Chenhong Li, Ph.D.

Contact Information

College of Fisheries and Life Science
Shanghai Ocean University
999 Hucheng Huan Road, Pudong New District
Shanghai 201306, China
Phone: +86 21 61900495
Fax: +86 21 61900263
email: chli at


Postdoctoral Fellow, College of Charleston, Charleston, SC, (2010.8-2012.8). Advisor: Gavin Naylor.
Visiting Scholar, University of York, UK, (2011.1-2011.5). Advisor: Michael Hofreiter.
Postdoctoral Research Associate, University of Nebraska – Lincoln, (2007.8-2010.8). Advisor: Guillermo Ortí.
Ph. D., Biological Sciences-Ecology, Evolution, and Behavior. University of Nebraska, Lincoln, NE (2007). Advisor: Guillermo Ortí.
Ph. D. student (transferred to UNL), Marine Biology. Florida Institute of Technology, Melbourne, FL (2001-2002). Advisor: Junda Lin.
M. S., Aquaculture. Shanghai Fisheries University, Shanghai, China (1996). Advisor: Sifa Li.
B. S., Hydrobiology. Shanghai Fisheries University, Shanghai, China (1993).


I am interested in inferring evolutionary history of fishes using genomic sequence data. We are currently using gene-capture method to collect sequences from thousands of single-copy coding loci. My other research focus is to investigate genetic changes underline adaptive evolution of fishes, such as adapted to different salinity or temperature range. We have started using whole genome sequences to screen those changes.

Book Chapters

  1. Ortí, G, Li, C. 2009. Phylogeny and Classification (Chapter 1). pp 1-24 in: Jamieson, B.G.M. (Eds.), Reproductive Biology and Phylogeny of Fishes. Science Publishers, Enfield, New Hampshire.

  2. Ortí, G, Li, C., Farias, I. P. 2005. Filogenia, filogeografíay estructura poblacional de las especies de Prochilodus (Prochilodontidae, Characiformes) en las principales cuencas fluviales de Sudamérica. In: Renno J. -F., García-Dávila C., Duponchelle F. and Nuñez J. (Eds.), Biología de las Poblaciones de Peces de la Amazoníay Piscicultura. Comunicaciones del Primer coloquio de la Red de Investigación sobre la Ictiofauna Amazónica, Iquitos, Perú, pp. 116-122.

Selected Publications

  1. Kuang T, L Tornabene, J Li, J Jiang, P Chakrabartye, J S Spark, G J.P. Naylor, C Li, 2018. Phylogenomic analysis on the exceptionally diverse fish clade Gobioidei (Actinopterygii: Gobiiformes) and data-filtering based on molecular clocklikeness. Molecular Phylogenetics and Evolution, 128, 192-202.

  2. Liu S, Wang C, Li C, 2018. Progress in Aquaculture Genetics and Breeding in China. Journal of World Aquaculture Society, 49 (2): 272-276.

  3. Xia J, Wu H, Li C, Wu Y, Liu S, 2018. A new species of Rhinogobius (Pisces: Gobiidae), with analyses of its DNA barcode. Zootaxa 4407 (4): 553-562.

  4. L C. Hughes, G Ortí, Y Huang, Y Sun, C C. Baldwin, A W. Thompson, D Arcila, R Betancur-R, C Li, L Becker, N Bellora, X Zhao, X Li, M W, C Fang, B Xie, Z Zhou, H Huang, S Chen, B Venkatesh, and Q Shi, 2018. Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proceedings of the National Academy of Sciences of the United States of America, 115(24): 6249-6254. doi:10.1073/pnas.1719358115

  5. Li H, Y. He, J. Jiang, Z. Liu, C. Li, 2018. Molecular systematics and phylogenetic analysis of the Asian endemic freshwater sleepers (Gobiiformes: Odontobutidae). Molecular Phylogenetics and Evolution, 121, 1–11.

  6. Liu J, Jiang J, Song S, Tornabene, L., Chabarria, R., Naylor, G. J. P., Li, C., 2017. Multilocus DNA barcoding - Species Identification with Multilocus Data. Scientific Reports 7, 16601.

  7. Song, S., Zhao, J., Li, C., 2017. Species delimitation and phylogenetic reconstruction of the sinipercids (Perciformes: Sinipercidae) based on target enrichment of thousands of nuclear coding sequences. Molecular Phylogenetics and Evolution, 111, 44-55.

  8. Wang, Q., Zhang, J., Matsumoto, H., Kim, J., Li, C. 2016. Population structure of elongate ilisha Ilisha elongata along the Northwestern Pacific Coast revealed by mitochondrial control region sequences. Fisheries Science, 82 (5): 771 - 785. doi:10.1007/s12562-016-1018-4.

  9. Yuan H, Jiang J, Jimenez FA, Hoberg EP, Cook JA, Galbreath KE, Li C. 2016. Target gene enrichment in the cyclophyllidean cestodes, the most diverse group of tapeworms. Molecular Ecology Resources, 16(5):1095-1106. doi: 10.1111/1755-0998.12532.

  10. PM Delser, Corrigan S., Hale M., Li C., Veuille M., Planes S., Naylor G., Mona S. 2016. Population genomics of C. melanopterus using target gene capture data: demographic inferences and conservation perspectives. Scientific Reports, (6): 33753. doi: 10.1038/srep33753

  11. Chenhong Li, Shannon Corrigan , Lei Yang , Nicolas Straube , Mark Harris , Michael Hofreiter , William T. White , Gavin Naylor, 2015. DNA Capture Reveals Trans Oceanic Gene Flow in Endangered River Sharks. Proceedings of the National Academy of Sciences of the United States of America,

  12. Nicolas Straube, Chenhong Li, Julien M. Claes, Shannon Corrigan and Gavin J. P. Naylor, 2015. Molecular phylogeny of Squaliformes and first occurrence of bioluminescence in sharks. BMC: Evolutionary Biology, 15:162. DOI 10.1186/s12862-015-0446-6.

  13. Li, C., M., Hofreiter, N., Straube, S., Corrigan, G. J. P. Naylor, 2013. Capturing protein-coding genes across highly divergent species. BioTechniques 54:321-326

  14. Betancur-R. R, Broughton RE, Wiley EO, Carpenter K, López JA, Li C, Holcroft NI, Arcila D, Sanciangco M, Cureton II JC, Zhang F, Buser T, Campbell MA, Ballesteros JA, Roa-Varon A, Willis S, Borden WC, Rowley T, Reneau PC, Hough DJ, Lu G, Grande T, Arratia G, Ortí G., 2013. The Tree of Life and a New Classification of Bony Fishes. PLOS Currents Tree of Life. 2013 Apr 18.

  15. Broughton RE, Betancur-R. R, Li C, Arratia G, Ortí G. Multi-locus phylogenetic analysis reveals the pattern and tempo of bony fish evolution. PLOS Currents Tree of Life. 2013 Apr 16.

  16. Li, C., Riethoven, J.-J. M., Naylor, G. 2012. EvolMarkers: a database for mining exon and intron markers for evolution, ecology and conservation studies. Molecular Ecology Resources, 12(5):967-71.

  17. Li, C., Lu, G., Ortí, G., 2008. Optimal data partitioning and a test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci. Systematic Biology, 57(4): 519- 539.

  18. Li, C., Ortí, G., Zhang, G., Lu, G., 2007. A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC: Evolutionary Biology, 7: 44.

  19. Li, C., Ortí, G., 2007. Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences, Molecular Phylogenetics and Evolution 44: 386-398.

  20. Li, S., Li, C., Dey, M., Dunham, R., 1999. Seinability of four strains of Nile tilapia, Oreochromis niloticus, in Chinese ponds. Aquaculture, 174: 223-227

Full list of publication


I am teaching undergraduate course: Introductory Zoology, Ichthyology, Undergraduate Seminar - Fish Diversity, and graduate course: Bioinformatics, Methods in Molecular Systematics and Ecology.