For Today:

• Work through example of Bayesian thinking (here).
• Does selection still play a role in human evolution? Read abstracts (or more) of articles on Natural selection in a contemporary human population, Natural and sexual selection in a monogamous historical human population, and Measuring selection in contemporary human populations.
• Read Wikipedia entry on Toxoplasma and behaviour
• Take home exam #7 is due

If time,

• listen to radiolab on parasites
• Do STDs increase frequency of behavious that leads to transmission?
• Does the same apply at the gene level? Do HEs that relay on "sex" of the host, impact sex frequency? (see here)

For Friday

• Refresh you knowledge of Baysian approaches to phylogenetic inference.
  Read the following sections in the Wikipedia entry http://en.wikipedia.org/wiki/Bayesian_inference_in_phylogeny: Intro, Bayesian Inference of Phylogeny, Background and Bases, Pitfalls and controversies, MRBAYES software for Bayesian Inference of Phylogeny)

For Monday

• read the Wikipedia entries on PSSMs, HMMER, , and at least skim through the entry for hidden Markov models
• Read through Wikipedia entries on modern synthesis and mutationism
• Read through first two entries of the curirous disconnect here and here (feel free to keep on reading)

Slides for today on role of duplications, sex and HGT in evolution, types of selection.

Goals since midterms (previous goals see class 12)

Goals class 21/22

• Know what the terms positive, negative, and neutral selection mean and what frequent synonyms for these terms are.
• Know how to infer the type of selection using synonymous and non-synonymous substitutions.
• Know that one can infer the type of selection from the rate with which a gene goes to fixation.
• Be able to discuss the terms positive and diversifying selection

Goals class 20

• Know the difference between mutation and substitution.
• Understand why for neutral mutations the mutation rate equals the substitution rate.
• Understand that even with very large populations, most mutations that provide a small selective advantage go extinct due to genetic drift.
• Understand how population size impacts the time it takes for fixation of a neutral mutation

Goals class 19:

• Know the names and characteristics of the different types of homology
• Know about the different ways the tree of life can be rooted.
• Know the reasons why a gene tree might be different from the species tree
• Be able to read bipartition tables
• Know the basic structure with which program in phylip work.

Goals Class 18:

• Know how bootstrap samples are created
• Know the principle behind parsimony analysis and Occam's razor (or Ockham's razor, aka lex parsimoniae)
• Know the similarity and differences between parsimony and maximum likelihood based phylogenetic reconstruction.
• Know about the relationship between maximum likelihood, posterior and prior probability.

Goals class 17:

• Understand the term "tree topology", and know that brancklengths provide important information.
• Be able to recognize indentical trees and trees with the same topology.
• Know about distance matrix, parsimony, maximum likelihood and Bayesian approaches to phylogenetic reconstruction.
• Know what bootstrapping is and what it is used for.

Goals class 16:

• Know the difference between global and local alignments, and know one commonly used program that implements this type of alignment
• Understand the principle behind dynamic programming algorithms that are guaranteed to find the best global alignment
• Understand the steps in progressive alignment of multiple sequences, and understand the problems generated through this approach

Goals class 15:

• Understand the controversy about the term monophyletic, and how the different interpretations lead to different taxonomies.
• Know that spliceosomal introns likely evolved from Group II Introns
• Understand the problems the intron early hypothesis encountered

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 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

Goals for class 13:

• Understand genome structure of prokaryotic genomes (Ori, leading/lagging strand, terminus of replication).
• Know about strand bias and how to use cumulative strandbias 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.