Assignment for Friday:
- Understand the patterns of within genome recombination events, their impact on genome organization and the possible reasons for only some recombination events occuring.
Assignment for Monday:
- Take home exam #4 will be posted later today and is due on Monday - ask questions on Friday
- Read through the following intron sections on Wikipedia
Assignment for
Wednesday next week
- Read the highlighted portion from the article on gratuitous complexity (highlighted in the Reading materials on WebCT)
Updated goals for class 13:
- Know the possible fates of duplicated genes (non-, sub-, and neo-functionalization), and the frequency of the different outcomes.
- Know how to compare two bacterial or archaeal chromosomes using a gene plot.
- Understand the power of simple script to run programs and to process the output of programs
- Appreciate the use of hashes as an efficient data structure linking keys and values
- (more discussion of the next couple of goals in class 14)
- Understand genome structure of prokaryotic genomes (Ori, leading/lagging strand, terminus of replication). (more discussion of this in class 14)
- Know about strand bias and how to use cumulative strand-bias to find the origin and terminus of replication.
- Understand the type of recombination that lead to gene plots where most of the matches are along the two diagonals.
- Know the possible reasons for this process.
Today:
Why do within genome recombinations mainly occur equidistant to the origin of replication? (Note: One could also say why do within genome recombinations mainly occur equidistant to the terminus of replication?) Slides here
cladistics (terms and concepts)
Discuss terms used in cladistics - rooted versus unrooted (clades versus clanns), homoplasies, monophyletic, paraphyletic, polyphyletic, Ashlock's holophyly
Tree of life - three domains, main endosymbiosis events, archaeplastida, other algae.
Slides on sequence space
Goals class 14:
- Know what the terms synapomorphy, sympleisiomorphy, autapomorphy, and homoplasy mean.
- Know how these terms are related to mono-, para, and polyphyletic groups.
- Know about Ashlock's redefinition of monophyletic
- Know the definition of a clade, and why it is not applicable in case of unrooted trees.
- Be able to discuss the goals of a natural taxonomy