DEEP-SEA ECOLOGY & EVOLUTION

Herrera Lab

The Herrera lab seeks to understand how diversity arises in, and interacts with, the ocean environment. We make use of high-throughput data-gathering techniques and computationally-intensive analytical approaches, in combination with oceanographic field expeditions and laboratory experiments, to generate and test ecological and evolutionary hypothesis using a range of non-model systems. Our research focuses on deep-sea and mesophotic benthic ecosystems, populations, species, and organisms. Our research is cross-disciplinary; we work closely with physical oceanographers, geochemists, molecular biologists, marine engineers, and natural resource managers.

We are always looking to recruit excellent PhD Students and Postdoctoral Researchers to join our team. Ongoing projects include topics such as: 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 contact Santiago via email (santiago [dot] herrera [at] lehigh [dot] edu) with your CV and a brief statement of research interests.

Herrera Lab

Current Members

 
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Santiago Herrera
Principal Investigator

Santiago is a Deep-Sea Biological Oceanographer trained at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution.

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PhD Student
NSF Graduate Research Fellow

Nicole is interested in the dispersal and recruitment in benthic communities. Before joining the lab, she was a Lab Technician at Harvard University and a Guest Student at the Woods Hole Oceanographic Institution.

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Penny Demetriades
Undergraduate Student

Penny is interested in the interactions between biodiversity and anthropogenic threats.​ 

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Sam Vohsen
Postdoctoral Researcher

Sam is a Microbial Ecologist trained at Pennsylvania State University and the Max Planck Institute for Marine Microbiology.

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Luke McCartin
PhD Student

Luke is interested in community structure, environmental DNA, and comparative evolution. Before joining the lab, he was a Research Assistant at the Woods Hole Oceanographic Institution.

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Syrmalenia Kortronaki
PhD Student

Syrmalenia is interested in population genomics and phylogenomics of deep-sea fauna. Before joining the lab, she was a Research Assistant at GEOMAR Helmholtz- Centre for Ocean Research Kiel

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Former Members

Matt Galaska
Postdoctoral Researcher

Went to work as a Research Scientist at the University of Washington and NOAA PMEL

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Susan Ambrose
Masters Student

 

    Maria Granquist
    Undergraduate Student

    Went to work as a Research Assistant at the Smithsonian National Museum of Natural History

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    Destiny West
    Undergraduate Student

    Went to work as a Research Assistant at the Harvard Medical School

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    Fieldwork

    Members of the Herrera lab have led or participated in more than 20 oceanographic research expeditions, totaling more than a year at sea. We have done over 250 dives with remotely operated vehicles (ROVs), to a maximum depth of ten kilometers. We have also used autonomous underwater vehicles (AUVs), towed camera systems, and the human occupied vehicle (HOV) Alvin in our research. Geographically, our work has taken place in the Atlantic, Pacific and Southern oceans, the Mediterranean, Celebes, and Caribbean seas, and most recently the Gulf of Mexico.

    Research cruises at sea

    *Indicates participation via telepresence

    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.

     

    Publications

    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. 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. 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

    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.

    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.

    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.

    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.

    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.

    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.