Publications

Alvarado-Cerón, V., Gómez-Corrales, M., Padilla-Souza, A. C., León-Pech, M. G., Rivera-Madrid, R., Arias-González, J. E., & Prada, C. (2025). Genomic insights into natural and restored populations of Acropora palmata: Implications for genetic diversity and conservation strategies. Marine Environmental Research, 107779. https://doi.org/10.1016/j.marenvres.2025.107779

Neely, K. L., Nowicki, R. J., Dobler, M. A., Toth, K. A., Macaulay, K. A., & Gallagher, S. M. (2025). Survival and reinfection rates of SCTLD-affected corals treated in situ with amoxicillin. Frontiers in Marine Science, 12. https://doi.org/10.3389/fmars.2025.1649646

Whitall, D., Williams, G. J., Aeby, G. S., Davies, A., Spring, D. L., & Walker, B. K. (2025). Terrestrial runoff and meteorology drive changes in coral reef water quality in southeast Florida. Marine Ecology Progress Series. https://doi.org/10.3354/meps14988

Ladd, M. C., Shantz, A. A., Harborne, A. R., Bauman, A. G., & Duran, A. (2025). The rise of long-sediment-laden algal turfs: An additional negative feedback process limiting reef resilience. Coral Reefs. https://doi.org/10.1007/s00338-025-02796-6

Gómez-Corrales, M., González Angel, A. M., Kamel, B., Medina, M., Knowlton, N., Levitan, D. R., & Prada, C. (2025). Speciation across depth gradients in reef corals. Nature Communications, 16(1), 10153. https://doi.org/10.1038/s41467-025-65226-9

Steindler, L., Durán Canché, M. A., Ilan, M., Bar-Shalom, R., Lopez, J. V., Hentschel, U., Oatley, G., Sinclair, E., Aunin, E., Gettle, N., Santos, C., Paulini, M., Niu, H., McKenna, V., O’Brien, R., Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory Team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, & Aquatic Symbiosis Genomics Project Leadership. (2025). The chromosomal genome sequence of the marine sponge Diacarnus erythraeanus Kelly-Borges & Vacelet, 1995, and its associated microbial metagenome sequences. Wellcome Open Research, 10, 466. https://doi.org/10.12688/wellcomeopenres.24763.1

Hirose, E., Lopez, J.V., Oatley, G., Sinclair, E., Aunin, E., Santos, C., Paulini, M., Niu, H., McKenna, V., O'Brien, R., Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory Team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. (2025). The chromosomal genome sequence of the photosymbiotic ascidian, Trididemnum clinides Kott, 1977 and its associated microbial metagenome sequences. Wellcome Open Research, 10, 357. https://doi.org/10.12688/wellcomeopenres.24563.1

Liberman, R., Hiley, A., Huebner, L. K., Colella, M. A., Ruzicka, R. R., Gilliam, D. S., & Jones, N. P. (2025). Octocoral dynamics over a decade on Florida’s coral reef. Scientific Reports, 15(1), 37635. https://doi.org/10.1038/s41598-025-21610-5

Manzello, D. P., Cunning, R., Karp, R. F., Baker, A. C., Bartels, E., Bonhag, R., Borreil, A., Bourque, A., Brown, K. T., Bruckner, A. W., Corbett, B., D’Alessandro, M., Dahlgren, C., Dilworth, J., Geiger, E., Gilliam, D. S., Gomez, M., Hanson, G., Harrell, C., … Williamson, O. M. (2025). Heat-driven functional extinction of Caribbean Acropora corals from Florida’s Coral Reef. https://doi.org/10.1126/science.adx7825

Chamberland V.F., Gómez-Corrales M., Marhaver K. L., Bongaerts P., Latijnhouwers K.R.W., Vergara-Flórez D.C., Snowden S., Sánchez J.A., Vermeij M. J. A. (2025). Discovery of Genetically Distinct,Sympatric Coral Lineages With Temporal but Not Gametic Reproductive Isolation. Molecular Ecology, n/a(n/a), e70138. https://doi.org/10.1111/mec.70138

Whitall, D., Williams, G. J., Aeby, G., Davies, A., Spring, D., & Walker, B. (Accepted/In press). Terrestrial runoff and meteorology drive changes in coral reef water quality in southeast Florida. Marine Ecology Progress Series. https://doi.org/10.3354/meps14988

Tardin, R., Maricato, G., Kiszka, J. J., Cantor, M., Maciel, I., Melo-Santos, G., May-Collado, L., Meirelles, A. C., Gonçalves, M. I. C., Daura-Jorge, F. G., Sousa-Lima, R. S., Le Pendu, Y., de Thoisy, B., Cremer, M. J., Simões-Lopes, P. C., Caballero, S., Rossi-Santos, M. R., Alves, M. A. S., Freitas, D. C., … Vale, M. M. (2025). Optimistic climate mitigation scenario halves projected range loss in a neotropical dolphin. Ocean & Coastal Management, 269, 107800. https://doi.org/10.1016/j.ocecoaman.2025.107800

Steel, D. J., Carroll, E. L., Baker, C. S., Caballero, S., Childerhouse, S., Corne, C., Garrigue, C., Gibbs, N., Kinsey, R., Ogle, M., Olavarría, C., Palacios, D., Poole, M. M., Rasmussen, K., Riekkola, L., Robbins, J., & Constantine, R. (2025). Genetic differentiation and population connectivity of humpback whales migrating through Aotearoa New Zealand waters. Pacific Conservation Biology, 31(5). https://doi.org/10.1071/PC25026

Toth, L. T., Johnson, S. A., Lyons, E. O., Spadaro, J., Stathakopoulos, A., Bloomer, S., Mallon, J., Jenkins, C. M., Williams, S. D., Combs, I., Craig, Z., & Muller, E. (2025). Coral restoration can drive rapid increases in reef accretion potential. Scientific Reports, 15(1), 28353. https://doi.org/10.1038/s41598-025-04818-3

Bernier-Graveline, A., Nash, S. B., Bierlich, K. C., Friedlaender, A., Johnston, D. W., Castrillon, J., Botero-Acosta, N., Caballero, S., & Christiansen, F. (n.d.). Drone-Based Photogrammetry Provides Estimates of the Energetic Cost of Migration for Humpback Whales Between Antarctica and Colombia. Marine Mammal Science, n/a(n/a), e70048. https://doi.org/10.1111/mms.70048

Neely, K. L., Morgan, R. M., O’Neil, K. L., Cox, N., Gilliam, D. S., Mair, M. B., Walker, B. K., Zummo, A., Harrell, C., & Ellis, A. (2025). Status of Florida’s pillar coral population: In situ declines and ex situ successes. Frontiers in Marine Science, 12. https://doi.org/10.3389/fmars.2025.1650422

Pitts, K. A., Scheuermann, M., Lefcheck, J. S., Ushijima, B., Danek, N., McDonald, E. M., Milanese, A. R., Schul, M. D., Meyer, J. L., Toth, K. A., Ferris, Z., De La Flor, Y. T., DeMarco, T., Noren, H. K. G., Walker, B. K., & Paul, V. J. (2025). Evaluating the effectiveness of field-based probiotic treatments for stony coral tissue loss disease in southeast Florida, USA. Frontiers in Marine Science, 12. https://doi.org/10.3389/fmars.2025.1480966

Dotson, K. W., Pisano, K., Gellman, E. R., Roman, P., & Lopez, J. V. (2025). Degradation of polyhydroxyalkanoate (PHA) drinking straws at an ocean shoreline. Journal of Environmental Chemical Engineering, 13(4), 117157. https://doi.org/10.1016/j.jece.2025.117157

Jones, N.P., Leinbach, S.E. & Gilliam, D.S. (2025) Interspecific variation in demographics reveals ecological winners and losers in a highly disturbed coral reef system. Coral Reefs. https://doi.org/10.1007/s00338-025-02681-2 

Figueiredo, J., Baird, A.H., Harii, S., & Connolly S.R. (2025) Predicting demography from species traits: larval development time and its sensitivity to warming depend on egg size in corals. Coral Reefs. https://doi.org/10.1007/s00338-025-02683-0.

Short, M.L., Close, H.G., Gilliam, D.S., & Figueiredo, J. (2025). A reproductive and trophic analysis of corals in a degraded environment. Coral Reefs 44, 967–982. https://doi.org/10.1007/s00338-025-02655-4.

Lopez J.V., Pomponi S.A., Hentschel U., Erpenbeck D., Pruzinksy N., Fiore C., Mulheron R., Oatley G., Sinclair E., Aunin E., Gettle N, Santos C., Paulini M., Niu H., McKenna V., & O'Brien R (2025). The chromosomal genome sequence of the giant barrel sponge, Xestospongia muta Schmidt 1870 and its associated microbial metagenome sequences. Wellcome Open Research, 10:336 https://doi.org/10.12688/wellcomeopenres.24173.1

Mallon, J. E., Altieri A. H., Cyronak, T., Melendez-Declet, C. V., Paul, V. J., & Johnson, M. D.  (2025). Sublethal changes to coral metabolism in response to deoxygenation. J Exp Biol 15 February 2025; 228 (4): JEB249638. doi: https://doi.org/10.1242/jeb.249638 

Mazurek, H.E., Neely, K.L., & Renegar, D.A. (2025). The impact of stony coral tissue loss disease and amoxicillin treatments on coral gametogenesis. Frontiers in Marine Science, 11. https://doi.org/10.3389/fmars.2024.1445735

Neely K.L., Whitehead R.F., Dobler M.A. (2024). The effects of disease lesions and amoxicillin treatment on the physiology of SCTLD-affected corals. Frontiers in Marine Science 11. https://doi.org/10.3389/fmars.2024.1460163  

Zamborain-Mason, J., Connolly, S.R., MacNeil, M.A., Barnes, M.L., Bauman, A.G., Feary, DA., Huertas, V., Januchowski-Hartley, F.A., Lau, J. D., Mihalitsis, M., & Cinner, J.E. (2025). Downscaling global reference points to assess the sustainability of local fisheries. Conservation Biology, n/a(n/a), e14440. https://doi.org/10.1111/cobi.14440

Neely, K. L., Nowicki, R. J., Dobler, M. A., Chaparro, A. A., Miller, S. M., & Toth, K. A. (2024). Too hot to handle? The impact of the 2023 marine heatwave on Florida Keys coral. Frontiers in Marine Science, 11. https://doi.org/10.3389/fmars.2024.1489273

Ladd, M. C., Shantz, A.A., Harrell, C., Hayes, N. K., Gilliam, D.S., Muller, E.M., O’Neil, K.L., Reckenbeil, B., Craig, Z., & Lirman, D. (2024). Acclimation and size influence predation, growth, and survival of sexually produced Diploria labyrinthiformis used in restoration. Scientific Reports, 14(1), 26362. https://doi.org/10.1038/s41598-024-73727-8

Sbragaglia, V., Cecapolli, E., Morroni, L., & Januchowski-Hartley, F.A. (2024). Advancing the understanding of spearfisher-fish behavioural interactions and its management implications. Journal of Applied Ecology, 61(11), 2594–2604. https://doi.org/10.1111/1365-2664.14796

Limer, B. D., Payne, O., Brancato, A., Mitchell, M., Abu-Kubie, C., Figueiredo, J., & Holstein, D. M. (2024). Life history and early ontogeny determine vertical swimming behaviors in the larvae of Caribbean corals. Journal of Experimental Marine Biology and Ecology, 578, 152035. https://doi.org/10.1016/j.jembe.2024.152035

Riegl, B., Bauman, A., Hadj-Hamou, J., & Burt, J. A. (2024). A decade of benthic changes on coral reefs in the Southern Persian/Arabian Gulf (2010–2020). Coral Reefs, 43(6), 1647–1657. https://doi.org/10.1007/s00338-024-02562-0

Díaz-Yayguaje, M., Caballero-Gaitan, S., & Valderrama-Aguirre, A. (2024). Unlocking epitope similarity: A comparative analysis of the American manatee (Trichechus manatus) IgA and human IgA through an immuno-informatics approach. PLOS ONE, 19(9), e0308396. https://doi.org/10.1371/journal.pone.0308396

Tezanos-Pinto, G., Bohorquez, L., Zaeschmar, J. R., Stockin, K., Carroll, E. L., & Caballero-Gaitán, S. (2025). Population structure and genetic diversity of false killer whales ( Pseudorca crassidens ) in New Zealand waters: Preliminary results. New Zealand Journal of Marine and Freshwater Research, 59(4), 670–684. https://doi.org/10.1080/00288330.2024.2353208

Gonzalez, C., Postaire, B., Driggers, W., Caballero, S., & Chapman, D. (n.d.). Sphyrna alleni sp. Nov., a new hammerhead shark (Carcharhiniformes, Sphyrnidae) from the Caribbean and the Southwest Atlantic. Retrieved September 12, 2025, from https://repository.library.noaa.gov/view/noaa/66984

Martinelli Marín, D., Lasso, C. A., & Caballero Gaitan, S. J. (2024). eDNA metabarcoding: An effective tool for vertebrate diversity studies in the Colombian Amazon and Orinoco basins. Frontiers in Ecology and Evolution, 12. https://doi.org/10.3389/fevo.2024.1409296

Laforest, K. V., Petrik, C. G., Hylton, A. A., Ionata, R. L., McDonald, E. M., Short, M. L., & Figueiredo, J. (2024). Induced sexual reproduction ex situ reveals bidirectional sex change of the coral Montastraea cavernosa. Coral Reefs. https://doi.org/10.1007/s00338-024-02546-0 

Whitall, D., Woodley, C., May, L., Karazsia, J., Serrano, X., Hayes, N., & Gilliam, D. (2024). Potential Impact of Dredging Activities at Port Everglades (Florida) on Coral Reef Communities: Assessment of the Threat of Sediment Associated Contaminants. https://repository.library.noaa.gov/view/noaa/61653

McGowen, M. R., Caballero, S., Flores, M. F. C., Murphy, K. R., Archer, F. I., Ayyagari, S., Beasley, I., Cohen, C. S., Dolar, M. L. L., Junchompoo, C., Kaewmong, P., Klinsawat, W., Kreb, D., Kuit, S. H., Robertson, K., Sabin, R., Sakornwimon, W., Smith, K. J., Teoh, Z. Y., … Hines, E. (2024). Range-wide phylogeographic structure of the endangered Irrawaddy dolphin (Orcaella brevirostris) using expanded sampling from contemporary and historical specimens. Marine Mammal Science, 40(4), e13159. https://doi.org/10.1111/mms.13159

Jones N.P. & Gilliam D.S. (2024). Spatial differences in recruit density, survival, and size structure prevent population growth of stony coral assemblages in southeast Florida. Frontiers in Marine Science, 11. https://www.frontiersin.org/articles/10.3389/fmars.2024.1369286

Renegar D.A., Noren H.K.G., Turner N.R., Figueiredo J., & Walker B.K. (2024). Southeast Florida large Orbicella faveolata are highly fecund without evident disease intervention effects. Frontiers in Marine Science, 11. https://doi.org/10.3389/fmars.2024.1369222

McGirl, M., Renegar, D. A., & Kerstetter, D. W. (2024). Extensive Microplastic Contamination in Southeastern Florida Forage Fishes. Caribbean Journal of Science, 54(1), 91–102. https://doi.org/10.18475/cjos.v54i1.a12

Jones N.P. & Gilliam D.S. (2024) Temperature and local anthropogenic pressures limit stony coral assemblage viability in southeast Florida. Marine Pollution Bulletin, 200:116098. https://doi.org/10.1016/j.marpolbul.2024.116098 

Grupstra, C.G.B., Gómez-Corrales, M., Fifer, J. E., Aichelman, H. E., Meyer-Kaiser, K. S., Prada, C., & Davies, S. W. (2024). Integrating cryptic diversity into coral evolution, symbiosis and conservation. Nature Ecology & Evolution, 8(4), 622–636. https://doi.org/10.1038/s41559-023-02319-y

Liberman R, Voolstra CR, Hume, BCC et al. (2024) Juvenile octocorals acquire similar algal symbiont assemblages across depths. Coral Reefs 43, 489–496. https://doi.org/10.1007/s00338-024-02470-3 

Toth, K. A., Buckley, S. F., Noren, H., Neely, K. L., & Walker, B. K. (2024). Broadscale coral disease interventions elicit efficiencies in endemic disease response. Frontiers in Marine Science, 10. https://doi.org/10.3389/fmars.2023.1302697

Klein, A. M., Sturm, A. B., Eckert, R. J., Walker, B. K., Neely, K. L., & Voss, J. D. (2024). Algal symbiont genera but not coral host genotypes correlate to stony coral tissue loss disease susceptibility among Orbicella faveolata colonies in South Florida. Frontiers in Marine Science, 11. https://doi.org/10.3389/fmars.2024.1287457