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

Publications ( 2015-2018 )
  1. 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, 119.
  2. 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. (SCI) (IF: 2.177; SCI ranking: 31.3%)
  3. 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. (SCI) (IF: 4.259; SCI ranking: 15.6%)
  4. 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. (SCI) (IF: 2.177; SCI ranking: 31.3%)
  5. 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. (SCI) (IF: 2.906; SCI ranking: 12.4%)
  6. 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. (SCI) (IF: 4.259; SCI ranking: 15.6%)
  7. 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. (SCI) (IF: 4.076; SCI ranking: 20.8%)
  8. 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.
  9. 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. (SCI) (IF: 1.008; SCI ranking: 52.1%)
  10. 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. (SCI) (IF: 3.979; SCI ranking: 25.1%,29.2%)
  11. 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. (SCI) (IF: 2.177; SCI ranking: 31.3%)
  12. 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. (SCI) (IF: 4.419; SCI ranking: 20.8%,19.2%,22.1%)
  13. 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. (SCI) (IF: 2.177; SCI ranking: 31.3%)
  14. 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. (SCI) (IF: 1.972; SCI ranking: 20.9%)
  15. 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. (SCI) (IF: 4.259; SCI ranking: 15.6%)
  16. 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. (SCI) (IF: 1.008; SCI ranking: 52.1%)
  17. 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. (SCI) (IF: 1.757; SCI ranking: 44.4%,40%,30%,40%)
  18. 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. (SCI) (IF: 2.806; SCI ranking: 23.4%)
  19. 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. (SCI) (IF: 2.906; SCI ranking: 12.4%)
  20. 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. (SCI) (IF: 2.134; SCI ranking: 60.8%)
  21. 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. (SCI) (IF: 1.646; SCI ranking: 44.8%,38.9%)
  22. 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. (SCI) (IF: 4.022; SCI ranking: 14.8%,21.6%,16.6%)
  23. J.-T. Wang*, C.-M. Hsu, C.-Y. Kuo, P.-J. Meng, C. A. Chen*, 2015, “Physiological Outperformance at the Morphologically-Transformed Edge of the Cyanobacteriosponge Terpios hoshinota (Suberitidae: Hadromerida) when Confronting Opponent Corals”, PLoS One, 10(6), e0131509. (SCI) (IF: 2.806; SCI ranking: 23.4%)
  24. Shang-Yin Vanson Liu, Chia-Ling Carynn Chan, Hernyi Justin Hsieh, Silvia Fontana, Carden C. Wallace, Chaolun Allen Chen*, 2015, “Massively parallel sequencing (MPS) assays for sequencing mitochondrial genomes: the phylogenomic implications for Acropora staghorn corals (Scleractinia; Acroporidae)”, MARINE BIOLOGY, 162(6), 1383-1392. (SCI) (IF: 2.136; SCI ranking: 29.5%)
  25. F.-W. Kuo, C.-Y. Kuo, T.-Y. Fan, M.-C. Liu, C. A. Chen*, 2015, “Hidden ecosystem function of rabbitfishes? Siganus fuscescens feeds on the soft coral, Sarcophyton sp.”, CORAL REEFS, 34(1), 57. (SCI) (IF: 2.906; SCI ranking: 12.4%)
  26. Pierre-Alexandre Château, Yuan-Chao Angelo Huang, Chaolun Allen Chen, Yang-Chi Chang*, 2015, “Integrated assessment of sustainable marine cage culture through system dynamics modeling”, ECOLOGICAL MODELLING, 299, 140-146. (SCI) (IF: 2.363; SCI ranking: 38.6%)
  27. S. de Palmas, V. Denis, L. Ribas Deulofeu, M. Loubeyres, S. Woo, S.J. Hwang, J.I. Song, C.A. Chen*, 2015, “Symbiodinium spp. associated with high-latitude scleractinian corals from Jeju Island, South Korea”, Coral Reefs, 34(3), 919-925. (SCI) (IF: 2.906; SCI ranking: 12.4%)
  28. Y.-Y. Chuang, C. A. Chen*, 2015, “The complete mitochondrial genomes of Pseudosiderastrea spp (Cnidaria, Scleractinia, Siderastreidae).”, Mitochondrial DNA, 27(6), 4065-4066. (SCI) (IF: 3.35; SCI ranking: 35.9%)

Lab members


電  話

顏綵葭    鄭雁文    陳彥嘉

吳欣儒    黃雅怡    楊松穎

林愛龍    夏翔柯(Shanky)

夏沛亞(Chateau Pierre)


許嘉閔    莊曜陽    高國瑋

鄭念昀    曹景昕    方慧玲

洪若譯    周文華    張添忠

高莉雁(Juliet) 高洛德(Rodrigo)



新溫室 204