Jarrett Phillips

My research uses mathematical, statistical and computational methods to answer fundamental and applied conservation questions in biodiversity science, evolutionary biology, ecology, genomics and bioinformatics, as they relate to molecular species identification and discovery through DNA barcoding and other DNA-based approaches.

• Agent-based, compartmental, and individual-based modelling
• Bayesian computing and statistics in R and Stan
• Biodiversity informatics (e.g., DNA barcoding, environmental DNA (eDNA) DNA sequences analysis)
• Data science
• Machine learning (e.g., association rule generation, clustering, classification, and dimensionality reduction of (e)DNA sequence data and related metadata)
• Nonparametric statistics (e.g., bootstrap resampling, local regression, kernel methods)
• Spatiotemporal modelling (e.g., conditionally autoregressive models (CARs)
• Gaussian processes (GPs)/Kriging, generalized additive models (GAMs), time series)
• Stochastic optimization (e.g., random search algorithms, genetic algorithms (GAs), simulated annealing)

1. Phillips, J.D., Athey, T.B.T., Hanner, R.H. and McNicholas, P.D. VLF: An R package for the analysis of very low frequency variants in DNA sequences. Biodiversity Data Journal, e96480. DOI: 10.3897/BDJ.11.e98480.

2. Phillips, J.D., Gillis, D.J. and Hanner, R.H. (2022). Lack of statistical rigor in DNA barcoding likely invalidates the presence of a true species’ barcode gap. Frontiers in Ecology and Evolution, 10: 859099. DOI: 10.3389/fevo.2022.859099.

3. D’Ercole, J., Dincă, V., Opler, P.A., Kondla, N.G., Schmidt, C.B., Phillips, J.D., Robbins, R., Burns, J.M., Miller, S.E., Grishin, N., Zakharov, E.V., deWaard, J.R., Ratnasingham, S. and Hebert, P.D.N. (2020). A DNA barcode library for the butterflies of North America. PeerJ, 9: e11157. DOI: 10.7717/peerj.11157.

4. Phillips, J.D., *French, S.H., Hanner, R.H. and Gillis, D.J. (2020). HACSim: An R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves. PeerJ Computer Science, 6(192): 1-37. DOI: 10.7717/peerj-cs.243.

5. Phillips, J.D., Gillis, D.J. and Hanner, R.H. (2019). Incomplete estimates of genetic diversity within species: Implications for DNA barcoding. Ecology and Evolution, 9(5): 2996-3010. DOI: 10.1002/ece3.4757.

6. Phillips, J.D., Gwiazdowski, R.A., Ashlock, D. and Hanner, R. (2015). An exploration of sufficient sampling effort to describe intraspecific DNA barcode haplotype diversity: examples from the ray-finned fishes (Chordata: Actinopterygii). DNA Barcodes, 3: 66-73. DOI: 10.1515/dna-2015-0008.

Raymond, K., Sobkowich, K.E., Phillips, J.D., Nguyen, L., McKechnie, I., Mohideen, R.N., Fitzjohn, W.,

Szurkowski, M., Davidson, J., Rushton, J., Stacey, D.A., and Bernardo T.M. (2024). GBADs informatics

strategy: User-centric tools, data quality, and model interoperability. WOAH Scientific and Technical

Review, 43: 96-107. DOI: 10.20506/rst.43.3522.

Phillips, J.D., Griswold, C.K., Young, R.G., Hubert, N., and Hanner, R.H. (2024). A Measure of the DNA

Barcode Gap for Applied and Basic Research. In: DeSalle, R. (eds) DNA Barcoding. Methods in Molecular

Biology, vol 2744. Humana, New York, NY.

URL: https://link.springer.com/protocol/10.1007/978-1-0716-3581-0_24

Hubert, N., Phillips, J.D., and Hanner, R.H. (2024). Delimiting Species with Single-Locus DNA

Sequences. In: DeSalle, R. (eds) DNA Barcoding. Methods in Molecular Biology, vol 2744. Humana, New

York, NY. URL: https://link.springer.com/protocol/10.1007/978-1-0716-3581-0_3