About the project
The Hawaiian Drosophila Genomes Project is a collaborative effort to sequence, assemble, and compare the genomes of all of the estimated 1,000 species of flies in the family Drosophilidae endemic to the Hawaiian Islands. This evolutionary radiation is one of the most remarkable examples of biological diversification in our modern world, and it provides an unparalleled opportunity to understand how evolution acts upon the genome to generate novel morphological, ecological, and behavioral traits. At the same time, threats from habitat loss and invasive species, among others, present an urgent need to monitor and conserve this unique biodiversity. Our objectives are to build a comprehensive and publicly available genomic resource that will unlock our understanding of the genetic basis of evolutionary innovation while providing new tools to aid in their conservation for generations to come.
Research Goals
- Sequence, assemble, and annotate genomes from all species of Hawaiian Drosophila and Scaptomyza
- Reconstruct the evolutionary relationships and history of the clade
- Analyze genomic variation, population structure, and signatures of selection
- Build genomic tools for species identification, monitoring, and conservation
Team
Samuel Church, PhD
New York University
Co-founder, Principal Investigator
Bernard Kim, PhD
Princeton University
Co-founder, Principal Investigator
Augusto Santos Rampasso, PhD
Princeton University
Postdoctoral Researcher
Taiya Jarva
New York University
Bioinformatician
Jocelyn Wang
Princeton University
PhD Student
Joseph Arguelles
New York University
Postdoctoral Associate
Cameron Morris
New York University
MSc Student
Selin Bayraktaroglu
New York University
MSc Student
Data & Resources
All new data generated for this work will be made publicly available and deposited at NCBI SRA and GenBank.
Data from previous publications is available under BioProject PRJNA1020440. The whole-genome alignment is archived at Dryad. Illumina-only assemblies, RepeatModeler2 libraries, variant calls, diploid assemblies, genomes, and phylogenetic trees are archived at Zenodo. Raw Nanopore signal data (fast5, pod5) are available upon email request due to large file sizes.
Publications
Research findings and discoveries from the Hawaiian Drosophila Genomes Project are published in peer-reviewed journals. Publications will be listed here as they become available.
- Kim, B. Y., Gellert, H. R., Church, S. H., Suvorov, A., Anderson, S. S., Barmina, O., Beskid, S. G., Comeault, A. A., Crown, K. N., Diamond, S. E., & Dorus, S. (2024). Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life. PLoS Biology, 22(7), e3002697. https://doi.org/10.1371/journal.pbio.3002697 [link to PDF]