Phylogeny is the evolutionary history and a tree is the graphical summary of the history. Poor metaphor. What about: hybridization, transfer of genes between organisms. More like a web.

Homology is a similarity in traits that is due to descent from a common ancestor. Synapomorphies are homologous traits that are shared among certain species and is similar because it was modified in a common ancestor.  

Describe what a “hierarchy” of synapomorphies is.  

Willi Hennig came up with Cladistics. It infers a phylogeny by determining which traits are more ancient and which are more derived by comparison with an outgroup. Tree construction that relies on synapomorphies.

By convention how are synapomorphies indicated on phylogenetic trees? 

Often with bars across a branch of a tree.

Combo of convergence and reversal: similarity not due to common ancestry. Reversal Is common b/c there are only 4 base pairs

Simplest explanation is the best. Tree w/ least number of changes is best.        

What is a “character” in the context of evolution? Which is more useful, morphological or molecular characters, for generating phylogenies?

How is it inferred that whales most likely evolved from hippos?

Be able to produce a hypothetical molecular data set and identify a synapomorphy within that data set.

ACTGGCTAG

ACTGCCTAG

ACTGCCTAG

How would you choose the right phylogeny given that there are so many?

A computer can calculate the most parsimonious tree in an exhaustive search, you can search only some parts of the tree while maximizing the probability of finding the most parsimonious tree,

What is the difference between maximum likelihood and Bayesian approaches?

ML is a mathematical approach to examine the likelihood that the DNA nucleotide sequence could have arrived a different way. Bayesian approach asks what the probability is of a particular tree being correct.

Bootstrapping tests confidence in a node of a phylogenetic tree by comparing trees with and without a branch to compute which is more likely.        

If bootstrap support for a branch is less than 50%, the branching pattern is uncertain and collapses into a point of uncertainty.        

What if two data sets produced different maximum likelihood phylogenies? What would you do?

What is systematics, and how has phylogenetic analysis contributed to that work?

The effort to name and classify species. Method of naming is moving away from morphological similarities (phenetic approach) and toward evolutionary relationships (cladistic approach)     

What is phylogenetic systematics?

Classification should be tree based on names and categories that reflect the actual sequence of branching events of monophyletic groups.

What is a paraphyletic group? Be prepared to draw one, and give 3 examples.

A group that includes some but not all descendants of a common ancestor. (eg. Dicots)          

Emile Zuckerkandle and Linus Pauling. It’s possible to address questions about the timing and rate of evolution by analyzing molecular traits that change at a steady rate. Natural Selection should decrease the rate of the molecular clock.

Non coding regions because they are not under natural selection. Neutral changes in DNA, because they should accumulate in populations at a rate equal to the mutation rate.

How do you calibrate a molecular clock?

Measure genetic distance between two taxa whose divergence dates are known from fossils or geological data.

When did humans start wearing clothes, and how was that discovered?

72,000 +/- 42,000 years. Divergence of body lice from head lice.

Explain what phylogeography is.

Using phylogenies to answer biogeographical questions.

What is coevolution?

Yes, DNA sequences estimated a phylogeny of 17 aphid species and their bacterial symbionts. Similarities in bacteria type between closely related taxa of aphid.