1. Systematics, Taxonomy, & Phylogenetics David L
Systematics, Taxonomy, & Phylogenetics David L. Reed, Mammalogy Class August 27, 2002

2. Systematics is ….
Systematics is the study of the diversity of organisms and the relationships among these organisms.
It provides the framework for studies of biological diversity & evolution

3. Systematics comprises:
Classification - ordering of organisms into groups (pigeon-holing)
Nomenclature - the naming of organisms
Identification- placement of a new organism into a previously described group

4. Linnaeus’ Binomial Nomenclature
Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species
Latin binomial (Genus species)
Hierarchical structure
Very flexible when changes need to be made
Book outlining all the rules for nomenclature
Work an example

5. Classifications Phenetic Phylogenetic
Based on overall similarity (Phenetic)
Pros-- easy to see similarity, intuitive
Cons--doesn’t account for evolutionary history
Phylogenetic
Based on shared derived characters
Pros--contains evolutionary history
Cons--computationally harder

6. Phenetic Classification:
Phenetic classification (grade-level classification) is based upon overall similarity (Numerical Taxomony)
Phenogram: a branching diagram (tree) that links taxa by estimates of overall similarity

7. Phenetic Groupings Kangaroos with kangaroo mice (jumping legs)
Sugar gliders with flying squirrels (gliding membrane)
Bats with birds (wings)
House cat
Mountain Lion
Domestic dog
Grey Fox
Bobcat
Grey Wolf
African Lion

8. Downfall of Phenetics
Overall similarity misled biologists into putting things in non-natural groups (i.e. Ungulata-Artiodactyls + Perrisodactyls)
Better to use characters that are evolutionarily shared among group members (synapomorphic characters)

9. Phylogenetic classification (cladistics):
Based upon evolutionary relationships (i.e. upon common ancestry)
Would put all marsupials together because of the synapomorphic pouch
Separates birds and bats because they have unique evolutionary origins for their wings

10. Diagrams for Cladistic Analyses
Cladogram is a tree diagram which depicts a hypothesised evolutionary history
A Phylogram is a tree which indicates by branch length the degree of change believed to have occurred along each lineage

11. Cladograms and phylograms
Bacteria 1
Bacteria 2
Cladograms show branching order - branch lengths are meaningless
Bacteria 3
Eukaryote 1
Eukaryote 2
Eukaryote 3
Eukaryote 4
Phylograms show branch order and branch lengths
Bacteria 1
Bacteria 2
Bacteria 3
Eukaryote 1
Eukaryote 2
Eukaryote 3
Eukaryote 4

12. Character Matrix
Characters
Taxa 1 2 3 4 5 A B C D

13. Unrooted Cladogram C A B D

14. Character Matrix
Characters
Taxa 1 2 3 4 5
A (out) B C D

15. Rooted Tree (requires additional information)B C D 5
(0-1)
Characters
Time 4
(0-1)
Taxa 1 2 3 4 5
A (out) B C D 3
(0-1) 2
(0-1) 1
(0-1)

16. Character Matrix
Characters
Taxa 1 2 3 4 5
A (out) B C D E

17. Rooted topology D B C A E 5 5 3 2 4 1 (0-1) Taxa 1 2 3 4 5 A (out) B CB C D E

19. Taxa
No. of Possible Unrooted Trees 4 3 5 15 6
105 7
945 8
10,395 9
135,135 10
2,027,025 11
34,459,425 12
654,729,075 13
13,749,310,575 14
316,234,143,225
7,905,853,580,625 16
213,458,046,676,875 17
6,190,283,353,629,375 18
191,898,783,962,510,625 19
6,332,659,870,762,850,625 20
221,643,095,476,699,771,875 21
8,200,794,532,637,891,559,375 < (2.5 Billion years to compute!!!!!!!!!!!!!)

20. What about Fossils? Fossils often have far fewer characters to measure
DNA sequencing usually isn’t possible
Result is that paleontology still uses phenetic classification, sometimes
However, phylogenetic analyses can still be done when data are available

21. Phylogenetic systematics
Uses tree diagrams to portray relationships based upon common ancestry
Monophyletic groups (clades) - contain species which are more closely related to each other than to any outside of the group

22. Monophyletic groups monophyletic groups (clades) Rodent outgroup Fox
Wolf
Coyote
Cougar
Bobcat
Domestic Cat
Lion

23. Paraphyly and Polyphyly
Rodent outgroup
Wolf
Coyote
Canidae (polyphyletic)
Fox
Dog
Bobcat
Domestic Cat
Felidae (paraphyletic)
Cougar

24. What can we use phylogenies for?
Character evolution
Host-parasite evolution
Systematics and Taxonomy
Evolutionary history
Comparative biology

25. Character Evolution - Amniota
Rayfinned fish
Rayfinned fish
salamaders
crocodiles
mammals
salamaders
mammals
crocodiles
turtles
lungfish
lizards
snakes
lungfish
turtles
lizards
snakes
frogs
birds
frogs
birds
amnion
absent
present
3 steps
1 step

27. Comparative Analyses

28. Comparative Analyses