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PrimeGSR: Integrated Model for Efficient Gene Sequence Evolution Analysis

PrimeGSR model by Åkerborg, Arvestad, Lagergren, and Sennblad provides a comprehensive approach for gene sequence evolution analysis, emphasizing gene duplication and loss reconciliation, relaxed clock modeling, and efficient algorithms. The model improves gene tree reconstruction, offers divergence time estimates, and includes synteny in species tree reconstruction.

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PrimeGSR: Integrated Model for Efficient Gene Sequence Evolution Analysis

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

  7. MHC revisited

  8. 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 • Åkerborg et al. Submitted (GSR) • Integrated GEM + SRT model

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

  10. Pr[D,T] Sequence data, F Trees, 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. 31.6 % 21.6 % Orthogroup 3176 42.4 % Single best SYNERGY tree

  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

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