1. Biological Classification: The science of taxonomy
Traditional and Molecular Aspects

2. The Taxonomic Hierarchy
Species are grouped into categories.
Categories are grouped into larger categories.
Smallest universally-agreed category is species. (Subspecies are designated in some cases, but the definition of such categories is vague.)
See Fig in text and know categories.

4. Basis for Classifications
Artificial: Decide on a key character in advance and classify based on it. (For example, number of legs, number of stamens)
Natural: Classify based on overall similarity in many characters. (Statistical clustering)
Phylogenetic: Classification should represent evolutionary relatedness “Phylogeny” = Evolutionary history

5. Phylogenetic classification
All groups should be monophyletic, i.e. should be descended from a single common ancestor and include all the descendants of that ancestor.
Avoid polyphyletic groups (2 unrelated ancestors)
Avoid paraphyletic groups (one ancestor, but excluding some of the descendants of that ancestor.

7. Molecular taxonomy and evolution
Information in biological molecules can be used as taxonomic characteristics.
Amino acid sequences of protein
Nucleotide sequences of DNA
Other characteristics like protein molecular weight or DNA fragment length
The more closely related two organisms are, the more similar their DNA and protein will be.

8. Many sequence variations are neutral
Redundancy of genetic code; different codons specify same amino acid.
Sometimes different amino acids don’t affect structure or function of protein.
but most importantly
Much of the DNA is never transcribed or translated.

9. Neutral molecular variation is a very useful thing to study
Similarities in selectively important characteristics can be analogies, but similarities in neutral characters are more likely to be homologies.
Mutation happens at a fairly regular rate, so sequence divergence provides a molecular clock, allowing us to estimate how long ago two lineages diverged.