Deep-Sea Ecology & Evolution
Herrera Lab


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

Our research focuses on understanding the consequences of interactions between marine life and their environment, from geological to organismal time scales. We make use of high-throughput data-gathering methods and computationally intensive approaches, in combination with oceanographic expeditions and laboratory experiments, to generate and test evolutionary and ecological hypothesis using a range of non-model biological systems.

We are currently looking for excellent PhD Students and Postodoctoral Researchers to join our team. Ongoing projects include topics such as: phylogenomics and conservation genomics of deep-sea and mesophotic corals, environmental epigenomics and transcriptomics of coastal and hydrothermal vent species, and biodiversity exploration through community metabarcoding and environmental DNA (eDNA). If you are interesed in getting involved, please contact Santiago via email (santiago [dot] herrera [at] lehigh [dot] edu) with your CV and a brief research statement.

Research Topics

  • Deep-Sea Ecology

    How widespread are species ranges at different depths?

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

    What drives biodiversity, or lack thereof, in extreme deep-sea ecosystems?

  • Dynamic Biogeography of the Deep Ocean

    What are the controls on faunal biodiversification in the deep ocean?

    What are the mechanisms responsible for similarities in evolutionary relationships and distributions of different species?

    How often do biological invasions to new ecosystems happen in and from/into the deep?

  • Cold-water corals

    How do cold-water coral ecosystems respond to environmental changes?

    How can corals with lifespans of hundreds to thousands of years adapt to rapid changes?

    Why are there twice as many coral species living in the deep ocean, relative to shallow seas?

  • Genomics and Epigenomics

    How do organisms respond and/or adapt to environmental stress at the DNA and protein levels?

    Can epigenetic modifications be a mechanism of rapid adaptation to changing environments in species with long lifespans?

    How does the genetic background constrain epigenetic plasticity?

  • Bioinformatics

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

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


Herrera Lab Members

Santiago Herrera

Principal Investigator

My CV is available here.

Luke McCartin

PhD Student


Katie Foley

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


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.