Faculty list

Dr. Chaolun Allen Chen

Research Fellow
PhD – James Cook, University ,Australia,1995
Research Fields
Evolutionary ecology and genetics of coral reefs, symbiosis and bleaching biodiversity
Major Research Achievements (2013-2017)
  • Evolutionary genetics and ecology of reef corals Scleractinian corals and coral reef-associated organisms have been the major research focus in my lab over the last 5 years. One of the major accomplishments is to develop molecular markers for corals and to address phylogenetic and population genetic questions. A paper on the mitochondrial genomes of two Acroporidae genera suggesting a genomic-wise unequal rate of molecular evolution in this family is published. This paper represents the first mt genomic research in my laboratory. A series of manuscripts regarding to the evolutionary mitogenomics of corals are either submitted or in preparation. In addition, a series of papers were published in elucidating the higher level of molecular phylogeny using mitochondrial DNA sequences. Except for the confirmation of two-clade hypothesis of evolutionary history of scleractinians , a recent collaboration with Knowlton’s group in the Scripps Institute of Oceanography, UCSD, demonstrated that congeneric Faviina have indeed evolved independently in both Pacific and Atlantic Oceans that may indicate 340 my divergence. A paper based on this result is appeared in Nature, April, 2004. This finding raises the concern of conservation priority for Atlantic scleractinian corals. Currently, the other joint publication is under preparation to describe a new scheme of modern scleractinian systematics. This manuscript will describe the phylogenetic relationship over 180 species of corals, representing the major scleractinian lineages. I believe this manuscript will be very influential to our understanding of coral evolution. In addition to the high-level phylogeny of corals, I am also involved in the population genetics and phylogeography of the marine organisms in the Indian Ocean and West Pacific, particularly on corals. A manuscript describing the cryptic status of a “lab-rat” coral, Stylophora pistillata, between the Red Sea and the West Pacific populations which are associated with different symbiotic algae. This work challenge the fundamental concept that corals associated with distinct symbiotic algae in different biogeographic provinces is a phenotypic plasticity acclimatizing to different environment.
  • Symbiosis and bleaching biodiversity Symbiont diversity and coral bleaching biodiversity is the other major research topic in my lab. We extend the survey to the zooxanthellae diversity in scleractinian corals from southern Taiwan and the Penghu Archipelago, a tropical coral reef and a subtropical non-reefal community, respectively. Zooxanthellae diversity was investigated in 52 species of scleractinian corals from 26 genera and 13 families. RFLP and phylogenetic analyses of nuclear-encoded ribosomal RNA genes showed that Symbiodinium clade C was the dominant zooxanthellae in scleractinian corals in the seas around Taiwan; Symbiodinium clade D was also found in some species. Both Symbiodinium clade C and D were found in colonies of 7 species of scleractinian corals. Symbiodinium clade D was associated with corals that inhabit either shallow water or the reef edge in deep water, supporting the hypothesis that Symbiodinium clade D is a relatively stress-tolerant zooxanthellae found in marginal habitats. Seasonal dynamics of different clades of Symbiodinium was observed in Acropora palifera, a coral inhabits in shallow (1-5 m), and the dynamic pattern is correlated to the seasonal seawater temperature fluctuation in Kenting. Reshuffling or completed shift different clades within the coral hosts do not need the occurrence of bleaching . Our recent international collaboration on the biogeographic distribution range of Symbiodinium clade D, a clade assumed to be “heat-tolerant” specialist, indicates that this particular clade can reach the high-latitude (>340N). This result highlights caution should be taken when we try to infer the physiological constraints of symbiotic algae based on their community characteristics.
Research Interests
  • Evolution of reef corals and reef-associated organisms
  • Coral bleaching and zooxathanellae diversity
    Ongoing projects
    • Phylogeny of scleractinian corals based on mitogenomic approaches (Academia Sinica Genomics grant, 2006-2007)
    • Coral bleaching, symbiont diversity, and photophysiological differentiation (Academia Sinica Thematic grant, 2006-2007)
    • Out of Africa: molecular deduction of scleractinian corals in the Indian Ocean (Academia Sinica Pilot Thematic grant, 2007-2008)
    • Coral holobiont biodiversity: the pattern and functional approaches to the coral-associated microbial diversity (Academia Sinica Thematic grant, 2008-2010)
    • Impact of marine cage culture on the subtropical coral community in Penghu (NSC grant, 2006-2009)
      Publications (2009-2017)
      1. 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, DOI 10.7717/peerj.2871. (SCI) (IF: 2.183; SCI ranking: 22.2%)
      2. 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: 3.792; SCI ranking: 27.7%,28.3%,29.1%)
      3. 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: 2.183; SCI ranking: 22.2%)
      4. 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: 1.844; SCI ranking: 19.3%)
      5. 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: 5.228; SCI ranking: 11.1%)
      6. 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: 0.885; SCI ranking: 56.5%)
      7. 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: 1.583; SCI ranking: 50%,32.7%,49.2%,48.1%)
      8. 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: 3.057; SCI ranking: 17.5%)
      9. 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: 3; SCI ranking: 8.7%)
      10. 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: 2.439; SCI ranking: 52.8%)
      11. 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: 1.915; SCI ranking: 34.6%,36.7%)
      12. 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: 3.985; SCI ranking: 13.8%,14.3%,18%)
      13. 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: 3.057; SCI ranking: 17.5%)
      14. 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: 2.375; SCI ranking: 20.2%)
      15. 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: 3; SCI ranking: 8.7%)
      16. 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: 2.275; SCI ranking: 40.7%)
      17. 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: 3; SCI ranking: 8.7%)
      18. 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: 1.76; SCI ranking: 74.7%)
      19. Vianney Denis, Stéphane De Palmas, Francesca Benzoni & Chaolun Allen Chen*, 2014, “Extension of the known distribution and depth range of the scleractinian coral Psammocora stellata: first record from a Taiwanese mesophotic reef”, MARINE BIODIVERSITY, 45(4), 619-620. (SCI) (IF: 1.915; SCI ranking: 34.6%,36.7%)
      20. S. Montano, W.-H. Chou, C. A. Chen, P Galli, J. D. Reimer, 2014, “First record of the coral-killing sponge Terpios hoshinota in the Maldives and Indian Ocean.”, BULLETIN OF MARINE SCIENCE, 91(1), 97-98. (SCI) (IF: 1.856; SCI ranking: 39.4%,39.3%)
      21. C.-M. Hsu, S. de Palmas, C.-Y. Kuo, V. Denis, C. A. Chen*, 2014, “Identification of scleractinian coral recruits using fluorescent census and DNA barcoding techniques”, Plos ONE, 9(9), e107366. (SCI) (IF: 3.057; SCI ranking: 17.5%)
      22. Vianney Denis, Lauriane Ribas-Deulofeu, Mathilde Loubeyres, Stéphane De Palmas, Sung-Jin Hwang, Seonock Woo, Jun-Im Song, Chaolun Allen Chen*, 2014, “Recruitment of the subtropical coral Alveopora japonica in the temperate waters of Jeju Island, South Korea”, BULLETIN OF MARINE SCIENCE, 91(1), 85-96. (SCI) (IF: 1.856; SCI ranking: 39.4%,39.3%)
      23. R. Arrigoni, ZT Richards, CA Chen, AH Baird, F Benzoni, 2014, “Taxonomy and phylogenetic relationships of the coral genera Australomussa and Parascolymia (Scleractinia, Lobophylliidae)”, CONTRIBUTIONS TO ZOOLOGY, 83(3), 195-215. (SCI) (IF: 1.844; SCI ranking: 19.3%)
      24. Shashank Keshavmurthy, Silvia Fontana, Takuma Mezaki, Laura del Caño González, C. A. Chen*, 2014, “Doors are closing on early development in corals facing climate change.”, Scientific Reports, 4, 5633. (SCI) (IF: 5.228; SCI ranking: 11.1%)
      25. V. Denis, L. Ribas Deulofeu, S. De Palmas, C. A. Chen*, 2014, “First record of the scleractinian coral Psammocora albopicta from Korean waters.”, Marine Biodiversity, 44(2), 157-158. (SCI) (IF: 1.915; SCI ranking: 34.6%,36.7%)
      26. D. Huang, W. Y. Licuanan, B. W. Hoeksema, C. A. Chen, P. O. Ang, H. Huang, D. J. W. Lane, S. T. Vo, Z. Waheed, A. Yang Amri, T. Yeemin, L. M. Chou, 2014, “Extraordinary diversity of reef corals in the South China Sea”, Marine Biodiversity, 45(2), 157-168. (SCI) (IF: 1.915; SCI ranking: 34.6%,36.7%)
      27. S. Keshavmurthy, P.-J. Meng, J.-T. Wang, C.-Y. Kuo, S.-Y. Yang, C.-M. Hsu, C.-H. Gan, C.-F. Dai, C. A. Chen*, 2014, “Can resistant coral-Symbiodinium associations enable coral communities to survive climate change? A study of a site exposed to long-term hot water input”, PeerJ, 2, e327. (SCI) (IF: 2.183; SCI ranking: 22.2%)
      28. Mei-Fang Lin, Marcelo Visentini Kitahara, Haiwei Luo, Dianne Tracey, Jonathan Geller, Hironobu Fukami, David John Miller* and Chaolun Allen Chen*, 2014, “Mitochondrial genome rearrangements in the Scleractinia / Corallimorpharia complex: implications for coral phylogeny.”, Genome Biology and Evolution, 6(5), 1086-1095. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
      29. M. Kitahara, M.-F. Lin S. Foret, G. Huttley, D. J. Miller, and C. A. Chen*, 2014, “The “naked coral” hypothesis revisited – evidence for and against scleractinian monophyly”, PLoS One, 9(4), e94774. (SCI) (IF: 3.057; SCI ranking: 17.5%)
      30. Takuma Mezaki*, Shashank Keshavmurthy, Chaolun Allen Chen, 2014, “An old and massive colony of Pavona decussata is sexually active at high latitude (32°N) in Japan”, CORAL REEFS, 33(1), 97. (SCI) (IF: 3; SCI ranking: 8.7%)
      31. V. Denis, M. Loubeyres, S. Doo, S. de Palmas, S. Keshavmurthy, H. J. Hsieh, C. A. Chen*, 2014, “Can benthic algae mediate larval behavior and settlement of the coral Acropora muricata?”, CORAL REEFS, 33(2), 431-440. (SCI) (IF: 3; SCI ranking: 8.7%)
      32. Woo S, Lee A, Denis V, Chen CA, Yum S, 2014, “Transcript response of soft coral (Scleronephthya gracillimum) on exposure to polycyclic aromatic hydrocarbons”, Environmental Science and Pollution Research, 21(2), 901-910. (SCI) (IF: 2.76; SCI ranking: 28.9%)
      33. E. Slooten*, J. Y. Wang, S. Z. Dungan, K. A. Forney, S. K. Hung, T. A. Jefferson, K. N. Riehl, L. Rojas-Bracho, P. S. Ross, A. Wee, R. Winkler, S.-C.Yang and C A. Chen, 2013, “Impacts of fisheries on the Critically Endangered humpback dolphin Sousa chinensis population in the eastern Taiwan Strait”, Endangered Species Research, 22, 99-114. (SCI) (IF: 1.325; SCI ranking: 44.9%)
      34. Chia-Min Hsu, Jih-Terng Wang, Chaolun Allen Chen*, 2013, “Larval release and rapid settlement of the coral-killing sponge, Terpios hoshinota, at Green Island, Taiwan”, Marine Biodiversity, 43(4), 259-260. (SCI) (IF: 1.915; SCI ranking: 34.6%,36.7%)
      35. Mohammad Reza Rahmani, Hassan Rahimian, Mahnaz Ardalan, Shashank Keshavmurthy, Silvia Fontana, Carden C Wallace, Chaolun Allen Chen*, 2013, “Acropora distribution patterns in the northern and northeastern Persian Gulf”, ZOOLOGICAL STUDIES, 52, 40. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      36. M.-F. Lin, C. A. Chen*, D. J. Miller, 2013, “Asexual reproduction by marginal budding in the tropical corallimorpharian, Ricordea yuma (Corallimorpharia; Ricordeidae)”, Galaxea, 15 (2), 41-42.
      37. Shang-Yin Vanson Liu, Chia-Ling Carynn Chan, Oceana Lin, Chieh-Shen Hu, Chaolun Allen Chen*, 2013, “DNA Barcoding of Shark Meats Identify Species Composition and CITES-Listed Species from the Markets in Taiwan”, PLoS One, 8(11), e79373. (SCI) (IF: 3.057; SCI ranking: 17.5%)
      38. J. H. Pinzon, E. Sampayo, E. Cox, L. J. Chauka, C. A. Chen, C. R. Voolstra, T. C. LaJeunesse*, 2013, “Blind to morphology: genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia)”, JOURNAL OF BIOGEOGRAPHY, 40(8), 1595-1608. (SCI) (IF: 3.997; SCI ranking: 10.2%,17.3%)
      39. Colin Kuo-Chang Wen, Kao-Song Chen, Hernyi Justin Hsieh, Chia-Min Hsu, Chaolun Allen Chen*, 2013, “High coral cover and subsequent high fish richness on mature breakwaters in Taiwan”, Marine Pollution Bulletin, 72(1), 55-63. (SCI) (IF: 3.099; SCI ranking: 24.9%,5.8%)
      40. Shashank Keshavmurthy, Sung-Yin Yang, Ada Alamaru, Yao-Yang Chuang, Michel Pichon,David Obura, Silvia Fontana, Stephane De Palmas, Fabrizio Stefani, Francesca Benzoni, Angus MacDonald, Annika M. E. Noreen, Chienshun Chen, Carden C. Wallace,Ruby Moothein Pillay, Vianney Denis, Affendi Yang Amri, James D. Reimer, Takuma Mezaki,Charles Sheppard, Yossi Loya, Avidor Abelson, Mohammed Suleiman Mohammed,Andrew C. Baker, Pargol Ghavam Mostafavi, Budiyanto A. Suharsono, Chaolun Allen Chen*, 2013, “DNA barcoding reveals the coral 'laboratory-rat', Stylophora pistillata encompasses multiple identities”, Scientific Reports, 3, 1520. (SCI) (IF: 5.228; SCI ranking: 11.1%)
      41. V. Denis, C. A. Chen*, J. I. Song, S. Woo, 2013, “Alveopora japonica beds thriving under kelp”, Coral Reefs, 32(2) ,503. (SCI) (IF: 3; SCI ranking: 8.7%)
      42. V. Denis, T. Mezaki, K. Tanaka, C.-Y. Kuo, S. del Palmas, S. Keshavmurthy, C. A. Chen* , 2013, “Coverage, diversity and functionality of a high latitude coral community (Tatsukushi, Shikoku Island, Japan)”, PLoS One, 8(1), e54330. (SCI) (IF: 3.057; SCI ranking: 17.5%)
      43. Y.-T. Lien, S. Keshavmurthy, Y. Nakano, S. Plathong, H. Huang, H. Fukami, Y. Yamashita, C. A. Chen*, 2013, “Host genetics and Symbiodinium D diversity in a stress-tolerant scleractinian coral, Oulastrea crispata, in the West Pacific.”, MARINE ECOLOGY PROGRESS SERIES, 473, 163-177. (SCI) (IF: 2.361; SCI ranking: 24.6%,38%,22.1%)
      44. S. Fotana, S. Keshavmurthy, H. J. Hsieh, V. Denis, C. Y. Kuo, C. M. Hsui, C. A. Chen* , 2012, “Molecular evidence shows low species diversity of coral-associated hydroids in Acropora corals”, PLoS One, 7(11), e50130. (SCI) (IF: 3.057; SCI ranking: 17.5%)
      45. J.-T. Wang, Y.-Y. Chen, K. S. Tew, P.-J. Meng, C. A. Chen, 2012, “Physiological and biochemical performances of menthol-induced aposymbiotic corals”, PLoS One, 7(9), e46406. (SCI) (IF: 3.057; SCI ranking: 17.5%)
      46. C.-Y. Kuo, P.-J. Meng, P.-H. Ho, J.-T. Wang, J.-P. Chen, Y.-W. Chiu, H.-J Lin,Y.-C. Chang, T.-Y. Fan, A. H. Baird, C. A. Chen*, 2012, “Recurrent disturbances and the degradation of hard coral communities in Taiwan”, PLoS One, 7(8), e44364. (SCI) (IF: 3.057; SCI ranking: 17.5%)
      47. S. Keshavmurthy, C.-H. Lan, C.-M. Hsui, P.-J. Meng, J.-T. Wang, C. A. Chen*, 2012, “Symbiont communities and host genetic structure of the brain coral Platygyra verweyi, at the outlet of a nuclear power plant and adjacent areas”, Molecular Ecology, 21(17), 4393-4407. (SCI) (IF: 5.947; SCI ranking: 12.1%,7.3%,10.9%)
      48. Mei-Fang Lin, Marcelo Visentini Kitahara, Hiroyuki Tachikawa, Hironobu Fukami, David John Miller, Chaolun Allen Chen*, 2012, “Novel organization of the mitochondrial genome in the deep-sea coral, Madrepora oculata (Hexacorallia, Scleractinia, Oculinidae) and its taxonomic implications ”, Molecular Phylogenetics and Evolution, 65(1), 323-328. (SCI) (IF: 3.792; SCI ranking: 27.7%,28.3%,29.1%)
      49. J.-T. Wang, E. Hirose, C.-M. Hsu, Y.-Y. Chen, P.-J. Meng, C. A. Chen, 2012, “Coral-killing sponge, Terpios hoshinota, releases larvae harbouring cyanobacterial symbionts: an implication of dispersal”, Zoological Studies, 51(3), 314-320. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      50. S.-Y. Yang, S. Keshavmurthy, D. Obura, C. Shappard, S. Visram, C. A. Chen*, 2012, “Diversity and distribution of symbiodinium associated with seven common coral species in the Chagos Archipelago, central Indian Ocean”, PLoS One, 7(5), e35836. (SCI) (IF: 3.057; SCI ranking: 17.5%)
      51. Y. A. Huang, S.-C. Huang, P.-J. Meng, H. J. Hsieh, C. A. Chen*, 2012, “Influence of seasonal monsoon winds on the water quality around a marine cage-culture zone in a semi-closed embayment in Taiwan”, Marine Pollution Bulletin, 64(4), 851-860. (SCI) (IF: 3.099; SCI ranking: 24.9%,5.8%)
      52. M.-F. Lin, M. Kitahara, H. Tachikawa, S. Keshavmurthy, C. A. Chen* , 2012, “A new unusual shallow-water species, Polycyathus chaishanensis sp. nov. (Scleractinia: Caryophylliidae), from Chaishan, Kaohsiung, Taiwan”, Zoological Studies, 51(2), 213-221. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      53. J. T. Wang, P. J. Meng, Y. Y. Chen, and C. A. Chen, 2012, “Determination of the thermal tolerance of Symbiodinium using the activation energy for inhibiting photosystem II activity”, Zoological Studies, 51(2), 137-142. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      54. J.-T. Wang, Y.-Y. Chen, P.-J. Meng, Y.-H. Sune, C.-M. Hsu, K.-Y. Wei, C. A. Chen, 2012, “Diverse interactions between corals and the coral-killing sponge, Terpios hoshinota (Suberitidae; Hadromerida)”, Zoological Studies, 51(2),150-159. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      55. S. Keshavmurthy, C.-M. Hsu, C.-Y. Kuo, V. Dennis, K.-L. J. Leung, S. Fronta, H. J. Hsieh, W.-S. Tsai, W.-C. Su, C. A. Chen*, 2012, “Larvae development of the fertilized “pseudo-gynodiecious” eggs in Galaxea fascicularis”, Zoological Studies, 51(2),143-149. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      56. M. Pichon*, Y.-Y. Chuang, C. A. Chen*, 2012, “Pseudosiderastrea formosa sp. nov. (Cnidaria: Anthozoa: Scleractinia) a New Coral Species Endemic to Taiwan”, Zoological Studies, 51(1), 93-98. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      57. N. V. Wei, H. J. Hsieh, C.-F. Dai, C. C. Wallace, A. H. Baird, C. A. Chen* , 2012, “Reproductive Isolation among Acropora Species (Scleractinia: Acroporidae) in a Marginal Coral Assemblage”, Zoological Studies, 51(1), 85-92. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      58. Y. A. Huang, S.-C. Huang, P.-J. Meng, H. J. Hsieh, C. A. Chen* , 2012, “Changes in sedimentation, sediment characteristics, and benthic macrofaunal assemblages around marine cage culture under seasonal monsoon scales in a shallow-water bay in Taiwan ”, JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY, 422-423, 55-63. (SCI) (IF: 1.796; SCI ranking: 42.3%,52.7%)
      59. Denis V, Leung JKL, Hsu CM, Hsieh HJ, Tsai WS, Chen CA* , 2012, “Dark survival of Oulastrea crispata”, Galaxea: Journal of Coral Reefs Studies, 14(1), 117-118. (J-Stage)
      60. Sheppard, C. R. C., M. Ateweberhan, B. W. Bowen, P. Carr, C. A. Chen, 2012, “Reefs and islands of the Chagos Archipelago, Indian Ocean: why it is the world's largest no-take marine protected area”, Aquatic Conservation-Marine and Freshwater Ecosystems, 22(2), 232-261. (SCI) (IF: 2.415; SCI ranking: 33.3%,15.3%,18.3%)
      61. Chia-Min Hsu, Shashank Keshavmurthy, Vianney Denis, Chao-Yang Kuo, Jih-Terng Wang, Pei-Jie Meng, and Chaolun Allen Chen*, 2012, “Temporal and Spatial Variations in Symbiont Communities of Catch Bowl Coral Isopora palifera (Scleractinia: Acroporidae) on Reefs in Kenting National Park, Taiwan”, ZOOLOGICAL STUDIES, 55(8), 1343-1353. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      62. H. J. Hsieh, K.-S. Chen Y. I. Lin, A. Baird, W.-S. Tsai, W.-C. Su, C. A. Chen*, 2011, “Establishment of a No-take Area (NTA) could not guarantee the preservation of coral Communities in Chinwan Inner Bay, Penghu, Taiwan”, ZOOLOGICAL STUDIES, 50(4), 443-453. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      63. C.-Y. Kuo, P.-J. Meng, P.-H. Ho, J.-T. Wang, J.-P. Chen, Y.-W. Chiu, H.-J Lin,Y.-C. Chang, T.-Y. Fan, C. A. Chen*, 2011, “Damage to the reefs of Siangjiao Bay marine protected area in Kenting National Park, Taiwan during Typhoon Morakot”, ZOOLOGICAL STUDIES, 50(1),85. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      64. F. Stafani, F. Benzoni, S.-Y. Yang, M. Pichon, C. A. Chen, 2011, “Comparison of morphological and genetic analyses reveals cryptic divergence and morphological plasticity in Stylophora (Cnidaria, Scleractinia) ”, Coral Reefs, 30(4), 1033-1049. (SCI) (IF: 3; SCI ranking: 8.7%)
      65. K.-S. Chen, H. J. Hsieh, S. Keshavmurthy, J. K. L. Leung, I.-T. Lien, Y. Nakano, S. Plathong, H Huang, C. A. Chen* , 2011, “Latitudinal gradient of morphological variation in zebra coral, Oulastrea crispata (Scleractinia; Faviidae) in the West Pacific”, ZOOLOGICAL STUDIES, 50(1), 43-52. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      66. Yuan-Chao Angelo Huang, Hernyi Justin Hsieh, Shou-Chung Huang, Pei-Jie Meng, Yung-Song Chen, Keshavmurthy Shashank, Yoko Nozawa, Chaolun Allen Chen*, 2011, “Nutrient enrichment caused by marine cage culture and its influence on subtropical coral communities in turbid waters”, Marine Ecology Progress Series, 423, 83-93. (SCI) (IF: 2.361; SCI ranking: 24.6%,38%,22.1%)
      67. J.-T. Wang, P.-J Meng, E. Sampayo, S.-L. Tang, C. A. Chen, 2011, “Photosystem II breakdown induced by reactive oxygen species (ROS) in the freshly-isolated Symbiodinium of Montipora (Scleractinia; Acropordiae) ”, Marine Ecology Progress Series, 422, 51-62. (SCI) (IF: 2.361; SCI ranking: 24.6%,38%,22.1%)
      68. M.-F. Lin, K. S. Luzon, W. Y. Licuanan, M. C. Ablan-Lagman, C. A. Chen*, 2011, “Seventy-four universal primers for characterizing the complete mitochondrial genomes of scleractinian corals (Cnidaria; Anthozoa) ”, Zoological Studies, 50(4), 513-524. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      69. S.-Y. Sheu, Jiang SR, C. A. Chen , Wang JT, Chen WM , 2010, “Paracoccus stylophorae sp. nov., isolated from the reef-building coral Stylophora pistillata”, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 61(9), 2221-2226. (SCI) (IF: 2.439; SCI ranking: 52.8%)
      70. C.-P. Chen, Tseng C.-H., C. A. Chen, S. L. Tang , 2010, “The dynamics of microbial partnerships in the coral Isopora palifera”, The ISME Journal, 5(4), 728-740. (SCI) (IF: 9.328; SCI ranking: 2.7%,6.5%)
      71. S.-Y., Sheu Jiang SR, C. A. Chen, Wang J.-T., Chen W.-M, 2010, “Vibrio stylophorae sp. nov., isolated from the reef-building coral Stylophora pistillata”, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 61(9), 2180-2185. (SCI) (IF: 2.439; SCI ranking: 52.8%)
      72. M.-H. Chen, Sheu SY, C. A. Chen, Wang JT, Chen WM , 2010, “Paracoccus isoporae sp. nov., isolated from the reef-building coral Isopora palifera ”, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 61(5), 1138-1143. (SCI) (IF: 2.439; SCI ranking: 52.8%)
      73. C.-S. Yang, Chen MH, Arun AB, C. A. Chen, Wang JT, Chen WM , 2010, “Endozoicomonas montiporae sp. nov., isolated from the encrusting pore coral Montipora aequituberculata ”, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 60(Pt 5), 1158-1162. (SCI) (IF: 2.439; SCI ranking: 52.8%)
      74. M.-H. Chen, Sheu SY, C. A. Chen, Wang JT, Chen WM , 2010, “Shimia isoporae sp. nov., isolated from the reef-building coral Isopora palifera”, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 61(4), 823-827. (SCI) (IF: 2.439; SCI ranking: 52.8%)
      75. P.-C. Tang, C.-M. Hsu, C.-Y. Kuo, C. A. Chen* , 2010, “An unexpectedly high Acropora species diversity in the inlet of a nuclear power plant within Kenting National Park, southern Taiwan”, ZOOLOGICAL STUDIES, 49(1), 71. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      76. P.-C. Tang, N. V. Wei, C. C. Wallace, C. A. Chen* , 2010, “Comparative study of genetic utility of AAT and GT/CT microsatellites in staghorn coral, Acropora”, ZOOLOGICAL STUDIES, 49(5), 657-668. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      77. S. Visram, M-C Yang, R. Moothien Pillay, S. Said, O. Henriksson, M. Grahn, C. A. Chen , 2010, “Genetic connectivity and historical demography of the blue barred parrotfish (Scarus ghobban) in the Western Indian Ocean”, MARINE BIOLOGY, 157(7), 1475-1487. (SCI) (IF: 2.375; SCI ranking: 20.2%)
      78. Hong, M.J., Y.T.Yu, C.A. Chen, P.W. Chiang, S.L. Tang, 2009, “Influence of Species Specificity and Other Factors on Bacteria Associated with the Coral Stylophora pistillata in Taiwan”, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 75(24),7797-7806. (SCI) (IF: 3.823; SCI ranking: 25.2%,20.5%)
      79. M. J. Yang, H.-L. Hsieh, C.-P. Chen, C. A. Chen* , 2009, “Is a Living Fossil about to Go Locally Extinct? No Mitochondrial Genetic Variation in Horseshoe Crab Juveniles Tachypleus tridentatus at Haomeiliao Nature Reserve, Budai, Taiwan ”, ZOOLOGICAL STUDIES, 48(6), 737. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      80. Sheu, S.Y., T.F.Chiu, J.H.Chou, D.S.Sheu, A.B.Arun, C.C.Young, C.A.Chen, J.T.Wang, W.M.Chen, 2009, “Andreprevotia lacus sp nov., isolated from a fish-culture pond”, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 59,2482-2485. (SCI) (IF: 2.439; SCI ranking: 52.8%)
      81. Sheu, S.Y., T.F. Chiu, N.T.Cho, J.H.Chou, D.S.Sheu, A.B. Arun, C.C.Young, C.A.Chen, J.T.Wang, W.M.Chen, 2009, “Flectobacillus roseus sp nov., isolated from freshwater in Taiwan”, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 59, 2546-2551. (SCI) (IF: 2.439; SCI ranking: 52.8%)
      82. Chou, J.H., Y.J. Chou, A.B.Arun, C.C. Young, C.A. Chen, J.T.Wang, W.M.Chen, 2009, “Vogesella lacus sp nov., isolated from a soft-shell turtle culture pond”, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 59,2629-2632. (SCI) (IF: 2.439; SCI ranking: 52.8%)
      83. Soong, K., S.L.Yang, C.A. Chen, 2009, “A Novel Dispersal Mechanism of a Coral-Threatening Sponge, Terpios hoshinota (Suberitidae, Porifera)”, ZOOLOGICAL STUDIES, 48(5),596-596. (SCI) (IF: 0.885; SCI ranking: 56.5%)
      84. Tsang, L.M., B.K.K. Chan, F.L. Shih, K.H. Chu, C.A.Chen, 2009, “Host-associated speciation in the coral barnacle Wanella milleporae (Cirripedia: Pyrgomatidae) inhabiting the Millepora coral”, MOLECULAR ECOLOGY, 18(7), 1463-1475. (SCI) (IF: 5.947; SCI ranking: 12.1%,7.3%,10.9%)
      85. Chen, I. P., C.Y. Chung, C.Y. Chiou, J.H. Hsui, N. V. Wei, C. C. Wallace, P. Muir, H. Wu, C. A. Chen*, 2009, “Comparative analyses of coding and noncoding DNA regions indicate that Acropora spp (Anthozoa; Scleractina) possess a similar evolutionary tempo of nuclear vs. mitochondrial genomes in plants”, MARINE BIOTECHNOLOGY, 11(1),141-152. (SCI) (IF: 3.062; SCI ranking: 29.8%,6.7%)