1. Phylogeny and the Tree of Life

2. Phylogenetic Trees
Used to represent the evolutionary history of a group of organisms
May follow the hierarchical classification of the group
Sometimes looks at particular characteristics

3. Phylogenetic Trees
The sequence of branching does NOT necessarily indicate the actual age of the species
Trees should be read in terms of patterns of descent unless otherwise stated
A taxon on a tree does not evolve from the taxon next to it, rather they both evolved from a common ancestor

4. Homologies vs. Analogies
Homologies are similarities due to shared ancestry
Include morphological and molecular (genetic) characteristics
Analogies are similarities that are a result of convergent evolution

5. Cladistics
Once homologous features are distinguished from analogous features, phylogeny must be inferred
Cladistics is often used
Common ancestry is the primary criterion and species are placed into clades

6. Shared Ancestral vs. Shared Derived Characteristics
These characteristics are used to help build clades
Shared Ancestral – a characteristic that originated in an ancestor of the taxon
Shared Derived – an evolutionary novelty unique to a particular clade, but not found in the ancestor

7. Maximum Parsimony and Likelihood
The most parsimonious tree will require the fewest evolutionary events or fewest base changes
The most likely tree will hold according to the rules of how DNA changes over time

8. Orthologous vs. Paralogous Genes
An organism’s genome holds extensive information about its past (this includes mtDNA and various RNA)
All of these nucleic acids change at different rates which allow them to be useful in different comparisons
Orthologous genes – homologous genes that are found in different species because of speciation
Paralogous genes – gene duplication that results in the same gene being found in multiple copies in the same genome

9. Molecular Clocks
The concept of the molecular clock is based on the assumption that:
The number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the species branched from the common ancestor
In paralogous genes, the number of substitutions is proportional to the time since the genes became duplicated
The gene must have a reliable average rate of change

10. Three Domains of Life
Today, the three domain system is most widely used with the kingdoms being placed within those domains
Archaea
Kingdom: Archaeabacteria
Bacteria
Kingdom: Eubacteria
Eukarya
Kingdoms: Fungi, Animalia, Plantae, Protista