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Trees in ProPhylER

Trees in ProPhylER. Tree Branching and Branch Lengths. A Species Tree. . . . . . . . . . . . . . . . . . . zebrafish. xenopus. chicken. platypus. elephant. mouse. human. . mammals. . jawedvertebrates. . . . . Branching order describes relatedness of the species. Termini are the extant species; inte

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Trees in ProPhylER

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    1. Trees in ProPhylER • Tree Branching and Branch Lengths • Orthologs and Paralogs • How ProPhylER Treats Paralogs

    2. Trees in ProPhylER Tree Branching and Branch Lengths

    3. A Species Tree

    4. A Species Tree to Scale

    5. Two Notes about Protein Trees

    6. A Protein Tree to Scale

    7. A Protein Tree with Branch Lenghts in Subs/Site

    8. Additivity of Branch Lengths

    9. A Note on Branch Lengths

    10. A Tree of Fairly Variable Orthologs

    11. A Tree of Rather Constrained Orthologs

    12. Summary of Branch Length Concepts Proteins tend to be constrained; their sequences therefore change more slowly than the neutral rate of evolution The unit of the evolutionary rate is “substitutions per site” In ProPhylER, substitutions are quantified per amino acid site, not per codon or per nucleotide site, and they represent the average over the high quality portions of the underlying multiple alignment The length of the tree branches is proportional to the number of substitutions per site when the tree is drawn to scale Each branch in ProPhylER’s protein trees is annotated with the best estimate of the number of substitutions per site that happened on it Branch lengths are additive and reflect the total amount of information present in the tree

    13. Trees in ProPhylER Orthologs and Paralogs

    14. Gene Duplication 1

    15. Gene Duplication 2

    16. Gene Duplication 3

    17. Gene Duplication 4

    18. Gene Duplication 5

    19. Gene Duplication Basics: Summary There are only three types of nodes in a tree Gene Duplications Speciation events Terminal nodes (which represent the extant sequences) ProPhylER’s trees distinguish duplications from speciations Gene duplicates are called Paralogs Orthologs are genes related by a speciation event; they are “the same gene” in different organisms Because orthologs are the “same gene”, their function is much less likely to change over evolutionary times than the function of paralogs after a duplication Functional divergence of paralogs poses special challenges for ProPhylER -- more next

    20. Trees in ProPhylER How ProPhylER Treats Paralogs

    21. Why Paralogs Pose a Special Challenge ProPhylER needs substantial evolutionary variation for functional predictions (ESF, Physicochemical profiles, and MAPP) Sequence (and high-quality gene predictions) is still limiting, so paralogs often provide important diversity of sequence that orthologs alone simply do not have But paralogs may have changed functionally, violating ProPhylER’s assumption that function has remained stable, and that the variation observed among all aligned sequences is consistent with that stable function

    22. Reasons for Survival of both Paralogs after Duplication Isofunctionalization occurs because a high expression level is needed by many copies of ‘the same gene’ E.g., Actins, Tubulins, Cow stomach lysozyme, rRNA concerted evolution after duplication by gene conversion or cycles of duplication and loss Neofunctionalization occurs by evolution of a new biochemical function or a new expression domain E.g., p53 vs p63 and p73, RNA polymerases, hemoglobins sequence evolution occurs independently in both paralogs after duplication Subfunctionalization occurs so that the original protein’s functions or expression regions are subdivided among the paralogs has happened in many developmental regulators in vertebrates sequence evolution occurs independently in both paralogs after duplication

    23. Paralogs’ Neo- and Subfunctionalization 1 For its predictive analyses, ProPhylER assumes that there have been no systematic functional shifts due to amino acid changes among the compared sequences As stated previously, this is a reasonable assumption for orthologs, at least in the sense that most amino acid changes that occurred during the evolution of the compared orthologs ought to be compatible with the protein’s conserved structure and function Is it a reasonable assumption for paralogs? Yes, if the functional shift is expression-regulatory “Regulatory” neofunctionalization or subfunctionalization No, if the functional shift is due to changes in amino acid sequence “Biochemical” neofunctionalization or subfunctionalization

    24. Paralogs’ Neo- and Subfunctionalization 2

    25. Paralogs in ProPhylER

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