1. Organizing Biodiversity with Evolutionary Trees
From the beginning people have sought to name and group things; trying to find order in the the mysteries of the universe…
Organizing Biodiversity with Evolutionary Trees

2. Classification & Taxonomy
Aristotle - first classification system
John Ray - developed classification system and a new concept of species
Carolus Linnaeus - system of hierarchical classification and binomial nomenclature
Several people have contributed to the development of classification systems throughout history. Notable influences by Aristotle, English naturalist John Ray in the late 1600’s, and Linnaeus in the mid-1700’s.
Aristotle -- plants and animals
John Ray -- “ When men do not know the name and properties of natural objects---they cannot see and record accurately”
Carolus Linnaeus - hierarchical system still widely in place Kingdom, Phlylum, Class. Family, Order Genus, Species. Genus species names in Latin give binomial nomenclature.

3. What is Systematics?
Systematics is the branch of Biology that seeks to classify biodiversity using everything known about an organism in order to understand its evolutionary relationship to other organisms.
Systematics connects classification and phylogeny ( evolutionary history)
As everything we know grows…so do advancements in systematics
Systematics is the study of biodiversity in an evolutionary context
Note: not all classification system seek/sought to organize in light of relationships (pre-darwinian) ---some groupings ( i.e. reptiles persist due to traditional teachings and do not necessarily reflect or accept new findings ) Also, rearranging groups causes a lot of debate.
Ask: what is “everything known”? Let’s list what kind of things we can learn about an organisms…

4. Early Classification vs. Modern Analysis
Organisms are grouped according to similar physical characteristics
Organisms are grouped according to evolutionary relationships
Pre- Darwinian
Post-Darwinian
Taxonomy and early classification system were developed before Darwin proposed his Theory of Evolution. Some of the methods and theories used to group organisms have been challenged as new techniques are developed.

5. Dichotomous Keys vs. Phylogentic Trees
How is the purpose of each of these diagrams different?
How is the structure different?

6. Tree of Life
All organisms are related, but some are more closely related than others.
To represent the idea that all living things, despite their diversity, share a common ancestor, Darwin used the metaphor of a “tree of life”.
The more characteristics two organisms share, the more closely related they are said to be. (to each other compared to a a third organism)
Sharing more characteristics suggests that they shared a more recent common ancestor (again compared to another organisms---outgroup)
For Example: A lion and tiger are more related than a lion and a fish because they have more common characteristics

7. Tree Thinking
“The affinities of all the beings of the same class have sometimes been represented by a great tree…The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species… As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life.”
The revolutionary idea that all living organism are related gave scientists a new structure for organizing living things
Charles Darwin, On the Origins of Species (1859)

8. Darwin’s Tree
This “tree” illustration was the only one included in Darwin’s Origin of Species.
The tree is a natural image that conveys the idea of ancestry through its roots and the splitting off of lineages into branches over time.
Image taken from

9. The Tree of Life Project
The Tree of Life Web Project (ToL) is a collaborative effort of biologists from around the world. The project seeks to create a “super tree” which organizes the diversity of organisms on Earth through their evolutionary history.

10. Creating Evolutionary Trees
Comparative studies and fossils may be used to create initial phylogentic hypotheses
Molecular techniques may be used to test or refine initial hypotheses
Computer programs are readily available to analyze vast amounts of phylogenetic data

11. Based on the following character table, draw a tree

12. Cladograms and Phylogenetic Trees

13. How to read a cladogram Lines represent history through time.
Nodes represent ancestors that are extinct, but common to organisms

14. Clade-istics
Clade--group of organisms that share their most recent common ancestor

15. Evolutionary trees are hypotheses!
Different sources of evidence may lead to the development of competing trees
The principle of parsimony (choosing the least complex hypothesis) guides systematists in their reconstruction of trees

16. What is Cladistics?
A method of analyzing evolutionary relationships between groups to construct a cladogram or “family tree”
The branching tips of a cladogram must represent a clade, an ancestral species and ALL its descendents.
Cladogram, family tree, phylogenetic tree!!! Lots of terms seem to be used somewhat interchangably in the literature ( tought for us!!!) In general a “tree” depicts lines of descent that connect several branch tips. Some additional information

17. Clades
No more
Reptiles??
Using cladistics, the traditional reptile grouping does not include ALL descendents

18. Methods
Cladistic analysis involves comparing similarities (homologies) between organisms in order to determine primitive vs. derived characteristics.
Primitive - characteristics that all members of a group share
Derived - modified characteristics that only some members share
Comparing primitive vs. derived characteristics allows us to determine “roots” for our tree. While any characteristics can be used to differentiate two groups, careful selection of traits is essential to creating a rooted tree vs. a non-rooted organizational structure.
Unique shared derived characteristics identify a clade.

19. Data Sources Morphology Fossils Behavior Physiology Geology Geography
Molecular Evidence
Ecology

20. Reading Read “Tree Thinking Challenge” Which tree is more accurate?
What is the basis for trees?
What do nodes represent?

21. Practice Try the “odds” today and the “evens” for homework.
You will get an answer key on Wednesday!
They get harder as you go on!

22. Today’s Activity
Birdwing Butterflies: We will use a combination of geographic, physical, and genetic evidence to determine the evolutionary history of birdwing butterflies.

23. More Activities Later in the Year
HIV Evolution: We will use a computer program to compare HIV virus and determine the evolutionary origin.

24. Tools Available Software for Phylogenetic Analysis
Molecular Data Bases on the Web
PAUP
Hennig
MacClade
Genbank
Protein Information Resource (PIR)

25. Resources
“A Science Primer: Classification and Phylogenetics”
Baum, D.A.,et al. “ The Tree Thinking Challenge” Science 310:
Campbell, N.A. and Reece, J. B. Biology 6th edition. San Francisco: Benjamin Cummings, 2002.
Clos, L.M. “What is Cladistics?” [6/8/06]
Filson, R. “Island Biogeography and Evolution: Solving a Phylogenetic Puzzle with Molecular Genetics”
Kramer, B. and Flammer, L. “Making Cladograms: Phylogeny, Evolution, and Comparative Anatomy” Evolution & Nature of Science Institutes (ENSI/SENSI), University of Indiana. [6/8/06]
“Names & classifying living things”
Singer, F., et al “The Comparative Method, Hypothesis Testing & Phylogentic Analysis” The American Biology Teacher 63(7):
Skelton, P. W., A. Smith, et al. (2002). Cladistics a practical primer on CD-ROM. Cambridge, The Open University; Cambridge University Press.
“The Tree of Life Web Project’
“Tree-thinking Group”
“Understanding Evolution: An Evolution Web Site for Teachers”
“What did Trex taste like? An introduction to how life is related”