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Mixture models of nucleotide sequence evolution

Mixture models of nucleotide sequence evolution. Csiro Ecosystem Sciences. Lars Jermiin | OCE Science Leader. 26 November 2013. “Common sense is actually rather uncommon…” — Christy McGeough (2006). Phylogenetics. Evolution of species. Evolution of genomes. Evolution of languages.

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Mixture models of nucleotide sequence evolution

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  1. Mixture models of nucleotide sequence evolution Csiro Ecosystem Sciences Lars Jermiin | OCE Science Leader 26 November 2013 “Common sense is actually rather uncommon…” — Christy McGeough (2006)

  2. Phylogenetics Evolution of species Evolution of genomes Evolution of languages Evolution of genes Evolution of manuscripts Phylogenetics Genome annotation Systematics & taxonomy Resurrection of enzymes Conservation & biodiversity Co-evolution of traits Epidemiology & biosecurity Co-evolution of species Mixture models of molecular evolution | Lars Jermiin | Page 2

  3. Common scenario Multiple sequence alignment (MSA) Phylogenetic method • Common phylogenetic assumptions • Evolutionary history is tree-like • Sites have evolved under IID conditions • Evolutionary process can be modelled by a time-reversible Markov model, R R R R R R R R R Mixture models of molecular evolution | Lars Jermiin | Page 3

  4. Reality check Compositional heterogeneity(CH) across the sequences is common –  CH across sequences implies that a more complex model of evolution is necessary R1 R4 R1 R1 R2 R3 R4 R5 Mixture models of molecular evolution | Lars Jermiin | Page 4

  5. Finding the optimal evolutionary model Top-down approach R1 R1 R1 R6 R1 R2 R3 R1 R4 R1 R1 R5 R7 R1 R8 R1 Bottom-up approach Syst. Biol. (accepted) Mixture models of molecular evolution | Lars Jermiin | Page 5

  6. Example – evolution of 8 yeast genomes 1 QuestionUnder what conditions have these genomes evolved? • Data42,337 second codon sites from 106 nuclear genes • MethodMatched-pairs tests of homogeneity (using SymTest) Source. Rokas et al.. Nature425, 798-804 [2003]. Mixture models of molecular evolution | Lars Jermiin | Page 6

  7. Example – evolution of 8 yeast genomes 2 QuestionHow complex is the evolutionary process given a ‘correct’ tree? • Data Output from our HAL-HAS mixture model Mixture models of molecular evolution | Lars Jermiin | Page 7

  8. Example – evolution of 8 yeast genomes 3 QuestionWhat are the characteristics of the ancestral sequence? • Data Output from our HAL-HAS mixture model Invariable (49.1%) ν1 (39.6%) ν2 (11.3%) fA 0.281 fC 0.167 fG 0.146 fT 0.406 fA 0.310 fC 0.416 fG 0.071 fT 0.202 fA 0.290 fC 0.307 fG 0.216 fT 0.188 Mixture models of molecular evolution | Lars Jermiin | Page 8

  9. Example – evolution of 8 yeast genomes 4 QuestionHow much have the variable sites (ν1 & ν2) evolved? • Data Output from our HAL-HAS mixture model Mixture models of molecular evolution | Lars Jermiin | Page 9

  10. Acknowledgement OCE Science Leader Scheme Thank you Lars JermiinOCE Science Leader Bioinformatics & PhylogenomicsTeam t +61 2 6246 4043 e Lars.Jermiin@csiro.au w www.csiro.au/people/Lars.Jermiin.html • CSIRO Ecosystem Sciences • Collaborators • Faisal Ababneh (Al-Hussein Bin Talal University) • VivekJayaswal (Queensland University of Technology) • Bernard Misof (University of Bonn) • Michael Ott(Liebniz-Rechenzentrum) • Leon Poladian (University of Sydney) • John Robinson (University of Sydney) • Thomas Wong (CSIRO Ecosystem Sciences)

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