Trees:

Topology and Branchlengths
Rooted vs Unrooted

Branches, splits, bipartitions
In a rooted tree: clades
Mono-, Para-, polyphyletic groups, cladists and a natural taxonomy

Intro to phylogenetic reconstruction

Phylogenetic analysis is an inference of evolutionary relationships between organisms.
Those relationships are usually represented by tree-like diagrams.
Note: the assumption of tree-likeliness of evolution is controversial.

Steps of the phylogenetic analysis:

Compilation of sequence dataset

Alignment

Determination of substitution model

Tree building

Tree evaluation

Terms from evolutionary biology that are commonly used among evolutionary biologists. On the long run, you want to add them to your vocabulary (at least the passive one).

The term cladogram refers to a strictly bifurcating diagram, where each clade is defined by a common ancestor that only gives rise to members of this clade. I.e., a clade is monophyletic (derived from one ancestor) as opposed to polyphyletic (derived from many ancestors).

A clade is recognized and defined by shared derived characters (= synapomorphies). Shared primitive characters (= sympleisiomorphies , aternativie spelling is symplesiomorphies) do not define a clade. (see in class example drawing ala Hennig).

To use these terms you need to have polarized characters; for most molecular characters you don't know which state is primitive and which is derived (exceptions:....).

Related terms:
autapomorphy = a derived character that is only present in one group; an autapomorphic character does not tell us anything about the relationship of the group that has this character ot other groups.
homoplasy = a derived character that was derived twice independently (convergent evolution). Note that the characters in question might still be homologous (e.g. a position in a sequence alignment, frontlimbs turned into wings in birds and bats).
paraphyletic = a taxonomic group that is defined by a common ancestor, however, the common ancestor of this group also has decendants that do not belong to this taxonomic group. Many systematists despise paraphyletic groups (and consider them to be polyphyletic). Examples for paraphyletic groups are reptiles and protists. Many consider the archaea to be paraphyletic as well.
holophyletic = same as above, but the common ancestor gave rise only to members of the group.

Questions on Midterm?

Studies on the Origin of Life

Top down approaches (fossil and molecular records, retrodiction of biochemical pathways)

Bottom up (prebiotic chemistry)

Primordial Soup (Miller -> see reading assignment) or Primordial Pizza (Wächtershäuser -> see reading assignments)

The RNA world

The currently favored scientific scenarios for the transition from chemistry to biology is somewhat as follows:

prebiotic chemistry either on Earth or in Space, in solution or on surfaces or in the gas phase

(autocatalytic chemical cycles and chemical networks)

self-replicating biopolymer

Emergence of cells, hypercycles or other means to co-select different genes

RNA world

Invention of protein biosynthesis

The existence of the RNA world as a transitory stage is supported by the following:

RNA molecules have catalytic activity. Famous ribozymes are the group I self splicing intron from Tetrahymena (ciliate) and the RNA portion of the E.coli Ribonuclease P (involved in tRNA processing)
RNA molecules have the potential to function as genetic material and as enzymes, or ribozymes (this solves the chicken vs. egg problem). This also allows for comparatively easy schemes to evolve RNAs in vitro to have new or different catalytic function (blind design by evolution).
Many enzymatic cofactors are nucleotides or nucleotide derived (FAD, ATP). Ribosomal protein synthesis relies on RNAs. RNA is an important part of the catalytic machinery that forms the peptide bond (see Noller et al.), tRNAs contain many strange bases suggesting that the catalytic potential of RNA molecules can go beyond what is possible with four bases only.

In vitro evolution has succeeded to evolving RNA's with novel properties, e.g. ATP binding. Jack Szostak's lab is working to evolve RNAs with template directed RNA polymerization capabilities. The principle selection scheme is depicted in this diagram at Szostak's web page.

In vitro selection became famous with Sol Spiegelman's experiments on the vitro replication of the Phage Qbeta RNA. In this case selection was for the fastest replicating molecules - they become shorter and lost their ability to infect bacteria.

Later inventions are the SELEX procedure to select for RNA with very specific binding properties (see left), and the selection of ribozymes with altered or new properties. In the latter case growth and selection can be either discrete or continuous. See reading materials for further discussion.

How can evolution be improved?

Genetic drift or the co-selection of slightly deleterious mutations lead to the fixation of deleterious mutations. These mutations can be eliminated if recombination occurs between different members of the population. Another advantage of recombination is that positive properties that arose independently in different parts of the molecules can be combined by recombination, molecular breeding, and sexual PCR.

Illustration for the power of recombination: Molecular Computation -> the traveling salesman problem Adleman's Science paper (JSTORE link)

In vitro evolution of proteins
Problem:
How to couple the functional protein to the genetic material.

Biological solution: cells contain the genetic material and the encoded proteins. Selection of cell that contain the more successful protein, will also select the gene encoding the protein.

Alternative: Link protein to encoding RNA. (see O'Keefe and Szostak's scheme h on RNA display here)

If time discuss sequence space (.ppt)

Reading assignment:

Work on Quiz #4
Try to learn terminology