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    Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus / sinensis complex (Poaceae)

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    Type
    Article
    Authors
    Huang, Chao-Li
    Ho, Chuan-Wen
    Chiang, Yu-Chung
    Shigemoto, Yasumasa
    Hsu, Tsai-Wen
    Hwang, Chi-Chuan
    Ge, Xue-Jun
    Chen, Charles
    Wu, Tai-Han
    Chou, Chang-Hung
    Huang, Hao-Jen
    Gojobori, Takashi cc
    Osada, Naoki
    Chiang, Tzen-Yuh
    KAUST Department
    Biological and Environmental Sciences and Engineering (BESE) Division
    Bioscience Program
    Computational Bioscience Research Center (CBRC)
    Bioscience Program
    Date
    2014-11-11
    Online Publication Date
    2014-11-11
    Print Publication Date
    2014-12
    Permanent link to this record
    http://hdl.handle.net/10754/575622
    
    Metadata
    Show full item record
    Abstract
    Young incipient species provide ideal materials for untangling the process of ecological speciation in the presence of gene flow. The Miscanthus floridulus/sinensis complex exhibits diverse phenotypic and ecological differences despite recent divergence (approximately 1.59million years ago). To elucidate the process of genetic differentiation during early stages of ecological speciation, we analyzed genomic divergence in the Miscanthus complex using 72 randomly selected genes from a newly assembled transcriptome. In this study, rampant gene flow was detected between species, estimated as M=3.36x10(-9) to 1.20x10(-6), resulting in contradicting phylogenies across loci. Nevertheless, beast analyses revealed the species identity and the effects of extrinsic cohesive forces that counteracted the non-stop introgression. As expected, early in speciation with gene flow, only 3-13 loci were highly diverged; two to five outliers (approximately 2.78-6.94% of the genome) were characterized by strong linkage disequilibrium, and asymmetrically distributed among ecotypes, indicating footprints of diversifying selection. In conclusion, ecological speciation of incipient species of Miscanthus probably followed the parapatric model, whereas allopatric speciation cannot be completely ruled out, especially between the geographically isolated northern and southern M.sinensis, for which no significant gene flow across oceanic barriers was detected. Divergence between local ecotypes in early-stage speciation began at a few genomic regions under the influence of natural selection and divergence hitchhiking that overcame gene flow.
    Citation
    Huang, C.-L., Ho, C.-W., Chiang, Y.-C., Shigemoto, Y., Hsu, T.-W., Hwang, C.-C., … Chiang, T.-Y. (2014). Adaptive divergence with gene flow in incipient speciation ofMiscanthus floridulus/sinensiscomplex (Poaceae). The Plant Journal, 80(5), 834–847. doi:10.1111/tpj.12676
    Sponsors
    The work is supported by the International Research Intensive Centers of Excellence of Taiwan, the Supercomputing Research Center of National Cheng Kung University, and the Aim for the Top University Project of National Cheng Kung University. We thank Peter Raven (President Emeritus of Missouri Botanical Garden) for his valuable comments.
    Publisher
    Wiley
    Journal
    The Plant Journal
    DOI
    10.1111/tpj.12676
    ae974a485f413a2113503eed53cd6c53
    10.1111/tpj.12676
    Scopus Count
    Collections
    Articles; Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Computational Bioscience Research Center (CBRC)

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