Current members (bold) and previous members (*) of the PMEL Ocean Molecular Ecology

2024:

Klymus, K.E., J. D. Baker, C. L. Abbot, R. J. Brown, J. M. Craine, Z. Gold, M. E. Hunter, M. D. Johnson, D. N. Jones, M. J. Jungbluth, and S. P. Jungbluth. (2024): The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data. Metabarcoding and Metagenomics, 8, p.e128689, https://doi.org/10.3897/mbmg.8.128689

 

Parsons, K., S. May, Z. Gold, M. Dahlheim, C. Gabriele, J. Straley, J. Moran, K. Goetz, A. Zerbini, L. Park, and P. Morin. (2024): Using eDNA to Supplement Population Genetic Analyses for Cryptic Marine Species: Identifying Population Boundaries for Alaska Harbour Porpoises. Molecular Ecology, e17563, https://doi.org/10.1111/mec.17563

 

Goodwin, K. D., C. M. Aiello, M. Weise, M. Edmondson,  K. Fillingham, D. Allen, A. Amerson,  M.L. Barton, A. Benson, G. Canonico, G., Z. Gold,  J. Gumm, M. Hunter, N. Joffe, R. Lance, A. Larkin, R. Letelier, C. Lipsky, D. McCoskey, C. Morrison, K. Clark, J.A. Darling, A-J. Demery, M. Everett, C. Fletcher-Hoppe, K.M. Nichols, K.M. Parsons, J. Price, K. Puglise, K. Scholl, M.K. Schwartz, A. Sepulveda, J. Shannon, W. Turner, T. White (2024): National Aquatic Environmental DNA Strategy. White House Office of Science, Technology, and Policy (OSTP), https://www.whitehouse.gov/wp-content/uploads/2024/06/NSTC_National-Aquatic-eDNA-Strategy.pdf

 

Stepien C. A.*, H. K. Schultz, S. M. McAllister, E. L. Norton, and J. E. Keister (2024): Evaluating Metabarcoding Markers for Identifying Zooplankton and Ichthyoplankton Communities to Species in the Salish Sea: Morphological Comparisons and Rare, Threatened or Invasive Species​. DNA, 4(1), 1-33, https://doi.org/10.3390/dna4010001

2023:

Galaska, M.P.*, S.D. Brown, and S.M. McAllister (2023): [Spotlight] Monitoring biodiversity impacts of a changing Arctic through environmental (e)DNA. Oceanography, 36(2–3), 109–113, https://doi.org/10.5670/oceanog.2023.221

McAllister, S.M., C. Paight*, E. Norton*, and M.P. Galaska* (2023): [Spotlight] REVAMP: Rapid Exploration and Visualization through an Automated Metabarcoding. Oceanography, 36(2–3), 114–119, https://doi.org/10.5670/oceanog.2023.231

Rabinowitz, C.N.*, S.D. Brown, S.M. McAllister, A.K. Winans, J.E. Keister, and M.P. Galaska* (2023): The complete mitochondrial genome of Cyphocaris challengeri (Amphipoda: Cyphocarididae). Mitochondrial DNA Part B, 8(10), 1128-1131, https://doi.org/10.1080/23802359.2023.2270206

Waters, T., K. Langlois, Z. Gold, S. Theroux , & R.A. Eagle (2023): Hidden in plain sight: The invasive macroalga Caulerpa prolifera evades detection by environmental DNA methods. Environmental DNA, 00(1–10), https://doi.org/10.1002/edn3.496

Kelly, R.P., D.M. Lodge, K.N. Lee, S. Theroux, A.J. Sepulveda, C.A. Scholin, J.M. Craine, E. Andruszkiewicz Allan, K.M. Nichols, K.M. Parsons, K.D. Goodwin, Z. Gold, F.P. Chavez, R.T. Noble, C.L. Abbott, M.R. Baerwald, A.M. Naaum, P.M. Thielen, A.L. Simons, C.L. Jerde, J.J. Duda, M.E. Hunter, J.A. Hagan, R.S. Meyer, J.A. Steele, M.Y. Stoeckle, H.M. Bik, C.P. Meyer, E. Stein, K.E. James, A.C. Thomas, E. Demir-Hilton, M.A. Timmers, J.F. Griffith, M.J. Weise, and S.B. Weisberg (2023): Toward a national eDNA strategy for the United States. Environmental DNA, 00, 1-10, https://doi.org/10.1002/edn3.432

Curd, E.E., L. Gal, R. Gallego, K. Silliman, S. Nielsen, and Z. Gold (2023): rCRUX: A rapid and versatile tool for generating metabarcoding reference libraries in R. Environmental DNA, 00, 1–16, https://doi.org/10.1002/edn3.489

Gold, Z., M.Q. Koch, N.K. Schooler, K.A. Emery, J.E. Dugan, R.J. Miller, H.M. Page, D.M. Schroeder, D.M. Hubbard, J.R. Madden, S.G. Whitaker, and P.H. Barber (2023): A comparison of biomonitoring methodologies for surf zone fish communities. PLoS ONE, 18(6), e0260903, https://doi.org/10.1371/journal.prone.0260903

Waters, T., Z. Gold, A. Obaza, R.F. Ambrose, and R.A. Eagle (2023): Environmental DNA metabarcoding reveals distinct fish assemblages supported by seagrass (Zostera marina and Zostera pacifica) beds in different geographic settings in Southern California. PLoS One, 18(10), e0286228, https://doi.org/10.1371/journal.pone.0286228

Hakimzadeh, A., A. Abdala Asbun, D. Albanese, M. Bernard, D. Buchner, B. Callahan, J.G. Caporaso, E. Curd, C. Djemiel, M. Brandström Durling, V. Elbrecht, Z. Gold, H.S. Gweon, M. Hajibabaei, F. Hildebrand, V. Mikryukov, E. Normandeau, E. Özkurt, J.M. Palmer, G. Pascal, T.M. Porter, D. Straub, M. Vasar, T. Větrovský, H. Zafeiropoulos, and S. Anslan (2023): A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses. Molecular Ecology Resources, 00, 1–17, https://doi.org/10.1111/1755-0998.13847

Gold, Z., A.O. Shelton, H.R. Casendino, J. Duprey, R. Gallego, A. Van Cise, M. Fisher, A.J. Jensen, E. D'Agnese, E. Andruszkiewicz Allan, A. Ramón-Laca, M. Garber-Yonts, M. Labare, K.M. Parsons, and R.P. Kelly (2022): Signal and noise in metabarcoding data. PLoS ONE, 18(5), e0285674, https://doi.org/10.1371/journal.pone.028567

Gold, Z., R.P. Kelly, A.O. Shelton, A.R. Thompson, K.D. Goodwin, R. Gallego, K.M. Parsons, L.R. Thompson, D. Kacev, and P.H. Barber (2023): Archived DNA reveals marine heatwave-associated shifts in fish assemblages. Environmental DNA, 00, 1-14, https://doi.org/10.1002/edn3.400

Satterthwaite, E.V., A.E. Allen, R.H. Lampe, Z. Gold, A.R. Thompson, N. Bowlin, R. Swalethorp, K.D. Goodwin, E.L. Hazen, S.J. Bograd, S.A. Matthews, and B.X. Semmens (2023): Toward identifying the critical ecological habitat of larval fishes: An environmental DNA window into fisheries management. In: Frontiers in Ocean Observing: Emerging Technologies for Understanding and Managing a Changing Ocean. E.S. Kappel, V. Cullen, M.J. Costello, L. Galgani, C. Gordó-Vilaseca, A. Govindarajan, S. Kouhi, C. Lavin, L. McCartin, J.D. Müller, B. Pirenne, T. Tanhua, Q. Zhao, and S. Zhao, eds, Oceanography, 36, 90-93, https://doi.org/10.5670/oceanog.2023.s1.29

2022:

Shelton, A.O., Z. Gold, E. Allen, E. D’Agnese, A. Van Cise, R. Gallego, K. Parsons, J. Duprey, H. Casedino, M. Garber-Yonts, M. Fisher, R. Kelly (2022): Towards Quantitative Metabarcoding. Ecology, 104(2), e3906, https://doi.org/10.1002/ecy.3906

Gold, Z., A.R. Wall, Teia M. Schweizer, N.D. Pentcheff, E.E. Curd, P.H. Barber, R.S. Meyer, R. Wayne, K. Stolzenbach, K. Prickett, J. Luedy, and R. Wetzer (2022): A manager's guide to using eDNA metabarcoding in marine ecosystems. PeerJ, 10, e14071, http://doi.org/10.7717/peerj.14071

Garber, A.I., C. R. Armbruster, S.E. Lee, V.S. Cooper, J.M. Bomberger, and S.M. McAllister (2022): SprayNPray: User-friendly taxonomic profiling of genome and metagenome contigs. BMC Genomics, 23(1), 1-8, https://doi.org/10.1186/s12864-022-08382-2

2021:

Galaska, M.P.*, G. Liu, D. West, K. Erickson, A. M. Quattrini, A. Bracco, and S. Herrera (2021): Seascape genomics reveals metapopulation connectivity network of Paramuricea biscaya in the northern Gulf of Mexico. Front. Mar. Sci., 8, 790929, https://doi.org/10.3389/fmars.2021.790929

Galaska, M.P.*, D.S. Wethey, A. Arias, S.F. Dubois, K.M. Halanych, and S.A. Woodin (2021): The impact of aquaculture on the genetics and distribution of the onuphid annelid Diopatra biscayensis. Ecol. Evol., 11(11), 6184-6194, https://doi.org/10.1002/ece3.7447

Resh, C.A., Galaska, M.P.*, K.C. Benesh, J.P.A. Gardner, K.-J. Wei, R.-J. Yan, and A.R. Mahon (2021): Using genomics to link populations of an invasive species to its potential sources. Front. Ecol. Evol., 9, 575599, https://doi.org/10.3389/fevo.2021.575599

Garber, A.I., G.A. Ramírez, S.M. McAllister, W. Orsi, and S. D’Hondt (2021): Cryptic metabolisms in anoxic subseafloor sediment. Environ. Microbiol. Rep., 13(5), 696-701, https://doi.org/10.1111/1758-2229.12983

2020:

Stepien, C.A.*, D. Leaman, and M.D. Niner. (2020): Chapter 4: Rhabdoviruses (with focus on Viral Hemorrhagic Septicemia Virus and other Novirhabdoviruses). In: Woo, P.T.K, J. Leong, & K. Buchmann. Climate Change and Infectious Fish Diseases. CABI, England, U.K.

2019:

Stepien, C.A.*, M.R. Snyder, A.E*. Elz. (2019): Invasion genetics of the silver carp Hypophthalmichthys molitrix across North America: Differentiation of fronts, introgression, and eDNA metabarcode detection. PLoS ONE, 14(3), e0203012., https://doi.org/10.1371/journal.pone.0203012

Marshall, N.T.*, C.A. Stepien*. (2019): Invasion genetics from eDNA and thousands of larvae: A targeted metabarcoding assay that distinguishes species and population variation of zebra and quagga mussels. Ecol. Evol., 9(6), 1-24, https://doi.org/10.1002/ece3.4985

Canonico, G., Buttigieg, P.L…Stepien, C.A.*, … et al. (2019): Global Observational Needs and Resources for Marine Biodiversity. Front. Mar. Sci., 6(367), https://doi.org/10.3389/fmars.2019.00367

Marshall, N.*, and C.A. Stepien* (2019): Dreissenidae. Chapter 42 in Freshwater Mollusks of the World: A Distribution Atlas, C. Lydeard and K.S. Cummings (eds.), Johns Hopkins University Press.

2018:

Stepien, C.A.*, D.J. Eddins, M.R. Snyder*, and N.J. Marshall* (2018): Genetic change versus stasis over the time course of invasions: Trajectories of two concurrent, allopatric introductions of the Eurasian ruffe. Aquat. Invasions, 13(4), 537–552, https://doi.org/10.3391/ai.2018.13.4.11

Stepien, C.A.*, M.R. Snyder*, and C.T. Knight (2018): Genetic divergence of nearby walleye spawning groups in central Lake Erie: Implications for management. N. Am. J. Fish. Manage., 38(4), 783–793, https://doi.org/10.1002/nafm.10176

Tajbakhsk, F., C.A. Stepien*, A. Abdoli, N. Tabatabaei, and B.H. Kiabi (2018): Geometric morphometric and meristic analysis of the deepwater goby, Ponticola bathybius (Kessler, 1877) (Teleostei: Gobiidae) in the Iranian waters of the Caspian Sea. Iran. J. Ichthyol., 5(1), 64–73.

Shepherd, B.S., A.R. Spear, A.M. Phillip, D.W. Leaman, C.A. Stepien*, O.J. Sepulveda-Villet, D.E. Palmquist, and M.M. Vijayan (2018): Effects of cortisol and lipopolysaccharide on expression of select growth-, stress- and immune-related genes in rainbow trout liver. Fish Shellfish Immunol., 74, 410-418, https://doi.org/10.1016/j.fsi.2018.01.003

2017:

Klymus, K.E., N.T. Marshall*, and C.A. Stepien* (2017): Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes. PLoS ONE, 12(5), e0177643, https://doi.org/10.1371/journal.pone.0177643

Trebitz, A., J. Hoffman, J. Darling, E. Pilgrim, J. Kelly, E. Brown, W. Chadderton, S. Egan, E. Grey, S. Hashsham, K. Klymus, A. Mahon, J. Ram, M. Schjuiltz, C.A. Stepien*, and J. Schardt (2017): Early detection monitoring for aquatic non-indigenous species: Optimizing surveillance, incorporating advanced technologies, and identifying research needs. J. Environ. Manage., 202(1), 299–310, https://doi.org/10.1016/j.jenvman.2017.07.045

Ke, Q., W. Weaver, A. Pore, B. Gorgoglione, J. Halo Wildschutte, P. Xiao, B.S. Shepherd, A. Spear, K. Malathi, C.A. Stepien*, V.N. Vakharia, and D.W. Leaman (2017): Role of Viral Hemorrhagic Septicemia Virus Matrix (M) protein in suppressing host transcription. J. Virol., 91(19), e00279-17, https://doi.org/10.1128/JVI.00279-17

Snyder, M.R.*, and C.A. Stepien* (2017): Genetic patterns across an invasion's history: A test of change versus stasis for the Eurasian round goby in North America. Mol. Ecol., 26(4), 1075–1090, https://doi.org/10.1111/mec.13997

Stepien, C.A*., S.I. Karsiotis, T.J. Sullivan, and K.E. Klymus (2017): Population genetic structure and comparative diversity of smallmouth bass Micropterus dolomieu: Congruent patterns from two genomes. J. Fish Biol., 90(5), 2125–2147, https://doi.org/10.1111/jfb.13296