Research Interests

Genome evolution, molecular evolution, population genetics and phylogenetics


2008 – 2014

Ph.D., Biology
Department of Biology, University of Konstanz, Germany

2005 – 2008

M.S. Biochemistry and Molecular Biology
College of Life Science, Northwest A&F University, China

2001 – 2005

B.S. Information and Computer Science
College of Science, Northwest A&F University, China

Work Experience

July – December 2014

Postdoctoral Researcher, Department of Biology, University of Konstanz, Germany



Chinese government awards for outstanding self-financed student abroad


Travel grant from Frontiers in Speciation Research for visiting Prof. Yves van de Peer, University of Ghent


DAAD doctoral stipend


ESF conserve genetics and thermal adaptation, travel grant to Ecological Genomics Workshop, Centro Residenziale Universitario di Bertinoro, Bertinoro (FC), Italy


Northwest A&F University, travel grant to Fifth International Bioinformatics Workshop, Weihai, China


  • Fan, S*, Hansen, ME*, Yancy, L*, and Tishkoff SA, Going global by adapting local: A review of recent human adaptation. Science 354(6308):54-59.
    (Cover article) *Co-first authorship

    Lin, Q*, Fan, S*, et al., (2016) The seahorse genome provides insights into the evolution of its specialized body plan. Nature 540:395–399.
    (Cover article) *Co-first authorship

    Fruciano, C, Franchini, P, Raffini, F, Fan, S, Meyer, A (2016) Are sympatrically speciating Midas cichlid fish special? Patterns of morphological and genetic variation in the closely related species Archocentrus centrarchus. Ecology and Evolution. DOI: 10.1002/ece3.2184

    Spotted Gar Genome Consortium. 2016. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics 48(4):427-437.

    Fan, S., Meyer, A (2014) Evolution of genomic structural variation and genomic architecture in the adaptive radiations of African cichlid fishes. Evolutionary and Population Genetics 5:163.

    Elmer, K., Fan, S. et al. (2014) Parallel evolution of Nicaraguan crater lake cichlid fishes via non-parallel routes. Accepted by Nature Communications.

    Cichlid Genome Consortium (2014) The genomic substrate for adaptive radiation: genomes of five African cichlid fish. Nature 513:375–381.

    Chalopin, D., Fan, S., Simakov, O., Meyer, A., Schartl, M. and J.-N. Volff (2013) Evolutionary active transposable elements in the genome of the coelacanth. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution.

    Gunter, H.M., Fan, S., Xiong, F., Franchini, P., Fruciano, C. and A. Meyer (2013) Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish. Molecular Ecology 22:4516-4531.
    Perspective on the article in the "News and Views" section of the journal 

    Amemiya, C.T., Alföldi, J., Lee, A.P., Fan, S., et al. The African coelacanth genome provides insights into tetrapod evolution. Nature 496: 311-316. [Cover article]

    Jones, J.C., Fan, S., Franchini, P., Schartl, M. and A. Meyer (2013) The evolutionary history of Xiphophorus fish and their sexually selected sword: a genome-wide approach using restriction site-associated DNA sequencing. Molecular Ecology 22:2986–3001.
    [Cover article]

    Elmer, K.R., Lehtonen, T.K, Fan, S., and A. Meyer (2013) Crater lake colonization by Neotropical cichlid fishes. Evolution 67:281-288.

    Fan, S., Elmer, K.R. and A. Meyer (2012) Genomics of adaptation and speciation in cichlid fishes: recent advances and analyses in African and Neotropical lineages. Philosophical Transactions of the Royal Society B 367:385-394.

    Fan, S., Elmer, K.R. and A. Meyer. (2011) Positive Darwian selection drives the evolution of the morphology-related gene, EPCAM, in particularly species-rich lineages of African cichlid fishes. Journal of Molecular Evolution 73:1-9. [Cover article]

    Elmer, K.R., Fan, S., Gunter, H.M., Jones, J.C., Boekhoff, S., Kuraku, S. and A. Meyer (2010) Rapid evolution and selection inferred from thetranscriptomes of sympatric crater lake cichlid fishes. Molecular Ecology 19(Suppl. 1):197–211.

    Gong, X, Fan, S  et al. (2008) Comparative analysis of essential genes and nonessential genes in Escherichia coli K12. Molecular Genetics and Genomics 279:87–94. 

    Thompson, WA, Fan, S, Weltman. JK (2008) Information entropy of influenza A segment 7. Entropy 10(4):736-744. 


Programming languages: Perl, BioPerl, R.

Genome and transcriptome assembly: Allpaths-LG, Trinity, Velvet, Tophat
Mapping software: BWA, Bowtie, Stampy.
Phylogenetic analysis: RaxML, Mrbayes, PhyML, MEGA.
Molecular evolution: PAML, MEGA.
Statistical software: R and Matlab.

Academic service

Reviewer for Molecular Ecology, BMC genomics and Molecular Ecology Resources.