Publications
2024
Niche–dependent sponge hologenome expression profiles and the host-microbes interplay: a case of the hawaiian demosponge. Liu, F., Ryu, T., Ravasi, T. et al. Mycale Grandis. Environmental Microbiome 19, 22 (2024). 4/8/2024https://doi.org/10.1186/s40793-024-00563-8
Fish and coral assemblages of a highly isolated oceanic island: The first eDNA survey of the Ogasawara Islands, Ayşe Haruka Oshima Açıkbaş, Haruhi Narisoko, Roger Huerlimann, Koki Nishitsuji, Noriyuki Satoh, James Davis Reimer, Timothy Ravasi. Environmental DNA, 2/20/2024, https://doi.org/10.1002/edn3.509
Ecological generalism and physiology mediate fish biogeographic ranges under ocean warming. Chloe Hayes, Angus Mitchell, Camille Mellin, David J Booth, Timothy Ravasi, Ivan Nagelkerken. Proceedings of the Royal Society B 1/31/2024 https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2023.2206
Tissue-specific transcriptional response of post-larval clownfish to ocean warming. Billy Moore, Jeffrey Jolly, Michael Izumiyama, Erina Kawai, Timothy Ravasi, Taewoo Ryu, Science of the Total Environment. 1/15/2024. https://www.sciencedirect.com/science/article/pii/S0048969723068481
2023
High abundances of zooxanthellate zoantharians (Palythoa and Zoanthus) at multiple natural analogues: potential model anthozoans? James Davis Reimer, Sylvain Agostini, Yimnang Golbuu, Ben P Harvey, Michael Izumiyama, Emmeline A Jamodiong, Erina Kawai, Hajime Kayanne, Haruko Kurihara, Timothy Ravasi, Shigeki Wada, Riccardo Rodolfo-Metalpa. Coral Reefs. 2023/4/15, https://link.springer.com/article/10.1007/s00338-023-02381-9
Research priorities for the sustainability of coral-rich western Pacific seascapes. Graeme S Cumming, Maja Adamska, Michele L Barnes, Jon Barnett, et al. Regional Environmental Change. 2023/4/21 https://link.springer.com/article/10.1007/s10113-023-02051-0
Development of a real-time PCR (qPCR) method for the identification of the invasive paddle crab Charybdis japonica (Crustacea, Portunidae) Tiffany JS Simpson, Claire M Wellington, Sherralee S Lukehurst, Roger Huerlimann, Heather Veilleux, Michael Snow, Joana Dias, Justin I McDonald. PeerJ 6/12/2023. https://peerj.com/articles/15522/
Brain transcriptome of gobies inhabiting natural CO2 seeps reveal acclimation strategies to long‐term acidification Sneha Suresh, Alice Mirasole, Timothy Ravasi, Salvatrice Vizzini, Celia Schunter. Evolutionary Applications 6/15/2023. https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/eva.13574
The effects of climate change on the ecology of fishes Ivan Nagelkerken, Bridie JM Allan, David J Booth, Jennifer M Donelson, Graham J Edgar, Timothy Ravasi, Jodie L Rummer, Adriana Vergés, Camille Mellin. PLOS Climate. 8/7/2023. https://journals.plos.org/climate/article?id=10.1371/journal.pclm.0000258
Two new pygmy squids, Idiosepius kijimuna n. sp. and Kodama jujutsu n. gen., n. sp. (Cephalopoda: Idiosepiidae) from the Ryukyu Islands, Japan Amanda Reid, Noriyoshi Sato, Jeffrey Jolly, Jan Strugnell, Marine Biology. 10/21/2023 https://onlinelibrary.wiley.com/doi/full/10.1002/edn3.509
Sharks and their relatives: can their past help predict their future? Aaron Hasenei, Jennifer M Donelson, Timothy Ravasi, Jodie L Rummer. Frontiers in Marine Science. 11/1/2023 https://doi.org/10.3389/fmars.2023.1268532
Tissue-specific transcriptional response of post-larval clownfish to ocean warming. Billy Moore, Jeffrey Jolly, Michael Izumiyama, Erina Kawai, Timothy Ravasi, Taewoo Ryu. Science of the Total Environment.11/2/2023. https://www.sciencedirect.com/science/article/pii/S0048969723068481
Neuromolecular responses in disrupted mutualistic cleaning interactions under future environmental conditions S Ramírez-Calero, Jose Ricardo Paula, Eve Otjacques, Timothy Ravasi, Rui Rosa, Celia Schunter. BMC biology. 11/14/2023 https://link.springer.com/article/10.1186/s12915-023-01761-5
Research priorities for the sustainability of coral-rich western Pacific seascapes. GS Cumming, M Adamska, ML Barnes, J Barnett, D Bellwood, J Cinner, P Cohen, J Donelson, K Fabricius, RQ Grafton, A Grech, GG Gurney, O Hoegh-Guldberg, AS Hoey, MO Hoogenboom, J Lau, C Lovelock, R Lowe, D Miller, TH Morrison, PJ Mumby, M Nakata, JM Pandolfi, GD Peterson, M Pratchett, T Ravasi, C Riginos, JL Rummer, B Schaffelke, T Wernberg, S Wilson. Regional Environmental Change. 2023, In press.
Anemonefishes: A Model System for Evolutionary Genomics. M Herrera, T Ravasi, and V Laudet. F1000Research, 2023, 12:204, doi: 10.12688/f1000research.130752.1 (2023).
The Clownfish Larvae Exhibit Faster Growth, Higher Metabolic Rates and Altered Gene Expression under future Ocean Warming. B Moore, J Jolly, M Izumiyama, E Kawai, T Ryu and T Ravasi. Science of the Total Environment 873, 2023, 162296, doi:10.1016/j.scitotenv.2023.162296, (2023).
The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into melanic pigmentation of anemonefish. B Moore, M Herrera, E Gairin, C Li, S Miura, J Jolly, M Mercader, M Izumiyama, E Kawai, T Ravasi, V Laudet and T Ryu. G3 Genes|Genomes|Genetics, 2023, jkad002,doi:10.1093/g3journal/jkad002, (2023).
Resilience and Adaptation to Local and Global Environmental Change. C Schunter, JM Donelson, PL Munday, T Ravasi. Evolution, Development and Ecology of Anemonefishes, 253-274, CRC Press, 2023.
Transcriptome assemblies of two deep-sea octocorals Calyptrophora lyra and Chrysogorgia stellata from West Pacific seamount, Godin Guyot, T Ryu, S-J Hwang, S Woo, Marine Genomics 67, 2023.101006, doi: 10.1016/j.margen.2022.101006 (2023).
2022
The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into melanic pigmentation of anemonefish
Moore B, Herrera M, Gairin E, Li C, Miura S, Jolly J, Mercader M, Izumiyama M, Kawai E, Ravasi T, Laudet V, Ryu T. G3: Genes|Genomes|Genetics in PRESS
Molecular responses of brains to cross-generational warming in a coral reef fish.
MA Bernal, E Schmidt, J Donelson, P Munday, T Ravasi. Frontiers in Marine Science
Rapid evolution fuels transcriptional plasticity to ocean acidification
J Kang, I Nagelkerke, JL Rummer, R Rodolfo-Metalpa, PL Munday, C Schunter, T Ravasi. Global Change Biology
A chromosome-scale genome assembly of the false clownfish, Amphiprion ocellaris
Taewoo Ryu, Marcela Herrera, Billy Moore, Michael Izumiyama, Erina Kawai, Vincent Laudet, Timothy Ravasi, bioRxive, 2022.1.17 https://doi.org/10.1101/2022.01.16.476524
2021
Plasticity to ocean warming is influenced by transgenerational, reproductive, and developmental exposure in a coral reef fish
Carbonne, C., Teixidó, N., Moore, B., Mirasole, A., Guttierez, T., Gattuso, J.P. and Comeau, S., Evolutionary Applications, 2021.12.17 https://doi.org/10.1111/eva.13337
Molecular basis of parental contributions to the behavioural tolerance of elevated pCO2 in a coral reef fish
Alison A. Monroe, Celia Schunter, Megan J. Welch, Philip L. Munday and Timothy Ravasi, Proceedings of the Royal Society B, 2021.12.8 https://doi.org/10.1098/rspb.2021.1931
Two temperate corals are tolerant to low pH regardless of previous exposure to natural CO2 vents
Moisés A. Bernal, Timothy Ravasi, Giverny G. Rodgers, Philip L. Munday, Jennifer M. Donelson, Limnology and Oceanography, 66(11), pp.4046-4061, 2021.10.1 https://doi.org/10.1002/lno.11942
The time course of molecular acclimation to seawater in a euryhaline fish
Celia Schunter, Michael D. Jarrold, Philip L. Munday, Timothy Ravasi, Molecular Ecology, 2021.8.17 https://doi.org/10.1038/s41598-021-97295-3
Diel pCO2 fluctuations alter the molecular response of coral reef fishes to ocean acidification conditions
Lucrezia C. Bonzi, Alison A. Monroe, Robert Lehmann, Michael L. Berumen, Timothy Ravasi & Celia Schunter, Scientific Reports 2021.9.13 https://doi.org/10.1111/mec.16124
Digital Droplet PCR-Based Environmental DNA Tool for Monitoring Cryptocaryon irritans in a Marine Fish Farm from Hong Kong
Hin Hung Tsang,Jose A. Domingos, Jacob A. F. Westaway, Maximilian H. Y. Kam, Roger Huerlimann and Giana Bastos Gomes, Diversity, 2021, 13(8), 350; https://doi.org/10.3390/d13080350
Using bacterial whole genome sequencing to identify toxin genes associated with disease outbreaks in black tiger shrimp (Penaeus monodon) aquaculture production
Kelly Condona,Roger Huerlimann, Tony Charles, Ryan Lowrey, Phoebe Arbon, Dean R.Jerry, Aquaculture, 2021, 7.29; https://doi.org/10.1016/j.aquaculture.2021.737255
The role of ligand-gated chloride channels in behavioural alterations at elevated CO2 in a cephalopod
Jodi T. Thomas, Blake L. Spady, Philip L. Munday, Sue-Ann Watson, Journal of Experimental Biology, 2021.7.8; https://doi.org/10.1242/jeb.242335
Phylogenomics illuminates the evolution of bobtail and bottletail squid (order Sepiolida)
Gustavo Sanchez, Fernando Á. Fernández-Álvarez, Morag Taite, Chikatoshi Sugimoto, Jeffrey Jolly, Oleg Simakov, Ferdinand Marlétaz, Louise Allcock & Daniel S. Rokhsar, Communications Biology, 2021, 6.29; https://doi.org/10.1038/s42003-021-02348-y
Neuro-molecular characterization of fish cleaning interactions
S. Ramírez-Calero, J. R. Paula, E. Otjacques, R. Rosa, T. Ravasi, C. Schunter, bioRxive, 2021.6.27, https://doi.org/10.1101/2021.06.22.449532
Desert fish populations tolerate extreme salinity change to overcome hydrological constraints
, bioRxive, 2021.5.16, https://doi.org/10.1101/2021.05.14.444120
Rapid multi-generational acclimation of coralline algal reproductive structures to ocean acidification.
Moore, B., Comeau, S., Bekaert, M., Cossais, A., Purdy, A., Larcombe, E., Puerzer, F., McCulloch, M.T. and Cornwall, C.E, Proceedings of the Royal Society B, 288(1950), p.20210130, https://doi.org/10.3390/d13080350
First detection of critically endangered scalloped hammerhead sharks (Sphyrna lewini) in Guam, Micronesia, in five decades using environmental DNA
Alyssa M.Budd, Madalyn K.Cooper, Agnès LePort, Tom Schils, Matthew S. Mills, Mari E. Deinhart, Roger Huerlimann, Jan M.Strugnell, Ecological Indicators, 27 April 2021 | https://doi.org/10.1016/j.ecolind.2021.107649
Improved detection sensitivity using an optimal eDNA preservation and extraction workflow and its application to threatened sawfishes
Madalyn K. Cooper, Roger Huerlimann, Richard C. Edmunds, Alyssa M. Budd, Agnès Le Port, Peter M. Kyne, Dean R. Jerry, Colin A. Simpfendorfer, Aquatic Conservation, 24 April 2021 | https://doi.org/10.1002/aqc.3591
Unexpected high abundance of aragonite-forming Nanipora (Octocorallia: Helioporacea) at an acidified volcanic reef in southern Japan
James Davis Reimer, Haruko Kurihara, Timothy Ravasi, Yoichi Ide, Michael Izumiyama & Hajime Kayanne, Marine Biodiversity, 2 February 2021 | https://doi.org/10.1007/s12526-021-01165-0
Sex and time specific parental effects of warming on reproduction and offspring quality in a coral reef fish
Rachel K. Spinks, Lucrezia C. Bonzi, Timothy Ravasi, Philip L. Munday, Jennifer M. Donelson, Evolutionary Applications, 18 December 2020 | https://doi.org/10.1111/eva.13187
2020
Proteomic responses to ocean acidification in the brain of juvenile coral reef fish
Hin Hung Tsang, Megan J. Welch, Philip L. Munday, Timothy Ravasi and Celia Schunter, Frontiers in Marine Science, 30 July 2020 | https://doi.org/10.3389/fmars.2020.00605
Methods matter in repeating ocean acidification studies
Philip L. Munday, Danielle L. Dixson, Megan J. Welch, Douglas P. Chivers, Paolo Domenici, Martin Grosell, Rachael M. Heuer, Geoffrey P. Jones, Mark I. McCormick, Mark Meekan, Göran E. Nilsson, Timothy Ravasi & Sue-Ann Watson, Nature 586, E20–E24 (2020). https://doi.org/10.1038/s41586-020-2803-x
First transcriptome assembly of a newly discovered vent mussel, Gigantidas vrijenhoeki, at Onnuri Vent Field on the northern Central Indian Ridge
aewoo Ryu, Jong Guk Kim, Jimin Lee, Ok Hwan Yu, Seungshic Yum, Dongsung Kim, Seonock Woo, Marine Genomics, 12 September 2020, 100819 (2020). https://doi.org/10.1016/j.margen.2020.100819
Viral ecogenomics across the Porifera
Cecília Pascelli, Patrick W. Laffy, Emmanuelle Botté, Marija Kupresanin, Thomas Rattei, Miguel Lurgi, Timothy Ravasi & Nicole S. Webster, Microbiome Volume 8, Article number: 144 (2020). https://doi.org/10.1186/s40168-020-00919-5
Symbiodiniaceae diversity of Palythoa tuberculosa in the central and southern Red Sea influenced by environmental factors
Hin Boo Wee, Michael L. Berumen, Timothy Ravasi and James Davis Reimer, Coral Reefs, 03 August 2020| https://doi.org/10.1007/s00338-020-01989-5
Probing SWATH‐MS as a tool for proteome level quantification in a nonmodel fish
Alison A. Monroe, Huoming Zhang, Celia Schunter, and Timothy Ravasi, Molecular Ecology Resources, 20 July 2020| https://doi.org/10.1111/1755-0998.13229
An Epigenetic Signature for Within-Generational Plasticity of a Reef Fish to Ocean Warming
Taewoo Ryu, Heather D. Veilleux, Philip L. Munday, Imgook Jung, Jennifer M. Donelson and Timothy Ravasi, Frontiers in Marine Science, 30 April 2020 | https://doi.org/10.3389/fmars.2020.00284
Species-specific molecular responses of wild coral reef fishes during a marine heatwave
Moisés A. Bernal, Celia Schunter, Robert Lehmann, Damien J. Lightfoot, Bridie J. M. Allan, Heather D. Veilleux, Jodie L. Rummer, Philip L. Munday, Timothy Ravasi, Science Advances, 18 Mar 2020: Vol. 6, no. 12, eaay3423 DOI: 10.1126/sciadv.aay3423
Neural effects of elevated CO2 in fish may be amplified by a vicious cycle
Celia Schunter, Timothy Ravasi, Philip L Munday, Göran E Nilsson, Conservation Physiology, Volume 7, Issue 1, 2020, coz100, https://doi.org/10.1093/conphys/coz100
2019
Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells
Muhammad Shuaib, Krishna Mohan Parsi, Manjula Thimma, Sabir Abdu Adroub, Hideya Kawaji, Loqmane Seridi, Yanal Ghosheh, Alexandre Fort, Bodor Fallatah, Timothy Ravasi, Piero Carninci, Valerio Orlando (2019), Cell Systems, Volume 9, Issue 5, 27 November 2019, Pages 446-458.e6 | https://doi.org/10.1016/j.cels.2019.09.005
Testing the Adaptive Potential of Yellowtail Kingfish to Ocean Warming and Acidification,
Philip L. Munday, Celia Schunter, Bridie J. M. Allan, Simon Nicol, Darren M. Parsons, Stephen M. J. Pether, Stephen Pope, Timothy Ravasi, Alvin N. Setiawan, Neville Smith and Jose A. Domingos (2019), Frontiers in Ecology and Evolution, 09 July 2019 | https://doi.org/10.3389/fevo.2019.00253
The full list of publications can be found here