useful things in his area Knowing the Earths Biodiversity: Challenges for the Infrastructure of Systematic Biology Expensive Information needs to be more accessible Taxonomy takes place in museums Systematics getting smaller and smaller. No one wants to study systematics and ppl are retiring Systemists are increasing in tropical areas of the world bc they have the organisms and the money now

How to get the information out there? Give them money, and databases Taxonomic Revival Computerizing databases. Putting them online to be accessed Funded by PEET grants. NSF partnership for enhancing expertise in taxonomy. They give you the money, but all the info has to be accessible online free Uses of databases: modeling and predicting where the species will be found by overlaying weather and species size and distribution data What will technology be like in 50 years? Very different. If you put it online now, will it be accessible? Will it be compatible with future technology? Maybe we should still have stuff in print

Week 1, Friday
Introduction
The Swedish naturalist Linnaues (Carl von Linne, 1707-1778) was the father of taxonomy Weird bc Candolle invented the word taxonomy only after Linnaeus died 95% of his lifes work was actually in economics His binomial method of nomenclature was consistently applied by him to animals in the 10th edition of his 10th edition Systema Naturae (1758) 10th edition he used his binomial nomenclature. Before he didnt Why binominal (two-names)? A story: Spearmint had a 6 word name and it was very descriptive (menthe floribus spicatis folis oblongis scoratis) Linnaeus reduced it down to Mantha spicata (spiked mint) 1749 His student reduced it down to two words: students had to write down what plants the farm animals ate everytime they ate something, and they got tired of writing down so many words. As short hand they wrote down just the first two words In linnaeuss new book Species Plantarum, he used the two word names 7700 plant, 4400 animal species named and described by Linnaeus Evolution wasnt a factor in any of this naming

Taxonomists had to be good artists Evolution was not a factor in this pre-Darwin taxonomy While the purpose (philosophy) has changed, the system of an unambiguous binomial nomenclature and a rigid hierarchy of categories proved useful to todays biologists, although this is now disputed by some

Original Linnaean hierarchy

Six categories Kingdom (bc he wrote two different books on plants and animals, so this was inferred)Class, order, genus, species, variety The genus has Linnaeus special category Basic form. Ex: turtles would be the genus. Genus (plural genera) gives the characteristics, not the other way around. Like essence Taxonomists need to know all 300 genera. But now maky of those genera have been moved up to family designation Variety was used by Linnaeus as an optional category for types of intraspecific variants Red rode or white rose are different varieties Later, family and phylum were added Kingdom, phylum, class, order, family, genus, species, variety

Todays taxonomic hierarchy (obligatory categories)

All species have these seven categories associated with them Kingdom, phylum, class, order, family, genus, species The category species is special for evolutionary biologists; however the discussion of species concepts is beyond the scope of this course. Other groups are human-made grouping. Species is an evolutionary and true biological meaning Uninomials are capitalized unless they are used as adjectives; they are plural nouns Each thing above species is a plural noun Replace the word with they and see if the verb tense makes sense

First letter is capitalized Names above genus can be used as an adjective and they its not capitalized Ex: Cyprinidae inhabit; She studied cyprinid fished Species and subspecies terms should not be used as uninomials Never capitalized Always used as nouns. Never as adjectives Some examples of good form Homo sapiens. Just never try to shorten it Genus, species, and subspecies are always italics or underlined. The other are never Species is a modifier of genus. Genus (essence) turtle. Species is spotted turtle. Adj should follow the noun, bc in latin language thats logical. Only in English its backwards

Added categories
The number of categories has been enhanced in two ways 1. Put modifiers on the terms Could put superorder before order Suborder after order Division of a suborder could be an infraorder Bias is to make subs 2. Invent completely new categories Hierarchy for animals (with optional categories) Empire, kingdom, subkingdom, phylum, subphylum, class (super, sub, infra), division (changes depending on if its zoological or botanical), order(SSI), family (SSI), Tribe (SS), Genus (subgenus, section, subsection, series, subseries), species, subspecies Compare the categories in bacteriology, botany, and zoology Ex phylum is a zoological term that botanists dont use Standardized ending; only a few are recognized One universally recognized is the ending for family idae (pronounced dee)

Most recognize standardized ending for order iformes Species concepts: why are you recognizing it as a different species?

Week 2, Monday
Introduction: the international commission on zoological nomenclature
The codes of nomenclature Three international codes: bacteriology, zoology, and botany Seven general principles applicable to all codes (Wiley 1981:385) 1 each code is completely independent of the other two codes 2 taxa are given in latin or latinized names: they have to be binominal for a species. Everything above species are uninominal (1 word) 3 taxa are assigned to certain categories and they only have one correct name 4 in general the correct name for a taxon is the earliest proposed name that is correctly published (the principle of priority) 5 in general, 2 taxa cannot have the same name: within, not between the codes. Cant have 2 animals with the same genus and species, but an animal and plant could have the same name 6 taxa assigned to certain categories are objectively defined in reference to type specimens 7 the most current codes are retroactive unless specifically stated otherwise. If a rule is changed everything in the past needs to be changed Recommendations, not laws The five tenets (not a rigid rule, but a principle)(Schuh and Brower 2009:179) 1 Priority: earliest name that was effectively published Linnaeus supported it, but didnt always follow it Published systema naturae and naming was stable for 50 years More ppl entered the field and weakened the authority of the book Species given multiple names Conflict between priority and stability Zoological code, the earliest name is the valid name

In botanical and bacteriological code its called the correct name 1 January 1758 systema naturae 10th ed is the date for animals which the date of name starts Exception: spiders: clerck 1757 For plants cut off date is 1753 Stability If theres a misspelling can take it to the commission Rule is 50 years: if scientific name hasnt been used for 50 years, then the more accepted name is official and the old name is called a nomenoblitum ( a forgotten name) First reviser principle: the first person who revises the paper can choose the real name (this person is beta level) if its lost they get to name a new one 2 Availability Effective publication of names 1 Latin and in English letters 2 Binominal 3 Appear in print in after the cutoff dates stated early Different meaning for effectively published Zoological: available Botanical: legitimate or validly published Bacteriological code: valid or validly published Legitimacy of being legitimately published Illegitimate things. Nomens Nomen oblitum: forgotten name Nomen superfluum: superfluous name Includes the type of another name that should have been used Description error Nomen ambiguum: ambiguous name Nomen dubium: dubious name

Not thorough enough to distinguish it enough from other things Nomen nudum: improperly published name Name published with no clothes on: no description 3 Typification 4 Homonymy 5 synonymy The five tenets: priority The five tenets: availability