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

Handle URI:
http://hdl.handle.net/10754/575622
Title:
Adaptive divergence with gene flow in incipient speciation of Miscanthus floridulus / sinensis complex (Poaceae)
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 ( 0000-0001-7850-1743 ) ; Osada, Naoki; Chiang, Tzen-Yuh
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.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division; Bioscience Program; Computational Bioscience Research Center (CBRC); Bioscience Program
Publisher:
Wiley-Blackwell
Journal:
The Plant Journal
Issue Date:
11-Nov-2014
DOI:
10.1111/tpj.12676
Type:
Article
ISSN:
0960-7412
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.
Appears in Collections:
Articles; Bioscience Program; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorHuang, Chao-Lien
dc.contributor.authorHo, Chuan-Wenen
dc.contributor.authorChiang, Yu-Chungen
dc.contributor.authorShigemoto, Yasumasaen
dc.contributor.authorHsu, Tsai-Wenen
dc.contributor.authorHwang, Chi-Chuanen
dc.contributor.authorGe, Xue-Junen
dc.contributor.authorChen, Charlesen
dc.contributor.authorWu, Tai-Hanen
dc.contributor.authorChou, Chang-Hungen
dc.contributor.authorHuang, Hao-Jenen
dc.contributor.authorGojobori, Takashien
dc.contributor.authorOsada, Naokien
dc.contributor.authorChiang, Tzen-Yuhen
dc.date.accessioned2015-08-24T08:34:25Zen
dc.date.available2015-08-24T08:34:25Zen
dc.date.issued2014-11-11en
dc.identifier.issn0960-7412en
dc.identifier.doi10.1111/tpj.12676en
dc.identifier.urihttp://hdl.handle.net/10754/575622en
dc.description.abstractYoung 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.en
dc.description.sponsorshipThe 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.en
dc.publisherWiley-Blackwellen
dc.titleAdaptive divergence with gene flow in incipient speciation of Miscanthus floridulus / sinensis complex (Poaceae)en
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentBioscience Programen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentBioscience Programen
dc.identifier.journalThe Plant Journalen
dc.contributor.institutionDepartment of Life Sciences; National Cheng Kung University; Tainan 701 Taiwanen
dc.contributor.institutionDepartment of Biological Sciences; National Sun Yat-sen University; Kaohsiung 804 Taiwanen
dc.contributor.institutionLife Science Systems Division; Fujitsu Ltd; Shinkamata Ota-ku Tokyo 144-8588 Japanen
dc.contributor.institutionHigh Altitude Experimental Station; Endemic Species Research Institute; Nantou 552 Taiwanen
dc.contributor.institutionDepartment of Engineering Science and Supercomputing Research Center; National Cheng Kung University; Tainan 701 Taiwanen
dc.contributor.institutionKey Laboratory of Plant Resources Conservation and Sustainable Utilization; South China Botanical Garden; Chinese Academy of Sciences; Guangzhou 510650 Chinaen
dc.contributor.institutionInternational Maize and Wheat Improvement Center; CP56130 Texcoco Mexicoen
dc.contributor.institutionResearch Centre for Biodiversity and Graduate Institute of Ecology and Evolutionary Biology; China Medical University; Taichung 404 Taiwanen
dc.contributor.institutionNational Institute of Genetics; Yata Mishima Shizuoka 411-8540 Japanen
kaust.authorGojobori, Takashien
All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.