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Professor Charles F. Aquadro ("Chip")


My primary interests are in molecular population genetics, molecular evolution, and comparative genomics. Our current research focuses on the molecular population genetics and evolution of genes that regulate Drosophila germline stem cell (GSC) maintenance and differentiation.  Our goal is to understand the types of natural selection shaping variation within and between species that is observed in GSC genes, to understand the functional consequences of this variation and diversification, and to test hypotheses as to the evolutionary forces driving the strong positive selection for protein diversification that we have observed at the key “switch” genes bag of marbles (bam) and benign gonial cell neoplasm (bgcn).  Of particular interest are the roles that bacterial endosymbionts (e.g., Wolbachia) and other germline “parasites” (including transposable elements and viruses) play in driving the rapid evolution of these and other GSC genes. As part of this work, we are also continuing our computational analyses of the evolutionary rate covariation (“ERC”) statistics developed with Nathan Clark when he was a postdoc in our group (he is now on the faculty at the University of Pittsburg School of Medicine).  Current work includes an extensive reanalysis of evolutionary rate correlations of all orthologous protein coding loci across 20 species of Drosophila.  I also have a productive and enjoyable collaboration with my colleague Eric Alani analyzing the mutational and population genetic consequences of variants in mismatch repair genes in the yeast Saccharomyces cerevisiae.

Faculty web page including recent publication list:

Jae Young Choi

Postdoc, Currently Postdoc with Michael Purugganan at NYU

My research focuses on two main areas related to Wolbachia and its coevolution with its host Drosophila and the impact on germline stem cell gene evolution. The first area involves studies of the evolution of germline stem cell regulating genes across the genus Drosophila. Previous studies have extensively studied the rapid evolution of “downstream” reproductive genes (seminal fluid proteins and gamete recognition proteins). The earliest stages of reproduction involving germline stem cell maintenance and initial differentiation have received much less attention though several key germline stem cell regulatory genes are extremely rapidly evolving due to natural selection of some form.  I am generating as well as using newly available comparative and population genomic datasets of multiple species of Drosophila in order to understand the evolutionary forces shaping the molecular and functional evolution of the germline stem cell regulatory system.  I am also investigating the evolution of other stem cell regulatory systems (i.e. neural stem cell) in order to understand the general patterns of evolution and forces occurring in genes with stem cell regulatory functions.

My second research area involves the genomic analysis of the insect endosymbiont Wolbachia pipientis. This bacteria infects probably three-quarters of all insects, and can cause significant manipulation of reproduction in these species.  I have investigated the evolutionary history of the infection of several species of Drosophila by W. pipentis, with a particular focus on the widespread Asian species Drosophila ananassae.  This species is of particular interest in that not only are many populations infected intracellularly by this endosymbiont, but many individuals also have the whole bacterial genome integrated into the host eukaryotic genome. I am using population genomic approaches to understand the evolutionary history and dynamics of the integration event and characterize the genomic and functional properties of the integrated bacterial genome in the host.


  • Choi, J.Y., K. Zeng and C.F. Aquadro.  2016.  Recent and long term selection across synonymous sites in Drosophila ananassae.  Journal of Molecular Evolution  in press.
  • Choi, J.Y. and C.F. Aquadro. 2015. Molecular evolution of Drosophila germline stem cell and neural stem cell regulating genes. Genome Biology and Evolution 7(11):3097-3114.
  • Choi, J.Y., J.E. Bubnell, and C.F. Aquadro.  2015. Population genomic analysis of the infectious and integrated Wolbachia pipientis genomes in Drosophila ananassae. Genome Biology and Evolution 7(8):236-82.
  • Choi, J.Y. and C.F. Aquadro. 2014. The coevolutionary period of Wolbachia pipientis infecting Drosophila ananassae and its impact on the evolution of the host germline stem cell regulating genes. Molecular Biology and Evolution  31(9):2457-2471.
  • Cutter, A.D. and J.Y. Choi. 2010. Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae. Genome Research 20: 1103-1111.



Jaclyn E. “Jackie” Bubnell

Graduate Student

I am interested in understanding the functional consequences of evolution in Drosophila using population genetic and functional approaches. Our lab and others have identified a set of germline stem cell genes that have been undergoing rapid, adaptive evolution in the sister species Drosophila melanogaster and Drosophila simulans. In D. melanogaster, these genes play key roles in the maintenance and differentiation of the germline, but their functions have not been defined in other Drosophila species. Have these genes been rapidly evolving due to changes in germline function, or is there an evolutionary conflict resulting in an “arms race,” thereby driving sequence diversification?

I’m currently working to functionally characterize these genes in D. simulans and other divergent Drosophila species to determine if core germline function has diverged. I plan to define both the expression patterns of these genes as well as protein function. I’m also exploring the possibility that the maternally inherited germline parasite Wolbachia pipientis has introduced an evolutionary conflict with the host germline and is thereby driving the positive selection of a subset of the rapidly evolving germline stem cell genes, especially bag of marbles which our lab has shown to be genetically interacting with Wolbachia.


  • Choi, J.Y., J.E. Bubnell, and C.F. Aquadro.  2015. Population genomic analysis of the infectious and integrated Wolbachia pipientis genomes in Drosophila ananassae. Genome Biology and Evolution 7(8):236-82.
  • Flores, H.A.F., J.E. Bubnell, C.F. Aquadro, and D.A. Barbash.  2015. The Drosophila bag of marbles gene interacts genetically with Wolbachia and shows female-specific effects of divergence. PLoS_Genetics  11(8):e1005453.
  • Choi, J.Y., J.E. Bubnell, and C.F. Aquadro.  2015. Population genomic analysis of the infectious and integrated Wolbachia pipientis genomes in Drosophila ananassae. Genome Biology and Evolution 7(8):236-82.
  • Bubnell J, Pfister P, Sapar ML, Rogers ME, Feinstein P. 2013. β2 Adrenergic Receptor Fluorescent Protein Fusions Traffic to the Plasma Membrane and Retain Functionality. PLoS ONE 8(9): e74941.








Kristen Rose Baxter

Undergrad Research Student

I’m an undergraduate working closely alongside Chip and Jackie to assist with their research. At Cornell, I’m studying Biology with a concentration in Genetics, Genomics, and Development. When I’m not in the lab, you can probably find me at Schoellkopf Stadium or Lynah Rink playing with the Big Red Marching Band and Big Red Pep Band.