Exam Sample

The exam will take place over one hour and will focus on both practice and theory. It will be structured as follows:

22 multiple-choice or fill-in-the-blank questions, each worth 1 point. There are no penalties for incorrect answers.
2 open-ended question (maximum three sentences), worth a total of 5 points.

multiple-choice questions:

The molecular clock ...

A. ... works perfectly in all evolutionary scenarios.
B. ... has never been observed to work in any case.
C. … in some cases, it can provide a reasonable approximation of evolutionary time.
D. ... what time is it again?

Which is not a perturbation approach?

A. Nearest Neighbor Interchange.
B. Metropolis-Hasting Criterion.
C. Subtree Pruning and Regrafting.
D. Tree Bisection and Reconnection.

To align a gene you use:

A. IQTREE
B. Astral
C. Gblocks
D. MAFFT

Fill-in-the-blank questions:

In phylogenetic analysis, a site is considered parsimony-informative if it contains at least _________________ different character states, each represented in at least _________________ sequences.

Sequence saturation occurs when multiple _________________ happen at the same site, making it hard to infer the true number of _________________ between sequences.

The Markov property in substitution models states that the probability of a nucleotide changing from one state to another depends only on its _________________ state, not on its _________________ one.

Open questions:

Briefly explain what an orthogroup is and how it relates to the concept of orthology. Also, what is a 1-to-1 orthogroup?
Explain what is the input for the Astral software(s) and which software can be used to generate it.
Define what we mean by character-based and distance-based methods in phylogenetics.