A statistical guide to the design of deep mutational scanning experiments

This new publication in Genetics comes from a collaboration between the Bank and Jensen labs; the statistical analyses were performed by Sebastian Matuszewski and Marcel Hildebrandt. The authors present a statistical guide (and web tool, implemented by Hermina) that can be used to design and improve your future experimental setup of a deep mutational scanning study. Deep mutational scanning is an approach in which hundreds or thousands of pre-engineered mutants are grown together and their relative abundance, directly related to their fitness, is assessed through deep sequencing at several time points.

The main requirements for the statistical model of the paper to be applicable are: 1) Large copy number of each mutant in the initial library; 2) Mutants need to grow exponentially during the experiment; 3) Both population and sample sizes need to be large; 4) You should to collect your data at two or more time points.

With the interactive tool that comes with the publication, it is possible to introduce and manipulate several experimental parameters, and it allows you to quantify and maximize not only your experimental resolution, but also to get estimates of the time and expenses for a particular experiment.

Btw, there is also an IGC paper video about the project, also featuring a Portuguese version!

Check out our “Walk of Life” board game at NOS Alive!

Our lab has created a fun board game called “Walk of Life” to explain fitness landscapes for the IGC kiosk at the NOS Alive festival. Andreia, Claudia, and Inês will be there playing the game and answering your burning questions about fitness landscapes on Thursday 7th and Friday 8th of July. To make sure you find us, here is a map of the festival; the IGC kiosk is labelled  “12”.

Fitness landscapes at BioSAM this Saturday

Claudia will be giving a talk this Saturday, April 16th at NEBFCUL’s Biological Science 1st Annual Meeting (BioSAM)! She will be presenting her recent work On the (un-)predictability of a fitness landscape in yeast (see abstract). All talks will be in the auditorium of C1 building, 3rd floor, room 14. Students are especially encouraged to attend since the congress is geared towards a general biologist audience and will feature a panel on evolutionary genetics!

The limits to parapatric speciation: Dobzhansky-Muller incompatibilities in a continent-island model

Despite their deleterious effects on hybrids, epistatic genetic interactions in the form of Dobzhansky-Muller incompatibilities (DMIs) seem to persist, and potentially even accumulate, in populations in the presence of gene flow.

In this paper, we provide a rigorous theoretical framework to study this phenomenon. We determine the maximum amount of gene flow that allows for the accumulation or maintenance of DMIs, and interpret our results with respect to the relative importance of ecological and mutation-order speciation; two concepts that are controversially discussed in the field of speciation.

Link to our paper in Genetics: The limits to parapatric speciation: Dobzhansky-Muller incompatibilities in a continent-island model