1. Phylogeny and the Tree of Life
Chapter 26

2. I. Phylogeny
The evolutionary history of a species or group of related species
Systematics-classifying organisms and their evolutionary relationships
1. Uses fossils, morphology, genes and molecular evidence
Domains est. 1990

3. C. Taxonomy – division of organisms into categories based on similarities and differences 1. Binomial nomenclature – two part naming system (genus and species) developed by Carolus Linnaeus)
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4. 2. The lower in this hierarchy that two species share a classification, the more closely related they are

5. II. Displaying Evolutionary relationships
Two types (both considered hypotheses of relationships)
1. Phylogenetic trees – show relationships AND time
a. Time is calibrated using fossil evidence and molecular clocks
*Note – length of line indicates passage of time

6. Cladograms – show relationships but do not indicate how much time passed or genetic distance
a. Clade – group of species which includes an ancestral species and all its descendants (monophyletic group)

7. B. Traits lost or gained during evolution are used to construct both types of diagrams
1. Shared derived characteristics – evolutionary novelties unique to a clade (ex. hair in mammals)
2. Shared ancestral characteristics – originated in an ancestor, shared by more than one clade (ex. all mammals have backbones, but so do all vertebrates)

8. 3. Conserved features and processes – indicate a shared common ancestor
Ex. The structure of the mitochondria is pretty much the same in all eukaryotes
Ex. The process of glycolysis occurs in pretty much the same way in all living organisms

9. C. Features of the diagrams
1. Root – The initial ancestor common to all organisms within the diagram (incoming line shows it originates from a larger clade)
2. Nodes – Each node corresponds to a hypothetical common ancestor that speciated to give rise to two (or more) daughter taxa (indicates speciation occurred)
3. Outgroup – The least closely related species to the rest in the diagram
4. Clades – A common ancestor and all of its descendants (i.e. a node and all of its connected branches)

10. Sister groups: most closely related
Outgroup: least related to the others
Node: showing common ancestor
Divergences indicated gain or loss of traits
Root

11. 5. Branches can be rotated around a node without changing relationship displayed
Emphasize that inverting the diagram top to bottom does not “change” the evolutionary history. The common ancestor remains the same.
The two phylogenetic trees illustrate the same evolutionary relationships. The vertical branches have been rotated.

12. D. Different types of evidence can suggest different relationships
A diagram based on multiple comparisons would be more accurate that a diagram only based on one type of evidence

13. 1. Many different types of evidence can be used
Characteristic
Example/reason
Morphology (Shape)
shape of plants seed coat
Shape of birds bill
Anatomy
Number of petals on a flower
Type of digestive system in invertebrate
Cytology
Structure and function of cells
Chemistry
Special organic compounds in plants
Chromosome number
Two species with same #, more closely related, the differing # of chromosomes
Molecular differences
Protein sequences
DNA sequences
Beats out all others

14. When new evidence is found, diagrams must be revised
a. Ex. Switch to 3 Domain system – first introduced in 1977, widely adopted in 1990
*Current hypothesis

15. How to read a Cladogram
This diagram shows a relationship between 4 relatives. These relatives share a common ancestor at the root of the tree.
Note that this diagram is also a timeline. The older organism is at the bottom of the tree.
Branches on the tree represent SPECIATION, the formation of a new species.
The four descendants at the top of the tree are DIFFERENT species. This is called SPECIATION.

16. How to read a Cladogram
Species B and C each have characteristics that are unique only to them.
But they also share some part of their history with species A. This shared history is the common ancestor

17. III. Evolutionary History & Genomes
Rate of DNA evolution varies within a genome
DNA that codes for ribosomal RNA changes slowly (useful for examining divergences that happened millions of years ago)
DNA that codes for mitochondrial DNA evolves rapidly (examined for more recent events)

18. B. The molecular clock hypothesis - among closely related species, a given gene usually evolves at reasonably constant rate. Used to measure time of evolutionary change based on the rates of genome changes

19. Molecular clocks can be used to study genomes that change rather quickly such as the HIV-1 virus (a retrovirus).
Using a molecular clock, it as been estimated that the HIV-1 virus entered the human population in 1960’s and the origin of the virus dates back to the 1930’s.

20. Membrane bound organelles
C. There is much evidence to indicate that all eukaryotes have a common ancestor 1. Membrane-bound organelles 2. Linear Chromosomes 3. Genes that contain introns
Characteristics
Bacteria
Archaea
Eukarya
Nuclear envelope No
Yes
Membrane bound organelles
Introns
Histone proteins associated with DNA
Circular chromosome