J Syst Evol ›› 2019, Vol. 57 ›› Issue (3): 268-277.doi: 10.1111/jse.12461

• Research Articles • Previous Articles     Next Articles

Analyses of genome‐scale variation reveal divergence of two Sinalliaria species (Brassicaceae) with continuous but limited gene flow

Tian-Jing Wang, Da-Fu Ru, Dan-Zhang, and Quan-Jun Hu*   

  1. Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
  • Received:2018-04-07 Accepted:2018-08-30 Online:2019-01-01 Published:2019-06-06

Abstract: Numerous biogeographic studies have suggested that geographic isolations triggered by Quaternary climatic changes could have contributed greatly to the high species diversity of eastern Asia. However, little is known about how speciation proceeded during the evolutionary divergence of sister species in this region. In this study, we examined genomic divergence and investigated the speciation process of the two species in the genus Sinalliaria endemic to eastern China, S. limprichtiana (Pax) X. F. Jin, Y. Y. Zhou & H. W. Zhang and S. grandifolia (Z. X. An) Huan Hu, com. nov. (Basionym: Alliaria grandifolia Z. X. An (Acta Phytotax. Sin. 23: 396, 1985)). We sequenced the transcriptomes of seven and eight S. limprichtiana and S. grandifolia individuals, respectively. Analysis of transcriptome single nucleotide polymorphism data indicated that both species were well‐delineated with strong genetic differentiation (mean FST?=?0.31). A total of 4000 genes showed differential expression between the two species. Based on these genome‐scale nucleotide variations, we used the allele frequency spectrum for modeling analysis with fastsimcoal to gain insights into the speciation process. Our results suggested divergence with continuous gene flow between the two species. These findings will add to our knowledge on the origin of species diversity in eastern Asia.

Key words: divergence, gene flow, genome-scale variation, Sinalliaria, speciation pattern

[1] Umar Zeb, Wan-Lin Dong, Ting-Ting Zhang, Ruo-Nan Wang, Khurram Shahzad, Xiong-Feng Ma, and Zhong-Hu Li. Comparative plastid genomics of Pinus species: Insights into sequence variations and phylogenetic relationships . J Syst Evol, 2020, 58(2): 118-132.
[2] Salvatore Cozzolino, Giovanni Scopece, Luca Roma, Philipp M. Schlüter. Different filtering strategies of genotyping‐by‐sequencing data provide complementary resolutions of species boundaries and relationships in a clade of sexually deceptive orchids . J Syst Evol, 2020, 58(2): 133-144.
[3] Joseph A. Kleinkopf, Wade R. Roberts, Warren L. Wagner, and Eric H. Roalson. Diversification of Hawaiian Cyrtandra (Gesneriaceae) under the influence of incomplete lineage sorting and hybridization . J Syst Evol, 2019, 57(6): 561-578.
[4] Shu-Li Wang, Lang Li, Xiu-Qin Ci, John G. Conran, and Jie Li. Taxonomic status and distribution of Mirabilis himalaica (Nyctaginaceae) . J Syst Evol, 2019, 57(5): 431-439.
[5] Xiao-Yue Yang, Ze-Fu Wang, Wen-Chun Luo, Xin-Yi Guo, Cai-Hua Zhang, Jian-Quan Liu, and Guang-Peng Ren. Plastomes of Betulaceae and phylogenetic implications . J Syst Evol, 2019, 57(5): 508-518.
[6] Wu-Qin Xu, Jocelyn Losh, Chuan Chen, Pan Li, Rui-Hong Wang, Yun-Peng Zhao, Ying-Xiong Qiu, Cheng-Xin Fu. Comparative genomics of figworts (Scrophularia, Scrophulariaceae), with implications for the evolution of Scrophularia and Lamiales . J Syst Evol, 2019, 57(1): 55-65.
[7] David J. Hearn, Margaret Evans, Ben Wolf, Michael McGinty, Jun Wen. Dispersal is associated with morphological innovation, but not increased diversification, in Cyphostemma (Vitaceae) . J Syst Evol, 2018, 56(4): 340-359.
[8] Man Zhao, Xiangxian Ying, Jie SunZhao Wang. Molecular evolution of Coq1 gene family in eukaryotes . J Syst Evol, 2017, 55(5): 417-425.
[9] Jonathan P. Spoelhof, Pamela S. Soltis, Douglas E. Soltis. Pure polyploidy: Closing the gaps in autopolyploid research . J Syst Evol, 2017, 55(4): 340-352.
[10] Si Xu, Zong-Yan Qin, Pi-Chang Gong, Qian-Li Dong, Ying Bao. Identification and characterization of Rubisco activase genes in Oryza punctata . J Syst Evol, 2017, 55(3): 200-207.
[11] Pan-Pan Wu, Hong-Wei Zuo, Genlou Sun, De-Xiang Wu, Bjorn Salomon, Qun-Wen Hu, Zhao-Rong Dong. Comparison of gene flow among species that occur within the same geographic locations versus gene flow among populations within species reveals introgression among several Elymus species . J Syst Evol, 2016, 54(2): 152-161.
[12] Weronika B. Żukowska, Witold Wachowiak. Utility of closely related taxa for genetic studies of adaptive variation and speciation: Current state and perspectives in plants with focus on forest tree species . J Syst Evol, 2016, 54(1): 17-28.
[13] Wei WANG, Hong-Lei LI, Xiao-Guo XIANG, Zhi-Duan CHEN. Revisiting the phylogeny of Ranunculeae: Implications for divergence time estimation and historical biogeography . J Syst Evol, 2014, 52(5): 551-565.
[14] Hong-Mei LIU, Li-Juan HE, Harald SCHNEIDER. Towards the natural classification of tectarioid ferns: Confirming the phylogenetic relationships of Pleocnemia and Pteridrys (eupolypods I) . J Syst Evol, 2014, 52(2): 161-174.
[15] Jin CHENG, Lei XIE. Molecular phylogeny and historical biogeography of Caltha (Ranunculaceae) based on analyses of multiple nuclear and plastid sequences . J Syst Evol, 2014, 52(1): 51-67.
Full text



[1] LIU Jun;ZHAO Lan-Yong;FENG Zhen;ZHANG Mei-Rong;WU Yin-Feng. Optimization Selection of Genetic Transformation Regeneration System from Leaves of Dendranthema morifolium[J]. Chin Bull Bot, 2004, 21(05): 556 -558 .
[2] Luo Jian-ping and Ja Jing-fen. Structure and Function of Plant Oligosaceaharins[J]. Chin Bull Bot, 1996, 13(04): 28 -33 .
[3] YANG Qi-He SONG Song-Quan YE Wan-HuiYIN Shou-HuaT. Mechanism of Seed Photosensitivity and FactorsInfluencing Seed Photosensitivity[J]. Chin Bull Bot, 2003, 20(02): 238 -247 .
[4] CUI Yue-Hua;WANG Mao and SUN Ke-Lian. Morphological Study of Gutta-containing Cells in Eucommia ulmoides Oliv.[J]. Chin Bull Bot, 1999, 16(04): 439 -443 .
[5] CHEN Shao-Liang LI Jin-Ke BI Wang-Fu WANG Sha-Sheng. Genotypic Variation in Accumulation of Salt Ions, Betaine and Sugars in Poplar Under Conditions of Salt Stress[J]. Chin Bull Bot, 2001, 18(05): 587 -596 .
[6] . Advances in Research into Low-Phytic-Acid Mutants in Crops[J]. Chin Bull Bot, 2005, 22(04): 463 -470 .
[7] Cong Ma, Weiwen Kong. Research Progress in Plant Metacaspase[J]. Chin Bull Bot, 2012, 47(5): 543 -549 .
[8] Chang’en Tian, Yuping Zhou. Research Progress in Plant IQ Motif-containing Calmodulin-binding Proteins[J]. Chin Bull Bot, 2013, 48(4): 447 -460 .
[9] Huawei Xu, Dianyun Hou. Research Advances in Protein Transport into Chloroplasts in Plant Cell#br#[J]. Chin Bull Bot, 2018, 53(2): 264 -275 .
[10] Li Jiandong, Zheng Huiying. ?ber die Anwendung der Braun-Blanquet's Methode in der Steppen-Untersuchung[J]. Chin J Plan Ecolo, 1983, 7(3): 186 -203 .