Department of Biology

Renn Lab

Student Project Ideas

(check back often as new ideas will be added)
(see previous ideas, some of which are still viable)

These pages include scientific ideas that supplement my own research interests. I provide a short summary and a few references but students are encouraged to propose independent ideas.


Cichlid fishes are one of the most well-known models in evolutionary biology. The species flock, composed of several hundred endemic species primarily located in the East African Great lakes, has diversified within an extremely short time span and represent one of the most successful "adaptive radiations" among vertebrates. This conspicuous diversity was dubbed "the cichlid problem" by the famous evolutionary biologist Ernst Mayr. However, this unusually diverse group is now proving to be an unusually informative system in which to study the genomic architecture of adaptation, the genetic processes that underlie speciation, and the patterns that contribute to parallel evolution. The information obtained from comparative genomic analysis of cichlids is likely to inform a broad range of questions applicable to many animals systems. Kuraku and Meyer (2009) have recently written a very good review on this topic.

1.A) Gene Duplication of Genomic Architecture of Adaptive Radiation *

It is now well established that gene duplication (and subsequent evolution of the duplicates) is a substantial force in evolutionary novelty, in fact, 30-65% of all genes are thought to have originated through duplication events. Gene duplications are known to be involved in adaptive evolution in response to diet, chemical challenge, reproductive incompatibility, cold adaptation, metabolic process etc. which can allow diversification into new niches, for example, through cold adaptation. When multiple copies of a gene are present one (or both copies) may 1) contribute to dosage effects on quantitative trait variation 2) partition the expression or function or 3) acquire novel functions through molecular divergence (for review see Taylor and Raes, 2004).  We aim to test the hypothesis that gene duplication has contributed to the diversification of cichlid species. We have identified several hundred duplicated loci (Machado et al, submitted) and now need to 1) characterize the copy number variation between species and 2) describe the sequence variation between paralogs.

1.B) Bioinformatic Analysis of Cichlid Genomes

For the majority of cichlid genes, all inter-species comparisons that are available suggest little sequence divergence among orthologs, especially in the protein coding regions (Watanabe et al. 2004; Salzburger et al. 2008; Loh et al. 2008). Among the five Malawi species for which genomic sequence information is available, nucleotide diversity (Watterson’s qw = 0.26%) and Jukes-Cantor genetic distance (0.23 – 0.29%) are low. We are interested to understand patterns of genome evolution in this evolutionarily remarkable lineage. Projects in this area may involve collaboration with Jim Fix or Albyn Jones in the Math department.



1. GENOME EVOLUTION (details):
1.A) Gene Duplication of Genomic Architecture of Adaptive Radiation *
1.B) Bioinformatic Analysis of Cichlid Genomes

2. MATERNAL BEHAVIOR: AFRICAN CICHLID Astatotilapia burtoni (details):
2.A) The Effect of Early Experience on Adult Behavior
2.B) The Influence of Metabolic Regulation on Maternal Behavior *
2.C) The Social Neural Circuit *
2.D) The Emergence of Leadership

3.A) Sex-Role Reversal *
3.B) RNA-seq may replace Microarray analysis. Are we ready?


(* indicates ongoing projects that are a main focus in our funded research programs)