Bibliography
Matthieu Leray
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.
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.
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.
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.
Gaither, Michelle R., DiBattista, Joseph D., Heyden, Sophie, and Leray, Matthieu. 2022. "Metabarcoding the marine environment: from single species to biogeographic patterns." Environmental DNA, 4, (1) 3–8. https://doi.org/10.1002/edn3.270.
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.
Flantua, Suzette G. A., Lueders-Dumont, Jessica A., Titcomb, Max C., Leray, Matthieu, and O'Dea, Aaron. 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
