Nancy Knowlton

• A.B., Harvard University
• Ph.D., University of California, Berkeley

Marine Biodiversity; ecology, behavior, evolution and systematics of coral reef organisms.

Systematics, evolution, ecology and behavior of marine invertebrates, particularly shrimps and corals, marine biodiversity, systematics, evolution, conservation.

Journal Article

• Yan, Helen F., Casey, Jordan M., Knowlton, Nancy, Duffy, J. Emmett, and Brandl, Simon J. 2023. "Examining the diversity, stability and functioning of marine fish communities across a latitudinal gradient." Global Ecology and Biogeography, 32, (1) 166–177. https://doi.org/10.1111/geb.13611.
• Borja, Angel, Elliott, Michael, Basurko, Oihane C., Muerza, Alex Fernandez, Micheli, Fiorenza, Zimmermann, Fabian, and Knowlton, Nancy. 2022. "#OceanOptimism: Balancing the Narrative About the Future of the Ocean." Frontiers in Marine Science, 9. https://doi.org/10.3389/fmars.2022.886027.
• Borja, Angel, Elliott, Michael, Basurko, Oihane C., Fernández Muerza, Alex, Micheli, Fiorenza, Zimmermann, Fabian, and Knowlton, Nancy. 2022. "Correction to OceanOptimism: Balancing the narrative about the future of the ocean (vol 9, 886027, 2022)." Frontiers in Marine Science, 9. https://doi.org/10.3389/fmars.2022.1027767.
• Di Lorenzo, Emanuele and Knowlton, Nancy. 2022. "The search for ocean solutions." PLOS Biology, 20, (10). https://doi.org/10.1371/journal.pbio.3001860.
• Machida, Ryuji J., Knowlton, Nancy, and Leray, Matthieu. 2022. "MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences." Environmental DNA, 4, (4) 894–907. https://doi.org/10.1002/edn3.303.
• Prada, Carlos, Lopez-Londono, Tomas, Pollock, F. Joseph, Roitman, Sofia, Ritchie, Kim B., Levitan, Don R., Knowlton, Nancy, Woodley, Cheryl, Iglesias-Prieto, Roberto, and Medina, Monica. 2022. "Linking photoacclimation responses and microbiome shifts between depth-segregated sibling species of reef corals." Royal Society Open Science, 9, (3). https://doi.org/10.1098/rsos.211591.
• Plaisance, Laetitia, Matterson, Kenan, Fabricius, Katharina, Drovetski, Sergei V., Meyer, Christopher P., and Knowlton, Nancy. 2021. "Effects of low pH on the coral reef cryptic invertebrate communities near CO2 vents in Papua New Guinea." PLOS ONE, 16, (12). https://doi.org/10.1371/journal.pone.0258725.
• Knowlton, Nancy. 2021. "Ocean Optimism: Moving Beyond the Obituaries in Marine Conservation." Annual Review of Marine Science, 13, (1) 479–499. https://doi.org/10.1146/annurev-marine-040220-101608.
• Knowlton, Nancy. 2021. "Local management matters for coral reefs." Science, 372, (6545) 908–909. https://doi.org/10.1126/science.abi7286.
• Silliman, Katherine, Indorf, Jane L., Knowlton, Nancy, Browne, William E., and Hurt, Carla. 2021. "Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama." Bmc Ecology and Evolution, 21, (1). https://doi.org/10.1186/s12862-021-01836-3.
• Martindale, Rowan C., Holstein, Daniel, Knowlton, Nancy, Voss, Joshua D., Weiss, Anna M., and Correa, Adrienne M. S. 2021. "Editorial: Gulf of Mexico Reefs: Past, Present and Future." Frontiers in Marine Science, 8. https://doi.org/10.3389/fmars.2021.713058.
• Sumaila, U. R., Skerritt, Daniel J., Schuhbauer, Anna, Villasante, Sebastian, Cisneros-Montemayor, Andr, Sinan, Hussain, Burnside, Duncan, Abdallah, Patrízia Raggi, Abe, Keita, Addo, Kwasi A., Adelsheim, Julia, Adewumi, Ibukun J., Adeyemo, Olanike K., Adger, Neil, Adotey, Joshua, Advani, Sahir, Afrin, Zahidah, Aheto, Denis, Akintola, Shehu L., Akpalu, Wisdom, Alam, Lubna, Alava, Juan José, Allison, Edward H., Amon, Diva J., Anderies, John M. et al. 2021. "WTO must ban harmful fisheries subsidies." Science, 374, (6567) 544–544. https://doi.org/10.1126/science.abm1680.
• Duarte, Carlos M., Agusti, Susana, Barbier, Edward, Britten, Gregory L., Castilla, Juan Carlos, Gattuso, Jean-Pierre, Fulweiler, Robinson W., Hughes, Terry P., Knowlton, Nancy, Lovelock, Catherine E., Lotze, Heike K., Predragovic, Milica, Poloczanska, Elvira, Roberts, Callum, and Worm, Boris. 2020. "Rebuilding marine life." Nature, 580, (7801) 39–51. https://doi.org/10.1038/s41586-020-2146-7.
• Leray, Matthieu, Knowlton, Nancy, Ho, Shian-Lei, Nguyen, Bryan N., and Machida, Ryuji J. 2020. "REPLY TO LOCATELLI ET AL.: Evaluating species-level accuracy of GenBank metazoan sequences will require experts' effort in each group." Proceedings of the National Academy of Sciences of the United States of America, 117, (51) 32213–32214. https://doi.org/10.1073/pnas.2019903117.
• Malhi, Yadvinder, Franklin, Janet, Seddon, Nathalie, Solan, Martin, Turner, Monica G., Field, Christopher B., and Knowlton, Nancy. 2020. "Climate change and ecosystems: threats, opportunities and solutions." Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 375, (1794). https://doi.org/10.1098/rstb.2019.0104.
• Nguyen, Bryan N., Shen, Elaine W., Seemann, Janina, Correa, Adrienne M. S., O'Donnell, James L., Altieri, Andrew H., Knowlton, Nancy, Crandall, Keith A., Egan, Scott P., McMillan, W. Owen, and Leray, Matthieu. 2020. "Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape." Scientific Reports, 10, (1) Article 6729. https://doi.org/10.1038/s41598-020-63565-9.
• Kandler, Nora, Wooster, Michael, Leray, Matthieu, Knowlton, Nancy, de Voogd, Nicole, Paulay, Gustav, and Berumen, Michael. 2019. "Hyperdiverse Macrofauna Communities Associated with a Common Sponge, Stylissa carteri, Shift across Ecological Gradients in the Central Red Sea." Diversity, 11, (2) 18. https://doi.org/10.3390/d11020018.
• Knowlton, Nancy. 2019. "Earth Optimism-recapturing the positive." Oryx, 53, (1) 1–2. https://doi.org/10.1017/S0030605318001333.
• Leray, Matthieu, Alldredge, Alice L., Yang, Joy Y., Meyer, Christopher P., Holbrook, Sally J., Schmitt, Russell J., Knowlton, Nancy, and Brooks, Andrew J. 2019. "Dietary partitioning promotes the coexistence of planktivorous species on coral reefs." Molecular ecology, 28, (10) 2694–2710. https://doi.org/10.1111/mec.15090.
• Leray, Matthieu, Knowlton, Nancy, Ho, Shian-Lei, Nguyen, Bryan N., and Machida, Ryuji J. 2019. "GenBank is a reliable resource for 21st century biodiversity research." Proceedings of the National Academy of Sciences of the United States of America, 116, (45) 22651–22656. https://doi.org/10.1073/pnas.1911714116.
• Baker, David M., Freeman, Christopher J., Wong, Jane C. Y., Fogel, Marilyn L., and Knowlton, Nancy. 2018. "Climate change promotes parasitism in a coral symbiosis." The ISME journal, 12 921–930. https://doi.org/10.1038/s41396-018-0046-8.
• Beyer, Hawthorne L., Kennedy, Emma, V., Beger, Maria, Chen, Chaolun Allen, Cinner, Joshua E., Darling, Emily S., Eakin, C. Mark, Gates, Ruth D., Heron, Scott F., Knowlton, Nancy, Obura, David O., Palumbi, Stephen R., Possingham, Hugh P., Puotinen, Marji, Runting, Rebecca K., Skirving, William J., Spalding, Mark, Wilson, Kerrie A., Wood, Sally, Veron, John E., and Hoegh-Guldberg, Ove. 2018. "Risk-sensitive planning for conserving coral reefs under rapid climate change." Conservation Letters, 11, (6). https://doi.org/10.1111/conl.12587.
• Knowlton, Nancy. 2018. "How rats wreak havoc on coral reefs." Nature, 559, (7713) 190–191. https://doi.org/10.1038/d41586-018-05355-y.
• Pearman, J. K., Leray, M., Villalobos, R., Machida, R. J., Berumen, M. L., Knowlton, Nancy, and Carvalho, S. 2018. "Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority." Scientific Reports, 8 8090–8090. https://doi.org/10.1038/s41598-018-26332-5.
• Altieri, Andrew H., Harrison, Seamus B., Seemann, Janina, Collin, Rachel, Diaz, Robert J., and Knowlton, Nancy. 2017. "Tropical dead zones and mass mortalities on coral reefs." Proceedings of the National Academy of Sciences of the United States of America, 114, (14) 3660–3665. https://doi.org/10.1073/pnas.1621517114.
• Balmford, Andrew and Knowlton, Nancy. 2017. "Why Earth Optimism?" Science, 356, (6335) 225–225. https://doi.org/10.1126/science.aan4082.
• Brandl, Simon J., Casey, Jordan M., Knowlton, Nancy, and Duffy, J. Emmett. 2017. "Marine dock pilings foster diverse, native cryptobenthic fish assemblages across bioregions." Ecology and Evolution, 7, (17) 7069–7079. https://doi.org/10.1002/ece3.3288.
• Hartmann, Aaron C., Baird, Andrew H., Knowlton, Nancy, and Huang, Danwei. 2017. "The Paradox of Environmental Symbiont Acquisition in Obligate Mutualisms." Current Biology, 27, (23) 3711–3716. https://doi.org/10.1016/j.cub.2017.10.036.
• Krupnick, Gary A. and Knowlton, Nancy. 2017. "Earth Optimism: Success Stories in Plant Conservation." Annals of the Missouri Botanical Garden, 102, (2) 331–340. https://doi.org/10.3417/D-16-00010A.
• Leray, Matthieu and Knowlton, Nancy. 2017. "Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding." PeerJ, 5, (e3006). https://doi.org/10.7717/peerj.3006.
• Machida, Ryuji J., Leray, Matthieu, Ho, Shian-Lei, and Knowlton, Nancy. 2017. "Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples." Scientific Data, 4, (170027). https://doi.org/10.1038/sdata.2017.27.
• Neal, Benjamin Paul, Khen, Adi, Treibitz, Tali, Beijbom, Oscar, O'Connor, Grace, Coffroth, Mary Alice, Knowlton, Nancy, Kriegman, David, Mitchell, B. G., and Kline, David I. 2017. "Caribbean massive corals not recovering from repeated thermal stress events during 2005-2013." Ecology and Evolution, 7, (5) 1339–1353. https://doi.org/10.1002/ece3.2706.
• Rouzé, H., Leray, Matthieu, Magalon, H., Penin, L., Gélin, P., Knowlton, Nancy, and Fauvelot, C. 2017. "Molecular characterization reveals the complexity of previously overlooked coral-exosymbiont interactions and the implications for coral-guild ecology." Scientific Reports, 7, (44923). https://doi.org/10.1038/srep44923.
• Webster, Michael S., Colton, Madhavi A., Darling, Emily S., Armstrong, Jonathan, Pinsky, Malin L., Knowlton, Nancy, and Schindler, Daniel E. 2017. "Who Should Pick the Winners of Climate Change?" Trends in Ecology and Evolution, 32, (3) 167–173. https://doi.org/10.1016/j.tree.2016.12.007.
• Al-Rshaidat, Mamoon, Snider, Allison, Rosebraugh, Sydney, Devine, Amanda M., Devine, Thomas D., Plaisance, Laetitia, Knowlton, Nancy, and Leray, Matthieu. 2016. "Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea." Genome, 59, (9) 724–737. https://doi.org/10.1139/gen-2015-0208.
• Huang, Danwei, Arrigoni, Roberto, Benzoni, Francesca, Fukami, Hironobu, Knowlton, Nancy, Smith, Nathan D., Stolarski, Jarosław, Chou, Loke Ming, and Budd, Ann F. 2016. "Taxonomic classification of the reef coral family Lobophylliidae (Cnidaria: Anthozoa: Scleractinia)." Zoological Journal of the Linnean Society, 178, (3) 436–481. https://doi.org/10.1111/zoj.12391.
• Leray, Matthieu and Knowlton, Nancy. 2016. "Censusing marine eukaryotic diversity in the twenty-first century." Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 371, (1702). https://doi.org/10.1098/rstb.2015.0331.
• O'Dea, Aaron, Lessios, Harilaos A., Coates, Anthony G., Eytan, Ron I., Restrepo-Moreno, Sergio, Cione, Alberto L., Collins, Laurel S., de Queiroz, Alan, Farris, David W., Norris, Richard D., Stallard, Robert F., Woodburne, Michael O., Aguilera, Orangel, Aubry, Marie-Pierre, Berggren, William A., Budd, Ann F., Cozzuol, Mario A., Coppard, Simon E., Duque-Caro, Herman, Finnegan, Seth, Gasparini, German M., Grossman, Ethan L., Johnson, Kenneth G., Keigwin, Lloyd D., Knowlton, Nancy et al. 2016. "Formation of the Isthmus of Panama." Science Advances, 2, (8). https://doi.org/10.1126/sciadv.1600883.
• Prada, Carlos, Hanna, Bishoy, Budd, Ann F, Woodley, Cheryl M, Schmutz, Jeremy, Grimwood, Jane, Iglesias-Prieto, Roberto, Pandolfi, John M, Levitan, Don, Johnson, Kenneth G, Knowlton, Nancy, Kitano, Hiroaki, DeGiorgio, Michael, and Medina, Mónica. 2016. "Empty Niches after Extinctions Increase Population Sizes of Modern Corals." Current Biology, 26, (23) 3190–3194. https://doi.org/10.1016/j.cub.2016.09.039.
• Baker, David M., Freeman, Christopher J., Knowlton, Nancy, Thacker, Robert W., Kim, Kiho, and Fogel, Marilyn L. 2015. "Productivity links morphology, symbiont specificity and bleaching in the evolution of Caribbean octocoral symbioses." The ISME journal, 9 2620–2629. https://doi.org/10.1038/ismej.2015.71.
• Fisher, Rebecca, O'Leary, Rebecca A, Low-Choy, Samantha, Mengersen, Kerrie, Knowlton, Nancy, Brainard, Russell E, and Caley, M. J. 2015. "Species Richness on Coral Reefs and the Pursuit of Convergent Global Estimates." Current Biology, 25, (4) 500–505. https://doi.org/10.1016/j.cub.2014.12.022.
• Jacquet, Jennifer, Estes, James, Jackson, Jeremy, Johnson, Ayana E., Knowlton, Nancy, Mcclenachan, Loren, Pauly, Daniel, and Sala, Enric. 2015. "Ocean Calamities: Hyped Litany or Legitimate Concern?" Bioscience, 65, (8) 745–746. https://doi.org/10.1093/biosci/biv087.
• LaJeunesse, Todd C., Lee, Sung Yeon, Gil-Agudelo, Diego, Knowlton, Nancy, and Jeong, Hae Jin. 2015. "Symbiodinium necroappetens sp. nov. (Dinophyceae): an opportunist ‘zooxanthella’ found in bleached and diseased tissues of Caribbean reef corals." European Journal of Phycology, 50, (2). https://doi.org/10.1080/09670262.2015.1025857.
• Leray, Matthieu and Knowlton, Nancy. 2015. "DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity." Proceedings of the National Academy of Sciences of the United States of America, 112, (7) 2076–2081. https://doi.org/10.1073/pnas.1424997112.
• Marko, Peter B., Eytan, Ron I., and Knowlton, Nancy. 2015. "Do large molecular sequence divergences imply an early closure of the Isthmus of Panama?" Proceedings of the National Academy of Sciences of the United States of America, 112, (43). https://doi.org/10.1073/pnas.1515048112.
• Bracken-Grissom, Heather, Collins, Allen Gilbert, Collins, Timothy, Crandall, Keith, Distel, Daniel, Dunn, Casey, Giribet, Gonzalo, Haddock, Steven, Knowlton, Nancy, Martindale, Mark, Medina, Monica, Messing, Charles, O'Brien, Stephen J., Paulay, Gustav, Putnam, Nicolas, Ravasi, Timothy, Rouse, Greg W., Ryan, Joseph F., Schulze, Anja, Worheide, Gert, Adamska, Maja, Bailly, Xavier, Breinholt, Jesse, Browne, William E., Diaz, M. Christina et al. 2014. "The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes." The Journal of Heredity, 105, (1) 1–18. https://doi.org/10.1093/jhered/est084.
• Connolly, Sean R., MacNeil, M. Aaron, Caley, M. Julian, Knowlton, Nancy, Cripps, Ed, Hisano, Mizue, Thibaut, Loic M., Bhattacharya, Bhaskar D., Benedetti-Cecchi, Lisandro, Brainard, Russell E., Brandt, Angelika, Bulleri, Fabio, Ellingsen, Kari E., Kaiser, Stefanie, Kroncke, Ingrid, Linse, Katrin, Maggi, Elena, O'Hara, Timothy D., Plaisance, Laetitia, Poore, Gary C. B., Sarkar, Santosh K., Satpathy, Kamala K., Schuckel, Ulrike, Williams, Alan, and Wilson, Robin S. 2014. "Commonness and rarity in the marine biosphere." Proceedings of the National Academy of Sciences of the United States of America, 111, (23) 8524–8529. https://doi.org/10.1073/pnas.1406664111.
• Huang, Danwei, Benzoni, Francesca, Fukami, Hironobu, Knowlton, Nancy, Smith, Nathan D., and Budd, Ann F. 2014. "Taxonomic classification of the reef coral families Merulinidae, Montastraeidae, and Diploastraeidae (Cnidaria: Anthozoa: Scleractinia)." Zoological Journal of the Linnean Society, 171, (2) 277–355. https://doi.org/10.1111/zoj.12140.
• Levitan, Don R., Boudreau, William, Jara, Javier, and Knowlton, Nancy. 2014. "Long-term reduced spawning in Orbicella coral species due to temperature stress." Marine Ecology Progress Series, 515 1–10. https://doi.org/10.3354/meps11063.
• Rocha, L. A., Aleixo, A., Allen, G., Almeda, F., Baldwin, Carole C., Barclay, M. V. L., Bates, J. M., Bauer, A. M., Benzoni, F., Berns, C. M., Berumen, M. L., Blackburn, D. C., Blum, S., Bolanos, F., Bowie, R. C. K., Britz, R., Brown, R. M., Cadena, C. D., Carpenter, K., Ceriaco, L. M., Chakrabarty, P., Chaves, G., Choat, J. H., Clements, K. D., Collette, Bruce B. et al. 2014. "Specimen collection: An essential tool." Science, 344, (6186) 814–815. https://doi.org/10.1126/science.344.6186.814.
• Baker, David M., Weigt, Lee A., Fogel, Marilyn, and Knowlton, Nancy. 2013. "Ancient DNA from Coral-Hosted Symbiodinium Reveal a Static Mutualism over the Last 172 Years." PLoS ONE, 8, (2) e55057. https://doi.org/10.1371/journal.pone.0055057.
• Hurt, C., Silliman, K., Anker, A., and Knowlton, Nancy. 2013. "Ecological speciation in anemone-associated snapping shrimps (Alpheus armatus species complex)." Molecular ecology, 22, (17) 4532–4548. https://doi.org/10.1111/mec.12398.
• Leslie, Heather M., Goldman, Erica, Mcleod, Karen L., Sievanen, Leila, Balasubramanian, Hari, Cudney-Bueno, Richard, Feuerstein, Amanda, Knowlton, Nancy, Lee, Kai, Pollnac, Richard, and Samhouri, Jameal F. 2013. "How Good Science and Stories Can Go Hand-In-Hand." Conservation Biology, 27, (5) 1126–1129. https://doi.org/10.1111/cobi.12080.
• Ruckelshaus, M., Doney, S. C., Galindo, H. M., Barry, J. P., Chan, F., Duffy, J. Emmett, English, C. A., Gaines, S. D., Grebmeier, J. M., Hollowed, A. B., Knowlton, Nancy, Polovina, Jeffrey J., Rabalais, N. N., Sydeman, W. J., and Talley, L. D. 2013. "Securing ocean benefits for society in the face of climate change." Marine Policy, 40 154–159. https://doi.org/10.1016/j.marpol.2013.01.009.
• Budd, Ann F., Fukami, Hironobu, Smith, Nathan D., and Knowlton, Nancy. 2012. "Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia)." Zoological Journal of the Linnean Society, 166, (3) 465–529. https://doi.org/10.1111/j.1096-3642.2012.00855.x.
• Doney, Scott C., Ruckelshaus, Mary, Duffy, J. Emmett, Barry, James, Chan, Francis, English, Chad A., Hines, Heather M., Grebmeier, Jacqueline M., Hollowed, Anne B., Knowlton, Nancy, Polovina, Jeffrey J., Rabalais, Nancy N., Sydeman, William J., and Talley, Lynne D. 2012. "Climate Change Impacts on Marine Ecosystems." Annual Review of Marine Science, 4 11–37. https://doi.org/10.1146/annurev-marine-041911-111611.
• Fogarty, N. D., Lowenberg, M., Ojima, M. N., Knowlton, Nancy, and Levitan, D. R. 2012. "Asymmetric conspecific sperm precedence in relation to spawning times in the Montastraea annularis species complex (Cnidaria: Scleractinia)." Journal of Evolutionary Biology, 25, (12) 2481–2488. https://doi.org/10.1111/j.1420-9101.2012.02625.x.
• Knowlton, Nancy. 2012. "Iconic coral reef degraded despite substantial protection." Proceedings of the National Academy of Sciences of the United States of America, 109, (44) 17734–17735. https://doi.org/10.1073/pnas.1215836109.
• Machida, Ryuji J. and Knowlton, Nancy. 2012. "PCR Primers for Metazoan Nuclear 18S and 28S Ribosomal DNA Sequences." Plos One, 7, (9) 1–11. https://doi.org/10.1371/journal.pone.0046180.
• Machida, Ryuji J., Kweskin, Matthew, and Knowlton, Nancy. 2012. "PCR Primers for Metazoan Mitochondrial 12S Ribosomal DNA Sequences." PLoS ONE, 7, (4) 1–6. https://doi.org/10.1371/journal.pone.0035887.
• Machlis, Gary, Frankovich, Thomas A., Alcolado, Pedro M., Garcia-Machado, Erik, Caridad Hernandez-Zanuy, Aida, Hueter, Robert E., Knowlton, Nancy, Perera, Erick, and Tunnell, John W., Jr. 2012. "OCEAN POLICY US-Cuba Scientific Collaboration Emerging Issues and Opportunities in Marine and Related Environmental Sciences." Oceanography, 25, (2) 227–231. https://doi.org/10.5670/oceanog.2012.63.
• Fisher, R., Radford, B. T., Knowlton, Nancy, Brainard, Russell E., Michaelis, F. B., and Caley, M. J. 2011. "Global mismatch between research effort and conservation needs of tropical coral reefs." Conservation Letters, 4, (1) 64–72. https://doi.org/10.1111/j.1755-263X.2010.00146.x.
• Fisher, Rebecca, Knowlton, Nancy, Brainard, Russell E., and Caley, M. Julian. 2011. "Differences among Major Taxa in the Extent of Ecological Knowledge across Four Major Ecosystems." PLoS ONE, 6, (11) e26556–8. https://doi.org/10.1371/journal.pone.0026556.
• Knowlton, Nancy. 2011. "Q&A Nancy Knowlton." Current Biology, 21, (8) R270–R271.
• Knowlton, Nancy and Jackson, Jeremy B. C. 2011. "Beyond the obituaries." Solutions: For a Sustainable and Desirable Future, 2, (1).
• Knowlton, Nancy and Jackson, Jeremy B. C. 2011. "The evolutionary diversity and ecological complexity of coral reefs." Paleontological Society Papers, 17 111–120.
• Levitan, Don R., Fogarty, Nicole D., Jara, Javier, Lotterhos, Katie E., and Knowlton, Nancy. 2011. "Genetic, Spatial, and Temporal Components of Precise Spawning Synchrony in Reef Building Corals of the Montastraea Annularis Species Complex." Evolution, 65, (5) 1254–1270. https://doi.org/10.1111/j.1558-5646.2011.01235.x.
• Mumby, Peter J., Iglesias-Prieto, Roberto, Hooten, Anthony J., Sale, Peter F., Hoegh-Guldberg, Ove, Edwards, Alasdair J., Harvell, C. Drew, Gomez, Edgardo D., Knowlton, Nancy, Hatziolos, Marea E., Kyewalyanga, Margareth S., and Muthiga, Nyawira. 2011. "Revisiting climate thresholds and ecosystem collapse." Frontiers in Ecology and the Environment, 9, (2) 94–96. https://doi.org/10.1890/11.WB.002.
• Nunes, Flavia L. D., Norris, Richard D., and Knowlton, Nancy. 2011. "Long Distance Dispersal and Connectivity in Amphi-Atlantic Corals at Regional and Basin Scales." Plos One, 6, (7) 1–12. https://doi.org/10.1371/journal.pone.0022298.
• Plaisance, Laetitia, Brainard, Russell, Caley, M. Julian, and Knowlton, Nancy. 2011. "Using DNA Barcoding and Standardized Sampling to Compare Geographic and Habitat Differentiation of Crustaceans: A Hawaiian Islands Example." Diversity, 3, (4) 581–591. https://doi.org/10.3390/d3040581.
• Plaisance, Laetitia, Caley, M. Julian, Brainard, Russell E., and Knowlton, Nancy. 2011. "The Diversity of Coral Reefs: What Are We Missing?" PLoS ONE, 6, (10) 1–7. https://doi.org/10.1371/journal.pone.0025026.
• Terk, Elizabeth and Knowlton, Nancy. 2010. "The role of SCUBA diver user fees as a source of sustainable funding for coral reef marine protected areas." Biodiversity, 11, (1-2) 78–84. https://doi.org/10.1080/14888386.2010.9712651.
• Anker, Arthur, Hurt, Carla, and Knowlton, Nancy. 2009. "Description of cryptic taxa within the Alpheus bouvieri A. Milne-Edwards, 1878 and A. hebes Kim and Abele, 1988 species complexes (Crustacea: Decapoda: Alpheidae)." Zootaxa, (2153) 1–23.
• Hurt, Carla, Anker, Arthur, and Knowlton, Nancy. 2009. "A Multilocus Test of Simultaneous Divergence Across the Isthmus of Panama using Snapping Shrimp in the Genus Alpheus." Evolution, 63, (2) 514–530. https://doi.org/10.1111/j.1558-5646.2008.00566.x.
• Nunes, F., Norris, R. D., and Knowlton, Nancy. 2009. "Implications of isolation and low genetic diversity in peripheral populations of an amphi-Atlantic coral." Molecular ecology, 18, (20) 4283–4297. https://doi.org/10.1111/j.1365-294X.2009.04347.x.
• Plaisance, Laetitia, Knowlton, Nancy, Paulay, Gustav, and Meyer, Christopher P. 2009. "Reef-associated crustacean fauna: biodiversity estimates using semi-quantitative sampling and DNA barcoding." Coral Reefs, 28, (4) 977–986. https://doi.org/10.1007/s00338-009-0543-3.
• Roth, M. S. and Knowlton, Nancy. 2009. "Distribution, abundance, and microhabitat characterization of small juvenile corals at Palmyra Atoll." Marine Ecology Progress Series, 376 133–142. https://doi.org/10.3354/meps07787.
• Anker, Arthur, Hurt, C., and Knowlton, Nancy. 2008. "Revision of the Alpheus websteri Kingsley, 1880 species complex (Crustacea: Decapoda: Alpheidae), with revalidation of A. arenensis (Chace, 1937)." Zootaxa, 1694 51–68.
• Anker, Arthur, Hurt, Carla, Jara, Javier A., and Knowlton, Nancy. 2008. "Revision of the Alpheus cylindricus Kingsley, 1878 species complex (Crustacea: Decapoda: Alpheidae), with revalidation of A. vanderbilti Boone, 1930." Zootaxa, (1943) 53–68.
• Anker, Arthur, Hurt, Carla, and Knowlton, Nancy. 2008. "Revision of the Alpheus cristulifrons species complex (Crustacea: Decapoda: Alpheidae), with description of a new species from the tropical eastern Atlantic." Journal of the Marine Biological Association of the United Kingdom, 88, (3) 543–562. https://doi.org/10.1017/S0025315408001136.
• Anker, Arthur, Hurt, Carla, and Knowlton, Nancy. 2008. "Revision of the Alpheus formosus Gibbes, 1850 complex, with redescription of A. formosus and description of a new species from the tropical western Atlantic (Crustacea : Decapoda : Alpheidae)." Zootaxa, (1707) 1–22.
• Dinsdale, E. A., Pantos, O., Smriga, S., Edwards, R. A., Angly, F., Wegley, L., Hatay, M., Hall, D., Brown, E., Haynes, M., Krause, L., Sala, E., Sandin, S. A., Thurber, R. V., Willis, B. L., Azam, F., Knowlton, Nancy, and Rohwer, F. 2008. "Microbial ecology of four coral atolls in the northern Line Islands." PLoS One, 3 1584–1601.
• Fukami, Hironobu, Chen, Chaolun Allen, Budd, Ann F., Collins, Allen Gilbert, Wallace, Carden, Chuang, Yao-Yang, Chen, Chienhsun, Dai, Chang-Feng, Iwao, Kenji, Sheppard, Charles, and Knowlton, Nancy. 2008. "Mitochondrial and Nuclear Genes Suggest that Stony Corals Are Monophyletic but Most Families of Stony Corals Are Not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria)." PLoS ONE, 3, (9) e3222. https://doi.org/10.1371/journal.pone.0003222.
• Hoegh-Guldberg, O., Mumby, P. J., Hooten, A. J., Steneck, Robert S., Greenfield, P., Gomez, E., Harvell, D. R., Sale, P. F., Edwards, A. J., Caldeira, K., Knowlton, Nancy, Eakin, C. M., Iglesias-Prieto, R., Muthiga, N., Bradbury, Roger H., Dubi, A., and Hatziolos, M. E. 2008. "Coral adaptation in the face of climate change - Response." Science, 320, (5874) 315–316. https://doi.org/10.1126/science.320.5874.315.
• Knowlton, Nancy. 2008. "Marine biodiversity in jeopardy: the attrition of the world's coral reefs signals far broader and graver problems." American Prospect Special Report: Oceans and Coasts, 19, (12) 15–16.
• Knowlton, Nancy. 2008. "Coral reefs." Current Biology, 18, (1) R18–R21. https://doi.org/10.1016/j.cub.2007.11.018.
• Knowlton, Nancy and Jackson, Jeremy B. C. 2008. "Shifting baselines, local impacts, and global change on coral reefs." Plos Biology, 6, (2) 215–220. https://doi.org/10.1371/journal.pbio.0060054.
• Nunes, F., Fukami, H., Vollmer, S. V., Norris, R. D., and Knowlton, Nancy. 2008. "Re-evaluation of the systematics of the endemic corals of Brazil by molecular data." Coral Reefs, 27 423–432.
• Ruckelshaus, M., Klinger, T., Knowlton, Nancy, and DeMaster, D. P. 2008. "Marine ecosystem-based management in practice: Considering resilience in a broader context." Bioscience, 58 53–63.
• Sandin, S. A., Smith, J. E., DeMartini, Edward E., Dinsdale, E. A., Donner, S. D., Friedlander, A. M., Konotchick, T., Malay, M., Maragos, James E., Obura, D., Pantos, O., Paulay, G., Richie, M., Rohwer, F., Schroeder, Robert E., Walsh, S., Jackson, Jeremy B. C., Knowlton, Nancy, and Sala, E. 2008. "Baselines and degradation of coral reefs in the northern Line Islands." PLoS One, 3 e1548–1559.
• Anker, Arthur, Hurt, C., and Knowlton, Nancy. 2007. "Revision of the Alpheus nuttingi (Schmitt) species complex (Crustacea: Decapoda: Alpheidae), with description of a new species from the tropical eastern Pacific." Zootaxa, 1577, (41) 60.
• Anker, Arthur, Hurt, Carla, and Knowlton, Nancy. 2007. "Three transisthmian snapping shrimps (Crustacea: Decapoda: Alpheidae: Alpheus) associated with innkeeper worms (Echiura: Thalassematidae) in Panamá." Zootaxa, 1626 1–23.
• Fukami, H., Chen, C. A., Chiou, C. -Y, and Knowlton, Nancy. 2007. "Novel group I introns encoding a putative homing endonuclease in the mitochondrial coxI gene of scleractinian corals." Journal of Molecular Evolution, 64 591–600.
• Hoegh-Guldberg, O., Mumby, P. J., Hooten, A. J., Steneck, Robert S., Greenfield, P., Gomez, E., Harvell, C. D., Sale, P. F., Edwards, A. J., Caldeira, K., Knowlton, Nancy, Eakin, C. M., Iglesias-Prieto, R., Muthiga, N., Bradbury, Roger H., Dubi, A., and Hatziolos, M. E. 2007. "Coral Reefs Under Rapid Climate Change and Ocean Acidification." Science, 318, (5857) 1737–1742. https://doi.org/10.1126/science.1152509.
• Mittelbach, Gary G., Schemske, Douglas W., Cornell, Howard V., Allen, Andrew P., Brown, Jonathan M., Bush, Mark B., Harrison, Susan P., Hurlbert, Allen H., Knowlton, Nancy, Lessios, Harilaos A., McCain, Christy M., McCune, Amy R., McDade, Lucinda A., McPeek, Mark A., Near, Thomas J., Price, Trevor D., Ricklefs, Robert E., Roy, Kaustuv, Sax, Dov F., Schluter, Dolph, Sobel, James M., and Turelli, Michael. 2007. "Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography." Ecology Letters, 10, (4) 315–331. https://doi.org/10.1111/j.1461-0248.2007.01020.x.
• Garren, M., Walsh, S. M., Caccone, A., and Knowlton, Nancy. 2006. "Patterns of association between Symbiodinium and members of the Monstastraea annularis species complex on spatial scales ranging from within colonies to between geographic regions." Coral Reefs, 25 503–512.
• Kline, D. I., Bryan, J., Kisflaudy, E., Rohwer, G., Nostropaur, F., Grayson, J., Knowlton, Nancy, and Rohwer, F. 2006. "The aquatic automated dosing and maintenance system (AADAMS)." Limnology and Oceanography, 4 184–192.
• Kline, D., Kuntz, N., Breitbart, M., Knowlton, Nancy, and Rohwer F. 2006. "Role of elevated organic carbon levels and microbial activity in coral mortality." Marine Ecology Progress Series, 314 119–125.
• Sala, E. and Knowlton, Nancy. 2006. "Global marine biodiversity trends." Annual Review of Environment and Resources, 31 93–122.
• Fukami, Hironobu and Knowlton, Nancy. 2005. "Analysis of Complete Mitochondrial DNA Sequences of Three Members of the Montastraea Annularis Coral Species Complex (Cnidaria, Anthozoa, Scleractinia)." Coral Reefs, (24) 410–417.
• Fukami, Hironobu, Budd, Ann F., Levitan, Don R., Jara, Javier A., Kersanach, Ralf, and Knowlton, Nancy. 2004. "Geographic Differences in Species Boundaries Among Members of the Montastraea Annularis Complex Based on Molecular and Morphological Markers." Evolution, (2) 324-337.
• Fukami, Hironobu, Budd, Ann F., Paulay, Gustav, Sole-Cava, Antonio, Chen, Chaolun Allen, Iwao, Kenji, and Knowlton, Nancy. 2004. "Conventional Taxonomy Obscures Deep Divergence Between Pacific and Atlantic Corals." Nature, (6977) 832–835.
• Knowlton, Nancy. 2004. "Multiple "stable" states and the conservation of marine ecosystems." Progress in Oceanography, 60 387–396.
• Levitan, Don R., Kukami, Hironobu, Jara, Javier A., Kline, David, McGovern, Tamara M., McGhee, Kathie E., Swanson, Cheryl A., and Knowlton, Nancy. 2004. "Mechanisms of Reproductive Isolation Among Sympatric Broadcast Spawning Corals of the Montastraea Annularis Species Complex." Evolution, (2) 308–323.
• Knowlton, Nancy and Rohwer, Forest. 2003. "Multispecies Microbial Mutualisms on Coral Reefs: The Host As a Habitat." American Naturalist, 162, (4) S51–S62.
• Williams, S. T., Knowlton, Nancy, Jara, J., and Gomez, E. 2003. "The marine Indo-West Pacific break: contrasting the resolving power of mitochondrial and nuclear genes." Integrative and Comparative Biology, 42 941–952.
• Rohwer, F., Seguritan, V., Azam, F., and Knowlton, Nancy. 2002. "High diversity and species-specific distribution of coral-associated bacteria." Marine Ecology Progress Series, 243 1–10.
• Toller, Wesley W., Rowan, Rob, and Knowlton, Nancy. 2002. "Genetic evidence for a protozoan (phylum Apicomplexa) associated with corals of the Montastraea annularis species complex." Coral Reefs, 21, (2) 143–146.
• Knowlton, Nancy. 2001. "The Future of Coral Reefs." Proceedings of the National Academy of Sciences of the United States of America, (10) 5419–5425.
• Knowlton, Nancy. 2001. "Coral Reef Biodiversity-Habitat Size Matters." Science, (5521) 1493–1495.
• Knowlton, Nancy. 2001. "Sea Urchin Recovery From Mass Mortality: New Hope for Caribbean Coral Reefs?" Proceedings of the National Academy of Sciences of the United States of America, (9) 4822–4824.
• Knowlton, Nancy. 2001. "Who are the players on coral reefs and does it matter? The importance of coral taxonomy for coral reef management." Bulletin of Marine Science, 69 10–13.
• Rohwer, F., Breitbart, Mya, Jara, Javier A., Azam, F., and Knowlton, Nancy. 2001. "Diversity of Bacteria Associated With the Caribbean Coral Montastraea Franksi." Coral Reefs, (1) 85–91.
• Toller, Wesley W., Rowan, Rob, and Knowlton, Nancy. 2001. "Zooxanthellae of the Montastraea annularis Species Complex: Patterns of Distribution of Four Taxa of Symbiodinium on Different Reefs and Across Depths." Biological Bulletin, 201 348–359.
• Toller, Wesley W., Rowan, Rob, and Knowlton, Nancy. 2001. "Repopulation of Zooxanthellae in the Caribbean Corals Montastraea annularis and M. faveolata Following Experimental and Disease-Associated Bleaching." Biological Bulletin, 201, (3) 360–373.
• Williams, Suzanne T. and Knowlton, Nancy. 2001. "Evidence for Three Major Clades Within the Snapping Shrimp Genus Alpheus Inferred From Nuclear and Mitochondrial Gene Sequence Data." Molecular Phylogenetics and Evolution, (3) 375–389.
• Williams, Suzanne T. and Knowlton, Nancy. 2001. "Mitochondrial Pseudogenes Are Pervasive and Often Insidious in the Snapping Shrimp Genus Alpheus." Molecular Biology and Evolution, (8) 1484–1493.
• Williams, Suzanne T., Knowlton, Nancy, Weigt, Lee A., and Jara, Javier A. 2001. "Evidence for Three Major Clades within the Snapping Shrimp Genus Alpheus Inferred from Nuclear and Mitochondrial Gene Sequence Data." Molecular phylogenetics and evolution, 20, (3) 375–389. https://doi.org/10.1006/mpev.2001.0976.
• Knowlton, Nancy. 2000. "Molecular Genetic Analyses of Species Boundaries in the Sea." Hydrobiologia, (1) 73–90.
• Herre, Edward Allen, Knowlton, Nancy, Mueller, Ulrich Gerhard, and Rehner, Stuart A. 1999. "The Evolution of Mutualisms: Exploring the Paths Between Conflict and Cooperation." Trends in Ecology and Evolution, (2) 49–53.
• Killingback, T., Doebeli, M., and Knowlton, Nancy. 1999. "Variable investment, the continuous prisoner's dilemma, and the origin of cooperation." Proceedings of the Royal Society B: Biological Sciences, 266 1723–1728.
• Lopez, Jose V., Kersanach, Ralph, Rehner, Stephen A., and Knowlton, Nancy. 1999. "Molecular Determination of Species Boundaries in Corals: Genetic Analysis of the Montastraea annularis Complex Using Amplified Fragment Length Polymorphisms and a Microsatellite Marker." Biological Bulletin, 196, (1) 80–93.
• Doebeli, Michael and Knowlton, Nancy. 1998. "The Evolution of Interspecific Mutualisms." Proceedings of the National Academy of Sciences of the United States of America, (15) 8676–8680.
• Knowlton, Nancy and Weigt, Lee A. 1998. "New Dates and New Rates for Divergence Across the Isthmus of Panamá." Proceedings of the Royal Society B: Biological Sciences, (1412) 2257–2263.
• Baker, Andrew C., Rowan, R., and Knowlton, Nancy. 1997. "Symbiosis ecology of two Caribbean acroporid corals." Proceedings of the 8th International Coral Reef Symposium, 2 1295–1300.
• Knowlton, Nancy, Mate, J. L., Guzmán, Héctor M., Rowan, R., and Jara, J. 1997. "Direct evidence for reproductive isolation among the three species of the Montastraea annularis complex in Central America (Panama, Honduras)." Marine Biology, 127 705–711.
• Lopez, Jose V. and Knowlton, Nancy. 1997. "Discrimination of sibling species in the Montastraea annularis complex using multiple genetic loci." Proceedings of the 8th International Coral Reef Symposium, 2 1613–1618.
• Rowan, R., Knowlton, Nancy, Baker, A., and Jara, J. 1997. "Landscape ecology of algal symbionts creates variation in episodes of coral bleaching." Nature, 388 265–269.
• Knowlton, Nancy. 1996. "Trench warfare on the shore: inter-clonal aggression in sea anemones." Trends in Ecology and Evolution, 11 271–272.
• Rowan, R. and Knowlton, Nancy. 1995. "Intraspecific diversity and ecological zonation in coral-algal symbiosis." Proceedings of the National Academy of Sciences of the United States of America, 92 2850–2853.
• Rowan, Rob and Knowlton, Nancy. 1995. "The Ecological Significance of Genetic Diversity in Corals and their Algal Symbionts." Journal of cellular biochemistry, 19B 334.
• Knowlton, Nancy. 1994. "A tale of two seas." Natural History, 6, (94) 66–68.
• Knowlton, Nancy and Jackson, Jeremy B. C. 1994. "New taxonomy and niche partitioning on coral reefs: jack of all trades or master of some?" Trends in Ecology and Evolution, 9 7–9.
• Knowlton, Nancy and Jackson, Jeremy B. C. 1994. "Taxonomy and coral reef ecology: a response to Sale." Trends in Ecology and Evolution, 9 398–398.
• Weil, E. and Knowlton, Nancy. 1994. "A multi-character analysis of the Caribbean coral Montastraea annularis (Ellis and Solander, 1786) and its two sibling species, M. faveolata (Ellis and Solander, 1786) and M. franksi (Gregory, 1895)." Bulletin of Marine Science, 55 151–175.
• Knowlton, Nancy. 1993. "Sibling species in the sea." Annual Review of Ecology and Systematics, 24 189–216.
• Knowlton, Nancy, Weight, Lee A., Solorzano, Luis Anibal, Mills, DeEtta K., and Bermingham, Eldredge. 1993. "Divergence in proteins, mitochondrial DNA, and reproductive compatibility across the Isthmus of Panamá." Science, 260, (5114) 1629–1632. https://doi.org/10.1126/science.8503007.
• Knowlton, Nancy. 1992. "Thresholds and multiple stable states in coral reef community dynamics." American Zoologist, 32 674–682.
• Knowlton, Nancy and Mills, D. E. K. 1992. "The systematic importance of color and color pattern: evidence for complexes of sibling species of snapping shrimp (Caridea: Alpheidae: Alpheus) from the Caribbean and Pacific coasts of Panamá." Proceedings of the San Diego Society of Natural History, 18 1–5.
• Knowlton, Nancy, Weil, E., Weigt, Lee A., and Guzmán, Héctor M. 1992. "Sibling species in Montastraea annularis, coral bleaching, and the coral climate record." Science, 255 330–333.
• Knowlton, Nancy. 1989. "A Coral Reef Directory: Coral Reefs of the World (Vols 103)." Trends in Ecology and Evolution, 4, (10) 305–305.
• Knowlton, Nancy, Lang, J. C., and Keller, Brian D. 1989. "Fates of staghorn coral isolates on hurricane- damaged reefs in Jamaica: the role of predators." Proceedings of the 6th International Coral Reef Symposium, 2 83–88.
• Knowlton, Nancy. 1988. "Coral Bleaching in Panama and Considerations for the Future." Mass Bleaching of Coral Reefs in the Caribbean: A Research Strategy, National Undersea Research Program Research Report, 88, (2) 35–37.
• Knowlton, Nancy. 1986. "Cryptic and sibling species among the decapod Crustacea." Journal of Crustacean Biology, 6 356–363.
• Knowlton, Nancy and Keller, Brian D. 1986. "Larvae which fall far short of their potential: highly localized recruitment in an alpheid shrimp with extended larval development." Bulletin of Marine Science, 39 213–223.
• Knowlton, Nancy and Keller, Brian D. 1985. "Two more sibling species of alpheid shrimps associated with the Caribbean sea anemones Bartholomea annulata and Heteractis lucida." Bulletin of Marine Science, 37 893–904.

Dataset

• Silliman, Katherine, Indorf, Jane L., Knowlton, Nancy, Browne, William E., and Hurt, Carla. 2021. [Dataset] Base-substitution mutation rate across the nuclear genome of Alpheus snapping shrimp and the timing of isolation by the Isthmus of Panama. Distributed by Dryad. https://doi.org/10.5061/DRYAD.QNK98SFGS.

Book Chapter

• Knowlton, Nancy and Leray, Matthieu. 2015. "Exploring Coral Reefs Using the Tools of Molecular Genetics." In Coral Reefs in the Anthropocene. Birkeland, Charles, editor. 117–132. Springer Netherlands. https://doi.org/10.1007/978-94-017-7249-5_6.
• Howard, Jennifer, Babij, Eleanora, Griffis, Roger, Helmuth, Brian, Himes-Cornell, Amber, Niemier, Paul, Orbach, Michael, Petes, Laura, Allen, Stewart, Auad, Guillermo, Auer, Carol, Beard, Russell, Boatman, Mary, Bond, Nicholas, Boyer, Timothy, Brown, David, Clay, Patricia, Crane, Katherine, Cross, Scott, Dalton, Michael, Diamond, Jordan, Diaz, Robert, Dortch, Quay, Duffy, J. Emmett, Fauquier, Deborah et al. 2013. "Oceans and Marine Resources in a Changing Climate." In Oceanography and Marine Biology. 1st ed. Scourse, James, editor. 71–192. Boca Raton, Florida: CRC Press-Taylor & Francis Group. In Oceanography and Marine Biology Annual Review, 51.
• Knowlton, Nancy. 2012. "Coral reefs." In Oxford Bibliographies in Ecology. Gibson, David, editor. New York: Oxford University Press.
• Machida, Ryuji J. and Knowlton, Nancy. 2012. "Ways to mix multiple PCR amplicons into single 454 run for DNA barcoding." In DNA Barcodes: Methods and Protocols. 355–361. Humana Press. In Methods in molecular biology, 858. https://doi.org/10.1007/978-1-61779-591-6_16.
• Knowlton, Nancy. 2011. "First steps as a scientist – preface." In In Pursuit of Natural History: Selected Readings and Commentaries. Graham, M. K., Parker, J., and Dayton, P. K., editors. Chicago: Univ. Chicago.
• Knowlton, Nancy, Brainard, Russell E., Fisher, Rebecca, Moews, Megan, Plaisance, Laetitia, and Caley, M. Julian. 2010. "Coral reef biodiversity." In Life in the World's Oceans: Diversity, Distribution, and Abundance. McIntyre, Alasdair D., editor. 65–77. Wiley-Blackwell.
• Knowlton, Nancy, Weight, Lee A., Solorzano, Luis Anibal, Mill, DeEtta K., and Bermingham, Eldredge. 2007. "Diferenciación de proteínas, ADN mitocondrial y compatibilidad reproductora a través del istmo de Panamá." In Ecología y evolución en los trópicos. Leigh, Egbert Giles, Jr., Herre, Edward Allen, Jackson, Jeremy B. C., and Santos-Granero, Fernando, editors. 402–406. Panama: Editora Nova Art.
• Rowan, Robert, Knowlton, Nancy, Baker, Andrew C., and Jara, Javier A. 2007. "Mutualismos entre especies de esponjas de los arrecifes de coral del Caribe." In Ecología y evolución en los trópicos. Leigh, Egbert Giles, Jr., Herre, Edward Allen, Jackson, Jeremy B. C., and Santos-Granero, Fernando, editors. 231–253. Panama: Editora Nova Art.
• Knowlton, Nancy. 2006. "Coral reef coda: what can we hope for?" In Coral Reef Conservation. Cote, I. and Reynolds, J., editors. 538–549. Cambridge University Press.
• Knowlton, Nancy and Budd, Ann F. 2001. "Recognizing coral species past and present." In Evolutionary Patterns: Growth, Form and Tempo in the Fossil Record. Jackson, Jeremy B. C., Lidgard, S., and McKinney, F. K., editors. 97–119. University of Chicago Press.
• Knowlton, Nancy and Jackson, Jeremy B. C. 2001. "The ecology of coral reefs." In Marine Community Ecology. Bertness, Mark D., Gaines, S., and Hay, M. E., editors. 395–422. Sunderland, MA: Sinauer.
• Williams, S. T., Knowlton, Nancy, and Weigt, Lee A. 1999. "Indo-Pacific molecular biogeography of the coral-dwelling snapping shrimp Alpheus lottini (Decapoda: Caridea: Alpheidae)." In Ecology of the Chagos Archipelago, Occassional Publications of the Linnean Society. Sheppard, C. R. C. and Seaward, M. R. D., editors. 195–206. London: Linnean Society.
• Knowlton, Nancy. 1998. "Hard Decisions and Hard Science: Research Needs for Coral Reef Management." In Coral Reefs: Challenges and Opportunities for Sustainable Management. Hatziolas, M., Hooten, A. J., and Fodor, M., editors. 183. World Bank.
• Knowlton, Nancy and Weigt, Lee A. 1997. "Species of marine invertebrates: a comparison of the biological and phylogenetic species concepts." In Species: the Units of Biodiversity, Systematics Association (UK) Special Volume Series 54. Claridge, M. F., Dawah, H. A., and Wilson, M. R., editors. 199–219. Chapman and Hall.
• Knowlton, Nancy and Jackson, Jeremy B. C. 1993. "Inbreeding and outbreeding in marine invertebrates." In The Natural History of Inbreeding and Outbreeding. Thornhill, N. W., editor. 200–249. University of Chicago Press.
• Knowlton, Nancy. 1988. "Coral bleaching in Panamá and considerations for the future." In Mass Bleaching of Coral Reefs in the Caribbean: A Research Strategy. Ogden, John C. and Wicklund, Robert A., editors. 35–37. U.S. Department of Commerce, National Oceanic and Atmospheric Administration, Oceanic and Atmospheric Research, Office of Undersea Research.
• Knowlton, Nancy. 1986. "Field studies of life cycles: focusing on individuals." In Indian Ocean: Biology of Benthic Marine Organisms. Thompson, M. -F, Sarojini, R., and Nagabhushanam, R., editors. 209–215. Oxford and IBH Publications.
• Knowlton, Nancy and Greenwell, Simon R. 1984. "Male sperm competition avoidance mechanisms: the influence of female interests." In Sperm Competition and the Evolution of Animal Mating Systems. Smith, R. L., editor. 61–84.. New York: Academic Press.

Book

• Knowlton, Nancy. 2010. Citizens of the sea : wonderous creatures from the census of marine life. Washington D.C.: National Geographic Society.
• Knowlton, Nancy, Lang, J. C., and Keller, Brian D. 1990. Case study of natural population collapse: post-hurricane predation on Jamaican staghorn corals. Washington, DC: Smithsonian Institution Press. In Smithsonian Contributions to the Marine Sciences. https://doi.org/10.5479/si.01960768.31.1.

Web Page / Electronic Publication

• Knowlton, Nancy. 2004. Ocean health and human health.

Book Review

• Knowlton, Nancy. 1984. [Book review] "The explanation of organic diversity by Mark Ridley." Science, 225, 160–161.