1. “It is less clear, however, whether our species demarcations provide this information for the vast majority of prokaryotes that are never going to cause gum disease, will never be weaponized and will never prove useful in treating raw sewage or making yoghurt.” (Gevers et al., 2005)

2. Species Are there species? How should we define species? Three major classes of concepts: –Biological species concept “Species are groups of actually or potentially interbreeding populations, which are reproductively isolated from other such groups” (Mayr, 1942) –Phylogenetic/genealogical species concept –Ecological species concept

3. Microbial species Are there microbial species? How are microbial species traditionally defined? –“…a category that circumscribes a (preferably) genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested under highly standardized conditions” (Stackebrandt et al., 2002) –“…characterized by a certain degree of phenotypic consistency, showing 70% of DNA-DNA binding and over 97% of 16S ribosomal RNA (rRNA) gene- sequence identity” (Vandamme et al., 1996)

4. Microbial species How much do genomes help? (Konstantinidis & Tiedje, 2005) Threshold definitions still an issue (Gevers et al., 2005)

5. How do new species emerge? Why do we care? –Species are a unit of evolution (present gene pool, shared past/future) How do species emerge? –Allopatric vs. sympatric Barriers to gene flow –Prezygotic vs. postzygotic –In microbes? Allopatric speciation Sympatric speciation

6. Restrictions upon HGT Homologous vs. illegitimate recombination “Prezygotic” = (likelihood of encounter x likelihood of recombination) “Postzygotic” = fitness effect & likelihood of fixation (Fraser et al., 2007)(Lawrence & Hendrickson, 2003) Bacillus subtilis Bacillus mojavensis Streptococcus pneumoniae E. coli

7. How much does HGT occur? Relative contribution of recombination vs. mutation –Estimate of 80:1 for Neisseria meningitidis MLST (multi-locus sequence typing) MLST for Streptococcus pneumoniae

8. Population genetic structure from MLST Plot using eBURST (Feil et al., 2004) Biological species for microbes? (Dykhuizen & Green, 1991) (Feil, 2004) high HGT modest HGT high HGT modest HGT

9. MLSA in taxonomy: Burkholderia Does B. mallei deserve rank of species? Tree of MLSA data shows it is a derived B. pseudomallei (Fraser et al., 2007)

10. What should a microbial species be? Ecotype concept –Subject to selective sweeps –Even ‘high’ recombination to weak to hinder divergence How determine ecotypes? –From genes –Don’t know real ecology… (Cohan, 2001)

11. Case of ecotypes: Prochloroccus Correspondence between: –Latitude –Niche –Distribution –Physiology –Genome content (Johnson et al., 2006)

12. Case of ecotypes: Vibrio Acinas et al., 2004 (uncorrected) 100% 99% 98% 97%

13. Case of ecotypes: Vibrio Distinct genome sizes with identical 16S rRNA (Thompson et al., 2005) HGT preferentially w/in clusters

14. Single rule may not always apply (Nesbø et al., 2006)