Phylogeography of Xanthopappus subacaulis(Asteraceae), an Endemic Species from the Northeastern of the Qinghai-Tibet Plateau

doi:10.7525/j.issn.1673-5102.2022.04.006

Abstract

Abstract:

Xanthopappus subacaulis is an endemic medicinal plant growing in the alpine meadow of the Qinghai-Tibet Plateau（QTP）. To explore the influence of Quaternary climatic oscillations on the population genetic structure and distribution pattern of X. subacaulis， 3 chloroplast DNA fragments（psbA-trnH， rbcL and psbI-psbK） from 123 individuals of 20 populations were sequenced and analyzed respectively in the present study. The results showed that 6 haplotypes were detected in X. subacaulis， among which H1 was an ancient haplotype. All populations of X. subacaulis had haplotype H1 except for P7. H3， H5 and H6 were private haplotypes， among which H3 was a private haplotype of population P7， and H5 and H6 only existed in P18. H2 and H4 were mainly distributed in the population of Qinghai Lake basin. The total genetic diversity（H_e） and nucleotide diversity（π） were 3.101 and 0.008 903， respectively. The genetic variation among populations（68.98%） was higher than that within populations（31.02%）， and the genetic differentiation among populations was relatively higher（F_ST=0.689 85，P<0.01）. The genetic differentiation coefficient N_ST of populations（0.727） was higher than that of G_ST（0.656）（P>0.05）， which indicated that there was no obvious phylogeographical structure in the sampling regions. The results of mismatch distributions and neutrality tests revealed that the population of X. subacaulis might have experienced recent expansion. Therefore， the study suggests there are micro-sanctuaries in Qinghai Lake basin of Qinghai Province and Lintan region of Gansu Province during the Quaternary glaciations， and suggests that the Quaternary climate change and QTP uplift shape the modern geographical distribution pattern of X. subacaulis.

Key words: Xanthopappus subacaulis, genetic structure, dynamic history, chloroplast DNA, Qinghai-Tibet Plateau

CLC Number:

Q948.2

Yang ZHANG, Zilan MA, Shanshan XU, Xu SU, Meiying LI. Phylogeography of Xanthopappus subacaulis(Asteraceae), an Endemic Species from the Northeastern of the Qinghai-Tibet Plateau[J]. Bulletin of Botanical Research, 2022, 42(4): 565-573.

References

1	AVISE J C， ARNOLD J， BALL R M，et al.Intraspecific phylogeography：the mitochondrial DNA bridge between population genetics and systematics［J］.Annual Review of Ecology and Systematics，1987，18：489-522.
2	AVISE J C.Phylogeography：the history and formation of species［M］.Cambridge：Harvard University Press，2000.
3	PROVAN J， BENNETT K D.Phylogeographic insights into cryptic glacial refugia［J］.Trends in Ecology & Evolution，2008，23（10）：564-571.
4	COMES H P， KADEREIT J W.The effect of Quaternary climatic changes on plant distribution and evolution［J］.Trends in Plant Science，1998，3（11）：432-438.
5	施雅风，李吉钧，李炳元.青藏高原晚新生代隆升与环境变化［M］.广州：广东科技出版社，1998.
5	SHI Y F， LI J J， LI B Y.Uplift and environmental changes of Qinghai-Xizang（Tibetan） Plateau in the late Cenozoic［M］.Guangzhou：Guangdong Science and Technology Press，1998.
6	ZHENG D.The system of physico-geographical regions of the Qinghai-Xizang（Tibet） Plateau［J］.Science in China（Series D），1996，39（4）：410-417.
7	QIU Y X， FU C X， COMES H P.Plant molecular phylogeography in China and adjacent regions：tracing the genetic imprints of Quaternary climate and environmental change in the world’s most diverse temperate flora［J］.Molecular Phylogenetics and Evolution，2011，59（1）：225-244.
8	WANG H， QIONG L， SUN K，et al.Phylogeographic structure of Hippophae tibetana（Elaeagnaceae） highlights the highest microrefugia and the rapid uplift of the Qinghai-Tibetan Plateau［J］.Molecular Ecology，2010，19（14）：2964-2979.
9	GAO Q B， ZHANG D J， DUAN Y Z，et al.Intraspecific divergences of Rhodiola alsia（Crassulaceae） based on plastid DNA and internal transcribed spacer fragments［J］.Botanical Journal of the Linnean Society，2012，168（2）：204-215.
10	WANG L Y， ABBOTT R J， ZHENG W，et al.History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau：Aconitum gymnandrum（Ranunculaceae）［J］.Molecular Ecology，2009，18（4）：709-721.
11	MENG L H， YANG R， ABBOTT R J，et al.Mitochondrial and chloroplast phylogeography of Picea crassifolia Kom.（Pinaceae） in the Qinghai-Tibetan Plateau and adjacent highlands［J］.Molecular Ecology，2007，16（19）：4128-4137.
12	YANG F S， LI Y F， DING X，et al.Extensive population expansion of Pedicularis longiflora（Orobanchaceae） on the Qinghai-Tibetan Plateau and its correlation with the Quaternary climate change［J］.Molecular Ecology，2008，17（23）：5135-5145.
13	陈生云，吴桂莉，张得钧，等.高山植物条纹狭蕊龙胆的分子亲缘地理学研究［J］.植物分类学报，2008，46（4）：573-585.
13	CHEN S Y， WU G L， ZHANG D J，et al.Molecular phylogeography of alpine plant Metagentiana striata（Gentianaceae）［J］.Journal of Systematics and Evolution，2008，46（4）：573-585.
14	张甜.核桃谱系地理学和转录组学遗传标记开发研究［D］.西安：西北大学，2016.
14	ZHANG T.Phylogeographic study and genetic marker development using transcriptomics of Juglans regia ［D］.Xi’an：Northwest University，2016.
15	石铸.中国植物志：第78卷［M］.北京：科学出版社，1987：61.
15	SHI Z.Flora of China：Vol.78［M］.Beijing：Science Press，1987：61.
16	吴征镒.云南植物志：第13卷［M］.北京：科学出版社，2004：614.
16	WU Z Y.Flora Yunnanica：Vol.13［M］.Beijing：Science Press，2004：614.
17	刘尚武.青海植物志：第3卷［M］.西宁：青海人民出版社，1996：437.
17	LIU S W.Flora Qinghaiica：Vol.3［M］.Xining：Qinghai People’s Publishing Press，1996：437.
18	史惠兰.青海湖地区4种荒漠植物抗逆性指标的研究［J］.安徽农业科学，2011，39（23）：14227-14229.
18	SHI H L.Study on the resistance indexes of four kinds of desert plants in Qinghai Lake area［J］.Journal of Anhui Agricultural Sciences，2011，39（23）：14227-14229.
19	张丽.三种药用植物次生代谢物结构及其生物活性研究［D］.兰州：兰州大学，2014.
19	ZHANG L.Studies on the secondary metabolites and their biological activity of three medicinal plants［D］.Lanzhou：Lanzhou University，2014.
20	尚冀宁.黄缨菊和赪桐化学成分研究［D］.兰州：兰州大学，2010.
20	SHANG J N.Studies on the chemical constituents of Xanthopappus subacaulis C.Winkl.and Clerodendrum japonicum（Thunb.） sweet［D］.Lanzhou：Lanzhou University，2010.
21	WANG Y J， LIU J Q， MIEHE G.Phylogenetic origins of the Himalayan endemic Dolomiaea，Diplazoptilon and Xanthopappus（Asteraceae：Cardueae） based on three DNA regions［J］.Annals of Botany，2007，99（2）：311-322.
22	BARRES L， SANMARTíN I， ANDERSON C L，et al.Reconstructing the evolution and biogeographic history of tribe Cardueae（Compositae）［J］.American Journal of Botany，2013，100（5）：867-882.
23	SANG T， CRAWFORD D J， STUESSY T F.Chloroplast DNA phylogeny，reticulate evolution，and biogeography of Paeonia（Paeoniaceae）［J］.American Journal of Botany，1997，84（8）：1120-1136.
24	尚宝龙.川木香属（菊科）的DNA条形码研究［D］.兰州：兰州大学，2015.
24	SHANG B L.DNA barcoding of the genus Dolomiaea（Asteraceae）［D］.Lanzhou：Lanzhou University，2015.
25	LAHAYE R， SAVOLAINEN V， DUTHOIT S，et al.A test of psbK-psbI and atpF-atpH as potential plant DNA barcodes using the flora of the Kruger National Park（South Africa） as a model system［J］.Nature Precedings，2008.doi：10.1038/npre.2008.1896.1 .
26	TAMURA K， STECHER G， PETERSON D，et al.MEGA6：molecular evolutionary genetics analysis version 6.0［J］.Molecular Biology and Evolution，2013，30（12）：2725-2729.
27	LIBRADO P， ROZAS J.DnaSP v5：a software for comprehensive analysis of DNA polymorphism data［J］.Bioinformatics，2009，25（11）：1451-1452.
28	PONS O， PETIT R J.Measuring and testing genetic differentiation with ordered versus unordered alleles［J］.Genetics，1996，144（3）：1237-1245.
29	EXCOFFIER L， LISCHER H E L.Arlequin suite ver 3.5：a new series of programs to perform population genetics analyses under Linux and Windows［J］.Molecular Ecology Resources，2010，10（3）：564-567.
30	SLATKIN M.A measure of population subdivision based on microsatellite allele frequencies［J］.Genetics，1995，139（3）：1463c.
31	PEAKALL R， SMOUSE P E.GenAlEx 6.5：genetic analysis in Excel.Population genetic software for teaching and research-an update［J］.Bioinformatics，2012，28（19）：2537-2539.
32	BANDELT H J， FORSTER P， R?HL A.Median-joining networks for inferring intraspecific phylogenies［J］.Molecular Biology and Evolution，1999，16（1）：37-48.
33	ZHANG D， GAO F L， JAKOVLI? I，et al.PhyloSuite：an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies［J］.Molecular Ecology Resources，2020，20（1）：348-355.
34	TAJIMA F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism［J］.Genetics，1989，123（3）：585-595.
35	FU Y X.Statistical tests of neutrality of mutations against population growth，hitchhiking and background selection［J］.Genetics，1997，147（2）：915-925.
36	ROGERS A R， HARPENDING H.Population growth makes waves in the distribution of pairwise genetic differences［J］.Molecular Biology and Evolution，1992，9（3）：552-569.
37	GAO L M， M?LLER M， ZHANG X M，et al ．High variation and strong phylogeographic pattern among cpDNA haplotypes in Taxus wallichiana（Taxaceae） in China and North Vietnam［J］.Molecular Ecology，2007，16（22）：4684-4698.
38	GAO Q B， ZHANG F Q， XING R，et al.Phylogeographic study revealed microrefugia for an endemic species on the Qinghai-Tibetan Plateau：Rhodiola chrysanthemifolia（Crassulaceae）［J］.Plant Systematics and Evolution，2016，302（9）：1179-1193.
39	WANG F Y， GONG X， HU C M，et al.Phylogeography of an alpine species Primula secundiflora inferred from the chloroplast DNA sequence variation［J］.Journal of Systematics and Evolution，2008，46（1）：13-22.
40	WANG J F， PAN Y Z， GONG X，et al.Chloroplast DNA variation and phylogeography of Ligularia tongolensis（Asteraceae），a species endemic to the Hengduan Mountains region of China［J］.Journal of Systematics and Evolution，2011，49（2）：108-119.
41	WANG L Y， IKEDA H， LIU T L，et al.Repeated range expansion and glacial endurance of Potentilla glabra（Rosaceae） in the Qinghai-Tibetan Plateau［J］.Journal of Integrative Plant Biology，2009，51（7）：698-706.
42	DYNESIUS M， JANSSON R.Evolutionary consequences of changes in species’ geographical distributions driven by Milankovitch climate oscillations［J］.Proceedings of the National Academy of Sciences of the United States America，2000，97（16）：9115-9120.
43	HEWITT G M.Genetic consequences of climatic oscillations in the Quaternary［J］.Philosophical Transactions of the Royal Society B：Biological Sciences，2004，359（1442）：183-195.
44	于海彬，张镱锂.青藏高原及其周边地区高山植物谱系地理学研究进展［J］.西北植物学报，2013，33（6）：1268-1278.
44	YU H B， ZHANG Y L.Advances in phylogeography of alpine plants in the Tibetan Plateau and adjacent regions［J］.Acta Botanica Boreali-Occidentalia Sinica，2013，33（6）：1268-1278.

[1]	Siru TANG, Tiejuan WANG, Fang XIU, Mengyao LIU, Hui ZHANG. Genetic Structure and Phylogeography Analysis of Artemisia intramongolica Based on Single Copy Nuclear Genes [J]. Bulletin of Botanical Research, 2022, 42(6): 956-963.
[2]	Ermei CHANG, Jianfeng LIU, Yuening HUANG, Hongli LI, Bingyan SHAN, Zeping JIANG, Xiulian ZHAO. Comparison of Genetic Diversity Between Wild and ex-situ Conservation Populations of Cupressus chengiana [J]. Bulletin of Botanical Research, 2022, 42(5): 772-779.
[3]	Pengcheng FU, Qiuqian WEI, Mingyang SHI. Genetic Divergence and Demographic History of Gentiana algida var. purdomii on the Qinghai-Tibet Plateau [J]. Bulletin of Botanical Research, 2022, 42(4): 556-564.
[4]	Hongbin ZHANG, Dong LÜ, Ming ZHAO, Hu ZHAO, Xingpeng ZHAO, Wei LI. Genetic Structure Analysis of Picea crassifolia Based on Genome-wide SNP Molecular Markers [J]. Bulletin of Botanical Research, 2022, 42(3): 373-382.
[5]	Qian CAO, Long-Hua XU, Jiu-Li WANG, Fa-Qi ZHANG, Shi-Long CHEN. Molecular Phylogeny of Subtribe Swertiinae [J]. Bulletin of Botanical Research, 2021, 41(3): 408-418.
[6]	Xu ZHANG, Xiu-Jiao ZHANG, Yong-Peng MA, Zheng-Hong LI, You-Ming WAN, Hong MA. Genetic Diversity Assessment of Rhododendron sinofalconeri with Genotyping by Sequencing(GBS) [J]. Bulletin of Botanical Research, 2021, 41(3): 429-435.
[7]	ZHANG Zhong-Hua, SONG Xiao-Qian, TANG Zhong-Hua, LIANG Zheng-Wei. An Assessment of Phylogenetic Diversity and Dissimilarity of Halophytes Across Different Provincial Region,China [J]. Bulletin of Botanical Research, 2020, 40(3): 330-338.
[8]	MA Wen-Mei, WANG Yi-Feng, ZHAO Xia-Wei, LI Lei. Altitude Differences in Reproductive Characteristics and Resource Allocation of Saussurea wellbyi [J]. Bulletin of Botanical Research, 2019, 39(5): 707-715.
[9]	TANG Nan, LI Miao-Miao, TANG Dao-Cheng. Characteristics of Leaf Epidermis of Meconopsis integrifolia under Different Altitudes in the Qinghai-Tibet Plateau [J]. Bulletin of Botanical Research, 2019, 39(2): 161-168.
[10]	LIU Yu-Ping, LÜ Ting, ZHU Di, ZHOU Yong-Hui, LIU Tao, SU Xu. Sequencing and Alignment Analysis of the Complete Chloroplast Genome of Littledalea tibetica,an Endemic Species from the Qinghai-Tibet Plateau [J]. Bulletin of Botanical Research, 2018, 38(4): 518-525.
[11]	HAO Jiu-Cheng, JIA Xin, MU Xiao-Hong, ZHANG Heng-Qing. Genetic Diversity between Island and Mainland Natural Populations of Polygonatum odoratum in Dalian Area by ISSR [J]. Bulletin of Botanical Research, 2017, 37(5): 709-714.
[12]	ZHANG Tian；WANG Ma-Li；ZHAO Peng. Sequence Analysis of Nuclear DNA JRD5680 for Determining Genetic Diversity and Genetic Structure Analysis of Common Walnut(Juglans regia* L.) [J]. Bulletin of Botanical Research, 2016, 36(2): 232-241.
[13]	LIN Le-Jing1,2；JIN Chu-Qi1；ZHENG Chun-Hao3；ZHOU Ya-Mei1；ZHOU Ying1. ISSR Analysis on the Genetic Diversity of Relic Plant Bretschneidera sinensis from Wuyishan Region [J]. Bulletin of Botanical Research, 2015, 35(4): 559-563.
[14]	XU Bin;ZHU Bao-Zhu;ZHANG Fang-Qiu;PAN Wen;WANG Yu-Xia. Genetic Diversity Analysis on Rhodoleia championii Wild Populations [J]. Bulletin of Botanical Research, 2014, 34(4): 479-484.
[15]	ZHANG Heng-Qing;FANG Xiao-Di;WU Jin-Mei;DU Yang;TAN Kun;FAN Qiang-Jun;ZHU En-Wei. Analysis on Genetic Diversity of Chenopodium album L. Populations in Four Natural Islands of South of Changdao,Shandong Province by ISSR [J]. Bulletin of Botanical Research, 2012, 32(5): 632-635.