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Showing 1-20 of about 28 results.
A new species of Alpheus Fabricius, 1798 (Decapoda: Caridea: Alpheidae) from the Caribbean coast of PanamaAnker, ArthurLeray, MatthieuPachelle, Paulo P. G.DOI: info:10.11646/zootaxa.4933.3.5v. 4933No. 3379–390
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
ID: 158779
Type: article
Authors: Anker, Arthur; Leray, Matthieu; Pachelle, Paulo P. G.
Abstract: Alpheus viserion sp. n. is described based on the material from Bocas del Toro archipelago on the Caribbean coast of Panama. The new species is morphologically closest to three members of the speciose A. armillatus H. Milne-Edwards, 1837 species complex, viz. A. carlae Anker, 2012, A. angulosus McClure, 2002, and A. tenuis Kim & Abele, 1988, differing from them, as well as from all the other species currently included in this complex, by a suite of morphological characters and a diagnostic colour pattern. With the description of yet another new shrimp species from Bocas del Toro, the authors hope to contribute to the awareness that this archipelago represents one of the most biologically diverse places in the Caribbean Sea and to encourage the preservation of the remaining natural habitats of this unique area.
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)Rodriguez-Ezpeleta, NaiaraMorissette, OlivierBean, Colin W.Manu, ShivakumaraBanerjee, PritamLacoursiere-Roussel, AnaisBeng, Kingsly C.Alter, S. ElizabethRoger, FabianHolman, Luke E.Stewart, Kathryn A.Monaghan, Michael T.Mauvisseau, QuentinMirimin, LucaWangensteen, Owen S.Antognazza, Caterina M.Helyar, Sarah J.de Boer, HugoMonchamp, Marie-EveNijland, ReindertAbbott, Cathryn L.Doi, HideyukiBarnes, Matthew A.Leray, MatthieuHablutzel, Pascal I.Deiner, KristyDOI: info:10.1111/mec.15942
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 https://doi.org/10.1111/mec.15942
ID: 159571
Type: article
Authors: 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.; Deiner, Kristy
Abstract: In a recent paper, "Environmental DNA: What's behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring," Pawlowski et al. argue that the term eDNA should be used to refer to the pool of DNA isolated from environmental samples, as opposed to only extra-organismal DNA from macro-organisms. We agree with this view. However, we are concerned that their proposed two-level terminology specifying sampling environment and targeted taxa is overly simplistic and might hinder rather than improve clear communication about environmental DNA and its use in biomonitoring. This terminology is based on categories that are often difficult to assign and uninformative, and it overlooks a fundamental distinction within eDNA: the type of DNA (organismal or extra-organismal) from which ecological interpretations are derived.
New findings of the stenopodidean shrimp Microprosthema looensis Goy & Felder, 1988 (Decapoda: Stenopodidea: Spongicolidae)Ferreira, Luciane Augusto De AzevedoLeray, MatthieuAnker, ArthurDOI: info:10.11646/zootaxa.4729.3.11v. 4729No. 3445–450
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
ID: 154357
Type: article
Authors: Ferreira, Luciane Augusto De Azevedo; Leray, Matthieu; Anker, Arthur
Abstract: The spongicolid genus Microprosthema Stimpson, 1860 is currently composed of 16 species inhabiting tropical and subtropical marine shallow waters worldwide, with six species found in the western Atlantic (one of them also present in the central and eastern Atlantic), one species in the eastern Pacific, and nine species in the Indo-West Pacific (Saito & Okuno 2011; Goy & Martin 2013; Saito & Anker 2014; De Grave et al. 2016). The genus is characterised by the somewhat depressed body; the carapace more or less densely covered by spines (except in one species); the third maxilliped with a long exopod; the first pereopod with a setiferous organ on the carpus and propodus; the third pereopod greatly enlarged and elongate; and the telson with one tooth on the lateral margin (Holthuis 1946; Poore 2004; Saito & Okuno 2011).
REPLY TO LOCATELLI ET AL.: Evaluating species-level accuracy of GenBank metazoan sequences will require experts' effort in each groupLeray, MatthieuKnowlton, NancyHo, Shian-LeiNguyen, Bryan N.Machida, Ryuji J.DOI: info:10.1073/pnas.2019903117v. 117No. 5132213–32214
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
ID: 157998
Type: article
Authors: Leray, Matthieu; Knowlton, Nancy; Ho, Shian-Lei; Nguyen, Bryan N.; Machida, Ryuji J.
Seabed mining could come at a high price for a unique faunaLeray, MatthieuMachida, Ryuji J.DOI: info:10.1111/mec.15678
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
ID: 157274
Type: article
Authors: Leray, Matthieu; Machida, Ryuji J.
Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascapeNguyen, Bryan N.Shen, Elaine W.Seemann, JaninaCorrea, Adrienne M. S.O'Donnell, James L.Altieri, Andrew H.Knowlton, NancyCrandall, Keith A.Egan, Scott P.McMillan, W. OwenLeray, MatthieuDOI: info:10.1038/s41598-020-63565-9v. 10No. 1Article 6729
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
ID: 155402
Type: article
Authors: 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; Leray, Matthieu
Abstract: Accurate, rapid, and comprehensive biodiversity assessments are critical for investigating ecological processes and supporting conservation efforts. Environmental DNA (eDNA) surveys show promise as a way to effectively characterize fine-scale patterns of community composition. We tested whether a single PCR survey of eDNA in seawater using a broad metazoan primer could identify differences in community composition between five adjacent habitats at 19 sites across a tropical Caribbean bay in Panama. We paired this effort with visual fish surveys to compare methods for a conspicuous taxonomic group. eDNA revealed a tremendous diversity of animals (8,586 operational taxonomic units), including many small taxa that would be undetected in traditional in situ surveys. Fish comprised only 0.07% of the taxa detected by a broad COI primer, yet included 43 species not observed in the visual survey. eDNA revealed significant differences in fish and invertebrate community composition across adjacent habitats and areas of the bay driven in part by taxa known to be habitat-specialists or tolerant to wave action. Our results demonstrate the ability of broad eDNA surveys to identify biodiversity patterns in the ocean. © 2020, The Author(s).
Hyperdiverse Macrofauna Communities Associated with a Common Sponge, Stylissa carteri, Shift across Ecological Gradients in the Central Red SeaKandler, NoraWooster, MichaelLeray, MatthieuKnowlton, Nancyde Voogd, NicolePaulay, GustavBerumen, MichaelDOI: info:10.3390/d11020018v. 11No. 218
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
ID: 150078
Type: article
Authors: Kandler, Nora; Wooster, Michael; Leray, Matthieu; Knowlton, Nancy; de Voogd, Nicole; Paulay, Gustav; Berumen, Michael
Dietary partitioning promotes the coexistence of planktivorous species on coral reefsLeray, MatthieuAlldredge, Alice L.Yang, Joy Y.Meyer, Christopher P.Holbrook, Sally J.Schmitt, Russell J.Knowlton, NancyBrooks, Andrew J.DOI: info:10.1111/mec.15090v. 28No. 102694–2710
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
ID: 150716
Type: article
Authors: Leray, Matthieu; Alldredge, Alice L.; Yang, Joy Y.; Meyer, Christopher P.; Holbrook, Sally J.; Schmitt, Russell J.; Knowlton, Nancy; Brooks, Andrew J.
Abstract: Theories involving niche diversification to explain high levels of tropical diversity propose that species are more likely to co-occur if they partition at least one dimension of their ecological niche space. Yet, numerous species appear to have widely overlapping niches based upon broad categorizations of resource use or functional traits. In particular, the extent to which food partitioning contributes to species coexistence in hyperdiverse tropical ecosystems remains unresolved. Here, we use a molecular approach to investigate inter- and intraspecific dietary partitioning between two species of damselfish (Dascyllus flavicaudus, Chromis viridis) that commonly co-occur in branching corals. Species-level identification of their diverse zooplankton prey revealed significant differences in diet composition between species despite their seemingly similar feeding strategies. Dascyllus exhibited a more diverse diet than Chromis, whereas Chromis tended to select larger prey items. A large calanoid copepod, Labidocera sp., found in low density and higher in the water column during the day, explained more than 19% of the variation in dietary composition between Dascyllus and Chromis. Dascyllus did not significantly shift its diet in the presence of Chromis, which suggests intrinsic differences in feeding behaviour. Finally, prey composition significantly shifted during the ontogeny of both fish species. Our findings show that levels of dietary specialization among coral reef associated species have likely been underestimated, and they underscore the importance of characterizing trophic webs in tropical ecosystems at higher levels of taxonomic resolution. They also suggest that niche redundancy may not be as common as previously thought. This article is protected by copyright. All rights reserved.
GenBank is a reliable resource for 21st century biodiversity researchLeray, MatthieuKnowlton, NancyHo, Shian-LeiNguyen, Bryan N.Machida, Ryuji J.DOI: info:10.1073/pnas.1911714116v. 116No. 4522651–22656
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
ID: 152934
Type: article
Authors: Leray, Matthieu; Knowlton, Nancy; Ho, Shian-Lei; Nguyen, Bryan N.; Machida, Ryuji J.
Abstract: Traditional methods of characterizing biodiversity are increasingly being supplemented and replaced by approaches based on DNA sequencing alone. These approaches commonly involve extraction and high-throughput sequencing of bulk samples from biologically complex communities or samples of environmental DNA (eDNA). In such cases, vouchers for individual organisms are rarely obtained, often unidentifiable, or unavailable. Thus, identifying these sequences typically relies on comparisons with sequences from genetic databases, particularly GenBank. While concerns have been raised about biases and inaccuracies in laboratory and analytical methods, comparatively little attention has been paid to the taxonomic reliability of GenBank itself. Here we analyze the metazoan mitochondrial sequences of GenBank using a combination of distance-based clustering and phylogenetic analysis. Because of their comparatively rapid evolutionary rates and consequent high taxonomic resolution, mitochondrial sequences represent an invaluable resource for the detection of the many small and often undescribed organisms that represent the bulk of animal diversity. We show that metazoan identifications in GenBank are surprisingly accurate, even at low taxonomic levels (likely <1% error rate at the genus level). This stands in contrast to previously voiced concerns based on limited analyses of particular groups and the fact that individual researchers currently submit annotated sequences to GenBank without significant external taxonomic validation. Our encouraging results suggest that the rapid uptake of DNA-based approaches is supported by a bioinformatic infrastructure capable of assessing both the losses to biodiversity caused by global change and the effectiveness of conservation efforts aimed at slowing or reversing these losses.
Recent and old duplications in crustaceans 'Internal Transcribed Spacer 1″: structural and phylogenetic implicationsVan Wormhoudt, AlainAdjeroud, MehdiRouzé, HeloiseLeray, MatthieuDOI: info:10.1007/s11033-019-04976-4v. 46No. 55185–5195
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
ID: 151786
Type: article
Authors: Van Wormhoudt, Alain; Adjeroud, Mehdi; Rouzé, Heloise; Leray, Matthieu
Abstract: Internal Transcribed Spacer structures are important in preserving accessibility to specific enzymes for the maturation of rRNAs. ITS1 sequences reported in the literature in Crustaceans range between 182 and 820 bp and are characterized by the absence of repeats or the presence of only a limited number of microsatellites. Here, we sequenced ITS1 for a range of shrimp families (infraorder Caridea) and show that most taxa have much larger ITS1 sequences. We find a high number of microsatellites in Alpheus hebes and Crangon crangon and we report repeat units in Pandalidae, Palaemonidae and mainly in Alpheidae species. Up to four repeats were found in A. vanderbilti (1915 bp), A. rostratus (1635 bp) and A. lottini (1625 bp). In general, four helices were found in ITS1. Repeat units led to extra hairpins and loops. No conserved positions occurred except in helix 4. Three clades were defined in A. lottini for the first time. We estimated the ITS1 divergence rate for the three clades of A. lottini collected in French Polynesia using existing calibrations of substitution rates. Rates of sequence evolution are largely influenced by repeat units, which likely evolve separately. By comparison with COI marker, we estimated the divergence rate of the whole ITS1 sequence to range from 0.5 to 1.4% Pmy and between 0.12 and 0.5% for the 3' end of ITS1 located outside the repeat units. Given the degree of identity between repeats, we suggest that a duplication event recently occurred in A. floridanus (98% identity) whereas an ancient duplication happened in A. sulcatus (50% identity) early at the origination of the group Alpheidae, approximately 50 mya ago. In conclusion, our results highlight an over representation of shorter ITS1 sequences in public repositories, and underlines the importance to further understand patterns of molecular evolution of this functionally important gene.
Host-associated microbiomes drive structure and function of marine ecosystemsWilkins, Laetitia G. E.Leray, MatthieuO'Dea, AaronYuen, BenedictPeixoto, Raquel S.Pereira, Tiago J.Bik, Holly M.Coil, David A.Duffy, J. EmmettHerre, Edward AllenLessios, Harilaos A.Lucey, Noelle M.Mejia, Luis C.Rasher, Douglas B.Sharp, Koty H.Sogin, Emilia M.Thacker, Robert W.Thurber, Rebecca VegaWcislo, William T.Wilbanks, Elizabeth G.Eisen, Jonathan A.DOI: info:10.1371/journal.pbio.3000533v. 17No. 111–15
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
ID: 153257
Type: article
Authors: 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.; Eisen, Jonathan A.
Abstract: Abstract: The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health...
Host-associated microbiomes and their roles in marine ecosystem functionsWilkins, Laetitia G. E.Leray, MatthieuYuen, BenedictPeixoto, RaquelPereira, Tiago J.Bik, Holly M.Coil, David A.Duffy, J. E.Herre, Edward AllenLessios, HarilaosLucey, NoelleMejia, Luis C.O'Dea, AaronRasher, Douglas B.Sharp, KotySogin, Emilia M.Thacker, Robert W.Thurber, Rebecca VegaWcislo, William T.Wilbanks, Elizabeth G.Eisen, Jonathan A.DOI: info:10.7287/peerj.preprints.27930v11–27
Wilkins, Laetitia G. E., Leray, Matthieu, Yuen, Benedict, Peixoto, Raquel, Pereira, Tiago J., Bik, Holly M., Coil, David A., Duffy, J. E., 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
ID: 153258
Type: article
Authors: Wilkins, Laetitia G. E.; Leray, Matthieu; Yuen, Benedict; Peixoto, Raquel; Pereira, Tiago J.; Bik, Holly M.; Coil, David A.; Duffy, J. E.; 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.; Eisen, Jonathan A.
Abstract: The significance of mutualisms between eukaryotic hosts and microbes extends from the organismal to the ecosystem level, and mutualistic symbioses underpin the health of Earth's most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes (microbiomes), very little is known about their interactions for the vast majority of marine host species. We outline research priorities to broaden our current knowledge of host-microbiome interactions and how they shape marine ecosystems. We argue that this research frontier will allow us to predict responses of species, communities, and ecosystems to stressors driven by human activity, and inform future management and mitigation.
Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organismd'Auriac, Ines GaltierQuinn, Robert A.Maughan, HeatherNothias, Louis-FelixLittle, MarkKapono, Clifford A.Cobian, AnaReyes, Brandon T.Green, KevinQuistad, Steven D.Leray, MatthieuSmith, Jennifer E.Dorrestein, Pieter C.Rohwer, ForestDeheyn, Dimitri D.Hartmann, Aaron C.DOI: info:10.1098/rspb.2018.1307v. 285No. 288420181307–20181307
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
ID: 148265
Type: article
Authors: 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.; Hartmann, Aaron C.
Abstract: Corals and humans represent two extremely disparate metazoan lineages and are therefore useful for comparative evolutionary studies. Two lipid-based molecules that are central to human immunity, platelet-activating factor (PAF) and Lyso-PAF were recently identified in scleractinian corals. To identify processes in corals that involve these molecules, PAF and Lyso-PAF biosynthesis was quantified in conditions known to stimulate PAF production in mammals (tissue growth and exposure to elevated levels of ultraviolet light) and in conditions unique to corals (competing with neighbouring colonies over benthic space). Similar to observations in mammals, PAF production was higher in regions of active tissue growth and increased when corals were exposed to elevated levels of ultraviolet light. PAF production also increased when corals were attacked by the stinging cells of a neighbouring colony, though only the attacked coral exhibited an increase in PAF. This reaction was observed in adjacent areas of the colony, indicating that this response is coordinated across multiple polyps including those not directly subject to the stress. PAF and Lyso-PAF are involved in coral stress responses that are both shared with mammals and unique to the ecology of cnidarians.
MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated databaseLeray, MatthieuHo, Shian-LeiLin, I. -JMachida, Ryuji J.DOI: info:10.1093/bioinformatics/bty454v. 34No. 213753–3754
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
ID: 146720
Type: article
Authors: Leray, Matthieu; Ho, Shian-Lei; Lin, I. -J; Machida, Ryuji J.
Abstract: Summary: We present MIDORI server, a user-friendly web platform that uses a curated reference dataset, MIDORI, for high throughput taxonomic classification of unknown metazoan mitochondrial-encoded gene sequences. Currently three methods of taxonomic assignments: RDP Classifier, SPINGO and SINTAX, are implemented. Availability: The web server is freely available at {{http://reference-midori.info/server.php}}. Contact: ryujimachida@gmail.com. Supplementary information: Details about the server and the MIDORI database can be found at {{http://www.reference-midori.info}}.
Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majorityPearman, J. K.Leray, M.Villalobos, R.Machida, R. J.Berumen, M. L.Knowlton, NancyCarvalho, S.DOI: info:10.1038/s41598-018-26332-5v. 88090–8090
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
ID: 146553
Type: article
Authors: Pearman, J. K.; Leray, M.; Villalobos, R.; Machida, R. J.; Berumen, M. L.; Knowlton, Nancy; Carvalho, S.
Abstract: Coral reefs harbor diverse assemblages of organisms yet the majority of this diversity is hidden within the three dimensional structure of the reef and neglected using standard visual surveys. This study uses Autonomous Reef Monitoring Structures (ARMS) and amplicon sequencing methodologies, targeting mitochondrial cytochrome oxidase I and 18S rRNA genes, to investigate changes in the cryptic reef biodiversity. ARMS, deployed at 11 sites across a near- to off-shore gradient in the Red Sea were dominated by Porifera (sessile fraction), Arthropoda and Annelida (mobile fractions). The two primer sets detected different taxa lists, but patterns in community composition and structure were similar. While the microhabitat of the ARMS deployment affected the community structure, a clear cross-shelf gradient was observed for all fractions investigated. The partitioning of beta-diversity revealed that replacement (i.e. the substitution of species) made the highest contribution with richness playing a smaller role. Hence, different reef habitats across the shelf are relevant to regional diversity, as they harbor different communities, a result with clear implications for the design of Marine Protected Areas. ARMS can be vital tools to assess biodiversity patterns in the generally neglected but species-rich cryptic benthos, providing invaluable information for the management and conservation of hard-bottomed habitats over local and global scales.
Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcodingLeray, MatthieuKnowlton, NancyDOI: info:10.7717/peerj.3006v. 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
ID: 142567
Type: article
Authors: Leray, Matthieu; Knowlton, Nancy
Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samplesMachida, Ryuji J.Leray, MatthieuHo, Shian-LeiKnowlton, NancyDOI: info:10.1038/sdata.2017.27v. 4No. 170027
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
ID: 142539
Type: article
Authors: Machida, Ryuji J.; Leray, Matthieu; Ho, Shian-Lei; Knowlton, Nancy
Abstract: Mitochondrial-encoded genes are increasingly targeted in studies using high-throughput sequencing approaches for characterizing metazoan communities from environmental samples (e.g., plankton, meiofauna, filtered water).
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 PolynesiaRansome, EmmaGeller, Jonathan B.Timmers, MollyLeray, MatthieuMahardini, AngkaSembiring, AndrianusCollins, Allen GilbertMeyer, Christopher P.DOI: info:10.1371/journal.pone.0175066v. 12No. 4
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
ID: 142624
Type: article
Authors: Ransome, Emma; Geller, Jonathan B.; Timmers, Molly; Leray, Matthieu; Mahardini, Angka; Sembiring, Andrianus; Collins, Allen Gilbert; Meyer, Christopher P.
Molecular characterization reveals the complexity of previously overlooked coral-exosymbiont interactions and the implications for coral-guild ecologyRouzé, H.Leray, MatthieuMagalon, H.Penin, L.Gélin, P.Knowlton, NancyFauvelot, C.DOI: info:10.1038/srep44923v. 7No. 44923
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
ID: 142768
Type: article
Authors: Rouzé, H.; Leray, Matthieu; Magalon, H.; Penin, L.; Gélin, P.; Knowlton, Nancy; Fauvelot, C.
Abstract: Several obligate associate crabs and shrimps species may co-occur and interact within a single coral host, leading to patterns of associations that can provide essential ecological services. However, knowledge of the dynamics of interactions in this system is limited, partly because identifying species involved in the network remains challenging. In this study, we assessed the diversity of the decapods involved in exosymbiotic assemblages for juvenile and adult Pocillopora damicornis types α and β on reefs of New Caledonia and Reunion Island. This approach revealed complex patterns of association at regional and local scales with a prevalence of assemblages involving crab-shrimp partnerships. Furthermore, the distinction of two lineages in the snapping shrimp Alpheus lottini complex, rarely recognized in ecological studies, reveals a key role for cryptic diversity in structuring communities of mutualists. The existence of partnerships between species that occurred more commonly than expected by chance suggests an increased advantage for the host or a better adaptation of associated species to local environmental conditions. The consideration of cryptic diversity helps to accurately describe the complexity of interaction webs for diverse systems such as coral reefs, as well as the functional roles of dominant associated species for the persistence of coral populations.
Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red SeaAl-Rshaidat, MamoonSnider, AllisonRosebraugh, SydneyDevine, Amanda M.Devine, Thomas D.Plaisance, LaetitiaKnowlton, NancyLeray, MatthieuDOI: info:10.1139/gen-2015-0208v. 59No. 9724–737
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
ID: 140854
Type: article
Authors: Al-Rshaidat, Mamoon; Snider, Allison; Rosebraugh, Sydney; Devine, Amanda M.; Devine, Thomas D.; Plaisance, Laetitia; Knowlton, Nancy; Leray, Matthieu
Abstract: High-throughput sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the northern Red Sea. Samples were obtained from standardized sampling devices (Autonomous Reef Monitoring Structures (ARMS)) deployed for 18 months. DNA barcoding of non-sessile specimens >2 mm revealed 83 OTUs in six phyla, of which only 25% matched a reference sequence in public databases. Metabarcoding of the 2 mm - 500 μm and sessile bulk fractions revealed 1197 OTUs in 15 animal phyla, of which only 4.9% matched reference barcodes. These results highlight the scarcity of COI data for cryptobenthic organisms of the Red Sea. Compared with data obtained using similar methods, our results suggest that Gulf of Aqaba reefs are less diverse than two Pacific coral reefs but much more diverse than an Atlantic oyster reef at a similar latitude. The standardized approaches used here show promise for establishing baseline data on biodiversity, monitoring the impacts of environmental change, and quantifying patterns of diversity at regional and global scales.