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The Tree of Life according to SSU ribosomal RNA (+)

strictly bifurcating no reticulation only extant lineages based on a single molecular phylogeny branch length is not proportional to time. The Tree of Life according to SSU ribosomal RNA (+). Eukaryotes. Bacteria. Archaea.

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The Tree of Life according to SSU ribosomal RNA (+)

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  1. strictly bifurcating • no reticulation • only extant lineages • based on a single molecular phylogeny • branch length is not proportional to time The Tree of Life according to SSU ribosomal RNA (+) Eukaryotes Bacteria Archaea PHYLOGENY: from Greek phylon, race or class, and -geneia, born. “the origin and evolution of a set of organisms, usually of a species” (Wikipedia); Cenancestor (aka MRCA or LUCA)as placed by ancient duplicated genes (ATPases, Signal recognition particles, EF) The “Root”

  2. “The tree of life should perhaps be called the coral of life, base of branches dead” Page B26 from Charles Darwin’s (1809-1882) notebook (1837) Tree, Web, or Coral of Life? Charles Darwin Photo by J. Cameron, 1869

  3. Which Type of Coral?

  4. Darwin’s coral was a red algae(Bossea orbignyana) The captivating coral. According to the ideas of Horst Bredekamp, parts of the diagram in Darwin's origin of species (centre) more or less directly reflect the branching properties of a specimen Darwin collected himself. From Florian Maderspacher: “The captivating coral--the origins of early evolutionary imagery.” Curr Biol 16: R476-8 2006

  5. The Coral of Life (Darwin)

  6. Popular view Gene transfer is a disruptive force in phylogenetic reconstruction. New view Events of ancient gene transfer are valuable tools for reconstructing organismal phylogeny. Gene Transfer and Phylogenetic Reconstruction: Friends or Foes?

  7. 1. Any ancient gene transfer to the ancestor of a major lineage implicitly marks the recipient and descendents as a natural group. 2. The donor must exist at the same time or earlier than the recipient. Ancient HGTs

  8. Presence of a transferred gene is a shared derived character that can be useful in systematics. Gene “ping-pong” between different lineages can be used to build correlations between different parts of the tree/net of life.

  9. The central dogma Why might this be wrong or incomplete

  10. Replication lagging and leading strand - strand bias

  11. Transcription

  12. Transcription • Prokaryotes • Eukaryotes

  13. RNA processing • Intron types • RNA can be the catalyst Simple illustration of a pre-mRNA, with introns (top). After the introns have been removed via splicing, the mature mRNA sequence is ready for translation (bottom).

  14. RNA enzymes:

  15. Ribosome

  16. Self-splicing introns

  17. Group II intron

  18. The RNA world concept • What arguments support an “RNA world” preceding a two biopolymer world?

  19. Protein structure:

  20. Angles in the protein backbone

  21. spdbf - viewer aka Deep View Free and powerful program Steep learning curve Interacts with modeling server available at http://ca.expasy.org/http://spdbv.vital-it.ch/ Gale Rhodes’ Tutorial is at http://www.usm.maine.edu/~rhodes/SPVTut/index.html

  22. Simplify the display • Show only alpha carbons • Color secondary structure • Turn 3 D display on

  23. 1HEW • Backbone as ribbon • Sidechains only in binding pocket • Substrate in yellow • Non-polar residues of binding pocket in turquoise

  24. mind map 1

  25. mind map 2

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