Peer Reviewed Publications

** co-first author

* student co-author

2023

50. Linsmayer L.B., Noel S.K., Leray M., Wangpraseurt D., Hassibi C., Kline D.I., Tresguerres M. 2023. Effects of bleaching on oxygen dynamics, energy metabolism, and genotype of symbiotic algae in two Caribbean coral species. Science of The Total Environment 919, 170753

49. Weinheimer AR, Aylward FO, Leray M, Scott J. 2023. Contrasting drivers of abundant phage and prokaryotic communities in tropical, coastal ecosystems across the Isthmus of Panama. ISME Communications 3, 127

48. Levy N, Simon-Blecher N, Ben-Ezra S, Yuval M, Doniger T, Leray M, Karako-Lampert S, Tarazi E, Levy O. 2023. Evaluating biodiversity for coral reef reformation and monitoring on complex 3D structures using environmental DNA (eDNA) metabarcoding. Science of The Total Environment 856, 159051

2022

47. O’Dea A, Flantua SGA, Leray M, Lueders-Dumont JA, Titcomb MC, 2022. Pleistocene sean level changes and crocodile population histories on the Isthmus of Panama: A comment on Avila-Cervantes et al. Evolution 76, 2778-2783

46. Clever F*, Sourisse JM*, Preziosi RF, Eisen JA, Rodriguez Guerra EC¥, Scott JJ, Wilkins LGE, Altieri AH, McMillan WO, Leray M. 2022. The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs. Communications Biology 5, 770

45. Leray M, Knowlton N, Machida R. 2022. MIDORI2: A collection of quality controlled, preformatted, and regularly updated reference databases for taxonomic assignment of eukaryotic mitochondrial sequences. Environmental DNA. 4, 894-907

44. Aguilar R, Prakash S, Ogburn MB, Pagenkopp Lohan KM, MacDonald KS III, Driskell AC, Ahyong ST, Leray M, McIlroy SE, Tuckey TD, Baeza JA. 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) ruab079

2021

43. Gaither MR, DiBattista JD, Leray M, von der Heyden S. 2021. Metabarcoding the marine environment: from single species to biogeographic patterns. Environmental DNA. 4, 3-8

42. Leray M**, Wilkins LGE**, Apprill A, Bik HM, Clever F, Connolly SR, De León ME, Duffy EJ, Ezzat L, Gignoux-Wolfsohn S, Herre EA, Kaye JZ, Kline DI, Kueneman JG, McCormick MK, McMillan OW, O’Dea A, Pereira TJ, Petersen JM, Petticord DJ, Torchin ME, Vega Thurber R, Videvall E, Wcislo WT, Yuen B, Eisen JA. 2021. Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution. PLoS Biology. 19, e3001322

41. Johnson MD**, Scott JJ**, Leray M**, Lucey N**, Bravo LMR, Wied WL, Altieri AH. 2021. Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef. Nature Communications. 12, 1-1240.

40. Osvatic JT**, Wilkins LGE**, Leibrecht L, Leray M, Zaunera S, Polzina J, Camacho Y, Gros O, van Gils JA , Eisen JA, Petersen JM, Yuen B. 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, e2104378118

39. Wells CD, Paulay G, Nguyen BN, Leray M. 2021. DNA metabarcoding provides insights into the diverse diet of a dominant suspension feeder, the giant plumose anemone Metridium farcimenEnvironmental DNA. 4, 147-156 

38. Rodriguez-Ezpeleta N, Morissette O, Bean C, Manu S, Banerjee P, Lacoursiere A, Ben K, Alter E, Roger F, Holman L, Stewart K, Monaghan M, Mauvisseau Q, Mirimin L, Wangensteen OS, Antognazza C, Helyar S, de Boer H, Monchamp ME, Nijland R, Abbott C, Doi H, Barnes M, Leray M, Hablützel P, Deiner K. 2021. Trade-offs between reducing complex terminology aand producing accurate interpretations from environmental DNA: Comment on “Environmental DNA: What’s behind the term?” Molecular Ecology. 00, 1-5 

37. Kline DI, Dehgan A, Bunje P, Selbe S, Chirayath V, Pizarro O, Leray M, Connolly S, Bongaerts P, Treibitz T, Levy O, Kriegman D, Andersson A, McField M, and Duffy JE. 2021. The coral reef sentinels program: A Mars shot for blue planet health. Marine Technology Society Journal 55, 118-119

36. Anker AA, Leray M, Pachelle PPG. 2021. 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. granulosus Ayón-Parente, Hendrickx & Galvan-Villa, 2015 (Decapoda: Caridea: Palaemonidae). Zootaxa. 4933, 379-390

35. Anker AA, Leray M, Pachelle PPG. 2021. A new species of Alpheus Fabricius, 1798 (Decapoda: Caridea: Alpheidae) from the Caribbean coast of Panama. Zootaxa. 4933, 379-390

2020

34. Leray M, Knowlton N, Ho S, Nguyen BN, Machida R. 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, 32213-32214

33. Leray M, Machida R. 2020. Seabed mining could come at a high price for a unique fauna. Molecular Ecology. 29, 4506-4509

32. Ferreira LAA, Leray M, Anker A. 2020. New findings of the stenopodidean shrimp Microprosthema looensis Goy & Felder, 1988 (Decapoda: Stenopodidea: Spongicolidae)Zootaxa 4729, 445-450

31. Nguyen BN**, Shen EW**, Seemann J, Correa AMS , O’Donnell JL, Altieri AH, Knowlton N, Crandall KA , Egan SP, McMillan WO, Leray M. 2020. Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape. Scientific Reports 10:6729

2019

30. Leray M, Knowlton N, Ho SL, Nguyen BN, Machida RJ. 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, 22651-22656

29. Wilkins LGE**, Leray M**, Yuen B, Peixoto R, Pereira TJ, Bik HM, Coil DA, Duffy JE, Herre EA, Lessios H, Lucey N, Mejia LC, O’dea A, Rasher DB, Sharp K, Sogin EM, Thacker RW, Vega Thurber R, Wcislo WT, Wilbanks EG, Eisen JA. 2019. Host-associated microbiomes drive structure and function of marine ecosystems. PLoS Biology 17, e3000533

28. Van Wormhoudt A, Adjeroud M, Rouzé H, Leray M. 2019. Recent and old duplications in crustaceans “Internal Transcribed Spacer 1″: structural and phylogenetic implications. Molecular Biology Reports 46, 5185–5195

27. Leray M, Alldredge AL, Yang JY, Meyer CP, Holbrook SJ, Schmitt RJ, Knowlton N, Brooks AJ. 2019. Dietary partitioning promotes the coexistence of planktivorous species on coral reefs. Molecular ecology 28, 2694–2710

26. Kandler NM*, Wooster MK, Leray M, Knowlton N, de Voogd NJ, Paulay G, Berumen ML. 2019. Hyperdiverse macrofauna communities associated with a common sponge, Stylissa carteri, shift across ecological gradients in the Central Red Sea. Diversity 11, 18

2018

25. Galtier d’Auriac I, Quinn RA, Maughan H, Nothias LF, Little M, Kapono CA, Cobian A, Reyes BT, Green K, Quistad SD, Leray M, Smith JE, Dorrestein PC, Rohwer F, Deheyn DD, Hartmann AC. 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, 20181307

24. Pearman JK, Leray M, Villalobos R*, Machida R, Berumen M, Knowlton N, Carvalho S. 2018. Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majorityScientific Reports 8, 8090

23. Pachelle PPG, Leray M, Anker AA, Lasley R. 2018. Five new records of marine shrimps (Decapoda: Caridea, Stenopodidea) from the Caribbean coast of PanamaZootaxa. 4438,128-136

22. Leray M, Ho S-L, Lin J, Machida R. 2018. MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated databaseBioinformatics bty454

2017

21. Ransome E, Geller JB, Timmers M, Leray M, Mahardini A, Sembiring A, Collins AG, Meyer CP. 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 PolynesiaPLoS One 12,e0175066

20. Rouzé H, Leray M, Magalon H, Penin L, Gélin P, Knowlton N, Fauvelot C. 2017. Molecular characterization reveals the complexity of previously overlooked coral-exosymbiont interactions and the implications for coral-guild ecologyScientific Report 7,44923

19. Leray M, Knowlton N. 2017. Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcodingPeerJ 5,e3006

18. Machida RJ, Leray M, Ho S-L, Knowlton N. 2017. Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samplesScientific Data 4,170027

2016

17. Leray M, Knowlton N. 2016. Censusing marine eukaryotic diversity in the twenty-first centuryPhilosophical Transactions of the Royal Society B 371,20150331

16. Al-Rshaidat MMD, Snider A*, Rosebraugh S*, Devine AM*, Devine TD*, Plaisance L, Knowlton N, Leray M. 2016. Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red SeaGenome 59,724-737

15. Leray M, Knowlton N. 2016. Visualizing patterns of marine eukaryotic diversity from metabarcoding data using QIIME. In, Bourlat S.J. (eds) Methods in Molecular Biology, Marine Genomics Methods and Protocols. Springer Protocols, pp 219-235

14. Bourlat SJ, Haenel Q, Finnman J, Leray M. 2016. Preparation of amplicon libraries for metabarcoding of marine eukaryotes using Illumina MiSeq, The dual-PCR method. In, Bourlat S.J. (eds) Methods in Molecular Biology, Marine Genomics Methods and Protocols. Springer Protocols, pp 197-207

13. Leray M, Haenel Q, Bourlat SJ. 2016. Preparation of amplicon libraries for metabarcoding of marine eukaryotes using Illumina MiSeq, The adapter ligation method. In, Bourlat S.J. (eds) Methods in Molecular Biology, Marine Genomics Methods and Protocols. Springer Protocols, pp 209-218

2015

12. Leray M, Meyer CP, Mills SC. 2015. Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist dietPeerJ 3, e1047

11. Knowlton N, Leray M. 2015. Exploring coral reefs using the tools of molecular genetics. In, Birkeland C. (eds) Coral Reefs in the Anthropocene. Springer Science+Business Media, Dordrecht, pp 117-132

10. Leray M, Knowlton N. 2015. DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversityProceedings of the National Academy of Sciences of the United States of America 112, 2076-2081

2014

9. Stier AC**, Leray M.** 2014. Predators alter community organization of coral reef cryptofauna and reduce abundance of coral mutualistsCoral Reefs 33,181-191

2013

8. Leray M, Yang JY, Meyer CP, Mills SC, Agudelo N*, Ranwez V, Boehm JT, Machida RJ. 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 contentsFrontiers in Zoology 10,34

7. Leray M, Agudelo N*, Mills SC, Meyer CP. 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 speciesPLoS One 8,e58076

2012

6. Leray M, Boehm JT, Mills SC, Meyer CP. 2012. Moorea BIOCODE barcode library as a tool for understanding predator-prey interactions, insights into the diet of common predatory coral reef fishesCoral Reefs 31,383-388

5. Leray M, Beraud M*, Anker A, Chancerelle Y, Mills S. 2012. Acanthaster planci outbreak, decline in coral health, coral size structure modification and consequences for obligate decapod assemblagesPLoS One 7,e35456

4. Stier AC, Gil MA, McKeon CS, Lemer S, Leray M, Mills SC, Osenberg CW. 2012. Housekeeping mutualisms, do more symbionts facilitate host performance? PLoS One 7,e32079

2010

3. Leray M, Beldade R, Holbrook SJ, Schmitt RJ, Planes S, Bernardi G. 2010. Allopatric divergence and speciation in coral reef fish, the three-spot Dascyllus, Dascyllus trimaculatus, species complexEvolution 64,1218-1230

2. Van Herwerden L, Howard Choat J, Newman SJ, Leray M, Hillersøy G. 2009. Complex patterns of population structure and recruitment of Plectropomus leopardus (Pisces, Epinephelidae) in the Indo-West Pacific, Implications for fisheries managementMarine Biology 156,1595-1607

2009

1. Leray M, Beldade R, Holbrook SJ, Schmitt RJ, Planes S, Bernardi G. 2009. Isolation and characterization of 13 polymorphic nuclear microsatellite primers for the widespread Indo‐Pacific three‐spot damselfish, Dascyllus trimaculatus, and closely related D. auripinnisMolecular ecology resources 9, 213-215

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