Cenancestor (aka MRCA or LUCA)as placed by ancient duplicated genes (ATPases, Signal recognition particles, EF)

The “Root”

• 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 (+)

PHYLOGENY: from Greek phylon, race or class, and -geneia, born.“the origin and evolution of a set of organisms, usually of a species” (Wikipedia);

Tree, Web, or Coral of Life?

Charles DarwinPhoto by J. Cameron, 1869

Page B26 from Charles Darwin’s (1809-1882) notebook (1837)

“The tree of life should perhaps be called the coral of life, base of branches dead”

“The tree of life should perhaps be called the coral of life, base of branches dead”

Which Type of Coral?

QuickTime™ and a decompressor

are needed to see this picture.

QuickTime™ and a decompressor

are needed to see this picture.

Darwin’s coral was a red algae(Bossea orbignyana)

From Florian Maderspacher: “The captivating coral--the origins of early evolutionary imagery.” Curr Biol 16: R476-8 2006

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.

The Coral of Life (Darwin)

Gene Transfer and Phylogenetic Reconstruction: Friends or Foes?

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.

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

Gene “ping-pong” between different lineages can be used to build correlations between different parts of the tree/net of life.

Presence of a transferred gene is a shared derived character that can be useful in systematics.

The central dogma

Why might this be wrong or incomplete

Replication

lagging and leading strand - strand bias

Transcription

Transcription

Prokaryotes

Eukaryotes

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).

RNA enzymes:

Ribosome

Self-splicing introns

Group II intron

The RNA world concept

What arguments support an “RNA world” preceding a two biopolymer world?

Protein structure:

Angles in the protein backbone

spdbf - viewer aka Deep View

Free and powerful programSteep learning curveInteracts 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

Simplify the display

Show only alpha carbons

Color secondary structure

Turn 3 D display on

1HEW

Backbone as ribbon

Sidechains only in binding pocket

Substrate in yellow

Non-polar residues of binding pocket in turquoise

mind map 1

mind map 2