1. Whole Genome Duplications (Polyploidy) Made famous by S. Ohno, who suggested WGD can be a route to evolutionary innovation (focusing on neofunctionalization) Ohno proposed in the 1970s that vertebrate lineage underwent two WGDs … later confirmed with whole-genome sequence data. WGDs are most common in plants but observed in vertebrates, fishes, yeast, and Paramecium, among other species

2. Major mechanisms of polyploidy 1.Gametic nonreduction - production of unreduced gametes caused by an error in meiosis 2.Somatic doubling - production of a cell with twice the normal chromosome number caused by an error in mitosis 3.Polyspermy – fertilization of multiple gametes Errors in meiosis/mitosis can be caused by genetic or environmental factors

3. Spindle error or failure Abnormal chromosome pairing Abnormal or absent cytokinesis Pre-meiotic doubling Produced at an average rate of 0.5% per gamete Bretagnolle and Thompson New Phytol. (1995) 129: 1-22 Production of 2n gametes

4. Types of Polyploidy Allopolyploidy – chromosomal duplications derived from different species … produce homeologs Autopolyploidy – chromosomal duplications derived from the same species … produce ohnologs

5. Timeline after WGD 1.Initial duplication of entire genome autopolyploid = identical genome 2.Gene loss is likely frequent immediately after (although some papers find no evidence of this) which copy is lost is initially random 2.As sequences diverge, loss may not be random sub/neofunctionalization may favor retention of specific ohnologs 4.Chromosomal rearrangements reduces 2X chromosome number 5.Reciprocal Gene Loss (RGL) in different individuals can promote speciation

6. From Kellis & Lander. Nature 2004

8. Reciprocal Gene Loss (RGL): differential loss of ohnologs can lead to speciation (due to problems pairing chromosomes) WGD event RGL in individuals Mating Difficulties during subsequent meiosis (F2s) Ancient WGD’s correlate with increased species diversity and even radiations WGD-driven speciation (via RGL) may be more likely to occur soon after WGD: rate of gene loss is highest soon after WGD and the copy lost is more likely to be random

9. The costs & benefits of WGD Costs: Doubles the DNA content and chromosome number More DNA = larger cells, larger volume, more proteins required Benefits: Doubles whole pathways of functionally related genes Maintains balanced expression across the genome

10. The Balance Hypothesis Single-gene duplication can = stoichiometric imbalance WGD maintains stoichiometry (at least initially) The Balance Hypothesis predicts that proteins in multi-subunit complexes and proteins that require precise stoichiometry are more likely to be influenced by WGD vs single-gene duplications

11. The fate of duplicate genes after WGD 1.‘Classical’ sub- or neo-functionalization (“6 – 36% of ohno. pairs have one with higher rate of divergence note this evolution can occur at the level of function OR expression

12. The fate of duplicate genes after WGD note this evolution can occur at the level of function OR expression 2. Buffering (?) 1.‘Classical’ sub- or neo-functionalization Observation: yeast genes with retained ohnologs have less phenotypic consequence of deletion … probably due to redundancy ? But is the driving force for their retention? ( seems weird that buffering could drive their retention )

13. 2. Buffering (?) note this evolution can occur at the level of function OR expression 1.‘Classical’ sub- or neo-functionalization The fate of duplicate genes after WGD 3. Benefit of copy number increase (maintaining stoichiometry across pathways) e.g. Most glycolytic enzymes & most ribosomal proteins in S. cerevisiae are retained Ohnologs

14. 2. Buffering (?) note this evolution can occur at the level of function OR expression 1.‘Classical’ sub- or neo-functionalization The fate of duplicate genes after WGD 3. Benefit of copy number increase (maintaining stoichiometry across pathways)

15. 2. Buffering (?) note this evolution can occur at the level of function OR expression 1.‘Classical’ sub- or neo-functionalization The fate of duplicate genes after WGD 3. Benefit of copy number increase (maintaining stoichiometry across pathways) 4. Need to maintain stoichiometry across pathways

16. 2. Buffering (?) note this evolution can occur at the level of function OR expression 1.‘Classical’ sub- or neo-functionalization The fate of duplicate genes after WGD 3. Benefit of copy number increase (maintaining stoichiometry across pathways) 4. Need to maintain stoichiometry across pathways 5. Evolution of new regulatory circuits (‘rewiring’)

17. Veron et al. Mol Biol Evol 2007

18. unicellular ciliate (eukaryote): evidence of three ancient and successive WGDs -find no evidence for rapid gene loss shortly after WGD -the latest WGD correlates with expansion of sister species -10-16% of ohnologs show asymetric evolutionary rates (i.e. one copy faster) -Gene retention driven by stiochiometric requirements (complexes) and expression abundance (higher expression = more likely to be retained)