Publications

Symbols represent: ^Equal contribution; *Graduate student; §Undergraduate student 

2025

• Tracy CB, CF Arias, E Tysall, MP Hoeppner, WO McMillan, O Puebla, and MA Bernal (2025). Comparative Genomics of Transisthmian Damselfishes (Abudefduf saxatilis and A. troschelii). bioRxiv, 2025-07. https://www.biorxiv.org/content/10.1101/2025.07.17.665425v1.abstract

• Bernal MA, Aguilar GL*, Sakmar J, Politis SN, Oglesby SL§, Nicholls A, Kelly AM, Roy LA, and IAE Butts. 2025. Transcriptome analyses reveal differences in the response to temperature in Florida and Northern largemouth bass (Micropterus spp.) during early life stages. PLOSOne 20, e0317563. 

2024

• Backenstose NJC, DJ MacGuigan, CA Osborne, MA Bernal, EK Thomas, E Normandeau, DL Yule, W Stott, AS Ackiss, VA Albert, L Bernatchez, and TJ Krabbenhoft. 2024. Origin of the Laurentian Great Lakes fish fauna through upward adaptive radiation cascade prior to the Last Glacial Maximum. Communications Biology 7: 978. doi: https://doi.org/10.1038/s42003-024-06503-z

• Lotterhos KE^, MA Bernal^, Phifer-Rixey M^, Hanley T^. 2024. Lighting pathways to success in STEM: a virtual Laboratory Meeting Programme (LaMP) mutually benefits mentees and host laboratories. Proceedings of the Royal Society B 291. doi: https://doi.org/10.1098/rspb.2024.0149

• Eaton KM*, TJ Krabbenhoft, NJC Backenstose, and MA Bernal. 2024 The chromosome-scale reference genome for the pinfish (Lagodon rhomboides) provides insights into their evolutionary and demographic history. G3: Genes, Genomes, Genetics 14. doi: https://doi.org/10.1093/g3journal/jkae096

• Swank AR*, CB Tracy*, MT Mendonça, and MA Bernal. 2024. Molecular plasticity to ocean warming and habitat loss in a coral reef fish. Journal of Heredity, esae024.  doi: https://doi.org/10.1093/jhered/esae024

2023

• Waldo B§^, K Moore§^, S Bickley*, CJ Anderson, and MA Bernal. 2023. Salinity fluctuations due to urbanization of coastal environments and their potential effect on the genetic divergence of the Gulf killifish (Fundulus grandis). Environmental Biology of Fishes 106: 1539-1550. doi: https://doi.org/10.1007/s10641-023-01433-x

• Aguilar GL, J Sakmar, A Nicholls, MK Litvak, HN Hess, TJ Bruce, HR Montague, AM Kelly, LA Roy, MA Bernal, SN Politis, and IAE Butts. 2023. Effects of temperature and subspecies during critical early life history stages of largemouth bass (Micropterus salmoides). Aquaculture 570: 739350. doi: https://doi.org/10.1016/j.aquaculture.2023.739350

• Hallaj A^, L Turner*^, C McArdle§, and MA Bernal. 2023. De novo transcriptomes for two species of snappers from the Western Atlantic (Lutjanus griseus and Lutjanus synagris). Marine Genomics 67:1-4. doi: https://doi.org/10.1016/j.margen.2022.101005

• Dornburg A, R Mallik, Z Wang, MA Bernal, B Thompson, EA Bruford, DW Nebert, V Vasiliou, LR Yohe, JA Yoder, and JP Townsend. 2023. Placing human gene families into their evolutionary context. Human Genomics 16:1-26. doi: https://doi.org/10.1186/s40246-022-00429-5

2022

• Ramírez-Castañeda, et al. (32 coauthors including MA Bernal). 2022. A set of principles and practical suggestions for equitable fieldwork in biology. PNAS. https://doi.org/10.1073/pnas.2122667119

• Bernal MA, DL Yule, W Stott, L Evrard, T Dowling, and TJ Krabbenhoft. 2022. Concordant patterns of morphological, stable isotope and genetic variation in a recent ecological radiation (Salmonidae: Coregonus spp.). Molecular Ecology 31, 4495-4509. doi: https://doi.org/10.1111/mec.16596

• Chan SKN, S Suresh, P Munday, T Ravasi, MA Bernal, and C Schunter. 2022. The alternative splicing landscape of a coral reef fish during a marine heatwave. Ecology and Evolution. https://pubmed.ncbi.nlm.nih.gov/35342554/

• Bernal MA, E Schmidt, JM Donelson, PM Munday, and T Ravasi. 2022. Molecular responses of brains to cross-generational warming in a coral reef fish. Frontiers in Marine Science. https://doi.org/10.3389/fmars.2022.784418

• Bernal MA, T Ravasi, GG Rodgers PM Munday, JM Donelson. 2022. Plasticity to ocean warming is influenced by transgenerational, reproductive, and developmental exposure in a coral reef fish. Evolutionary Applications. https://doi.org/10.1111/eva.13337

• Eaton KM*, A Hallaj, JA Stoeckel, MA Bernal. 2022. Ocean warming leads to increases in aerobic demand and changes to gene expression in the pinfish (Lagodon rhomboides).  Frontiers in Ecology and Evolution. https://doi.org/10.3389/fevo.2021.809375

2021

• Turner L*, NJ Backenstose, SJ Brandl, MA Bernal. 2021. Range expansion and complete mitochondrial genome of the highfin blenny (Lupinoblennius nicholsi). Molecular Biology Reports. https://doi.org/10.1007/s11033-021-06932-7

• Pelosi J, MA Bernal, TJ Krabbenhoft, S Galbo, C Prada, MA Coffroth, HR Lasker. 2021. Fine-scale genomic, morphological, reproductive, and symbiont differences delimit the Caribbean octocorals Plexaura homomalla and P. kükenthali. Coral Reefs. https://doi.org/10.1371/journal.pone.0030410

2020

• Eaton KM*, MA Bernal, NJ Backenstose, and TJ Krabbenhoft. 2020. Nanopore amplicon sequencing reveals molecular convergence and local adaptation of opsin genes. Genome Biology and Evolution. evaa237, https://doi.org/10.1093/gbe/evaa237. Cover of Volume 13. 

• Bernal MA^, CM Schunter^, R Lehmann, D Lightfood, B Gibbs, H. Veilleux, J Rummer, P Munday and T Ravasi. 2020. Molecular Responses of Coral Reef Fishes to a Marine Heatwave. Science Advances. eaay3423, https://doi.org/10.1126/sciadv.aay3423. *Denotes equal contribution. Press coverage by: KAUST discovery, Eureka Alert, Phys.org, SciMex, James Cook University 

• Salas E, JP Hobbs, MA Bernal, WB Simison, ML Berumen, G Bernardi, and LA Rocha. 2020. Distinct patterns of cryptic hybridization across a suture zone in a coral reef fish (Dascyllus trimaculatus). Ecology and Evolution. doi.org/10.1002/ece3.6068

2019

• Bernal MA, GB Dixon, MV Matz and LA Rocha. PeerJ. Comparative transcriptomics of sympatric species of coral reef fishes (genus: Haemulon). e6541. doi: 10.7717/peerj.6541 

• WB Ludt, Bernal MA, E Kenworthy, E Salas and P Chakrabarty. 2019. Investigating species limits of vagile surgeonfishes of the Eastern Pacific (Acanthuridae: Prionurus). Ecology and Evolution 9, 4001-4012. doi: 10.1002/ece3.5029 

• Schunter C, R Lehmann, MA Bernal and T Ravasi. 2019. Unusual bilateral color pattern in a regal angelfish from the Red Sea. Bulletin of Marine Science 95, 113-1. 

2018

• Bernal MA, Donelson JM, Veilleux HD, Ryu T, Munday PL and Ravasi T. 2018. Phenotypic and molecular consequences of step-wise temperature increase across generations in a coral reef fish. Molecular Ecology. doi:10.1111/mec.14884. Press coverage by: La Prensa Panamá

• Crandall ED, RJ Toonen, ToBo Laboratory‡ and KA Selkoe. 2018. A coalescent sampler successfully detects biologically meaningful population structure overlooked by F‐statistics. Evolutionary Applications. doi:10.1111/eva.12712 ‡Group of 18 collaborators including MA Bernal.

2017

• Bernal MA, MR Gaither, B Simison and LA Rocha. 2017. Introgression and selection shaped the evolutionary history of sympatric sister species of coral-reef fishes (genus: Haemulon). Molecular Ecology 26:639–652. doi:10.1111/mec.13937 

2016

• Selkoe KA, OE Gaggiotti, EA Treml, JL Wren, MK Donovan, Hawai‘i Reef Connectivity Consortium§ and RJ Toonen. 2016. The DNA of coral reef biodiversity: predicting and protecting genetic diversity of reef assemblages. Proceedings of the Royal Society B 283. doi:1098/rspb.2016.0354. §Group of 31 collaborators including MA Bernal 

2015

• Gaither MR, MA Bernal, I Fernandez-Silva, M Mwale, SA Jones, C Rocha and LA Rocha. 2015. Two deep evolutionary lineages in the circumglobal Glasseye, Heteropriacanthus cruentatus (Teleostei, Priacanthidae) with admixture in the Western Indian Ocean. Journal of Fish Biology 87:715-727. doi:10.1111/jfb.12754

• Sellas AB, K Bassos-Hull, JC Perez-Jimenez, JA Angulo-Valdes, MA Bernal and RE Hurt. 2015. Population structure and seasonal migration of the spotted eagle ray, Aetobatus narinari. Journal of Heredity 106:266-275. doi: 10.1093/jhered/esv011

• Bernal MA, SR Floeter, MR Gaither, GO Longo, R Morais, CEL Ferreira, MJA Vermeij and LA Rocha. 2015. High prevalence of dermal parasites among coral reef fishes of Curacao. Marine Biodiversity. doi: 10.1007/s12526-015-0322-z

• Gaither MR, MA Bernal, R Coleman, B Bowen, S Jones, WB Simison and LA Rocha. 2015. Genomic signatures of geographic isolation and natural selection in coral reef fishes. Molecular Ecology. doi: 10.1111/mec.13129. Cover of the issue. Press coverage by Molecular Ecologist

2014

• Selkoe KA, OE Gaggiotti, ToBo Laboratory‡, BW Bowen, RJ Toonen. 2014. Emergent patterns of population genetic structure for a coral reef community. Molecular Ecology 23, 3064-3079. doi: 10.1111/mec.12804. ‡Group of 19 collaborators including MA Bernal. 

• Bernal MA, NL Sinai, C Rocha, MR Gaither, F Dunker and LA Rocha. 2014. Long-term sperm storage in the Brownbanded Bamboo Shark Chiloscyllium punctatum Müller & Henle, 1838 (Chondrichthyes: Hesmiscyliidae). Journal of Fish Biology 86(3): 1171-1176. doi: 10.1111/jfb.12606. Press coverage by: Scientific American, BBC Earth, California Academy of Sciences, Washington Post, Science Codex, Phys.org, Yakima Herald, IOLscitech, IFLS, Scienceblog.com, The Earth Times.

2013-2011

• Rocha LA, MA Bernal, MR Gaither and ME Alfaro. 2013. Massively parallel DNA sequencing: the new frontier in biogeography. Frontiers of Biogeography 5.1

• Ludt W, MA Bernal, BW Bowen and LA Rocha. 2012. Living in the Past: Phylogeography and Population Histories of Indo-Pacific Wrasses (genus Halichoeres) in Shallow Lagoons versus Outer Reef Slopes. PLoS One  7(6): e38042. doi: 10.1371/journal.pone.0038042 

• Jones FA, DL Erickson, MA Bernal, E Bermingham, WJ Kress, EA Herre, HC Muller-Landau and BL Turner. 2011. The roots of diversity: below ground richness and rooting distributions in a tropical forest revealed by DNA barcodes and inverse modeling. PLoS One 6(9): e24506. doi: 10.1371/journal.pone.0024506

• Bernal MA and LA Rocha. 2011 Acanthurus tractus Poey, 1860, a valid Western Atlantic species of surgeonfish (Teleostei, Acanthuridae), distinct from Acanthurus bahianus Castelnau, 1855. Zootaxa 2905: 63–68

Non-Peer Reviewed: 

• Bernal MA and LA Rocha. 2012. Speciation with gene flow in coral reef fishes? Proceedings of the American Academy of Underwater Sciences 31st Symposium: 114-118. ·      

• Bernal MA. 2008. Caracterización molecular de peces de arrecife del Archipiélago de Bocas del Toro utilizando códigos de barra de ADN mitochondrial. Undergradute Thesis, Universidad de Panamá.