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Some sticky issues

Some sticky issues. Short branches and ortholog/paralog inference Short branches and rearrangement Species tree Multiple roots. FA. CA 1. MA 1. HA 1. CA 2. HA 2. Very short branches imply non-binary nodes. FA. CA 1. HA 1. CA 2. HA 2. MA 1. FA. CA 1. MA 1. HA 1. CA 2. HA 2.

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Some sticky issues

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  1. Some sticky issues • Short branches and ortholog/paralog inference • Short branches and rearrangement • Species tree • Multiple roots

  2. FA CA1 MA1 HA1 CA2 HA2 Very short branches imply non-binary nodes FA CA1 HA1 CA2 HA2 MA1

  3. FA CA1 MA1 HA1 CA2 HA2 FA HA1 CA1 MA1 CA2 HA2 FA CA1 HA1 MA1 CA2 HA2 Alternate Hypotheses FA CA1 MA1 HA1 CA2 HA2

  4. FA CA1 MA1 HA1 CA2 HA2 D D FA MA1 CA1 HA1 CA2 HA2 FA CA1 HA1 MA1 CA2 HA2 Each alternate hypothesis yields a different set of orthologs Orthologs: (MA1,CA1) Paralogs: (HA1,CA1), (HA1,MA1) Orthologs: (HA1,CA1) Paralogs: (MA1,CA1), (HA1,MA1) All three are orthologs

  5. Some sticky issues • Short branches and ortholog/paralog inference • Short branches and rearrangement • Species tree • Multiple roots

  6. D Rearrangement will prefer hypothesis 1, but is that a better choice? HA2 CA2 FA CA1 HA1 CA2 FA HA1 HA2 CA1 D Hypothesis 2: Hypothesis 1: CA1 HA1 FA CA2 HA2 FA CA1 HA1 CA2 HA2

  7. Some sticky issues • Short branches and ortholog/paralog inference • Short branches and rearrangement • Species tree • Multiple roots

  8. Baldauf, Science 2003

  9. General agreement on unrooted Eukaryotic tree Plasmodium Dictyostelium Fungi Animals Plants

  10. Cavalier-Smith’s root

  11. Arisue’s root

  12. Some sticky issues • Short branches and ortholog/paralog inference • Short branches and rearrangement • Species tree • Multiple roots

  13. Beta Crystalin family CrybB2 Notung: All bold branches have the same score CrybA2 Crybb2 CrybA4 CrybA3 CrybB1 CrybA1 Ruvinsky and Silver, Genomics, 1997

  14. Beta Crystalin family Ruvinsky and Silver: Root provided by biochemical information A2 A4 A3 A1 B1 B2 B3 basic acidic

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