African cichlids are a great model organism for understanding the genetic basis of adaptive traits because we can do controlled experiments in the lab, and then compare our findings to ecological and population genetic data from the wild. We have hybrid crosses between species which can be used to directly connect genotype to phenotype–to identify regions in the genome that are associated with our traits of interest. Each individual can be measured for many traits, allowing us to answer many questions with the same genetic resource. Once we know the general regions in the genome to look at, we can narrow down our candidates with population genomic comparisons in those regions.
In the Roberts Lab, one such gene mapping line is between a sand-dwelling invertivore and a rock-dwelling omnivore. I’ve photographed and measured exploratory behavior in almost 500 offspring, used whole-genome genotypes (ddRAD sequences, if you’re curious about these sorts of things) to make a genetic map, and performed gene mapping that has identified multiple regions across the genome that influence those behaviors (quantitative trait locus, or QTL, mapping).
One of the neat aspects of these genetic resources is that undergraduates can find a trait that they’re interested in and perform the gene mapping experiment themselves. My undergraduate Sophie is currently working on a project to find the genes involved in an ecologically relevant trait that we identified from photographs: tail shape (see figure 1). One parent species of the cross (Aulonocara) has a forked tail, which reduces drag for endurance swimming. The other species (Metriaclima) has a more paddle-shaped tail, which increases power, but also drag.
Figure 1. Differences in tail shape by species
Because the DNA sequencing was performed and the genetic map constructed prior to Sophie starting her project, she has been able to focus on choosing how to measure her trait and analyse her data. She has full ownership of the project, and a very good chance of finishing a publishable manuscript by the end of the semester.