Centre for Philosophy of Science Applied Evolutionary Epistemology Lab

Francisco Dionísio

Symbiogenesis, LGT & Hybridization

Course description

This course addresses the causes for the presence of certain accessory DNA elements within cells in general, with a particular focus on bacterial cells. Bacterial cells often contain plasmids (some of them able to transfer to other cells), viruses (mostly without causing any harm to the host cell), insertion sequences, transposons, restriction-modification systems, toxin-antitoxin loci, and other accessory elements. Apparently, they are not useful to the cell, but they actually form long standing relationships with the cell; why is that so? Are they mutualistic or parasitic elements? And what about accessory elements found in eukaryotic cells, including our own?

By the end of this course, I expect that the students are able to reason about the presence of accessory DNA elements and relate these alien presences in terms of what is life all about.

The audience of the course is very diverse: biologists and non-biologists, theoreticians and experimentalists, all of them having in common a strong interest in learning evolutionary biology. So, I expect that all the students will strongly interact with each other and make an effort to avoid that any student gets lost with experimental details, mathematical treatments, or bioinformatics data. Read the papers and try to explain them to your colleagues.


Day-by-Day Program


Lecture 1: Introduction: life, replication, and natural selection

  1. Introduction to the course
  2. What is Life? Maynard-Smith’s definition  versus  other definitions
  3. What is Natural Selection?
  4. Levels of selection: the example of mitochondria and saccharomyces: Taylor, Zeyl, and Cooke PNAS 2002
  5. So many plasmids: Smillie et al 2010 Microbiology and Molecular Reviews


Lecture 2: How come plasmids are so common? (1)

  1. Levin et al 1979 PLASMIDS
  2. Gordon DM 1992 J Gen Microbiology
  3. Dionisio et al 2002 Genetics
  4. Ghigo et al 2001 Nature
  5. Gerdes et al 2005 Nat Rev Microb


Lecture 3: How come plasmids are so common? (2)

  1. Silva et al 2011 PLoS Genetics
  2. Dahlberg and Chao 2003 Genetics
  3. Bouma and Lenski 1988 Nature
  4. Dionisio et al 2005 Genetics


Lecture 4: Plasmids, TA-loci, Bacteriophages and Restriction –Modification systems

  1. Korona and Levin 1993 Evolution
  2. Naito et al 1995 Science
  3. Rocha et al 2001 Genome Research


Lecture 5: Viruses and plasmids as mutualistic parasites

  1. Brown et al 2006 Current Biology
  2. Dionisio 2007 Evolutionary Ecology Research
  3. Gama et al 2013 PLoS ONE
  4. Arnaud et al 2008 PLoS Genetics
  5. Feschotte and Gilbert 2012 Nat Rev Genet


Other Reading Materials Recommended

  1. Smith_2001 Proc Roy Soc
  2. Nogueira et al 2009 Current Biology
  3. Dionisio et al 2005 Biology Letters