Leray, Matthieu

Smithsonian Tropical Research Institute staff

Using both broad-scale environmental sampling and experimental manipulations of small scale model systems, I focus in particular on the following three questions: (1) What are the nature and causes of biodiversity patterns in the ocean? (2) How do these biodiversity patterns influence ecosystem function? (3) How do ecological interactions (i.e., trophic and symbiotic) promote the stability and resilience of marine communities?

Background And Education

Education And Training

Ph.D. in Marine molecular ecology, Université Pierre et Marie Curie 2008 - 2012

Research And Grants

Investigator On

Characterizing the biodiversity of selected offshore seamounts to improve management awarded by Central Caribbean Marine Institute

Publications

Selected Publications

Article
- 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
- 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
- Rouzé, Héloïse, Knowlton, Nancy, Anker, Arthur, Hurt, Carla, Wirshing, Herman H., Van Wormhoudt, Alain, and Leray, Matthieu. 2024. "An integrative phylogeography for inferring cryptic speciation in the Alpheus lottini species complex, an important coral mutualist." iScience, 27, (10). https://doi.org/10.1016/j.isci.2024.111034. 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
- McIlroy, Shelby E., Guibert, Isis, Archana, Anand, Chung, Wing Yi Haze, Duffy, J. E., Gotama, Rinaldi, Hui, Jerome, Knowlton, Nancy, Leray, Matthieu, Meyer, Christopher, Panagiotou, Gianni, Paulay, Gustav, Russell, Bayden, Thompson, Philip D., and Baker, David M. 2024. "Life goes on: Spatial heterogeneity promotes biodiversity in an urbanized coastal marine ecosystem." Global Change Biology, 30, (4). https://doi.org/10.1111/gcb.17248. 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
- Weinheimer, Alaina R., Aylward, Frank O., Leray, Matthieu, and Scott, Jarrod J. 2023. "Contrasting drivers of abundant phage and prokaryotic communities revealed in diverse coastal ecosystems." ISME Communications, 3, (1) 127. https://doi.org/10.1038/s43705-023-00333-6. 2023
- 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
- Leray, Matthieu, Knowlton, Nancy, and Machida, Ryuji J. 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. 2022
- 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
- Clever, Friederike, Sourisse, Jade M., Preziosi, Richard F., Eisen, Jonathan A., Guerra, E. Catalina Rodriguez, Scott, Jarrod J., Wilkins, Laetitia G. E., Altieri, Andrew H., McMillan, W. Owen, and Leray, Matthieu. 2022. "The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs." Communications Biology, 5, (1). https://doi.org/10.1038/s42003-022-03679-0. 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
- Johnson, Maggie D., Scott, Jarrod J., Leray, Matthieu, Lucey, Noelle, Bravo, Lucia M. Rodriguez, Wied, William L., and Altieri, Andrew H. 2021. "Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef." Nature Communications, 12, (1). https://doi.org/10.1038/s41467-021-24777-3. 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
- 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. 2020
- 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, 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. 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
- 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. 2019
- 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. 2019
- 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
- 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. 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
- 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. 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
- 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. 2017
- 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. 2017
- 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. 2017
- 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 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. 2016
- 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. 2016
- 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. 2015
- 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
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. 2015
Dataset
- Clever, Friederike, Sourisse, Jade M., Preziosi, Richard F., Eisen, Jonathan A., Rodriguez-Guerra, E. Catalina, Scott, Jarrod J., Wilkins, Laetitia G. E., Altieri, Andrew H., McMillan, W. Owen, and Leray, Matthieu. 2021. [Dataset] The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs. Distributed by Dryad. https://doi.org/10.5061/DRYAD.M905QFV28. 2021

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Leray, Matthieu

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Leray, Matthieu

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Background And Education

Education And Training

Research And Grants

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Selected Publications

Article

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Dataset

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