1. Evolution of Duplicated Genomes Talline Martins 4.24.07

2. Possible Consequences of Polyploidization Null hypothesis Interlocus gene conversion Loss of homoeologue Wendel, 2000

3. Genomic changes Many genome-level changes may occur as a result of genomic ‘shock’ –Increased transposable element activity –Elevated levels of DNA methylation Homoeologous recombination Inter-genomic concerted evolution Non- and reciprocal translocations Processes involved in diploidization What happens to the duplicate genes that remain???

4. Persistence of Duplicate Genes Classical model: –The most common fate of duplicated genes is to become null through deleterious mutations. The only mechanism for preservation of duplicate genes is through fixation of beneficial mutations (neofunctionalization). Problems with the classical model: –Fraction of genes preserved is higher than predicted –Evidence for purifying selection can be found in both loci –Relative lack of null alleles segregating in extant populations

5. The Duplication-Degeneration- Complementation (DDC) Model Degenerative mutations facilitate rather than hinder the preservation of duplicate functional genes. –Duplicate genes lose different regulatory subfunctions –They must complement each other to retain all ancestral functions

6. Possible Fates of Duplicate Genes

7. Probability of Subfunctionalization The probability of maintenance of duplicate genes increases with number of number of regulatory elements z P S = Σ P S,i i=2

8. Complex Regulatory Regions Why are some duplicates expressed in some tissues together but not in others? Embedded and overlapping regulatory regions may reduce the number of subfunctions

9. Relaxed Selection Among Duplicate Regulatory Genes in Lamiales

10. LFY/FLO & AP3/DEF

11. Why are the duplicates still around? Role of selection –Non-synonymous/synonymous substitution Dn/ds (  ) –If  < 1; purifying selection  = 1; no selection (neutral)  > 1; positive selection

12. Codon Substitution Models Branch and fixed-sites models Sites and branch-site models

13. Branch and Fixed-Sites Models Branch models: Models R1-R4 Fixed-sites model: compare  ’s between paralogs –Model C (single  ) –Model E (allows separate  ’s for paralogs)

14. Results LFY/FLO = paralogs diverging more quickly relative to single-copy lineages (R2), and significantly different from each other (model E). AP3/DEF = paralogs diverging more quickly relative to single-copy lineages (R2), but not significantly different from each other (models C and E).

15. Sites and Branch-Sites Models (more powerful way to test for positive selection) Sites models: “hold  constant among all branches while allowing  to take on multiple values among site classes” –Models: M1a, M2a, M7, M8 Branch-sites models:  1 set as foreground branches, allowing for different  ’s over different branches and sites. –Reflects initial positive selection on duplicates followed by purifying selection on ancestral lineages –Model A and Model A null. (  2 is fixed at 1)

16. Results

17. Is  different among functional domains of LFY/FLO & AP3/DEF ? DEF: MADS (DNA-binding site), I, K, and C-terminus FLO: N- and C-terminus (putative DNA- binding site) How: used sites, fixed-sites, and branch models in addition to Bayes

18. Results 1. DNA-binding domain in FLO and MADS domain in DEF are under stronger purifying selection than other domains. 3. DEF’s increase in  is due to I, K, and C-terminus domains 2. FLOB has higher  than FLOA in both domains FLO DEF

19. Conclusions…. Continuous purifying selection on both paralogs for both genes, although relaxed in comparison to single-copy taxa (supports the DDC model). Relaxed constraint in some domains may be an indication of subfunctionalization. –Subfunctionalization rather than adaptive evolution contributes to preservation of duplicate genes

20. Alternative explanations Gene Dosage –Unlikely, because duplicates have diverged and because of partial functional redundancy Transcriptional regulatory interactions –FLO and DEF paralogs may have co- evolved (concerted divergence) –Still needs to be tested

21. References Chen, ZF and Z Ni. 2006. Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. BioEssays 28:240-252. Adams, KL and JF Wendel. 2005. Polyploidy and genome evolution in plants. Curr. Op. Plant Bio. 8:135-141 Wendel JF. 2000. Genome evolution in polyploids. Plant Mol. Bio. 42:225-249. Force et al. 1999. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151:1531- 1545. Aagard JE, Willis JH, and PC Phillips. 2006. Relaxed selection among duplicate floral regulatory genes in Lamiales. J Mol. Evol. 63:493-503.

22. Time to Subfunctionalization Fates of duplicated genes are determined shortly after polyploidization Ratio of mutation rate in regulatory and coding regions is a weak factor in expected degree of resolution * *