Biodiversity Research Center, Academia Sinica

Dr. Chaolun Allen Chen Research Fellow

Lab PI

Dr. Chaolun Allen Chen

Research Fellow

PhD – James Cook, University ,Australia,1995

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Office:Greenhouse Builiding 204


Research Fields
  • Coral and coral reef evolution
  • Coral reef ecosystem and environmental change
  • Symbiosis

Research Directions

  • Coral reef hosts high biodiversity which provides a foundation stone for human civilization. Due to the disturbances from human activities, including overfishing, pollution, habitat destruction, and synergetic effect of ocean warming and acidification caused by climate change, coral reef are facing severe degradation worldwide. Corals are facing mass extinction and coral reef ecosystem are losing its ecological function and service towards end of this century, if the human-induced disturbances were not ceased. We address several important questions regarding to response mechanisms of corals and coral reefs under the impact of environmental change. First, will corals acclimatize or adapt to environmental change, particularly the impact of rising seawater temperature? If so, who are the winners? Who are the loosers? Second, what kind of mechanisms behind these winners to survive under the future scenarios? Is it driven by host corals or symbionts? Third, will the coral communities composed by the winner perform a similar ecological function as we observe from present coral reef ecosystem? Forth, what are management and conservation implications for the future coral reefs based on our research? Based on the long-term ecological research approach, we incorporate genomics, molecular ecology, physiology, and community ecology to address these questions.


Latest published paper

期刊論文 ( 2016 - 2021 )

  1. Ming-Jay HO, Chao-Yang KUO, Hung-Yi WU, Ming-Shiou JENG, Shiahn-Wern SHYUE*, Chaolun Allen CHEN*, 2020, “Fishing pressure occurs down to the lower mesophotic coral ecosystem in Lyudao, Taiwan”, Galaxea, Journal of Coral Reef Studies, 22(1), 29-30. Link
  2. Shashank Keshavmurthy, Chao-Yang Kuo, Ya-Yi Huang, Rodrigo Carballo-Bolaños, Pei-Jei Meng*, Jih-Terng Wang* and Chaolun Allen Chen*, 2020, “Correction: Keshavmurthy, S., et al. Coral Reef Resilience in Taiwan: Lessons from Long-Term Ecological Research on the Coral Reefs of Kenting National Park (Taiwan). Journal of Marine Science and Engineering 2019, 7, 338”, Journal of Marine Science and Engineering, 8(12), 964. (SCIE) (IF: 2.033; SCIE ranking: 46.2%,84.8%) Link
  3. Shashank Keshavmurthy*, Morgan Beals, Hernyi Justin Hsieh, Kwang-Sik Choi, Chaolun Allen Chen*, 2020, “Physiological plasticity of corals to temperature stress in marginal coral communities”, Science of The Total Environment, 143628. (SCIE) (IF: 6.551; SCIE ranking: 8.3%) Link
  4. Juliet Furaha Karisa, David Obare Obura, Chaolun Allen Chen*, 2020, “Spatial heterogeneity of coral reef benthic communities in Kenya”, PLOS ONE, 15(8), e0237397. (SCIE) (IF: 2.74; SCIE ranking: 38%) Link
  5. Chao-Yang Kuo, Shashank Keshavmurthy, Aichi Chung, Ya-Yi Huang, Sung-Yin Yang, Yei-Chia Chen & Chaolun Allen Chen*, 2020, “Demographic census confirms a stable population of the critically-endangered caryophyllid coral Polycyathus chaishanensis (Scleractinia; Caryophyllidae) in the Datan Algal Reef, Taiwan”, SCIENTIFIC REPORTS, 10, 10585 (2020). (SCIE) (IF: 3.998; SCIE ranking: 23.9%) Link
  6. Ya-Yi Huang, Rodrigo Carballo-Bolaños, Chao-Yang Kuo, Shashank Keshavmurthy & Chaolun A. Chen*, 2020, “Leptoria phrygia in Southern Taiwan shuffles and switches symbionts to resist thermal-induced bleaching”, SCIENTIFIC REPORTS, 10, 7808. (SCIE) (IF: 3.998; SCIE ranking: 23.9%) Link
  7. Shashank Keshavmurthy​, Hwee Sze Tee​, Kuo-Wei Kao, Jih-Terng Wang​*, Chaolun Allen Chen​*, 2020, “Specificity trumps flexibility—location-based stable associations between Symbiodiniaceae genera and Platygyra verweyi (Scleractinia; Merulinidae)”, PEERJ, 8:e8791. (SCIE) (IF: 2.379; SCIE ranking: 45.1%) Link
  8. Ji Hyoun Kang, Ji Eun Jang, Jae Hwan Kim, Sangil Kim, Shashank Keshavmurthy, Sylvain Agostini, James D. Reimer, Chaolun Allen Chen, Kwang-Sik Choi, Sang Rul Park and Hyuk Je Lee*, 2020, “The Origin of the Subtropical Coral Alveopora japonica (Scleractinia: Acroporidae) in High-Latitude Environments”, FRONTIERS IN ECOLOGY AND EVOLUTION, 8(12). (SCIE) (IF: 2.416; SCIE ranking: 41.4%) Link
  9. Rodrigo Carballo-Bolaños*, Derek Soto* and Chaolun Allen Chen*, 2019, “Thermal Stress and Resilience of Corals in a Climate-Changing World”, Journal of Marine Science and Engineering, 8(1), 15. (SCIE) (IF: 2.033; SCIE ranking: 46.2%,84.8%) Link
  10. Shashank Keshavmurthy, Chao-Yang Kuo, Ya-Yi Huang, Rodrigo Carballo-Bolaños, Pei-Jei Meng*, Jih-Terng Wang*, and Chaolun Allen Chen*, 2019, “Coral Reef Resilience in Taiwan: Lessons from Long-Term Ecological Research on the Coral Reefs of Kenting National Park (Taiwan)”, Journal of Marine Science and Engineering, 7(11), 388. (SCIE) (IF: 2.033; SCIE ranking: 46.2%,84.8%)
  11. Emily S. Darling, Tim R. McClanahan, […], Chaolun Allen Chen,[…],David Mouillot , 2019, “Social–environmental drivers inform strategic management of coral reefs in the Anthropocene”, NATURE ECOLOGY & EVOLUTION, 3(9), 1341-1350. (SCIE) (IF: 12.543; SCIE ranking: 1.8%,5.9%) Link
  12. Jih-Terng Wang*, Yu-Ting Wang, Shashank Keshavmurthy, Pei-Jei Meng, Chaolun Allen Chen*, 2019, “The coral Platygyra verweyi exhibits local adaptation to long-term thermal stress 2 through host-specific physiological and enzymatic response”, Scientific Reports, 9, 13492. (SCIE) (IF: 3.998; SCIE ranking: 23.9%) Link
  13. Chao-Yang KUO, Aichi CHUNG, Shashank KESHAVMURTHY, Ya-Yi HUANG, Sung-Yin YANG, and Chaolun Allen CHEN*, 2019, “Lonely giant on the sand: unexpected massive Taiwanese coral, Polycyathus chaishanensis in the Datan algal reef demands a conservation focus”, Galaxea, Journal of Coral Reef Studies, 21(1), 11-12.
  14. Rodrigo Carballo-Bolaños, Vianney Denis, Ya-Yi Huang, Shashank Keshavmurthy, Chaolun Allen Chen*, 2019, “Temporal variation and photochemical efficiency of species in Symbiodinaceae associated with coral Leptoria phrygia (Scleractinia; Merulinidae) exposed to contrasting temperature regimes”, PLOS ONE, 14(6): e0218801. (SCIE) (IF: 2.74; SCIE ranking: 38%) Link
  15. Ren Min Oh1*, Mei Lin Neo, Nicholas Wei Liang Yap, Sudhanshi Sanjeev Jain, Ria Tan, Chaolun Allen Chen & Danwei Huang, 2019, “Citizen science meets integrated taxonomy to uncover the diversity and distribution of Corallimorpharia in Singapore”, RAFFLES BULLETIN OF ZOOLOGY, 67, 306–321. (SCIE) (IF: 0.907; SCIE ranking: 64.5%) Link
  16. Carolin Nieder, Chen-Pan Liao, Chaolun Allen Chen, Shao-Lun Liu*, 2019, “Filamentous calcareous alga provides substrate for coral-competitive macroalgae in the degraded lagoon of Dongsha Atoll, Taiwan”, PLOS ONE, 14(5): e0200864. (SCIE) (IF: 2.74; SCIE ranking: 38%) Link
  17. Carolin Nieder, Pin-Chen Chen, Chen, Chaolun Allen Chen, Shao-Lun Liu*, 2019, “New record of the encrusting alga Ramicrusta textilis overgrowing corals in the lagoon of Dongsha Atoll, South China Sea”, Bulletin of Marine Science, (SCIE) (IF: 1.432; SCIE ranking: 51.4%,65.7%) Link
  18. Shashank Keshavmurthy, Sung-Yin Yang, Chun-Yu Su, Yu-Wen Chiu, Chaolun Allen Chen*, 2019, “Association between massive Porites and the hidden hermit crab, Calcinus latens (Decapoda, Diogenidae)”, BULLETIN OF MARINE SCIENCE, 95(1), 115-116. (SCIE) (IF: 1.432; SCIE ranking: 51.4%,65.7%) Link
  19. Parisa Alidoost Salimi, Pargol Ghavam Mostafavi*, Chaolun Allen Chen, Seyed Mohammad Reza Fatemi, and Michel Pichon, 2018, “The Scleractinia (Cnidaria: Anthozoa) of Abu-Musa and Sirri Islands, Persian Gulf”, ZOOLOGICAL STUDIES, 57(56). (SCIE) (IF: 1.257; SCIE ranking: 46.2%) Link
  20. Kuo-Wei Kao, Shashank Keshavmurthy*, Cing-Hsin Tsao, Jih-Terng Wang, and Chaolun Allen Chen*, 2018, “Repeated and Prolonged Temperature Anomalies Negate Symbiodiniaceae Genera Shuffling in the Coral Platygyra verweyi (Scleractinia; Merulinidae)”, ZOOLOGICAL STUDIES, 57, 55. (SCIE) (IF: 1.257; SCIE ranking: 46.2%) Link
  21. Hawthorne L. Beyer, Emma V. Kennedy, Maria Beger, Chaolun Allen Chen, Joshua E. Cinner, Emily S. Darling, C. Mark Eakin, Ruth D. Gates, Scott F. Heron, Nancy Knowlton, David O. Obura, Stephen R. Palumbi, Hugh P. Possingham, Marji Puotinen, Rebecca K. Runting, William J. Skirving, Mark Spalding, Kerrie A. Wilson,Sally Wood, John E. Veron, Ove Hoegh‐Guldberg, 2018, “Risk‐sensitive planning for conserving coral reefs under rapid climate change”, Conservation Letters, 11(6),e12587. (SCIE) (IF: 6.766; SCIE ranking: 3.4%) Link
  22. Stephane De Palmas, Derk R. Sato, Min-Jay Ho, Vianney Denis*, Chaolun Allen Chen* , 2018, “Molecular assessment of Pocillopora verrucosa (Scleractinia; Pocilloporidae) distribution along a depth gradient in Ludao, Taiwan. ”, PeerJ, 6, e5797. (SCIE) (IF: 2.379; SCIE ranking: 45.1%) Link
  23. Sung-Yin Yang, Hsing-Ju Chen, Ming-Jay Ho, Yen-Jia Chen, Ya-Yi Huang, Wenhua Savanna Chow, Sen-Lin Tang, Ming-Shiou Jeng, Chaolun Allen Chen*, 2018, “Outbreak of coral-killing cyanobacteriasponge, Terpios hoshinota, in Taiping Island (Itu Aba), Spratlys, South China Sea”, BULLETIN OF MARINE SCIENCE, 94(4), 1543-1544. (SCIE) (IF: 1.432; SCIE ranking: 51.4%,65.7%) Link
  24. Derek Soto, Stephane De Palmas, Ming Jay Ho, Vianney Denis*, Chaolun Allen Chen*, 2018, “Spatial variation in the morphological traits of Pocillopora verrucosa along a depth gradient in Taiwan”, PLoS One, 13(8), e0202586. (SCIE) (IF: 2.74; SCIE ranking: 38%) Link
  25. Maria Dornelas*, Laura H. Antão, Faye Moyes, Amanda E. Bates, Anne E. Magurran, Dušan Adam, Asem A. Akhmetzhanova, Ward Appeltans, José Manuel Arcos, Haley Arnold, Narayanan Ayyappan, Gal Badihi, Andrew H. Baird, Miguel Barbosa, Tiago Egydio Barreto, Claus Bässler, Alecia Bellgrove, Jonathan Belmaker, Lisandro Benedetti‐Cecchi, Brian J. Bett, Anne D. Bjorkman, Magdalena Błażewicz, Shane A. Blowes, Christopher P. Bloch, Timothy C. Bonebrake, Susan Boyd, Matt Bradford, Andrew J. Brooks, James H. Brown, Helge Bruelheide, Phaedra Budy, Fernando Carvalho,Edward Castañeda‐Moya, Chaolun Allen Chen, ...etc., 2018, “BioTIME: A database of biodiversity time series for the Anthropocene”, GLOBAL ECOLOGY AND BIOGEOGRAPHY, 27(7), 760-786. (SCIE) (IF: 6.446; SCIE ranking: 6.5%,4%) Link
  26. Sung-Yin Yang, Wai-Ling Fong, Wenhua Savanna Chow, Chia-Min Hsu, Chia-Ling Carynn Chan, Shashank Keshavmurthy*, Chaolun Allen Chen*, 2018, “Development of Novel Polymorphic Microsatellite Markers in Catch Bowl Coral, Isopora palifera (Scleractinia; Acroporidae) Using Next-generation Sequencing”, ZOOLOGICAL STUDIES, 57, 32. (SCIE) (IF: 1.257; SCIE ranking: 46.2%) Link
  27. Carolin Nieder, Chaolun Allen Chen, Shao-Lun Liu*, 2018, “Long-term blooming filamentous calcareous alga provides substrate for other coral-competitive macroalgae in the degraded lagoon of Dongsha Atoll (Pratas), Taiwan”, bioRxiv, Link
  28. Sonny T. M. Lee, Shashank Keshavmurthy*, Silvia Fontana, Mezaki Takuma, Wen-Hua Chou and Chaolun Allen Chen*, 2018, “Transcriptomic response in Acropora muricata under acute temperature stress follows preconditioned seasonal temperature fluctuations.”, BMC research notes, 11(1), 119. Link
  29. Katrina S. Luzon*, Mei-Fang Lin*, Ma. Carmen A. Ablan Lagman, Wilfredo Roehl Y. Licuanan and Chaolun Allen Chen*, 2017, “Resurrecting a subgenus to genus: molecular phylogeny of Euphyllia and Fimbriaphyllia (order Scleractinia; family Euphyllidae; clade V)”, PeerJ, 5, e4074. (SCIE) (IF: 2.379; SCIE ranking: 45.1%) Link
  30. Jia-Ho Shiu, Shashank Keshavmurthy, Pei-Wen Chiang, Hsing-Ju Chen, Shueh-Ping Lou, Ching-Hung Tseng, Hernyi Justin Hsieh, Chaolun Allen Chen & Sen-Lin Tang*, 2017, “Dynamics of coral-associated bacterial communities acclimated to temperature stress based on recent thermal history”, SCIENTIFIC REPORTS, 7(1), 14933. (SCIE) (IF: 3.998; SCIE ranking: 23.9%) Link
  31. Jih-Terng Wang​*, Shashank Keshavmurthy, Tzu-Ying Chu, Chaolun Allen Chen​*, 2017, “Diverse responses of Symbiodinium types to menthol and DCMU treatment”, PeerJ, 5, e3843. (SCIE) (IF: 2.379; SCIE ranking: 45.1%) Link
  32. Ching-Yu Liou, Sung-Yin Yang*, Chaolun Allen Chen*, 2017, “Unprecedented calcareous algal reefs in northern Taiwan merit high conservation priority”, CORAL REEFS, 36(4), 1253. (SCIE) (IF: 3.536; SCIE ranking: 8.4%) Link
  33. Vianney Denis*, Lauriane Ribas-Deulofeu, Nicolas Sturaro, Chao-Yang Kuo & Chaolun Allen Chen, 2017, “A functional approach to the structural complexity of coral assemblages based on colony morphological features”, SCIENTIFIC REPORTS, 7(1), 9849. (SCIE) (IF: 3.998; SCIE ranking: 23.9%) Link
  34. Yang S-H, Tseng C-H, Huang C-R, Chen C-P, Tandon K, Lee STM, Chiang P-W, Shiu J-H, Chen CA and Tang S-L, 2017, “Long-Term Survey Is Necessary to Reveal Various Shifts of Microbial Composition in Corals”, Frontiers in Microbiology, 8, 1094. (SCIE) (IF: 4.236; SCIE ranking: 25%) Link
  35. James Davis Reimer, Maria Eduarda Alves Santos, Hiroki Kise, Mei Lin Neo, Chaolun Allen Chen, Keryea Soong, 2017, “Diversity of Zoantharia (Anthozoa: Hexacorallia) at Dongsha Atoll in the South China Sea”, Regional Studies in Marine Science, 12, 49-57. (SCIE) (IF: 1.183; SCIE ranking: 62.6%,76.9%) Link
  36. Yaoyang Chuang, Marcelo Kitahara, Hironobu Fukami, Dianne Tracey, David J. Miller*, Chaolun Allen Chen*, 2017, “Loss and Gain of Group I Introns in the Mitochondrial Cox1 Gene of the Scleractinia (Cnidaria; Anthozoa)”, ZOOLOGICAL STUDIES, 56, 9. (SCIE) (IF: 1.257; SCIE ranking: 46.2%) Link
  37. Mei-Fang Lin, Aurelie Moya, Hua Ying, Chaolun Allen Chen, Ira Cooke, Eldon E. Ball, Sylvain Forêt, David J. Miller, 2017, “Analyses of Corallimorpharian Transcriptomes Provide New Perspectives on the Evolution of Calcification in the Scleractinia (Corals)”, Genome Biology and Evolution, 9(1),150-160. (SCIE) (IF: 3.462; SCIE ranking: 35.3%,34.8%) Link
  38. Shashank Keshavmurthy, Kuo-Hsun Tang, Chao-Yang Kuo, Keryea Soong, Chaolun Allen Chen*, 2017, “Symbiodinium spp. associated with scleractinian corals from Dongsha Atoll (Pratas), Taiwan in the South China Sea”, PeerJ, 5, e2871. (SCIE) (IF: 2.379; SCIE ranking: 45.1%) Link
  39. Roberto Arrigoni, Michael L Berumen, Chaolun Allen Chen, Tullia I Terraneo, Andrew H Baird, Claude Payri, Francesca Benzoni, 2016, “Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species”, MOLECULAR PHYLOGENETICS AND EVOLUTION, 105, 146-159. (SCIE) (IF: 3.496; SCIE ranking: 33.3%,41.4%,34.3%) Link
  40. Mei Fang Lin, Wen Hwa Chou, Marcelo V Kitahara, Chao Lun Allen Chen, David John Miller, Sylvain Foret​, 2016, “Corallimorpharians are not “naked corals”: insights into relationships between Scleractinia and Corallimorpharia from phylogenomic analyses”, PeerJ, 4, e2463. (SCIE) (IF: 2.379; SCIE ranking: 45.1%) Link
  41. Roberto Arrigoni*, Francesca Benzoni*, Danwei Huang, Hironobu Fukami, Chaolun Allen Chen, Michael L. Berumen, Mia Hoogenboom, Damian P. Thomson, Bert W. Hoeksema, Ann F. Budd, Yuna Zayasu, Tullia I. Terraneo, Yuko F. Kitano, Andrew H. Baird, 2016, “When forms meet genes: revision of the scleractinian genera Micromussa and Homophyllia (Lobophylliidae) with a description of two new species and one new genus”, CONTRIBUTIONS TO ZOOLOGY, 85(4), 387-422. (SCIE) (IF: 1.242; SCIE ranking: 47.9%) Link
  42. S.-T. Hsiao, S.-C. Chuang, K.-S. Chen, P.-H. Ho, C.-L. Wu, C. A. Chen*, 2016, “DNA barcoding reveals that the common cupped oyster in Taiwan is the Portuguese oyster Crassostrea angulata (Ostreoida; Ostreidae), not C. gigas”, Scientific Reports, 6, 34057. (SCIE) (IF: 3.998; SCIE ranking: 23.9%) Link
  43. H. J. Hsieh, C. K-C. Wen, Y.-C. Huang, K.-S. Chen, C.-F. Dai, C. A. Chen*, 2016, “Spatial patterns and environmental settings of non-reefal coral communities across the Tropics of Cancer in the Penghu Archipelago (Pescadores), Taiwan”, ZOOLOGICAL STUDIES, doi:10.6620/ZS.2016.55-45. (SCIE) (IF: 1.257; SCIE ranking: 46.2%) Link
  44. Christophe Vieira, Shashank Keshavmurthy, Se-Jong Ju, Kiseong Hyeong, Inah Seo, Chang-Keun Kang, Hyun-Ki Hong, Chaolun Allen Chen and Kwang-Sik Choi, 2016, “Population dynamics of a high-latitude coral Alveopora japonica Eguchi from Jeju Island, off the southern coast of Korea”, MARINE AND FRESHWATER RESEARCH, 67, 594-604. (SCIE) (IF: 1.488; SCIE ranking: 50%,49.1%,48.6%,61.2%) Link
  45. L. R. Deulofeu, V. Denis, S. De Palmas, C.-Y. Kuo, H. J. Hsieh, C. A. Chen*, 2016, “Structure of benthic communities along the Taiwan latitudinal gradient”, PLoS One, 11(8), e0160601. (SCIE) (IF: 2.74; SCIE ranking: 38%) Link
  46. G. Suzuki, S. Keshavmurthy, T. Hayashibara, C. C. Wallace, Y. Shirayama, C. A. Chen, H. Fukami, 2016, “Genetic evidence of peripheral isolation and low diversity in marginal populations of the Acropora hyacinthus complex”, CORAL REEFS, 35(4), 1419-1432. (SCIE) (IF: 3.536; SCIE ranking: 8.4%) Link
  47. Wen-Ming Chen, Li-Ping Liu, Chaolun Allen Chen, Jih-Terng Wang, Shih-Yi Sheu, 2016, “Thalassotalea montiporae sp. nov., isolated from the encrusting pore coral Montipora aequituberculata.”, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 66, 4077-4084. (SCIE) (IF: 2.415; SCIE ranking: 63.2%) Link
  48. M.-J. Ho, C.-M. Hsu, C. A. Chen*, 2016, “Wall of orange cup coral, Tubastraea coccinea, at the inlet breakwaters of a nuclear power plant, southern Taiwan”, Marine Biodiversity, DOI: 10.1007/s12526-016-0469-2. (SCIE) (IF: 1.487; SCIE ranking: 63.8%,49.5%) Link
  49. D. Huang, B. W. Hoeksema, A. Yang Amri, P. O. Ang, C. A. Chen, H. Huang, D. J. W. Lane, W. Y. Licuanan, Ouk Vibol, S. T. Vo, T. Yeemin, L. M. Chou, 2016, “ Conservation of reef corals in the South China Sea based on species and evolutionary diversity”, BIOLOGICAL CONSERVATION, 25(2), 331-344. (SCIE) (IF: 4.711; SCIE ranking: 10.3%,12.4%,18.5%) Link