Genomes are frequently in conflict with selfish DNAs – genetic elements that can spread in genomes and populations without offering any benefit, and many times even causing harm, to their hosts. Our lab integrates genomic, cytological and molecular approaches to study selfish DNA and its impact on genome evolution. Our primary interest is in satellite DNA (repetitive DNA typically found at centromeres and telomeres) and meiotic drive. Our work is funded by the NSF MCB and the NIH NIGMS. Lab projects focus on the following areas:


I. The functional and evolutionary genomics of satellite DNA

Drosophila melanogaster mitotic chromosomes labeled with a 1.688 family satellite probe.

Satellite DNAs are tandem repeats typically found at centromeres and telomeres. We use genomic, modeling, cytologenetic and molecular approaches to study the functional genomics of satellite DNAs and their dynamic evolution across taxa.




II. Molecular mechanisms of meiotic drive

A cyst of individualizing sperm in Drosophila affinis sex ratio males.

Meiotic drivers are selfish genetic elements that gain a transmission advantage through the germline. We use genetic, genomic and cytological approaches to determine the molecular mechanism of different drive systems. Our primary focus is on the selfish Segregation Distorter complex of D. melanogaster.



III. Y chromosome evolution

Drosophila guanche mitotic chromosomes: sex chromosomes are labeled with an rDNA probe.

Drosophila Y chromosomes are dense in repetitive sequences and carry few protein-coding genes, but in most species are important for male fertility.  We use  Drosophila species as models to study Y chromosome organization, function, and evolution.


IV. Evolution of centromere organization

The pileup of CENP-A (centromeric histone variant) ChIPseq reads on the complex island corresponding to the centromere on the 4th chromosome. Figure from Chang et al. 2019 PLOS Biology
Centromeres are essential chromosomal regions required for proper chromosome segregation during cell division. Disruptions in centromere function can lead to chromosomal instability, one of the hallmarks of cancer. Despite their essential function, centromeres evolve rapidly. In many species, centromeres are located in highly repetitive genome regions but the contribution of DNA sequences to centromere function is unclear, as centromere identity is determined by a centromere-specific histone variant. Drosophila species are fantastic models to study centromere function and evolution: they have small but complex genomes and are powerhouse model organisms for doing genetics. We combine comparative (epi)genomic and cytogenetic approaches to study the evolution of centromere organization in Drosophila species. Together with our collaborators, we discovered that Drosophila melanogaster centromeres correspond to islands of retroelements embedded in satellite DNA. Our current focus is on the role of centromeric DNA in centromere function and the evolutionary forces shaping the rapid evolution. We see dramatic shifts in centromere composition and organization over short evolutionary time periods in Drosophila species. We are testing the hypothesis that genetic conflicts contribute to the rapid evolutionary dynamics at centromeres.
Photinus pyralis
Genome size and organization can differ widely across species.  We are interested in the role of repetitive DNA sequences in the evolution of genome organization. We use beetles, especially fireflies, as models for genome evolution.