1. Molecular Phylogeny
Similarity among organisms (and their genes) is the result of descent from a common ancestor. Variation occurs via genetic drift and selection. The ultimate repository of fixed variation is the genome. Sequence divergence is related to the time since sharing a common ancestor. There is not a specific relationship between the rate of sequence divergence and time since genes vary in their freedom to change and the factors governing rates of change are not well constrained.
Although the most complete understanding of relationship would derive from sequencing of entire genomes (now a reality), the preferred alternative is to select an appropriate region of the genome for comparison (i.e., pick a specific gene or selected set of genes common to all organisms evaluated).
The gene(s) must meet certain requirements:
1. Be homologous - be derived from the same ancestral sequence
2. Not subject to lateral transfer - they are inherited via descent from common ancestor.
3. Have high information content
4. Be conserved - sequence does not change so rapidly as to erase the record of change.

2. Biological Molecules as Documents of Evolutionary History

3. From MacGregor 2002

4. The Prokaryotic Ribosome is composed of two subunits: small (30S subunit) and large (50S subunit), initially named according to their sedimentation behavior during ultracentrifugation. Each subunit is composed of ribosomal RNA (~2/3 of mass) and protein (~1/3 of mass). Translation requires the association of the two subunits into a holocomplex (70S ribosome). The eukaryotic version is larger (80S), but derived from the same ancestral components.
Large subunit: 16S rRNA (ca nt) and
~20 proteins.
Small subunit: 5S rRNA (ca. 120 nt) and 23S rRNA (ca nt) and ~30 proteins.

5. The RNA components of the ribosome (rRNAs)
16S rRNA sequence variation has proven to be generally useful for microbial phylogeny and monitoring (identification)
Provide for Organism- and Group-specific (Phylogenetic) Molecular Signatures. Can be detected without amplification
16S rRNA

6. Other Relevant Definitions
Molecular Phylogeny
Other Relevant Definitions
There are several types of homology that must be distinguished
Orthologous - the common ancestry of two sequences can be traced back to a speciation event.
Paralogous - the common ancestry of two sequences can be traced back to a gene duplication event
Xenologous - sequences related through horizontal transfer (i.e., not derived via vertical descent. Conjugative transfer of genes is the best understood mechanism of lateral transfer.)

7. The consequences of using orthologous versus paralogous genes to infer phylogeny. (A) The phylogeny of a set of homologous genes in three species (1-3). A gene duplication event in the ancestor of the three species gave rise to two sets of paralogoous genes (A and B), and two subsequent speciation events gave rise to orthologous genes in each of three species. (B) The phylogeny inferred from comparison of either set of orthologus genes (notice that this is the correct species phylogeny). (C) The phylogeny inferred from comparison of two orthologous and one paralogous sequences (this is the correct gene phylogeny, but not the correct species phylogeny!!).
Hillis et al. 1996

8. From G.Olsen,
University of Illinois

9. From MacGregor 2002

10. The Diversity of Life as Inferred from 16S rRNA Sequence Divergence
C.R. Woese 1990
16S rRNA

11. Recognized Diversity of Life
1,413,000 Species

12. Recognized Diversity of Life
Prokaryotes
Eukaryotes
Bacteria
Archaea
Euryarchaeota
Green nonsulfur
bacteria
Methanosarcina
Animals
Halophiles
Methobacterium
Purple bacteria
Gram-
positives
Fungi
Methanococcus
Slime Molds
T. celer
Plants
Crenarchaeota
Entamoebae
Ciliates
Cyanobacteria
Thermoproteus
Pyrodictium
Flavobacteria
Flagellates
Trichomonads
Thermotogales
Microsporidi
Diplomonads

13. Known Phylogenetic Span of Bacteria: 1987
Hugenholtz et al. 1998

14. Today
Adapted from Hugenholtz et al. 1998

15. Mechanisms of prokaryotic DNA exchange: 3 general categories
1. Conjugation: Requires cell-cell contact. DNA transferred and “machinery” of transfer general plasmid encoded
2. Transduction: Virus mediated. “Defective” virus incorporates a portion of host DNA during infection/lysis and transfers it to another cell during infection.
3. Transformation: Uptake of “naked” DNA from the environment

16. Exchange of DNA between two prokaryotic cells (E. coli) via conjugation. Plasmid DNA from the donor is passed to the recipient via a sex pilus.
From Neidhardt et al. 1990

19. NAM = N-acetyl muramic acid
Basic structure of the peptidoglycan cell wall is a network of polysaccharide chains cross-linked via short chains of amino acids (peptides). Penicillin inhibits the cross-linking reaction, causing cell to lyse. The cell wall provides shape and mechanical protection (e.g., from osmotic shock) but it does not limit the passage of nutrients or most toxic compounds.
NAM = N-acetyl muramic acid
NAG = N-acetyl glucosamine
From Neidhardt et al. 1990

20. *
Hugenholtz et al. 1998

21. Endospore Forming Gram-positive Bacteria

22. References