Ms Michelle Achlatis

Coral reefs are the result of a constant battle between constructive and destructive forces. When it comes to biologically-driven destruction, erosion by excavating sponges is one of the most important yet understudied mechanisms. Global warming and acidification are predicted to enhance the impact of these sponges on reefs, tipping the balance to the disadvantage of corals and other calcifying organisms. Using Cliona orientalis as her model species, Michelle’s current work aims to decipher the metabolic dynamics of bioerosion and to evaluate the resilience of excavating sponges to future environmental conditions. Michelle joined the Coral Reef Ecosystems lab as a PhD student in 2014 after she finished her Master’s at the University of Amsterdam working on Caribbean reef sponges and majoring in science communication. She completed her first degree at the University of Crete in her homeland Greece.

Installing equipment on the reef crest of Heron Island

harries bommie

The bioeroding sponge Cliona orientalis growing on Heron Island reef







Contact details
Coral Reef Ecosystems Lab
School of Biological Sciences  |  University of Queensland
Level 7 Gehrmann Laboratories (60)
St. Lucia, QLD 4072  |  Australia



Alexander B. E., Achlatis M., Osinga R., van der Geest H.G., Cleutjens J. P. M., Schutte B. , de Goeij J.M. (2015). Cell kinetics during regeneration in the sponge Halisarca caerulea: how local is the response to tissue damage? PeerJ 3:e820

Achlatis M., van der Zande R.M., Schönberg C.H.L., Fang J.K.H., Hoegh-Guldberg O., Dove S. (2017). Sponge bioerosion on changing reefs: ocean warming poses physiological constraints to the success of a photosymbiotic excavating sponge. Sci Rep 7: 10705.​ doi:10.1038/s41598-017-10947-1

Ramsby, B. D., Hill, M. S., Thornhill, D. J., Steenhuizen, S. F., Achlatis, M., Lewis, A. M. and LaJeunesse, T. C. (2017). Sibling species of mutualistic Symbiodinium clade G from bioeroding sponges in the western Pacific and western Atlantic oceans. J. Phycol.. doi:10.1111/jpy.12576

Achlatis M., Pernice M., Green K., Guagliardo P., Kilburn M.R., Hoegh-Guldberg O., Dove S. (2018). Single-cell measurement of ammonium and bicarbonate uptake within a photosymbiotic bioeroding sponge. ISME J DOI 10.1038/s41396-017-0044-2

Fang J.K.H., Schönberg C.H.L., Mello-Athayde M.A., Achlatis M., Hoegh-Guldberg O., Dove S. (2018). Bleaching and mortality of a photosymbiotic bioeroding sponge under future carbon dioxide emission scenarios. Oecologia 10.1007/s00442-018-4105-7

Dr Annamieke Van Den Heuvel

Sunset – Heron Island

Annamieke has been with the CRE lab for a number of years, first as a Honours student and then when undertaking her PhD. During her time as a CRE student, she researched the effects increased levels of exogenous nitrogen had on the relationship between coral and their symbiotic algae, Symbiodinium. These effects were examined on both a genetic and physiological level to develop an overall picture of a coral holobionts response to increasing levels of nitrogen.

Currently Annamieke is the Laboratory Manager for the Coral Reef Ecosystems Lab. She helps in keeping the lab running and responds to applications to work with the lab.

inside the mesocosm
A view into the Mesocosm ‘Mini-Reef’

In addition to her Lab manager role, Annamieke regularly travels to Heron Island to check and sample the mesocosm experiment currently underway. These mesocosems are representative ‘mini reefs’ comprised of several species of hard and soft coral, algae assemblages, various invertebrates and some herbivorous fish. The experiment, being run by A/Prof Sophie Dove, looks at the effects of climate change on coral reef ecosystems. The four treatments explores the effects of increased temperature and pCO2 on coral reef communities both in combination and separately.

Dr Nela Rosic (DECRA Research Fellow)


I grew up in Serbia and start thinking about Science due to my love for genetics. I received a BSc (Hons First Class) in Molecular Biology and Physiology and a MSc in Plant Biology from the University of Belgrade. After moving to Brisbane, I completed a PhD at the University of Queensland. I have been awarded with a UQ Postdoctoral Fellowship for Women (2011-2013) and a prestigious Discovery Early Career Researcher Award by ARC (2012-2014).

Research Interests

  • Reprogramming Symbiodinium epigenome for higher temperature conditions
    Coral reefs represent one of the most diverse marine ecosystems housing an estimated 25% of all marine species. Exposure to thermal stress has been recognized as an important abiotic factor leading to the loss of algal symbionts from coral tissue and coral bleaching. The goal of this project is to enhance our understanding of the capacity of coral algae to tolerate thermal stress using an ancient epigenetic mechanism DNA methylation for reprogramming their epigenomes.
  • Coral algae as a source of UV-absorbing compounds
    Reef-building corals form mutualistic symbioses with unicellular photosynthetic dinoflagellate of the genus Symbiodinium. Exposure to ultraviolet radiation especially when combined with thermal stress, has been recognized as an important abiotic factor leading to oxidative stress and break down of the coral-algal endosymbiosis. In nature, many marine organisms use Mycosporine-like Amino Acids (MAAs) as biological sunscreens in UV protection and the prevention of oxidative stress. Corals acquire MAAs from their symbiotic algae and diet. Until now the complete enzymatic pathway of MAA synthesis is not known nor is the extent of their regulation by environmental conditions.
  • Transcriptomics for detection of stress in coral
    Changes to the environment as a result of human activities can result in a range of impacts on reef building corals that include reduced concentrations of algal symbionts and coral bleaching. We investigate the expression of genes in the colonies of the reef-building coral during environmental perturbations including elevated sea temperatures and nutrient enrichment. Our results will provide new insights into the transcriptional profiles of the coral holobiont and transcriptional regulation prior bleaching. In addition, we will identify a range of potential stress biomarkers that could be used for the development of the early warning signs of stress in reef-building corals.



Book Chapter

  • Rosic, Nela (2013). DNA shuffling of cytochromes P450 for indigoid pigment production. In Ian R. Phillips, Elizabeth A. Shepherd and Paul R. Ortiz de Montellano (Ed.), Cytochrome P450 protocols 3rd ed. (pp. 205-224) New York, NY, United States: Humana Press. doi:10.1007/978-1-62703-321-3_18

Journal Article

Conference Publication

  • Rosic, N. and Dove, S. (2013). How can dinoflagellates help in reducing coral reef vulnerability to environmental stress?. In: M. Dennis Hanisak, James A. Nienow and Akshinthala K. S. K. Prasad, Abstracts of Papers to be Presented at the 10th International Phycological Congress. 10th International Phycological Congress, Orlando, Florida, United States, (94-94). 4-10 August 2013.

  • Rosic, Nela, Pernice, Mathieu, Hoegh-Guldberg, Ove and Dove, Sophie (2011). Differential Regulation of Heat Shock Proteins and Cytochrome P450 Genes in Symbiotic Dinoflagellates Under Thermal Stress. In: Fifth European Phycological Congress: EPC5 Programme and Abstracts. 5th European Phycological Congress, Rhodes, Greece, (145-145). 04-09 September 2011. doi:10.1080/09670262.2011.613192

  • Rosic, Nela, Kaniewska, Pauline, Ling, Edmund, Edwards, David, Dove, Sophie and Hoegh-Guldberg, Ove (2011). Transcriptomics of the coral-algal symbiosis in response to environmental stress. In: Fifth European Phycological Congress: EPC5 Programme and Abstracts. 5th European Phycological Congress, Rhodes, Greece, (97-97). 04-09 September 2011. doi:10.1080/09670262.2011.613190

  • Rosic, Nedeljka, Lonhienne, Thierry G.A., DeVoss, James J. and Gillam, Elizabeth M.J. (2003). Directed evolution of mammalian cytochrome P450 enzymes involved in xenobiotic metabolism. In: Drug Metabolism Reviews: Proceedings 8th European Meeting of the International-Society-for-the-Study-of-Xenobiotics (ISSX). 8th European Meeting of the International-Society-for-the-Study-of-Xenobiotics (ISSX), Dijon, France, (46-46). 27 April – 1 May, 2003. doi:10.1081/DMR-120020120

Dr Pim Bongaerts

PimBongaerts3.jpg?itok=RWndFd8aPim is a post-doctoral research fellow in the CRE lab and lead scientist for the “Deep Reef” component of the Catlin Seaview Survey ( The Deep Reef survey looks into the effects of climate change on one of the least known ecosystems on the planet – the deep-water reefs or mesophotic coral ecosystems (between 30-100m). The project aims to provide a comprehensive study of the biodiversity and connectivity of mesophotic reefs across the globe, with a major focus on the Great Barrier Reef, the Coral Sea and the Southern Caribbean.




  1. Bongaerts P, Carmichael M, Hay KB, Tonk L, Frade PR, Hoegh-Guldberg O (2015) Symbiont zonation plays a crucial role in the vertical distribution of coral species. Royal Society Open Science – in press
  2. Pantos O, Bongaerts P, Dove S, Hoegh-Guldberg O (2015) Microbial associations in the scleractinian coral Seriatopora hystrix across depths, locations and host/symbiont genotypes. ISME Journalin press
  3. Bongaerts P, Frade PR, Englebert N, Hay KB, Vermeij MJH, Hoegh-Guldberg O (2015) Deep down on a Caribbean reef: lower mesophotic depths harbor a specialized coral-endosymbiont community. Nature Scientific Reports 5:7652
  4. Muir P, Wallace C, Bridge TCL, Bongaerts P (2015) Diverse Staghorn Coral Fauna on the Mesophotic Reefs of North-East Australia. PLoS One – in press
  5. González-Rivero M, Bongaerts P, Beijbom O, Pizarro O, Friedman A, Rodriguez-Ramirez A, Upcroft B, Laffoley D, Kline DI, Vevers R, Hoegh-Guldberg O (2014) The Catlin Seaview Survey – kilometre-scale seascape assessment, and monitoring of coral reef ecosystems. Aquatic Conservationin press
  6. Englebert N* & Bongaerts P*, Muir P, Hay KB, Hoegh-Guldberg O (2014) Deepest zooxanthellate corals of the Great Barrier Reef and Coral Sea. Marine Biodiversityin press
  7. Bongaerts P, Frade PR, Ogier JJ, Hay KB, van Bleijswijk J, Englebert N, Vermeij MJH, Bak RPM, Visser PM, Hoegh-Guldberg O (2013) Sharing the slope: depth partitioning of agariciid corals and associated Symbiodinium across shallow and mesophotic habitats (2-60 m) on a Caribbean reef. BMC Evolutionary Biology 13:205
  8. Bongaerts P, Muir PR, Bridge TCL, Englebert N, Hoegh-Guldberg O (2013) Cyclone damage at mesophotic depths on Myrmidon Reef (GBR). Coral Reefs 32:935
  9. Bridge TCL, Hughes TP, Guinotte JM, Bongaerts P (2013) Call to protect all coral reefs. Nature Climate Change 3:528-530
  10. Tonk L* & Bongaerts P*, Sampayo EM, Hoegh-Guldberg (2013) SymbioGBR: a web-based database of Symbiodinium associated with cnidarian hosts on the Great Barrier Reef. BMC Ecology 13:7
  11. Foster R, Bridge T, Bongaerts P (2012) The first record of Hippocampus denise from Australia. Aqua – International Journal of Ichthyology 18:55-57
  12. Bongaerts P, Hoeksema B, Hay K, Hoegh-Guldberg O (2012) Mushroom corals overcome live burial through pulsed inflation. Coral Reefs 2:399
  13. Bongaerts P, Riginos C, Hay K, van Oppen MJH, Hoegh-Guldberg O, Dove S (2011) Adaptive divergence in a scleractinian coral: physiological adaptation of Seriatopora hystrix to shallow and deep reef habitats. BMC Evolutionary Biology 11:303 (cover article)
  14. Bridge TCL, Fabricius KE, Bongaerts P, Wallace CC, Muir P, Done TJ, Webster JM (2011) Diversity of Scleractinia and Octocorallia in the mesophotic zone of the Great Barrier Reef, Australia. Coral Reefs 31:179-189
  15. Bongaerts P, Sampayo EM, Bridge TLC, Ridgway T, Vermeulen F, Englebert N, Webster JM, Hoegh-Guldberg O (2011) Symbiodinium diversity of mesophotic coral communities on the GBR: a first assessment. Marine Ecology Progress Series 439:117-126
  16. Bongaerts P* & Bridge T*, Kline DI, Muir PR, Wallace CC, Beaman RJ, Hoegh-Guldberg O (2011) Mesophotic coral ecosystems on the walls of Coral Sea atolls. Coral Reefs 30:335
  17. Van Oppen MJH, Bongaerts P, Underwood JN, Peplow LM, Cooper TF (2011) The role of deep reefs in shallow reef recovery: an assessment of vertical connectivity in a brooding coral from west and east Australia. Molecular Ecology 20:1647-1660
  18. Bongaerts P, Riginos C, Ridgway T, Sampayo EM, van Oppen MJH, Englebert N, Vermeulen F, Hoegh-Guldberg O (2010) Genetic Divergence across Habitats in the Widespread Coral Seriatopora hystrix and its Associated Symbiodinium. PLoS One 5(5):e10871
  19. Bongaerts P, Ridgway T, Sampayo EM, Hoegh-Guldberg O (2010) Assessing the ‘deep reef refugia’ hypothesis: focus on Caribbean reefs. Coral Reefs 29:309–327
  20. Frade PR, Bongaerts P, Winkelhagen AJS, Tonk L, Bak RPM (2008) In situ photobiology of corals over large depth ranges: a multivariante analysis on the roles of environment, host and algal symbiont. Limnology and Oceanography 53:1-14
  21. Sampayo EM, Ridgway T, Bongaerts P, Hoegh-Guldberg O (2008) Bleaching susceptibility and mortality of corals are determined by fine-scale differences in symbiont type. PNAS 105:10444-10449


Dr. Benjamin P. Neal


Neal2 (1)

Outreach and Media



Coral Reef Ecosystems Lab / Catlin Seaview Survey
Global Change Institute, The University of Queensland
St Lucia, QLD, Australia, 4067
Cell: +61 0421 727 846
Office: +61 7 336 56009




Research Interests

– Contemporary dynamics and change in tropical marine ecosystems
– Coral reef ecosystem response to global and local stressors
– Optical, remote, and in situ sensing and monitoring of coral reef ecosystems

Ben joins the Coral Reef Ecology Lab as a lead researcher for the Catlin Seaview Survey. Hailing from the Scripps Institution of Oceanography at the University of California, he works on coral reef image interpretation and analysis, generating coral cover and other ecological data, and creating outreach and scientific products. He completed his PhD in 2013, studying the growth and genetic response of Caribbean corals to thermal stress and bleaching. He has conducted marine research in a variety of tropical and temperate locations, has been a commercial fisherman in Alaska, and has worked for federal and state ocean management bodies in the United States. When not diving, he enjoys getting out into nature with his wife Loren, a professor of marine biology, and their young daughter Sonora.


2013   Ph.D.   Scripps Institution of Oceanography, University of California San Diego: Marine Biology. Dissertation: Long-term coral recovery and endosymbiont changes following the major 2005 thermal disturbance in Bocas del Toro, Panama. Co-advisors: B. Greg Mitchell and Richard Norris.

2007   M.Sc.    Scripps Institution of Oceanography, University of California San Diego: Marine Biology. Co-advisors: Jeremy Jackson and Enric Sala.

1993   B.A.     Dartmouth College, Hanover, New Hampshire: Geography/Environmental Studies.



Outreach and Media

Media coverage of our work:

Time Magazine: Breaking the waves – Catlin Seaview Survey digitizes the endangered oceans

360 Degree Solomon Islands: A film from our expedition with the Khaled bin Sultan Living Oceans Foundation

EuroNews: Mapping the oceans’ coral reefs to try and save them from extinction

Dive the great reefs of the world on Google Street View: Mother Nature News

Jakarta MetroTV News: An underwater sketch of Karimunjawa National Park (in Bahasa Indonesian)


Blogs from recent expeditions:

Reflections on the Maldives (30 March – 21 April 2015)

Contemplating the Chagos Archipelago: Outpost for Coral (9 – 28 February 2015)

Catlin Seaview Survey joins forces with the Living Oceans Foundation in the Solomon Islands (30 October – 12 November 2014)

Karimunjawa National Park (13 September – 10 October 2014)

An introduction to Timor-Leste (23 July – 6 August 2014)

We’re off to the Philippines, first stop Tubbataha Reefs Natural Park (14 – 25 March 2014)


Peer Reviewed Publications

Neal, B. P.; R. N. Winter; H. Lin; T. Trebitz; D. Kline; B. G. Mitchell. Improved estimation of two-dimensional area of coral colonies from underwater photographs. In press: Environmental Monitoring and Assessment.

Beijbom, O.; Edmunds, P.J; Roelfsema, C.; Smith, J.; Kline, D.I.; Neal, B.P.; Dunlap, M.; Moriarty, V.; Fan, T.; Tan, C.; Chan, S.; Trebitz, T.; Gamst, A.; Mitchell, B.G.; Kriegman, D. Automated analysis of community composition in underwater imagery using machine learning enabled algorithms. PLOS ONE: DOI: 10.1371/journal.pone.0130312. 

Treibitz, T.; Neal, B.P.; Kline, D.I.; Beijbom, O.; Roberts, P.; Mitchell, B. G.; Kriegman, D. 2014. Wide Field-of-View Fluorescence Imaging of Coral Reefs. Nature Scientific Reports 5.

Lavi, A.; Neal, B.P.; Loya, Y.; Keren, R.; Eyal, G. A quick, easy, and non-intrusive method for underwater volume and surface area evaluation of benthic organisms by 3D computer modelling. Methods in Ecology and Evolution (DOI: 10.1111/2041-210X.12331).

McClenachan; L., Neal, B.P.; Al-Abdulrazzak, D., Witkin, T., Fisher, K., and Kittinger, J. 2014. Do Community Supported Fisheries (CSFs) improve sustainability? Fisheries Research 157:62-69.

Neal, B. P.; Condit, C.; dos Santos, S.; Liu, G.; Kahru, M.; Kline, D.; Mitchell, B.G. 2013. When depth is no refuge: Cumulative thermal stress increases with depth for corals in Bocas del Toro, Panama. Coral Reefs. 33:193-205.

Beijbom, O; Edmunds, P.J; Fan, T.; Smith, J.; Roelfsema, C.; Dunlap, M.; Moriarty, V.; Neal, B.P., Chan, S.; Treibitz, T.; Kline, D.I.; Mitchell, B.G.; Kriegman, D. 2012. Towards Automated Annotation of Scientific Image Data: A Coral Reef Ecology Study. IEEE Proceedings on Computer Vision and Pattern Recognition (CVPR).

Manuscripts in Progress

Neal, B. P.; Kline, D.; Coffroth, M.A. Changes in Symbiodinum genetic diversity and temporal variation over time and depth for three Caribbean corals. In preparation.

Neal, B. P.; Winter, R.; Treibitz, T.; Beijbom, O.; Kline, D.; Coffroth, M.A.; Mitchell, B. G. Long term, in-situ growth and recovery of the scleractinians Montastrea franksii and Siderastrea siderea following the 2005 Caribbean bleaching event. In preparation.

Selected Recent Presentations

Rapid, high definition, automated underwater sensing of coral reef ecosystems: The Catlin Seaview Survey. International Marine Conservation Congress, Glasgow, Scotland, 14-18 August 2014

Hydrological conditions contributing to the severe heat bleaching in the Caribbean in 2005. American Society of Limnology and Oceanography Aquatic Sciences Meeting, New Orleans, LA. 17-22 February 2013

Long term, in-situ growth and recovery of the scleractinian Montastrea franksii following the 2005 Caribbean bleaching event. International Coral Reef Symposium, Cairns, Australia. 9-13 July 2012

Semi-automated photographic processing of coral reef photographs from time series observations at Bocas del Toro, Panama. American Society of Limnology and Oceanography Aquatic Sciences Meeting, San Juan, Puerto Rico. 13-18 February 2011





Driving the SeaView-II (SV-II) camera system in the Maldives, with a camera calibration transect on the bottom



Healthy Acroporid corals and abundant fish in the western Maldives.


Chagos ben big coral

Surveying large coral colonies in the world’s largest marine protected area in the Chagos Archipelago (British Indian Ocean Territory).

Dr Alberto Rodriguez-Ramirez

BETO in field

Postdoctoral Research Fellow

CGRR Image Analysis and Data Base Manager

Global Change Institute, The University of Queensland

Room 708 (Level 7), Gehrmann Laboratories (Building #60),
St. Lucia, Brisbane, QLD 4072, Australia



Alberto Rodríguez-Ramírez has been an active coral reef researcher for 17 years, studying and monitoring long-term trajectories in marine ecosystems, including seagrass and mangroves, as well as coral reefs in the Caribbean region and the Great Barrier Reef (GBR). He completed his PhD at The University of Queensland focusing on the reconstruction of historic disturbances to coral reefs, coral responses and water quality changes for the southern GBR using geochemical proxies from coral archives and secondary sources of information.

Currently he is the Image Analysis and Database Manger of the Catlin Global Reef Record, conducting the post-processing of coral reef images and quantitative/ecological analysis.



Peer Review Journals

  1. Rodriguez-Ramirez A., CA Grove, J. Zinke, J.M. Pandolfi and J-x. Zhao. 2014. Coral Luminescence Identifies the Pacific Decadal Oscillation as a Primary Driver of River Runoff Variability Impacting the Southern Great Barrier Reef. PLoS ONE 9(1): e84305. doi:10.1371/journal.pone.
  2. van Tussenbroek B., Cortés, R. Collin, A.C. Fonseca, P.M.H. Gayle, H.M. Guzmán, G.E. Jácome, R. Juman, K.H. Koltes, H. A. Oxenford,  A. Rodriguez-Ramirez, J. Samper-Villarreal, S.R. Smith, J.J Tschirky, and E. Ernesto Weil. Caribbean. 2014. Wide, Long-Term Study of Seagrass Beds Reveals Local Variations, Shifts in Community Structure and Occasional Collapse. PLoS ONE 9(3): e90600. doi:10.1371/journal.pone.0090600
  3. Gonzalez-Rivero M., P. Bongaerts, O. Beijbom, O. Pizarro, A. Friedman, A. Rodriguez-Ramirez, B. Upcroft, D. Laffoley, D. Kline, R. Vevers, and O. Hoegh-Guldberg. 2014. The Catlin Seaview Survey – kilometre-scale seascape assessment, and monitoring of coral reef ecosystems. Aquatic Conserv: Mar. Freshw. Ecosyst. 24(Supp. 2): 184-198.
  4. Grove et al., (including  A. Rodriguez-Ramirez). In press. Spectral Luminescence Scanning: Updates and Developments. Special Issue, DPER volume: Micro-XRF Studies of Sediment Cores
  5. Rodriguez-Ramirez A. and F.A Zapata. 2012. An atypical corallum morphology in a species of Pocillopora. Coral Reefs, 31:253. doi 10.1007/s00338-011-0854-z.
  6. Eakin C.M., J.A. Morgan, S.F. Heron, T.B. Smith, G. Liu, L. Alvarez-Filip, B. Baca, E. Bartels, C. Bastidas, C. Bouchon, M. Brandt, A.W. Bruckner, L. Bunkley-Williams, A. Cameron, B.D. Causey, M. Chiappone, T.R.L. Christensen, M.J.C. Crabbe, O. Day, E. de la Guardia, G. Díaz-Pulido, D. DiResta, D.L. Gil-Agudelo, D.S. Gilliam, R.N. Ginsburg, S. Gore, H.M. Guzmán, J.C. Hendee, E.A. Hernández-Delgado, E. Husain, C.F.G. Jeffrey, R.J. Jones, E. Jordán-Dahlgren, L.S. Kaufman, D.I. Kline, P.A. Kramer, J.C. Lang, D. Lirman, J. Mallela, C. Manfrino, J.-P. Maréchal, K. Marks, J. Mihaly, W.J. Miller, E.M. Mueller, E.M. Muller, C.A. Orozco Toro, H.A. Oxenford, D. Ponce-Taylor, N. Quinn, K.B. Ritchie, S. Rodríguez, A. Rodriguez-Ramirez, S. Romano, J.F. Samhouri, J.A. Sánchez, G.P. Schmahl, B.V. Shank, W.J. Skirving, S.C.C. Steiner, E. Villamizar, S.M. Walsh, C. Walter, E. Weil, E. H. Williams, K.W. Roberson, and Y. Yusuf. 2010. Caribbean Corals in Crisis: Record Thermal Stress, Bleaching, and Mortality in 2005. PLoS ONE, 5(11): e13969. doi:10.1371/journal.pone.0013969.
  7. Rodriguez-Ramirez A., J. Garzon-Ferreira, A. Batista-Morales, D. L. Gil, D.I. Gomez-Lopez, K. Gomez-Campo, T. Lopez-Londoño, R. Navas-Camacho, M.C. Reyes-Nivia, and J. Vega-Sequeda. 2010. Temporal patterns in coral reef, seagrass and mangrove communities from Chengue bay CARICOMP site (Colombia): 1993-2008. Revista de Biología Tropical, 58 (Suppl. 3): 45-62.
  8. Rodriguez-Ramirez A., M.C. Reyes-Nivia, S. Zea, P. Herron, R. Navas-Camacho, J. Garzón-Ferreira, S. Bejarano, and C. Orozco.  2010. Recent dynamics and condition of coral reefs in the Colombian Caribbean. Revista de Biología Tropical, 58(Suppl. 1): 107-131.
  9. Garzón-Ferreira J. and A. Rodriguez-Ramirez. 2010. SIMAC: Development and implementation of a coral reef monitoring network in Colombia. Revista de Biología Tropical, 58(Suppl. 1): 67-80.
  10. Zapata F.A., A. Rodriguez-Ramirez, C. Caro-Zambrano, and J. Garzón-Ferreira. 2010. Mid-term coral-algal dynamics and conservation status of a Gorgona Island (Tropical Eastern Pacific) coral reef. Revista de Biología Tropical, 58(Suppl. 1): 81-94.
  11. Navas-Camacho R., A. Rodríguez-Ramírez, M.C. Reyes-Nivia, D.L. Gil-Agudelo, and J. Garzón-Ferreira. 2010.Coral diseases and bleaching on Colombian Caribbean coral reefs. Revista de Biología Tropical, 58(Suppl. 1): 95-106.
  12. Navas-Camacho R., A. Rodríguez-Ramírez, and M.C. Reyes-Nivia. 2010. Agents of coral mortality on reef formations of the Colombian Pacific. Revista de Biología Tropical, 58(Suppl. 1): 133-138.
  13. Sánchez J.A., R. Navas-Camacho, A. Rodríguez-Ramírez, P. Herron, V. Pizarro, A.R. Acosta, P.A. Castillo, J.C. Martínez , P. Montoya, and C. Orozco. 2010. White plague-like coral disease in remote reefs of the Western Caribbean Revista de Biología Tropical, 58(Suppl. 1): 145-154.
  14. Gil-Agudelo D.L., R. Navas-Camacho, A. Rodríguez-Ramírez, M.C. Reyes-Nivia, S. Bejarano, J. Garzón-Ferreira, and G.W. Smith. 2009. Enfermedades coralinas y su investigación en los arrecifes colombianos. Boletin de Investigaciones Marinas y Costeras, 38(2): 189-224.
  15. Paddack M.J., J.D. Reynolds, C. Aguilar, R.S. Appeldoorn, J. Beets, E.W Burkett, P.M. Chittaro, K. Clarke, R. Esteves, A.C. Fonseca, G.E Forrester, A.M. Friedlander, J. García-Sais, G. González-Sansón, L.K.B. Jordan, D.B. McClellan, M.W. Miller, P.P Molloy, P.J. Mumby, I. Nagelkerken, M. Nemeth, R. Navas-Camacho, J. Pitt, N.V.C. Polunin, M.C. Reyes-Nivia, D.R. Robertson,  A. Rodríguez-Ramírez, E. Salas, S.R.  Smith, R.E. Spieler, M.A. Steele, I.D. Williams, C.L. Wormald, A.R. Watkinson, and I.M. Côté. 2009. Recent region-wide declines in Caribbean reef fish abundance. Current Biology, 19(7): 590-595.
  16. Vega-Sequeda, J.,  A. Rodríguez-Ramírez, M.C. Reyes-Nivia, and R. Navas-Camacho. 2008. Formaciones coralinas del área de santa: estado y patrones de distribución espacial de la comunidad bentónica. Boletín de Investigaciones Marinas y Costeras, 37(2): 87-105.
  17. Rodríguez-Ramírez A. and M.C. Reyes-Nivia. 2008. Evaluación rápida de los efectos del huracán Beta en la Isla de Providencia (Caribe colombiano). Boletín de Investigaciones Marinas y Costeras, 37(1): 217-224.
  18. Olaya-Restrepo J., M.C. Reyes-Nivia, and A. Rodríguez-Ramírez. 2008. Ensamblajes de peces arrecifales del área de Santa Marta y el Parque Nacional Natural Tayrona. Boletín de Investigaciones Marinas y Costeras, 37(1): 111-127.
  19. Zapata F.A., A. Rodríguez-Ramírez, M. Rodríguez-Moreno, C. Muñoz, and M. López Victoria. 2007. Confirmation of the occurrence of the coral Pavona chiriquiensis (Cnidaria: anthozoa: Agariciidae) in the Colombian Pacific. Boletín de Investigaciones Marinas y Costeras, 36(1): 307-312.
  20. Reyes-Nivia M.C., J. Garzón-Ferreira, and A. Rodríguez-Ramírez. 2004. Depredación de coral vivo por peces en las bahías de Chengue y Gayraca, Parque Nacional Natural Tayrona (Caribe colombiano). Revista de Biología Tropical., 52(4): 883–895.
  21. Rodríguez-Ramírez A., J. Nivia-Ruíz, and J. Garzón-Ferreira. 2004. Características estructurales y funcionales del manglar de Avicennia germinans en la Bahía de Chengue (Caribe colombiano). Boletín de Investigaciones Marinas y Costeras, 33: 223-244.
  22. Reyes-Nivia M.C.,  A. Rodríguez-Ramírez, and J. Garzón-Ferreira. 2004. Peces asociados a arrecifes coralinos de cinco áreas del Caribe colombiano: listado de especies y nuevos registros. Boletín de Investigaciones Marinas y Costeras, 33: 101-116.
  23. Santodomingo N.,  A. Rodríguez Ramírez, and J. Garzón Ferreira. 2002. Territorios del pez Stegastes planifrons en formaciones coralinas del Parque Nacional Natural Tayrona, Caribe Colombiano: un panorama general. Boletín de Investigaciones Marinas y Costeras, 31: 65-84.
  24. Acero A.,  A. Rodríguez-Ramírez, and J. Garzón-Ferreira. 1995. Nomeus gronovii (Gmelin) (Pisces: Nomeidae) en el Caribe colombiano: primer registro para la costa noroccidental de América del Sur. Anales del Instituto de Investigaciones Marinas de Punta de Betin, 23: 173-176.
  25. Mejía L.S., O.D. Solano, and  A. Rodríguez-Ramírez. 1995. Ocho nuevos registros para la fauna íctica de Islas del Rosario, (Mar Caribe colombiano). Anales del Instituto de Investigaciones Marinas de Punta de Betin, 23: 189-192.



  1. Rodríguez-Ramírez A. and J. Garzón-Ferreira. 2003. Monitoreo de arrecifes coralinos, pastos marinos y manglares en la Bahía de Chengue (Caribe Colombiano): 1993-1999. INVEMAR, Serie de Publicaciones Especiales No.8, Santa Marta, 170p. ISBN 958-97264-6-1


Book Chapters 

  1. Rodríguez-Ramírez A., C. Bastidas, J. Cortés, H. Guzmán, Z. Leão, J. Garzón-Ferreira, R. Kikuchi, B. Padovani Ferreira, J.J. Alvarado, C. Jiménez, A.C. Fonseca, E. Salas, J. Nivia, C. Fernández, S. Rodríguez, D. Debrot, A. Croquer, D. Gil, D.I. Gómez, R.Navas-Camacho, M.C. Reyes-Nivia, A. Acosta, E. Alvarado, V. Pizarro, A. Sanjuan, P. Herrón, F.A. Zapata, S. Zea, M. López-Victoria, and J.A. Sánchez. 2008. Status of coral reefs and associated ecosystems in Southern Tropical America: Brazil, Colombia, Costa Rica, Panamá and Venezuela. pp 281-294. In: Wilkinson, C. (Ed.). Status of coral reefs of the world: 2008. Global Coral Reef Monitoring Network and Reef and Rainforest Research Centre, Townsville, Australia. ISSN 1447-6185.
  2. Rodríguez-Ramírez A., C. Bastidas, S. Rodríguez, Z. Leão, R. Kikuchi, M. Oliveira, D. Gil, J. Garzón-Ferreira, M.C. Reyes-Nivia, R.Navas-Camacho, N. Santodomingo, G. Díaz-Pulido, D. Venera-Ponton,L. Florez-Leiva, A. Rangel-Campo, C. Orozco, J.C Márquez, S. Zea, M. López-Victoria, J.A. Sánchez, and M.C. Hurtado. 2008. The effects of coral bleaching in the Southern Tropical America: Brazil, Colombia, and Venezuela. pp 105-114. In: Wilkinson C. and D. Souter (Eds.). Status of Caribbean coral reefs after the bleaching and hurricanes of 2005. GCRMN and RRRC, Townsville, Australia. ISSN 1447 6185
  3. Rodríguez-Ramírez A., R. Navas-Camacho, C. Reyes-Nivia, S. Bejarano-Chavarro, and J. Garzón-Ferreira. 2007. Implementación del SIMAC en la isla de Malpelo. pp 97-112. In: DIMAR-CCCP and UAESPNN-DTSO (Eds.). Santuario de Fauna y Flora Malpelo: descubrimiento en marcha, DIMAR, Bogotá. Colombia.
  4. Rodríguez-Ramírez A., J. Garzón-Ferreira, M.C. Reyes-Nivia, R. Navas-Camacho, S. Bejarano, G. Duque, and F.A. Zapata. 2006. Sistema nacional de monitoreo de arrecifes coralinos en Colombia Simac: logros y resultados 1998-2004. Tomo II. pp 365-370. In: Chaves M.E. and M. Santamaría (Eds). Informe nacional sobre el avance en el conocimiento y la información de la biodiversidad 1998 -2004. Instituto de Investigación de Recursos Biológicos Alexander von Humboldt. Bogotá D.C., Colombia. 2 Tomos. ISBN 958-8151-78-3
  5. Duque G., J. Garzón-Ferreira, and A. Rodríguez Ramírez. 2006. Funcionamiento y monitoreo de ecosistemas marinos. Tomo II. pp 352-364. In: Chaves M.E. and M. Santamaría (Eds). Informe nacional sobre el avance en el conocimiento y la información de la biodiversidad 1998-2004. Instituto de Investigación de Recursos Biológicos Alexander von Humboldt. Bogotá D.C., Colombia. 2 Tomos. ISBN 958-8151-78-3
  6. Garzón Ferreira J. (15 authors included  A. Rodríguez-Ramírez). 2006. SIMAC: Vigilando nuestros arrecifes coralinos. pp 72-73. In: 70 casos de investigación científica, tecnológica e innovación en Colombia 1990-2004. COLCIENCIAS, Bogotá, Colombia. ISBN 958-8290-13-9.
  7. Garzón-Ferreira J., J. Cortés, A. Croquer, H. Guzmán, Z. Leao, and  A. Rodríguez-Ramírez. 2004. Southern Tropical America: coral reef status and consolidation as GCRMN regional node. V2: pp 509-522. In: Wilkinson C. (Ed). Status of coral reefs of the world: 2004. AIMS, Townsville, Queensland, Australia. ISSN 1447-6185.
  8. Andrade A. (33 authors included A. Rodríguez-Ramírez). 2004. Ecosistemas. pp 105-216. In: Costa C. and C.A. Buitrago (Eds.): Informe anual sobre el estado del medio ambiente y los recursos naturales renovables de Colombia. IDEAM, Bogotá, Colombia.
  9. Rodríguez-Ramírez A. 2003. Peces bentónicos asociados a praderas de Thalassia testudinum en Isla Grande e Isla Rosario. pp 106-110. In: Díaz J.M., L.M Barrios., and D.I. Gómez-López (Eds). 2003. Las praderas de pastos marinos en Colombia: Estructura y distribución de un ecosistema estratégico. INVEMAR, Serie de publicaciones especiales No.10, Santa Marta, Colombia. ISBN 958-97301-9-5.
  10. Garzón-Ferreira J. and A. Rodríguez-Ramírez. 2003. Diez años de monitoreo en una pradera de Thalassia. pp 71-74. In: Díaz J.M., L.M Barrios., and D.I. Gómez-López (Eds). Las praderas de pastos marinos en Colombia: Estructura y distribución de un ecosistema estratégico. INVEMAR, Serie de Publicaciones Especiales No.10, Santa Marta, Colombia. ISBN 958-97301-9-5.
  11. Garzón-Ferreira J., J. Cortés, A. Croquer, H. Guzmán, Z. Leao, and A. Rodríguez-Ramírez. 2002. Status of coral reefs in Southern Tropical America in 2000-2002: Brazil, Colombia, Costa Rica, Panama and Venezuela. pp 343-348. In: Wilkinson C. (Ed). Status of coral reefs of the World: 2002. AIMS, Townsville. ISSN 1447-6185.
  12. Garzón-Ferreira J., J. Cortés, A. Croquer, H. Guzmán, Z. Leao, and A. Rodríguez-Ramírez. 2000. Status of coral reefs in Southern Tropical America: Brazil, Colombia, Costa Rica, Panama and Venezuela. pp 331-348. In: Wilkinson C. (Ed). Status of Coral Reefs of the World: 2000. AIMS, Townsville. ISBN 0642322090.


Conference Papers 

  1. Rodríguez-Ramírez A., M.C. Reyes-Nivia, R. Navas-Camacho, S. Bejarano, J. Garzón-Ferreira, and F.A. Zapata. 2006. Status of the coral reefs of Colombia in 2003. Proc. 10th Int. Coral Reef Symp., 976-981.
  2. CARICOMP (42 authors included A. Rodríguez-Ramírez). 2002. Status and temporal trends at CARICOMP coral reef sites. Proc. 9th Int. Coral Reef Symp.,1:325-330
  3. CARICOMP (22 authors included A. Rodríguez-Ramírez). 1997. Meteorological and oceanographic characterization of coral reef, seagrass and mangrove habitats in the Winder Caribbean. Proc. 8th Int. Coral Reef Symp., 1:657-662.
  4. CARICOMP (30 authors included A. Rodríguez-Ramírez). 1997. Studies on Caribbean coral bleaching, 1995-96. Proc. 8th Int. Coral Reef Symp., 1:673-678.
  5. Torres D., A. Rodríguez-Ramírez, L.S. Mejía, and C.A. Buitrago. 1992. Las comunidades del bajo arrecifal profundo Imelda, Isla Barú, Caribe colombiano: VII. Evaluación preliminar de la ictiofauna. Memorias del VIII seminario de ciencias y tecnologías del mar, 350-361.


Technical reports 

  1. CARICOMP (33 authors included A. Rodríguez-Ramírez). 2004. Caribbean Coastal Marine Productivity Program. 1993-2003. CARICOMP, 91pp. ISBN 97-66106-24-X
  2. Garzón-Ferreira J, M.C. Reyes-Nivia, and A. Rodríguez-Ramírez. 2002. Manual de métodos del SIMAC. INVEMAR, Santa Marta, Colombia, 102pp.
  3. Friedlander et al. (Several authors included A. Rodríguez-Ramírez). 2014. Colombia. pp 191-201. In: Jackson et al. (Eds.). Status and trends of Caribbean coral reefs: 1970-2012. GCRMN, IUCN, Gland, Switzerland.