{"id":106,"date":"2023-08-28T14:45:03","date_gmt":"2023-08-28T14:45:03","guid":{"rendered":"https:\/\/striresearch.si.edu\/matthieuleray\/?page_id=106"},"modified":"2025-01-10T21:50:33","modified_gmt":"2025-01-10T21:50:33","slug":"publications","status":"publish","type":"page","link":"https:\/\/striresearch.si.edu\/matthieuleray\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n<div class=\"wp-block-cover is-light has-parallax\" style=\"min-height:50px;aspect-ratio:unset;\"><span aria-hidden=\"true\" class=\"wp-block-cover__background has-background-dim-30 has-background-dim\"><\/span><div class=\"wp-block-cover__image-background wp-image-745 has-parallax\" style=\"background-position:50% 50%;background-image:url(https:\/\/striresearch.si.edu\/matthieuleray\/wp-content\/uploads\/sites\/154\/2023\/08\/CoverPublications-scaled.jpg)\"><\/div><div class=\"wp-block-cover__inner-container is-layout-flow wp-block-cover-is-layout-flow\">\n<div style=\"height:25vh\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n<style>.wp-block-kadence-advancedheading.kt-adv-heading106_27ed75-de, .wp-block-kadence-advancedheading.kt-adv-heading106_27ed75-de[data-kb-block=\"kb-adv-heading106_27ed75-de\"]{text-align:center;font-style:normal;color:#ffffff;}.wp-block-kadence-advancedheading.kt-adv-heading106_27ed75-de mark.kt-highlight, .wp-block-kadence-advancedheading.kt-adv-heading106_27ed75-de[data-kb-block=\"kb-adv-heading106_27ed75-de\"] mark.kt-highlight{font-style:normal;color:#f76a0c;-webkit-box-decoration-break:clone;box-decoration-break:clone;padding-top:0px;padding-right:0px;padding-bottom:0px;padding-left:0px;}<\/style>\n<h1 class=\"kt-adv-heading106_27ed75-de wp-block-kadence-advancedheading\" data-kb-block=\"kb-adv-heading106_27ed75-de\"><strong>Peer Reviewed Publications<\/strong><\/h1>\n\n\n\n<div style=\"height:25vh\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n<\/div><\/div>\n\n\n\n<div style=\"height:80px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n<style>.kb-row-layout-id106_b7e1e3-06 > .kt-row-column-wrap{align-content:start;}:where(.kb-row-layout-id106_b7e1e3-06 > .kt-row-column-wrap) > .wp-block-kadence-column{justify-content:start;}.kb-row-layout-id106_b7e1e3-06 > .kt-row-column-wrap{column-gap:var(--global-kb-gap-md, 2rem);row-gap:var(--global-kb-gap-md, 2rem);padding-top:var(--global-kb-spacing-sm, 1.5rem);padding-bottom:var(--global-kb-spacing-sm, 1.5rem);}.kb-row-layout-id106_b7e1e3-06 > .kt-row-column-wrap > div:not(.added-for-specificity){grid-column:initial;}.kb-row-layout-id106_b7e1e3-06 > .kt-row-column-wrap{grid-template-columns:minmax(0, 1fr) minmax(0, 6fr) minmax(0, 1fr);}.kb-row-layout-id106_b7e1e3-06 > .kt-row-layout-overlay{opacity:0.30;}@media all and (max-width: 1024px){.kb-row-layout-id106_b7e1e3-06 > .kt-row-column-wrap > div:not(.added-for-specificity){grid-column:initial;}}@media all and (max-width: 1024px){.kb-row-layout-id106_b7e1e3-06 > .kt-row-column-wrap{grid-template-columns:minmax(0, 1fr) minmax(0, 6fr) minmax(0, 1fr);}}@media all and (max-width: 767px){.kb-row-layout-id106_b7e1e3-06 > .kt-row-column-wrap > div:not(.added-for-specificity){grid-column:initial;}.kb-row-layout-id106_b7e1e3-06 > .kt-row-column-wrap{grid-template-columns:minmax(0, 1fr);}}<\/style><div class=\"kb-row-layout-wrap kb-row-layout-id106_b7e1e3-06 alignnone wp-block-kadence-rowlayout\"><div class=\"kt-row-column-wrap kt-has-3-columns kt-row-layout-center-exwide kt-tab-layout-inherit kt-mobile-layout-row kt-row-valign-top\">\n<style>.kadence-column106_3be3d0-c0 > .kt-inside-inner-col,.kadence-column106_3be3d0-c0 > .kt-inside-inner-col:before{border-top-left-radius:0px;border-top-right-radius:0px;border-bottom-right-radius:0px;border-bottom-left-radius:0px;}.kadence-column106_3be3d0-c0 > .kt-inside-inner-col{column-gap:var(--global-kb-gap-sm, 1rem);}.kadence-column106_3be3d0-c0 > .kt-inside-inner-col{flex-direction:column;}.kadence-column106_3be3d0-c0 > .kt-inside-inner-col > .aligncenter{width:100%;}.kadence-column106_3be3d0-c0 > .kt-inside-inner-col:before{opacity:0.3;}.kadence-column106_3be3d0-c0{position:relative;}@media all and (max-width: 1024px){.kadence-column106_3be3d0-c0 > .kt-inside-inner-col{flex-direction:column;justify-content:center;}}@media all and (max-width: 767px){.kadence-column106_3be3d0-c0 > .kt-inside-inner-col{flex-direction:column;justify-content:center;}}<\/style>\n<div class=\"wp-block-kadence-column kadence-column106_3be3d0-c0\"><div class=\"kt-inside-inner-col\">\n<p class=\"has-text-align-center\">** co-first author<\/p>\n\n\n\n<p class=\"has-text-align-center\">* student co-author<\/p>\n<\/div><\/div>\n\n\n<style>.kadence-column106_611886-5e > .kt-inside-inner-col,.kadence-column106_611886-5e > .kt-inside-inner-col:before{border-top-left-radius:0px;border-top-right-radius:0px;border-bottom-right-radius:0px;border-bottom-left-radius:0px;}.kadence-column106_611886-5e > .kt-inside-inner-col{column-gap:var(--global-kb-gap-sm, 1rem);}.kadence-column106_611886-5e > .kt-inside-inner-col{flex-direction:column;}.kadence-column106_611886-5e > .kt-inside-inner-col > .aligncenter{width:100%;}.kadence-column106_611886-5e > .kt-inside-inner-col:before{opacity:0.3;}.kadence-column106_611886-5e{position:relative;}@media all and (max-width: 1024px){.kadence-column106_611886-5e > .kt-inside-inner-col{flex-direction:column;justify-content:center;}}@media all and (max-width: 767px){.kadence-column106_611886-5e > .kt-inside-inner-col{flex-direction:column;justify-content:center;}}<\/style>\n<div class=\"wp-block-kadence-column kadence-column106_611886-5e\"><div class=\"kt-inside-inner-col\">\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2024<\/h2>\n\n\n\n<p>54. Rouz\u00e9 H, Knowlton N, Anker A, Hurt C, Wirshing H, Von Wormhoudt A,\u00a0Leray M. 2024. An integrated phylogeographic approach for inferring cryptic speciation in the\u00a0<em>Alpheus lottini<\/em>\u00a0species complex, an important coral mutualist.\u00a0<em>iScience\u00a0<\/em>27<em>,\u00a0<\/em>111034<\/p>\n\n\n\n<p>53. Morel-Letelier I, Yuen B, K\u00fcck AC, Camacho-Garc\u00eda YE, Petersen JM, Lara M, Leray M, Eisen JA, Osvatic JT, Gros O, Wilkins LGE. 2024. Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts. <em>PLoS Genetics<\/em> 20, e1011295<\/p>\n\n\n\n<p>52. Seymour M, Guibert I, Jeunen GJ, Helstrom M, Leray M, Elbrecht V, Lau A, How CM, Ho Ip JC, Liu Z, Moffitt J, Qian L, Qin X, Tse CM, Wang Y, Wang Z, Zeng X, Zhao M. 2024.The first International eDNA workshop in Hong Kong: A beginner\u2019s guide for the next generation eDNA researcher. <em>Environmental DNA <\/em>6, e552<\/p>\n\n\n\n<p>51. McIlroy SE, Guibert I, Archana A, Haze Chung WY, Duffy JE, Gotama R, Hui J, Knowlton N, Leray M, Meyer CP, Panagiotou G, Paulay G, Russell B, Thompson PD, Baker DM. 2024. Life goes on: spatial heterogeneity promotes biodiversity in an urbanized coastal marine ecosystem. <em>Global Change Biology <\/em>30, e17248<\/p>\n\n\n\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2023<\/h2>\n\n\n\n<p>50. Linsmayer LB, Noel SK, Leray M, Wangpraseurt D, Hassibi C, Kline DI, Tresguerres M. 2023. Effects of bleaching on oxygen dynamics, energy metabolism, and genotype of symbiotic algae in two Caribbean coral species. <em>Science of The Total Environment<\/em> 919, 170753<\/p>\n\n\n\n<p>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. <em>ISME Communications<\/em> 3, 127<\/p>\n\n\n\n<p>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. <em>Science of The Total Environment <\/em>856, 159051<\/p>\n\n\n\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2022<\/h2>\n\n\n\n<p>47. O\u2019Dea 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. <em>Evolution <\/em>76, 2778-2783<\/p>\n\n\n\n<p>46. Clever F*, Sourisse JM*, Preziosi RF, Eisen JA, Rodriguez Guerra EC\u00a5, Scott JJ, Wilkins LGE, Altieri AH, McMillan WO, Leray M. 2022. The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs. <em>Communications Biology<\/em> 5, 770<\/p>\n\n\n\n<p>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. <em>Environmental DNA<\/em>. 4, 894-907<\/p>\n\n\n\n<p>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 <em>Lysmata vittata Stimpson<\/em>, 1860 (Decapoda: Caridea: Lysmatidae) species complex and recent introduction of <em>Lysmata vittata sensu<\/em> stricto in the western Atlantic. <em>Journal of Crustacean Biology<\/em> 42(1) ruab079<\/p>\n\n\n\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2021<\/h2>\n\n\n\n<p>43. Gaither MR, DiBattista JD, Leray M, von der Heyden S. 2021. Metabarcoding the marine environment: from single species to biogeographic patterns. <em>Environmental DNA<\/em>. 4, 3-8<\/p>\n\n\n\n<p>42. Leray M**, Wilkins LGE**, Apprill A, Bik HM, Clever F, Connolly SR, De Le\u00f3n ME, Duffy EJ, Ezzat L, Gignoux-Wolfsohn S, Herre EA, Kaye JZ, Kline DI, Kueneman JG, McCormick MK, McMillan OW, O\u2019Dea A, Pereira TJ, Petersen JM, Petticord DJ, Torchin ME, Vega Thurber R, Videvall E, Wcislo WT, Yuen B, Eisen JA.&nbsp;2021. Natural experiments and long-term monitoring are critical to understand and predict marine host-microbe ecology and evolution.&nbsp;<em>PLoS Biology<\/em>. 19, e3001322<\/p>\n\n\n\n<p>41. Johnson MD**, Scott JJ**, Leray M**, Lucey N**, Bravo LMR, Wied WL, Altieri AH.&nbsp;2021. Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef.&nbsp;<em>Nature Communications<\/em>. 12, 1-1240. <\/p>\n\n\n\n<p>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.&nbsp;Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups.&nbsp;<em>Proceedings of the National Academy of Sciences of the United States of America<\/em>. 118, e2104378118<\/p>\n\n\n\n<p>39. Wells CD, Paulay G, Nguyen BN, Leray M. 2021.&nbsp;DNA metabarcoding provides insights into the diverse diet of a dominant suspension feeder, the giant plumose anemone&nbsp;<em>Metridium farcimen<\/em>.&nbsp;<em>Environmental DNA<\/em>. 4, 147-156&nbsp;<\/p>\n\n\n\n<p>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, Habl\u00fctzel P, Deiner K. 2021.&nbsp;Trade-offs between reducing complex terminology aand producing accurate interpretations from environmental DNA: Comment on \u201cEnvironmental DNA: What\u2019s behind the term?\u201d&nbsp;<em>Molecular Ecology<\/em>. 00, 1-5&nbsp;<\/p>\n\n\n\n<p>37.&nbsp;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.&nbsp;The coral reef sentinels program: A Mars shot for blue planet health.&nbsp;<em>Marine Technology Society Journal<\/em>&nbsp;55, 118-119<\/p>\n\n\n\n<p>36.&nbsp;Anker AA, Leray M, Pachelle PPG. 2021.&nbsp;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 Ay\u00f3n-Parente, Hendrickx &amp; Galvan-Villa, 2015 (Decapoda: Caridea: Palaemonidae).&nbsp;<em>Zootaxa<\/em>. 4933, 379-390<\/p>\n\n\n\n<p>35. Anker AA, Leray M, Pachelle PPG. 2021.&nbsp;A new species of Alpheus Fabricius, 1798 (Decapoda: Caridea: Alpheidae) from the Caribbean coast of Panama.&nbsp;<em>Zootaxa<\/em>. 4933, 379-390<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2020<\/h2>\n\n\n\n<p>34. Leray M, Knowlton N, Ho S, Nguyen BN, Machida R. 2020.&nbsp;Reply to Locatelli et al.: Evaluating species-level accuracy of GenBank metazoan sequences will require experts\u2019 effort in each group.&nbsp;<em>Proceedings of the National Academy of Sciences of the United States of America<\/em>. 117, 32213-32214<\/p>\n\n\n\n<p>33. Leray M, Machida R. 2020.&nbsp;Seabed mining could come at a high price for a unique fauna.&nbsp;<em>Molecular Ecology<\/em>. 29, 4506-4509<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">32. Ferreira LAA, Leray M, Anker A. 2020.&nbsp;<a href=\"https:\/\/www.mapress.com\/j\/zt\/article\/view\/zootaxa.4729.3.11\" target=\"_blank\" rel=\"noreferrer noopener\">New findings of the stenopodidean shrimp Microprosthema looensis Goy &amp; Felder, 1988 (Decapoda: Stenopodidea: Spongicolidae)<\/a><a href=\"https:\/\/www.pnas.org\/content\/116\/45\/22651.short\" target=\"_blank\" rel=\"noreferrer noopener\">.&nbsp;<\/a><em><a href=\"https:\/\/www.pnas.org\/content\/116\/45\/22651.short\" target=\"_blank\" rel=\"noreferrer noopener\">Zootaxa 4729,&nbsp;<\/a><\/em><a href=\"https:\/\/www.pnas.org\/content\/116\/45\/22651.short\" target=\"_blank\" rel=\"noreferrer noopener\">445-450<\/a><\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">31. Nguyen BN**, Shen EW**, Seemann J, Correa AMS , O&#8217;Donnell JL, Altieri AH, Knowlton N, Crandall KA , Egan SP, McMillan WO, Leray M. 2020.&nbsp;<a href=\"https:\/\/www.nature.com\/articles\/s41598-020-63565-9\" target=\"_blank\" rel=\"noreferrer noopener\">Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape<\/a><a href=\"https:\/\/www.nature.com\/articles\/s41598-020-63565-9\" target=\"_blank\" rel=\"noreferrer noopener\">.<\/a>&nbsp;<em>Scientific Reports&nbsp;<\/em>10:6729<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2019<\/h2>\n\n\n\n<p class=\"has-black-color has-text-color\">30. Leray M, Knowlton N, Ho SL, Nguyen BN, Machida RJ. 2019.&nbsp;<a href=\"https:\/\/www.pnas.org\/content\/116\/45\/22651.short\" target=\"_blank\" rel=\"noreferrer noopener\">GenBank is a reliable resource for 21st century biodiversity research.&nbsp;<\/a><em><a href=\"https:\/\/www.pnas.org\/content\/116\/45\/22651.short\" target=\"_blank\" rel=\"noreferrer noopener\">Proceedings of the National Academy of Sciences of the United States of America 116,&nbsp;<\/a><\/em><a href=\"https:\/\/www.pnas.org\/content\/116\/45\/22651.short\" target=\"_blank\" rel=\"noreferrer noopener\">22651-22656<\/a><\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">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&#8217;dea A, Rasher DB, Sharp K, Sogin EM, Thacker RW, Vega Thurber R, Wcislo WT, Wilbanks EG, Eisen JA. 2019.&nbsp;Host-associated microbiomes drive structure and function of marine ecosystems.&nbsp;<em>PLoS Biology<\/em>&nbsp;17, e3000533<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">28. Van Wormhoudt A, Adjeroud M, Rouz\u00e9 H, Leray M. 2019.&nbsp;Recent and old duplications in crustaceans \u201cInternal Transcribed Spacer 1\u2033: structural and phylogenetic implications.&nbsp;<em>Molecular Biology Reports<\/em>&nbsp;46, 5185\u20135195<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">27. Leray M, Alldredge AL, Yang JY, Meyer CP, Holbrook SJ, Schmitt RJ, Knowlton N, Brooks AJ. 2019.&nbsp;<a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1111\/mec.15090\" target=\"_blank\" rel=\"noreferrer noopener\">Dietary partitioning promotes the coexistence of planktivorous species on coral reefs.&nbsp;<em>Molecular ecology<\/em>&nbsp;28, 2694\u20132710<\/a><\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">26. Kandler NM*, Wooster MK, Leray M, Knowlton N, de Voogd NJ, Paulay G, Berumen ML. 2019.&nbsp;<a href=\"https:\/\/www.mdpi.com\/1424-2818\/11\/2\/18\" target=\"_blank\" rel=\"noreferrer noopener\">Hyperdiverse macrofauna communities associated with a common sponge,&nbsp;<em>Stylissa carteri<\/em>, shift across ecological gradients in the Central Red Sea.&nbsp;<em>Diversity<\/em>&nbsp;11, 18<\/a><\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2018<\/h2>\n\n\n\n<p class=\"has-black-color has-text-color\">25. Galtier d&#8217;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.&nbsp;<a href=\"https:\/\/royalsocietypublishing.org\/doi\/full\/10.1098\/rspb.2018.1307\" target=\"_blank\" rel=\"noreferrer noopener\">Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism.&nbsp;<em>Proceedings of the Royal Society B: Biological Sciences<\/em>&nbsp;285, 20181307<\/a><\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">24. Pearman JK, Leray M, Villalobos R*, Machida R, Berumen M, Knowlton N, Carvalho S. 2018.&nbsp;<a href=\"https:\/\/www.nature.com\/articles\/s41598-018-26332-5\" target=\"_blank\" rel=\"noreferrer noopener\">Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority<\/a>.&nbsp;<em>Scientific Reports<\/em>&nbsp;8, 8090<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">23. Pachelle PPG, Leray M, Anker AA, Lasley R. 2018.&nbsp;<a href=\"https:\/\/www.researchgate.net\/publication\/325879337_Five_new_records_of_marine_shrimps_Decapoda_Caridea_Stenopodidea_from_the_Caribbean_coast_of_Panama\" target=\"_blank\" rel=\"noreferrer noopener\">Five new records of marine shrimps (Decapoda: Caridea, Stenopodidea) from the Caribbean coast of Panama<\/a>.&nbsp;<em>Zootaxa<\/em>. 4438,128-136<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">22. Leray M, Ho S-L, Lin J, Machida R. 2018.&nbsp;<a href=\"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/21\/3753\/5033384?searchresult=1\" target=\"_blank\" rel=\"noreferrer noopener\">MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database<\/a>.&nbsp;<em>Bioinformatics<\/em>&nbsp;bty454<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2017<\/h2>\n\n\n\n<p class=\"has-black-color has-text-color\">21. Ransome E, Geller JB, Timmers M, Leray M, Mahardini A, Sembiring A, Collins AG, Meyer CP. 2017.&nbsp;<a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0175066\" target=\"_blank\" rel=\"noreferrer noopener\">The importance of standardization for biodiversity comparisons, A case study using autonomous reef monitoring structures (ARMS) and metabarcoding to measure cryptic diversity on Mo\u2019orea coral reefs, French Polynesia<\/a>.&nbsp;<em>PLoS One&nbsp;<\/em>12,e0175066<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">20. Rouz\u00e9 H, Leray M, Magalon H, Penin L, G\u00e9lin P, Knowlton N, Fauvelot C. 2017.&nbsp;<a href=\"https:\/\/www.nature.com\/articles\/srep44923\" target=\"_blank\" rel=\"noreferrer noopener\">Molecular characterization reveals the complexity of previously overlooked coral-exosymbiont interactions and the implications for coral-guild ecology<\/a>.&nbsp;<em>Scientific Report&nbsp;<\/em>7,44923<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">19. Leray M, Knowlton N. 2017.&nbsp;<a href=\"https:\/\/peerj.com\/articles\/3006\/\" target=\"_blank\" rel=\"noreferrer noopener\">Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding<\/a>.&nbsp;<em>PeerJ<\/em>&nbsp;5,e3006<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">18. Machida RJ, Leray M, Ho S-L, Knowlton N. 2017.&nbsp;<a href=\"https:\/\/www.nature.com\/articles\/sdata201727\" target=\"_blank\" rel=\"noreferrer noopener\">Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples<\/a>.&nbsp;<em>Scientific Data<\/em>&nbsp;4,170027<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2016<\/h2>\n\n\n\n<p class=\"has-black-color has-text-color\">17. Leray M, Knowlton N. 2016.&nbsp;<a href=\"https:\/\/royalsocietypublishing.org\/doi\/full\/10.1098\/rstb.2015.0331?url_ver=Z39.88-2003&amp;rfr_id=ori:rid:crossref.org&amp;rfr_dat=cr_pub%3dpubmed\" target=\"_blank\" rel=\"noreferrer noopener\">Censusing marine eukaryotic diversity in the twenty-first century<\/a>.&nbsp;<em>Philosophical Transactions of the Royal Society B<\/em>&nbsp;371,20150331<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">16. Al-Rshaidat MMD, Snider A*, Rosebraugh S*, Devine AM*, Devine TD*, Plaisance L, Knowlton N, Leray M. 2016.&nbsp;<a href=\"https:\/\/www.nrcresearchpress.com\/doi\/10.1139\/gen-2015-0208?url_ver=Z39.88-2003&amp;rfr_id=ori:rid:crossref.org&amp;rfr_dat=cr_pub%3dwww.ncbi.nlm.nih.gov#.XOIoiS_Mw1g\" target=\"_blank\" rel=\"noreferrer noopener\">Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea<\/a>.&nbsp;<em>Genome<\/em>&nbsp;59,724-737<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">15. Leray M, Knowlton N. 2016.&nbsp;<a href=\"https:\/\/www.researchgate.net\/publication\/305673509_Visualizing_Patterns_of_Marine_Eukaryotic_Diversity_from_Metabarcoding_Data_Using_QIIME\" target=\"_blank\" rel=\"noreferrer noopener\">Visualizing patterns of marine eukaryotic diversity from metabarcoding data using QIIME<\/a>. In, Bourlat S.J. (eds)&nbsp;<em>Methods in Molecular Biology, Marine Genomics Methods and Protocols<\/em>. Springer Protocols, pp 219-235<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">14. Bourlat SJ, Haenel Q, Finnman J, Leray M. 2016.&nbsp;<a href=\"https:\/\/www.researchgate.net\/publication\/305673406_Preparation_of_Amplicon_Libraries_for_Metabarcoding_of_Marine_Eukaryotes_Using_Illumina_MiSeq_The_Dual-PCR_Method\" target=\"_blank\" rel=\"noreferrer noopener\">Preparation of amplicon libraries for metabarcoding of marine eukaryotes using Illumina MiSeq, The dual-PCR method<\/a>. In, Bourlat S.J. (eds)&nbsp;<em>Methods in Molecular Biology, Marine Genomics Methods and Protocols<\/em>. Springer Protocols, pp 197-207<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">13. Leray M, Haenel Q, Bourlat SJ. 2016.&nbsp;<a href=\"https:\/\/www.researchgate.net\/publication\/305673701_Preparation_of_Amplicon_Libraries_for_Metabarcoding_of_Marine_Eukaryotes_Using_Illumina_MiSeq_The_Adapter_Ligation_Method\" target=\"_blank\" rel=\"noreferrer noopener\">Preparation of amplicon libraries for metabarcoding of marine eukaryotes using Illumina MiSeq, The adapter ligation method<\/a>. In, Bourlat S.J. (eds)&nbsp;<em>Methods in Molecular Biology, Marine Genomics Methods and Protocols<\/em>. Springer Protocols, pp 209-218<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2015<\/h2>\n\n\n\n<p class=\"has-black-color has-text-color\">12. Leray M, Meyer CP, Mills SC. 2015.&nbsp;<a href=\"https:\/\/peerj.com\/articles\/1047\/\" target=\"_blank\" rel=\"noreferrer noopener\">Metabarcoding dietary analysis of coral dwelling predatory fish demonstrates the minor contribution of coral mutualists to their highly partitioned, generalist diet<\/a>.&nbsp;<em>PeerJ<\/em>&nbsp;3, e1047<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">11. Knowlton N, Leray M. 2015.&nbsp;<a href=\"https:\/\/www.researchgate.net\/publication\/295258953_Exploring_Coral_Reefs_Using_the_Tools_of_Molecular_Genetics\" target=\"_blank\" rel=\"noreferrer noopener\">Exploring coral reefs using the tools of molecular genetics<\/a>. In, Birkeland C. (eds)&nbsp;<em>Coral Reefs in the Anthropocene<\/em>. Springer Science+Business Media, Dordrecht, pp 117-132<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">10. Leray M, Knowlton N. 2015.&nbsp;<a href=\"https:\/\/www.pnas.org\/content\/112\/7\/2076\" target=\"_blank\" rel=\"noreferrer noopener\">DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity<\/a>.&nbsp;<em>Proceedings of the National Academy of Sciences of the United States of America<\/em>&nbsp;112, 2076-2081<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2014<\/h2>\n\n\n\n<p class=\"has-black-color has-text-color\">9. Stier AC**, Leray M.** 2014.&nbsp;<a href=\"https:\/\/www.researchgate.net\/publication\/260528073_Predators_alter_community_organization_of_coral_reef_cryptofauna_and_reduce_abundance_of_coral_mutualists\" target=\"_blank\" rel=\"noreferrer noopener\">Predators alter community organization of coral reef cryptofauna and reduce abundance of coral mutualists<\/a>.&nbsp;<em>Coral Reefs<\/em>&nbsp;33,181-191<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2013<\/h2>\n\n\n\n<p class=\"has-black-color has-text-color\">8. Leray M, Yang JY, Meyer CP, Mills SC, Agudelo N*, Ranwez V, Boehm JT, Machida RJ. 2013.&nbsp;<a href=\"https:\/\/frontiersinzoology.biomedcentral.com\/articles\/10.1186\/1742-9994-10-34\" target=\"_blank\" rel=\"noreferrer noopener\">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<\/a>.&nbsp;<em>Frontiers in Zoology&nbsp;<\/em>10,34<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">7. Leray M, Agudelo N*, Mills SC, Meyer CP. 2013.&nbsp;<a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0058076\" target=\"_blank\" rel=\"noreferrer noopener\">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<\/a>.&nbsp;<em>PLoS One<\/em>&nbsp;8,e58076<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2012<\/h2>\n\n\n\n<p class=\"has-black-color has-text-color\">6. Leray M, Boehm JT, Mills SC, Meyer CP. 2012.&nbsp;<a href=\"https:\/\/www.researchgate.net\/publication\/257398164_Moorea_BIOCODE_barcode_library_as_a_tool_for_understanding_predator-prey_interactions_Insights_into_the_diet_of_common_predatory_coral_reef_fishes\" target=\"_blank\" rel=\"noreferrer noopener\">Moorea BIOCODE barcode library as a tool for understanding predator-prey interactions, insights into the diet of common predatory coral reef fishes<\/a>.&nbsp;<em>Coral Reefs<\/em>&nbsp;31,383-388<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">5. Leray M, Beraud M*, Anker A, Chancerelle Y, Mills S. 2012.&nbsp;<a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0035456\" target=\"_blank\" rel=\"noreferrer noopener\">Acanthaster planci outbreak, decline in coral health, coral size structure modification and consequences for obligate decapod assemblages<\/a>.&nbsp;<em>PLoS One<\/em>&nbsp;7,e35456<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">4. Stier AC, Gil MA, McKeon CS, Lemer S, Leray M, Mills SC, Osenberg CW. 2012.&nbsp;<a href=\"https:\/\/journals.plos.org\/plosone\/article?id=10.1371\/journal.pone.0032079\" target=\"_blank\" rel=\"noreferrer noopener\">Housekeeping mutualisms, do more symbionts facilitate host performance?<\/a>&nbsp;<em>PLoS One<\/em>&nbsp;7,e32079<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2010<\/h2>\n\n\n\n<p class=\"has-black-color has-text-color\">3. Leray M, Beldade R, Holbrook SJ, Schmitt RJ, Planes S, Bernardi G. 2010.&nbsp;<a href=\"https:\/\/www.researchgate.net\/publication\/40680082_Allopatric_divergence_and_speciation_in_coral_reef_fish_The_three-spot_dascyllus_Dascyllus_trimaculatus_species_complex\" target=\"_blank\" rel=\"noreferrer noopener\">Allopatric divergence and speciation in coral reef fish, the three-spot Dascyllus, Dascyllus trimaculatus, species complex<\/a>.&nbsp;<em>Evolution<\/em>&nbsp;64,1218-1230<\/p>\n\n\n\n<p class=\"has-black-color has-text-color\">2. Van Herwerden L, Howard Choat J, Newman SJ, Leray M, Hillers\u00f8y G. 2009.&nbsp;<a href=\"https:\/\/www.researchgate.net\/publication\/225509870_Complex_patterns_of_population_structure_and_recruitment_of_Plectropomus_leopardus_Pisces_Epinephelidae_in_the_Indo-West_Pacific_Implications_for_fisheries_management\" target=\"_blank\" rel=\"noreferrer noopener\">Complex patterns of population structure and recruitment of Plectropomus leopardus (Pisces, Epinephelidae) in the Indo-West Pacific, Implications for fisheries management<\/a>.&nbsp;<em>Marine Biology<\/em>&nbsp;156,1595-1607<\/p>\n\n\n\n<div style=\"height:30px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<h2 class=\"wp-block-heading has-text-color\" style=\"color:#006a3a\">2009<\/h2>\n\n\n\n<p class=\"has-black-color has-text-color\">1. Leray M, Beldade R, Holbrook SJ, Schmitt RJ, Planes S, Bernardi G. 2009.&nbsp;<a href=\"https:\/\/www.researchgate.net\/publication\/51119408_Isolation_and_characterization_of_13_polymorphic_nuclear_microsatellite_primers_for_the_widespread_Indo-Pacific_three-spot_damselfish_Dascyllus_trimaculatus_and_closely_related_D-auripinnis\" target=\"_blank\" rel=\"noreferrer noopener\">Isolation and characterization of 13 polymorphic nuclear microsatellite primers for the widespread Indo\u2010Pacific three\u2010spot damselfish,&nbsp;<em>Dascyllus trimaculatus<\/em>, and closely related&nbsp;<em>D. auripinnis<\/em><\/a>.&nbsp;<em>Molecular ecology resources<\/em>&nbsp;9, 213-215<\/p>\n<\/div><\/div>\n\n\n<style>.kadence-column106_dee347-9f > .kt-inside-inner-col,.kadence-column106_dee347-9f > .kt-inside-inner-col:before{border-top-left-radius:0px;border-top-right-radius:0px;border-bottom-right-radius:0px;border-bottom-left-radius:0px;}.kadence-column106_dee347-9f > .kt-inside-inner-col{column-gap:var(--global-kb-gap-sm, 1rem);}.kadence-column106_dee347-9f > .kt-inside-inner-col{flex-direction:column;}.kadence-column106_dee347-9f > .kt-inside-inner-col > .aligncenter{width:100%;}.kadence-column106_dee347-9f > .kt-inside-inner-col:before{opacity:0.3;}.kadence-column106_dee347-9f{position:relative;}@media all and (max-width: 1024px){.kadence-column106_dee347-9f > .kt-inside-inner-col{flex-direction:column;justify-content:center;}}@media all and (max-width: 767px){.kadence-column106_dee347-9f > .kt-inside-inner-col{flex-direction:column;justify-content:center;}}<\/style>\n<div class=\"wp-block-kadence-column kadence-column106_dee347-9f\"><div class=\"kt-inside-inner-col\"><style>.wp-block-kadence-advancedbtn.kb-btns106_c7901e-48{gap:var(--global-kb-gap-xs, 0.5rem );justify-content:center;align-items:center;}.kt-btns106_c7901e-48 .kt-button{font-weight:normal;font-style:normal;}.kt-btns106_c7901e-48 .kt-btn-wrap-0{margin-right:5px;}.wp-block-kadence-advancedbtn.kt-btns106_c7901e-48 .kt-btn-wrap-0 .kt-button{color:#555555;border-color:#555555;}.wp-block-kadence-advancedbtn.kt-btns106_c7901e-48 .kt-btn-wrap-0 .kt-button:hover, .wp-block-kadence-advancedbtn.kt-btns106_c7901e-48 .kt-btn-wrap-0 .kt-button:focus{color:#ffffff;border-color:#444444;}.wp-block-kadence-advancedbtn.kt-btns106_c7901e-48 .kt-btn-wrap-0 .kt-button::before{display:none;}.wp-block-kadence-advancedbtn.kt-btns106_c7901e-48 .kt-btn-wrap-0 .kt-button:hover, .wp-block-kadence-advancedbtn.kt-btns106_c7901e-48 .kt-btn-wrap-0 .kt-button:focus{background:#444444;}<\/style>\n<div class=\"wp-block-kadence-advancedbtn kb-buttons-wrap kb-btns106_c7901e-48\"><style>ul.menu .wp-block-kadence-advancedbtn .kb-btn106_9a928a-0f.kb-button{width:initial;}.wp-block-kadence-advancedbtn .kb-btn106_9a928a-0f.kb-button{color:#000000;background:rgba(0,0,0,0);border-top-color:rgba(0,0,0,0);border-top-style:solid;border-right-color:rgba(0,0,0,0);border-right-style:solid;border-bottom-color:rgba(0,0,0,0);border-bottom-style:solid;border-left-color:rgba(0,0,0,0);border-left-style:solid;}.kb-btn106_9a928a-0f.kb-button .kb-svg-icon-wrap{font-size:30px;--kb-button-icon-size:30px;}.wp-block-kadence-advancedbtn .kb-btn106_9a928a-0f.kb-button:hover, .wp-block-kadence-advancedbtn .kb-btn106_9a928a-0f.kb-button:focus{background:rgba(0,0,0,0);}@media all and (max-width: 1024px){.wp-block-kadence-advancedbtn .kb-btn106_9a928a-0f.kb-button{border-top-color:rgba(0,0,0,0);border-top-style:solid;border-right-color:rgba(0,0,0,0);border-right-style:solid;border-bottom-color:rgba(0,0,0,0);border-bottom-style:solid;border-left-color:rgba(0,0,0,0);border-left-style:solid;}}@media all and (max-width: 767px){.wp-block-kadence-advancedbtn .kb-btn106_9a928a-0f.kb-button{border-top-color:rgba(0,0,0,0);border-top-style:solid;border-right-color:rgba(0,0,0,0);border-right-style:solid;border-bottom-color:rgba(0,0,0,0);border-bottom-style:solid;border-left-color:rgba(0,0,0,0);border-left-style:solid;}}<\/style><span class=\"kb-button kt-button button kb-btn106_9a928a-0f kt-btn-size-standard kt-btn-width-type-auto kb-btn-global-outline kt-btn-has-text-true kt-btn-has-svg-true  wp-block-kadence-singlebtn\"><span class=\"kt-btn-inner-text\">Google Scholar<\/span><span class=\"kb-svg-icon-wrap kb-svg-icon-fe_arrowRightCircle kt-btn-icon-side-right\"><svg viewBox=\"0 0 24 24\"  fill=\"none\" stroke=\"currentColor\" stroke-width=\"2\" stroke-linecap=\"round\" stroke-linejoin=\"round\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\"  aria-hidden=\"true\"><circle cx=\"12\" cy=\"12\" r=\"10\"\/><polyline points=\"12 16 16 12 12 8\"\/><line x1=\"8\" y1=\"12\" x2=\"16\" y2=\"12\"\/><\/svg><\/span><\/span><\/div>\n<\/div><\/div>\n\n<\/div><\/div>","protected":false},"excerpt":{"rendered":"<p>** co-first author * student co-author 2024 54. Rouz\u00e9 H, Knowlton N, Anker A, Hurt C, Wirshing H, Von Wormhoudt A,\u00a0Leray M. 2024. An integrated phylogeographic approach for inferring cryptic speciation in the\u00a0Alpheus lottini\u00a0species complex, an important coral mutualist.\u00a0iScience\u00a027,\u00a0111034 53. Morel-Letelier I, Yuen B, K\u00fcck AC, Camacho-Garc\u00eda YE, Petersen JM, Lara M, Leray M, Eisen &hellip; <a href=\"https:\/\/striresearch.si.edu\/matthieuleray\/publications\/\">Continued<\/a><\/p>\n","protected":false},"author":61,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"inline_featured_image":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_exactmetrics_skip_tracking":false,"_exactmetrics_sitenote_active":false,"_exactmetrics_sitenote_note":"","_exactmetrics_sitenote_category":0,"footnotes":""},"class_list":["post-106","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v25.7 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Publications - Symbiosis &amp; Resilience Lab<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/striresearch.si.edu\/matthieuleray\/publications\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Publications - Symbiosis &amp; Resilience Lab\" \/>\n<meta property=\"og:description\" content=\"** co-first author * student co-author 2024 54. 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