Deep-Sea Ecology & Evolution
Herrera Lab


Welcome to the Herrera Lab at the Department of Biological Sciences of Lehigh University.

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, species, and organisms. Our research is cross-disciplinary. We work closelly with physical oceanographers, geochemists, molecular biologists, marine engineers, and natural resource managers.

We are always looking to recruit excellent PhD Students and Postodoctoral 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 interesed in joining the lab, please contact Santiago via email (santiago [dot] herrera [at] lehigh [dot] edu) with your CV and a brief research statement.

Research Topics

  • Benthic Ecology

    How widespread are species found at different depth ranges?

    How homogeneous is genetic diversity within the range of a deep-sea species?

    What drives biodiversity patterns in extreme deep-sea ecosystems?

  • Dynamic Biogeography

    What factors define the limits for animal colonization in the deep ocean?

    Are there general mechanisms that can explain global diversity patterns?

    What are the mechanisms of adaptation in response to depth-drivent enviromental gradients?

  • Threats and Conservation

    To what degree marine protected areas allow connectivity among populations in the mesophotic and the deep-sea.

    How do deep-sea species, populations and ecosystems respond to environmental changes?

    Can we adequately restore deep benthic ecosystems after a catastrophy?

  • Genomics and Epigenomics

    How do organisms, and their microbiomes, respond and/or adapt to environmental stress at the molecular level?

    Are epigenetic modifications important in the process of acclimation or adaptation to changing environments in marine species with long lifespans?

    What is the potential of eDNA sequecing methods for studying the ecology of remote deep-sea ecosystems?

  • Bioinformatics

    How do we extract meaningful information from massive 'omics' datasets?

    How can different kinds of 'big data' be integrated to understand biological processes in the ocean?


Herrera Lab Members

Santiago Herrera

Principal Investigator

My CV is available here.

Sam Vohsen


Microbiome & Symbiosis

Katie Foley

PhD Student


Luke McCartin

PhD Student


Susan Ambrose

Masters Student

Earth and Environmental Science

Destiny West

Undergraduate Student

Biology. Learn about Destiny here.

Former Members


Matt Galaska (went to work at University of Washington/NOAA PMEL)

Undergraduate Students

Maria Granquist (went to work at the Smithsonian Institution)

Omar Ahmed (went to Grad School for a Master's at Lehigh University)

Emily Bushta

Alondra Maldonado


These are some of our current and past projects.

eDNA - From Surface to Bottom

Defining Scales

RESTORE Deepwater Corals

Gulf of Mexico

Connectivity of Coral Ecosystems

Mesophotic Banks and Reefs


In Peer-Reviewed Journals


21. 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.

20. 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.

19. 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.

18. 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.


17. 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.

16. 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.

15. 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.

14. 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 .


13. 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.

12. 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.


11. 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.

10. 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.


9. 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. Git code repository:

8. 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.

7. 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.


6. 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. *Indicates equal contributions.


5. 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.

4. 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.


3. 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.


2. 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

1. 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.

In Non-Refereed Journals

3. Mills S., D. Leduc, J. C. Drazen, P. Yancey, A.J. Jamieson, M.R. Clark, A.A. Rowden, D. J. Mayor, S. Piertney, T. Heyl, D. Bartlett, J. Bourque, W. Cho, A. Demopoulos, P. Fryer, M. Gerringer, E. Grammatopoulou, S. Herrera, M. Ichino, B. Lecroq, T.D. Linley, K. Meyer, C. Nunnally, H. Ruhl, G. Wallace, C. Young & T.M. Shank (2016). 10,000 m under the sea: an overview of the HADES expedition to Kermadec Trench. In B. Golder and A. Connell (Eds.) Proceedings of Kermadec – Discoveries and Connections. Paper presented at Kermadec – Discoveries and Connections, Wellington, New Zealand (Pp 36–38). The Pew Charitable Trusts.

2. Herrera S. & Sánchez J.A. (2013) Un coral a la conquista de los océanos profundos (A coral conquering the deep oceans). Revista Hipótesis: apuntes científicos uniandinos. Universidad de los Andes. Bogotá. (Special Anniversary Number): 76-79.

1. Herrera S., C.A. Hernandez & E. Bahamón (2008) Guerreros fantasmales: comportamiento competitivo en el cangrejo Ocypode gaudicaudii de la isla Gorgona (Ghostly warriors: competitive behavior of the crab Ocypode gaudicaudii in the Gorgona island). Revista Hipótesis: apuntes científicos uniandinos. Universidad de los Andes. Bogotá. (9): 34-35.

Fieldwork in the Deep Ocean

Footage courtesy of the NOAA Office of Ocean Exploration and Research, 2010 INDEX-SATAL.

We have lead and participated in more than a dozen scientific expeditions to deep-sea hydrothermal vents, hydrocarbon seeps, active volcanoes, mid-ocean ridges, continental margins, seamounts, ocean trenches and abyssal plains. In doing so, we have explored regions of the Atlantic, Pacific, and Southern Oceans, the Gulf of Mexico, and the Celebes, Caribbean and Mediterranean Seas and conducted over 320 days of fieldwork and 110 submersible dives.