title: Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus/sinensis complex (Poaceae).
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 1.59 million 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 = 3.36 × 10(-9) to 1.20 × 10(-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.
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.
authors.forename: Chao-Li
authors.initials: CL
authors.lastname: Huang
authors.forename: Chuan-Wen
authors.initials: CW
authors.lastname: Ho
authors.forename: Yu-Chung
authors.initials: YC
authors.lastname: Chiang
authors.forename: Yasumasa
authors.initials: Y
authors.lastname: Shigemoto
authors.forename: Tsai-Wen
authors.initials: TW
authors.lastname: Hsu
authors.forename: Chi-Chuan
authors.initials: CC
authors.lastname: Hwang
authors.forename: Xue-Jun
authors.initials: XJ
authors.lastname: Ge
authors.forename: Charles
authors.initials: C
authors.lastname: Chen
authors.forename: Tai-Han
authors.initials: TH
authors.lastname: Wu
authors.forename: Chang-Hung
authors.initials: CH
authors.lastname: Chou
authors.forename: Hao-Jen
authors.initials: HJ
authors.lastname: Huang
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
authors.forename: Naoki
authors.initials: N
authors.lastname: Osada
authors.forename: Tzen-Yuh
authors.initials: TY
authors.lastname: Chiang
mesh_terms: D002681:China; D060146:Ecotype; D051456:Gene Flow; D049810:Genetic Speciation; D014644:Genetic Variation; D005828:Genetics, Population; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D010802:Phylogeny; D006109:Poaceae / Q000235:genetics*; D013624:Taiwan
keywords: Miscanthus; diversifying selection; gene flow; incipient speciation; local adaptation; outlier loci; parapatric speciation