Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. ociOsozawa Soichi Recent the at and rates mid-Cretaceous substitution base accelerated timetree, Spermatophyta h oooyo h eutn ierewscnrle yteclbainpitaddt e n h selection the and set date and point calibration the by controlled are was data timetree sequence resulting the including the of species If topology and Angiospermae The representative included. paleodicots for are of analyzed order system ourselves Whole APG we trichopoda GenBank, in monocots. Amborella / lineages as DDBJ older well in available with as not eudicots dicots of include we order representative Angiospermae, GenBank. For / Cycadales. 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(BI) have events BEAST inference evolutionary Bayesian of botanical a version prepared of We advanced correlation 2015). the Escapa, be & may (Wilf botany of goal A radiation level order the Introduction reflecting Ma, triggered 120 time. around the Cretaceous found and middle was plants the rate at C4 endemic substitution including Angiospermae of base diversity of of generation Spermatophyta diversification rise of was increasing and Another cause the species. in potential resulted Viola a have and and might base system, that Asarum rate in APG suggested raised increase the The and exponential to the change. and concordant time, discovered climatic was genera we geologic ITS, Quaternary topology 20 analyses, recent resultant ribosomal BEAST for in The the Jurassic nuclear Through rate the genera. the phylogeny. 6 to substitution the for applying up dated Ma ages precisely X 1.55 and fossil of successfully applying we age v1. by event done BEAST geological were Quaternary employing calibrations a multipoint by and Robust timetree rbcL. Spermatophyta and matK of chloroplastic whole a constructed We Abstract 2020 11, September 3 2 1 aionaSaeUiest,Fresno University, State Systematics California Plant for Society Japanese Institute Bio-Geology Molecular KawaOso 21) r o eddfrti iutnoscmie eeaayi nBATv.X eselected We X. v1. BEAST in analysis gene combined simultaneous this for needed not are (2015), . tal et 1 ui Nackejima Cunio , n ilnwyula oal 1seies(al 1). (Table specimens 91 totally upload newly will and , ,21;Beulieu 2010; ., moel trichopoda Amborella ikobiloba Ginkgo tal et 2 n onWakabayashi john and , ,21) h rtclo airto ssml oipttetime the input to simply is calibration of protocol The 2015). ., tal et Gngia) n ersnaieseiso iae (conifers) Pinales of species representative and (Ginkgoidae), osdrda h letseisi nisemei every in Angiospermae in species oldest the as considered , ,21) eas rdbetmte fSpermatophyta of timetree credible a because 2018), ., 1 tal et 3 21)adAGI 21) and (2016), IV APG and (2011) . et Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. usiuinrt Fg ne) hr r opeiu oaia tde fti yei hsiln region 1) island (Table and sampling this Taxon dispersal in Nakamura simple type and a this Methods (2017) assume Setoguchi and of cannot base main & Materials studies the Takahashi model a to by evolutionary botanical relative straightforward supposed as previous radiation as a Spermatophyta no and process because endemism whole are colonization possibly their There of of Asia, inset). details timetree East the 3 of robust assess (Fig. to built rate attempts newly also substitution and the 3), under (Fig. of islands, subject Taiwan especially and analyses phylogenetic Ryukyu, included includes additionally paper We islands. This Ryukyu islands. the Taiwan of and part Ryukyu, a Japan, islands, Amami study our the and in of , eudicots), progress case Proteales, in relatively of the is in species radiation in tree Spermatophyta include this of analyses species-richness evaluates all with (our for correlate also Proteaceae rates rate the substitution substitution in higher that diversification base showed and (2013) the Bromham evaluate (Osozawa & can Duchene time time. we that recent this at using by exist and fragmentation not calibration, range did distribution bridge have of land to to MRCA suitable due the expected a was 1.55 is diversification China, at radiation from the began this suggested dispersal that and (2017) islands 2006), Setoguchi Sugawara, these & 2; of Takahashi and isolation 1 by triggered (Figs. been islands considered Taiwan and they Ryukyu, although requires Japan, age. rates, rates Quaternary mutation lower of accelerated prior those of Genus the as issue such the to ages revisit compared To younger (Quaternary) overestimation. with later systematic Ma calibration a acquired 2 rates probably to accelerated was the 1 richness after species rate extant mutation Ho roots, evolutionary Quaternary). deep (= have substitution diversity base the functional clock increase relaxed may and radiation the adaptive by the previous suspected (Magallon and any rate time, as in Cretaceous time posterior in used the diversified probability, fully was through not Angiosperm posterior rates was inconsistent show function the (Drummond to This paper BEAST function node. this of each a in model at found has Cohen others we is and and and scale rate, tree, paper, time substitution BI the base consequent of mean is generation age, the the available the version by draws recent to standardized v1.4.2 most related been FigTree the paper asso- has writing explanatory the of this scale the of of dates time and version as radio-isotopic This recent v2020/03, http://www.stratigraphy.org; most v on at on 2015). available the based is Escapa, age/stage and generally (www.stratigraphy.org) scale & an (ICS) time are radio-isotopic (Wilf to Stratigraphy ranges on localities on assigned age based Commission global biostratigraphy employedInternational absolute key are on which and in Some based for (2010), strata are data. scale, ciated bellow. al. output others time the Methods et whereas geologic as in Smith strata, the well by shown as fossil-bearing as as Q the such to BEAST dates dating A reviews run calibration of calibration repeatedly reliable ages fossil and input chronologically calibration including other the the literatures shows the to reset surveyed 3 from contrast We we different Figure in topology ages, one, one. “active” unreasonable output reasonable has an and get timetree is to topology input must the calibration until established mismatched the If v.1.X 3 the and and BEAST following Figure calibration. system the BEAUti monocots, “passive” APG in that and in a shown means eudicots checked employs (output) This than that as software older age monophyletic system. be APG posterior be must the must and paleodicots of monocots (input) the and of age age eudicots, prior crown Paleodicots, and BEAUti, coincident. in be species ingroup of Lilium Asarum and , Heterotropa Pinus tal et section , ,21) hyas rdcsta hl usata mut fagopr morphological angiosperm of amounts substantial while that predicts also They 2015). ., o h utrayclbain eas h nei pce r nw lofo the from also known are species endemic the because calibration, Quaternary the for tal et Heterotropa nei pce nteeilnswsipta 1.55 as input was islands these in species endemic 20) eeoeso ES .. (Drummond v.1.3 BEAST of developers (2005), . tal et Heterotropa ,2012). ., ssial o utraycalibration. Quaternary a for suitable is Matsuda . 2 Heterotropa tal et ± 21)as one u htthe that out pointed also (2017) . .5M (Osozawa Ma 0.15 idgnescletdfo h Japan, the from collected gingers wild ± Heterotropa .5M o elgclevent geological a for Ma 0.15 tal et tal et tal et tal et ,20) oe higher noted 2006), ., ,21) h ieof time The 2012). ., (2010). . sdvrie nthe in diversified is ,21) Whereas 2012). ., tal et (2013). . Asarum Viola Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. rmr sdfrapicto fclrpatcrc eercF(-AGTACACAAAGGACT GAG ACA CAA CCA TCA ATG (5- rbcLF were rbcL chloroplastic of amplification TGT for TTG primer, CBOL used upstream the Primers CTT was following matKR GTA TTC-3), and TGG ACA primer, TCT downstream CGT AAA was matKF TGG (5- ATC actually. that matKF TCC Notice BOL CAG (2009). were ACC Group Plant Working (5- matK China Plant matKR chloroplastic the and CGT following of G-3), AGT -3), CGA amplification TTA AGA GC TAT for AGG TGA used GGA TAT GCT (5- Primers TCC ITS5F TCC were (5- ITS 1.5 ITS4R (2011). ribosomal in and Group nuclear -3) solution the EDTA G of AAG and AAC Tris amplification 1% for with used cleaned Primers were specimens found leaf and young tube. trial, mL first crushed the operation, by as this GenElute analyzed X the Before We v1. using analyses. done BEAST was their in extraction in set) DNA data improved. data much ITS concatenated was the the resolution include by the not the (not that did genes addition, 2016) these In 2009, combining (2009). 2003, the (1998, Group APG Working ( marker the Plant suitable although amplify CBOL additional to an the be primers by to Yamaji suitable markers known is of as gene lack use ITS nuclear the for was recommended plants were to genes method (Kanno phylogenetic variation molecular recognizable alignment shown applying sequence are problem and A photos amplification, calyx reaction chain representative polymerase Some GenBank. extraction, 1. / DNA Table DDBJ in the on in information shown available additional are become endemic and stem recently Many numbers, and 2. accession leaf, These Fig. GenBank. calyx, in Voucher / platform. of DDBJ the character under the the space in the registered filling are gel silica collectors with of desiccator diversification a in extraordinary Asarum stored the were explain samples proposed leaf to speciation, Collected applied allopatric simply Therefore, be distributed 2013). cannot sympatrically (Maeda, mostly (2017), Heterotropa Oshima are Setoguchi these Amami & and Takahashi including 1), by Table island 1; an (Fig. such species within endemic plural yield island, Oshima endemic of ability dispersal of The pollinators the structure, Sinn flower 1978; 1). of of (Table paper basis 2019 published the in recently On a released for were except our they 1) submitted and we (Fig. 2015, that islands in Taiwan Note and (2017). Ryukyu, Setoguchi Japan, & Takahashi the Yamaji of entirety by the species over into subdivided these and of studied relationship was phylogenetic The species). two al section islands; Taiwan on and focused Ryukyu sections, the from previous known 1998; not Kelly, duous; in species 16 (Tablestolon; University Tohoku genus Sciences, The Pharmaceutical of Experimental School from Graduate collected Endemic were Studies, 1). GenBank Plant / Medical DDBJ for in unavailable Station specimens Angiospermae Some Tokyo. of trichopoda Amborella 21a) h hlgn fsection of phylogeny The (2015ab). . tal et Heterotropa pcmn eeas rprd pcmnnmes( slt) oaiis( onr) pce,and species, country), (= localities isolate), (= numbers Specimen prepared. also were specimens Asarum tal et nteJpnRuy-awnislands. Japan-Ryukyu-Taiwan the in Viola ,20;CiaPatBLGop 01 Sinn 2011; Group, BOL Plant China 2007; ., ,21b,adsesmyb are/rnpre yat Mea 03 ine l,2015b). al., et Sinn 2013; (Maeda, ants by carried/transported be may seeds and 2015b), ., n teswr olce Tbe1,claoae the collaborated 1), (Table collected were others and ossso he etosof sections three of consists pce Tkhsi&Stgci 07.Nt,hwvr htsm sad,sc sAmami as such islands, some that however, Note, 2017). Setoguchi, & (Takahashi species e aeoi rgn a ffrdb h osiaaBtnclGre,teUniversity the Garden, Botanical Koishikawa the by offered was origin, Caledonia New , Heterotropa Asarum Euasarum, tal et pce r lokonfo hn,adteCieesqec aahave data sequence Chinese the and China, from known also are species ,20;Fazekas 2004; ., a esal(uaaa 06,adti a eafco ngenerating in factor a be may this and 2006), (Sugawara, small be may a tde yKly(98,Sugawara (1998), Kelly by studied was Asiasarum Asarum TM Heterotropa amla eoi N iirpKtb Sigma-Aldrich. by Kit Miniprep DNA Genomic Mammalian Heterotropa tal et eae ySinn by renamed ; tal et itiue nEs sa nldn h aa islands, Japan the including Asia, East in distributed , 3 20) Section (2007). . ,20) oee,teclrpatcmt n rbcL and matK chloroplastic the However, 2008). ., eegen ansection), main (evergreen, Heterotropa tal et r rbbytn isadmliee (Hiura, millipedes and flies tiny probably are Asarum ,21a;Tkhsi&Stgci 2017), Setoguchi, & Takahashi 2015ab; ., tal et el,19;Sugawara 1996; Kelly, : eunedt oDB GenBank / DDBJ to data sequence Asarum Heterotropa ,21b,and 2015b), ., tal et apigbelow. sampling Euasarum a o enanalyzed been not has 20) n Sinn and (2005), . Asiasarum tal et (deciduous, ,2005; ., (deci- et Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. ieg fploiosi h P ytm n h tmaewsapidas s130.7 as also applied was age (Sun stem Ranunculaceae the whole E: and the point system, than 130.7 Calibration APG rather was (monophyletic), the date paleodicots in of the paleodicots age fossil and of crown No tuff, the lineage D2: silicic for point intercalated date this Calibration to applied Angiospermae. applied We 2006). method al. Ar-Ar et the (He by dated lower was 2011) The Angiospermae. as such of species genus cycad extinct D1: that point Note Calibration geochronology. (31.8 by NP23 constrained well zone not nannoplankton are Nilssonia Australia calcareous as to such corresponds cycads and 2016), Kovar-Eder, ± 2014; fossil (Kvacek, also but strata Modern rocks. Antarctica C: these Formation, point for Meseta Calibration age La 3) Eocene Fig. the 1992; from Clarke, reported & were woods fossil (Pujana 3). Conifer (Fig. B: age point stem (Jiang Calibration and China input northern prior 160.7 the province, of as ages Liaoning latter Ar-Ar the reported from 2014) reported (2009, was wood fossil at: A: manual” point operating Calibration “BEAST the see software, this of must http://kawaosombgi.livedoor.blog/ operation Library the BEAGLE of the software, explanation Sampling graphic BEAST Analysis For the Evolutionary operating (Bayesian Before 2018 order. downloaded. June ascending be 10th in on FigTree, and released tator, X v1. Suchard Trees; BEAST software 3; the (Fig. using tree (BI) inference Bayesian A in reflected are CALIBRATION data EVENT BEAST by GEOLOGICAL such checkedBY checked + and was FOSSIL also WITH GenBank, GenBank. sequences ASSOCIATED were ANALYSES / / rbcL PHYLOGENETIC DDBJ sequences DDBJ and the by These matK in offered the data Tool) Tool. for registered Search Resource for translation our Alignment Bioinformatics readable Codon Local were tool, (Basic resting. bp) Translate BLAST the (544 ExPASy- to gene the similar rbcL using were chloroplastic was pair the gap base and No of bp), 2016). (833 al., gene et matK (Kumar X for MEGA in even for incorporated sequences aligned ClustalW was in using Sequencing observed done Promega. was System, was alignment Clean-Up extension Sequence PCR final and Gel and Japan. SV times, Macrogen Wizard 35 by using cycled done purified was seconds, product 60 matK; PCR for for (56@C The 72@C ITS minutes. for at was 53@C 5 extension incubation at for of seconds, annealing 72@C 60 temperature seconds, at 30 the for for and rbcL) 94@C Promega, at for Working denaturation Mix, 54@C with Plant Master seconds, CBOL Green 60 G2 the for GoTaq 94@C following by CG-3), done CCR was CCA Amplification AGT TCA AAA GTA (2009). (5- Group rbcLR and GC-3), AAA . a n lntncfrmnfr oeP8(32.9 P18 zone foraminifera planktonic and Ma) 2.2 tal et Aristolochia antb dpe o airto dates. calibration for adopted be cannot ,21) n aiemcolntncfsisidct raoin(35.95 Priabonian a indicate fossils microplanktonic marine and 2014), ., tal et tal et ,21) unn EUi(aeinEouinr nlssUiiy,BAT TreeAnno- BEAST, Utility), Analysis Evolutionary (Bayesian BEAUti running 2018), ., efutsmirus Leefructus okobiloba Gonkgo Archaefructus pce eaiet the to relative species ,21) h oslhrznwti h ideYxa omto (Sun Formation Yixian middle the within horizon fossil The 2011). ., Asarum Archaefructus rmteJhlBoa otes hn,i netntbteris known earliest but extinct an is China, northeast Biota, Jehol the from sotndsrbda iigfsi n netn eu,and genus, extant an and fossil living a as described often is lofo rmteJhlBoai nlddi aa uio aiyof family eudicot basal a in included is Biota Jehol the from from also Heterotropa lhuhgpswr on nISrgo o h etn sequences resting the for region ITS in found were gapes although , ± Ceratozamia Asarum . aad166.7 and Ma 0.4 Amborella oslhrznwti h iinFrain(Sun Formation Yixian the within horizon fossil reetnst h ih nti iga)wsconstructed was diagram) this in right the to extends tree 4 eune.TeISgn 64b) h chloroplastic the bp), (694 gene ITS The sequences. ± a eotdfo h uoenOioeebasinal Oligocene European the from reported was a o enfud u hsseisi h oldest the is species this but found, been not has . a i.3.Fsi oaiiso te modern other of localities Fossil 3). Fig. Ma; 0.9 ± . a epciey n eaotdthe adopted we and respectively, Ma, 1.0 tal et Asarum 06.Cage al. et Chang 2016). , ± ± . Ma. 1.4 .5M;Cocozza Ma; 2.05 n h number the and tal et ± Gonkgo ,2011) ., . Ma 1.4 tal et ., Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. yCutl ffrdb DJ n h odn a yuigteIpr aao lsbto.Partitions button. plus or box. Partition Data the Import in the appeared files using sequences nexus by gene into rbcL was converted and loading were matK, the files ITS, and fasta the Partitions: DDBJ, by used. defined by the were in offered settings included ClustalW software were by following species the these BEAUti, and In 2012), Watababe, & date. (Osozawa 1). Formation calibration (Table Guga fossil analyses the the from with found concordant also is ( calibration formosana event Liquidambar geologic above of the Fossils and 2012), Watababe, of Similarly, fossil A6: cone and A Q5 point and Calibration islands, Ryukyu the in especially are (A4). species endemic Viola Similarly, okinawensis Q4: to Q2 point Calibration 1.55 at Osozawa radiate in to presented (15.35 began the separation method simultaneously that Ar-Ar 1) considered the (Fig. by We islands dated Q1: was L: point tuff point Calibration silicic Calibration the 2009). Lee, and & 1990), Perkins Lindqvist Parker, Ma; shown; & 0.85 not (Tidwell are Nevada (errors from Ma found 23.2 of 27.23 age of Ar-Ar age an U-Pb of an Fossils with K2: Ethiopia in strata 51.25 from of age Ar-Ar an A I: Lies 51.25 including Aristolochiaceae as of input MRCA is 51.25 of Radivo- age of time and the age (Matenco for age Ar-Ar Accordingly, in 2003). an Eocene Miocene) and Ma; older, 1984), 7.24 an (Grande, - contrast, (11.62 In Tortonian 2012). as estimated jevic, and of 2014) fossil (Meller, Austria A H: point Calibration (Martinez America the including South from Colombia, reported in were seams of leaves fossils Fossil G: eudicots) point (F2, Calibration Ericales (91.85 and (106.75 USA eudicots) Group Formation, (F1, Potomac Raritan Turonian Saxifragales Albian F: he point from were Calibration fossils paleodicots), (106.75 eudicots) E3, (E5, Jordan Piperales; Proteales + of ± and Laurales E Albian eudicots), + and from (Magnoliales (E4, D Magnoliidae Buxuales were of paleodicots), fossils calibration (E2, above Chloranthales paleodicots) 2008). the (E1, to Nymphaeales conflicts statement. it E: this but follow m.y., not 10 do Smith least we and at Portugal system, by western APG dicots of the of (119 sequences and was radiation time continental date the Aptian Cretaceous the in preceded Early was and it the radiation tuff, of monocot silicic that data intercalated revealed Palynological in F: included point sanidine Calibration to applied method Ar-Ar 124.60 the by dated was .5M;Caee l,19;Cae&Hrnen 1996). Herendeen, & Crane 1994; al., et Crane Ma; 6.25 tal et Typha tal et ± unnhmalanceolata Cunninghamia 21)rvee ooo osldt plcbet u oslclbain Fg ) airto point Calibration 3). (Fig. calibrations fossil our to applicable data fossil monocot reviewed (2015) . .5M (Yang Ma 0.25 Piper oslwsrpre lofo h re ie omto Gad,18)wt bv mentioned above with 1984) (Grande, Formation River Green the from also reported was fossil + 21)rvee io osldt plcbet u oslclbain Fg ) Calibration 3). (Fig. calibrations fossil our to applicable data fossil dicot reviewed (2010) . Earina .grypoceras V. , .luchuensis P. Houttuynia tal et ± and ,1998) ., ± .1M Fg 3). (Fig. Ma 0.31 tal et Dendrobium .1M (Smith Ma 0.31 Saxifragales), (A2), , Aristolochia 2007). . a on rmte15 aGg omto,Oiaailn Ooaa& (Osozawa island Okinawa Formation, Guga Ma 1.55 the from found was Aristolochia tal et il amamiana Viola (Pinidae), Piper eerpre rmsrt nNwZaad(Conran Zealand New in strata from reported were (2012). . aslii rsa( crista Caesalpinia iimalexandrae Lilium Pprls aedct)wr eotdfo h asrcta coal Maastrichtian the from reported were paleodicots) (Piperales, ± tal et Aristolochia and , ± .5M;Hermsen Ma; 2.05 ebr aga ( manghas Cerbera Pprls a eotdfo h etr anna Basin, Pannonian western the from reported was (Piperales) tal et .1M a enrpre rmteercs(Smith rocks these from reported been has Ma 0.31 Heterotropa ,20) airto on :A J: point Calibration 2003). ., Asarum + ± 05,s h ieo RAo l pce fPiperales of species all of MRCA of time the so 2015), . 5 .tashiroi V. . a(Pan Ma 0.1 oslwsrpre rmteGenRvrFormation River Green the from reported was fossil ± a 69.05 was ± .5M,floigtegooia vn fisland of event geological the following Ma, 0.15 a (Hochuli Ma) 6 nei pce fteJapan-Ryukyu-Taiwan the of species endemic and aae) and Fabales), tal et A) and (A3), iu luchuensis Pinus Gentianales), tal et ± ,20;Nxn&Cee,2003). Crepet, & Nixon 2003; ., .5M Fg 3). (Fig. Ma 3.05 Aristolochia ,21) airto on 1and K1 point Calibration 2014). ., il yedoensis Viola uru salicina Quercus tal et ciawlihi( wallichii Schima Dioscorea ± ,20) hysae that stated They 2006). ., r nei nRyukyu. in endemic are .5M;Tye tal., et Tayler Ma; 6.25 and Asarum tal et + oslwsfound was fossil Protoyucca .betonicifolia V. Fgls were (Fagales) ,20)with 2009) ., h prior the , Ericales), tal et Viola was ± ., Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. section Sinn and into henryi Aristolochiaceae Saruma differentiation and these level and Ma. and Ma, Genus 76.17 Ma, 48.91 Ma. at 16.77 at at Piperales 58.08 dated differentiated to at Saururaceae sister differentiated of also Magnoliales asister were and Ma. is Ma, 106.84 Piperaceae 66.6 at Piperales, at differentiated In differentiated Magnoliidae sister of a sister is a Laurales is Chloranthales and Ma. the 105.3 to 3). at concordant (Fig. differentiated almost below was ages paleodicots, eudicot node and In the monocot, describe paleodicot, we of and each system, the topology APG Consequently, Internal respectively. system. monophyletic, (including as APG paleodicots represented the were of species (including topology ingroup paleodicots these Angiospermae calibrated and we Ma, As 120.38 Ma. 34.24 and 132.44 since at differentiated estimated and was Ma, rella Angiospermae 69.13 of consists at age Cycadales crown node basal Ma. The basal the 26.8 order the with since in with level Pinaceae genus separation Zamiaceae and into and the Cupressaceae differentiation Cycadaceae and of Ma. began of Cycadales, clades and clades two of Ma, two 37.8 of sister of at consists a level Pinales is family Ma. Pinales for 116.38 Gymnospermae. node at of Ma. estimated 179 species is be other level to the estimated of was sister age a root tree Gymnospermae, The In Angiospermae. of sister a is Gymnospermae 3) (Fig. shown tree age” time (“Node Spermatophyta age vs FigTree) inset). in 3 node (Fig. Results each diagram at FigTree) shown in median” node (“rate each rate at 3. substitution Fig. constant) base in (not In made shown median” confusion. posterior We are “rate avoid highest to and these 3 95% ages”), and Fig. The in (“Node output, shown TreeAnnotator. age be not was into but posterior can FigTree, tree input (“posterior”), in consequent were output probability The be files posterior BEAUti. can FigTree, tree ages by of the made intervals confidence that, file for input for density xml v1.4.2, each FigTree incorporating by by drawn done was BEAST Distribution: Running Prior 10,000,000. as above chain: noted of date Length deviation. point MCMC: Standard calibration and the Mean from the input was and MRCA) Normal, distribution, of (time log-normal tmrca under (Drummond Priors: rate branches Process. three evolutionary Yule of own Speciation: median Prior: its Tree rate have Trees: the to is tree rate phylogenetic node the a clocks and The of relaxed Uncorrelated Off. branch Lognormal. 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HKY the Taxon Heterogenety in and Model: screen: set case), were left Substitution by dates case The Sites: calibration in button. checked 3, plus were Fig. box the in stem using output and by As all, was for checked ingroup were as boxes taxa of Loading Taxa: ,edct,admnct t107 2.,ad19M,tecondtswr siae t124,124.62, 132.44, at estimated were dates crown the Ma, 119 and 124.6, 130.7, at monocots and eudicots, ), Euasarum tal et sasse fada ugopseisrltv othe to relative species outgroup an and of sister a is 21a) Section (2015ab). . moel trichopoda Amborella sasse fsection of sister a is ikobiloba Ginkgo Saruma and sa l ieg,addtdbc o1.3my scalibrated. as m.y. 16.63 to back dated and lineage, old an is Asiasarum Asarum steods ieg.Asrbieae n ypaae sasister a is Nymphaeales and Austrobaileyales lineage. oldest the is Heterotropa eedtda 05 Ma. 10.54 at dated were sasse fsection of sister a is Amborella nsection In . 6 ,edct,admnct a ocratto concordant was monocots and eudicots, ), Asiasarum Aristolochia Asarum Euasarum tal et ,2006). ., , pce ssonb el (1998) Kelly by shown as species .sieboldii A. section + and Saruma sntdifferentiated not is Heterotropa + Asarum .biloba G. Ambo- and , was is Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. ne-pce n nr-pce ieetaini eonzd lhuhwt tln o ln rpgto (no propagation plant Chinese for The section stolons In with specimen. Korean although the recognized, for to is stolon relative differentiation differentiated intra-species is and but inter-species Japan, in sites collection among forbesii aegn,btta fedct xeddt h egn.Gnsseislvldffrnito a fe the after to was differentiation mid-Cretaceous the level the during Genus-species was from Neogene. differentiation was the level Family to diversification Paleogene. extended then late eudicots and the of to differentiation that extended level but eudicots Paleogene, order of that 3, but Fig. Paleogene, in rate shown substitution As base in 1.55 increase exponential by and species Diversification calibrated of additional A6 for and found (monocots) was relation sympatric Sister of sister a and with species yedoensis although distributed Ma, 25.93 Ma. Neogene). at 90.14 to Viola differentiated to (Paleogene and Ma up analyses, 17.25 was to our age for 63.77 in stem date from (Caryophyllales) the Neogene at Amaranthaceae found level were C4 order differentiation Gymnospermae. included differentiation This level We and level family Asterales. Order monocots of and also nodes clades. Apiales 16 and major Totally for paleodicots two Ma the for 31.16 to younger at relative much continued Ma is asterids but 98.83 eudicots of Ma, at clades 98.26 date two to at crown the a Ericales began into with Soltis from classification lineage system, asterids this basal APG and and the the Caryophyllales Proteales, followed Malpighiales, clades; basically Buxuales, to rosids major Celastrales and two from system. have rosids Ma, eudicots APG and 91.62 next orders, the Lamiales, above before the to the differentiated is than common lineages Ranunculales Other Ma, system. older Ma, APG 108.55 are the 120.31 at to Saxifragales of common third and lineage also the Gunnerales, oldest Sabiales Vitales, the C4 and Trochodendrales, and as Ma, Ma, expressed 116.48 34.97 was the at at Poales Ceratophyllales and differentiation Poales. level Ma. eudicots, Ma, of genus 15.58 for Poaceae 83.22 In started from Ma and at differentiation monocots, 50.62 Typhaceae started differentiation at in for and were lineage level Ma differentiations generated youngest order 62.33 level Poales the Family at of absolutely and Liliales. start not Asparagales, and is and Dioscoreales of for Iridaceae node Ma and basal 59.91 Asparagaceae the at is with consists descendent one Poales The youngest Ma). + 63.77 Alismatales + at Iridaceae) and differentiated Liliales Ma, + Araceae of at106.79 of groups sister differentiated clade a was two is Acorales of (Aponogetonaceae Ma. Ma 59.91 94.74 at same at differentiated was the Dioscoreales distinct on of clade genetically sister distinct a of a occurrence into Monocots, differentiation sympatric found. In relationship, were However, sister relationships to 1). sister a common tends Table inter-island have without differentiation to and 2; island The tends island, single (Fig. Ma. clade each a 1.55 leaf of within of species and species event The calyx geological clades. distinct the of constitutes be characteristics therein to and islands, considered within was occur time divergence the section and of species section Endemic in included also were species data. Chinese matK 14 additional an but Heterotropa Mlihae;rdd)hsconnd f1.9M.Endemic Ma. 15.49 of node crown has rodids) (Malpighiales; h Japan-Ryukyuan-Taiwan the + sdffrnitdi ahiln fRuy,Tna,adHongKong. and Tanwan, Ryukyu, of island each in differentiated is Heterotropa .grypoceras V. orCieeseiswt bLdt nteDB eBn r nlddi u analyses, our in included are GenBank / DDBJ the in data rbcL with species Chinese Four . Heterotropa rlimsmalli Trillium Pinus ). . excluding il amamiana Viola Heterotropa (conifers). Llae)wsrpeetda h letlnae although lineage, oldest the as represented was (Liliales)

isoels+Aprgls(rhdca) n saaae (Asparagaeae Asparagales and (Orchidaceae), Asparagales + Dioscoreales .forbesii A. .yedoensis V. Heterotropa eesvrl ieetae nteJpnRuy-awnislands Japan-Ryukyu-Taiwan the on differentiated severely were mm sia sasse of sister a is Oshima, Amami , =section (= . and , tal. et 7 .forbesii A. Longistylis 21) n Magallon and (2011), Longistylis il okinawensis Viola ± sasse fteJapan-Ryukyu-Taiwan the of sister a is Sinn ; .5M o oe fA of A5 of nodes for Ma 0.15 .tashiroi V. tal et il betonicifolia Viola ld ae nsll T and ITS solely on based clade tal et ,21b sasse of sister a is 2015b) ., 21) atllsis Santalales (2015). . Iriomote-jima. , sasse fwidely of sister a is Lilium Llae is ) (Liliales Euasarum sasimilar a is Lilium Viola A. , Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. xeddt h one g hnteohrsc sploios n h iesfiainadeouinwas evolution and diversification the and was paleodicots, eudicots as of such differentiation other level eudicots. Soltis the order for that system, than event Note APG younger age clade. the the younger asterids to the the third, common to of the are Asterales extended Sabiales rosids and next, and Apiales the between asterids Ma is of Ranunculales clades two lineage, descendent oldest al. the the and is others, Ceratophyllales basically and eudicots, is to Poales (2000). restricted + Bremer of If (Asparagaeae) phylogeny clades two level Asparagales descendent Our order and the 2000). the Liliales, gene and (Bremer, to Alismatales, and + gene common and dates Dioscoreales rbcL Acorales and + the of 1993), (Orchidaceae) selecting lineages (Swofford, variance, older Asparagales PAUP* of the by we including analysis made by topology but was calculated monocot reported tree been was have phylogenetic fossil rates the any substitution monocots, paleodi- although to in papers, lineage restricted other oldest If many that. the satisfy and represented to it system BEAUti and APG in Ma, the set 126.23 to at concordant Amborellales also of et cots, age (Elder crown beta estimated 2.0 also We raxmlGUI using is (2018) version Brown recent & most 2007). Smith the (Stamatakis Rambaut, by that RAxML was note Smith using phylogeny but 2019). conducted plant 2014), al., seed also (Stamatakis, inclusive was 8.2.11 broadly analysis v. The this phylogenyRAxML limitations. Angiosperm but same Other (2010), Soltis Qiu the 2006). al. by by Stamatakis, with et 7.1; genes genes Smith (vers. 15 mitochondrial by RAxML other in rbcL four and calibrate selecting age matK, presented to (Sokolof and possible was phylogeny it rbcL on not Angiosperm affects chloroplastic is The much it 2002). both and but (Swofford, botany selecting PAUP* systematic by software of concatenated older presented base the a the to was now connected of by is use hampered IV the rbcL be APG chloroplastic and to and of the appears analyses 1998) selected work APG for recent (APG, 2016). most set IV, (APG) the data Ma APG even Group and but 116.01 2009; genes, Phylogeny was III, other two Angiosperm APG age and 2003; the node II, level (APG by times order presented several updated The was fossil. phylogeny living Angiosperm a The actually is Cycadales. species and this Pinales that between suggesting 3), (Fig. Ma of ours. age to calibration crown no comparable The has is PAUP* phylogeny Although level 1998). and (Swofford, high PAUP* (Gymnospermae this using and Spermatophyta function, Rydin genes whole nuclear by two and and presented relation, chloroplastic, was sister phylogeny a have Angiospermae) Angiospermae and radiation Gymnospermae Angiospermae (mid-Cretaceous). mid-cretaceous Ma reflecting curve 130 phylogeny, (red around level time rate Order for the peak through another rate shows maximum curve with Discussion This plots 3). connecting Fig. smoothly in by inset “trendline” on a drew also for We calibration Ma equation 1.55 the the and and 3), 3. Neogene), Fig. (Miocene; in Ma the inset All 10 differentiation the since the on increased A6, shown exponentially is to trendline A1 has of of rate Ma substitution 1.55 Quaternary. base calibrated the The of species event the an for was and diversification Neogene, and mostly and Paleogene late 21) n Magallon and (2011), Heterotropa tal. et ikobiloba Ginkgo ae eels hn00 ssoni oe ae nlf adfiueof figure hand left on rates lower in shown as 0.01 than less were rates 21)as aetmte mlyn le eso fBATv.. Dumn & (Drummond v1.4.7 BEAST of version older employing timetree made also (2010) tal et 21) h onetdt fodrlvlbacigfredct a t31.16 at was eudicots for branching level order of date youngest The (2015). . a siae t166 a eetn h airto aeo :166.7 N: of date calibration the reflecting Ma, 166.63 at estimated was Heterotropa i o ffc h nraigrt nQaenr time. Quaternary in rata increasing the affect not did 8 tal et tal et 20) yslcigclrpatcrc,other rbcL, chloroplastic selecting by (2002), . 21)adslcigte ee including genes tree selecting and (2010) . tal et ,21) iia phylogeny Similar 2018). ., Heterotropa tal et tal et (2011), . ,2008) ., (Fig. ± 22 et Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. dpierdaino aa-Ruy-Taiwan Ryukyu- and Japan- Ma, of and 17.25 level radiation Nelumbonaceae, genus-species to Adaptive by for 61.66 succeeded Results. from Ma was in at 34.03 It noted found monocots. at as were and event since level differentiation paleodicots eudicots genus than level for dates oldest family younger differentiation recent. of The much until Poaceae. nodes events to 50.62 speciation succeeded 15 and at many it totally Typhaceae by Aponogetonaceae, eudicots, succeeded for and was for Ma Ma Araceae As 51.2 62.33 for at at Typhaceae Ma for and 63.77 speciation Iridaceae, at or and differentiation was Asparagaceae differentiation for level out family Ma found monocots, also + for was Piperaceae for As It Ma for 51.26 Saururaceae. Ma after and was 51.26 differentiation Piperaceae at level was for Genus and Aristolochia Pinaceae (Nymphaeales). Ma Piperales, Cabombaceae and 16.77 and in Ma, at Nymphaeaceae found between and 26.32 were Aristolochiaceae, after differentiations and level was Saururaceae family Cupressaceae paleodicots, Pinales, for of and As Ma, case 39.56 a after was In Ma. Cycadaceae Ma. 21.79 of differentiation 34.35 after level after genus was estimated We Zamiaceae Neogene. 37.99 the at in differentiation. event age young Cycadales node for level Ma family 69.36 the Nagalingum at estimated We and ours. differentiation to Pinales comparable for was Ran Ma (Nagalingum clades to calibrations Zamiaceae (Drummond Cycadales, and common v.1.3 fossil for Cycadaceae As BEAST Pinidae, by 2007). by and (Yang, and drawn MCMCTree Cupressaceae genes successfully and of was 2014) (Stamatakis, timetree clades v.8.2.4 the two RAxML of employed who consists radiation (2018), Pinales angiospermae recent Gymnospermae, relatively notable. In the be reflecting phylogeny, should level event to species differentiation concordant to contemporaneous contemporaneous, Family the almost such and eudicots, paleodicots; Ma, and Ma, 120.31 monocots, 132.44 eudicots: at paleodicots, estimated and was Magallon Ma, Angiospermae by 116.68 of and timetree age at crown 3 monocots above, (Fig. noted Ma, eudicots as 131.53 Fig.3 basal to of the began timetree our as diversity In expressed extant thus Ceratophyllales tricolpate. angiosperm is clade, that of system) Note single contemporaneous components APG Cretaceous.” a nearly the major middle being to the distincti- the as membership therefore, in morphologically estimated indicate diversify monocots; which were are unequivocally eudicots and 1989), grains The and paleodicots Doyle, pollen calibration. fossils, with Tricolpate & good as Donoghue clade. exceptionally tri- preserved this 1984; an by Walker, become providing of characterized & easily lineage younger Walker morphologically can stem the condition; are ve, the to this “Eudicots on estimated statements: from evolved studies derived the probably previous (or to the from According pollen difference eudicots. colpate noteworthy of a ours. date was to crown which comparable calibrations monocots, their and to (Drum- cots due v1.7.5 Ma BEAST 120 of and Magallon version 140 older between differentiated generation contemporaneously two was but recent We these more below. reflecting by mond probably drawn differentiation inset), was level 3 timetree genus-species (Fig. Angiosperm estima- and tendency we some family phylogeny with as radiations. but dated Therefore, well valuable and a robust. were differentiations as building rates were differentiation, abo- paleodicots, substitution through calibrations level base of papers but our order found topology topology, however, referenced of concordant Angiospermae that, and dates generate the Note system to ted not system. APG satisfy was APG to the contribution the calibrations our to to BEAUti eudicots concordant set and whole we monoicots, word, a other as The was ve. topology Angiospermae Our tal et tal et ,20)slcigrc,mt,adohrtregns(Magallon genes three other and matK, rbcL, selecting 2006) ., and tal et 21)fudta rw uiosaeapoiaeycneprnoswt rw paleodi- crown with contemporaneous approximately are eudicots crown that found (2015) . Asarum 21)pitdotta yaae salvn osl u ahseito sarelatively a is speciation each but fossil, living a is Cycadales that out pointed (2011) . tal et n h etns n ucee ni eet See recent. until succeeded and restings, the and 21)btas h P ytm ahrta h re ftebaciginto branching the of order the than Rather system. APG the also but (2015) . Heterotropa tal et 9 ,21) n hi ya ierecnitn fthe of consisting timetree Cycad their and 2011), ., tal et Viola ,20)slcigrc n matK and rbcL selecting 2006) ., Asarum tal et pcainwssc radiation such was speciation ,21) n vr family every and 2015), ., aito,nx section. next radiation, tal et . Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. lc oe.W a o ics h aibert,truhbidn rdbeSemtpyatmte by X. timetree v1. Spermatophyta BEAST credible of a functions building partition through and rate, calibrations variable point the multiple (Drummond discuss applying rate now evolutionary fully can same We the to model. and according clock glacier evolves branch of every al start that rate et assumes to substitution model related base clock in be strict increases may A mid-Cretaceous date and Ma. This recent 2.58 the 1). since for time Triggers (Fig. Quaternary Ma the 1.91 of at change climatic differentiate of inter-glacier to ancestor started common single and a habitat, Ma, the 3.72 and At river Yangze Ma). 2.63 the since radiated also were of accumulation. Chinese species size snow other increased heavy the the to the originally that relation to premise (1978) adaptation the Hiura indicated included forbesii 1). this period Asarum (Fig. and growth Honshu month climate, snowy several northern a the in to during radiated adaptation calyx and of environment idea the snowy proposed heavy a to adapted to Similar and species, distinct (Matsuda if progress as celsum in leaf A. be and silversword calyx may Hawaiian of radiation the morphotypes adaptive for observed have Oshima, that might ancestral Amami to On 3) single Blonder similar and a 1998; left), 1 Sanderson, 2 from (Fig. and Figs. radiation continent (Baldwin right; adaptive Asia alliance original 1 of of Fig. mechanism margin expansion; the wet,eastern morphological consequent from the and resulted and of genetic rather Osozawa result winter, simultaneous 1; a the (=the the (Fig. as during coast islands islands, the Sea Sea water consequence, Japan Japan Japan sea a the the the the As along into of warmed snowfall flow Honshu heavy current to caused the This began further wind of current, strength 1). seasonal their Kuroshio case northwestern (Fig. maintained the event the and of rifting In passed sea branch the once 2015). the a Wakabayashi, tracks over current, Typhoon remained & warm patterns. rifting (Osozawa Tsushima storm rerouted, the course affected thus after also their this current, but mainland and energy, this along the was, lost and once from and 1), (Osozawa mainland land islands (Fig. Sea the over Ryukyu trough China where the the each East seaways present through around or of current the form sea separation warmed Kuroshio to The and the began input. into reefs of flowed detrital inflow coral en- this so the other of locations, in and these resulted absence sediment climatic reaching detrital to the prevented from tied in also rivers also Asia Yellow island is continental and Ma from Yangtze 1.55 islands the at Ryukyu from Ryukyu of of isolation islands The changes. isolated Osozawa vironmental formed (cf., that colored) event speciation Amami red geological vicariant bottom; The the right the on 3 by 2015). Wakabayashi, as (Fig. solely & clades such Osozawa generated distinct island, 2017abc; been three an into have splitting not within species may sympatric differentiated base these partly of many All constant yields populations but Oshima species. and island Amami allopatric 2013). allopatric always suspected (Maeda, on islands not a Oshima acted are applied have species and to model). endemic expected data, clock is (strict matK) calibration speciation (or for Allopatric /m.y.) ITS (0.0413 solely ITS of by rate analyzed substitution v.1.7.5, BEAST ed solely 1.55 Regarding at here A6 discuss to we radiation. A1 and by radiation, calibrated extensive groups species Six ,20) u h aeadbac eghi lal o rprinl n hsw hudapyrelaxed apply should we thus and proportional, not clearly is length branch and rate the but 2006), ., au crenata Fagus and , .pellucidum A. sasse fteisland the of sister a is Heterotropa Heterotropa Fg ;atog h RAaei siae t2.9Ma), 20.39 at estimated is age MRCA the although 3; (Fig. Heterotropa Heterotropa u ierei oprbet aaah eouh 21) hyemploy- They (2017). Setoguchi & Takahashi to comparable is timetree our , ihdsic opooy(i.3rgtcenter). right 3 (Fig. morphology distinct with nei pcainadsvr iest nteJpn yku Taiwan Ryukyu- Japan- the in diversity severe and speciation endemic ooie h atr rao h sa otnn atyoelpe in overlapped partly continent Asian the of area eastern the colonized Heterotropa, (section Heterotropa tal et Longistylis 10 ± ,21;c. liepat nBoucher in plants Alpine cf., 2015; ., n tdffrnitda .1M;teehv sister a have these Ma; 1.91 at differentiated it and ( Asarum .5M Fg )wr yia xmlsreflecting examples typical were 3) (Fig. Ma 0.15 .fudsinoi A. Heterotropa ieetae t37 a(i.3; (Fig. Ma 3.72 at differentiated ) tal et rsoohaee ieae;paleodicots) Piperales; Aristolochiaceae; ; ,21) h itn vn eutdi a in resulted event rifting The 2012). ., sgntclysmlrt other to similar genetically is tal et pce,adw nlzdsxendemic six analyzed we and species, ,2017). ., tal et .forbesii A. .megacalyx A. Heterotropa Asarum ,21,21a,2016, 2015ab, 2014, ., .fudsinoi A. tal et naie along inhabited naiigthe inhabiting tal et u these but , ih have might Longistylis ,2015). ., a many has .gusk A. ,2012). ., , Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. seilydct,iiitdagoa clgcltasomto oad h rtcosboiest Jnde species, (Jan plant biodiversity angiosperm Cretaceous broad-leaved the Also Acknowledgements towards plant. transformation food ecological the of global as a radiation Boer Angiospermae initiated level of dicots, order co-radiation been have especially the of (Hunt beetles to start Insect time in tie Cretaceous 3). a differentiated middle to (Fig. extensively express around Neogene also were may the peak until monocots which Gunter rate eudicots and a inset), for have paleodicots especially 3 to level, the clarified family both then (Fig. and Thereafter, level, trendline order 3). red the (Fig. by the Angiospermae angiosperms shown and Note of as CO2 abundance 2017). ecological atmospheric Ma Salzmann, and (Friis diversity in 3). & mid-Cretaceous phylogenetic Pound drop Fig. in the c.f., increase rapid around (Eocene; dramatic Ma; Ma and a 39.56 (33.9 37.99 indicates large to transition at record diversification Fossil a estimated Oligocene level with also to genus is coincides Eocene this radiation the date of conifer at a initiation that also Such the cooling for inset). of 3). estimate 3 onset the Fig. (Fig. revises Quaternary (Oligocene; result the Our 1997). Ma of al., Miocene. Ma Miocene et the 2.58 late (Cerling in at the not period in Ma, glacial–interglacial 10 beginning present Nagalingum at America the grasses started (Uno South C4 concerning rate of Africa day, and increasing expansion savannah present eastern America that The C4 the Note in North 2008). Pakistan, to al., including Ma Group, et persisting also 9.9 Siwalik (Badgley Ma and sub-Himalayan phenomena at 6.0 the global and started mammalian from 8.5 a plants between from tooth was woodland C4 ratios fossil and isotope into forest mammalian C3 Carbon change started the replaced and Ma). these diet Also appeared 25.93 that because plants 2011). from Poales show (Taira, layers, eudicots ., C4 enamel C4 concentration coal and 3; 2004), tooth thick CO2 (Saga, (Fig. fossil form fixation atmospheric Ma CO2 may to 15.58 such decreased glaciations for from ferns consequently efficient Permian diversification tree are the that plants terrestrial and glaciations C4 fixation of Quaternary Poales, 2007). carbon development prevailing The grasses the increased glaciation. land by on processes of onset triggered expansion the been by triggering have triggered in biologic from role been feedback a have be 2005), to in played Muller, of may appear & also factor trigger history (Rohde have Permian Earth change a end possible in may environment the be episodes development severe A as glacial may such such the configuration Whereas this landmass and event. by important. above, cycle influenced actual more noted interglacial probably an was and As islands glacial is of isolation time. of rate start Quaternary substitution the the base been clock. in have strict increasing substitution may if recently base are rate as of equations the increasing rate changing the constant that drastic and a justified reflecting assuming trendlines not We by their by but the although incorrect time, discuss actually Therefore, to the are needed through gene. users timetrees rates the concatenated their is such ours, or and rate to BEAST, gene increasing of similar each of versions reason every old the in for and dates possible rate date, not younger ( were Quaternary as calibration that analyses well the relaxed Note gene Quaternary by as although combined the rate. calibrated Jurassic model, to solely rapid as clock not a such only strict Ma, dates produced unrelated as 1.55 older calibration (like of including date node Quaternary dates Quaternary each of multi a at by that constant calibrated found be instantaneously They to we (Ho assumed applied). is was primates run model as every clock such at (Ho rate taxa v.1.3 a for BEAST and shown but showed points, been We (Papadopoulo calibration shown had multiple v.1.4 2008). as phenomenon applying Recent (Ho, simultaneously This the calibrated run toward to be (Papadopoulo inset). exponentially insects to 3 and increased needs 2011) has clock (Fig. 2005, Spermatophyta absolute trendline of the even the rate time but by over substitution clock, rate base constant molecular relatively the relaxed a that at of evolve case sequences DNA a that in states hypothesis clock molecular The tal et tal et ,2012). ., tal et ,21;Toussaint 2016; ., 21)soe htccd newn ersnhoosgoa iesfiainbeginning diversification global synchronous near a underwent cycads that showed (2011) . tal et ,21)nee ornrpael yapyn aea vr airto point, calibration every at date a applying by repeatedly run to needed 2010) ., tal et tal et tal et ,21;Zhang 2016; ., ,20) n hseetmyb idt nte aepa rud130 around peak rate another to tied be may event this and 2006), ., ,21) u eeae iteatnin ES 1 spossible is X v1. BEAST attention. little generated but 2010), ., Asarum 11 tal et ae eeetmtdls hn00) lont that note Also 0.01). than less estimated were rates ,21) n h nraigrt a explained was rate increasing the and 2018), ., Heterotropa tal et ,20;McKenna 2007; ., aito,atog physical although radiation, tal et ,20)adBEAST and 2005) ., tal et ,2015; ., tal et tal et ., Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. hn C hn ,HmigS,MsoG,Fn .(04 0r3A g osrit nteHaifanggou the on constraints bloom? age flowers 40Ar/39Ar 277-284. first (2014) the , Y. did Fang When GT, formations: Mesko Lanqi SR, and Hemming H, Zhang SC, Chang Lanqi plants. basal angiosperm the of on constraints origin 1–10. age the 40Ar/39Ar , for High-precision implications (2009) Global its Y. (1997) Fang and PR, JR. Formation Renne Ehleringer HC, V, Zhang S, Eisenmann Chang J, boundary. Quade Miocene/Pliocene MG, the Leakey through BJ, change MacFadden vegetation JM, Harris plants. TE, land Cerling for barcode DNA A Sciences (2009) of Group. Working Plant CBOL plants. flowering USA monocot Sciences, of lineages of common Cretaceous is Early divergence (2000) niche K. Bremer little with speciation Allopatric Primulaceae. (2015) Alpine E. among Conti functional NE, leaf Zimmermann in FC, (Asteraceae). macroevolution Boucher and alliance Variation silversword (2015) Hawaiian RH. the Robichaux in BJ, traits Enquist BG, Angiosperms. Baldwin for alliance B, and Estimate Evolution Blonder silversword Molecular Age of Triassic Hawaiian Rates the the MJ4.Heterogeneous Explain Donoghue of Could (2015) P. Diversification diversification Crane BC, of O’Meara JM, rate Beaulieu and Age (1998) PNAS MJ. (Compositae). Sanderson BG, Baldwin Ecological forcing. (2008) USA climatic D. prolonged Sciences, Pilbeam of of TE?, impact Academy Cerling show record AK, of Behrensmeyer mammalian families SV, Miocene Nelson in and ME, changes orders Morgan the JC, Barry for C, classification Badgley Group Phylogeny Angiosperm IV. of the APG families of plants: and update flowering orders An the (2016) for IV. classification APG Group Phylogeny of Angiosperm III. families the APG and of plants. orders update flowering the An for (2009) classification III. Group APG Phylogeny Angiosperm II. the APG of plants: update flowering An (2003) II. plants. flowering APG of families the for classification Garden ordinal An (1998) APG. Ltd., Co., Sugawara Engineering fund. Kohei this CTI Survey), References to Corporation), contributing Geological Techno sup- for for Material Fang Inc. Office Hua-Te (Mitsubishi NEWJEC, (Nunohara and Momose and Datun-shan Nunohara Ho, Atsushi Keiji Mt. Jen-Zon GSK), thank a (Ecofarm Tsai, We for Chin-Ho Osozawa University. 2016), Kyoji Tohoku Taiwan. December and in 1 collections samples, sample (deceased Kyushu ported Jahn the Bor-ming all for sample. Studies, Watanabe Plant Kinichi Japan northern Medical sample, for for Nagano Tsunoda Iichi Station thank We Experimental for University. Tohoku from samples Sciences, collected Pharmaceutical of were School species Graduate endemic including specimens trichopoda Amborella 85 531–553. , 106 Asarum 12794-12797. , 97 yj szw n koKmn o eta aa ape,KnioOuafrthe for Ogura Kanjiro samples, Japan central for Komano Akio and Osozawa Kyoji , 4707–4711. , 95 a ffrdb h osiaaBtnclGre,teUiest fTko Some Tokyo. of University the Garden, Botanical Koishikawa the by offered was oaia ora fteLnenSociety Linnean the of Journal Botanical 9402-9406. , oaia ora fteLnenSociety Linnean the of Journal Botanical oaia ora fteLnenSociety Linnean the of Journal Botanical ora fBiogeography of Journal 105 12145–12149. :

hspoetwsprl nne hog h szw ud(former), Fund Osozawa the through financed partly was project This 43 12 591-602. , elgclScey odn pca Publications Special London, Society, Geological ora fEcology of Journal Nature at n lntr cec Letters Science Planetary and Earth 141 181 389 161 rceig fteNtoa Academy National the of Proceedings rceig fteNtoa Academy National the of Proceedings 399–436. , 1–20. , 5-158. 153- , 105–121. , naso h isuiBotanical Missouri the of Annals ytmtcBiology Systematic 104 rceig fteNational the of Proceedings 219–228. , 64 869-78. , 378 279 Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. eme J adloM,NxnK,Cee L 20)Dvssyu e.Nv a.Ieca) fossil a Iteaceae), (aff. Nov. USA. gen. Jersey, Divisestylus New (2003) of WL. Cretaceous 40Ar/39Ar late Crepet The the KC, (2006) from Nixon RX. saxifrage MA, Zhu boundary? Gandolfo A, China. EJ, Boven K-Pg northern Hermsen X, Province, the Ding Hebei Fengning, LK, at Yang from co-extinction F, Biota Wang Jehol Geosystems mass ZH, early Zhou the a F, of suffer Jin dating XL, also Wang HY, they He did Scarabaeinae) dinosaurs, (Scarabaeidae: beetles with dung If PLoSONE association (2015) SL. Cameron in L, Bocak arose fauna. A, fish the Slipinksi TA, the Weir of of NL, review Gunter component a with prominent Bulletin Formation River a Wyoming Green of the plants: Survey of Paleontology Normapolles (1984) L. (2006) plant Grande J. discriminate Schonenberger genome diversification. plastid R, rosid the Pedersen Cretaceous from K. barcodes EM, DNA for Friis multilocus toolkit and Multiple interface well. (2008) graphical equally a species al. beta: et 2.0 chloroplast AJ https://doi.org/10.1101/800912 raxmlGUI Fazekas doi: (2019) plants: bioRxiv, D. in RAxML. 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New from Epidendroideae) (Orchidaceae: 36 11 7 199-204. , oeua ilg n Evolution and Biology Molecular ln ytmtcEouin(Supplement) Evolution Systematic Plant 001 o:012/05C003IS:1525-2027 ISSN: doi:10.1029/2005GC001083 Q04001. , e0153570. , eiwo aaooayadPalynolog and Palaeobotany of Review 7 4 4 214. , 355–362. , 8.hts/diog 10.1371/journal.pbio.0040088. https://doi.org/ e88. , PLoSONE 108 19641–19646. , 63 3 3 p. 333 , ln ytmtc n Evolution and Systematics Plant e2802. , Phytotaxa 29 1969-1973. , 13 19 90 8 mrcnJunlo Botany of Journal American 51–72. , 55–70. , 319–337. , mrcnJunlo Botany of Journal American 260 M vltoayBiology Evolutionary BMC 107–140. , rceig fteNational the of Proceedings eceity Geophysics, Geochemistry, 90 96 1373–1388. , Dendrobium 466–474. , h Geological The 13 M Evo- BMC 65. , and Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. xicint iesf uigteCeaeu ersra revolution. terrestrial Cretaceous the during diversify to characteristics extinction floral differentiated DD, Highly McKenna wild islands: insular sympatric continental among on cohesion genotypes. species Aristolochiaceae) undifferentiated Tight versus (2017) spp. H. Setoguchi (Asarum J, gingers Nagasawa Y, de- Maeda Dinarides. Constraints J, and Matsuda Basin: Carpathians Pannonian the between the area of junction evolution the and doi:10.1029/2012TC003206 of formation structure the the On from (2012) rived D. 437– Radivojevic diversity. L, phylogenetic Matenco 207: plant metacal- Phytologist flowering A of New metacalibrated 2015. rise A diversity. Hernandez-Hernandez. early 437–453. 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All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. szw ,St ,WkbysiJ 21a utrayvcrac flotic of lentic vicariance with Quaternary contrasted (2017a) lands J. Wakabayashi F, Sato S, Osozawa aaool ,Aatso ,Vge P 21)Rvstn h netmtcodilmlclrcok The clock: molecular mitochondrial insect the Miocene Revisiting early (2010) calibration. and AP. trench Vogler Oligocene mid-Aegean I, late Anastasiou the A, from Papadopoulo fossils Dioscoreaceae (2014) pia. ED. northwestern Ethio- of Currano flora of BF, River Jacobs Guang AD, Ma) (27.23 Pan Oligocene Late the the from of fossils origin Ethiopia. leaf the Rutaceae and (2010) current AD. Pan Kuroshio by ( Dispersion beetles islands: Carabid oceanic populations. (2016) Izu-Bonin insular J. Wakabayashi isles, Y, O-shima Oba and S, Nii-jima Osozawa S, Ogino K, of Osozawa vicariance islands. 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(Gliding 159 eiotr Science Lepidoptera 46 15 188–194. , 54 1-16. , 175 noooia Research Entomological 1369-1388. , 108 17–28. , 27 8-8.DI 10.1093/biolinnean/esx007 DOI: 280-287. , 116 1659–1672. : Mycalesis Pyrocoelia 412-422. , ora fErhSine&Climatic & Science Earth of Journal 66 Coeliccia Ypthima 8-14. , utris pcae vicari- speciated butterflies, Lmyia;fiey nthe in firefly) (Lampyridae; 46 aau blaptoides Carabus nteRuy-awnis- Ryukyu-Taiwan the in utris(Lepidoptera, butterflies 122-127. , noooia Science Entomological mrcnJunlof Journal American olgclJunlof Journal Zoological Platypleura 121 ora fBio- of Journal 8-9.doi: 185-199. , Palaeontologia Cicindela (Cicadi- from ) Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. uhr A ee ,BeeG ye L rmodA,RmatA 21)Bysa hlgntcand phylogenetic Bayesian (2018) A. Rambaut 1.10. AJ, web-servers. BEAST Drummond RAxML using DL, integration Ayres the data G, for phylodynamic Baele algorithm P, Lemey bootstrap MA, rapid Suchard A (2008) J. Biology Rougemont Systematic P, Hoover A, Stamatakis of thousands CA, with models. Rushworth analyses mixed phylogenetic Z, RG, and likelihood-based taxa Xi Maximum Olmstead RAxML-VI-HPC: RS, D, taxa. (2006) Beaman 640 A. Diouf MJ, Stamatakis genes, C, 17 Sanderson phylogeny: Black CC, Angiosperm S, Davis (2011) Crawley PS. KW, Botany Soltis Walker M, Hilu MJ, NF, YL, Latvis Donoghue Refulio-Rodriguez Qiu WS, CD, SF, Judd KJ, Bell Brockington Sytsma BS, DC, MA, Tank Carlsward Gitzendanner KJ, MJ, Wurdack N, Moore Cellinese JB, whorled SA, flower Smith angiosperm DE, ancestral Soltis the Was (2018) Rudall. of PJ Journal Bateman, throughout? American RM phylogeny. Remizowa, plant MV DD, seed Sokoloff inclusive broadly earlier a an Constructing (2018) suggests Botany JW. analysis Brown relaxed-clock SA, uncorrelated Smith Formation, An River (2010) Green plants. MJ. flowering Eocene Donoghue for the JM, origin of Beaulieu geochronology SA, Ar Smith Ar/39 autonomous 40 (2003) in of A. diversification loss Carroll increased Wyoming. B, mimicry, with Singer brood-site ME, correlated Smith floral significantly Putative are (2015b) growth vegetative JV. rum reduced Freudenstein and LM, selfing, Kelly BT, in Sinn relationships classification. Phylogenetic revised (2015a) a JV. and Freudenstein coni- tioning LM, of Kelly monophyly photosynthesis. BT, Gnetales C4 the Sinn of of and evolution position problems, The systematic (2004) rooting the RF. data, Sage and Conflicting relationships DNA: plant chloroplast Seed and (2002) fers. nuclear EM. Friis on R, based Kallersjo C, Rydin temperate diverse most world’s Tracing the regions: in adjacent change (2010) and environmental China ZD. and in Chen climate phylogeography flora. Quaternary YH, molecular of Plant Hudson imprints (2011) Y, genetic HP. the Comes Liu CX, genes. JW, Fu Brown YX, mitochondrial Qiu RQ, four Li of TA, Hendry sequences JY, from Evolution Xue inferred B, phylogeny Wang Angiosperm LB, the Li during change YL, climate Qiu transition. terrestrial and Oligocene vegetation early global to province. in silicic Eocene Range Heterogeneity of late and (2017) source U. Basin Salzmann and northern MJ, age, the Pound Sequence, of basins (1998) Miocene W. Bulletin late McIntosh America to SK, of middle Williams in WP, tuffs Nash fallout FH, Brown ME, Perkins a H hnT,Wn M agX.(08 hlgnmc eovstede hlgn fse plants seed of angiosperms. phylogeny and deep Gnetales B the between resolves Society evolution Phylogenomics Royal homoplastic (2018) the or convergent XQ. Wang partial MM, indicates Wang and TT, Shen JH, Ran nentoa ora fPatSciences Plant of Journal International (Aristolochiaceae). oeua hlgntc n Evolution and Phylogenetics Molecular 105 98 48 elgclSceyo mrc Bulletin America of Society Geological 704–740. , 302-314. , mrcnJunlo Botany of Journal American 9–425. 391– , 75 285 110 758–771. , oeua hlgntc n Evolution and Phylogenetics Molecular Bioinformatics 0802 http://dx.doi.org/10.1098/rspb.2018.1012 20181012. , 344–360. , PNAS 107 mrcnJunlo Botany of Journal American 5897–5902. , 22 cetfi Reports Scientific 105 2688–2690. , 163 59 5–15. , 225–244. , 197–214. , 115 iu Evolution Virus 16 e Phytologist New 549–565. , 7 89 38.di 10.1038/srep43386 doi: 43386. , 102 ,194–204. 4 765–779. , vey016. , 161 341–370. , Asarum ora fSseaisand Systematics of Journal ffc fdt parti- data of effect : mrcnJunlof Journal American elgclSociety Geological rceigof Proceeding Asa- Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. loarc etfiue rgnl( a aiaso igeacsrlseisi h rt-Japan-Ryukyu- proto- the in species ancestral always not single of are that a continent), species Asia island of the same habitats of the area Ma) that marginal of Note (2 (= history unit. islands Original Taiwan island Evolutionary or figure: (2018) island Left P. an allopatric. from Zhang species A. endemic reflect Slipinski Colors Adam species. H, and 1 Pang genes Fig. D, of Liang sampling extensive Y, by Li revealed Phylogeny-based LH, Coleoptera of order Che in SQ, arranged Tokyo. Liaoning: Zhang Japan Hokuryukan, of of Japanese). plants (in vascular dinosaurs the pp feathered of 213 Syllabus the system, (2013) of J. China. Merata age northeast K, Cretaceous Sihetun, Yonekura in for Formation evidence Yixian New the 177-182. of (2007) , dating B. SHRIMP Jiang U-Pb S, zircon Li W, Yang likelihood. maximum by analysis phylogenetic 1591. 4: 1586– PAML H, (2007) Sasaki Z. Yang S, DNA. Takeda ribosomal T, nuclear Morota of K, (ITS) Evolution sequences Kondo and spacer CS, in transcribed Yang phylogeography internal CZ, and in evolution Zhou cumented Reticulate JH, and (2007) Pak origin M. J, Yokoyama the Maki T, and Fukuda pollen H, angiosperm Yamaji Cretaceous plants. Lower flowering of of Ultrastructure speak evolution Patagonia (1984) early Gondwanan AG. from Walker fossils JW, Plant Walker herbivor- clock? African megabiased (2011) East or Web radiations. among N. Green evolutionary Nakaya change (2015) on Hideo diet IH. Escapa differential M, P, Nakatsukasa of Wilf MG, record Leakey isotope Y, (2016) carbon A. Kunimatsu Pliocene es. Fikacek JM, to AEZ, Harris Miocene Short TE, Late L, Cerlinga Sekerka KT, D, Uno KraL beetles. J, dating HaJek of E, peril Arriaga-Varela The M, with U.S.A. Seidel monocotyledon Nevada, EFA, arborescent northwestern Toussaint an of nov., Miocene sp. middle et the gen. Palynology shadishii from living Protoyucca to growth fossils (1990) secondary leaf LR. related Parker of WD, relationships Tidwell the and Jordan, of Cretaceous lower (2008) genera. the SH. from plant Basha fossil GJ, aquatic of Brenner implications DW, sequences. taxonomic Taylor matK and and phylogeny ITS Molecular on 4b10. based (2017) version chiaceae) H. methods), Setoguchi other D, (*and Takahashi parsimony using USA. analysis Massachusetts, Sunderland, Sin- Phylogenetic Sinauer, PAUP*: 4. version (2002) methods), DL. other Swofford (*and parsimony USA. using Massachusetts, analysis Sunderland, Phylogenetic auer, PAUP*: (1998) DL. Swofford phylogenetic and Geobotanica characters karyological et and nomica Molophological (2005) J. of Murata relationship K, Senni N, Fujii T, Sugawara 368-386. Japan: (2006) T. Sugawara rceig fteNtoa cdm fSciences of Academy National the of Proceedings ih gr:Peet( a aiasof habitats Ma) (0 Present figure: Right mrcnJunlo Botany of Journal American 62 44 79–95. , srmcordifolium Asarum 863–884. , Asarum 56 247-255. , ytmtcEntomology Systematic e Phytologist New n wtuiK, Iwatsuki In: . naso h isuiBtnclGarden Botanical Missouri the of Annals ...Fsh(rsoohaee curn nMyanmar. in occurring (Aristolochiaceae) Fisch C.E.C. 95 340–352. : 207 ln pce Biology Species Plant ctflu jordanicum Scutifolium Heterotropa tal et 283–290. , O:10.1111/syen.12198 DOI: , 108 17 ,eios lr fJpn o.IIa Vol. Japan, of Flora editors. ., 6509–6514. : nteJpnRuy-awnilnsadChina. and islands Japan-Ryukyu-Taiwan the in Asarum srmforbesii Asarum aueCommunications Nature o:10.1111/1442-1984.12189 doi: . sect. e.e.s.nv Cbmaee,an (Cabombaceae), nov. sp. et. gen. oeua ilgclEvolution Biological Molecular Asiasarum 71 ln h agz ie,and River, Yangtze the along eiwo aaooayand Palaeobotany of Review 464–521. , oeua Phylogenetics Molecular rtcosResearch Cretaceous Aitlcica)do- (Aristolochiaceae) . Asarum oasa Tokyo, Kodansha, 9 caPhytotaxo- Acta 205. : (Aristolo- 24 28 , Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. lnsatrteacceptance. than the Other after time. shown. blanks the also through rate are maximum characteristics with plots function, Excel connecting 1 by by Table drawn drawn trendline for Exponential trendline figure equation: handed enlarged with Free curve Laterally curve: Black bottom: diagram. Red Right node) APG each 2013). the at Murata, shown to and age according (Yonekura names species Christenhusz order each after and of Asarum to family aside according Angiospermae, shown names For is order (2013). 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Data may be preliminary. 20 Posted on Authorea 11 Sep 2020 — The copyright holder is the author/funder. All rights reserved. No reuse without permission. — https://doi.org/10.22541/au.159986856.60354858 — This a preprint and has not been peer reviewed. Data may be preliminary. 21