1. GSR The Gene Sequence evolution model with iid Rate variation over tree Örjan Åkerborg, KTH Lars Arvestad, KTH Jens Lagergren, KTH Bengt Sennblad

2. What? Gene evolution through duplication and loss Sequence evolution

3. Why? Base reconciliation analysis directly on data –Avoid information loss –Addresses uncertainty better Gene tree reconstruction should mirror generation

4. When? Arvestad et al. 2003, –MrBayes + GEM –Flawed model

5. 60s ribosomal data

6. Arvestad et al. 2003, –MrBayes + GEM –Flawed model Arvestad et al. 2004 –Intergrated GEM + Substitution model –Mathematically correct model –Molecular clock –Sampling algorithm - slow When?

7. MHC revisited

8. Åkerborg et al. Submitted (GSR) –Integrated GEM + SRT model When? Arvestad et al. 2003, –MrBayes + GEM –Flawed model Arvestad et al. 2004 –Intergrated GEM + Substitution model –Mathematically correct model –Molecular clock –Sampling algorithm - slow

9. How? GSR –GEM Reconciled trees – duplication and loss –SRT Relaxed clock model (iid) Substitution model –Fast algorithm Discretized time space

10. Trees, T Sequence data, F Pr[D,T] Self-consistency

11. Self-consistency – the X%-test

12. Application to Yeast data Compare to prev. Results –YGOB –Orthogrups (SYNERGY) Both synteny-based

13. Synteny -- gene order

14. Application to Yeast data Compare to prev. Results –YGOB –Orthogrups (SYNERGY) Both synteny-based –Whole genome duplication Challenge! Genome-wide analysis! –4809 gene families (orthogroups)

15. Comparison YGOB results

16. Molecular clock?

17. Comparison SYNERGY results

18. Sequence vs. synteny data No sequence diff –36% of data sets are >85% similar Strong divergence –25% of data set are <40% similar –Long-branch attraction Conflicting sequence-synteny signal

19. Sequence vs. synteny data

20. Orthogroup 3176 42.4 % Single best SYNERGY tree 21.6 % 31.6 %

21. Summary primeGSR –Integrated model Reconciliation – gene duplication loss Relaxed clock Sequence evolution –Efficient algorithms –Improved gene tree reconstruction Future prospects –Divergence time estimates (MAP) –Species tree reconstruction –Include synteny