Biodiversity conservation relies upon accurate species taxonomy to support decision-making. Stony corals in the genus Pocillopora are critical ecosystem engineers in the Eastern Tropical Pacific (ETP); however, Pocillopora species diversity in the region is still unresolved due to high phenotypic plasticity, lack of diagnostic morphological characters, and low-resolution genetic markers used in previous studies. To address this gap, we leveraged low-coverage whole-genome sequencing for 342 Pocillopora coral samples collected from Panamá, Costa Rica, Colombia, Ecuador, and Clipperton Atoll (France). Sequence data were used to recover mitochondrial genomes and barcode loci, ultraconserved elements, and genome-wide single-nucleotide polymorphisms (SNPs) for species delimitation. Together, our data revealed the existence of four distinct Pocillopora species in the ETP, corresponding to the nominal species P. effusa (Veron, 2000), P. meandrina Dana, 1846, P. capitata Verrill, 1864, and P. lacera Verrill, 1869. Two P. capitata population subclusters with moderate genetic differentiation were separated between offshore islands and continental sites, and individual colonies with signatures of admixture between P. effusa and P. lacera were identified at Isla del Coco, Costa Rica. Additionally, Pocillopora-associated algal symbiont community profiling identified Cladocopium and Durusdinium as dominant genera that varied according to the host species, with P. lacera demonstrating higher specificity for associations with Cladocopium. This study highlights the power of genome skimming as an affordable, high-resolution approach to rapidly assess coral species diversity and algal symbiont associations, thereby empowering marine conservation.
@article{Connelly_2026,author={Connelly, MT and Glynn, VM and Cornejo, A and Villalobos-Cubero, T and Kleypas, J and Alvarado, JJ and Brandt, M and Logan, CA and Palacio-Castro, AM and Flot, J-F and Leray, M and Connolly, SR and Quattrini, AM},title={Genome Skimming Illuminates Hidden Species Diversity and Symbiodiniaceae Associations in East Pacific <i>Pocillopora</i> Corals},journal={Genome Biology and Evolution},abbr={Genome Biol. Evol},volume={18},number={2},year={2026},doi={10.1093/gbe/evaf235},html={https://doi.org/10.1093/gbe/evaf235}}
2025
Aquat. Geochem
Statistical prediction of in situ coral reef carbonate dynamics using endmember chemistry, hydrodynamic models, and benthic composition
HK Hirsh , TA Oliver , T Dobbelaere , AM Palacio-Castro , and 4 more authors
@article{hirsh_2025,title={Statistical prediction of in situ coral reef carbonate dynamics using endmember chemistry, hydrodynamic models, and benthic composition},author={Hirsh, HK and Oliver, TA and Dobbelaere, T and Palacio-Castro, AM and Barkley, HC and Webb, AE and Hanert, E and Enochs, IC},journal={Aquatic Geochemistry},abbr={Aquat. Geochem},volume={31},number={4},html={https://link.springer.com/article/10.1007/s10498-025-09438-x},doi={10.1007/s10498-025-09438-x},language={en},urldate={2025-02-26},year={2025}}
Genotypes of Acropora cervicornis in Florida show resistance to either elevated nutrients or disease, but not both in combination
AM Palacio-Castro , D Kroesche , IC Enochs , C Kelble , and 3 more authors
@article{PalacioResistada2025,title={Genotypes of <i>Acropora cervicornis</i> in Florida show resistance to either elevated nutrients or disease, but not both in combination},author={Palacio-Castro, AM and Kroesche, D and Enochs, IC and Kelble, C and Smith, I and Baker, AC and SM, Rosales},journal={PLOS One},volume={31},number={1},issn={1380-6165},html={https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0320378},doi={10.1371/journal.pone.0320378},code={https://github.com/anampc/Acer_NH4_disease},year={2025},}
Elevated temperature decreases stony coral tissue loss disease transmission, with little effect of nutrients
AM Palacio-Castro , N Soderberg , Z Zagon , K Cooke , and 5 more authors
@article{PalacioCastro2025_SCTLD,title={Elevated temperature decreases stony coral tissue loss disease transmission, with little effect of nutrients},author={Palacio-Castro, AM and Soderberg, N and Zagon, Z and Cooke, K and Studivan, MS and Gill, T and Kelble, C and Christian, T and Enochs, IC},journal={Scientific Reports},volume={15},number={1},issn={1380-6165},html={https://doi.org/10.1038/s41598-025-06322-0},doi={10.1038/s41598-025-06322-0},code={https://github.com/anampc/SCTLD_environment},year={2025},}
Three-dimensional photogrammetry-based monitoring to enhance site-level carbonate budget assessments of coral reefs
JT Morris , CB Edwards , A Webb , H Barkley , and 10 more authors
@article{Morris2025_PBCB,title={Three-dimensional photogrammetry-based monitoring to enhance site-level carbonate budget assessments of coral reefs},author={Morris, JT and Edwards, CB and Webb, A and Barkley, H and Viehman, TS and Palacio-Castro, AM and Wong, M and Ramos-Rosado, A and Hirsh, HK and Besemer, N and Petrovic, V and Perry, CT and Simmons, KR and Enochs, IC},journal={Limnol Oceanogr Methods},html={https://doi.org/10.1002/lom3.70000},doi={10.1002/lom3.70000},code={https://doi.org/10.5281/zenodo.16578499},year={2025},}
Ecol. Evol
Differences in Molecular Responses to a Thermally Variable Preconditioning Treatment for Two Caribbean Coral Species
A DeMerlis , MS Studivan , K Wong , N Soderberg , and 15 more authors
@article{enochs_sequential_2024,title={Sequential {Treatment} {Application} {Robot} ({STAR}) for high-replication marine experimentation},author={Enochs, IC and Soderberg, N and Palacio-Castro, AM and Eaton, K},volume={18},journal={HardwareX},issn={24680672},html={https://doi.org/10.1016/j.ohx.2024.e00524},code={https://github.com/ienochs/STARSystem},doi={10.1016/j.ohx.2024.e00524},year={2024},pages={e00524},}
Rubble Persistence under Ocean Acidification threatened by accelerated bioerosion and lower-density coral skeletons
AE Webb , AM Palacio-Castro , K Cooke , K Eaton , and 9 more authors
@article{Webb2024stones,title={Rubble Persistence under Ocean Acidification threatened by accelerated bioerosion and lower-density coral skeletons},author={Webb, AE and Palacio-Castro, AM and Cooke, K and Eaton, K and Chomitz, B and Soderberg, N and Chakraborty, M and Zagon, Z and Boyd, A and Kiel, PM and DeMerlis, A and Perry, CT and Enochs, IC},journal={Global Change Biology},volume={30},number={6},year={2024},abbr={GCB},html={https://doi.org/10.1111/gcb.17371},pdf={2024_Webb_GCB.pdf}}
Sediment source and dose influence the larval performance of the threatened coral Orbicella faveolata
XM Serrano , SM Rosales , MW Miller , AM Palacio-Castro , and 3 more authors
@article{serrano_sediments_2024,title={Sediment source and dose influence the larval performance of the threatened coral <i>Orbicella faveolata</i>},author={Serrano, XM and Rosales, SM and Miller, MW and Palacio-Castro, AM and Williamson, OM and Gomez, A and Baker, AC},journal={PLOS One},volume={19},number={6},html={https://doi.org/10.1371/journal.pone.0292474},code={https://anampc.github.io/Sediments_Larvae/},year={2024},}
2023
Coral disease outbreak at the remote Flower Garden Banks, Gulf of Mexico
MA Johnston , MS Studivan , IC Enochs , A Correa , and 7 more authors
@article{johnston2023coral,title={Coral disease outbreak at the remote Flower Garden Banks, Gulf of Mexico},author={Johnston, MA and Studivan, MS and Enochs, IC and Correa, A and Besemer, N and Eckert, RJ and Edwards, K and Hannum, R and Hu, X and Nuttall, M and others},journal={Frontiers in Marine Science},volume={10},pages={100},year={2023},publisher={Frontiers},abbr={Front. mar. sci.},html={https://doi.org/10.3389/fmars.2023.1111749}}
Increased dominance of heat-tolerant symbionts creates resilient coral reefs in near-term ocean warming
AM Palacio-Castro , TB Smith , V Brandtneris , GA Snyder , and 6 more authors
Proceedings of the National Academy of Sciences, 2023
@article{palacio2023increased,title={Increased dominance of heat-tolerant symbionts creates resilient coral reefs in near-term ocean warming},author={Palacio-Castro, AM and Smith, TB and Brandtneris, V and Snyder, GA and van Hooidonk, R and Mat{\'e}, JL and Manzello, D and Glynn, PW and Fong, P and Baker, AC},journal={Proceedings of the National Academy of Sciences},volume={120},number={8},pages={e2202388120},year={2023},publisher={National Academy of Sciences},abbr={PNAS},html={https://doi.org/10.1073/pnas.2202388120},pdf={2023_PNAS.pdf},}
@article{connelly2023antibiotics,title={Antibiotics reduce <i>Pocillopora</i> coral-associated bacteria diversity, decrease holobiont oxygen consumption and activate immune gene expression},author={Connelly, Michael T and Snyder, Grace and Palacio-Castro, AM and Gillette, PR and Baker, AC and Traylor-Knowles, N},journal={Molecular Ecology},year={2023},abbr={Mol. Ecol},html={https://doi.org/10.1111/mec.17049},pdf={2023_Molecular Ecology.pdf}}
Comparación de tres métodos para el estudio de las comunidades bentónicas sésiles en arrecifes coralinos
AM Palacio Castro , and FA Zapata
In BUCEO CIENTÍFICO: Procedimientos y metodologı́as , 2023
@incollection{palacio2023comparacion,title={Comparaci{\'o}n de tres m{\'e}todos para el estudio de las comunidades bent{\'o}nicas s{\'e}siles en arrecifes coralinos},author={Palacio Castro, AM and Zapata, FA},booktitle={BUCEO CIENT{\'I}FICO: Procedimientos y metodolog{\'\i}as},pages={221},year={2023},html={https://www.accefyn.org.co/2023/Publicaciones-recientes-de-los-Academicos/Manual-de-buceo.pdf#page=221},pdf={2023_ManualBuceo_Cap_18.pdf},code={https://anampc.github.io/Metodos_Cobertura/}}
Coral Reef Carbonate Chemistry Reveals Interannual, Seasonal, and Spatial Impacts on Ocean Acidification Off Florida
AM Palacio-Castro , IC Enochs , N Besemer , A Boyd , and 8 more authors
@article{palacio2023coral,title={Coral Reef Carbonate Chemistry Reveals Interannual, Seasonal, and Spatial Impacts on Ocean Acidification Off Florida},author={Palacio-Castro, AM and Enochs, IC and Besemer, N and Boyd, A and Jankulak, M and Kolodziej, G and Hirsh, HK and Webb, AE and Towl, E K and Kelble, C and Smith, I and others},journal={Global Biogeochemical Cycles},volume={37},number={12},year={2023},abbr={GBC},html={https://doi.org/10.1029/2023GB007789},pdf={2023_Global Biogeochemical Cycles.pdf},code={https://anampc.github.io/FLK_2021/}}
2022
Microbiome signatures in Acropora cervicornis are associated with genotypic resistance to elevated nutrients and heat stress
AM Palacio-Castro , SM Rosales , CE Dennison , and AC Baker
@article{palacio2022microbiome,title={Microbiome signatures in <i>Acropora cervicornis</i> are associated with genotypic resistance to elevated nutrients and heat stress},author={Palacio-Castro, AM and Rosales, SM and Dennison, CE and Baker, AC},journal={Coral Reefs},pages={1--15},year={2022},publisher={Springer},abbr={Coral Reefs},html={https://doi.org/10.1007/s00338-022-02289-w},pdf={2022_Coral Reefs.pdf},code={https://github.com/anampc/Nutrients_Genotypes}}
2021
Variation in susceptibility among three Caribbean coral species and their algal symbionts indicates the threatened staghorn coral, Acropora cervicornis, is particularly susceptible to elevated nutrients and heat stress
AM Palacio-Castro , CE Dennison , SM Rosales , and AC Baker
@article{palacio2021variation,title={Variation in susceptibility among three Caribbean coral species and their algal symbionts indicates the threatened staghorn coral, <i>Acropora cervicornis</i>, is particularly susceptible to elevated nutrients and heat stress},author={Palacio-Castro, AM and Dennison, CE and Rosales, SM and Baker, AC},journal={Coral Reefs},volume={40},number={5},pages={1601--1613},year={2021},publisher={Springer Nature},abbr={Coral Reefs},html={https://link.springer.com/article/10.1007/s00338-021-02159-x},pdf={2021_Coral Reefs.pdf},code={https://github.com/anampc/NutrientsHeat_Caribbean}}
2020
Increased algal symbiont density reduces host immunity in a threatened Caribbean coral species, Orbicella faveolata
LE Fuess , AM Palacio-Castro , CC Butler , AC Baker , and 1 more author
@article{fuess2020increased,title={Increased algal symbiont density reduces host immunity in a threatened Caribbean coral species, <i>Orbicella faveolata</i>},author={Fuess, LE and Palacio-Castro, AM and Butler, CC and Baker, AC and Mydlarz, LD},journal={Frontiers in Ecology and Evolution},volume={8},pages={369},year={2020},publisher={Frontiers},abbr={Front. ecol. evol.},html={https://doi.org/10.3389/fevo.2020.572942}}
Coral reef resilience to thermal stress in the Eastern Tropical Pacific
M Romero-Torres , A Acosta , AM Palacio-Castro , EA Treml , and 3 more authors
@article{romero2020coral,title={Coral reef resilience to thermal stress in the Eastern Tropical Pacific},author={Romero-Torres, M and Acosta, A and Palacio-Castro, AM and Treml, EA and Zapata, FA and Paz-Garc{\'\i}a, DA and Porter, JW},journal={Glob Chang Biol},volume={26},number={7},pages={3880--3890},year={2020},abbr={GCB},html={https://doi.org/10.1111/gcb.15126},pdf={2020_GCB.pdf}}
2019
Abiotic controls on endosymbiotic algal communities and their implications for coral bleaching susceptibility and recovery
@phdthesis{palacio2019abiotic,title={Abiotic controls on endosymbiotic algal communities and their implications for coral bleaching susceptibility and recovery},author={Palacio-Castro, Ana M},year={2019},school={University of Miami},abbr={UM},html={https://www.proquest.com/openview/c2c679c4f958b73926b337474ab8e96e/1?pq-origsite=gscholar&cbl=18750&diss=y}}
2017
Source location and food availability determine the growth response of Orbicella faveolata to climate change stressors
EK Towle , AM Palacio-Castro , AC Baker , and C Langdon
@article{towle2017source,title={Source location and food availability determine the growth response of <i>Orbicella faveolata</i> to climate change stressors},author={Towle, EK and Palacio-Castro, AM and Baker, AC and Langdon, C},journal={Regional studies in marine science},volume={10},pages={107--115},year={2017},publisher={Elsevier},abbr={Reg. Stud. Mar. Sci},html={https://doi.org/10.1016/j.rsma.2017.01.007},pdf={2017_Regional Studies.pdf}}
