Charles Aquadro

The Aquadro lab closed after 40+ years and Chip retires the end of 2025.

I have been a research scientist and educator. I view these responsibilities part of a continuum that runs from current students to alumni to the general public. My research focused on discovering basic principles that determine the amount of diversity that exists within and between the genomes of organisms, and how we can use that diversity to understand organismal diversity, to discover novel genes, to maximize human health, and to advance agriculture. Our research was carried out primarily with Drosophila, though past work has included mammals and plants. Our most recent research aimed to evaluate the evolutionary flexibility of the genes that regulate germline stem cell maintenance and differentiation using combined population and functional genomic approaches. My teaching covered the concepts and methodologies of population genetics and comparative genomics, and personal genomics and medicine.

Recent Journal Publications

• Arnce, LR, JE Bubnell, CF Aquadro. 2025. Comparative functional and evolutionary analysis of essential germline stem cell genes across the genus Drosophila and two outgroup species. G3 (Bethesda). 2025 Oct 3:jkaf224. doi: 10.1093/g3journal/jkaf224
• Arnce, LR, JE Bubnell, CF Aquadro. 2025. Comparative analysis of Drosophila Bam and Bgcn sequences and predicted protein structure evolution. Journal of Molecular Evolution 93(2): 278-291.
• Kagemann, C.H., JE Bubnell, BG Colocho, D Arana and CF Aquadro. 2024. Wolbachia pipientis modulates germline stem cells and gene expression associated with ubiquitination and histone lysine trimethylation to rescue fertility defects in Drosophila.  Genetics Dec 18:2024.12.17.628990. doi. 10.1101/2024.12.17.628990.
• Kagemann, CH, GM Colocho, CF Aquadro. 2024. Non-ovarian Wolbachia pipientis titer correlates with fertility rescue of a Drosophila melanogaster bag of marbles hypomorph. Micropublication Biology  10.17912/micropub.biology.001233.
• Shen, R., Wenzel, M.J., Messer, P.W., and Aquadro, C.F. 2023. Evolution under a model of functionally buffered deleterious mutations can lead to positive selection in protein-coding genes.  Evolution 2023 Jul 19; qpad131. doi: 10.1093/evolut/qpad131.
• Wenzel, M.J. and Aquadro, C.F. 2023. Wolbachia infection as least partially rescues of several the fertility and ovary defects of several new Drosophila melanogaster bag of marbles protein-coding mutants. PLoS Genetics 19(10): e1011009 https:// doi.org/10.1371/journal.pgen.1011009
• Wenzel, M.J. and Aquadro, C.F. 2023. Wolbachia genetically interacts with the bag of marbles germline stem cell gene in male D. melanogaster. microPublication Biology. 0.17912/micropub.biology.000845.
• Kagemann, C.H., G. Colocho, and C.F. Aquadro. 2023. Gene expression changes in Drosophila melanogaster females associated with the rescue of the bag of marbles (bam)  hypomorph fertility defect by W. pipientis.  ​www.biorxiv.org/content/10.1101/2023.09.22.558898v1
• Bubnell, J.E., Ulbing, C.K.S., Fernandez Begne, P., Aquadro, C.F., Functional divergence of the bag of marbles gene in the Drosophila melanogaster species group, Molecular Biology and Evolution, 2022, msac137
• Johri, P, Charles F. Aquadro, CF, Beaumont, M, Brian Charlesworth, B, Excoffier, L, Eyre-Walker, A, Keightley, PD, Lynch, M, McVean, G, A. Payseur, BA, Pfeifer, SP, Stephan, W, and Jensen, JD. 2022. Recommendations for improving statistical inference in population genomics. PLoS Biology 20(5):e3001669

• 2022 Lifetime Achievement Award from the Society for Molecular Biology and Evolution
• Honorary Doctor of Science (2016) St. Lawrence University
• Stephen H. Weiss Presidential Fellow (2016) Cornell University
• Charles A. Alexander Professor of Biological Sciences (2007) Cornell University
• President (2013) Society for Molecular Biology and Evolution
• 2012 Russell Distinguished Teaching Award (2012) College of Arts & Sciences, Cornell University
• Appointed House Faculty Fellow, Hans Bethe House, Cornell University West Campus, 2009 – 2016
• Named the Charles A. Alexander Professor of Biological Sciences, Cornell University, 2007 - present
• Accomplished Alumnus Award, Department of Biology, University of Vermont, 2006
• Elected Fellow, American Association for the Advancement of Science, 1993
• Genetics Society of Australia "Society Visitor for 1994

Most recently I developed and taught a large undergraduate class in personal genomics and medicine (BioMG1290). I had previously taught the core Population Genetics course at Cornell since 1986. I also had given explorations for introductory biology students, alumni and public lectures on the genetics of diversity and genomics, and served as scientific advisor to science television (NOVA, WGBH, Discovery Channel).