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Biology Faculty Publications and Presentations Department of Biological Sciences
1-1-1993 Phylogenetic Hypotheses for the Monocotyledons Constructed from rbcL Sequence Data James F. Smith Boise State University
This document was originally published by Biodiversity Heritage Library in Annals of the Missouri Botanical Garden. Copyright restrictions may apply. Image courtesy of Biodiversity Heritage Library. http://biodiversitylibrary.org/page/553094 See article for full list of authors. PH YLOGENETTC ,\left ,;" N. D Il[)(dl. ~ "liclwd T Clegg. ".! HYPOTHESES l\lurk Ir. Chase, !·1 It". Ih>lI f1 i.~ Clark," 11". Joh" Kress." lIarold G. lIills.' H FOR THE MO NOCOTYLEDO NS 1.llis I:', I:'glliarte. ~ J (lfII('.~ I:. Smith. ." CONSTR UCTED FROM H ralldun S. CallI,".! 1~'Ii=flIJC lh .-1. Zill/mer,M rbe l SEQ UENCE DATA' ((fld C(>fald II. Learn. Jr. :!
A Il:-;'I'HACT
DNA l>t!(IIICIlCes for the 1'1a~l i d lo('lb that cncOI.ie.-. tht' larp;(' ~lIhllll il of riblllo~c I .S.lm'l'ho~phale carlooxvla-..,' oXYAt'Il:I~C (rbc L) were determined for 18 "pecie:; of 1II0llucotrb1oll;' ill 15 falllilie:.-. TheM' data were allulyzt.'d IOj!t'tlwr ..,jlh "etlllt'I]!;C" for 60 other 1II0nocoi -,=,pecies in a total of 52 falllilic" by the maximum likt·1i hoOtI method produnll/o! Ollt'. prt'",ulllably optimal. topology. A II additional 26 "'pent'" ..• .. t'r!:' added ( I 04 Iotal lIlotlO('ot ,..peeie,..) and anah.wd b\' the ""r,.imon} melhod \Iilh an olllJ~rollp of 18 dieot !-pecic,; producing 109 In~t',. of :I,()]:! ,.tep", The rhd. data ,.holl' at I{'ast moderate support for ~c I· l.'n lineage;: corrc;: pollding to the following order!-, Hlpt·rorders. or ('olllbillation~: ..\ n'l·anal': tbparagales (exclm!ing lI ypoxidaceae) plus Ifidaccac: Cyclanthanac plu~ Pumi
Ill llmiitioll" for the manipida liull of Ilucleic acid,. li lleagc,. of rnoll o("oly l('d o n ~ kl"t'd 011 rlwl. .. t'· and ad va nCl';; ill compllt.'!" h'chllOlogy IIOW permil q Il PI U' f' da ta ha v(' llef'n :lllt'III]lII'd prt'\·ioll ... I~ for : ]l llylogt'lll' tit' a nalysis of Il0I1101()~t)u" ,. t'q ucl lces of (I) Arc('aceae (\'\'il"oll l'1 <.II.. 19<)0): (2) Brollll'li . DNA from large lIu mbt'r.<; of organi." rn ." . T hcse base·
For computer analyse" \Ie than].. G. J. Ol",en (Ulli\'ert-ity of Illilloi". Urbana), H. Ow·rI-"·t'].. l l\ l a t hemilli('~ and Corrrplltt'r Science. Argonnc i\atiOiral La lJO ratory. Argonnc, IlIlinois), the Concllrn'l1t ~upl'r( __ omputing Con .. ortiu/ll, B. \~ · hitkll1>. P. LO\l'e (both, l ' nivt'ft-itl of CalifoTllia. Ri ven,ide) a nd ~ 1. Berres (l1 nil' er~ it v of ~ I inne"ota. St. Paul). \,'t. 1I1.~o thank D. Jarrell (Ur1l\t' rloit\' of California. Hi\'crside). n. Olmstead (Urliver,.ity of Colorado. Boulder).
ANN. M,sso" B' BOT. GA B". 80: 607- 6 19. 199:1. 608 Annals of the Missouri Botanical Garden
cotyledons usin g DNA sequence da ta fraln the ruc L dideoxynuc leotide c hain-te rmina tiOlI method using locus for a set of species tha t represent ed the a set of conserved, syntheti c, interna l rbe L primers breadth of taxonomic di versit y in the group. (obtained from C. Zurawski, DNAX Corp.). Both the rbe L coding stra nd a nd the complementary strand we re seque nced for all species. The 18 rbe L MATERIA LS AND METHODS sequences produced for this study were entered DNA sequences of rbc L from 104 species in 52 into "CcnBank" under the accession numbe rs list of 104 monocol famil ies were analyzed (sec Ap ed in T able I . pendix in this issue for species, locations of vouch The maximum likelihood method of phylogene ti c ers, sequencing me thods, extent of sequences. and analysis wa s selected for use here because it is less authors). Eighteen of those seque nces Crable I ) biased by the heterogeneous nucleotide substitution we re produced specifica ll y for this stud y by the rates that have been obse rved for rbc L a nlong followin g me thods. Total DNA was extracted from different lin eages of monocotyledons (CaUl c t a I. , fresh leaf tissue by the method of Doyle & Doyle 1992) than are othe r methods (Felsenstein, 1981 ). ( 1987) for 16 species, the method of Palmer ( 1986) Furthe rmore. under this method , li kelihood scores for Cyperus aft.cnufolius. a nd the method of Ja rrell may be calculated for a lt erna te topologies and sub el a l. (1992) for L eml/(( m ;lIusC/I/a. Approximately jected to compara ti ve tests of sta tistical signifi I Jig of each DNA pre para tion was used to provide cance. However, onl y a subse t of the entire rbe L template for "flu/-mediated amplification of the rbcL database could be a nalyzed since the method is gene using the protocol provid ed with '/'aq DNA computer.intensive. [To establish all esti mate of pol yme rase by the supplier (Proillega Corp.). The the compute r burde n, a maximum likelihood a nal · prime rs for the reaction were two highly conse rved ysis of 79 rbe L sequences using the program, sequences from the rbc L coding region of Spinaeia DN AM L in PH Y LI P 3 .4 2 (Felsenstein, 199 1), was oferacea . The 5' primer consisted of the fi rst 30 e xec ut ed 0 11 a C RAY " Y - MP8 / 86 1 ~ " supercom. ba se pairs of that seque nce and the 3' (reverse) puter. The a nalysis spanned I I days wi th a run prime r corresponded to posit ions 135 1 to 1380 time of about 5 1 C P U hr. AI this speed, ten ex on the complementary stra nd. Ampli fica tions uti· ecut ions of the progra nl wil11 diffe rent in put orders lizing these primers produced 1,320 ba se pa irs of (typica ll y recommended) of the 79 rbe L seq uences the coding sequence of rbc L. Primers tha t a re would have required over three mo nths of real time external to the coding seque nce occasionally re utilizing more tha n 20 CP U days on this mac hine.] sulted in successful amplifications of more of the Consequently, 78 of the o ri gi nal 104 monocot spe rbc L coding sequence. For S pargallilllll wlleri cies were selected for maximum likelihood analysis C(lfIllIll. a 27 base pair seque nce al the promote r with Sallrurus eem/Ill s as the outgroup (79 species region for rbe L deri\'ed from positions 53742- total). Eac h of the followi ng taxa, Aga\'aceae, Are 53768 in the plastid genome of O,)':;a saril'a wa s caceae, Bromeliaceae, Nolin aceae. Poaceae, and used as the 5' prime r . For Gymn() .~/ a('hys (III Ce p 8. Zi ngibe ra les, in va ria bl y constituted a monophyleti c Trade8canl.ia afr. paffida. a nd Typha fali/olia. a lineage in prelimina ry phylogenetic analyses that 24 base pai r sequence at a ribosome control sit e included mult iple species in each. T he subset was downstream of the coding seq uence derived from thus selec ted 10 conlain re presentatives from each positions 59 146-59123 (complement ) in the plas. of the 52 families whil e e xcluding some of the tid genome of Nicoliana labacllm was used as the multiple species in these six taxa, preserving the 3' primer. Up to 1,428 base pai rs of rbe L were potential for in vestigating hig her orde r relatioll produced , depe nding on the prime rs Ihat were used ships . The species tha t we re retained in the subset in the a mplifi cation rea ctio ns. For the rb eL se are: Agavaceae- Man/rcda m(fclIlo.w and }'Ilcca quences from the monocotyledons ana lyzed he re, recurVifolia; Areca ceae - Car)'ola mitis, Ph oenix 5.7% of the sequence data was missing largely ree/illata, a nd S erenoa (('pens; Bromelia ceae because of the use of internal primers in the am· A eehmea challtinii a nd Til/al/dsia efi:abetltae; plifi cation reac tions. Nolina c eae- Noli na ( Beall ea f"fI ca) recu rva I.a ; Single -stra nded DNA was produced ill a second Poaceae- Oryza sa ti,la and Zca ma),s; and Zin round of a mplification using the double-stra nded gibe rales-Calalltea loeseneri, CostllS barballl s, product as template a nd the two prime rs indi \'id Globba cur/isii, H f'd)'ehillfll gardl/eria'lIlfli. Nel ua ll y. These single-stranded prod ucts were precip icoll ia la/ispal.ha. 1\!1 aranla leucofl eura, l\!1l1 sa itated (7.5% polyeth yle ne glycol -8000, 0.94 M (, avendi.shii, Orchidantha fimbria/a, Phellako NaCI). the DNA pelle ts were wa shed twi ce wit h Spermlll1l gllyarUlcnse, R avenafa madagascar. e tha nol, and sequencing was accomplished by the iel/sis. a nd Tapeinoelleilos Of/ aI/OSMIC. Volume 80. Number 3 Duvall et al. 609 1993 Phylogenetic Hypotheses for the Monocotyledons
T.o\lI t E I. Eighteen species for which rb(" L was SC(llICllcc\1 for this st udy. Vouchers (herbaria), acces..... ion IIlIJUIX'T!'o fo r the rbe l sequences submitted to Gcn lJank. superordinu l. ordinal, and familial alignments arc given. Idcntitic:. for the remaining 104 species that were analyzed may be found in the Appendix for this issue.
Vouchers Gcnl3ank Species (herbaria ) Family accessIon•
Aranac ..\r ales Acorus Cal(/mll.~ L. rrcl/('h 2:J2 (CI-I) Acorace,1\" i\1 9 1625 Gym'/O$/{/chy ,~ /IIICI!PS R. ilr. lIo1NIrI/ 11325 (n 'C ) Araceae M91629 IJistia slmliales L. Fr('l/('h 2JJ (CI-I) Araceat' M96963 !-cr1llUl milll/scllla Herter /Jw'all 191)20501 (UCH) Lelllnaeeac ~1 9 1 630
BrolT1clianae Typhales "I )pha latifolia L. /j rad/!')" :!IIY-;,I (Gi\I UF) T)'phaccac 1'19163 4- Sparg(lllilOlI aml'riC(lllll1ll Nut I. ehav 257 (NCU) Spargalliaceae 1'191 63] COlnmelinanae COll1l11elinales Tradeseal/tifl aff. pallida Brrulll'Y 24980 (GM UF) COIl III IC lina ccae L050·11 '/'rades(,(lII/i(l :f'brirw hon. ex Bosse COllllllclillaccac LO S04:! Cyperales C)pCTIl .( fl/r('mi/o/iIlS L. Dlll'olI 19920602 (UCR) CypcraCl"ilC ~ 1 91627
Liliallae Asparagales A/oc ,'cra (L. ) Burm. Bradh'), 24977 (G M UF) tbphodel:.lccac L0 5029 I/(//('o rtll;" slIbfilsciata Baker Brad/('y 24978 (GM UF) Asphodcl:.lccae L050% Chlorophytllffl ("omosum (Thunb.) Jacques ilrad/ey 7331 (C M UF) Antheri('aceae L05031 C/il'it! miniata Regel Bradley 211976 (CMUF) Amar yl lida('cac L0503 2 .vo/ino (/3ew/("ornea) rccur]"(ltll ( Len!.) Hellls1. PI'/('(.(O ll 12606 (US) Nolinaceac L0503 0 Liliales Iris xgerm(trliclllfI L. J3 radh,y 25976 (Ci\I UF) Iridaceae L05037 \1('Ii("o/fI ,·irJ.!ITmlfm (L. ) i\ l.'rri\J /lffld/t')' 24Y-;2 (CM UF) U"ularian'al' ~ 1 9 16 1 :l Zingiberanae Zingi beralcs ,\laranla ICl/ cof/cl/ra E. Morri,., Bradley 24979 (G M UF) Ma ralltaccac L05 040 /I (,((l'chill m go rei fl crio flllf1I Ker Ca ..... !. Bradley 24915 (Ci\ 1 f) Zingibcraceae 1\1 91628
The analysis wa s executed 0 11 the fastest ex isting a!.. 1986; Hit land & Clegg, 1987). Hegional alld compu ter, the TOllc hstone Delta Pa rallel Process· local bra nc h swapping weT{' employed. T hi., portioll ing Supercompute r. usin g "fastDNAml version of the analysis. whi ch included data fr oll! 7·1 of 1.0.3" (Olsen e t al.. 1992). Thir ty.three replica. the 79 species. consumed 125 hours of computer tions of th e analysis we re perforilled with diffe rent time. randomly determi ned orders of input. The "cate· t\fter the init ial a naly:,is wa s performed. tlu.' gories option:' wh ich permits specifi cation of dif· remaining five species (AIr'(ris /i/ril/owl. Hum/(/I/. fe rent substitll tion rates by codon position, was "ia bijlora. Sparg(Hlillm (1I1H'rinltIlOIl, SI('Ko/cpi., invoked using re la tive rates of 1.00. 0.85. a nd allenii. and '/)pha [aft/olia: total :o pecie3: 79) ,,·jth 5.80 for hrst, second . and third codoll posit ions, equivocal phylogenetic POSiliOils in prclinlinaq respecti vely. These va lues arc IJa"ed on re ported a ll al)'ses were added to th e optirnal topology from substitution ra tes a t each codoll posit io n (Clegg e t the previous step wi th 50 (of 120 possi hl e) random 610 Annals of the Missouri Botanical Garden
TA BI . ~ 2. Distribulioll of polymorphic sites. constant phyletic clades were conduc ted . The selected spe sites. and sites shared by two or more species (i.e., in cies groups we re; ( I) CO lllmclina nae (1 3 spp.); (2) fonn aliv~ sites), among codon positions of rbe L. Sites un.' Al islll a tanac (4 i:i PP ,), and Ara llae (4 spp.), to· calculated fo r 1.4 28 base pairs and 79 species. l3as(' gethe r wi th .·korus ('(1/(1111I1S: and (3) each of nine substitutions were optimized on the topology of Figures .l superorders sensu Da hlgren e t
Fl<:II KE I . Topology for 78 monocotyledons and the outgroup dicot),ledon S(lllfllfllS cerllllllS (79 spp. total) prod uced by the maximum likelihood me thod wit h a log likel ihood of - 18.8 78 .2 1. T he analysis was executed using the computer program fastDNAml 1.0.3 (Olsen et al.. 1992). on the Touchstolle Delta Parall el P rocessing Super. computer. the fastest existing computer. T he initial phase of the analysis included 74 of these species. employed regional alld local branch swapping. specified substi tution rates of 1.00. 0.85. ali(I 5.80 for first. second. and third eodon posi tion substitutions. respectively. under the "categories" option. was performed wit h 33 replications of thc input order. a nd consumed more than 125 hours of supercomputer time. Fi ve additional species. Aletris ! arifWS (/ . IJll mulfIflia bijlora. S/,Ilf'grlf/ill ffl (lffH'ri(,(IfHlfll. Stegull'fJi.~ all,'nii, and Typhll la/ijillia. were added more than SO ti mes to the initial topology wit h the largest log likelihood score. Add it iona l rea rra ngemcnts of the tree with the largest li keli hood score produced the tree shown here. Scale har indicates 1. 0 % maxi mum li kelihood dista nce units as cnlculuted under the assumptions specifi ed above. Specie!> are indicated by genera onl)'. For complete bi nomials see Appendix in this issue. Volume 80 , Number 3 Duvall et al. 611 1993 Phylogenetic Hypotheses for the Monocotyledons
Oryza Zea Elegl8 Ragellana Spa!gamum Typm. PnofJum Carex Cype"" Oxychloe Juncus Aechmea Til/BooS/a SlegoJeps PfJensKospermum He/looma Mu,a G/obba 1.0% QrchJdanltla Costus Hedychium MafEUlta Tapemochellos GaJafhea RavenaJa Ptilydrum Tradescanfla aIt_ pal.da
T. zebnna T. soccnuscana Pontedena L__ .:===::- -::;;;;;;;Arigozanlh us Serenoa CBfYO/8 Phoenix elMS. Bowiea Sanseviena Danae Nolina racuNa/a Xanthorrnoea Haworth/a- L-;=~::~=~DianeJla KnipfJJfl8 Chlorophytum MBnfreda YUCC8 Cyanastrum Iris Aroma/hees. Burmaml8 Hypoxis Curcullgo Oncid,um Neuwl8dia Oioscorea Ta= Sphaeradenia Freydneti8 Vellozia Alstroemena Burchard/a Colchicum ChamaeliriJm Smilax Medeola Ulium Aletris Pfee. Gymnostachys SpaftiphyJlum Lemna Pistia Potamogeton Alisma 5<:¥]irtana grammea 5. larifa/is. ____ Saururus 612 Annals of the Missouri Botanical Garden
72 Costaceae (2 spp.) N_. Heliconia :::I 62 Orchidantha CO_ . 93 Musa Calathea CT 0 1 2 Maranta C1) Phenakospermum .., Ravenala III 6 5 - Zingiberaceae (2 spp.) C1) 1 00 I/) 70 Tradescantia (3 spp.) Bromelianae (3 spp.)
Stegolepis 1 00 Bromeliaceae (2 spp.) 1 00 "tI 59 Poaceae (2 spp.) 0 Elegia III Flagellaria - 7 8 Typhaes (2 spp. ) C1) I/) 1 00 Byrex 9 0 7 1 perus l> 7 1 Oxxchloe .., Ju cus C1) Prionium 1 00 53 Caryota (") Phoenix III 1 00 Serenoa :::I Orchidales (2 spp .) III Burmannia C1) 98 Hypoxidaceae (2 spp.) 99 90 Agavaceae (2 spp.) l> I/) 1 00 Chlorophytum 73 1 00 Asphodelaceae (3 spp.) "0 III 50 96 Sansevieria .., 79 Nolina III Danae CO 7 1 Bowiea Dianella III ~r,nthorrh o ea -C1) IVla 54 I/) 97 9Yanastrum Irldaceae (2 S&p .) 1 00 Dioscoreales 2 spp.) 95 Freycinetia 53 ~haeraden ia ~ / loz ia 94 99 ilium Medeola Smilax 1 00 Colchicum 1 00 Burchardia Alstroemeria l> Melanthia les (3 spp.) .., 69 Pistia III :::I 53 67 Lemna Spathiphyllum III Gymnostachys C1) 1 00 Alisma 67 1 00 l> Sagittaria (2 spp.) -_. Potamogeton I/) Acarus 3 Saururus III -III :::I III C1) Volume 80, Number 3 Duvall et al. 613 1993 Phylogenetic Hypotheses for the Monocotyledons
T.\IILE 3. Support for clades corresponding to ta xa SCrlcil! Dllhlgrcn ct
Boot"trap Taxa (number of s p ec ie ~) vulue!; ( PI, ) Decay indi('l''' Length" Ali ... ma tanac (4-) 6 7 > -'J 37 (3) Aranac (·H 53 > -') I. ( I ) Arccantlc (3) 100 > -'J 31 (.) Brornclianae (8) < 50 0 Brornci iaceae (2) 100 > -'J I. (0 ) Typhales (2) 78 > -? 21 ( 11) Cuttlllwlimmae ( 13) < 50 0 Cypcrales (5) 71 > -.J 26 (I) Poalcs (3 of 4-) 59 -.J '") 1 (2) '" .J I' uaq ' a ~' (2) 100 > - 66 (7) Trru/esc(l Tltia (3) 100 > -'J · ~8 (3) Cy cl;ltlt lia nae (I) plus Pa ndalla ll1l e (I) 95 > -.J I 3 ( I ) Lilia na(' (32) < 50 0 A:-paragales ( 14- of 16) plll :-- Iridaceac (2) 8. > -.,.J IJ ( I ) Agavaceae (2) 90 > .-, 3 (0 ) :\"phodelaceat' (3) 100 > - 2 I ( I ) 1-1 vpoxidaccae (2) 100 > -" 18 II ) Dio';(:oreales (2 of 3) 98 > -? 27 (2) Orchidales (2) 100 -.J 2 :1 ( I ) '" ? Zirlgiberanae (II) 93 > - 20 II ) Co:--taceae (2) 72 > -'J ZillE!iberaceae (2) 65 > -'J ~I Oll ot' otyled ons excluding .·/n"ll$ f'(li(/II/I/$ (77 spp.) 73 > -'J 13 ( I )
IIwlCICrtninc d . value s . S(,V(' rI lilleage:o; found ill the IwO including: Agavac(·,w. t\ ~ I.I,()(I {'la{'{ ' ; I( " l{rll. !n FiLl tn: 2. ~'ia j oril y ru le (50(';) con !' cn :-'II~ tree fo r 79 species. The bootst rap analp. i ~ .... a :-- ('o]]{lut' ted u1> irlA PA l '!' 3.0s willi 200 bootst rap su b.~ a lllp l c,.. of the data lIla trix. Percentage valuc!> for tho"c bra ne1ws o('('urring in at Il'a,.., 50('i of the bootstrap topologies arc shown. Selected taxa are identified. Branch length,.. are a rLitrary. Decav va llH' ", up to two Sh:ps longer are indit'ateJ as \'crtical ba rs of va rying thickness overlaid 011 tht' boohtrap topol0!-iv. 'I'll!' thickest lines indicate clades supported ill trees at least two steps longer. The thi nnest lilll':-- illdicate:: clade:-- .'o uppor\t'd only in maximuill parsimony tree,,_ 614 Annals of the Missouri Botanical Garden o""C IIIo ~ Po ales (13 spp.) ~ ~ ~ ~ ] Cyperales (5) ::::::I Typhales (2) Bromeliaceae (7) Zingiberanae (14) Arecanae (7) Asparagales (21), Orchidales (2) , Iridaceae (2), and Melanthiales (1). Lilianae (7), Cyclanthanae (1) , Pandananae (1) , and Velloziales (1) . Dioscoreales (2 of 3), and Burmanniales (1). Alismatanae (4), Arecanae (4) , and Melanthiales (1). ------Acarus calamus Outgroup: Dicotyledonous Paleoherbs. Volume 80 , Number 3 Duvall et al. 615 1993 Phylogenetic Hypotheses for the Monocotyledons . The rnaXlml l 1ll likelihood Iree (1 9 ~ Pl' " Fi g. I ) bia ~ occurre d ill pa rt bec a use of extilln ioll (' vents. and th e resoh'cd portions of th e C OIl:-i{' II S U S tree or that the o r iginal radia t ions O( ' (, III'I'I'd rapid ly . produced by pa rsimony ( 122 spp., Fig. :~) arc 'r he fossil re c ord. a nd e specia ll y tliat o ffo s~ i l pollen. largely congruent with rc ~ pcc l to the ('onstitllent for a ngiosperms in gcne ral ( Do yle & liicke y. 1970) speci es of the seven lineages li sted al,uw! a nd the and pro bably fo r the monocotyle dolls as w(, 11 ( Do yle . order of di\'c rgcllcc of those lineages. Exceptio ns 19 7.1) is certa inl y c onsi stent wi th tile hypolhesi." arc: (I) Dioscorea les (cniliding Smilax g/al/('(I ) of ra pid rad ia tion. d ive rge earlier in the pa rsimony Ire{',;; (2) one : k u r ll.~ r a l a mll s o (' c upies a ull iq ut'. ha,.; al po species ea ch of Cyclantha nae. Pallda nanClc. a lld s itioll ill a ll the trees gene ra ted fo r thi,.; s tudy . Vellozialcs make up an isolated .. la de ill tilt' ma x Althoug h .·k orus wa s tra dit io na ll y c ia",.; irIC d in :\ ra imulll likelihood tree. whic h is found c mhedded ceae hec a u.sc o f sllpnficial mo rphologic al " illlila r with in a cladc of seven species of Lili a lla e in the it ic;; with the Austra lian a roid G I'IIIIIO .~ /(fdl\ S IIf/ - . . parsimony tree: (.1) l1urlllflllllia Ii/Jlort! i:-; fOlllld in ( ' ( 'p.~. a roid aut ho r it ies ha ve rc cenlly genus witll otll('r The ord e r of di vergence o f th(' ~ ( ' \ T tl lI1a jor monoc ot spe cies . if. as we sugg .. ,.;!. ·/1-" " 1., i. ., di,, lill('age s in our phylogene tit: a ll a l y~es i" ill gelle ra l tingllis hed as the lllo ~ t basal e xtantlill( 'agt' uf Il lono agree lllellt wi th wid e ly accepted \ - i ('w ~ O il Ihe e \-o cot yledons . Ilit ion of the m o noco tyledons . Becog ll ilioll o f the Several o the r a "Jlcc ts o f the trec of F I/! lJft, I. ea rl y di ve rg('llCes of Alism a t FIt:1 HE 3 . Overview of the stri ct C ()II.~ell '; \I ;; of 10 9 eq ua ll y parsimonious tree" for 104- JJJ onocots and 18 J ico"'_ T hese trees are of length 3.9 32, haye consistelH.:Y indices excluding ullinformative characters of 0 .267. antI retention indices of 0 .6 3 3. Note thaI the unresolved portions of this topology are within the terminal clades correspoll ding to: (I) Brollleiiaceae; (2) that conta ining Corrllileli naceae and three species of llrorllelianae; (3) Zingibenmae: (4) A~l)<\ r · agates; and (5) that consisting of Al ismatanae , Arecanae, and one species of Melanthiales. T he terminul ;; pt'cit'" a rt' identified in the Appendix ill this issue and as genera in Figures 4 and 5 . T he llllrJl ber of species anulyze,l frorll i'ach taxon is given parenthetica ll y. 616 Annals of the Missouri Botanical Garden -::9 Sorghum ....rC~n~~:u. L..penn/aetum 'Neurachne Avena ,ftlC u,fucclnellia _ Hordeum Aeglfopa =--OryzlJ -t £1"9Ia Flagellarls Juncua Cyperua C .rex Prlon/urn Typha Spafg.nlum Stego/tlpia Aecflmea _ ...:.Aaan •• Puy. GlomeropitclJirnitJ Catopa/a Tlllanda/a Hechtia ______:::!=:2~T"'~d~e.c.T. zebrinnatf. ,. f f. pallid. T. aoconuacana Phil d, m Ponted"ri.= Anigolanmua Ravena/,. ...r 5trefitzia ~ Phenakoapermum Marant. C ,. I at h ea Hedychlum Riede/e. Zing/be, Globba Co.tus rape/nochel/o. c.ryor. Ny!?. 20 ~ Phoenix ~ ...... Drymophloeu. I I r :-CChamaedore. scale I L C./amu. I Sereno. FIGUHE 4. Terminal portion of one arbitrarily selected tree from the set of 109 trees (see consensus tree. Fig. 3) of length 3,932. consistency index of 0.267. a nd retelltion index of 0.633. T his portion of the tree includes species of Commeli nanae. Bromelianae. Zingibcra nae. and Arecanae (see Fig. 5 for the remainder of the tree). Branch lengths correspond to the number of substitutions opt imized alollg the branches. T he scale bar is proportional to a branch length of 20 sleps. strap (84% ) and deca y (at least two steps longer) more a ncient groups than Arecanae. Inclusion of analyses. Duvall ct al. (in rcview) have a nal yzed rbel data for a second species of Panda nanae, rb d ~ seque nce da ta from four marc spccies in three P(/ n d (('I/1 .~ veit,hii does not a lt er this rcsult (Duvall additional fa mil ies of Aspa ragales thaI furthe r sup ct aI. , in review). porI the common ancestry of this large orde r. a nd The rb d ~ trees suggest that Smilax glallca is thcy note tha t the a lli ance bet wcCil Iridaceac and a lli ed wi th species of Liliales and isola ted fr om the Asparagales has morphological a nd a na tomical sup two ot her species of Dioscorealcs (Di():Kurea puly port . gOlloidt's and T(l a {1 illteg rijo/ia). Among the three The historical treat/nellt of Arccanae. Cyclan species a closer relationship has been proposed thanae, a nd Panda na nae as al least margi nall y between the laller two , a nd Smilax has been placed rela ted taxa has been contradic ted by subsequent outside of Dioscorcales becausc of a la c k of simi ta xonomi c schemes tha t treat each as a n unrelated la rities in secondary chemistry (Dahlgren e t al. . supe rorde r (Thorne. 1983) or as separate supe r 198 1). The more recent decision to pla ce Smilax orders wit h a loose a lli ance be tween Arecallae a nd jn Dioscoreales wa s based on " leaf morphology a nd Cyclanthanae (Dahlgre n et al.. 1985). Phyloge flo ral a ppeara nce:- a lt hough Smila x is hypothe netic hypotheses based on the rlw L data support sized to form a "bridge ,- between Dioscoreales a nd F'rt:y cifl cti.(/ (Pandananae) a nd Sphocrrrr/f>fli(l (Cy species of Lili anae (Da hlgren e t a I. , 19 85). cla ntha nae) as siste r specics only distantl y related Included in our a nalyses arc I I species of Poales to sevcn species of Arecanae. This a rra ngement a nd fi ve species of the related Cyperales. Phylo suggests tha t Pa ndananae a nd Cyclanthullae arc gene tic a nalyses of rbe l sequences of Poaceae Volume 80, Number 3 Duvall et al. 61 7 1993 Phylogenetic Hypotheses for the Monocotyledons Xanthorrhoea .... 1.___ Knlphofla I _ --.r Aloe I ~ '--'2'_ Haworth/a I _;:::====- OBow/e.f_nella ' Chlorophytum rl r-- ....-:-C Yucca Beacharne,l. L.. Hespera/oe L- Agave Manfred. San.evlerla Danae Nolina r"CUrvata OuyJlrJon L Nalina IIndhe/meriana ClivI. Iris "-_ r--[ Anomatheca - -L- Cyane.trum Curcullgo Hypoxia Alerr;. Neuw/edl. -{ Oncldlum Smilax Lflium I Medeola Afatroemerfa Colchicum -{ Burchard/a Cham.allf/um Velloz/. --{ Freye/net/a Sphaeradenl. r Dlaacor.a races Burmann;. Plees ,-- ===[S~P~.~t~h~/P~h~Y~/~/U~m~~ PI,rI. Lemn. L ____= Gymnostachy. Sagfttar/a gram/nes Alfam_ Pot8mogeton Acarus Amborella r Eurr.' r"- Vic orf. r- Nuphar" __ :=~B~r. sen/a L Cabo m ba ~ Barcl.y. L ,Nymphae. Schl •• ndr. -{ IJlieiurn AU.frob.lley. Chloranthua Sa rum. Asarum 20 Houttuynfa I Saururus Scale P"peromia r lCl · H ~. 5. HClIlainder of the trCI' partially shown in Figure 4. This portion of the trce incl udes species of Aranat:', Alismatanae. Lilianac. ou tgrollp ,licotyledons, and A ('oflls I"ll/rWIII S (see Fig. 4 for the remaindcr of the tree). Branch lengths ('orrcspond to the number of sub! have been tho roughl y discl1 !':-ocd ( Doebley ct aI. , inven;iolls in the plas tid gC IlOUlt.'S o r these taxa 1990). \'(I e hcre not e tha t pooid a nd pa nico id g rass ( Doylc ct al.. 1992) tha t rurther p redicts tha t J oi n es arc s('gregated inlo sis te r ('lades in Figu re 2, vil leaceae arc immedia tely hasal 10 Poaceae. T hi ~ a nd that Ory::.o .~ (/fil · (1 occu piC':-- the llIost basal predic tion has been confirmcd by analysi:; or r/JI'L posit ion o r Poaceac. In the dade cOllsisting or Poales data as well (D u vall ct al.. in rc\·i(·\\,). (Fig. 3), a s pecies or Restionaceac i:-- mos t closely III our analyse:. Commelinaccae (Ihree specie,) related 10 Poaceae. a nd Cyperalt.'~ are round as a clusle r with three species o r Bro!l1clianae: '''ofl/rd(,. componcllt o r a sis te r clade which al~o ('ontains ria .~ (/g i lfflrifl . Philydmrll 1r1f1ll;:iIlOSllfII. a nd /11- T y pha les contra Dahlg re n e l a!. ( 1985). T his 10- ig(j::.afl/hll .~ f!m'idll s in a dade that i ~ ~ i :- Ier 10 po logy is ill ag reemen t with the d i~ lr i lJUl ion or three Zingi bcranac a nd separated rrom 18 other ~ I'c('it· ~ 618 Annals of the Missouri Botanical Garden of Commelinanae (Fig. 4). A parsimony tree over c ules. T hese furthe r studies witt undoubtedly re fin e the 79 species subset constrained to include 13 methods of the ph ylogeneti c a na lysis of molecular spp. of Commelinanae as monophyle tic (llot shown) data. is 15 sleps longer than the tree wi thout constraints. Parsimony analysis of (he L thus does 11 0 1 support LITERAT URE CrrED the recognition of a monophyle tic Commelinanae. e IlA:';; £. M. W., R. MOIlGAN. P i .~tia has been tentativ el y aligned wi th 1. ('111 1/(/ D. E. SoLT I ~ . G. Ol~t SH: .,\ D . D. D . H. LB . B. D. MI S HL[f~. M. R . D UVALL. R . A. based on similarities of seed li ng struc ture (Grayum, P Rln:. H. G. HILLS, Y .-L. Q IU, K. A. K RO N, J. H. 1991). Analysis of rb e L seque nces supports this RtT rI:;, E. CONTI, J. O. P ,\LMER. J. R. M :\ NIII\ IIT, a lignment a t a bootstrap va lue of 6 9% a nd a decay K . J. SYTS MA, H . J. MICII M:J5;. W . J. Kllt::5S, K. C. index value of at least Iwo. K AHOL , W. D. CLARK. M, H EUR EN. 13 . S. CA I IT, R. Three spec ies of Mc lanthiaccae are found ill K . l\NSE;..' , K .• J. KIM . C. F . \·VIMI'EE. J. f. S~ H TlI, G. B. FtJltNIEII. S. H . STRAUSS. Q.-Y. XIANC. C. M. three different primary lineages . T hese species ex PU INKETr, P. S . SoLTIS, S. SWEN:--EN. S. E. W IL hibit a g reat deal of \'ariation a nd when cornbincd Li:\ ,\t:-- . P . A. C ADEK. C. J. QUINN. L. E. EC LIIAHTE, into a single family a rc considered a "diffic ult·· E. GOLENIJEIlG. C . H. LEA!!N, J!! ., S. W . CIl,\IIAM. treatme nt (Dahlgren el a I. , 1985). Our result s sup S. C. H. B A IH~E1T, S. D AYr\N,\ NOAN & V. A. ALBEIIT. 1993. Phylogcnctics of seed plants: An analysis of port the suggestion (Dahlgren ct a I. , 1985) that nucleotide sequences from the plastid gene rbe L. the Mela nthiaceae should be divided into several Anll. Mis."ouri Bot. Gard . 80: 528- 560. families. a nd we furthc r suggest tha t those fa milies CLt:cc;. ~L K. R rn.AND & G. ZIlIIAWSKI . 1986. Pro Iliay not be closely related to eac h other. cesses of chloroplast DNA evolution. Pp. 275- 294 The phylogenetic a nal ysis presented here offers in S . Karlin & E. Nevo (editors). Evolulionary Pro cesses and T heory. Academic Press. New York. suppo rt fo r the recognition of seven primary lin CHON!)1 t ~ T. A. 1981. An Integrated System of Classi eages of monocotylerlons that di verged over a re l fica tion of Flowering Plants. Colurnbiu Univ . Press. a tively short period of geologic tillle. As notcd, this New York. result is in agreement wi th the taxonomic treatme nt D.. \lILCII E:-':, R .. H. CUFrilIl D & P. YEO. 1985. The Families of the Monocotyledons. Springer-Verlag. New of Dahlgren et al. ( \985). However, a pa rsimony York. tree for the 79 species subse t constraincd to include --- . S. RO:-- END:\L-J EN:--EN & B. NIEL"' EN . 1981. A nine of ten supe rorde rs se nsu Dahlgren e t al. (1985) rcvised classifi cation of the angiosperms wilh com as monophyle tic groups (not shown) was consid mCllts 011 correlations between chemical and other e rabl y less parsimonious (52 ste ps longer). (N ote characters. Pl'. 149- 204 ill O. Young & D. Seigler (editors ). Phytochemistry a nd Angiosperm Phyloge that the tenth supe rorde r. Triurirla nae. is compo::i ed ny. Praeger Scientifi c. New York. exclusively of ac hlorophyllous species unlikely to D OERI.EY. L M. O IllWIN. E. GOLENrlEIl G, M. Cu :c c & D. possess a phylogenetica ll y meaningful copy of the MA. 1990. Evolutionary analysis of Ihe large sub rbcL sequence.) \'\lith regard to the paraphylctic unil of carboxylase (rb eL) nucleotide sequence aJllong Ihe grasses (Gramineae). Evolution 44: 1097- 1108. arrangeme nt s of Bromelianae. COII Hnei illaJlae, a nd DOYLE, J. A. 1973. T he monocolyledons: T heir evo· Lil ia nae. the ph ylogene tic hypotheses presented lution a nd compurative biology. Quarl. Re \,. BioI. 48: here a re a l odds with those based 011 morphological, 399- 413. anatomical, che mical. a nd other c ha racte rs. These --- & L. H ICKE Y. 1976. Pollen and leaves from disc re pa nc ies ma y reflect a new understa nding of the mid·Cretaceous Polomac Group and Iheir bearing on early angiosperm evolution. Pp. 139- 206 ill C. the cdTi nities a mong these taxa. However. insuffi l3eck (editor). Origin and Early Evolution of Angio cient sa mpli ng of the rbd.. da ta for these groups sperms. Columbia Univ. Press, New York . of species may a lso be a factor. For example, we D OYLE. J. J. & J. L. OOYLE. 1987. A rapid DNA isola lion have he re in cluded rhcL data fro III onl y half of the procedure from small quantities of fresh leaf tissue. Phylochem. Bull. 19: I 1- 15. ,52 famili es of Lilianae. Additional sa mpling of mo ---. J. I. D HI:-' . R . J. SoHNC. D. G.. \J\\ IN & M. J. lecula r characters may resolve these disc repan<.:ies A NUEl\:--ON. 1992. Chloropla !> 1 DNA inversions and or offer furthe r insight into the phylogcnetics of Ihe origin of the grass falllily (Poaceue). Proc. Natl. the monocotyledons. AClifl. Sci. U.S.A. 89: 7722- 7726. The foc us of this project was the phylogenetic Oll\·.. \I.L. M .. M. CHASE. D. SOLTI::; & 1'1.1. Cu:cc. A phylogeny of seed plants result ing from analysis of framework supported by the rI)("L da ta ,,('1 fo r the ONA sequence variation among the rbel loci of 475 Illonocotyledons . Another va lu able feature of the species wilh particular emphasis on alliances among data set, now generall y available in CenBank. will monocotyledons. III P. l'loch (editor). Ex perimental be to furthe r develop our understa nding of the and Molecular Approaches to Plant l3i osysteJJl 1991. PJ-IYLIP (Phylogeny Inference Pack 01_"'':,"", G .. H . NA~l · D ... , R. H ,\C'-;'IIH}\' & H. OHIUlH" , age) Version 3.4. University of Washington, Seattle. 1992. FaSIDNAml Version 1.0.3. Uniw:r,.itv of II· G'\"T. B .. S. M,,,.:. W. O. CI\UK & M . ClEC\ ;. 1992. linois, Urbana and Argonne National La boratory. Relative rates of nucleotide substitution at the , 1.1I'L ArgolJne, Illinois. loc us of monocotyledonous plants. J. i\ lolce. EvoL PAL\!EIl , J. 1986. Isolation and ~ tructural una l", "i,. of 35, 292 ~ 303. chloroplast DNA. Melh. Enzymology 118: I b 7 lU6. GOlIlIIEIH':, A. 1989. Classification, evolution, and phy . Hm .. NIl, K. & ~1. CI.EI;C, 1987. Evolutiollarv anal v,.i... logeny of the families of monocotyledon,:, 51111Ih,,01l of plant DNA sequencet> . AlIler. Naturalit> t 1] 0. ,.up· ian Contr. 1301. 71. Smithsonian Instit ution '''rc,.,,;. plelllcnt: 574·5100. Washington, D. C. 5\11 1"11, L W. J. K HL,.... &: E. t\ . Z,\,\I[H. 199 : ~ . Pin · GU .\Yl IM. M. 1987. A summary of CVilicllce ami ar logenetic analysis of tilt.' Zingibcrales ba"ed on rI,,' L guments supporting the rClllo \'al of . -/r'Ofl/S frolll the "eqUt·lIrC '" An n. Missouri Bot. Card. 80: 1):!O (dO. .'"\raceae.' . T axon 36-.,-?3 _ - -'9I _ . 5\\ ( )FHHI)l, D. 1991. PA U P : Phylogenetic Anal, ,.i .. l ' .... . ----. 1991. Syste matic embryology of the Araccac. ing Par,.illlony. \ 'ersion 3.D !'> . \'ompu,cr proWll lll