An optimized eDNA protocol for fish tracking in estuarine environments
Published in Scientific Reports, 2025
Optimizing MiFish Metabarcoding for Estuaries
Publications
You can also find my articles on my Google Scholar profile.
Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect.
Published in Evolutionary Applications, 2024
QTL crosses for populations of killifish that have rapidly evolved resistance to the developmental toxicity of PCBs and PAHs. We map population re-sequencing samples to the QTL map to intersect population genetic outliers and each QTLs in each cross
Developing a High-Quality Linkage Map for the Atlantic Killi sh Fundulus heteroclitus
Published in G3: Genes | Genomes | Genetics, 2019
Mapping a scaffold-level genome assembly to chromosomes with RAD-Seq
Publications:
Roback, E.,Ferrufino, E., Moran, R., Mulliniks, C., Shennard, D., Gallop, J., Weagley, J., Miller, J., Rohner, N., Kowalko, J., McGaugh, S. (2025) Population genomics of premature termination codons in cavefish with substantial trait loss. Molecular Biology and Evolution DOI: 10.1093/molbev/msaf012
El Baidouri, F., Miller, J., Kelly, M., Sevigny, J., Gilbert, H., Thomas, W. K., and Watts, A. (2025) An Optimized eDNA Protocol for Fish Tracking in Estuarine Environments. Scientific Reports, DOI: 10.21203/rs.3.rs-4740372/v1
Miller J., Clark, B., Reid, N., Nacci, D., Champlain, D., Whitehead, A. (2024) Independently evolved pollution resistance in four killifish populations is largely explained by few variants of large effect. Evolutionary Applications, DOI: 10.1101/2023.04.07.536079
Garduno-Sanchez, M., Hernandez-Lozano, J., Moran, R.L., Gamboa, R.M., Gross, J.B., Rohner, N., Elliott, W., Miller, J., Lozano-Vilano, L., McGaugh, S., Orneles-Garcia, P. (2023) Phylogeographic relationships and morphological evolution between cave and surface Astyanax mexicanus populations (De Fillipi 1853) (Actinopterygii, Characidae). Molecular Ecology, DOI: 10.22541/au.166979535.59484815/v1
Duvernell, D., Remex, N., Miller, J., Schaefer, J. (2023) Variable rates of hybridization among contact zones between a pair of topminnow species, Fundulus notatus and F. olivaceus), Ecology and Evolution, DOI: 10.1002/ece3.10399
Leland, N., Crocker Pearson, K., Burke, M., Miller, J., Watts,. A., Haney, J. (2023) Isolation of Picocyanobacteria (Order Synechococcales) and Occurrence of the Cyanotoxin Anatoxin-A in a Shallow Mesotrophic Pond. Journal of Water Resource and Protection, DOI: 10.4236/jwarp.2023.156017
Zivanovic, A., Miller, J., Munro, S., Li, Y., Passow, C., Simonaitis, P., Lynch, M. Oseth, L., Zhao, S., Feng, F., Wikström, P., Corey, E., Morrissey, C., Henzler, C., Raphael, B., Dehm, S. (2023) Co-evolution of AR gene copy number and structural complexity in endocrine therapy resistant prostate cancer. NAR Cancer, DOI: 10.1093/narcan/zcad045
Lee, R., Knutson, T., Munro, S., Miller, J., Heltemes-Harris, L., Jepsen, K., and Farrar, M. (2022) Nuclear corepressors NCOR1/NCOR2 regulate B cell development, maintain genomic integrity, and prevent transformation. Nature Immunology, 1-14, DOI: 10.1038/s41590-022-01343-7
Jellison, B., Elsmore, K., Miller J., NG, G., Ninokowa, A., Hill, T., and Gaylord, B. (2022) Low-pH Seawater Alters Indirect Interactions in Rocky-Shore Tidepools. Ecology and Evolutionary Biology, DOI: 10.1002/ece3.8607
Warren, W., Aspiras, A., Boggs, T.E., Borowsky, R., Carlson, B., Damen, F., Ferrufino, E., Gross, J., Keene, A., Kenzior, A., Kowalko, J., Lemieux, M. E., McGaugh, S., Miller, J. T., Mommersteeg, M., Moran, R., Peuß, R., Riddle, M., Sifuentes-Romero, I., Stahl, B., Sung, J. Y., Tabin, C., Thakur, S., Rohner, R. (2021) A Chromosome-level Genome of Astyanax mexicanus.\ Surface Fish for Comparing Population-specific Genetic Differences Contributing to Trait Evolution. Nature Communications, DOI: 10.1038/s41467-021-21733-z
Miller, J., Reid, N., Nacci, D., Whitehead, A. (2019) Developing a High-Quality Linkage Map for the Atlantic Killifish Fundulus heteroclitus.\ G3: Genes, Genomes, Genetics, DOI: 10.1038/srep14340
Rochman, C., Tahir, A., Williams, S., Baxa, D., Lam, R., Miller, J., Teh, F.C., Werorilangi, S., Teh, S. J. (2015) Plastic in seafood: Plastic Debris in Fish and Bivalves Sold for Human Consumption. Scientific Reports, DOI: 10.1534/g3.119.400262
Dubansky, B., Whitehead, A., Miller, J., Rice, C. D., & Galvez, F. (2013) Multitissue Molecular, Genomic, and Developmental Effects of the Deepwater Dorizon Oil Spill on Resident Gulf killifish (Fundulus grandis). Environmental Science and Technology, DOI: 10.1021/es400458p
Kolok, A., Miller, J., Schoenfuss, H. (2012) The Mini Mobile Environmental Monitoring Unit: a Novel Bio-Assessment Tool. Journal of Environmental Monitoring, DOI: 10.1039/C1EM10703H
Wisenden, B., Karst, J, Miller, J., Miller, S.D. Fuselier, L. (2008) Anti-Predator Behavior in Response to Chemical Cues in Umbra limi.\ Environmental Biology of Fishes, DOI: 10.1007/s10641-007-9255-0