For Friday:

Review gene and genome rearrangements.

• How would a misplaced origin of replication look like if two similar genomes are compared in a gene plot?
• Which part of a circular bacterial genome is least conserved?
• How would an inversion inside a protein coding gene look like in dotlet? (If you compare the two proteins? If you compare one protein to the encoding DNA sequence?)
• How would a large inversion look like in a gene plot?
• Check Monday's slides for example on genome rearrangement.

• Read through taxplot info below
• Bring user numbers and passwords for cluster
• PLEASE, fill out the online class evaluation! (Thank you to the 7 students that did already!)

For today

• Bring at least one question to class for discussion/review (check the take home exams for things that aren't clear to you).

Discuss lessons from the tardigrade (aka water bears, moss piglets, or Bärtierchen) genome fiasco - secrecy, competition, data sharing

Slides for today on supertrees, supermatrix, decomposition approaches.

Goal class 26:

• Know about the difference between supertree and supermatrix approaches, and appreciate the advantages and disadvantages of each approach.

Goals class 25:

• Understand how taxplot, or similar approaches (HGT index), can provide preliminary identification of horizontally transferred genes.
• Know about the problems associated with shotgun genome sequencing of multicelluar organisms that live with their symbionts and other bacteria - these genome sequences should be considered metagenome sequences.
• Understand that binning based on composition and coverage can help identify genes from the host and differentiate them form bacterial genes. (But might classify genes recently transferred to the host as belonging to bacteria.)
• Understand the demonstration that the UNC tardigrade genome contigs contained many genes not part of the tardigrade genome.

Goals Class 24

• Understand the different approaches to detect genes under positive selection.
• Know that HGT helped create biochemical pathways that changed the face of this planet (acetoclastic methanogenesis, oxygen producing photosynthesis).
• Understand that neutral processes lead to more complex intermolecular relations that at least initially do not provide a selective advantage to the organism.
• Understand the purifying selection in small populations is less effective, and that even slightly deleterious changes in gene and genome architecture (gene and mRNA editing, self splicing and spliceosomal introns, split inteins) can be fixed by genetic drift.

Goals class 23:

• Know that the dN/dS>1 approach to detect positive selection is often difficult to apply (alignment uncertainty)
• Know that dN/dS<1 approach to detect purifying selection may not always reflect a selection for function.
• Understand the link between positve selection and selective sweep.
• Know different approaches of how selective sweeps can be detected.
• Know about archaic admixtures to modern human populations
• Understand the mitochondrial Eve and Y chromosome Adam concept, and why this does not work for other genes.
• Know that HGT is an important force in evolution that created new metabolic pathways that changed the face of our planet. (and it also leads to adaptation of organisms to new ecological niches)

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 branch lengths provide important information.
• Be able to recognize identical 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 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.