I.

II.

III.

Classification of organisms
a. Arrangement into groups
b. Taxonomy
i. Science of classification
c. Systematics
i. Science of systems of classification
ii. Define the diff classes/ways to classify classes
d. For:
i. Treating organism
ii. Guess abilities (when new in nature) based on name
iii. Classifying new organisms, especially unknown ones on this planet
1. Ex: bacteria in our bodies
2. 80% unknown
Relatidness
a. Separate organisms (relationships)
b. Phenetic (based on phenotype)
i. Morphology
1. Look alike
2. Visual characteristics
3. Ex: eukaryotes/prokaryotes: nucleus
ii. Metabolism/biochemical
1. Similar lifestyles
2. Ex: plants/algae: photosynthesis, release oxygen, etc
iii. Motility/physiology
1. Move or not, method of movement
c. Hard to distinguish bacteria by these above 3 phenetic tests
i. Morphology 2 diff classes (round/long)
ii. Metabolism/physiology time consuming, similar characteristics anyway
d. => Group based on genetics and evolution (phylogenetics)
i. More common
ii. Similar/dissimilar DNA sequences
iii. Common ancestors
Bergeys Manual (bible for taxonomy)
a. Of Systematic bacteriology
i. More common
ii. 9 volumes, 3rd or 4th edition
b. Of Determinative Bacteriology
i. Key - list how to identify organisms
c. Identify organisms
d. rDNA genes
e. Phenetic rules
i. Cell wall
ii. Morphology
iii. Metabolism/physiology

IV.

f. Gram +/gram -, oxidase tests, etc

g. Important
i. Conduct tests in orderly fashion (decision tree), not every test
h. Journal of systematics
i. Publish and include genetic testing, rDNA, other analyses, description
ii. -> put into literature
iii. Vs GenBank
1. Doesnt use real names
2. Use what people submit
Trees
a. Show how organisms relate
b. Whittaker Tree
i. 1840/1850-1967
ii. First tree
iii. Animals, plants, fungi
1. Common ancestor
iv. Prostista
v. Bacteria (monera)
vi. 5 kingdom tree
vii. Wrong (obsolete)
1. 4 eukaryotes groups, bacteria are separate from archaea
viii. Dr. shneegurt doesnt approve
c. Current tree
i. Tree base on ribosomal RNA genes
ii. Started with: 5s
iii. Now: 16s (bacteria/archaea), 18s (eukaryotes)
1. Small subunit
iv. 1500 bp long
1. =>1500 characteristics!
2. Ex: morphology round/rod; ferments glucose yes/no
3. Each position along gene = characteristic
v. Bacteria
vi. Archaea and eukaryote (plants, animals, fungi, protists, algae)
1. Same branch -> common ancestor
2. Archaea more related to eukaryotes than w/ other prokaryotes (bacteria)
vii. More diversity in bacteria and archaea than eukaryotes
viii. Naming in bacteria
1. Not by reproductive isolation?
ix. Carl Woese
1. 1990
2. 2000 defending tree
x. Problem in bacteria
1. Two lineages
a. Blue and green

2. Binary fission
3. Linear (vertical) inheritance
a. Parent -> child
4. However bacteria do horizontal gene transfer
a. Evolution
b. More important
c. Making new organisms, evolutionary processes, mutation
5. Doolittle
a. Famous biologist
b. Anti-darwinist
c. Ex: lineages of genes
i. Evolutionary processes and species that branch off
ii. Gene transfer within a population
1. Unnoticeable lateral gene transfer
2. Doesnt make much difference (pretty equivalent)
3. Transfer easy
a. vs interchanging between two diff species
6. rRNA
a. ancient
b. highly conserved regions
i. similar among all organisms
c. variable regions
i. not important to function
ii. diff between diff organisms
d. all cellular organisms have
e. Advantages
i. make PCR primers for everything
ii. make good trees (make sense)
f. little/slow lateral transfer
g. integrated early on
i. => no/little lateral transfer
7. Making into tree
a. 16s rRNA sequences
i. Experimental
ii. Control (GenBank, ribosomal database project -RDP)
b. Algorithms compare sequenes
i. Alignment
1. Program: Clustal W
2. Packages: include all programs
a. MEGA
3. All sequences -> stack into positions
4. E. coli gene as guide
5. Compare
a. Similarity match

ii. Parsimony analysis

1. Program PAUP
2. Statistically treatment
a. Ex: neighbor joining, maximum likelyhood
3. Provides similarity matrix/distance map
a. Ex: sequence ABC how similar they are to
each other
iii. Making tree
1. Program Tree Plot, PAUP
2. Root
a. Common ancestor
3. Outlier
a. Ex: gram + tree, use gram as outlier
b. Ex: bacteria tree, use archaea as outlier
c. For comparison (depth in tree)
d. Unrooted tree?
iv. Tree
1. Branching
a. Common ancestor
2. Branch lengths
a. How long since diverge
b. Phylogenetic
c. Mutations
d. Guess rate of mutation
i. Jukes-Canter, Kimura 2
3. Move slightly
a. By changing sequences
4. Determine how good branches are
a. Add random sequence of bases (not on
tree; not related) -> run tree -> see if
branches end up same for everyone else
b. Add diff unrelated sequences x a lot
c. Bootstrap analysis/ Jackknife
i. Statistical
ii. Numbers on nodes- % branch
support
iii. Typically not less than 50% branch
recorded
V.

Fig. building a cladogram

a.