J Syst Evol ›› 2019, Vol. 57 ›› Issue (3): 278-286.doi: 10.1111/jse.12460

• Research Articles • Previous Articles     Next Articles

Nuclear simple sequence repeat markers are superior to DNA barcodes for identification of closely related Rhododendron species on the same mountain

Ji Wang1+, Jian Luo2+, Ya-Zhen Ma1, Xing-Xing Mao1, and Jian-Quan Liu1*   

  1. 1Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610025, China
    2College of Tibet Agriculture and Animal Husbandry, Nyingchi, Tibet 860000, China
  • Received:2018-05-01 Accepted:2018-08-16 Online:2019-01-01 Published:2019-06-06

Abstract: Accurate species delimitation of sampled biological material is critical for a range of studies. Although the DNA barcodes developed in recent years are useful for identifying numerous well differentiated species that have not experienced frequent gene flow, they fail to delimit recently diverged species, especially those with extensive introgressions. Here we use five Rhododendron species growing together on the same mountain as a model system to compare the species delimitation effectiveness of the DNA barcodes (internal transcribed spacer, matK, psbA‐trnH, and rbcL) previously proposed versus 15 pairs of microsatellite markers. Using these markers, we genotyped 129 individuals, which were members of five species according to morphological identification. We identified five simple sequence repeat genetic clusters (independently evolving lineages) corresponding to the morphological identification. However, we found that numerous individuals contained cryptic hybrid introgressions from the other species. The four DNA barcodes could not delimit three out of four closely related species that showed clear morphological differentiation and cryptic introgressions. Even after excluding all cryptic hybrids, two closely related species could not be successfully identified. The low discrimination ability of the DNA barcodes for closely related Rhododendron species could result from two, not mutually exclusive factors: introgressive hybridization and incomplete lineage sorting. Our results highlight the importance of simple sequence repeat markers in delimiting closely related species and identifying cryptic introgressions in the absence of morphological changes.

Key words: closely related species, cryptic introgression, DNA barcoding, Rhododendron, SSR

[1] Chuan Chen, Li Zheng, Qing Ma, Wen-Bin Zhou, Yin Lu, Yun-Peng Zhao, and Cheng-Xin Fu. Impacts of domestication on population genetics of a traditional Chinese medicinal herb, Atractylodes macrocephala (Asteraceae) . J Syst Evol, 2019, 57(3): 222-233.
[2] Lian-Ming Gao, Yan Li, Loc Ke Phan, Li-Jun Yan, Philip Thomas, Long Ke Phan, Michael Möller, De-Zhu Li. DNA barcoding of East Asian Amentotaxus (Taxaceae): Potential new species and implications for conservation . J Syst Evol, 2017, 55(1): 16-24.
[3] Gezahegn Girma, Charles Spillane, Melaku Gedil. DNA barcoding of the main cultivated yams and selected wild species in the genus Dioscorea . J Syst Evol, 2016, 54(3): 228-237.
[4] Wei Gong, Ying Liu, Jing Chen, Yu Hong, Hang-Hui Kong. DNA barcodes identify Chinese medicinal plants and detect geographical patterns of Sinosenecio (Asteraceae) . J Syst Evol, 2016, 54(1): 83-91.
[5] Yong-Peng MA, Zhi-Kun WU, Kun DONG, Wei-Bang SUN, Tobias MARCZEWSKI. Pollination biology of Rhododendron cyanocarpum (Ericaceae): An alpine species endemic to NW Yunnan, China . J Syst Evol, 2015, 53(1): 63-71.
[6] Yun-Rui MAO, Yong-Hua ZHANG, Koh NAKAMURA, Bi-Cai GUAN, Ying-Xiong QIU. Developing DNA barcodes for species identification in Podophylloideae (Berberidaceae) . J Syst Evol, 2014, 52(4): 487-499.
[7] Zhao-Ming CAI, Yu-Xiao ZHANG, Li-Na ZHANG, Lian-Ming GAO, De-Zhu LI. Testing four candidate barcoding markers in temperate woody bamboos (Poaceae: Bambusoideae) . J Syst Evol, 2012, 50(6): 527-539.
[8] Yong LI, Hai-Fei YAN, Xue-Jun GE. Phylogeographic analysis and environmental niche modeling of widespread shrub Rhododendron simsii in China reveals multiple glacial refugia during the last glacial maximum . J Syst Evol, 2012, 50(4): 362-373.
[9] Jian-Ping HAN, Lin-Chun SHI, Xiao-Chen CHEN, Yu-Lin LIN. Comparison of four DNA barcodes in identifying certain medicinal plants of Lamiaceae . J Syst Evol, 2012, 50(3): 227-234.
[10] Jakub SAWICKI, Vítèzslav PLÁŠEK,Monika SZCZECIŃSKA. Molecular data do not support the current division of Orthotrichum (Bryophyta) species with immersed stomata . J Syst Evol, 2012, 50(1): 12-24.
[11] Jiao-Jun YU, Chiaki KURODA, Xun GONG. Natural hybridization and introgression in sympatric Ligularia species (Asteraceae, Senecioneae) . J Syst Evol, 2011, 49(5): 438-448.
[12] He REN, Lu LU, Hong WANG, De-Zhu LI. DNA Barcoding of Gaultheria L. in China (Ericaceae: Vaccinioideae) . J Syst Evol, 2011, 49(5): 411-424.
[13] Lin-Chun SHI, Jin ZHANG, Jian-Ping HAN, Jing-Yuan SONG,Hui YAO,Ying-Jie ZHU,Jia-Chun LI,Zhen-Zhong WANG,Wei XIAO, Yu-Lin LIN, Cai-Xiang XIE,Zhong-Zhi QIAN, Shi-Lin CHEN. Testing the potential of proposed DNA barcodes for species identification of Zingiberaceae . J Syst Evol, 2011, 49(3): 261-266.
[14] Xiao-Guo XIANG, Jing-Bo ZHANG, An-Ming LU, Rui-Qi LI. Molecular identification of species in Juglandaceae: A tiered method . J Syst Evol, 2011, 49(3): 252-260.
[15] Hai-Fei YAN, Gang HAO, Chi-Ming HU, Xue-Jun GE. DNA barcoding in closely related species: A case study of Primula L. sect. Proliferae Pax (Primulaceae) in China . J Syst Evol, 2011, 49(3): 225-236.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
[1] . [J]. Chin Bull Bot, 2002, 19(01): 121 -124 .
[2] ZHANG Shi-Gong;GAO Ji-Yin and SONG Jing-Zhi. Effects of Betaine on Activities of Membrane Protective Enzymes in Wheat (Triticum aestivum L.) Seedlings Under NaCl Stress[J]. Chin Bull Bot, 1999, 16(04): 429 -432 .
[3] HE Wei-Ming and ZHONG Zhang-Cheng. Effects of Soil Fertility on Gynostemma pentaphyllum Makino Population Behavior[J]. Chin Bull Bot, 1999, 16(04): 425 -428 .
[4] SHE Chao-WenSONG Yun-Chun LIU Li-Hua. Analysis on the G_banded Karyotypes and Its Fluctuation at Different Mitotic Phases and Stages in Triticum tauschii (Aegilops squarrosa)[J]. Chin Bull Bot, 2001, 18(06): 727 -734 .
[5] Guijun Yang, Wenjiang Huang, Jihua Wang, Zhurong Xing. Inversion of Forest Leaf Area Index Calculated from Multi-source and Multi-angle Remote Sensing Data[J]. Chin Bull Bot, 2010, 45(05): 566 -578 .
[6] Man Chen, YishengTu, Linan Ye, Biyun Yang. Effect of Amino Acids on Thallus Growth and Huperzine-A Accumulation in Huperzia serrata[J]. Chin Bull Bot, 2017, 52(2): 218 -224 .
[7] Yefei Shang, Ming Li, Bo Ding, Hao Niu, Zhenning Yang, Xiaoqiang Chen, Gaoyi Cao, Xiaodong Xie. Advances in Auxin Regulation of Plant Stomatal Development[J]. Chin Bull Bot, 2017, 52(2): 235 -240 .
[8] CUI Xiao-Yong, Du Zhan-Chi, Wang Yan-Fen. Photosynthetic Characteristics of a Semi-arid Sandy Grassland Community in Inner Mongolia[J]. Chin J Plan Ecolo, 2000, 24(5): 541 -546 .
[9] LI Wei, ZHANG Ya-Li, HU Yuan-Yuan, YANG Mei-Sen, WU Jie, and ZHANG Wang-Feng. Research on the photoprotection and photosynthesis characteristics of young cotton leaves under field conditions[J]. Chin J Plan Ecolo, 2012, 36(7): 662 -670 .
[10] HU Bao-Zhong, LIU Di, HU Guo-Fu, ZHANG A-Ying, JIANG Shu-Jun. Random Amplified Polymorphic DNA Study of Local Breeds in Chinese lfalfa[J]. Chin J Plan Ecolo, 2000, 24(6): 697 -701 .