Genetic Divergence and Demographic History of Gentiana algida var. purdomii on the Qinghai-Tibet Plateau

doi:10.7525/j.issn.1673-5102.2022.04.005

Abstract

Abstract:

The Qinghai-Tibet Plateau（QTP） is one hotspot of studies about biodiversity， speciation and adaptive evolution. Gentiana algida var. purdomii， belonging to Gentianaceae， is endemic to the QTP and has high value in medicine. Based on populations across the QTP， we assessed its genetic structure， divergence and demographic history based on plastid and nuclear DNA sequences in this study. Palaeo-distribution was also reconstructed by species distribution model. High level of genetic diversity was observed in G. algida var. purdomii. Genetic differentiation was high in plastid data（F_ST=0.452） but low in ITS data（F_ST=0.022）， indicating high level of gene flow in G. algida var. purdomii. Neutrality test and mismatch distribution analysis both showed signatures of recent population expansion. Species distribution modelling showed slight range expansion from the Last Glacial Maximum to the present day. Divergence time estimates suggested that the onset of intraspecific diversification generally fell into the Quaternary. The results indicated that the intraspecific divergence in G. algida var. purdomii should be related to geographical isolation and range fragmentation in glaciations. This study provides insights into genetic differentiation， adaptive evolution and conversation in Gentiana as well as alpine plants in the QTP.

Key words: Gentiana algida var. purdomii, genetic divergence, demographic history, species distribution model, Qinghai-Tibet Plateau

CLC Number:

S792.153

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.

References

1	MARCHESE C.Biodiversity hotspots：a shortcut for a more complicated concept［J］.Global Ecology and Conservation，2015，3：297-309.
2	LIU J Q， DUAN Y W， HAO G，et al.Evolutionary history and underlying adaptation of alpine plants on the Qinghai-Tibet Plateau［J］.Journal of Systematics and Evolution，2014，52（3）：241-249.
3	FAVRE A， P?CKERT M， PAULS S U，et al.The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan biotas［J］.Biological Reviews，2015，90（1）：236-253.
4	SUN H， ZHANG J W， DENG T，et al.Origins and evolution of plant diversity in the Hengduan Mountains，China［J］.Plant Diversity，2017，39（4）：161-166.
5	XING Y E， REE R H.Uplift-driven diversification in the Hengduan Mountains，a temperate biodiversity hotspot［J］.Proceedings of the National Academy of Sciences of the United States of America，2017，114（17）：E3444.
6	YE X Y， MA P F， YANG G Q，et al.Rapid diversification of alpine bamboos associated with the uplift of the Hengduan Mountains［J］.Journal of Biogeography，2019，46（12）：2678-2689.
7	DING W N， REE R H， SPICER R A，et al.Ancient orogenic and monsoon-driven assembly of the world’s richest temperate alpine flora［J］.Science，2020，369（6503）：578-581.
8	LIU J Q， SUN Y S， GE X J，et al.Phylogeographic studies of plants in China：advances in the past and directions in the future［J］.Journal of Systematics and Evolution，2012，50（4）：267-275.
9	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.
10	付鹏程，高庆波，张发起，等.基于查尔酮合酶基因探讨鲜卑花的种群动态历史与遗传分化［J］.植物研究，2014，34（5）：700-705.
10	FU P C， GAO Q B， ZHANG F Q，et al.Demography history and genetic divergence of Sibiraea laevigata（Rosaceae） based on Chalcone synthase gene［J］.Bulletin of Botanical Research，2014，34（5）：700-705.
11	MUELLNER-RIEHL A N.Mountains as evolutionary arenas：patterns，emerging approaches，paradigm shifts，and their implications for plant phylogeographic research in the Tibeto-Himalayan Region［J］.Frontiers in Plant Science，2019，10：195.
12	LIANG Q L， XU X T， MAO K S，et al.Shifts in plant distributions in response to climate warming in a biodiversity hotspot，the Hengduan Mountains［J］.Journal of Biogeography，2018，45（6）：1334-1344.
13	HO T N， LIU S W.A worldwide monograph of Gentiana ［M］.Beijing：Science Press，2001：2-51.
14	FAVRE A， MICHALAK I， CHEN C H，et al.Out-of-Tibet：the spatio-temporal evolution of Gentiana（Gentianaceae）［J］.Journal of Biogeography，2016，43（10）：1967-1978.
15	董琦，吉文鹤，肖远灿，等.HPLC法同时测定藏药岷县龙胆中4种有效成分的含量［J］.天然产物研究与开发，2014，26（4）：561-563.
15	DONG Q， JI W H， XIAO Y C，et al.Simultaneous determination of four active components in Tibetan herb Gentiana purdomii Marq.by HPLC［J］.Natural Product Research and Development，2014，26（4）：561-563.
16	钟世浚，张碧东，赖世婷，等.红花龙胆组培快繁体系研究［J］.植物研究，2021，41（5）：753-759.
16	ZHONG S J， ZHANG B D， LAI S T，et al.Tissue culture and rapid propagation system of Gentiana rhodantha ［J］.Bulletin of Botanical Research，2021，41（5）：753-759.
17	HO T N， PRINGLE J M.Gentiana［M］//WU Z Y，RAVEN P H.Flora of China.Beijing：Science Press，2003：73-74.
18	孙姗姗，付鹏程.龙胆族（龙胆科）分类与进化研究进展［J］.西北植物学报，2019，39（2）：363-370.
18	SUN S S， FU P C.Study on taxonomy and evolution of Gentianeae（Gentianaceae）［J］.Acta Botanica Boreali-Occidentalia Sinica，2019，39（2）：363-370.
19	FAVRE A， PRINGLE J S， HECKENHAUER J，et al.Phylogenetic relationships and sectional delineation within Gentiana（Gentianaceae）［J］.Taxon，2020，69（6）：1221-1238.
20	FU P C， SUN S S， TWYFORD A D，et al.Lineage-specific plastid degradation in subtribe Gentianinae（Gentianaceae）［J］.Ecology and Evolution，2021，11（7）：3286-3299.
21	DOYLE J J， DOYLE J L.A rapid DNA isolation procedure for small quantities of fresh leaf material［J］.Phytochemical Bulletin，1987，19：11-15.
22	TABERLET P， GIELLY L， PAUTOU G，et al.Universal primers for amplification of three non-coding regions of chloroplast DNA［J］.Plant Molecular Biology，1991，17（5）：1105-1109.
23	FU P C， TWYFORD A D， SUN S S，et al.Recurrent hybridization underlies the evolution of novelty in Gentiana（Gentianaceae） in the Qinghai-Tibetan Plateau［J］.AoB Plants，2021，13（1）：plaa068.
24	KEARSE M， MOIR R， WILSON A，et al.Geneious basic：an integrated and extendable desktop software platform for the organization and analysis of sequence data［J］.Bioinformatics，2012，28（12）：1647-1649.
25	LIBRADO P， ROZAS J.DnaSP v5：a software for comprehensive analysis of DNA polymorphism data［J］.Bioinformatics，2009，25（11）：1451-1452.
26	STEPHENS M， SMITH N J， DONNELLY P.A new statistical method for haplotype reconstruction from population data［J］.American Journal of Human Genetics，2001，68（4）：978-989.
27	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 Resource，2010，10（3）：564-567.
28	EXCOFFIER L， SMOUSE P E， QUATTRO J M.Analysis of molecular variance inferred from metric distances among DNA haplotypes：application to human mitochondrial DNA restriction data［J］.Genetics，1992，131（2）：479-491.
29	PONS O， PETIT R J.Measwring and testing genetic differentiation with ordered versus unordered alleles［J］.Genetics，1996，144（3）：1237-1245.
30	FU Y X.Statistical tests of neutrality of mutations against population growth，hitchhiking and background selection［J］.Genetics，1997，147（2）：915-925.
31	TAJIMA F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism［J］.Genetics，1989，123（3）：585-595.
32	NGUYEN L T， SCHMIDT H A， HAESELER A VON，et al.IQ-TREE：a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies［J］.Molecular Biology and Evolution，2015，32（1）：268-274.
33	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.
34	BOUCKAERT R， HELED J， KüHNERT D，et al.BEAST 2：a software platform for Bayesian evolutionary analysis［J］.PLoS Computational Biology，2014，10（4）：e1003537.
35	DRUMMOND A J， SUCHARD M A， XIE D，et al.Bayesian phylogenetics with BEAUti and the BEAST 1.7［J］.Molecular Biology and Evolution，2012，29（8）：1969-1973.
36	PHILLIPS S J， DUDíK M， SCHAPIRE R E.Maxent software for modeling species niches and distributions（Version 3.4.1）［EB/OL］.［2021-05-07］.
37	ZHANG X L， YUAN Y M， GE X J.Genetic structure and differentiation of Gentiana atuntsiensis W. W. Smith and G.striolata T. N. Ho（Gentianaceae） as revealed by ISSR markers［J］.Botanical Journal of the Linnean Society，2007，154（2）：225-232.
38	LUO D， YUE J P， SUN W G，et al.Evolutionary history of the subnival flora of the Himalaya-Hengduan Mountains：first insights from comparative phylogeography of four perennial herbs［J］.Journal of Biogeography，2016，43（1）：31-43.
39	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.
40	SPICER R A， FARNSWORTH A， SU T.Cenozoic topography，monsoons and biodiversity conservation within the Tibetan region：an evolving story［J］.Plant Diversity，2020，42（4）：229-254.
41	HE K， JIANG X L.Sky islands of southwest China.I：an overview of phylogeographic patterns［J］.Chinese Science Bulletin，2014，59（7）：585-597.
42	DENG J Y， FU R H， COMPTON S G，et al.Sky islands as foci for divergence of fig trees and their pollinators in southwest China［J］.Molecular Ecology，2020，29（4）：762-782.
43	ZHANG X， SUN Y X， LANDIS J B，et al.Genomic insights into adaptation to heterogeneous environments for the ancient relictual Circaeaster agrestis（Circaeasteraceae，Ranunculales）［J］.New Phytologist，2020，228（1）：285-301.
44	BAGHERI A， MAASSOUMI A A， RAHIMINEJAD M R，et al.Molecular phylogeny and divergence times of Astragalus section Hymenostegis：an analysis of a rapidly diversifying species group in Fabaceae［J］.Scientific Reports，2017，7（1）：14033.
45	LIU J， YAN H F， GE X J.The use of DNA barcoding on recently diverged species in the genus Gentiana（Gentianaceae） in China［J］.PLoS One，2016，11（4）：e0153008.
46	FU P C， SUN S S， KHAN G，et al.Population subdivision and hybridization in a species complex of Gentiana in the Qinghai-Tibetan Plateau［J］.Annals of Botany，2020，125（4）：677-690.
47	YUAN Y M， KüPFER P.The monophyly and rapid evolution of Gentiana sect.Chondrophyllae Bunge s.l.（Gentianaceae）：evidence from the nucleotide sequences of the internal transcribed spacers of nuclear ribosomal DNA［J］.Botanical Journal of the Linnean Society，1997，123（1）：25-43.

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