Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. aze Liu Wanzhen southern of regions montane China F.P. the chuniana to Cercis endemic in (Fabaceae) cycles Metcalf glacial to linked dynamics Population atAi umrmnonadcniuu aia vial o cuain ope hsorpyplus physiography Complex occupation. for available intensified habitat with continuous China, simula- in coalescent and and period monsoon interglacial modeling Lushan-Tali summer niche geographical warm was Asia ecological the as by isolation East during function inferred Geographical occurred to As contact thought east. Pleis- physiography. secondary ranges, the complex middle tions, mountain to their the adjacent those to 11 in in from due among located separated barriers occurred variation populations Mts. divergence genetic the Nanling of between population the detected pattern that in spatial revealed populations dynamics. the when estimation population investigate tocene, time its to elucidate Bayesian dis- (GBS) on to narrowly sequencing China, focused populations. of subtropical we by evolution in climate Here genotyping ranges the Pleistocene used species. mountain affected We southern widespread geo- to have the more the response China to than driving endemic southern in studied species in processes less populations ranges the is plant mountain investigating species of key tributed for radiation the system How and excellent biodiversity fluctuations. an of are distribution China graphic southern of mountains The how ecosystems. understanding montane are our China approaches advances southern Abstract genomic study in population This species plant that of species. shows history distributed work evolutionary narrowly Our the occupation. of affected for have dynamics expansion began. available cycles demographic population migration glacial habitat the the contemporary continuous facilitated detecting which cycles and Lushan-Tali As in from glacial effective warm monsoon Mts., across physiography. the summer Nanling conditions complex during Asia the ecological their occurred stable in East to long-term contact intensified due plus secondary with physiography barriers simulations, Complex China, geographical coalescent in populations as and the variation period function between modeling detected interglacial genetic to niche was of isolation thought ecological Geographical pattern by when ranges, east. Pleistocene, spatial inferred mountain the middle elucidate to the adjacent the to those in investigate in from China, occurred separated to located divergence subtropical Mts. (GBS) population in Nanling that ranges sequencing the revealed Here in mountain by estimation populations southern time species. genotyping Bayesian the widespread used populations. to more We 11 than endemic among studied species dynamics. less woody in is ranges population a species mountain chuniana, its key distributed of Cercis the narrowly distribution How on of geographic fluctuations. focused evolution the climate we the driving Pleistocene affected processes to have the response China investigating in for southern populations plant system of excellent radiation an and are biodiversity China southern of mountains The Abstract 2020 22, June China 510650, Guangzhou Sciences, of Academy Chinese 3 Garden, Botanical China 2 1 Gong Wei and oaia eerhIsiueo ea,10 nvriyDie otWrh X717 USA 76107, TX Worth, Fort Drive, University 1700 Texas, of Institute South Research Utilization, Botanical Sustainable and Conservation Resources Plant of Laboratory Key University Agricultural China South 1 inun Xie Jianguang , 1 1 u Zhou Hui , 1 agu Kong Hanghui , 1 2 agHao Gang , ecschuniana Cercis 1 ee Fritsch Peter , woody a , 3 , Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. nulse aa 00.A ihiscneesi hn,i xiisa dpaint ei environments mesic to adaptation an exhibits al the it et (Fritsch near China, apex resolved in blade congeners is leaf its acuminate species with its The through As morphologically. 2020). identifiable data, easily unpublished it the and Wuyi makes of the which and base from sizes 1940), extending population Metcalf, larger distribution, increasingly 2010; geographical with narrow Mountains among a Nanling Unique the has densities. to It westwards China. Mountains species. widespread China southern et Eastern distributed on of Liu narrowly focused STEBF of 2016; has the evolution al., research to the with this et affect involved of might (Gong chuniana most scenarios ranges China Cercis However, mountain the southern 2020). key elucidated Wang, how in has & ignored species Bao, research and Wang, plant species Previous Ye, have of 2015). Tian, expansions history al., 2012; range evolutionary al., et rapid postglacial Tian or and 2011; localized glacial Comes, subsequent & which diversity Fu, of genetic al Qiu, of out et genetic centres China, (Chen with and correlated inferred southern isolation refugia been in glacial geographical elevation Multiple identified both in 2006). habitat for been Su, lowering of & opportunity have belts Cui, degree vegetation the (Shi, the providing with occur China, to range, periods, southern divergence geographic glacial 105 In during in 1980). to contracting decreased Wu, (east have & and to China Pu, now thought (Duan, eastern are is Glacials data in Tali connectivity considerable and periods debate, Lushan under glacial Dagu, still Poyang, four populations, Although support al of 2009). Skov, to history et & available demographic Li Normand, the 2004; Svenningm, shaping 2018; (Hewitt, important and Suding, an regions biodiversity as montane considered of in also pattern are particularly distribution and Pleistocene the the biodiversity during driving al of cycles fluctuations. factor glacial et distribution climate with (Li geographic Pleistocene associated cycles oscillations to the Climatic glacial response driving in Pleistocene processes populations and the plant events investigating of orogenic radiation for both arising system presumably with excellent 2011) line 2011; Ge, an in of al & Comes, rates years, well et Ying, high & Liu million Sun, and exhibit L´opez-Pujol, Fu, 1979; Zhang, 5 endemics, 2017; world subtropical predominantly last (Qiu, al., the is species, et the biota plant in (Hou mountains within their north-temperate radiation forests these of rapid the Many such of and of 2012). continuous local type Shi, elements largest vegetation & relictual Tang, the primary Fang, ancient Wang, Zhong, of The harbouring & one for Zhang, 2012). (STEBF), known Chen, complex 2016; Shi, forest to Zeng, al., attributed & broadleaved (Qiu, et been Tang, gradients evergreen has (Gong elevational uniqueness Fang, habitat species steep Wang, local plant or Their 2013; various longitudinal 2019). to for with Zhang, suggested (Hou, correlated & corridors Wu, been directions topography colonization Xiong, have northeast-southwest 2018; or ranges al., or diverse barriers et topographically north-south Tian geographical these either either 2001), in to as Ying, oriented part serve 1992b; large Often Wang, al in 1992a; et Wang, due 2016). (Fan is 1983; ranges Huang, China mountain & southern its Yao, Ruth, of of Dick, & biodiversity heterogeneity (Colin high physiographical isolation The geographic extreme 1964). of the episodes Simpson, because frequent habitats 2019; by montane Muellner-Riehl, afforded in 2006; opportunities diversification ecological rapid increased prompt the to of suggested is heterogeneity physiographical High INTRODUCTION ranges mountainous China China Southern southern contact, in secondary species plant our of advances KEYWORDS: history study This evolutionary the species. affected distributed approaches ecosystems. have narrowly genomic montane of cycles population dynamics that glacial shows population how work the Nan- understanding Our the detecting in began. in expansion effective migration demographic contemporary are the which facilitated from cycles Mts., glacial ling across conditions ecological stable long-term Cercis . 03 h,L,&L,19;Wn tal et Wang 1998; Li, & Li, Shi, 2013; , .P ecl Fbca:Crioda;Aaie l,21)i ml reo hu endemic shrub or tree small a is 2017) al., et Azani Cercidoideae; (Fabaceae: Metcalf P. F. ecschuniana Cercis hlgntcte,wt netmtdaeo .0M Fishe al et (Fritsch Ma 2.40 of age estimated an with tree, phylogenetic Cercis . 02 og hn oe,F,&Kc,20;L,Sa,L,Zag i,2012; Qiu, & Zhang, Lu, Shao, Li, 2008; Koch, & Fu, Dobes, Chen, Gong, 2012; , pce,i a naymtia efbae(hn hn,Lre,&Vincent, & Larsen, Zhang, (Chen, blade leaf asymmetrical an has it species, eorpi oeig egahcioain litcn lca cycles, glacial Pleistocene isolation, geographic modeling, demographic , . 08 sl,17;WnelnLre,&Lre,1981). Larsen, & Larsen, Wunderlin 1975; Isely, 2018; , 2 . . 00.Teecaatrsismk otenChina southern make characteristics These 2010). , 09 eqia ilan end oeod & Rosemond, Bernad, Tillmann, Mesquita, 2019; , º )drn h litcn,ie the i.e. Pleistocene, the during E) . 08 ue l,21;Yang, 2017; al., et Xu 2018; , . 08 i tal., et Liu 2018; , . , Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. ihtetsu ooeie iseye-6(hnhiJnxnIdsra eeomn o,Ld.Total beads (Doyle glass method Ltd). with (CTAB) Co., bromide tubes ammonium Development in trimethyl ground cetyl Industrial was modified Jingxin the tissue with (Shanghai Leaf extracted Tissuelyser-96 was -80. DNA homogenizer at genomic stored tissue and the nitrogen with filtering liquid quality in and immersed calling instantly SNP of (GBS), average. leaves sequencing on Tender by or factors month genotyping climate each extraction, influential in DNA most thus the temperature 2.3 The is in and the approach error precipitation 2007). under This omission including Peterson, area compared, zero 1997). & the also maintaining Bell, Nakamura, evaluating were while Raxworthy, & by possible (Fielding (Pearson, assessed area performance dataset was predicted model training minimum accuracy good the al Model show in identifying et to conservative, as (Phillips (2016). considered plot all current/past were (ROC) were al. 0.70 points, characteristic iterations et than receiver-operating of occurrence Gong the occur number the and of maximum to (AUC) including (2011) and considered curve threshold settings, populations al. convergence parameter of the et locations and as Dai well the pipelines as determine analysis variables specimen to bioclimatic en- The Herbarium used maximum were the present. 2006). locations used at Schapire, collection We & sample Anderson, our 2005). as (Phillips, Jarvis, v3.3.2 & estimates Maxent Jones, of high-resolution with records Parra, downscaled method Cameron, provides modeling which (Hijmans, Community Holocene database the 2006), tropy parameters of WorldClim al., Middle climate simulation et the model the Ma), circulation (Collins from of from 0.02 (CCSM) obtained downloaded were Model were data System [?] MH variables Climate and (LGM, LGM, Bioclimatic LIG, Maximum The current. Glacial resolution. the and Last for Ma), Ma), inferred ( data 0.006 0.12 paleoclimate distribu- ˜ [?] high-resolution spatial 0.14 on (MH, the analysis (LIG, characterize the Interglacial to based Last 2005) We Peterson inferences. for & biological conditions historical Soberon suitable (ENM; of modeling tion niche ecological used We and individuals through modeling NLW1 20 Mts. collected niche Wuyi whereas also We Mts., the Ecological 1). Nanling between Table 2.2 1, the located (Figure of is Mts. of part Nanling LXS2 population Mountains. the respectively. eastern and of one Mts., the Nanling part Mts. from Wuyi western in Luoxiao the and the located in the of are Luoxiao, located of parts are NLE2 Wuyi, NLW5 from western end and the and collected southern NLE1 eastern were Mts. the including the Luoxiao populations in China, in five located located southern to is are one LXS1 in WYS2 from ranges and Anywhere WYS1 mountain 1). Populations Table the of 1, of (Figure individuals each species 112 the and of populations distribution 11 collected We narrowly of and sampling history Population China evolutionary 2.1 the southern on its in METHODS environment ranges elucidate AND this MATERIALS mountain 2) of 2 impact of species, the roles hoped the of thereby the We of understanding species. distribution. infer distributed structure better geographic to and a population diversification gain data its and to driving of the diversity in analyses use fluctuations genetic genetic climatic 3) population Pleistocene investigate nonmodel and for 1) SNPs history, for to genome-wide analysis demographic collected aimed genome-wide and We a GBS . for al used et genotyping, we Davey tool and 2016; Here, cost-effective Hohenlohe, discovery 2017). & Luikart, genome and marker Miller, reference with high-throughput, Good, a genetic (Andrews, combination al require rapid, species investigating In not et a does (SNPs). Niu for GBS provides 2010; polymorphisms approach enzymes, Metzker, GBS nucleotide restriction genomic 2017; with single Li, reduction a detect & genomic as to on Pang, based Zhang, used is Hou, widely it (Chen, Because been structure population has and (GBS) diversity sequencing by Genotyping http://worldclim.org/download .chuniana C. .chuniana C. rmnn ebra(,IE,IK BC U,LG MH EadSF)a well as SCFI) and PE NMNH, LBG, KUN, IBSC, IBK, IBEC, (A, herbaria nine from .chingii C. .chuniana C. and ik&Hjas 07 o h ordffrn tgswt .-iuespatial 2.5-minute with stages different four the for 2017) Hijmans, & Fick ; hnlctdi hceghni hjagProvince. Zhejiang in Chichengshan in located Chun .chingii C. n oaeptnildsrbtoa ra ncnucinwith conjunction in areas distributional potential locate and eesmldadpae nocnrfg ue,wihwere which tubes, centrifuge into placed and sampled were 3 .chuniana C. rmtruhu h urn geographic current the throughout from . 01 cee,Bte,&Edwards, & Batley, Scheben, 2011; , . 06,weesoe higher scores where 2006), , .chuniana C. . 2019). , Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. mlmne nFsSrcuev. Rj tpes rthr,21) eue h eal etn with setting default the (MCMC) used We model Carlo 2014). Monte of Pritchard, individuals Chain & 112 Markov the Stephens, Bayesian on of cross-validation (Raj, a analysis 10-fold v1.0 with hierarchical FastStructure 1984). structure a in Cockerham, genetic implemented and & (AMOVA) Weir population variance 1996; estimated Weir, molecular We 1992; of Quattro, 0.1.16 & analysis vcftools Smouse, used (Excoffier, with we subdivision calculated populations, ( were populations within among SNPs and differences of selected values pairwise the calculating for frequencies ( allele heterozygosity and al et alleles (Petr of number admixture The and assignment population diversity, al Genetic et trees (Bouckaert ( 2.5 remaining v.1.4.3 v2.4.7 FigTree TreeAnnotator the with with edited from intervals were 2014). chronogram trees time Rambaut, final (MCC) confidence The (ESS) credibility 95% BEAST. size in and clade 2014) sample heights maximum effective mean the the nodal that generated with (Rambaut, check then v1.6 to for four Tracer and and BEAST and used convergence option, We in assess model simulations to generation. I MCMC 2014) 1000th + was Drummond, the every and G & sampled ran uncorrelated + Xie, parameters We with Suchard, GTR the with setting covered branches. the Clock generations which Strict the million with the Ma, 10 across conducted and 0.2 variation were prior, of rate Population analyses Constant deviations log-normal-distributed time Coalescent standard divergence a and The categories, distributions rate range. prior HPD normal a 95% with point calibration chuniana C. ( al PhyML-SMS substitution et (Fritsch in nucleotide within 1974) of times Akaike, model Divergence (AIC; The criteria information 2014). Akaike (Alexandros, Gateway the montpellier.fr/phymL/ v8 Science with RAxML CIPRES selected the in was in pseudoreplicates GBS al available the bootstrap cluster et on ML computer Miller based high-performance extracted (www.phylo.org; the SNPs 3.3 on the performed using were trees yses phylogenetic generate of to populations dataset. analysis 11 (ML) the likelihood among mum relationships phylogenetic estimation reconstruct 50% time To of divergence heterozygosity and at observed population locus. of analysis maximum For rate per Phylogenetic a genotyping populations a 2.4 Stacks. specified five and also with of 0.05 We calling number least at minimum populations. SNP of a within for (MAF) and individuals frequency individuals allele of 132 minor 80% by a used least with We assembled SNPs were extracted sorting. we of format and analysis, individual fastq one mapping DNA with in sequence (Illumina, and 2013) Reads for analyses Cresko, platform advanced & sequencing Further reads. Amores, HiSeq Bassham, low-quality sequencing. glabra Hohenlohe, Illumina remove 150 (Catchen, The to v2.2 (PE) STACKS paired-end performed using selected for Ltd. were were used fragments assembly was Co. desired library USA) Novogene the of CA, in and combination Diego, constructed construction San a was library with amplification GBS multiplex digested for after was barcodes libraries DNA to representation genomic ligation reduced al The generating et for workflow (Heffelfinger 2016). streamlined sequencing a Illumina is for (GBS) of sequencing Scientific, concentration (Thermo by DNA spectrophotometer Genotyping final Nanodrop a a and with USA), quantified was CA, concentration Carlsbad, DNA 1986). Doyle, & > ap srfrne W 078(i&Dri,20)adSMol 131(ie l,20)wr used were 2009) al., et (Li v1.3.1 SAMtools and 2009) Durbin, & (Li v0.7.8 BWA reference. as Pamp. 0 o ahprmtr edsaddtefis 0 ftesa uni ihtema oeheights node mean the with burn-in as trees of 10% first the discarded We parameter. each for 200 ecschingii Cercis . 01.T esr eei iest,w siae xetdhtrzgst ( heterozygosity expected estimated we diversity, genetic measure To 2011). , . eue ES 247(ocar tal et (Bouckaert v2.4.7 BEAST used we , 08 i tal et Liu 2018; , Ho .W sdAlqi 35(xoe ice,21)t siaegntcdffrnito by differentiation genetic estimate to 2010) Lischer, & (Excoffier v3.5 Arlequin used We ). eot ogeil,&Gsul 2017). Gascuel, & Longueville, Lefort, ; a sdt ottetes sbsdo h eut fFish&Cu 21) Anal- (2012). Cruz & Fritsch of results the on based as trees, the root to used was Cercis . nulse aa 00.Teeoe oetmt h iegnetm within time divergence the estimate to Therefore, 2020). data, unpublished , ae ntefsi eodsgetdthat suggested record fossil the on based . 05.TeM nlsswr efre iutnosywt 1000 with simultaneously performed were analyses ML The 2015). , . 04 lt ya,&Hr,21;Ml,Bral,&Hale, & Bartaula, Melo, 2014; Hare, & Nydam, Ilut, 2014; , .chuniana C. . 4 04 n ple h g f24M stesecondary the as Ma 2.4 of age the applied and 2014) , > 0ng/ 30 Fst etn o uppltos( subpopulations for testing , .T opr oeua iest between diversity molecular compare To ). Mse μ http://tree.bio.ed.as.uk/software/figtree/ a used. was L and I .chuniana C. .chuniana C. Nla I nye.Subsequent enzymes. III eepoe maxi- a employed we , He rgntd24Ma 2.4 originated K http://www.atgc- n observed and ) agn from ranging ) Cercis . ; , Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. . hrceiainaddsrbto fSNPs of of distribution range No distribution and suitable Characterization region. LGM for May 3.2 subtropical factor April, climate the Chinese in influential Precipitation the most of current. the of and of S1). be map most (Table MH to distribution between occupying revealed geographical vegetation evident was MH, were June The the distribution a and temperate geographical into during 2001). semi-arid the to widely Adams, in contracted in partially changes expanded & data distribution and have (Ray 7) geographical these to 3) (number continu- (number inferred steppe the compared scrub forest a LGM inside or We yielded mainly the woodland located Results during were areas 2b). contrast, distribution respectively). mod- In (Figure the 0.9966, areas (http://intarch.ac.uk/journal/issue11/2/map/download that 2a). and indicated fragmented (Figure 0.9976 data three LIG sample = the of test (AUC and ing distribution power training geographical predictive both ous high on based had performance els model of Evaluation modelling data. niche the Ecological of fit 3.1 best the (AIC). as criterion information chosen RESULTS Akaike models were the 3 demographic AIC on lowest complex based 10,000 were models the arbitrarily with models best-fit with of using model demographic models by likelihood each calculated The 10 composite was under All SFS The given analyses estimation. the S2-S4). FSC2 under likelihood Tables replicate composite S2, 100 (Figure and for ran compared parameters calculated We been optimal 1999). has for Mao, rate simulations & mutation 1.16 genomic Chen of no 1998; rate because (Aldworth, 2020), mutation data, substitution/site/generation unpublished the al., Cercis We et used (Liu scenario. we research each values, to our subjected real was into that estimates source split the as recent ( used migration ( or alternatively size by were applied. (AMIG) population followed also ES effective ancient were or estimated isolation groups (EXP) including NL two expansion (IS), Models model, demographic the only each and (SEC). migration, with In isolation contact one-way models (NIS), or secondary bidirectional demographic isolation or (RMIG), migration without 10 (BOT), of effect are: construction bottleneck models the (MIG), The as on populations based S2). remaining (SFS), (Figure the and and spectrum group (NL), frequency monophyletic group site ( a one easySFS formed as used which considered We were (ES). Mts., effects, another bottleneck Nanling location, Huerta- contact, geographic the secondary distinct in Dupanloup, divergence, a populations of Excoffier, showed The evidence (FSC2; model expansion. provide fastsimocoal2 demographic to and program 2013) Foll, the over & averaged S-DIVA. with Sousa, are with Sanchez, simulations reconstructions detected ancestral coalescent also the the applied were from in events We node derived With vicariance a tree 2016). or at Favre, credibility area Dispersal & ancestral clade trees. an Sun, maximum all of Muellner-Riehl, the frequencies (Matuszak, and the The TreeAnnotator method, trees 2015). and this MCMC He, BEAST & BEAST with Blair, the analysis Harris, Yu, Bayesian on 1997; based of (Ronquist v3.2 was groups RASP analysis seven in implemented used analysis we analysis) vicariance reconstruction, area ancestral For history demographic of ( Inference Lama Tanya 2.6 of 2012) scripts package. al., the R et Illustrator. (Zheng the using SNPRelate Adobe in results in with function the optimal PCA edited the the visualized and using choose and represented (PCA) to analysis graphically used component were was principal FastStructure Results performed in We likelihood. K marginal Choose script the python maximizes The 11. to 1 M NL-ES eetmtdagnrto ieo v er for years five of time generation a estimated We . n M and ES-NL o h w rusi ahmdlfo otro itiuin.T cl parameter scale To distributions. posterior from model each in groups two the for ) https://github.com/isaacovercast/easySFS .chuniana C. Ne ,tm ( time ), T cossvrlmuti agsi otenCiadur- China southern in ranges mountain several across n irto ae nidvda irnsprgeneration per migrants individual in rates migration and ) 5 page .chuniana C. .chuniana C. https://github.com/ECOtlama/SNPRelate.git shm,bsdo hc h he fragmented three the which on based js.htm), ae netmtsfriscongeners its for estimates on based o -IA(ttsia dispersal- (statistical S-DIVA for otasomSP noafolded a into SNPs transform to ) K .. h au that value the i.e., , .chuniana C. × 10 .chuniana C. -7 ae on based was ) Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. olwdb eodr otc SC n eorpi xaso EP al ,Fgr ,S,TbeS2-S4). Table S2, model 5, isolation Figure an 3, indicating Table SECEXP, (EXP; model expansion later. is demographic populations FSC2 and western with (SEC) the analysis and contact demographic and NLE2] secondary the first, by + for followed species vicariance [NLE1 model the six fit of separating the best rest rest Across Mts., The the the NLW5. Nanling from the and through of western diverged NLW2 LXS1 in rest and populations and between NLW1 located eastern the eastern is between the LXS2, V4 is and the events, and V6 between WYS2/LXS2 Mts. WYS2 whereas is Nanling between NLW5], between the through V5 is [NLW1 is in V3 V2 populations. populations the respectively. the populations. and Mts., of the LXS1 Luoxiao of including southern rest populations, and the the and (Figure Mts. analysis WYS1 S-DIVA Wuyi the between western from is inferred were V1 regions geographical 1). the among (V1-V6) events vicariance Six differentiation history genetic demographic significant of indicated Inference NLW5]. 2). 3.5 data through (Table [NLW2 GBS variation and total the NLW1, the on of NLE2], based 96.28% + as ( [NLE1 variance populations LXS2, molecular among LXS1, the the WYS2, the with of of WYS1, together in groups Analysis results populations seven analyses: phylogenetic circumscribed the further and ultimately from PCA, we for separate FastStructure, populations, distinctly the of were Considering locations these geographical S1). and (Figure together Mts. LXS2 Nanling and LXS1 clustered analysis when for clustering groups optimal remaining when the the ( populations from east remaining separated the the and in from populations average, other separated the WYS1 On of those to (0.19). comparable LXS2 highest in The detected 1). Table (0.31; highest of The former spanning differentiation 4). estimated the and (Figure Ma, respectively, diversity 0.51 periods ones, Genetic to Interglacial Population eastern 0.34 3.4 the period. from the and Interglacial calculated 0.29 Glacial Dagu-Lushan in were to the Dagu-Lushan LXS1-2) Ma in 0.20 the and latter 0.37 from both (WYS1-2 the to range east and occurring the 0.35 period Mts. in as Glacial from Nanling diversifications estimated Lushan in and were the diversifications which during populations of Population is 0.58 western which both 4). the Ma, Pleistocene, ca. (Figure 0.51 in Middle period populations Nanling ca. NLW1-NLW5 Ma in Glacial the populations western China Dagu Within western the the in rest 4). Mts. from in the (Figure period Nanling diverged debate from glacial NLW1 under the populations while third still in NLE1/NLE2 Ma, are the populations ranges eastern within the time the arose interglacial and was Mts., and times LXS2 LSX1 glacial and divergence between exact WYS2 Both divergence the between the although occurring Ma. the whereas divergence from 0.68 The Ma, diverging 0.72 period. WYS2/LXS2 ca. Glacial by ca. Poyang followed the as populations, of during estimated time remaining Ma The the 0.85 Mts. from ca. Nanling divergent NLE1 western rest and first the NLE2 was WYS2, in with others WYS1 populations the group, 4). the from monophyletic separate by a clade formed followed a of forming branch, Mts. origin first-diverging Nanling Mts. Nanling the the eastern in at the (Figure populations in values positioned The bootstrap be LXS1. high to and mostly revealed LXS2 with was population WYS1 each in for 3). monophyly deposited yielded been analysis have phylogenetic mean times The data The divergence The and 85.00%. S5). relationships (Table [?] Phylogenetic criteria Q30 3.3 extraction and SNP 92.23% for the XXX). SNPs [?] (DOI: with 61,748 Q20 Figshare detected agreed We with SNPs quality 37.84%. 10,761,958 32,890 high from was which identified content was were C tags data High-quality + sequence reads. G The clean GB 200 reads. and reads GB-PE raw GB 200.8 produced GBS .chuniana C. He a eetdi L2(.8 olwdb L5(.5;telws a eetdi LXS2 in detected was lowest the (0.35); NLW5 by followed (0.38) NLW2 in detected was Fst a siae s23 9%HD=19–.4 adrn h al litcn (Figure Pleistocene early the during Ma 1.97–2.74) = HPD (95% 2.36 as estimated was 0.99, = .chuniana C. H O P a eetdi L1(.4 olwdb L2(.3;telws was lowest the (0.33); NLW2 by followed (0.34) NLW1 in detected was .0,o hc h aito mn h ee rusacutdfor accounted groups seven the among variation the which of 0.00), = Fgr ) ieigsihl rmteFsSrcuersl,tePCA the result, FastStructure the from slightly Differing 4). (Figure He and K Ho .Svnsbouain ( subpopulations Seven 3. = nteNnigMs ( Mts. Nanling the in 6 K He .chuniana C. .WS n X2cutrda n group one as clustered LXS2 and WYS2 2. = 0.32; = Ho with .7.I attutr analysis, FastStructure In 0.27). = .chingii C. He K 0.33; = )wr eemndas determined were 7) = .chuniana C. sotru,among outgroup, as Ho .9 were 0.29) = populations Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. ouainsz,w ovre h iegnetm ewe LadE notenme fgnrto times, generation of number the into ES and NL between time divergence are the T (ES) converted regions we on eastern size, Based and population (NL) as value. calculated Mts. AIC population was size Nanling lowest effective population the into the of diversity on nucleotide sizes and based of population 57,495 confirmed effective estimates current genome-wide was The the Ma) converted sizes. (2.74 we generations rate, 548,000 mutation the of scale time The uxa t. ihanrhsuhoinain r sue osrea egahcbrirpriual for central particularly the barrier Notably, geographic 2013). a as al., serve et and 3). to Yan isolation 1, assumed geographical 1984; (Figures are cause (Liu, orientation, other to to China north-south each reported attributed southern a been from was in with has populations (V1) Mts., species Pleistocene the WYS2 Luoxiao many early geographic separate and the for to during and WYS1 divergence barrier between Mts. flow genetic Wuyi geographical isolation poorly gene of study, as as rising limited our acting considered The In to are Mts. contributing Wuyi 2018). sometimes thus the al., ranges et Mountain dispersal, 2017). (Oyama long-distance Ree, 2). isolation geographic & facilitating (Table Xing ( when flow for divergence 2018; gene conducive especially population Filatov, high inter-population occur & significantly low Hughes with Hughes, to variance 2017; indicates Contreras-Ortiz, thought molecular suggesting Hughes, Nevado, the 2018; is 3), 2017; of Reeder, This Analysis 1, & Kadereit, Higham, (Figure 2015; Hollingsworth, diversification. Atchison, regions (Harrington, & role local geographical dominant with via a plays aligned mostly isolation closely evolved and they monophyletic that are os- climatic populations Pleistocene All with ranges associated western mountain divergence and and eastern population cillations the ranges and between mountain isolation variation Geographical the and genetic (NLE1 4.2 of of physiography Mts. pattern short- Nanling and geographic the and orientation the of of to the south populations populations contributes Therefore, the to have in to north NLW5). seen diversification, appear through from is population NLW1 as more allowing retreat divergence and promoting Mts., younger gradual thus NLE2, and Nanling facilitate periods, size the interglacial can population of and larger species, glacial orientation populations during north-south plant eastern migrations the the of distance in Conversely, seen shifts is cooler LXS2). elevational as population of divergence and various increasing older times LXS1 an for in to disadvantageous WYS2, contributed migrations is have (WYS1, southward may which and blocking expansion, diversification, barriers and population geographical size orientations postglacial present different northward the to or be thought climate to are likely al is Mts. west et and China (Chen east ranges the between mountain diversification of of level genetic and of time al divergence (Chen, pattern et distributions general Gong wide with the 2018; species al with Sun, plant The agrees other & in pattern Zhou, were China 4). This western and Deng, group and (Figure monophyly eastern populations. sizes a between recent eastern formed observed population more divergence the Mts. where larger Nanling from Mts., the with distinctly Nanling of Ma) the populations separated that of within (0.37-020 revealed than range also occurred sizes analysis geographic diversification phylogenetic population the population smaller of with rapid and portion and Ma) eastern (0.51-0.34 the older in be divergence populations western population and The eastern between divergence Genetic 4.1 S3). Table 5, Figure DISCUSSION 1980; 3, 4 (Table Wu, 2). constant & (Figure less ( present or Pu, smaller divergence. at more much ES (Duan, than remained be and China sizes higher to rate population 5 in estimated migration ES was period ca. The the NL was Interglacial contrast, of and In Lushan-Tali size increased present. the population temperature effective within when ancestral is 2004), The Jackson, time & This Liu, Zhu, Ma. 0.10 = DIV . 08 i,Ga,F,&Cms 09.Oemi atrcnrbtn otedffrne fpopulation of differences the to contributing factor main One 2009). Comes, & Fu, Guan, Qiu, 2018; , 1,7 eeain g,ie,aot16M.Scnaycnat(E)wsetmtda ca. at estimated was (SEC) contact Secondary Ma. 1.6 about i.e., ago, generations 319,472 = Ne ES .chuniana C. 495 epciey rmtecreteetv ouainsz,teacsrleffective ancestral the size, population effective current the From respectively. 14,955, = M NL-ES 21)wsmc ihrthan higher much was (2.14) . . Ne 08.Tesuhetnrhatoinaino h uiMs n East and Mts. Wuyi the of orientation southwest-northeast The 2018). , ANC . 08 a i,Co,&Km 08 omn ta. 08 uet Lu 2018; al., et Hohmann 2018; Kim, & Choi, Kim, Ha, 2008; , 5,5 Tbe3 iue5 al 3.Uigteacsrleffective ancestral the Using S3). Table 5, Figure 3, (Table 755,955 = 7 M ES-NL 03) ihmgainocrigatrNL after occurring migration with (0.33), .chuniana C. Fst N e-pre-exp 0.99, = 6)ta at than 866) = setmtdto estimated is P .0 also 0.00) = Ne T NL SEC = Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. hntepeet(un u u 90 h ta. 04.Ti ugssta h eodr otc may contact secondary the that suggests This 2004). higher al., even still et be it Zhu to Ma), estimated 1980; (0.12˜0.14 was Wu, and LIG & increased the Pu, temperature continuous than (Duan, when present a younger China with the is in when than coincides period period 1980), interglacial Ma) Wu, interglacial the Lushan-Tali (0.10 & within the analysis lies Pu, Although our (Duan, from 2a). Ma) contact (Figure (0.10-0.20 secondary China of of in distribution time geographic period estimated expansion interglacial demographic The Lushan-Tali and contact the 5). secondary by Figure followed other isolation 3, of of migrations (Table model that best-fit west-to-east a to contemporary indicate analyses analogous and FSC2 expansion be demographic not contact, may Secondary refugia conditions glacial 4.3 climatic isolated several the where although ENM, LGM, in cycles. cycles the apparent glacial the glacial also affected Pleistocene during is for Lushan primarily identified populations role and of period were dominant period distribution The Glacial Interglacial geographic diversification. Dagu-Lushan Dagu the population the on The affected whereas northern primarily west, in 4). of and period lowlands (Figure distribution east Glacial to the cycles geographical forests between glacial fir the divergence spruce study, Pleistocene population drive and the our to dry with In 2017; shown The be associated been al., to ranges. have 1988). distribution tended et Pleistocene contracted (Liu, periods (Foster with Middle glacial elevations China estimates the lower The during in to time climate FSC2. shifting period The smaller in populations glacial setting the 2017). generate favor Barker, log-uniform to would & the the which thought Hong, under when cool, Zhang, is range estimation 1980), Kong, Wu, time time BEAST i.e. Bayesian 2017; & wider in of Kong, Pu, older, the results used (Duan, to is the attributed period calibration between FSC2 Glacial Periglacial partially discrepancy secondary Xixiabangma in Sizishan be The the the may model present. geographical of or FSC2 at fit the glacial 2016), and than Quaternary best lower al., shaped known 10 et the and was (Wan earliest genetic of east, temperature Ma the the time 1.6 with the drove overlaps divergence ca. to glaciation which 1980). estimated period those (last) 5), Wu, The and (Figure third & Glacial Ma Middle the Pu, variation. Mts. Kunlun 1.60 primarily the (Duan, genetic Nanling 1980), Wu, uncertain, Interglacial in the of Poyang-Dagu & & is China in patterns Pu, or Xu, glaciations in populations Duan, Zheng, 2011), the between period Ma; Wang, Ma; for divergence (0.5–0.6 glacial (0.5–0.7 & the time period period third Shi, in the Glacial Glacial Zhao, last populations Although Naynayxungla Dagu Ma; the the the 1998), (0.62–0.78 with between in Li, period fall Ma) & coincides may Zhou (0.68 east time 2002; al divergence the The have Shen, et of of to 4). Qu time those thought (Figure 2010; the are and Pleistocene (Knowles, and estimation, isolation habitat Bayesian Mts. geographic suitable on Nanling with changed Based coupled data periodically expansion and cycles 2011). and markers These contraction molecular range cycles. of traditional promoted glacial divergence with the population analyzed by that affected were as suggests which such study of China, Our all subtropical in 2019), range Li, distribution & wide analysis. Li, a with Cheng, species (Shen, directly plant isolation have other historical pauhoi many the Mts. Machilus the in to Nanling contributing from found and factor been distant Luoxiao, barriers major have geographically Wuyi, a geographical and considered the the are including Therefore, of Mts. and ranges colonization V6. Nanling populations mountain long-distance involving the the associated limited vicariance of with the the contrast ridge by in In one formed resulting on thus V5. alone populations, involving has that disadvantageous the remaining as also vicariance located (V4) infer within infer events to we is populations east We which contributing NLW1 (V6) Vicariance orientation, the northwest NLW2˜5, thus north-south and to general 3). orientation. colonization, middle a those the present east-west west-to-east 1, as and for Mts. a well (Figures Nanling as with The V3) (V5) Mts. Mts. corridors eastern and Nanling Nanling and geographical currently western (V2 the the of are between of populations which lack exist Mts., populations western the Luoxiao the or through the between in eastern arisen LXS2 isolation their and geographical of LXS1 the to each apply from to isolated appears This colonization. east-west .chuniana C. ouain Jag u eg 09 ie al et Li 2019; Deng, & Xu, (Jiang, populations Zue al et (Zhu .chuniana C. . 2017), , ooeau chinense Loropetalum ln h onanrne nsuhr hn a eetdb ENM by detected was China southern in ranges mountain the along .chuniana C. 8 Gn tal et (Gong . 09 age al et Yang 2019; , curdi h litcn n a been has and Pleistocene the in occurred .chuniana C. . 06 and 2016) , . nsuhr hn salso is China southern in 09.Smlrpatterns Similar 2019). , iidnrnchinense Liriodendron . , Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. kie .(94.Anwlo ttesaitclmdlidentification. model statistical the at look new A 19 Control, (1974). H. Akaike, XXX). (DOI: Figshare REFERENCES in authors deposited All been manuscript. have analyzed the data F. wrote PW. The and and G., results sample W. the statement and K., discussed Accessibility HH. investigation G. L., Data field manuscript. W. WZ. conducted the and work. with L. F. lab agree PW. the WZ. and out L., carried read research. WZ. Z. the data. H. designed and genomic X. the and JG. supervised L., WZ. H. collection. G. for and Yan information. G. Haifei and fossil W. and sampling providing Yi, for with Wang Huiqin help Qi Liu, for Tongjian contributions Prof. Zhang 31470319; Meier, to Author Zhong Joana goes (31470312; Ravinet, and thank (2016A030303048). Mark Huang, China Special Sun, China Yemei analyses. of Zhixia Li, Province, data thank Foundation Bo Guangdong We Zhou, Science of trips. Juan Natural field Wang, Project National Xiaolan Planning thank Technology the We and by Science supported 31970231), was work This the facilitate across may areas which stepping-stone adjacent ones, ACKNOWLEDGEMENTS closely eastern via the ones than for lower ranges. ecological to Mts. refugia mountain elevations Nanling stable the glacial higher the long-term more the from in diverged and migration of elevations phytogeography former west-to-east higher one the distinct relatively whereas with be at east, Mts., to present the Nanling thought towards The is Mts. condition, latter. Nanling the the than from recently inferred is direction migration in STEBF of history long a has ridges, distinct five of al composed with et are inferred (Fan diversification which was population Mts., China Mts. local Nanling high Nanling southern indicating The the 5), in Figure 3). expansion 3, (Table (Figure demographic size model, population intensified effective same increased monsoon the notably al In summer et Asia S1). (Liu (Table East period precipitation that interglacial the considering in the that especially during thought habitat, precipitation is more al with it et temperature Moreover, Meng increased to time. due warmer then this during occur rce rmrl rmteNnigMs otees.Mn xmlso ln pce nEs saehbta al exhibit et Asia Wang East 1992b; in species 1992a; plant Wang, of 2018; examples as al., Many such et east. route, (Tian migration the and to with pattern Mts. distribution divergence, Nanling similar ES the and from NL primarily relatively after proceed with occurring species migrations the bidirectional M for indicated even analysis dynamics, FSC2 using sampling, Additionally, population generation conducted population next the is the intensive detect research on to more previous based distribution. ways approaches the with narrow genomic effective of population methods, more Most consider are analysis We sequencing study. 2009). data current Huang, and the & with markers compared Lowe, molecular Kang, traditional Gao, Wang, the China, Mts. 2018; subtropical in increase al., Nanling species size et widespread the population in climatic in documented in resulting been Jiang, as from conditions have finally & such cases diversity, buffer ecological (Tian Similar population current a preserve stable expansion. as to demographic as long-term period and thought glacial served are plus last cycles physiography has the glacial during complex and across precipitation Therefore, periods annual same glacial the 2016). during almost had mountains It al these change. et to (Shen conditions shifts ecological longitudinal or elevational NL-ES uyoybscavaleriei Eurycorymbus 21)hge than higher (2.14) . 6,7673 doi:10.1109/TAC.1974.1100705 716–723. (6), 08 age l,19;Wn ta. 07 age l,21) hspoiigmr suitable more providing thus 2012), al., et Wang 2007; al., et Wang 1999; al., et Wang 2018; , . M 08 ue al et Xu 2018; , ES-NL , ooeau chinense Loropetalum .chuniana C. 03)(al ,Fgr ) h irtosin migrations The 5). Figure 3, (Table (0.33) . . 09 h tal et Zhu 2019; , 07.Isvgtto scaatrzdb ihyvaried highly by characterized is vegetation Its 2017). , saatdt ei niomnsadms nune by influenced most and environments mesic to adapted is . 9 05.Teqeto rssa owycontemporary why to as arises question The 2015). , ersim hemsleyanum Tetrastigma and .chuniana C. oeo chionantha Eomecon . 07,wihcnesrltvl stable relatively confers which 2017), , ouain of Populations . EETascin nAutomatic on Transactions IEEE and Gn ta. 06 Tian 2016; al., et (Gong .chuniana C. oeo chionantha Eomecon .chuniana C. . emto seem 2018; , are Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. ol,J,&Dye .(96.ArpdDAioainpoeuefo ml uniiso rs eftissues. leaf fresh of quantities (2011). small L. from M. procedure isolation Blaxter, DNA & rapid A M., 19 J. (1986). Bull, J. Catchen, Phytochem Doyle, Q., & J. J., Doyle, sequencing. Boone, next-generation D., using climatic P. genotyping Profound 12 Etter, and (2011). Genetics, discovery A., M. (2006). and marker P. F. models genetic R. Lei, niche Hohenlohe, Genome-wide J., ecological W., X. Smith, by Yang, J. revealed B., Davey, Aegithalidae), J., Gao, (Ave: T., Carton, tits C. black-throated Lin, analysis. Asian C., J., phylogeographic East W. two Bretherton, Wang, on N., effects G., Zhao, Y., (CCSM3). C. Bonan, 3 Dai, Version M., Model Blackmon, system doi:10.1175/JCLI3761.1 C., climate community Bitz, The W., Collins, diversification plant of rates Exceptional scale: Andes. continental 103 a the on of radiation Island uplift after (2006). E. Ruth, & H., of Colin, characteristics not? ecological or and ancient Technology composition flora population Plant & Asian Forestryence (1999). diversity, East Yunnan F. the Mao, Genetic Is & Z., (2018). Chen, H. (2017). Sun, & Y. Z., Y. Zhou, 5 T., Review, Li, Deng, S., & Y. markers. Chen, M., of SSR X. collection and core Pang, genotyping-by-sequencing a doi:10.3389/fpls.2017.00575 Y., by of variation Z. developed disequilibrium Geographic SNPs Zhang, linkage (2012). L., X. and C. Hou, structure, Fu, & W., R., Y. Chen, Mao, H., Yang, F., doi:10.1111/j.1759-6831.2012.00210.x Shi, 374–385. in J., DNA Zeng, chloroplast L., of Zhang, (2010). C., A. S. M. tool Chen, Vincent analysis & an China. S., Beijing, Stacks: S. Press: Larsen, (2013). Science A. D., W. Zhang, Cresko, D., & Chen, A., Amores, genomics. S., population Bassham, for BEAST A., set P. (2014). Hohenlohe, J. J., A. Catchen, Drummond, analysis. D., evolutionary Xie, Bayesian H., for C. Wu, platform doi:10.1371/journal.pcbi.1003537 T., software Vaughan, A a D., (2017). Kuhnert, 2: E. J., Zimmerman, phylogeny. Heled, B., comprehensive R., the R. Bouckaert, taxonomically Pinto, Harnessing a R., on A. based (2016). Barbosa, Leguminosae A. H., the 66 Banks, P. of D., classification Hohenlohe, C. subfamily Bailey, & new M., G., Babineau, genomics. N., Luikart, evolutionary Azani, R., and M. ecological Miller, for M., doi:10.1038/nrg.2015.28 phylo- RADseq J. large of of Good, post-analysis power and R., analysis K. phylogenetic Andrews, for tool a 8: version genies. RAxML (2014). S. Alexandros, Species Hundred (1998). J. S. Aldworth, 1,4–7 doi:10.12705/661.3 44–77. (1), 2) 03–03.doi:10.1073/pnas.0601928103 10334–10339. (27), iifrais 30 Bioinformatics, 6,9092 doi:10.1093/nsr/nwx156 920–932. (6), 7,4950 doi:10.1038/nrg3012 499–510. (7), oaSaeUiest,Dprmn fBotany. of Department University, State Iowa : 1,11–15. (1), ltcrastrobilacea Platycarya re n huso h apso oaSaeUiest:AWligTu fOne of Tour Walking A University: State Iowa of Campus the of Shrubs and Trees rceig fteNtoa cdm fSine fteUie ttso America, of States United the of Sciences of Academy National the of Proceedings lsOe 6 One, Plos 9,11–33 doi:10.1093/bioinformatics/btu033 1312–1313. (9), oeua clg,22 Ecology, Molecular 1,01. (1), . 1) 239.doi:10.1371/journal.pone.0029329 . e29359 (12). (Juglandaceae). 1) 1434.doi:10.1111/mec.12354 3124-3140. (11), 10 lsCmuainlBooy 10 Biology, Computational Plos Cercis ora fSseaisadEouin 50 Evolution, and Systematics of Journal iihsjujuba Ziziphus aueRvesGntc,17 Genetics, Reviews Nature ora fCiae 19 Climate, of Journal In . rnir nPatSine 8 Science, Plant in Frontiers lr fChina of Flora ecsyunnanensis Cercis sesdwt genome-wide with assessed Vl 0 p 5–6): pp. 10, (Vol. ainlScience National 1) 2122-2143. (11), aueReviews Nature 4,e1003537. (4), 2,81–92. (2), Coppice. Taxon, 575. , (4), Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. eefigr . rgs,C . oeo .A,Oetn .D,Mtigr .P,Za,H . elpra S. Dellaporta, Y., H. Zhao, studies. P., population J. for Mottinger, strategies climatic D., genotyping-by-sequencing J. Pleistocene scalable 15 Overton, and A., Flexible (2018). M. (2014). Moreno, W. L. A., T. C. Fragoso, ( Reeder, C., rattlesnake Heffelfinger, & diamond red E., the T. in contact Higham, secondary California. D., and B. isolation drive Hollingsworth, fluctuations M., S. (Oleaceae) shrubs. Forsythieae Harrington, of temperate dating Eurasian and phylogeny of Molecular history (2018). H. Miocene doi:10.3389/fpls.2018.00099 J. the Kim, into & K., insight Choi, provide C., Kim, wide H., to Y. refugia Ha, glacial From fos- (2016). X. living D. Zhang, a 0252-4 & forest. A., of broadleaved M. evergreen Phylogeography of Koch, ical S., expansion Kaneko, demographic L., (2008). range: Gu, distribution Z., A. W. M. Liu, W., Koch, Gong, & X., expansion. C. doi:10.1016/j.ympev.2008.05.003 postglacial Fu, forced subsequent C., glaciations limited Dobes, Pleistocene C., sil: evolution Chen, the Delgado-Salinas, for W., & implications O., Gong, D. Cercis: Burge, American C., North B. in floras. Cruz, boundaries W., dry species Gong, and of T., adaptations S. Leaf L. (2018). Leatherman, A. F., C. Nowell, biogeography. W., P. Fritsch, historical of transatlantic Phylogeny for (2017). Implications evolutionary W. 62 (2012). Evolution, Y. angiosperm C. regions: S. the B. plastid Ho, of Cruz, four & estimates & M., Bayesian W., Rossetto, P. on Fritsch, H., priors McPherson, and M., data Merwe, genomic der of timescale. conserva- Van in impact H., errors the prediction Sauquet, of Evaluating P., assessment the S. (2018). for C. methods Y. global Foster, of for review Z. A surfaces Zhang, climate (1997). models. F. resolution & presence/absence J. spatial tion X., Bell, 1-km & Y. new H., A. 2: Kou, Fielding, WorldClim M., (2017). S. J. of R. Cheng, areas. hotspots Hijmans, diversity land X., & species Z. E., with S. Sun, comparison Fick, A L., China: H. subtropical plants. Hu, in seed plants woody H., seed J. of metric hotspots Huang, data. from Evolutionary restriction M., inferred variance DNA D. molecular mitochondrial Fan, of human Analysis to (1992). application M. J. haplotypes: 131 Quattro, DNA & among E., distances P. Smouse, L., Excoffier, demographic Robust doi:10.1111/j.1755-0998.2010.02847.x (2013). M. Foll, & C., V. data. Sousa, SNP E., and quaternary. genomic Huerta-Sanchez, the from I., during inference China Dupanloup, in L., variations Excoffier, Climatic (1980). X. Wu, doi:10.1007/BF00214217 & 515–524. Q., Pu, W., Duan, xoe,L,&Lshr .E .(00.Alqi ut e .:anwsre fporm operform to programs of series new a 3.5: ver suite Arlequin Windows. and (2010). Linux L. under E. analyses H. genetics Lischer, population & L., Excoffier, 1,99 doi:10.1186/1471-2164-15-979 979. (1), 2,479–491. (2), ytmtcBooy 66 Biology, Systematic ora fBoegah,45 Biogeography, of Journal nentoa ora fCiaooy 37 Climatology, of Journal International mrcnJunlo oay 105 Botany, of Journal American 3,8685 doi:10.1016/j.ympev.2011.11.016 816–825. (3), rnir nGntc,9 Genetics, in Frontiers niomna osrain 24 Conservation, Environmental raim iest vlto,16 Evolution, & Diversity Organisms 3,3831 doi:10.1093/sysbio/syw086 338–351. (3), ikobiloba Ginkgo lsGntc,9 Genetics, Plos 1,6–5 doi:10.1111/jbi.13114 64–75. (1), 3.doi:10.3389/fgene.2018.00333 333. , oeua hlgntc n vlto,48 Evolution, and Phylogenetics Molecular ooeau chinense Loropetalum 9,17-54 doi:10.1002/ajb2.1155 1577-1594. (9), .(ikoca)it w eueaesi hn with China in areas refuge two into (Ginkgoaceae) L. 11 1) 3241.doi:10.1002/joc.5086 4302-4315. (12), Cercis 1) 1095 doi:10.1371/journal.pgen.1003905 e1003905. (10), oeua clg eore,10 Resources, Ecology Molecular ae nDAsqecso ula T and ITS nuclear of sequences DNA on based 1,3–9 doi:10.1017/s0376892997000088 38–49. (1), Hmmldca)i hns subtrop- Chinese in (Hamamelidaceae) 1,2–8 doi:10.1007/s13127-015- 23–38. (1), rnir nPatSine 9 Science, Plant in Frontiers oeua hlgntc and Phylogenetics Molecular rtlsruber Crotalus M Genomics, BMC eJunl 4 GeoJournal, 3,1094–1105. (3), 3,564–567. (3), Genetics, nBaja in ) 99. , , Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. i . ubn .(09.Fs n cuaesotra lgmn ihBrosWelrtransform. Burrows-Wheeler with alignment read short accurate PhyML. and in Fast selection (2009). model R. smart 25 SMS: Durbin, Bioinformatics, & (2017). H., O. Li, Gascuel, & 34 Evolution, E., and J. Biology Longueville, V., informing Lefort, Both reconstruction phylogenetic Multilocus (2017). (2017). M. 303 S. Kang, M. Evolution, Barker, M., & of Moller, Y., relationships Hong, B., polyploid Y., ecosystems Pan, Zhang, karst H., L., the H. in J. Kong, diversification Chen, plant driven J., have China. A. monsoons southern Harris, Asian from East L., and vascu- F. fluctuations models Condamine, temperature high refugial H., explicit of of H. Tests Kong, evolution divergence? promote of the glaciations studies Pleistocene grasshoppers. for the phylogenetic montane Did diversification in of (2001). interpretation species L. L. and situ Knowles, review Alps. in Alps-A the of European of role doi:10.1016/j.ppees.2017.03.002 the flora in The endemic diversity the species rare (2017). plant the of W. lar dynamics J. distribution and Kadereit, patterns genetic Spatial (2019). M. doi:10.3390/f10090821 Deng, & B., G. Caesalpinioideae. Oak Xu, Subfamily L., II. X. Jiang, States. United the Garden of representation Botanical Leguminosae reduced York restriction-based (1975). in clustering. D. optimal loci Isely, for Defining diagnostics the and (2014). to bias P. Andes of M. sources the Hare, International from species: & nonmodel radiations: L., from plant data M. genomic alpine Nydam, 114 of C., ubiquity D. America, The Ilut, of (2015). States W. hotspot? G. United biodiversity Mountains. Atchison, global Hengduan the & a E., of C. becoming Sciences Hughes, to of routes different Academy many National there doi:10.1073/pnas.1703798114 re- the and Are expansion of Iteration (2017). ceedings (2017). E. Y. X. C. Ding, Hughes, & Y., Q. Xue, distribution. T., 7 Z. geographical Reports, Niu, of its S., phylogeography Y. to evolution: Zhang, gional J., reference Luo, with W., B. China Hou, of Vegetation 70 Garden, (2018). Botanical A. (1983). Missouri M. Y. Koch, resolution H. P., Y. high Hou, Zhao, Very M., Kiefer, doi:10.1186/s12864-018-4673-2 (2005). B., 299. W. A. (1), Zhou, Jarvis, P., Rigault, & M., biloba G., E. P. Wolf, N., Jones, Hohmann, L., areas. J. 359 land Parra, Quaternary. global doi:10.1002/joc.1276 Sciences, for E., 1978. the B-Biological surfaces S. in climate Series Cameron, interpolated oscillations London J., climatic R. of Hijmans, of Society consequences Royal Genetic the doi:10.1098/rstb.2003.1388 of (2004). Transactions M. ical G. Hewitt, uru chungii Quercus sfopito yai litcn itr ae akol 9,0 er ago. years 390,000 only back dates history Pleistocene dynamic of footprint ’s 1,455 doi:10.1038/srep43525 43525. (1), . 6,7774 doi:10.1007/s00606-017-1406-y 727–744. (6), 2014 1) 7416.doi:10.1093/bioinformatics/btp324 1754–1760. (14), doi:10.1155/2014/675158 . mlctosfrboiest osraini otes China. Southeast in conservation biodiversity for Implications : oeua clg,26 Ecology, Molecular e htlgs,207 Phytologist, New . Aconitum oeua clg,10 Ecology, Molecular 9,22–44 doi:10.1093/molbev/msx149 2422–2424. (9), 3,5959 doi:10.2307/2992085 509–549. (3), esetvsi ln clg vlto n ytmtc,26 Systematics, and Evolution Ecology Plant in Perspectives edoimofficinale Dendrobium subgenus 2,2522 doi:10.1111/nph.13230 275–282. (2), 2) 4462.doi:10.1111/mec.14367 6414–6429. (22), Lycoctonum 3,6171 doi:10.1046/j.1365-294x.2001.01206.x 691-701. (3), 12 nentoa ora fCiaooy 25 Climatology, of Journal International n orrltdtx nsuhr China. southern in taxa related four and Rnnuaee nChina. in (Ranunculaceae) ln ytmtc and Systematics Plant oet,10 Forests, eor fteNew the of Memoirs M eois 19 Genomics, BMC 1) 4275–4277. (17), imdResearch Biomed 14) 183-195. (1442), naso the of Annals 1) 1965– (15), Philosoph- Molecular Scientific 9,821. (9), 28–38. , Ginkgo Pro- Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. ecl,F .(90.Egtnwseiso euioa rmSuhatr China. To- Southeastern from Leguminosae (2018). of N. species new K. Eight , Suding, a (1940). & P. across F. C., (1972–2008) Metcalf, change K. climate Rosemond, Colorado. to D., Ridge, C. response doi:10.1080/15230430.2018.1504492 Niwot vegetation Bernard, of S., landscape, Pleistocene L. patterns evidence mountain early Mineralogical explains Tillmann, the (2018). heterogeneity d., during F. B. pographic plateau J. P. loess Ji, C. Chinese & J., the Mesquita, Chen, on W., rainfall Balsam, monsoon T., summer C. interglacials. Asian X. SNP Wang, East for W., reduced pipeline L. of Liu, reference-optional Q., a X. GBS-SNP-CROP: Meng, genotyping-by-sequencing (2016). paired-end I. length, variable Hale, using & data. characterization germplasm R., biodiversity plant Bartaula, and between O., discovery routes of T. Dispersal history A. Evolutionary Melo, (2016). (2018). A. genus D. Favre, mountain Z. & the Chen, of H., case relatives. L., the Sun, H. Asia: N., Li, in A. in B., hotspots Liu, Muellner-Riehl, endemism F., plant S., J. of Matuszak, Ye, Centres China. T., of Yang, (2011). flora F., angiosperm S. L. the Mao, Ge, M., & L. S., Lu, T. Ying, Q., speciation? for H. or 2699.2011.02504.x Sun, survival for M., places in F. China: Changes Zhang, (2018). Province. J., Fujian C. Mountains, Lopez-Pujol, Science Wuyi S. Natural the Xie, of University & characteristics Nanjing variation. morphological H., of Monsoon and J. nal Summer origin Huang, Asian The East (1984) Y., Z.Z. to C. Liu related Tang, ka J., ecological 75 J. since and Plateau Pan, Geological 510 Palaeoecology, Loess H., Palaeoclimatology Palaeogeography Chinese Yang, (2013). the J., Z. on T. type D. vegetation Algeo, Li, Interpreting hotspot. S., & biodiversity J. (2012). C., a Liu, M. R. in F. Poudel, yews M., Lei, of L. & of speciation doi:10.1111/nph.12336 Gao, J., models cryptic J., niche Fjeldsa, Provan, drive ecological H., M., factors and S. Moller, phylogeography Li, J., the H., Liu, integrating Y. by Qu, China G., in Song, endemism the J., behind W. process Wang, the temperate T., a of H. phylogeography Chloroplast Liu, (2012). X. Y. Qiu, & P., doi:10.1111/j.1759-6831.2012.00203.x X. Zhang, C., Lu, W., China. tree J. of Shao, H., forests X. and Li, temperate period,amplitude the the of on discussion history doi:10.1016/0277-3791(88)90089-3 A Quaternary 1–20. (1979). (1988) B. plateau. K. Li, Qinghai-Xizang & Liu, the B., of Zheng, uplift F., phylogeographic the Wang, Molecular Q., of Zhang, type (2019). S., Y. Wen, J., Li, Li, Y., Wu, M., Motokawa, that S., reveal plex. Zhang, delimitations K., species project Wang, and Genome analyses L., Kong, (2009). R. H., SAMtools. Durbin, Li, and N., format Homer, Alignment/Map J., doi:10.1093/bioinformatics/btp352 Ruan, Sequence T., 2079. The Fennell, S: A., processing Wysoker, data B., Handsaker, H., Li, 19 tcyiossruficeps Stachyridopsis trcli tatarinowii Pteroceltis 549-563. , nertv olg,14 Zoology, Integrative M iifrais 17 Bioinformatics, BMC ora fBoegah,43 Biogeography, of Journal at n lntr cec etr,486 Letters, Science Planetary and Earth . Umca)i China. in (Ulmaceae) lsOe 7 One, Plos 5,4455 doi:10.1111/1749-4877.12378 494–505. (5), aue 554 Nature, 1,2.doi:10.1186/s12859-016-0879-y 29. (1), 3,5050 doi:10.1111/jbi.12617 580–590. (3), 1) 471 doi:10.1371/journal.pone.0046761 e46761. (10), , 79) 3 28 doi:10.1038/nature25485 –238. 234 (7691), ora fBoegah,38 Biogeography, of Journal 3 eplay edwardsi Leopoldamys 567–578. , Tripterospermum rtcAtrtcadApn eerh 50 Research, Alpine and Antarctic Arctic cetaSnc,22 Sinica, Scientia ora fSseaisadEouin 50 Evolution, and Systematics of Journal 13 2–3.doi:10.1016/j.palaeo.2018.02.030 124–139. , 16.doi:10.1016/j.epsl.2017.12.048 61–69. , Gninne etaaee n t close its and Gentianaceae) (Gentianinae, e htlgs,199 Phytologist, New Rdni:Mrde saseiscom- species a is Muridae) (Rodentia: 1314–1328. , utraySineRves 7 Reviews, Science Quaternary 7,16-20 doi:10.1111/j.1365- 1267-1280. (7), Bioinformatics iga cec Journal Science Lingnan , 4,1093–1108. (4), 25 1,e1504492. (1), 4,325–333. (4), 1) 2078– (16), Jour- (1), Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. a,A,Sehn,M,&Picad .K 21) atTUTR:vrainlifrneo population of inference variational http://tree.bio.ed.ac.uk/software/figtree/ software. from 1.4.3 fastSTRUCTURE: FigTree (2014). (2014). A. K. Rambaut, sets. J. data his- Pritchard, SNP and large & diversification in Lineage M., structure (2011). Stephens, M. A., F. Lei, Raj, & S., Himalayas. F. Zou, eastern G., the Song, bird of montane Y., diverse a R. most of Zhang, demography world’s X., torical the Luo, in H., Y. change regions: Qu, environmental adjacent and and China in climate phylogeography Quaternary molecular al- Plant flora. of promote temperate (2011). imprints P. interglacials H. genetic Comes, and/or the & Tracing X., glacials C. Fu, Did on X., Y. analyses Qiu, (2009). coalescent H. and Phylogeographic Comes, & plants? doi:10.1016/j.ympev.2009.01.016 X., temperate in Asian divergence C. and East Fu, isolation refugial in pattern C., distribution speciation B. Vegetation incipient Guan, lopatric (2013). X., M. Zhong, Y. China. & Qiu, basin, G., river C. hilly Zhang, and mountainous C., 23 subtropical C. Sciences, in Chen, gradient geographic Y., altitudinal species C. of along Zeng, modeling W., entropy B. Maximum variantQiu, (2006). The E. R. (2011). Schapire, T. & S. P., Sherry, R. distributions. A., Anderson, M. J., Depristo, S. B., Phillips, Eric, A., C. VCFtools. Madagascar. distribu- Albers, and in species A., format geckos Goncalo, call Predicting cryptic A., using Adam, (2007). case D., T. test Petr, A. a Peterson, records: & occurrence M., of 34 Biogeography, Nakamura, numbers small J., from C. Raxworthy, tions G., R. populations Pearson, among Ruiz- connectivity A., and 11 C. diversity Science, Torres-Miranda, genetic Conservation P., Tropical Genetic High E. (2018). A. (2019). A. Pedraza, P. of Gonzalez-Rodriguez, M., X. & J. Wen, E., Penaloza-Ramirez, W., Sanchez, W., Z. Ramirez-Toro, Chen, genotyping-by-sequencing. K., by G., Oyama, developed D. SNPs Zhao, genome-wide 19 H., using ( Biology, plant D. plateau, Plant tea Guizhou Qiao, the center, drive of H., origin analysis cycles Koiwa, structure an population glacial F., and Q. Pleistocene disequilibrium, Andes. linkage Song, diversity, high-elevation Z., (2018). the S. A. Niu, in D. speciation Filatov, & and C., doi:10.1111/nph.15243 flow Hughes, gene N., isolation, Contreras-Ortiz, B., A. Nevado, Region. M. Tibeto-Himalayan O’Leary, the 10 in Science, H., Research Paradigm Plant Phylogeographic Approaches, R. Plant in Emerging for Patterns, Scheuermann, Implications Gateway. Their Arenas: B., Evolutionary Science and as Shifts, CIPRES Mountains E. the (2019). Klem, N. via A. Tools H., Muellner-Riehl, Phylogenetic Sherry, to E., Access B. for 11 API Pickett, Bioinformatics, RESTful S., A Terri, gen- (2015). A., next technologies-the M. Sequencing Miller, sequencing. next-generation of Applications eration. (2010). L. M. Metzker, uru candicans Quercus aueRvesGntc,11 Genetics, Reviews Nature 2,2727 doi:10.1007/s11442-013-1007-9 247–257. (2), clgclMdlig 190 Modelling, Ecological oeua hlgntc n vlto,59 Evolution, and Phylogenetics Molecular 1,1217 doi:10.1111/j.1365-2699.2006.01594.x 102–117. (1), 1,38 doi:10.1186/s12870-019-1917-5 328. (1), 1) 34.doi:10.4137/EBO.S21501 43–48. (11), 9.doi:10.3389/fpls.2019.00195 195. , , uru crassifolia Quercus iifrais 27 Bioinformatics, M vltoayBooy 11 Biology, Evolutionary BMC eeis 197 Genetics, yom versipellis Dysosma 90898615 doi:10.1177/1940082918766195 1940082918766195. , arlxelliotii Garrulax 1,3–6 doi:10.1038/nrg2626 31–46. (1), 34,2129 doi:10.1016/j.ecolmodel.2005.03.026 231–259. (3-4), and , nttt fEouinr ilg,Ui.Edinburgh Univ. Biology, Evolutionary of Institute 1) 1625.doi:10.1093/bioinformatics/btr330 2156–2158. (15), 2,53 8.doi:10.1534/genetics.114.164350 589. 573– (2), uru castanea Quercus 14 mlctosfrtePesoeeeouinr history evolutionary Pleistocene the for implications - . oeua hlgntc n vlto,51 Evolution, and Phylogenetics Molecular 1,14 doi:10.1111/j.1365-294X.2008.03998.x 174. (1), 1,2524 doi:10.1016/j.ympev.2011.01.012 225–244. (1), nahtrgnoslnsaei Mexico. in landscape heterogeneous a in e htlgs,219 Phytologist, New aelasinensis Camellia ora fGeographical of Journal 2,779–793. (2), Evolutionary Retrieved . ora of Journal 281-293. , Frontiers from ) BMC Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. ag . in,L,Sn . u . ag .G,Sn,Z . hn,W .(00.Phylogeographic (2010). J. W. Zhang, P., Z. Song, G., (2016). Y. Wang, L. Plateau. F., Opgenoorth, Qinghai-Tibetan Lu, the & K., G., Sun, of Miehe, L., structure W., Qiong, Y. H., for East Duan, Wang, implications and S., conservation perennial, K. China and herbaceous Mao, 6 dynamics, over endemic Evolution, C., distribution Plateau climate D. potential Qinghai-Tibet maximum Jiang, history, a glacial J., evolutionary J. Quaternary last Feng, The Revisiting S., D. Wan, (2016). Asia. B. East D. in simulations. species doi:10.1016/j.palaeo.2016.04.020 PMIP3 Jiang, using tree patterns & monsoon the relict P., shape Asian a processes Z. Different of range (2020). genomes Repeated Tian, F. chloroplast H. Wang, and (2015). & nuclear Y. L., 10 Bao, the Z. Evolution, M., in T. Zhang, Wang, divergence L., W., of J. Q. Ye, Y., Meng, X. phylogeography. B., Tian, chloroplast Li, by L., 85 revealed Evolution, L. China and of Deng, subtropical routes W., in recolonization Hu, (Lardizabalaceae) inter-/postglacial Q., and S. expansions Lei, Phylogeography S., (2018). Y. Tian, Z. Zhang, J., corridor. Lopez-Pujol, dispersal R., D. het- a Li, and L., geographic Yuan, R., and Z. change Zhang, of X., climate Y. Kou, Plio-Pleistocene S., Tian, (2009). F. relationships. Skov, diversity-environment & 0587.2008.05732.x species’ plant S., and in niches Normand, erogeneity ecological C., fundamental of J. models Svenning, of Interpretation (2005). areas. A. distributional Peterson, in & Plateau J., Qinghai-Tibetan Soberon, mammals. of recent changes American environmental North and of density Uplift doi:10.2307/2411825 Species (1998). (1964). Y. G. B. Simpson, Li, China: Guangzhou, & J., Cenozoic. J. Late the Li, F., Press. Technology Y. (2006). and Shi, Z. Science Su, Hebei & China: J., Shijiazhuang, Z. . Cui, geospatial F., and chinense. Y. analysis phylogeographic Liriodendron Shi, Integrating of refugia (2019). glacial G. H. and Li, routes & dispersal doi:10.3390/f10070565 Q., historical K. infer Li, to L., methods Y. Cheng, F., application. Y. crop Shen, right characterize the to for approaches Genotyping-by-sequencing tool right (2017). doi:10.1111/pbi.12645 bio- the D. historical choosing Edwards, of & maximum quantification genomes: J., glacial the from Batley, to last A., Retrieved approach the Scheben, new at a 6. world the analysis: of Dispersal-vicariance v1. geography. map Tracer (1997). vegetation F. GIS-based Ronquist, A (2014). J. (2001). M. A. BP). J. Drummond, (25,000-15,000 Adams, & & N., D., Ray, Xie, A., M. http://beast.bio.ed.ac.uk/Tracer Suchard, A., Rambaut, oeo chionantha Eomecon ytmtcBiology Systematic ippa tibetana Hippophae 7,17–95 doi:10.1002/ece3.2019 1977–1995. (7), 1) 3144.doi:10.1002/ece3.6200 4331–4342. (10), 3–4.doi:10.1016/j.ympev.2015.02.016 238–246. , idvriyIfrais 2 Informatics, Biodiversity nentAcaooy 11 Archaeology, Internet nsbrpclCia h ulrlso h aln onan sagailrefugium glacial a as Mountains Nanling the of roles dual the China: subtropical in M vltoayBooy 18 Biology, Evolutionary BMC oeua clg,19 Ecology, Molecular , Eaanca)hglgt h ihs irrfgaadterpdulf of uplift rapid the and microrefugia highest the highlights (Elaeagnaceae) 46 1,1523 doi:10.2307/2413643 195–203. (1), undn cec n ehooyPress Technology and Science Guangdong h utraygaitosadevrnetlvrain nChina in variations environmental and glaciations Quaternary The aaoegah aaolmtlg aaoclg,453 Palaeoecology, Palaeoclimatology Palaeogeography doi:10.11141/ia.11.2 . 0.doi:10.17161/bi.v2i0.4 (0). 15 1) 9427.doi:10.1111/j.1365-294x.2010.04729.x 2964–2979. (14), 1,2.doi:10.1186/s12862-017-1093-x 20. (1), nsdstanguticus Anisodus cgah,32 Ecography, agnooacuneata Sargentodoxa ln itcnlg ora,15 Journal, Biotechnology Plant ytmtcZooy 13 Zoology, Systematic 1,1–1 doi:10.1111/j.1600- 13–21. (1), (Solanaceae). . Oi. ed tWils. et Rehd. (Oliv.) oeua Phylogenetics Molecular oet,10 Forests, 2,149-161. (2), clg and Ecology clg and Ecology 2,57–73. (2), 115–126. , 7,565. (7), Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. ag .H,Dc,C . a,X . un,H .(06.Ipcso igorpi itr and history biogeographic of Impacts (2016). of W. study H. case Huang, a & limits: H., range X. species ge- Zhang, Yao, 6 on the & Reports, W., genetics driving J. C. population in Che, Dick, marginal fluctuations R.W., H., Murphy, climatic A. J., Pleistocene Yang, Jin, than K., role Jiang, larger Y., a Hotspot 10.1111/mec.12153 Wang, of play (2017). Z., events structure X. Yuan, Geological Y. netic H., Jiang, Zhao, & (2013). G., W., China. Y. R. in Zhou, moun- Zang, plants F., H., Wuyi woody Yan, J. from broadleaved Huang, granite evergreen H., for Z. a Wang, gaps 7 of X., Reports, conservation L. behavior significant Ying, Mechanical indicate H., analyses Z. (2019). Shen, Y., H. Xu, S. Approaches. Zhang, Strain-Based & from C., doi:10.1007/s00603-018-1617-8 Insights S. temperate Wu, a tain: Mountains, F., Hengduan L. the Xiong, in diversification Uplift-driven doi:10.1073/pnas.1616063114 (2017). E3444–E3451. (17), H. Raven, R. & Ree, R.M. hotspot. biodiversity & Polhill, W., In Y. Bronn. Xing, Cercideae 3. Tribe (1981). Garden. S.S. Larsen, structure. & population P.H.(Eds.), K. of Larsen, analysis R.P., the Wunderlin, for F-statistics Estimating (1984). 38 C. tion, Cockerham, of & diversity B., beta Weir, Publishers. the Inc. in Associates, patterns Sinauer USA: Geographical Massachusetts, (1996). (2012). size. B. L. range Weir, and Shi, environment & space, Y., of Z. influence Tang, the doi:10.1111/j.1600-0587.2012.06988.x Y., plants: J. woody Fang, China’s H., phylogeogra- Z. Molecular China. Wang, (2015). subtropical X. in C. forest Fu, doi:10.1111/nph.13261 evergreen & 852–867. of X., (2), dynamics Y. climber, range Qiu, herbaceous S., Plio-Pleistocene widespread F. into a of Hu, insights P., modelling H. niche ecological Comes, and Asiatic M., phy eastern W. the Jiang, in H., found Y. routes Wang, migration some and patterns Quaternary distribution (Cont.). Asiatic some eastern region On (2007). the (1992b). in F. T. found J. W. routes Wang, migration Chen, some H., and patterns R. distribution orbital Chen, some and region. On R., volume ice (1992a). J. global T. Li, monsoon, W. Asian Wang, J., East to Tian, Linkages S., Sea: W. China South Xiao, forcing. the M., in records Z. opal East biogenic Jian, China (1999). J., South U. R. the Pflaumann, from Wang, case records S., sediment Heilig, the High-resolution P., Pleistocene: refugia: Grootes, Late within J., Sea. the Refugia Grimalt, during climate H., monsoon (2009). Erlenkeuser, Asian W. M., Sarnthein, H. L., Huang, Wang, & J., A. ( doi:10.1111/j.1365-2699.2009.02165.x Lowe, tree 2156–2164. M., canopy Kang, a of X., study P. Gao, J., Wang, aieGooy 156 Geology, Marine caPyoaooiaSnc,30 Sinica, Phytotaxonomica Acta cec nCiaSre -at cecs 50 Sciences, D-Earth Series China in Science 3817.doi:10.1111/j.1558-5646.1984.tb05657.x 1358–1370. , 1,262 doi:10.1038/srep25632 25632. (1), doi:10.1038/s41598-017-02098-0 1–10. (1), dacsi eueSseais at1 Part Systematics, Legume in Advances caPyoaooiaSnc (China) Sinica Phytotaxonomica Acta eei aaAayi.MtosfrDsrt ouainGntcData Genetic Population Discrete for Methods Analysis. Data Genetic uspaboulengeri Quasipaa rceig fteNtoa cdm fSine fteUie ttso mrc,114 America, of States United the of Sciences of Academy National the of Proceedings uyoybscavaleriei Eurycorymbus 14,2524 doi:10.1016/S0025-3227(98)00182-0 245-284. (1–4), Aua Dicroglossidae). (Anura: 1,1–24. (1), okMcaisadRc niern,52 Engineering, Rock and Mechanics Rock nsbrpclChina. subtropical in ) 16 p.1716.Sre,U:Kw oa Botanical Royal Kew: UK: Surrey, 107–116). (pp. . 02,97–117. 30(2), , 5,7074 doi:10.1007/s11430-007-0041-9 710-724. (5), oeua Ecology Molecular ersim hemsleyanum Tetrastigma iidnrnchinense Liriodendron ora fBoegah,36 Biogeography, of Journal cgah,35 Ecography, , e htlgs,206 Phytologist, New 22 1) 1092–1102. (12), 4,1120–1133. (4), Sunderland, . 3,719–736. (3), . (Vitaceae): Scientific Scientific Evolu- (11), Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. X2Wuzhifeng, Jinggangshan, LXS2 LXS1 4 Wuyi 3 WYS2 Tonglingshan, WYS1 2 Location Population 1 No. ( heterozygosity expected 1 TABLE Chinese Phylogeographic FIGURES in AND fabrics (2017). TABLES magnetic Y. the X. of significance Chen, ( Paleoenvironmental & interglacial doi:10.1016/S0012-821X(04)00103-7 (2004). last S., M. the X. Jackson, since & Hu, loess-paleosols Q., M., Liu, X. of R., Zhu, Deng, distribution the C., in J. 12 dispersal Li, One, northeastward P., Plos general Li, Mountains. a Y., Har suggests Bayan B. pattern the Liao, in Q., glaciation Quaternary Zhu, of sequence The (1998). J. International Li, & computing data. S., high-performance SNP Zhou, A of (2012). analysis B. Weir, component & principal C., glacial and 28 Laurie, S., relatedness Quaternary Gogarten, for and J., toolset Shen, change in D., climate Levine, State between X., Zheng, relationship speculation. Ancestral and The review (Reconstruct (2002). the Plateau: Y. RASP and doi:10.1016/s1040-6182(02)00054-x Qinghai–Tibetan China Shen, the in & on Glaciations Q., cycles Quaternary (2015). Xu, between Comparison B., J. Schema. (2011). Zheng, Improved X. J.. (MIS):An Wang Stage & Isotope He, F., Oxygen Y. Marine & Shi, D., biogeography. C., J. Zhao, historical Blair, for J., tool doi:10.1016/j.ympev.2015.03.008 A. A Harris, Phylogenies): China. Y., in into plants insight seed Yu, New of (2019). pattern X. distribution F. and Yu, 393–398. diversity & (4), Species Q., (2001). Y. China. Li, J. subtropical Y., Ying, western T. within Liu, mixture P., genetic L. and Liu, split J., lineage S. of Liu, pattern D., phylogeographic the Y. Zhong, H., A. Yang, 2) 3632.doi:10.1093/bioinformatics/bts606 3326–3328. (24), ceso nomto n eei iest aaeeso bevdhtrzgst ( heterozygosity observed of parameters diversity genetic and information Accession , 9,e145.doi:10.1371/journal.pone.0184456 e0184456. (9), 45 3–4.doi:10.1016/s1040-6182(97)00011-6 135–142. , He Jiangxi Ganzhou, Jiangxi Ji’an, Fujian ping, Nan- Mts., Zhejiang zhou, Wen- o h 11 the for ) iidnrnchinense Liriodendron < .chuniana C. 3 ka). 130 Mts. Luoxiao Southern Mts. Luoxiao Southern Mts. Wuyi Western Mts. Wuyi Eastern range Mountain at n lntr cec Letters Science Planetary and Earth oeua hlgntc n vlto,87 Evolution, and Phylogenetics Molecular 17 Mgoica)rvae yclrpatDA east-west DNA: chloroplast by revealed (Magnoliaceae) populations. 426.00 26.78 14 9 27.94 27.82 9 8 N caGorpiaSinica Geographica Acta utrayInternational Quaternary er,7 Peerj, iifrais(xod England), (Oxford, Bioinformatics aiueLongitude Latitude ahlspauhoi Machilus 65.doi:10.7717/peerj.6355 e6355. , º º º º 114.15 N 113.90 N 117.77 N 119.85 N hns idvriy,9 Biodiversity., Chinese , 66 , 7,867-884. (7), 221 nSuhChina. South in , º º º º 6-2 0.31/0.19 369-722 0.32/0.30 E 264-509 E 0.34/0.28 460-712 0.32/0.31 E 264-727 E 97 14,55–69. (1-4), Quaternary Ho 93–101. , 46–49. , and ) ag (m) range Elevation He/Ho Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. mn rus636.8 706896.28% 1.38% 38.49802 3458.143 2.34% 0.53215** 37.06608 111 3367.488 53.747 0.89979** 101 36.908 6 Indices Fixation Total 4 populations Within groups within populations Among groups Among variation of Source 2 TABLE Mao’ershan NLW5 Nanshan NLW4 11 Dupoxiang, NLW3 10 Tianpingshan, 9 NLW2 Yindianshan 8 NLW1 Dadongshan 7 NLE2 Mangshan 6 NLE1 Location Population 5 No. nlsso oeua aine(MV)rslsfrglobal for results (AMOVA) Variance Molecular of Analysis Guangxi Guilin, Reserve, Nature National Hunan Shaoyang, Yard, Log Hunan hua, Huai- Guangxi Guilin, Reserve, Nature ingshan Huap- Guangxi Guilin, Reserve, Nature Guangdong Qingyuan, Reserve, Nature Hunan zhou, Chen- Reserve, Nature Fsc d.f. 0.6284** : Mts. Nanling Western Mts. Nanling Western Mts. Nanling Eastern Mts. Nanling Eastern range Mountain Mts. Nanling Western Mts. Nanling Western Mts. Nanling Western 18 Fst variation of Percentage components Variance squares of Sum 0.9862** : 25.89 26.18 7 26.07 14 13 25.61 5 24.91 11 24.92 10 24.98 12 N Fct Fst aiueLongitude Latitude 0.9628 : ttsisof statistics º º º º º º º 110.38 N 110.19 N 109.47 N 109.90 N 110.96 N 112.72 N 112.89 N .chuniana C. º º º º º º º 0-5 0.35/0.25 700-852 0.32/0.30 E 611-703 0.32/0.30 E 612-657 E 0.38/0.33 852 0.33/0.34 E 700 0.32/0.32 E 774 0.32/0.21 E 716 E . ag (m) range Elevation He/Ho Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. ttebto fe h pi ewe h aln t.(L n h atr onan E) h migration The (ES). box mountains grey eastern shown the top and are The (NL) sizes Mts. ( ES. population right. Nanling rates current the the corresponding The between on and split size. shown directions the population after periods bottom effective interglacial the with or at populations glacial ancestral ( our corresponding the divergence represents the in of with investigated Time lines, models (Ma). dashed demographic time shows fit line best braces, bar. vertical the the the by above of indicated latter representation are study. the frame. periods Schematic line while interglacial dotted bar 5 and the the FIGURE glacial within below Various distinguished is bottom. are which [?] the of Mts. (P at former Nanling shown probabilities the the is high in bar with Populations scale (V1–V6) nodes. events Time for Vicariance corresponding shown areas. are in ancestral 95% 0.70), shown and indicate are regions bars FastStructure geographical blue in different light clusters The different estimation. with to time colours assigned Bayesian Individuals the struc- intervals. in population reconstruction. simulations confidence estimates, (MCMC) area time Carlo divergence ancestral Monte for chain and tree Bayesian clustering the tural of Chronogram 4 FIGURE outgroup. the as used factors influential of method. most tree The Phylogenetic study. 3 present FIGURE simulated the The for S1. (c) localities Table collected representing steppe- samples in steppe. dots and black dry 4, listed with 8, data are scrub; thorn range, and specimen or distribution tropical steppe; herbarium potential woodland forest current on 1, 7, temperate The based LGM: desert; (d) semi-arid temperate MH. the 3, at 6, at range desert; woodland; distribution alpine types boreal and vegetation open polar different 5, 2, tundra; contact represent woodland; secondary 1-8 scrub during Numbers and temperature scrub LGM. The at the ranges. map in mountain suitability indicated relevant vegetation are habitat to period the point each represents arrows in ( LIG; red variations (a) where temperature respectively, The boxes. and grey, gray 44.93%. Suitable and than current. red higher and probability) in (MH), (occurrence Holocene indicated Middle are the habitats (LGM), Maximum unsuitable Glacial Last the (LIG), temperature. Interglacial in variation corresponding and (ENM) **: ae ihtinls iaineeet eetdi -IAaesonwt lelns h e tbottom at key for The 1. areas Table indi- lines. suitable in are blue given Potentially east with is the 2 shown information in FIGURE are accession populations S-DIVA Additional circles; in ranges. black detected elevational with events indicates indicated Vicariance right are triangles. Mts. of with Nanling locations cated the sampling in study. the sampled this showing Populations in China, southeastern used of ulations Map 1 FIGURE LEGENDS FIGURE collections; all among differences T SEC P sidctd b oetal utbeaespoetdi oprsnwt ae fGIS-based of layer a with comparison in projected areas suitable Potentially (b) indicated. is ) < oe ae n h aaeescrepn otoei alsS n 3 epciey h left The respectively. S3, and S2 Tables in those to correspond parameters the and names Model 0.001; otta ecnae ( percentages Bootstrap K ,3ad7 ih7a h pia au.I h -IAaayi,clu eed indicate legends colour analysis, S-DIVA the In value. optimal the as 7 with 7, and 3 2, = Fct ieec mn groups; among difference , h onanrne novdi h td r hw noag shadows. orange in shown are study the in involved ranges mountain The d.f. > M 0 nteM reaeidctdaoetebranches. the above indicated are tree ML the in 50) .chuniana C. ere ffreedom. of degrees , ES nidvda irnsprgnrto r hw ewe Land NL between shown are generation per migrants individual in ) .chuniana C. Fsc T ouain ae nmxmmlklho (ML) maximum-likelihood on based populations 19 DIV ieecsaogcletoswti groups; within collections among differences , n eodr otc ( contact secondary and ) ordffrn eid eeapid .. h Last the i.e., applied, were periods different Four rnhlntswr rnfre i Markov via transformed were lengths Branch rdce yeooia ih modeling niche ecological by predicted T SEC .chuniana C. ecschingii Cercis r niae as indicated are ) pop- Fst was , Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. 20 Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. 21 Posted on Authorea 22 Jun 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159285541.11256769 — This a preprint and has not been peer reviewed. Data may be preliminary. 22