Article

• Zhang, Yan, Zhang, Heng, Akashi, Hiroshi, Albouy, Camille P., Andres, Kara J., Barquin, Jose, Brantschen, Jeanine, Connon, Richard E., Craine, Joseph M., Gleeson, Deirdre, Goldenberg-Vilar, Alejandra, Gonzalez-Ferreras, Alexia M., Hatzenbuhler, Chelsea, Hupalo, Kamil, Hyde, Josephine, Iwasaki, Wataru, Johnson, Mark D., Katz, Aron D., Kuzovlev, Vyacheslav V., Larson, Courtney E., Lecaudey, Laurene A., Leese, Florian, Leray, Matthieu, Li, Feilong, Macher, Till-Hendrik et al. 2026. "A unified analysis of global riverine eDNA reveals common associations of fish biodiversity with drainage characteristics." Nature Ecology & Evolution, https://doi.org/10.1038/s41559-026-03106-1. 2026
• Lardinois, Laura L., Hinojosa, Natasha A., Quintero-Arrieta, Helio, Sellers, Andrew J., Leray, Matthieu, and Barrett, Rowan D. H. 2026. "Host matters: coral reef fish species show distinct skin microbiome responses to upwelling-driven environmental changes." BMC Microbiology, https://doi.org/10.1186/s12866-026-05036-1. 2026
• Zhang, Yan, Zhang, Heng, Akashi, Hiroshi, Albouy, Camille P., Andres, Kara J., Barquín, José, Brantschen, Jeanine, Connon, Richard E., Craine, Joseph M., Gleeson, Deirdre, Goldenberg‐Vilar, Alejandra, González‐Ferreras, Alexia M., Hatzenbuhler, Chelsea, Hupało, Kamil, Hyde, Josephine, Iwasaki, Wataru, Johnson, Mark D., Katz, Aron D., Kuzovlev, Vyacheslav V., Larson, Courtney E., Lecaudey, Laurène A., Leese, Florian, Leray, Matthieu, Li, Feilong, Macher, Till‐Hendrik et al. 2026. "Integrated Reanalysis of Global Riverine Fish eDNA Datasets Shows Robustness and Congruence of Biodiversity Conclusions." Molecular ecology, 35, (8). https://doi.org/10.1111/mec.70340. 2026
• O'Dea, Aaron, Dillon, Erin M., Brandl, Simon J., Cramer, Katie L., Cybulski, Jonathan D., De Gracia, Brigida, García-Méndez, Kimberly, Griswold, Katherine, Lin, Chien-Hsiang, Leray, Matthieu, Lueders-Dumont, Jessica A., Sellers, Andrew J., and Wake, Thomas A. 2025. "Prehistoric archives reveal evidence of predator loss and release in Caribbean reef fish communities." Proceedings of the National Academy of Sciences of the United States of America, 122, (27). https://doi.org/10.1073/pnas.2503986122. 2025
• Hultgren, K. M., Paulay, G., Cummings, B., Leray, Matthieu, and Winans, G. 2025. "Salish Sea crustacean biodiversity is remarkably high and increases with oceanic influences." Marine Biodiversity, 55, (6) 121. https://doi.org/10.1007/s12526-025-01609-x. 2025
• Morel-Letelier, Isidora, Yuen, Benedict, Orellana, Luis H., Kück, A. Carlotta, Camacho-García, Yolanda E., Lara, Minor, Leray, Matthieu, and Wilkins, Laetitia G. E. 2025. "Seasonal transcriptomic shifts reveal metabolic flexibility of chemosynthetic symbionts in an upwelling region." Msystems, https://doi.org/10.1128/msystems.01686-24. 2025
• Glynn, Victoria M., de Barros Marangoni, Laura Fernandes, Guglielmetti, Maxime, Tapia, Eunice R., Ali, Viviane, Quintero, Helio, Rodriguez Guerra, E. Catalina, Yuval, Matan, Kline, David I., Leray, Matthieu, Connolly, Sean R., and Barrett, Rowan D. H. 2025. "The role of holobiont composition and environmental history in thermotolerance of Tropical Eastern Pacific corals." Current Biology, https://doi.org/10.1016/j.cub.2025.05.035. 2025
• Morel-Letelier, Isidora, Yuen, Benedict, Kück, A. Carlotta, Camacho-García, Yolanda E., Petersen, Jillian M., Lara, Minor, Leray, Matthieu, Eisen, Jonathan A., Osvatic, Jay T., Gros, Olivier, and Wilkins, Laetitia G. E. 2024. "Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts." Plos Genetics, 20, (5). https://doi.org/10.1371/journal.pgen.1011295. 2024
• Linsmayer, L. B., Noel, S. K., Leray, Matthieu, Wangpraseurt, D., Hassibi, C., Kline, D. I., and Tresguerres, M. 2024. "Effects of bleaching on oxygen dynamics and energy metabolism of two Caribbean coral species." Science of The Total Environment, 919 170753. https://doi.org/10.1016/j.scitotenv.2024.170753. 2024
• Seymour, Mathew, Guibert, Isis, Jeunen, Gert‐Jan, Hellström, Micaela, Leray, Matthieu, Elbrect, Vasco, Lau, Anthony, Cutracci, Maxine, How, Chun Ming, Ip, Jack Chi Ho, Liu, Zifang, Moffitt, Jessica, Qian, Cheng, Qin, Xian, Tse, Cham Man, Wang, Yifu, Wang, Zhi, Zeng, Xiaoyi, and Zhao, Meihong. 2024. "The First International eDNA Workshop in Hong Kong: A beginner's guide for the next‐generation eDNA researcher." Environmental DNA, 6, (3). https://doi.org/10.1002/edn3.552. 2024
• Levy, Natalie, Simon-Blecher, Noa, Ben-Ezra, Shachaf, Yuval, Matan, Doniger, Tirza, Leray, Matthieu, Karako-Lampert, Sarit, Tarazi, Ezri, and Levy, Oren. 2023. "Evaluating biodiversity for coral reef reformation and monitoring on complex 3D structures using environmental DNA (eDNA) metabarcoding." Science of The Total Environment, 856. https://doi.org/10.1016/j.scitotenv.2022.159051. 2023
• Gaither, Michelle R., DiBattista, Joseph D., Leray, Matthieu, and Heyden, Sophie. 2022. "Metabarcoding the marine environment: from single species to biogeographic patterns." Environmental DNA, 4, (1) 3–8. https://doi.org/10.1002/edn3.270. 2022
• O'Dea, Aaron, Flantua, Suzette G. A., Leray, Matthieu, Lueders-Dumont, Jessica A., and Titcomb, Max C. 2022. "Pleistocene sea level changes and crocodile population histories on the Isthmus of Panama: A comment on Avila-Cervantes et al. (2020)." Evolution, https://doi.org/10.1111/evo.14610. 2022
• Aguilar, Robert, Prakash, Sanjeevi, Ogburn, Matthew B., Lohan, Katrina M. Pagenkopp, Macdonald, Kenneth S., Driskell, Amy C., Ahyong, Shane T., Leray, Matthieu, McIlroy, Shelby E., Tuckey, Troy D., and Baeza, J. Antonio. 2022. "Unresolved taxonomy confounds invasive species identification: the Lysmata vittata Stimpson, 1860 (Decapoda: Caridea: Lysmatidae) species complex and recent introduction of Lysmata vittata sensu stricto in the western Atlantic." Journal of Crustacean Biology, 42, (1). https://doi.org/10.1093/jcbiol/ruab079. 2022
• Anker, Arthur, Leray, Matthieu, and Pachelle, Paulo P. G. 2021. "A new species of Alpheus Fabricius, 1798 (Decapoda: Caridea: Alpheidae) from the Caribbean coast of Panama." Zootaxa, 4933, (3) 379–390. https://doi.org/10.11646/zootaxa.4933.3.5. 2021
• Osvatic, Jay T., Wilkins, Laetitia G. E., Leibrecht, Lukas, Leray, Matthieu, Zauner, Sarah, Polzin, Julia, Camacho, Yolanda, Gros, Olivier, van Gils, Jan A., Eisen, Jonathan A., Petersen, Jillian M., and Yuen, Benedict. 2021. "Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups." Proceedings of the National Academy of Sciences of the United States of America, 118, (29). https://doi.org/10.1073/pnas.2104378118. 2021
• Leray, Matthieu, Wilkins, Laetitia G. E., Apprill, Amy, Bik, Holly M., Clever, Friederike, Connolly, Sean R., De Leon, Marina E., Duffy, J. Emmett, Ezzat, Leila, Gignoux-Wolfsohn, Sarah, Herre, Edward Allen, Kaye, Jonathan Z., Kline, David I., Kueneman, Jordan G., McCormick, Melissa K., McMillan, W. Owen, O'Dea, Aaron, Pereira, Tiago J., Petersen, Jillian M., Petticord, Daniel F., Torchin, Mark E., Vega Thurber, Rebecca, Videvall, Elin, Wcislo, William T., Yuen, Benedict et al. 2021. "Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution." Plos Biology, 19, (8). https://doi.org/10.1371/journal.pbio.3001322. 2021
• Kline, David, I., Dehgan, Alex, Bunje, Paul, Selbe, Shah, Chirayath, Ved, Pizarro, Oscar, Leray, Matthieu, Connolly, Sean, Bongaert, Pim, Treibitz, Tali, Levy, Oren, Kriegman, David, Andersson, Andreas, McField, Melanie D., and Duffy, J. Emmett. 2021. "The Coral Reef Sentinels Program: A Mars Shot for Blue Planetary Health." Marine Technology Society Journal, 55, (3) 118–118. https://doi.org/10.4031/MTSJ.55.3.51. 2021
• Rodriguez-Ezpeleta, Naiara, Morissette, Olivier, Bean, Colin W., Manu, Shivakumara, Banerjee, Pritam, Lacoursiere-Roussel, Anais, Beng, Kingsly C., Alter, S. Elizabeth, Roger, Fabian, Holman, Luke E., Stewart, Kathryn A., Monaghan, Michael T., Mauvisseau, Quentin, Mirimin, Luca, Wangensteen, Owen S., Antognazza, Caterina M., Helyar, Sarah J., de Boer, Hugo, Monchamp, Marie-Eve, Nijland, Reindert, Abbott, Cathryn L., Doi, Hideyuki, Barnes, Matthew A., Leray, Matthieu, Hablutzel, Pascal I. et al. 2021. "Trade-offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on "Environmental DNA: What's behind the term?" by Pawlowski et al., (2020)." Molecular ecology, 30, (19) 4601–4605. https://doi.org/10.1111/mec.15942. 2021
• Anker, Arthur, Pachelle, Paulo P. G., and Leray, Matthieu. 2021. "p Two new species of Typton Costa, 1844 from tropical American waters, with taxonomic notes on T. tortugae McClendon, 1911 and a new record of T. granulosusAyon-Parente, Hendrickx & Galvan-Villa, 2015 (Decapoda: Caridea: Palaemonidae)." Zootaxa, 4950, (2) 267–295. https://doi.org/10.11646/zootaxa.4950.2.3. 2021
• Ferreira, Luciane Augusto De Azevedo, Leray, Matthieu, and Anker, Arthur. 2020. "New findings of the stenopodidean shrimp Microprosthema looensis Goy & Felder, 1988 (Decapoda: Stenopodidea: Spongicolidae)." Zootaxa, 4729, (3) 445–450. https://doi.org/10.11646/zootaxa.4729.3.11. 2020
• Leray, Matthieu and Machida, Ryuji J. 2020. "Seabed mining could come at a high price for a unique fauna." Molecular ecology, https://doi.org/10.1111/mec.15678. 2020
• Wilkins, Laetitia G. E., Leray, Matthieu, Yuen, Benedict, Peixoto, Raquel, Pereira, Tiago J., Bik, Holly M., Coil, David A., Duffy, J. Emmett, Herre, Edward Allen, Lessios, Harilaos, Lucey, Noelle, Mejia, Luis C., O'Dea, Aaron, Rasher, Douglas B., Sharp, Koty, Sogin, Emilia M., Thacker, Robert W., Thurber, Rebecca Vega, Wcislo, William T., Wilbanks, Elizabeth G., and Eisen, Jonathan A. 2019. "Host-associated microbiomes and their roles in marine ecosystem functions." PeerJ, 1–27. https://doi.org/10.7287/peerj.preprints.27930v1. 2019
• Wilkins, Laetitia G. E., Leray, Matthieu, O'Dea, Aaron, Yuen, Benedict, Peixoto, Raquel S., Pereira, Tiago J., Bik, Holly M., Coil, David A., Duffy, J. Emmett, Herre, Edward Allen, Lessios, Harilaos A., Lucey, Noelle M., Mejia, Luis C., Rasher, Douglas B., Sharp, Koty H., Sogin, Emilia M., Thacker, Robert W., Thurber, Rebecca Vega, Wcislo, William T., Wilbanks, Elizabeth G., and Eisen, Jonathan A. 2019. "Host-associated microbiomes drive structure and function of marine ecosystems." PLoS biology, 17, (11) 1–15. https://doi.org/10.1371/journal.pbio.3000533. 2019
• Van Wormhoudt, Alain, Adjeroud, Mehdi, Rouzé, Heloise, and Leray, Matthieu. 2019. "Recent and old duplications in crustaceans "Internal Transcribed Spacer 1″: structural and phylogenetic implications." Molecular biology reports, 46, (5) 5185–5195. https://doi.org/10.1007/s11033-019-04976-4. 2019
• d'Auriac, Ines Galtier, Quinn, Robert A., Maughan, Heather, Nothias, Louis-Felix, Little, Mark, Kapono, Clifford A., Cobian, Ana, Reyes, Brandon T., Green, Kevin, Quistad, Steven D., Leray, Matthieu, Smith, Jennifer E., Dorrestein, Pieter C., Rohwer, Forest, Deheyn, Dimitri D., and Hartmann, Aaron C. 2018. "Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism." Proceedings of the Royal Society B: Biological Sciences, 285, (2884) 20181307–20181307. https://doi.org/10.1098/rspb.2018.1307. 2018
• Pachelle, Paulo P. G., Leray, Matthieu, Anker, Arthur, and Lasley, Robert. 2018. "Five new records of marine shrimps (Decapoda: Caridea, Stenopodidea) from the Caribbean coast of Panama." Zootaxa, 4438, (1) 128–136. https://doi.org/10.11646/zootaxa.4438.1.5. 2018
• Leray, Matthieu, Ho, Shian-Lei, Lin, I. -J, and Machida, Ryuji J. 2018. "MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database." Bioinformatics (Oxford, England), 34, (21) 3753–3754. https://doi.org/10.1093/bioinformatics/bty454. 2018
• Ransome, Emma, Geller, Jonathan B., Timmers, Molly, Leray, Matthieu, Mahardini, Angka, Sembiring, Andrianus, Collins, Allen Gilbert, and Meyer, Christopher P. 2017. "The importance of standardization for biodiversity comparisons: A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on Mo'orea coral reefs, French Polynesia." PLOS ONE, 12, (4). https://doi.org/10.1371/journal.pone.0175066. 2017
• Leray, Matthieu, Meyer, Christopher P., and Mills, Suzanne C. 2015. "Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet." PeerJ, 3. https://doi.org/10.7717/peerj.1047. 2015
• Leray, Matthieu, Yang, Joy Y., Meyer, Christopher P., Mills, Suzanne C., Agudelo, Natalia, Ranwez, Vincent, Boehm, Joel T., and Machida, Ryuji J. 2013. "A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents." Frontiers in Zoology, 10 34. https://doi.org/10.1186/1742-9994-10-34. 2013
• Leray, Matthieu, Agudelo, Natalia, Mills, Suzanne C., and Meyer, Christopher P. 2013. "Effectiveness of Annealing Blocking Primers versus Restriction Enzymes for Characterization of Generalist Diets: Unexpected Prey Revealed in the Gut Contents of Two Coral Reef Fish Species." PLoS ONE, 8, (4) e58076. https://doi.org/10.1371/journal.pone.0058076. 2013
• Stier, Adrian C., Gil, Michael A., McKeon, C. Seabird, Lemer, Sarah, Leray, Matthieu, Mills, Suzanne C., and Osenberg, Craig W. 2012. "Housekeeping Mutualisms: Do More Symbionts Facilitate Host Performance?" Plos One, 7, (4) 1–6. https://doi.org/10.1371/journal.pone.0032079. 2012
• Leray, Matthieu, Boehm, J. T., Mills, S. C., and Meyer, Christopher P. 2012. "Moorea BIOCODE barcode library as a tool for understanding predator-prey interactions: insights into the diet of common predatory coral reef fishes." Coral Reefs, 31, (2) 383–388. https://doi.org/10.1007/s00338-011-0845-0. 2012