Charles Aquadro
Professor of Population Genetics

Population genetics and molecular evolution

Charles Aquadro




Department of Molecular Biology and Genetics
235 Biotechnology Building
Cornell University
Ithaca, NY 14853-2703


Web Sites

Lab Web Site
Department Profile


Charles ("Chip") Aquadro is the Charles A. Alexander Professor of Biological Sciences, and Professor of Population Genetics in the Department of Molecular Biology and Genetics, with a joint appointment in the Department of Ecology and Evolutionary Biology. He received a B.S. in Biology at St. Lawrence University in 1975, an M.S. in Zoology at the University of Vermont in 1978 (with C.W. Kilpatrick) and a Ph.D. in Genetics at the University of Georgia in 1981 (with J.C. Avise). Prior to joining the Cornell faculty in 1985, he was a member of the Laboratory of Genetics with C.H. Langley at the National Institute of Environmental Health Sciences (NIH). He currently serves on the Council of the Society of Molecular Biology and Evolution, has served as Associate Editor for “Molecular Biology and Evolution” and “Evolution”, on the editorial board for “Genome Research”, and on numerous NIH proposal review panels. A founding member of the Cornell Genomics Initiative in 1997, he chaired the Evolutionary Genomics and the Computational and Statistical Genomics focus groups, served as a member of the Provost's Life Science Advisory Council, and chaired the Department of Molecular Biology and Genetics from 2004-2007. He was elected Fellow of the American Association for the Advancement of Science in 1993, and selected as the Genetics Society of Australia's "Society Visitor" for 1994. From 1998-2001, he was a member of the Scientific Advisory Board for the seven show PBS TV series, "Evolution", with WGBH/NOVA ( Aquadro's research has been supported by the National Institutes of Health, the National Science Foundation, the USDA, and the Alfred P. Sloan Foundation. He is a member of the graduate fields of Genetics and Development, and Ecology and Evolutionary Biology. He teaches Population Genetics, an Exploration on Genomic Diversity for Introductory Biology, and contributes to teaching Problems in Genetics and Development.

Research Description

Our research efforts are aimed at discovering the principles and processes that determine the nature, amount, distribution, and functional significance of genetic variation within and between natural populations and among related species. We draw on the tools of experimental and theoretical population genetics, molecular evolution, and comparative genomics to study the structure and evolution of the genome, natural populations, to resolve the evolutionary forces acting on individual genes, and to functionally annotate the genome (particularly that of Drosophila). Our work includes experimental studies of sequence variation and gene structure and function, as well as the development and refinement of statistical and computational methods for detecting selection on synonymous sites, distinguishing natural selection from population demography, and for detecting molecular coevolution (the statistical and computational studies in collaboration with Carlos Bustamante, Rasmus Nielsen and Rick Durrett). Current work focuses on the molecular genetic basis of adaptation in insects, mammals and plants, the functional significance of synonymous (“silent”) variation, the genomic distribution of recombination and its influence on levels and the genomic and geographic distribution of DNA sequence variation, and on the use of evolutionary diversification to understand molecular and evolutionary processes that modulate fertilization and regulate germ line stem cell maintenance and differentiation in Drosophila. See the Aquadro Lab website for additional detail, as well as the publications listed below.

Selected Publications

Demogines, A., A. Wong, C. Aquadro and E. Alani. 2008. Incompatibilities involving yeast mismatch repair genes: role for genetic modifiers and implications for disease penetrance and variation and genomic mutation rates. PLoS Genetics 4(6):e1000103.

Wong, A., M.C. Turchin, M.F. Wolfner and C.F. Aquadro. 2008. Evidence for positive selection on Drosophila melanogaster seminal fluid protease homologs. Molecular Biology and Evolution, 25:497-506.

Jensen, J.D., K. Thornton, and C.F. Aquadro. 2008. Inferring selection in partially sequenced regions. Molecular Biology and Evolution, 25:438-446.

Singh, N.D., V.L. Bauer DuMont, M.J. Hubisz, R. Nielsen, and C.F. Aquadro. 2007. Patterns of mutation and selection at synonymous sites in Drosophila. Molecular Biology and Evolution 24:2687-2697.

Jensen, J.D., A. Wong, and C.F. Aquadro. 2007. Approaches for identifying targets of positive selection. Trends in Genetics 23:568-577.

Drosophila Comparative Genome Sequencing and Analysis Consortium. 2007. Evolution of genes and genomes in the context of the Drosophila phylogeny. Nature 450:203-218.

Bauer DuMont, V.L., H.A. Flores, M.H. Wright, and C.F. Aquadro. 2007. Recurrent positive selection at Bgcn, a key determinant of germline differentiation, does not appear to be driven by simple co-evolution with its partner protein Bam. Molecular Biology and Evolution 24:182-191.

Wong, A., J.D. Jensen, J.E. Pool and C.F. Aquadro. 2007. Phylogenetic incongruence in the Drosophila melanogaster species group. Molecular Phylogenetics and Evolution 43:1138-1150.

Pool, J.E. and C.F. Aquadro. 2007. The genetic basis of adaptive pigmentation variation in Drosophila melanogaster. Molecular Ecology 16:2844-2851. (see News and Views by Kohn & Wittkopp 2007. Molec. Ecol. 16:2831-2833).

Jensen, J.D., V. Bauer DuMont, A.B. Ashmore, A. Gutierrez, and C.F. Aquadro. 2007. Patterns of sequence variability and divergence at the diminutive gene region of Drosophila melanogaster: complex patterns suggest an ancestral selective sweep. Genetics 177:1071-1085.

Jensen, J.D., K.R. Thornton, C.D. Bustamante, and C.F. Aquadro. 2007. On the utility of linkage disequilibrium as a statistic for identifying targets of positive selection in non-equilibrium populations. Genetics 176:2371-2379.

Nielsen, R., V.L. Bauer DuMont, M.J. Hubisz, and C.F. Aquadro. 2007. Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila. Molecular Biology and Evolution, 24:228-235.

Hamm, D., B.S. Mautz, M.F. Wolfner, C.F. Aquadro, and W.J. Swanson. 2007. Evidence for amino acid diversity-enhancing selection within humans and among primates at the candidate primate sperm-receptor gene PKDREJ. American Journal of Human Genetics 81:44-52.

Williams, B., G. Leung, H. Maiato, A. Wong, Z. Li, E.V. Williams, C. Kirkpatrick, C.F. Aquadro, C.L. Rieder, and M.L. Goldberg. 2007. Mitch: a rapidly-evolving component of the Ndc80 kinetochore complex required for proper chromosome segregation in Drosophila. Journal of Cell Science 120:3522-3533.

Pool, J.E., V. Bauer DuMont, J.L. Mueller, and C.F. Aquadro. 2006. A scan of molecular variation leads to the narrow localization of a selective sweep affecting both Afrotropical and cosmopolitan populations of Drosophila melanogaster. Genetics 172:1093-1105.

Heck, J.A., J.L. Argueso, Z. Gemici, R.G. Reeves, A. Bernard, C.F. Aquadro and E.Alani. 2006. Negative epistasis between natural variants of the Saccharomyces cerevisiae MLH1 and PMS1 genes results in a defect in mismatch repair. Proc. Natl. Acad. Sci. USA. 103:3256-3261.

Hamblin, M.T., A.M. Casa, H. Sun, S.C. Murray, A.H. Paterson, C.F. Aquadro, and S. Kresovich. 2006. Challenges of detecting directional selection after a bottleneck: lessons from Sorghum bicolor. Genetics 173:953-962.

Reed, F.A., and C.F. Aquadro. 2006. Mutation, selection and the future of human evolution. Trends in Genetics 22:479-484.

Pool, J.E., A. Wong, and C.F. Aquadro. 2006. Finding of male-killing Spiroplasma infecting Drosophila melanogaster in Africa implies transatlantic migration of this endosymbiont. Heredity 97:27-32.

Casa, A.M., S.E. Mitchell, J.D. Jensen, M.T. Hamblin, A.H. Paterson, C.F. Aquadro and S. Kresovich. 2006. Evidence for a selective sweep on chromosome 1 of cultivated sorghum. The Plant Genome, a Suppl. to Crop Science 46:S-27 – S-40.

Pool, J.E. and C.F. Aquadro. 2006. History and structure of sub-Saharan populations of Drosophila melanogaster. Genetics 174:915-929.

Bauer DuMont, V. and C.F. Aquadro. 2005. Multiple signatures of positive selection downstream of Notch on the X chromosome in Drosophila melanogaster. Genetics 171:639-653.

Reed, F.A., J. Akey and C.F. Aquadro. 2005. Fitting a background-selection model to levels of nucleotide variation and divergence along the human autosomes. Genome Research, 15:1211-1221.

Jensen, J.D., Y. Kim, V. Bauer DuMont, C.F. Aquadro and C.D. Bustamante. 2005. Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170:1401-1410.

Mueller, J.L., K.R. Ram, L.A. McGraw, M.C. Bloch Qazi, E.D. Siggia, A.G. Clark, C.F. Aquadro, and M.F. Wolfner. 2005. Cross-species comparison of Drosophila male accessory gland protein genes. Genetics 171:131-143.

Reed, F.A., R.G. Reeves and C.F. Aquadro. 2005. Evidence of susceptibility and resistance to cryptic X-linked meiotic drive in natural populations of Drosophila melanogaster. Evolution, 59:1280-1291.

Casa, A.M., S.E. Mitchell, M.T. Hamblin, H. Sun, J.E. Bowers, A.H. Paterson, C.F. Aquadro and S. Kresovich. 2005. Diversity and selection in sorghum: simultaneous analyses using simple sequence repeats. Theoretical and Applied Genetics 111:23-30.

Mueller, J.L., D.R. Ripoll, C.F. Aquadro and M.F. Wolfner. 2004. Comparative structural modeling and inference of conserved protein classes in Drosophila seminal fluid. Proc. Natl. Acad. Sci. USA. 101:13542-13547.

Swanson, W.J., A. Wong, M.F. Wolfner and C.F. Aquadro. 2004. Evolutionary expressed sequence tag analysis of Drosophila female reproductive tracts identifies genes subjected to positive selection. Genetics 168:1457-1465.

Sainudiin, R., R.T. Durrett, C.F. Aquadro and R. Nielsen. 2004. Microsatellite mutation models: Insights from a comparison of humans and chimpanzees. Genetics 168:383-395.

Bauer DuMont, V., J.C. Fay, P.P. Calabrese and C.F. Aquadro. 2004. DNA variability and divergence at the Notch locus in Drosophila melanogaster and D. simulans: A case of accelerated synonymous site divergence. Genetics 167:171-185.

Reed, F.A., E. J. Kontanis, K.A.R. Kennedy, and C.F. Aquadro. 2003. Ancient DNA prospects from Sri Lankan highland dry caves support an emerging global pattern. American Journal of Physical Anthropology 121(2):112-116.

Amos, W., C.M. Hutter, M.D. Schug, and C.F. Aquadro. 2003. Directional evolution of size coupled with ascertainment bias for variation in Drosophila microsatellites. Molecular Biology and Evolution. 20:660-662.

Odgers, W.A., C.F. Aquadro, C.W. Coppin, M.J. Healy, and J.G. Oakeshott. 2002. Nucleotide polymorphism in the Est6 promoter, which is widespread in derived populations of Drosophila melanogaster, changes the level of Esterase 6 expressed in the male ejaculatory duct. Genetics 162:785-797.

Swanson, W.J. and C.F. Aquadro. 2002. Positive Darwinian selection promotes diversity amongst members of the antifreeze protein multigene family. Journal of Molecular Evolution 54:403-410.

Aquadro, C.F., V. Bauer DuMont, and F.A. Reed. 2001. Genome-wide variation in the human and fruitfly: a comparison. Current Opinion in Genetics & Development 11:627-634.

Schmid, K.J. and C.F. Aquadro. 2001. The evolutionary analysis of "orphans" from the Drosophila genome identifies incorrectly annotated and rapidly evolving genes. Genetics 159:589-598.

Calabrese, P.P., R.T. Durrett, and C.F. Aquadro. 2001. Dynamics of microsatellite divergence under stepwise mutation and proportional slippage/point mutation models. Genetics 159:839-852.

Swanson, W.J.. A.G. Clark, H.M. Waldrip-Dail, M.F. Wolfner and C.F. Aquadro. Evolutionary EST analysis identifies rapidly evolving male reproductive genes in Drosophila. Proc. Natl. Acad. Sci. USA, 98:7375-7379.

Pascual, M., C.F. Aquadro, V. Soto, and L. Serra. 2001. Microsatellite variation in colonizing and Paelarctic populations of Drosophila obscura. Mol. Biol. Evol. 18:731-740.

Swanson, W.J., Z. Yang, M.F. Wolfner and C.F. Aquadro. 2001. Positive Darwinian selection drives the evolution of female reproductive proteins in mammals. Proc. Natl. Acad. Sci. USA 98:2509-2514.

Swanson, W. J., C. F. Aquadro, and V. D. Vacquier. 2001. Polymorphism in abalone fertilization proteins is consistent with the neutral evolution of the egg's receptor for lysin (VERL) and positive Darwinian selection of sperm lysin. Mol. Biol. Evol. 18:376-383.

Click here to view Dr. Aquadro's PubMed listings.