Parsons, K.M., May, S.A., Gold, Z., Dahlheim, M., Gabriele, C., Straley, J.M., Moran, J.R., Goetz, K., Zerbini, A.N., Park, L. and Morin,
P.A., 2025. Using eDNA to Supplement Population Genetic Analyses for Cryptic Marine Species: Identifying Population Boundaries
for Alaska Harbour Porpoises. Molecular Ecology, p.e17563.
Theroux, S., Sepulveda, A., Abbott, C.L., Gold, Z., Watts, A.W., Hunter, M.E., Klymus, K.E., Hirsch, S.L., Craine, J.M., Jones, D.N. and
Brown, R.J., 2025. What is eDNA method standardisation and why do we need it? Metabarcoding and Metagenomics, 9,
p.e132076.
Gold, Z., Kelly, R., Shelton, A.O., Goodwin, K., Gallego, R., Parsons, K., Thompson, L., Kacev, D., Thompson, A., Barber, P.H, 2024.
Archived DNA reveals impacts of a marine heatwave on fish assemblages over multiple decades. Environmental DNA, 6(1),
p.e400.
Klymus, K.E., Baker, J.D., Abbott, C.L., Brown, R.J., Craine, J.M., Gold, Z., Hunter, M.E., Johnson, M.D., Jones, D.N., Jungbluth, M.J.
and Jungbluth, S.P., 2024. The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data.
Metabarcoding and Metagenomics, 8, p.489.
Curd, E.E., Gal, L., Gallego, R., Silliman, K., Nielsen, S. and Gold, Z., 2024. rCRUX: A rapid and versatile tool for generating
metabarcoding reference libraries in R. Environmental DNA, 6(1), p.e489.
Waters, T., Langlois, K., Gold, Z., Theroux, S., & Eagle, R. (2024). Hidden in plain sight: the invasive macroalga Caulerpa prolifera
evades detection by environmental DNA methods due to negligible shedding. Environmental DNA, 6(1), p.e496.
Hakimzadeh, A., Abdala Asbun, A., Albanese, D., Bernard, M., Buchner, D., Callahan, B., Caporaso, J. G., Curd, E., Djemiel, C.,
Brandström Durling, M., Elbrecht, V., Gold, Z., Gweon, H. S., Hajibabaei, M., Hildebrand, F., Mikryukov, V., Normandeau, E., Özkurt, E.,
M. Palmer, J. … Anslan, S. (2024). 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., Shelton, A.O., Casendino, H.R., Duprey, J., Gallego, R., Van Cise, A., Fisher, M., Jensen, A.J., D’Agnese, E., Andruszkiewicz
Allan, E. and Ramón-Laca, A., (2023). Signal and noise in metabarcoding data. Plos one, 18(5), e0285674.
Kelly, R. P., Lodge, D. M., Lee, K. N., Theroux, S., Sepulveda, A. J., Scholin, C. A., Craine, J. M., Andruszkiewicz Allan, E., Nichols, K. M.,
Parsons, K. M., Goodwin, K. D., Gold, Z., Chavez, F. P., Noble, R. T., Abbott, C. L., Baerwald, M. R., Naaum, A. M., Thielen, P. M.,
Simons, A. L. … Weisberg, S. B. (2023). Toward a national eDNA strategy for the United States. Environmental DNA, 00, 1–10.
https://doi.org/10.1002/edn3.432
Andruszkiewicz Allan, E., Kelly, R. P., D'Agnese, E. R., Garber‐Yonts, M. N., Shaffer, M. R., Gold, Z., & Shelton, A. O. Quantifying impacts
of an environmental intervention using environmental DNA. Ecological Applications, e2914.
Shelton, A.O., Gold, Z., Allen, E., D’Agnese, E., Van Cise, A., Gallego, R., Parsons, K., Duprey, J., Casedino, H., Garber-Yonts, M., Fisher,
M., Kelly, R., Toward quantitative metabarcoding. (2022). Ecology 104( 2): e3906.
Waters, T., Gold, Z., Obaza, A., Ambrose, R. F., & Eagle, R. A. (2024). 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.
Gold, Z., Koch, M.Q., Schooler, N.K., Emery, K.A, Dugan, J.E., Miller, R.J., Page, H.M, Schroeder, D.M., Hubbard, D.M., Madden, J.,
Whitaker, S.G., Barber, P.H. (2023). A Comparison of Biomonitoring Methodologies for Surf Zone Fish Communities. PLOS
One,18(6), p.e0260903.
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(Supplement 1):90–93,
https://doi.org/10.5670/oceanog.2023.s1.29.
Gold, Z., Wall, A.R., Schweizer, T.M., Pentcheff, N.D., Curd, E.E., Barber, P.H., Meyer, R.S., Wayne, R., Stolzenbach, K., Prickett, K. and
Luedy, J., (2022). A manager’s guide to using eDNA metabarcoding in marine ecosystems. PeerJ, 10, p.e14071.
Gold, Z., Curd, E., Goodwin, K., Choi, E., Frable, B., Thompson, A., Burton, R., Kacev, D., and Barber, P., (2021). Improving
Metabarcoding Taxonomic Assignment: A Case Study of Fishes in a Large Marine Ecosystem. Molecular Ecology Resources, 21
(7), 2546-2564.
Gold, Z., Sprague, J., Kushner, D. J., Zerecero Marin, E., & Barber, P. H. (2021). eDNA metabarcoding as a biomonitoring tool for
marine protected areas. PLOS One, 16(2), e0238557.
Min, M. A., Barber, P. H., & Gold, Z. (2021). MiSebastes: An eDNA metabarcoding primer set for rockfishes (genus
Sebastes). Conservation Genetics Resources, 1-10.
Ely, T., Barber, P. H., Man, L., & Gold, Z. (2021). Short-lived detection of an introduced vertebrate eDNA signal in a nearshore rocky
reef environment. PLOS One, 16(6), e0245314.
Monuki, K., Barber, P., & Gold, Z. (2021). eDNA Captures Depth Partitioning in a Kelp Forest Ecosystem. PLOS One, 16 (11),
e0253104.
Marwayana, O.N., Gold, Z., Meyer C., and Barber, P.H., (2021). Environmental DNA in a Global Biodiversity Hotspot: Lessons from
Coral Reef Fish Diversity Across the Indonesian Archipelago. Environmental DNA 4(1), pp.222-238.
Willette, D. A., Navarrete-Forero, G., Gold, Z., Lizano, A. M. D., Gonzalez-Smith, L., & Sotil, G. (2021). Characterizing Industrial and
Artisanal Fishing Vessel Catch Composition Using Environmental DNA and Satellite-Based Tracking Data. Foods, 10(6), 1425.
Lin, M., Simons, A.L., Curd, E.E., Harrigan, R.J., Schneider, F.D., Ruiz-Ramos, D.V., Gold, Z., Osborne, M.G., Shirazi, S., Schweizer, T.M.
and Moore, T.N., (2020). Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity
in California. Ecological Applications, e2379.
Meyer R., Ramos M., Lin M., Schweizer T., Gold Z., Ramos D., Shirazi S., Kandlikar G., Kwan W., Curd E., Freise A., Parker J., Sexton J.,
Wetzer R., Pentcheff N., Wall A., Pipes L., Garcia-Vedrenne A., Mejia M., Moore T., Orland C., Ballare K., Worth A., Beraut E.,
Aronson E., Nielsen R., Lewin H., Barber P., Wall J., Kraft N., Shapiro B., Wayne R. (2021). The CALeDNA program: Citizen
scientists and researchers inventory California's biodiversity. California Agriculture, 75(1):20-32.
https://doi.org/10.3733/ca.2021a0001.
Gold, Z., Wall, A.R., Curd, E.E., Kelly, R.P., Pentcheff, N.D., Ripma, L., Barber, P.H. and Wetzer, R., (2020). eDNA metabarcoding
bioassessment of endangered fairy shrimp (Branchinecta spp.). Conservation Genetics Resources, 12(4), pp.685-690.
Gold, Z., 2020. Design and implementation of environmental DNA metabarcoding methods for monitoring the Southern California
marine protected area network (Doctoral dissertation, UCLA).
Curd, E. E., Gold, Z., Kandlikar, G. S., Gomer, J., Ogden, M., O'Connell, T., Pipes, L., Schweizer, T. Rabichow, L., Lin, M., Shi, B., Barber,
P.H., Kraft, N., Wayne, R., Meyer, R. (2019). Anacapa Toolkit: an environmental DNA toolkit for processing multilocus metabarcode
datasets. Methods in Ecology and Evolution, 10(9), 1469-1475.
Gold, Z., & Palumbi, S. R. (2018). Long-term growth rates and effects of bleaching in Acropora hyacinthus. Coral Reefs, 37(1), 267-
277.
Kandlikar, G. S., Gold, Z. J., Cowen, M. C., Meyer, R. S., Freise, A. C., Kraft, N. J., Moberg-Parker, J., Sprague, J., Kushner, D. J., Curd,
Emily E (2018). ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and
interactive visualizations. F1000Research, 7.
P.A., 2025. Using eDNA to Supplement Population Genetic Analyses for Cryptic Marine Species: Identifying Population Boundaries
for Alaska Harbour Porpoises. Molecular Ecology, p.e17563.
Theroux, S., Sepulveda, A., Abbott, C.L., Gold, Z., Watts, A.W., Hunter, M.E., Klymus, K.E., Hirsch, S.L., Craine, J.M., Jones, D.N. and
Brown, R.J., 2025. What is eDNA method standardisation and why do we need it? Metabarcoding and Metagenomics, 9,
p.e132076.
Gold, Z., Kelly, R., Shelton, A.O., Goodwin, K., Gallego, R., Parsons, K., Thompson, L., Kacev, D., Thompson, A., Barber, P.H, 2024.
Archived DNA reveals impacts of a marine heatwave on fish assemblages over multiple decades. Environmental DNA, 6(1),
p.e400.
Klymus, K.E., Baker, J.D., Abbott, C.L., Brown, R.J., Craine, J.M., Gold, Z., Hunter, M.E., Johnson, M.D., Jones, D.N., Jungbluth, M.J.
and Jungbluth, S.P., 2024. The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data.
Metabarcoding and Metagenomics, 8, p.489.
Curd, E.E., Gal, L., Gallego, R., Silliman, K., Nielsen, S. and Gold, Z., 2024. rCRUX: A rapid and versatile tool for generating
metabarcoding reference libraries in R. Environmental DNA, 6(1), p.e489.
Waters, T., Langlois, K., Gold, Z., Theroux, S., & Eagle, R. (2024). Hidden in plain sight: the invasive macroalga Caulerpa prolifera
evades detection by environmental DNA methods due to negligible shedding. Environmental DNA, 6(1), p.e496.
Hakimzadeh, A., Abdala Asbun, A., Albanese, D., Bernard, M., Buchner, D., Callahan, B., Caporaso, J. G., Curd, E., Djemiel, C.,
Brandström Durling, M., Elbrecht, V., Gold, Z., Gweon, H. S., Hajibabaei, M., Hildebrand, F., Mikryukov, V., Normandeau, E., Özkurt, E.,
M. Palmer, J. … Anslan, S. (2024). 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., Shelton, A.O., Casendino, H.R., Duprey, J., Gallego, R., Van Cise, A., Fisher, M., Jensen, A.J., D’Agnese, E., Andruszkiewicz
Allan, E. and Ramón-Laca, A., (2023). Signal and noise in metabarcoding data. Plos one, 18(5), e0285674.
Kelly, R. P., Lodge, D. M., Lee, K. N., Theroux, S., Sepulveda, A. J., Scholin, C. A., Craine, J. M., Andruszkiewicz Allan, E., Nichols, K. M.,
Parsons, K. M., Goodwin, K. D., Gold, Z., Chavez, F. P., Noble, R. T., Abbott, C. L., Baerwald, M. R., Naaum, A. M., Thielen, P. M.,
Simons, A. L. … Weisberg, S. B. (2023). Toward a national eDNA strategy for the United States. Environmental DNA, 00, 1–10.
https://doi.org/10.1002/edn3.432
Andruszkiewicz Allan, E., Kelly, R. P., D'Agnese, E. R., Garber‐Yonts, M. N., Shaffer, M. R., Gold, Z., & Shelton, A. O. Quantifying impacts
of an environmental intervention using environmental DNA. Ecological Applications, e2914.
Shelton, A.O., Gold, Z., Allen, E., D’Agnese, E., Van Cise, A., Gallego, R., Parsons, K., Duprey, J., Casedino, H., Garber-Yonts, M., Fisher,
M., Kelly, R., Toward quantitative metabarcoding. (2022). Ecology 104( 2): e3906.
Waters, T., Gold, Z., Obaza, A., Ambrose, R. F., & Eagle, R. A. (2024). 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.
Gold, Z., Koch, M.Q., Schooler, N.K., Emery, K.A, Dugan, J.E., Miller, R.J., Page, H.M, Schroeder, D.M., Hubbard, D.M., Madden, J.,
Whitaker, S.G., Barber, P.H. (2023). A Comparison of Biomonitoring Methodologies for Surf Zone Fish Communities. PLOS
One,18(6), p.e0260903.
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(Supplement 1):90–93,
https://doi.org/10.5670/oceanog.2023.s1.29.
Gold, Z., Wall, A.R., Schweizer, T.M., Pentcheff, N.D., Curd, E.E., Barber, P.H., Meyer, R.S., Wayne, R., Stolzenbach, K., Prickett, K. and
Luedy, J., (2022). A manager’s guide to using eDNA metabarcoding in marine ecosystems. PeerJ, 10, p.e14071.
Gold, Z., Curd, E., Goodwin, K., Choi, E., Frable, B., Thompson, A., Burton, R., Kacev, D., and Barber, P., (2021). Improving
Metabarcoding Taxonomic Assignment: A Case Study of Fishes in a Large Marine Ecosystem. Molecular Ecology Resources, 21
(7), 2546-2564.
Gold, Z., Sprague, J., Kushner, D. J., Zerecero Marin, E., & Barber, P. H. (2021). eDNA metabarcoding as a biomonitoring tool for
marine protected areas. PLOS One, 16(2), e0238557.
Min, M. A., Barber, P. H., & Gold, Z. (2021). MiSebastes: An eDNA metabarcoding primer set for rockfishes (genus
Sebastes). Conservation Genetics Resources, 1-10.
Ely, T., Barber, P. H., Man, L., & Gold, Z. (2021). Short-lived detection of an introduced vertebrate eDNA signal in a nearshore rocky
reef environment. PLOS One, 16(6), e0245314.
Monuki, K., Barber, P., & Gold, Z. (2021). eDNA Captures Depth Partitioning in a Kelp Forest Ecosystem. PLOS One, 16 (11),
e0253104.
Marwayana, O.N., Gold, Z., Meyer C., and Barber, P.H., (2021). Environmental DNA in a Global Biodiversity Hotspot: Lessons from
Coral Reef Fish Diversity Across the Indonesian Archipelago. Environmental DNA 4(1), pp.222-238.
Willette, D. A., Navarrete-Forero, G., Gold, Z., Lizano, A. M. D., Gonzalez-Smith, L., & Sotil, G. (2021). Characterizing Industrial and
Artisanal Fishing Vessel Catch Composition Using Environmental DNA and Satellite-Based Tracking Data. Foods, 10(6), 1425.
Lin, M., Simons, A.L., Curd, E.E., Harrigan, R.J., Schneider, F.D., Ruiz-Ramos, D.V., Gold, Z., Osborne, M.G., Shirazi, S., Schweizer, T.M.
and Moore, T.N., (2020). Landscape analyses using eDNA metabarcoding and Earth observation predict community biodiversity
in California. Ecological Applications, e2379.
Meyer R., Ramos M., Lin M., Schweizer T., Gold Z., Ramos D., Shirazi S., Kandlikar G., Kwan W., Curd E., Freise A., Parker J., Sexton J.,
Wetzer R., Pentcheff N., Wall A., Pipes L., Garcia-Vedrenne A., Mejia M., Moore T., Orland C., Ballare K., Worth A., Beraut E.,
Aronson E., Nielsen R., Lewin H., Barber P., Wall J., Kraft N., Shapiro B., Wayne R. (2021). The CALeDNA program: Citizen
scientists and researchers inventory California's biodiversity. California Agriculture, 75(1):20-32.
https://doi.org/10.3733/ca.2021a0001.
Gold, Z., Wall, A.R., Curd, E.E., Kelly, R.P., Pentcheff, N.D., Ripma, L., Barber, P.H. and Wetzer, R., (2020). eDNA metabarcoding
bioassessment of endangered fairy shrimp (Branchinecta spp.). Conservation Genetics Resources, 12(4), pp.685-690.
Gold, Z., 2020. Design and implementation of environmental DNA metabarcoding methods for monitoring the Southern California
marine protected area network (Doctoral dissertation, UCLA).
Curd, E. E., Gold, Z., Kandlikar, G. S., Gomer, J., Ogden, M., O'Connell, T., Pipes, L., Schweizer, T. Rabichow, L., Lin, M., Shi, B., Barber,
P.H., Kraft, N., Wayne, R., Meyer, R. (2019). Anacapa Toolkit: an environmental DNA toolkit for processing multilocus metabarcode
datasets. Methods in Ecology and Evolution, 10(9), 1469-1475.
Gold, Z., & Palumbi, S. R. (2018). Long-term growth rates and effects of bleaching in Acropora hyacinthus. Coral Reefs, 37(1), 267-
277.
Kandlikar, G. S., Gold, Z. J., Cowen, M. C., Meyer, R. S., Freise, A. C., Kraft, N. J., Moberg-Parker, J., Sprague, J., Kushner, D. J., Curd,
Emily E (2018). ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and
interactive visualizations. F1000Research, 7.
Technical & Government Reports
Gold, Z., Brown, S., Collins, A., Girard, M., Goodwin, K., McAllister, S., Meyer, C., Parsons, K., Patin, N., Rouse, G., Sala, L.,
Satterthwaite, E., Seid, C., Theroux, S., & Wetzer, R. (2025). Introduction to Developing DNA Reference Barcode Sequences (v1.0). The West Coast Ocean Biomolecular Observing Network. Zenodo. https://doi.org/10.5281/zenodo.14867763
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, National Aquatic Environmental DNA Strategy. White House Office of Science,
Technology, and Policy (OSTP), 2024.
Introduction to Using eDNA for Environmental Management (2024). Mobilizing eDNA for Environmental Management in the
Northeast Pacific Workshop. https://www.ednacollab.org/wp-content/uploads/2025/01/eDNA-primer-web.pdf
Theroux, S., and Gold, Z. (2022). eDNA 101: An Introduction to environmental DNA and its applications in marine science.
Prepared for the 2nd National Workshop on Marine eDNA. Southern California Coastal Watershed Research Project.
Satterthwaite, E., Seid, C., Theroux, S., & Wetzer, R. (2025). Introduction to Developing DNA Reference Barcode Sequences (v1.0). The West Coast Ocean Biomolecular Observing Network. Zenodo. https://doi.org/10.5281/zenodo.14867763
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, National Aquatic Environmental DNA Strategy. White House Office of Science,
Technology, and Policy (OSTP), 2024.
Introduction to Using eDNA for Environmental Management (2024). Mobilizing eDNA for Environmental Management in the
Northeast Pacific Workshop. https://www.ednacollab.org/wp-content/uploads/2025/01/eDNA-primer-web.pdf
Theroux, S., and Gold, Z. (2022). eDNA 101: An Introduction to environmental DNA and its applications in marine science.
Prepared for the 2nd National Workshop on Marine eDNA. Southern California Coastal Watershed Research Project.