DEEP-SEA ECOLOGY & EVOLUTION
Herrera Lab
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The Herrera lab seeks to understand how biodiversity arises in and interacts with the ocean environment, focusing on deep-sea ecosystems. We apply high-throughput omics techniques, computationally-intensive analytical tools, oceanographic field expeditions, and laboratory experiments to generate and test consequential hypotheses in ecology and evolution. We apply our work to inform the management of marine ecosystems vulnerable to environmental change and other threats. Our research is cross-disciplinary; we work closely with physical oceanographers, geochemists, molecular biologists, marine engineers, and natural resource managers.
We always seek to recruit excellent Ph.D. Students and Postdoctoral Researchers to join our team. Ongoing projects include comparative population genomics of corals and their microbiomes, phylogeography of widespread taxa, exploration of biodiversity patterns through community metabarcoding and environmental DNA (eDNA) sequencing, connectivity, restoration of degraded ecosystems, and conservation. If you are interested in joining the lab, please get in touch with Santiago via email (santiago [dot] herrera [at] lehigh [dot] edu) with your CV and a brief statement of research interests.
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Herrera Lab
Current Members
Santiago Herrera
Principal Investigator
Santiago is a Deep-Sea Biological Oceanographer trained at the Massachusetts Institute of Technology, the Woods Hole Oceanographic Institution, and la Universidad de los Andes.
Nicole Pittoors
NSF Graduate Research Fellow
Nicole is interested in dispersal and recruitment in benthic communities. Before joining the lab, Nicole was a Lab Technician at Harvard University and a Guest Student at the Woods Hole Oceanographic Institution.
Sam Vohsen
Postdoctoral Research Fellow
Sam is a Microbial Ecologist interested in the microbial associates of deep-sea corals. Sam was trained at the Pennsylvania State University and the Max Planck Institute for Marine Microbiology.
Luke McCartin
Graduate Researcher
Luke is interested in community structure, environmental DNA, and comparative evolution. Before joining the lab, Luke was a Research Assistant at the Woods Hole Oceanographic Institution.
Syrmalenia Kotronaki
Graduate Researcher
Syrmalenia is interested in the population genomics of deep-sea fauna. Before joining the lab, she was a Research Assistant at GEOMAR Helmholtz- Centre for Ocean Research in Kiel, Germany.
Milan Sengthep
Graduate Researcher
Milan is interested in environmental DNA in the deep-sea. Before joining the lab, Milan was a Lab Supervisor at Boise State University and studied at Oregon State University.
Sophia Mihalek
Undergraduate Researcher
Sophia is interested in the diversity of animals in the mesophotic and the deep sea. She is a double major in Biology and Earth and Environmental Sciences.
Elizabeth Whitson
Laboratory Manager
Elizabeth is interested in the mysterious life in the deep sea. Before joining the lab, Elizabeth completed a Masters at the University of Miami Rosenstiel School of Marine and Atmospheric Science.
Former Members
Omar Ahmed
Undergraduate Researcher
Went to pursue a Ph.D. in Computer Science at Johns Hopkins University in Baltimore, MD.
Emily Bushta
Undergraduate Researcher
Went to work at Earth Engineering Incorporated.
Alondra Maldonado
Undergraduate Researcher
Wen to work as an Emergency Medical Technician at the Easton Emergency Squad.
Matt Galaska
Postdoctoral Research Fellow
Went to work as a Principal Investigator at the University of Washington - NOAA Pacific Marine Environmental Laboratory in Seattle, Washington.
Maria Granquist
Undergraduate Researcher
Went to work as a Research Assistant at the Smithsonian National Museum of Natural History in Washington, DC.
Destiny West
Undergraduate Researcher
Went to work as a Research Assistant at the Harvard Medical School in Boston, Massachussetts.
Susan Ambrose
Masters Researcher
Went to work as an Environmental Chemist at M.J. Reider Associates
Penny Demetriades
Undergraduate Researcher
Went to pursue a Ph.D. in Marine Sciences at the University of South Alabama and the Dauphin Island Sea Lab.
Luis Caceres
Undergraduate Researcher
Is now a Senior at Lehigh University. Pursuing a dual degree in Biology + Sociology and Anthropology.
Fieldwork
Members of the Herrera lab have led or participated in more than 25 oceanographic research expeditions. We have done over 500 dives with remotely operated vehicles (ROVs), from the mesophotic to some of the deepest oceanic trenches. We have also used autonomous underwater vehicles (AUVs), towed camera systems, and the human-occupied vehicle (HOV) Alvin for our research. Geographically, our work has occurred in the Atlantic, Pacific, and Southern oceans, the Mediterranean, Celebes, and Caribbean seas, and most recently, the Gulf of Mexico.
Research cruises
*Indicates participation via telepresence
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2023 R/V Nancy Foster, ROV Global Explorer, NF23-06 IMPACT, U.S. Gulf of Mexico.
2023 R/V Falkor (too), ROV SuBastian, FKt230812, Eastern Galapagos Spreading Center.
2023 R/V Pisces, ROV Mohawk, PC23-02 Deepwater Horizon NRDA MDBC, U.S. Gulf of Mexico.
2023 R/V Pelican, ROV Beagle, PE23-04 MERCI, U.S. Gulf of Mexico.
2023 R/V Falkor (too), ROV SuBastian, FKt230417, Pulse, Puerto Rico.
2023 R/V Atlantis, HOV Alvin and AUV Sentry, AT50-07, East Pacific Rise 9° 50’N.
2022 R/V Point Sur, ROV Mohawk, PS22-22 Deepwater Horizon NRDA MDBC SALT3, U.S. Gulf of Mexico.
2022 R/V Nancy Foster, ROV Mohawk, PC22-02 Deepwater Horizon NRDA MDBC, U.S. Gulf of Mexico.
2022 R/V Point Sur, ROV Mohawk, PS22-22 Deepwater Horizon NRDA MDBC SALT2, U.S. Gulf of Mexico.
2022 R/V Nancy Foster, ROV Global Explorer, Illuminating Biodiversity in Deep Waters of Puerto Rico, Puerto Rico.
2021 R/V Point Sur, ROV Global Explorer, ConnectivitY of CoraL Ecosystems (CYCLE), U.S. Gulf of Mexico.
2021 R/V Roger Revelle, ROV Jason and AUV Sentry, RR2102, East Pacific Rise 9° 50’N.
2019 R/V Manta, AUV Mesobot, Environmental DNA Exploration of the Mesopelagic, eDNA MT19, U.S. Gulf of Mexico.
2019 R/V Pelican, ROV Global Explorer, ConnectivitY of CoraL Ecosystems (CYCLE), U.S. Gulf of Mexico.
2018 R/V Atlantis, HOV Alvin and AUV Sentry, AT42-06 Early Career Scientist (ECS) cruise, East Pacific Rise 8° 20’ - 9° 50’N.
2018 R/V Manta, ROV Mohawk, Connectivity of Deepwater Corals (RESTORE) MT18, U.S. Gulf of Mexico.
2017 R/V Manta, ROV Mohawk, Connectivity of Deepwater Corals (RESTORE) MT17, U.S. Gulf of Mexico.
2017 M/V Ocean Project, ROV Comanche, Connectivity of Deepwater Corals (RESTORE) OP17, U.S. Gulf of Mexico.
2017 M/V Ocean Intervention II, ROV Global Explorer, ECOGIG OI2 Jewels of the Deep, U.S. Gulf of Mexico.
2017 R/V Okeanos Explorer, ROV Deep Discoverer, EX1702 American Samoa Expedition. American Samoa.
2015 *R/V Okeanos Explorer, ROV Deep Discoverer, EX1502 Océano Profundo 2015. Caribbean Sea.
2014 R/V Thomas G. Thompson, HROV Nereus, TN309 Hadal Ecosystems Studies (HADES), Kermadec Trench, New Zealand.
2014 R/V Tangaroa, DTIS Towed Camera, TAN1402 Vulnerable Marine Ecosystems survey of the Louisville Seamounts, New Zealand.
2013 *R/V Okeanos Explorer, ROV Deep Discoverer, EX1304 Northeast U.S. Canyons Expedition 2013. North Atlantic Ocean.
2013 Technical scuba diving, Cold-Water Coral Collection Expedition in British Columbia Fjords. British Columbia, Canada.
2012 R/V Falkor, ROV Global Explorer MK3, Deep-Sea Coral Shakedown. Gulf of Mexico.
2012 *R/V Okeanos Explorer, ROV Little Hercules, EX1202 GoMEX 2012: Gulf of Mexico Expedition 2012. Gulf of Mexico.
2011 M/V Holiday Chouest, ROV UHD-34, NRDA Impacts to Coral Communities from the Deepwater Horizon Oil Spill. Gulf of Mexico.
2011 *R/V Okeanos Explorer, ROV Little Hercules, EX1103 GALREX 2011: Galápagos Rift Expedition 2011. Galapagos Rift, Ecuador.
2011 RSS James Cook, ROV Isis, JC055 Cruise: Chemosynthetic Ecosystems of the Southern Ocean. Southern Ocean, Antarctica.
2010 *E/V Nautilus, ROV Hercules, NA010, cruise: Nautilus 2010, Anaximander Seamounts. Anaximander Seamounts, Turkey.
2010 R/V Okeanos Explorer, ROV Little Hercules, EX1004 leg 3, cruise: INDEX-SATAL 2010. Sangihe Talaud, Indonesia.
2010 *R/V Okeanos Explorer, ROV Little Hercules, EX1004 leg 2, cruise: INDEX-SATAL 2010. Sangihe Talaud, Indonesia.
2010 R/V Tangaroa, DTIS Towed Camera, TAN1007 KARMA Kermadec ARc MinerAls. Kermadec arc, New Zealand.
2009 R/V Ronald H. Brown, ROV Jason II, Lophellia II Deepwater Coral Expedition: Reefs, Rigs, and Wrecks. Gulf of Mexico.
2009 SSV Corwith Cramer, Jake Peirson Summer Cruise. Atlantis Canyon, North Atlantic Ocean.
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Publications
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Herrera S., & E. Cordes (2023) Genome assembly of the deep-sea coral Lophelia pertusa. GigaByte. 78. https://doi.org/10.46471/gigabyte.78
Herrera S., W.W. Chadwick, M.G. Jackson, J. Konter, L. McCartin, N. Pittoors, E. Bushta, S. Merle (2023) From basalt to biosphere: Early non-vent community succession on the erupting Vailulu’u deep seamount. Frontiers in Marine Science. 10: 1110062 https://doi.org/10.3389/fmars.2023.1110062
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Govindarajan A.F., A. Adams, E. Allan, S. Herrera, A. Lavery, J. Llopiz, L. McCartin, D. Yoerger, W. Zhang (2023) Advances in Environmental DNA Technology for Observing Ocean Twilight Zone Biodiversity. Oceanography. 36(1):27 https://doi.org/10.5670/oceanog.2023.s1.27
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Govindarajan A.F. , L. McCartin, A. Adams, E. Allane, M. Belani, R. Francolinig, J. Fujii, A. Kukulya, F. Marin, K. Tradd, D. Yoerger, J. McDermott & S. Herrera (2022) Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies. Deep-Sea Research Part I: Oceanographic Research Papers. 189: 103871
https://doi.org/10.1101/2022.01.12.475892
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McDermott J. M., R. Parnell-Turner, T. Barreyre, S. Herrera, C. Downing, N. Pittoors, K. Pehr, S. Vohsen, W. Dowd, J. Wu, M. Marjanovic & D. Fornari (2022) Discovery of Active Off-Axis Hydrothermal Vents at 9°54’N East Pacific Rise. Proceedings of the National Academy of Sciences. 119(30):e2205602119. https://doi.org/10.1073/pnas.2205602119.
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McCartin L., S. Vohsen, S. Ambrose, M. Layden, C. McFadden, E. Cordes, J. McDermott & S. Herrera (2022) Temperature Controls eDNA Persistence Across Physicochemical Conditions in Seawater. Environmental Science & Technology. 56(12):8629–8639. https://doi.org/10.1021/acs.est.2c01672
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Quattrini A.M., S. Herrera, M. Adams, J. Grinyo, L. Allcock, A. Shuler, H. Wirshing, E.E.Cordes, & C.S. McFadden (2022) Phylogeography of Paramuricea: The role of depth and water mass in the evolution and distribution of deep-sea corals. Frontiers in Marine Science. 8:849402 https://doi.org/10.3389/fmars.2022.849402
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Liu G., A. Bracco, A. M. Quattrini, & S. Herrera (2021) Kilometer-scale larval dispersal processes predict metapopulation connectivity pathways for Paramuricea biscaya in the northern Gulf of Mexico. Frontiers in Marine Science, 8:790927. https://doi.org/10.3389/fmars.2021.790927
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Galaska M., G. Liu, D. West, K. Erickson, A.M. Quattrini, A. Bracco & S. Herrera (2021) Seascape genomics reveals metapopulation connectivity network of Paramuricea biscaya in the northern Gulf of Mexico. Frontiers in Marine Science, 8:790929. https://doi.org/10.3389/fmars.2021.790929
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Stefanoudis P.V., L.M. Biancani, S. Cambronero-Solano, M. Clark, J.T. Copley, E. Easton, F. Elmer, S.H.D. Haddock, S. Herrera, I. Inglesias, A.M. Quattrini, J. Sigwart, C. Yesson & A. Glover (2021) Moving conferences online: lessons learned from an international virtual meeting. Proceedings of the Royal Society B. 288(1961):20211769 https://doi.org/10.1098/rspb.2021.1769
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Voolstra C.R., K. Quigley, S.W. Davies, J.E. Parkinson, R.S. Peixoto, M. Aranda, A.C. Baker, A. Barno, D.J. Barshis, F. Benzoni, V. Bonito, D. Bourne, C. Buitrago-Lopez, T. Bridge, C. Xin Chan, D.J. Combosch, J. Craggs, J.C. Frommlet, S. Herrera, A.M. Quattrini, T. Rothig, J.D. Reimer, E. Rubio-Portillo, D. Suggett, H. Villela, M. Ziegler & M. Sweet (2021) Consensus guidelines for advancing coral holobiont genome and specimen voucher deposition. Frontiers in Marine Science. 8:701784 https://doi.org/10.3389/fmars.2021.701784
Dueñas L., J. León, V. Puentes, & S. Herrera (2021) Fauna associated with cold seeps in the deep Colombian Caribbean. Deep-Sea Research Part I: Oceanographic Research Papers. 173:103552. https://doi.org/10.1016/j.dsr.2021.103552
Frometa J., P.J. Etnoyer, A.M. Quattrini, S. Herrera & T.W. Greig (2021) Genetic diversity of Swiftia exserta, a gorgonian octocoral impacted by the DWH oil spill. Diversity. 13(4): 172. https://doi.org/10.3390/d13040172
De Leo D.M., A. Glazier, S. Herrera, A. Barkman & E.E. Cordes (2021) Transcriptomic responses of deep-sea corals experimentally exposed to crude oil and dispersant. Frontiers in Marine Science. doi:10.3389/fmars.2021.649909
​Buff L., M.G. Jackson, K. Konrad, J.G. Konter, M. Bizimis, A. Price, E.F. Rose-Koga, J. Blusztajn, A.A.P. Koppers, & S. Herrera (2021) “Missing links” for the long-lived Macdonald and Arago hotspots, South Pacific Ocean. Geology, https://doi.org/10.1130/G48276.1
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Glazier A., S. Herrera, A. Weinnig, M. Kurman, C. Gómez, & E. Cordes. (2020) Regulation of ion transport and energy metabolism enables certain coral genotypes to maintain calcification under experimental ocean acidification. Molecular Ecology. 103189. https://doi.org/10.1111/mec.15439
Bracco A., G. Liu, M. Galaska, A. M. Quattrini, & S. Herrera (2019) Integrating physical circulation models and genetic approaches to investigate population connectivity in deep-sea corals. Journal of Marine Systems. 198:103189. https://doi.org/10.1016/j.jmarsys.2019.103189
Dueñas L.F., C. Cedeño-Posso, A. Grajales, S. Herrera, E. Rodriguez, J.A. Sánchez, J. Leon, & V. Puentes (2019) First visual occurrence data for deep-sea cnidarians in the South-western Colombian Caribbean. Biodiversity Data Journal. 7:e33091. https://doi.org/10.3897/BDJ.7.e33091
Bors E., S. Herrera, J. Morris & T.M. Shank. (2019) Population genomics of the rapidly invading Lionfish in the Caribbean. Ecology & Evolution. 9(6): 3306-3320. https://doi.org/10.1002/ece3.4952
Sigwart J.D., M.K. Wicksten, M. Jackson & S. Herrera (2019) Deep sea video technology tracks a monoplacophoran to the end of its trail (Mollusca, Tryblidia). Marine Biodiversity. 49(2):825-832. https://doi.org/10.1007/s12526-018-0860-2
Herrera S., W.C. De Vega, D. Ashbrook, S.O. Vernon & P.O. McGowan (2018) Genome-Epigenome Interactions Associated with Chronic Fatigue Syndrome. Epigenetics. 13 (12): 1174-1190. https://doi.org/10.1101/237958
De Leo D.M., S. Herrera, S.D. Lengyel, A.M. Quattrini, R.J. Kulathinal & E.E. Cordes (2018) Gene expression profiling reveals deep-sea coral response to the Deepwater Horizon oil spill. Molecular Ecology. 27 (20): 4066-4077. https://doi.org/10.1111/mec.14847
Herrera S., M. Jackson, J. Konter, M. Lobecker & K. Elliott (2018) American Samoa Expedition: Suesuega o le Moana Amerika Samoa. Oceanography. 31 Suppl. (1): 72-73. https://doi.org/10.5670/oceanog.2018.supplement.01
Mullineaux L.S., A. Metaxas, S.E. Beaulieu, M. Bright, S. Gollner, B. Grupe, S. Herrera, J. Kellner, L. Levin, S. Mitarai, M. Neubert, A. Thurnherr, V. Tunnicliffe, H. Watanabe & Y. Won (2018) Exploring the ecology of deep-sea hydrothermal vents in a metacommunity framework. Frontiers in Marine Science. 5: 49. https://doi.org/10.3389/fmars.2018.00049
Quattrini A.M., B.C. Faircloth, L.F. Dueñas, T. Bridge, M. Brugler, I.F. Calixto-Botía,, D.M. DeLeo, S. Forêt, S. Herrera, S. Lee, D.J. Miller, C. Prada, G. Rádis-Baptista, C. Ramírez-Portilla,, J. Sánchez, E. Rodríguez & C.S. McFadden (2018) Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems. Molecular Ecology Resources. 18(2): 281-295. http://doi.org/10.1111/1755-0998.12736
De Vega W.C., S. Herrera, S.O. Vernon & P.O. McGowan (2017) Epigenetic modifications and glucocorticoid sensitivity in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS). BMC Medical Genomics. 10(1):11. http://doi.org/10.1186/s12920-017-0248-3
Herrera S. & Shank T.M. (2016) RAD sequencing enables unprecedented phylogenetic resolution and objective species delimitation in recalcitrant divergent taxa. Molecular Phylogenetics and Evolution. 100: 1055-7903. http://dx.doi.org/10.1016/j.ympev.2016.03.010
Cordes E.E., D.O. Jones, T.A. Schlacher, D.J. Amon, A.F. Bernadino, B.J. Bett, S. Brooke, R. Carney, D.M. DeLeo, K.M. Dunlop, Elva G. Escobar-Briones, A.R. Gates, L. Genio, J. Gobin, Lea-A. Henry, S. Herrera, S. Hoyt, S. Joye, S. Kark, N.C. Mestre, A. Metaxas, S. Pfeifer, K. Sink, A.K. Sweetman & U.F. Witte (2016) Environmental impacts of the deep-water oil and gas industry: a review to guide management strategies. Frontiers in Environmental Science. 24:58. http://doi.org/10.3389/fenvs.2016.00058
Herrera S., P.H. Reyes-Herrera & T.M. Shank (2015) Predicting RAD-seq marker numbers across the eukaryotic tree of life. Genome Biology and Evolution. 7(12): 3207-3225. http://dx.doi.org/10.1093/gbe/evv210. Git code repository: https://github.com/phrh/PredRAD.
Reyes-Herrera P.H., C.A. Speck-Hernandez, C.A. Sierra & S. Herrera (2015) BackCLIP: a tool to identify common background presence in PAR-CLIP datasets. Bioinformatics. 31 (22): 3703-3705. http://doi.org/10.1093/bioinformatics/btv442.
Herrera S., Watanabe H. & T.M. Shank (2015) Evolutionary history and biogeographical patterns of barnacles from deep-sea hydrothermal vents. Molecular Ecology, 24(3): 673-689. http://doi.org/10.1111/mec.13054.
Reitzel A.M.*, S. Herrera*, M.J. Layden, M.Q. Martindale & T.M. Shank (2013) Going where traditional markers have not gone before: utility and promise for RAD-sequencing in marine invertebrate phylogeography and population genomics . Molecular Ecology, 22(11): 2953-2970. Special Issue: Genotyping by Sequencing. http://doi.org/10.1111/mec.12228. *Indicates equal contributions.
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Herrera S., T.M Shank & Sánchez J.A. (2012) Spatial and temporal patterns of genetic variation in the widespread antitropical deep-sea coral Paragorgia arborea. Molecular Ecology, 21(24): 6053-6067. http://doi.org/10.1111/mec.12074.
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Shank T.M., E.T Baker, R.W. Embley, S. Hammond, J.F. Holden, S. White, S.L. Walker, M. Calderón, S. Herrera, et al. (2012) Exploration of the deepwater galápagos region. Oceanography 25: 50-51. http://dx.doi.org/10.5670/oceanog.2011.supplement.01.
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Shank T.M., S. Herrera, W. Cho, C.N. Roman, K.L.C. Bell (2011) Exploration of the Anaximander mud volcanoes. Oceanography 24 Suppl.: 22-23. http://dx.doi.org/10.5670/oceanog.24.1.supplement.
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Herrera S., A. Baco & J.A. Sánchez (2010) Molecular systematics of the bubblegum coral genera (Paragorgiidae, Octocorallia) and description of a new deep-sea species. Molecular Phylogenetics and Evolution, 55(1):123-135 http://dx.doi.org/10.1016/j.ympev.2009.12.007.
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Sánchez J.A., S. Herrera, R. Navas-Camacho, A. Rodriguez-Ramirez, P. Herron, V. Pizarro, A.R. Acosta, P.A. Castillo, P. Montoya & C. Orozco (2010) White plague-like coral disease in remote reefs of the Western Caribbean. International Journal of Tropical Biology and Conservation, 58(Suppl. 1): 145-154. http://www.scielo.sa.cr/pdf/rbt/v58s1/art10v58s1.pdf.
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