Topics will include (incomplete - open to student input):

• inspection and comparison of protein structures, convergence versus common ancestry
• alignment of protein structures
• What is life? (phages and viruses as part of a living system)
• Gaia hypothesis
• Natural selection - evolution as algorithm
• sequence space
• data bank searches
• Entrez at the NCBI
• evolution of the universe
• prebiotic evolution, the origin of life
• self-replicating biopolymers, the RNA-world,
• in vitro selection, experimental evolution
• from single genes to metabolic networks and hypercycles
• exon/domain shuffling
• What is the unit of selection? Genes, individuals, populations?
• gene duplications versus gene transfer
• biochemical innovation
• alignment of nucleotide and amino acid sequences (pairwise and multiple; global and local)
• detecting divergent homologs using PSI blast
• molecular trees (phylogenetic reconstructions)
• species concepts
• introns, inteins, molecular parasites, homing
• selfish genes, selfish operons
• rare genes in microbial population
• cooperation between genes - ecology of the genome
• analyses of complete genomes
• comparative genome analyses
• horizontal gene transfer
• Is there an organismal tree of life?
• co-evolution
• emergence of cooperation
• evolution of the holobiont / the hologenome
• What is the genome of an organism? Pan-genomes of population and species.
• black and red queen hypotheses
• Does a division of labor arise within microbial populations?
• neutral evolution
• evolution of complexity (non-adaptive pathways towards complexity, constructive neutral evolution)
• networks (small world networks, interaction networks, hubs, the rich get richer)

Frequent examples will be ATP synthases, Inteins, Aeromonas, Thermotoga, Haloarchaea

Last modified: August 27, 2021