713 Lecture 2

1. 713 Lecture 2 The species problem

2. What is a bacterial species? • Phenotypic similarity • Similarity in DNA sequence • Similarity in genome content • Entire genome? • Core genome? • Frequency of recombination

3. Mayr’s biological species concept • Species were once conceived by taxonomists as groups of similar organisms • Mayr introduced the need for biological cohesive forces maintaining the group • Recombination • Selection (natural and sexual)

4. Importance of the BSC • Emphasized importance of reproductive isolation • Focused studies of underlying mechanisms (not physical but evolutionary) • Identified distinct species within phenotypically similar groups and lumped other groups

5. Does the BSC work for prokaryotes?

6. Strategies for speciating bacteria • Phenotypic similarity • FAME • Biolog/API • DNA-DNA hybridization • 16s ribosomal DNA sequence similarity

8. Bacterial classification strategies • Problem: lacks fundamental principle • 1st, cluster on basis of phenotype • 2nd, find DNA:DNA hybridization values that fit phenotype clusters • New method: average nucleotide identity, or ANI • 3rd, find value for 16s sequence similarity that fits DNA:DNA hybridization value

9. Does the BSC work for prokaryotes?

10. Prokaryotic population genetics • Population sizes (N) are usually huge, so genetic drift is typically ineffective • Mutation rates are typically low, but N is large, so genetic variation is abundant • Recombination rates are VERY LOW, relative to typical diploid sexual species (and even relative to infrequent outcrossing species, like plants) • How frequent is bacterial recombination?

11. More challenges to fit prokaryotes into the eukaryotic BSC • Promiscuity of homologous recombination (not just within species) • Constraints on exchange • Ecology • Vectors • % DNA similarity:1-3% animals, 25% bacteria • Size of DNA fragment • HGT = horizontal gene transfer = nonhomologous recombination

12. The alternative: the ecotype (Cohan) The ecotype is a lesser unit than a species that highlights niche specificity and local adaptation Motivation: apparently low recombination rates undermine the BSC

13. Origin of ecotypes • New mutation generates new opportunity or selective advantage • Little/no recombination, so new subpopulation diverges without constraint • problem: a clean theoretical definition but realistic to find?

14. Periodic selection • Simply: the purging of genetic diversity within a population by the selective sweep of a beneficial mutation

15. Do ecotypes become species? (it depends on recombination)

16. Are these ecotypes the beginning of speciation? Poltak and Cooper

17. The relationship between ecotype and genotype • Do genotypes coincide with ecotypes? • Periodic selection should purge diversity within the lineage • Ecotypes should form single, coalescent sequence clusters • What about dispersal?

18. MLST Sequence conserved loci (genes) Each nucleotide substitution defines a new allele Changes at each locus occur independently and randomly Similarity = identity by descent Shared changes = recombination

20. MLST, eBURST  ecotype?

21. “Why does MLST work so well?” • How long do ecotypes last? • Can MLST divine species barriers?

22. What’s the best model to explain how your favorite bacterial species arose?