Goal class 25 &26:
- Know about different approaches to detect HGT events (phylogenetic conflict, gene presence absence, composition based)
- Know about the advantages and disadvantages to use bipartion and quartet based analysis to identify phylogenetic conflict.
- Understand why embedded quartets are advantagous.
- 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.
- Know about the difference between supertree and supermatrix approaches, and appreciate the advantages and disadvantages of each approach.
Goals class 24
- Know the principle behind PSI blast searches
- Understand the meaning of the E-value cut-off for inclusion in the next iteration
- Know about the problem in estimating the expected numbers of false positives in PSI blast searches
- Know the meaning of the E-value of a hit in a PSI blast search
- Appreciate that building the profile / scoring matrix can use a different databank as compared to the final search
- Know a few possible applications for PSI or Hmmer searches
Goals class 23
- Know that dN/dS>1 approach to detect positive selection is often difficult to apply (alignment)
- Know that dN/dS<1 approach to detect purifying selection may not always reflect a selection for function.
- Understand the link between positive 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.
Goals Computer lab #12
- Be able to perform a maximum likelihood ratio test to test the appropriateness of nested models.
- Be able to run MrBayes and interpret the program's output
- Understand that biased sampling results in an easy approach to calculate posterior probabilities and confidence intervals
- Understand the codon model that MrBayes uses to identify codons under positive selection
Goals class 22
- Know that selection still occurs in human populations.
- 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
- Understand the concept of the holobiont, and implications this has for HGT in eukaryotes
- Know which roles HGT plays and has played in evolution
Goals class 21
- 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
- Understand that individual genes have evolved from an ancestral gene, but that if one considers many genes, these ancestral genes did not exist in a single organism.
- This is true for Y-chromosome Adam and mitochondrial Eve (and for all the other genes found in humans), but also applies to the "tree" of life.
Goals Computer lab #11
- Be able to spot possible long branch attraction artifacts in phylogenetic trees
- Know which approaches are sensitive to long branch attraction
- Appreciate that sequence alignment acerbates LBA.
- Understand that LBA is a systematic error that is not reflected in low bootstrap support values.
Goals class 20
- 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.
- Understand the reasons why molecular phylogenies can differ from the species tree.
Goals class 19:
- Understand that in many microbial populations recombination occurs frequently - the probability of a nucleotide to change through a recombination event is much higher than the probability for the mutation of a single base.
Goals Computer lab #10
- Know how the display of a tree can be rearranged without changing the tree
- Know how to re-root a tree, and how to editorialize a tree
- Be familiar with figtree
- Understand some of the advantages/disadvantages of different programs to reconstruct evolutionary history from sequence data
Goals Class 18:
- Understand practical species definitions used for prokaryotes
- Know how ANI and in silico hybridization can help to delineate species
Goals class 17:
- Know about distance matrix, parsimony, maximum likelihood and Bayesian approaches to phylogenetic reconstruction.
- Know what bootstrapping is and what it is used for.
Goals Computer lab #9
- Know how to calculate multiple sequence alignments
- Understand that different parts of the sequence can show very different levels of sequence conservation.
- Know about different programs to filter alignments for conserved sites
Goals class 16:
- Understand the term "tree topology", and know that branchlengths provide important information.
- Be able to recognize identical trees and trees with the same topology.
- Understand what the intron early versus late debate is about, and be able to critically discuss the attempt for synthesis
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 Computer lab #8
- Know how to use dotlet, how to adjust the display, and how to interpret results.
- Know that the size of introns usually is NOT a multiple of three
- Understand the value of comparative approaches to determine intron/exon boundaries
- Know how to use jalview and understand the concept of the principle component analysis of sequences depicted as point in 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
- Know the difference between global and local alignments
- Know about different approaches to calculate multiple sequence alignments, and know about possible problems associated with the different approaches.
Goals for class 13:
- Know how to compare two bacterial or archaeal chromosomes using a gene plot.
- 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.
- Understand the principles of cladistics and know the commonly used terms.
Goals Computer lab #7
- Know how to assemble a data base that can be used for database searches using BLAST from a multiple FASTA sequence file
- Know how simple Perl scripts can be used to process data tables and multiple FASTA files.
- Understand the principle behind comparing genomes using gene plots.
- Know how to create scatter plots in Excel and/or using gnuplot
Goals Computer lab #6
- Know how to move up an down in the directory hierarchy using the unix command line
- Be able to transfer files to and from the bioinformatics cluster
- Be able to use the programs that are part of the blast + package
- Know how to get information on the different parameters you can set
- Know how to use the arrow keys to move back in the command history
- Know how to use the tab key for line completion