MOLECULAR PHYLOGENETICS OF BROMUS (POACEAE: POOIDEAE) BASED ON CHLOROPLAST AND NUCLEAR DNA SEQUENCE DATA

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1 Alis 2, pp , Ranch Santa Ana Btanic Garden MOLECULAR PHYLOGENETICS OF BROMUS (POACEAE: POOIDEAE) BASED ON CHLOROPLAST AND NUCLEAR DNA SEQUENCE DATA JEFFERY M. SAARELA,'-' PAUL M. PETERSON, RYAN M. KEANE, JACQUES CAYOUETTE,* AND SEAN W. GRAHAM' Department f Btany and UBC Btanical Garden and Centre fr Plant Research, University f British Clumbia, Vancuver, British Clumbia, V6T 1Z4, Canada; -Department f Btany, Natinal Museum f Natural Histry, MRC- 166, Smithsnian Institutin, Washingtn, D.C , USA; Department f Bilgy, Imperial Cllege f Science, Technlgy and Medicine, Silwd Park, Asct, Berkshire, SL5 7PY, UK; "Eastern Cereal and Oilseed Research Centre (ECORC), Agriculture and Agri-Fd Canada, Central Experimental Farm, Wm. Saunders Building, Ottawa, Ontari, KIA C6, Canada Crrespnding authr: (jsaarela interchange.ubc.ca) ABSTRACT We cnducted a phylgenetic analysis t cliaracterize relatinsiiips amng Brmus and test the mnphyly f five f the seven mrphlgically distinct grups within Brmus (Paceae: Pideae) that have been treated as sectins, subgenera, r genera. We sequenced the chlrplast /;«L (UAA) intrn, the '-end f the chlrplast ndh gene, and the internal transcribed spacers (ITS) f the nuclear ribsmal DNA regin fr 46 species that represent a large prprtin f the mrphlgical and gegraphical diversity in the genus. Independent analyses f plastid and nuclear ribsmal data identified several lineages in Brmus, but there is sme evidence f incngruence between these linkage grups. Nuclear ribsmal trees indicate that tw clades cmprising sme Nrth and Suth American species f sect. Brmpsis are the successive sister grups f the rest f the genus, and that Old Wrld species f sect. Brmpsis are mre clsely related t sects. Ceratchla and Nebrmus than they are t the remaining Nrth American species f sect. Brmpsis. In cntrast, plastid trees indicate a clse relatinship between Old Wrld and sme Nrth American species f sect. Brmpsis. In the nuclear ribsmal trees, sects. Genea and Brmus (if sect. Tiiniusia is included within it, as treated by mst authrs) are mnphyletic and nt clsely related. In the plastid trees, species f these tw sectins are intermixed, supprting a hybrid rigin fr B. pectinatus. The mnphyly f sect. Ceratchla is supprted in the plastid and nuclear ribsmal trees, and the mnphyly f sect. Nebrmus is rbustly supprted in the nuclear ribsmal trees. Current classificatin schemes d nt reflect phylgenetic relatinships in Brmus. Tentative evidence f cnflict amng nuclear and plastid data partitins needs clarificatin with mre rbustly supprted plastid and nuclear ribsmal gene trees. Key wrds: Brmeae, Brmus, ITS, ndh, phylgenetics, Paceae, Pideae, / L intrn. INTRODUCTION that Littledalea and Brmus d nt frm a clade, thus Brmeae may nt be mnphyletic (J. M. Saarela unpubl. data). Brmus is a large genus that is widely distributed in tem- Q believed previusly t be clsely related t perate and muntainus regins f the Nrthern and Suth- ßrmus, based n mrphlgical similarities, include Meern hemispheres. Several species are imprtant frage grass- giachne Steud., Metcalfia Cnert, Pseuddanthnia Br & es (e.g., Ferdinandez and Culman 2; Ferdinandez et al. c. E. Hubb., and Sinchasea Keng (Smith 197; Stebbins 21; Puecher et al. 21); sme were imprtant cereal 1981), but these genera are nw cnsidered distantly related crps in the past (Schlz and Ms 1994); and many are (ciaytn and Renvize 1986; Sreng et al. 2). Phylgeinvasive weeds (e.g., Ainuche et al. 1999; Nvak and Mack (i analyses f chlrplast DNA restrictin site variatin 21; Ogle et al. 2). Brmus is distinguished frm ther NA sequence data indicate that Brmeae are the sister grass genera by the cmbinatin f several mrphlgical gp f Triticeae (e.g., Davis and Sreng 199; Catalán et characters, including: leaf sheath margins that are cnnate j jjilu et al. 1999; Hsia et al. 1999; Sreng and fr mst f their length; awns that are almst always sub- Davis ' GPWG 2 D apically inserted; hairy apical bilabiate appendages f the vary; and simple starch grains (Wagnn 1952; Smith 197). Taxnmy and Classificatin Phylgenetic Psitin Brmus is a taxnmically difficult genus with a cmplex nmenclatural histry (see Wagnn 1952, Smith 197, and The eastern Asian genus Littledalea Hemsl., with three Aced and Llamas 1999 fr cmprehensive reviews), and species, was believed by Stebbins (1981) t be the clsest many species are difficult t distinguish due t their high living relative f Brmus; tribe Brmeae currently cmprises degree f mrphlgical similarity. As with many ther genthese tw genera (Smith 197; Claytn and Renvize 1986; era f grasses, many species are plyplids, and hybridiza- Tsvelev 1989; Grass Phylgeny Wrking Grup [GPWG] tin is believed t have played an imprtant rle in the ev- 21). Hwever, preliminary plastid sequence data indicate lutin f many species in the genus (Stebbins 1981). The

2 VOLUME 2 Mlecular Phylgenetics f Bimus 451 cmplexity f Brmus is exemplified in the mre than 12 taxa that have been described, accrding t the Internatinal Plant Names Index (24). The mst recent estimates f the number f species in the genus are 16 (Aced and Llamas 21) and 142 (Claytn et al. 22 nwards), althugh estimates have ranged frm arund 1 (Guld and Shaw 198) t 4 (Sderstrm and Beaman 1968). Several species cmplexes have been the subject f recent taxnmic investigatins (e.g., Schlz 1981; Naranj et al. 199; Sales and Smith 199; Sales 199, 1994a; Smith and Sales 199; Zajac 1996<, b; Allisn et al. 21; Bacic and Jgan 21; Petersn et al. 22; Spaltn 22a; J. M. Saarela and P. M. Petersn unpubl. data), and new taxa cntinue t be cllected and described (e.g.. Smith 1985a; Veldkamp et al. 1991; Aced and Llamas 1997; Schlz 1997, 1998; Petersn and Planchuel 1998; Bmble and Schlz 1999; Hlmström and Schlz 2; Spaltn 21; J. M. Saarela and P M. Petersn unpubl. data). Because f its large size, taxnmic cmplexity, and wide gegraphic range, n cmprehensive wrldwide treatment f all species in Brmus exists, but many flristic treatments and keys f Brmus have been published fr varius gegraphic regins in the New Wrld (e.g.. Shear 19; Wagnn 1952; Mitchell 1967; Sderstrm and Beaman 1968; Pint-Escbar 1981, 1986; Matthei 1986; Allred 199; Pavlick 1995; Gutiérrez and Pensier 1998; Planchuel and Petersn 2) and the Old Wrld (e.g., Veldkamp et al. 1991; Förde and Edgar 1995; Chen and Kuh 2; Spaltn 22 ), 24). Genetic variatin within and amng many species has been studied using data frm iszymes (Kahler et al. 1981; Ainuche et al. 1995, 1999; Oja 1998, 1999, 22a, b, 27; Bartlett et al. 22), as well as an array f DNA-based mlecular techniques, including RAPDs and AFLPs (Ferdinandez et al. 21; Massa et al. 21; Puecher et al. 21; Ferdinandez and Culman 22) and micrsatellites (Green et al. 21; Ramakrishnan et al. 22). A physical map f the chlrplast genme has been cnstructed fr ne species, B. inermis (Pillay 199). The infrageneric classificatin f Brmus has received cnsiderable study. The genus has been variusly split int several grups that have been recgnized as sectins, subgenera, r generic segregates (Table 1). Smith (197) reviewed the mrphlgical characteristics and nmenclature f the cmmnly recgnized grups in the genus, and accepted five distinct sectins, characterized by minr differences in the spikelets. Using data frm crssing experiments, Stebbins (1981) recgnized seven subgenera (althugh ne, Bissiera, is nt validly published at this rank) based n their mrphlgical distinctiveness and the apparent high degree f genetic divergence amng them. He argued that the subgenera f Brmus are t distinct t be treated as sectins, since they seemed mre distantly related t ne anther than are several ther genera f grasses. Other authrs believe that these grups are sufficiently distinct t be regarded as genera (e.g., Tsvelev 1976). N taxnmic cnsensus exists, and infrageneric taxa in Brmus are recgnized currently as distinct genera (e.g.. Catalán et al. 1997; Green et al. 21; Spaltn 22 >, 24), subgenera (e.g.. Aced and Llamas 1999), r sectins (e.g.. Smith 1985.; Pavlick 1995; Planchuel and Petersn 2). The sectinal classificatin f Smith (197) has been fllwed by mst recent Nrth American authrs, and is emplyed here, incrprating later md- ificatins by Smith (1985a) and Schlz (1998); all species mentined belw are treated as species f Brmus. Each sectin f Brmus can be identified using a cmbinatin f several mrphlgical characters, including the number f nerves n the first and secnd glumes, spikelet shape and cmpressin, and lemma and awn mrphlgy (Table 2). Additinal data frm embry mrphlgy (Ksina 1996), flral micrstructures (Ksina 1999), micrmrphlgy f the lemmas and paleas (Aced and Llamas 21), and anatmy (Aced and Llamas 1999) have recently been cllected t aid in the infrageneric classificatin. Insights btained frm these studies generally agree with the classificatin schemes based n macrmrphlgical evidence. Sectin Brmpsis is the largest sectin, cmprising apprximately 6 species that ccur naturally in Eurasia, Africa, and Nrth and Suth America, and thus is represented in all regins where brme grasses are native (Stebbins 1981; Armstrng 1991). The sectin includes diplids, tetraplids, hexaplids, ctplids, and pentaplids (Stebbins 1981). Sectin Brmpsis cmprises at least tw gegraphically, mrphlgically, and cytlgically distinct grups. Nrth American taxa, and the B. ramsus cmplex frm the Old Wrld, are lsely tufted (nnrhizmatus), shrt-lived perennials r biennials (except B. texensis (Shear) Hitchc, an annual) with small anthers and large chrmsmes, and the majrity are diplids (Wagnn 1952; Armstrng 1981, 198, 1991; Stebbins 1981). Old Wrld taxa and B. pumpellianus, which ccurs in Nrth America and the Old Wrld, are densely tufted r rhizmatus, lng-lived perennials with large anthers and smaller chrmsmes, and the majrity are plyplids (tetra-, hexa-, ct-, and decaplids) (Wagnn 1952; Armstrng 1981, 198, 1991; Stebbins 1981). Armstrng (198, 1991) suggested that these tw grups might have separate evlutinary histries, based n difficulties in crssing Nrth American and Eurasian taxa, and nted that valid names are available at sectinal rank fr each f these grups if such recgnitin becmes apprpriate. Cytlgy and evlutinary relatinships f the Suth American species are prly knwn (Stebbins 1981). Sectin Brmus cmprises diplid and tetraplid annual species native t Eurpe and Asia. One species, B. arenarius Labill., is thught by sme authrs t be the nly native Brmus species in Australia; thers believe the species is intrduced there (e.g., Stebbins 1981). Many species are invasive and widely distributed in ther regins f the wrld. Fr example, the 11 species f sect. Brmus that ccur in Nrth America are all intrduced (Pavlick 1995). Species in the sectin are mrphlgically similar (e.g.. Smith and Sales 199; Oja et al. 2), and several subsectinal classificatins have been prpsed (Smith 1972). The tetraplid species in sect. Brmus are believed t be allplyplids (Stebbins 1981), and their putative intrasectinal rigins have been elucidated using serlgy (Smith 1972), allzymes (Ainuche et al. 1995; Oja 1998), and DNA sequence data (Ainuche and Bayer 1997; Ainuche et al. 1999). One grup f tetraplid species, the B. pectinatus cmplex, is believed t be f hybrid rigin between sects. Brmus and Genea (Stebbins 1956, 1981; Schlz 1981). Sectin Ceratchla cmprises 1 16 perennial species native t Nrth and Suth America. All taxa in this sectin are plyplids (ct-, hexa-, and 12-plid) (Stebbins 1981;

3 452 Saarela, Petersn, Keane, Cayuette, and Graham ALISO Pavlick 1995). Species bundaries in sect. Ceratchla are uncertain due t hybridizatin and mrphlgical intergradatin, which have resulted in varius taxnmic treatments (e.g., Sderstrm and Beaman 1968; Stebbins 1981; Pavlick 1995; Planchuel and Petersn 2). Sme species cmplexes in the sectin have recently been revised. Based n genetic and mrphlgical studies f six hexaplid and ctplid species frm Patagnia, Massa et al. (21, 24) distinguished nly tw mrphlgically and genetically distinct taxa, which they treated as tw species. Similar revisinary wrk is necessary t characterize mrphlgical and mlecular variatin amng Nrth American taxa f sect. Ceratchla. Sectin Genea cmprises diplid, tetraplid, hexaplid, and ctplid annual species native t the Mediterranean, suthwestern Asia, and nrthern Eurpe. Several species are invasive (e.g., cheatgrass [B. tectrum L.], ripgut grass [ß. diandrus], and red brme [B. madritensis subsp. rubens\) and have becme widely distributed far beynd their native ranges (e.g., Pavlick 1995). Species in the sectin are highly variable mrphlgically, and many taxa have been prpsed. Recent revisinary wrk has reduced the number f species t five, including several infraspecific taxa (Sales 199, 1994a). Sectin Genea is thus the nly gegraphically widespread sectin f Brmus that has received mngraphic-level taxnmic attentin. Based n this taxnmic framewrk. Sales (1994 >) prpsed hyptheses fr the rigins f taxa and patterns f adaptive radiatin that have ccurred within the sectin. Iszyme data have indicated that the three diplid species f sect. Genea are putative dnrs f genmes in the rigins f the plyplid species in the sectin (e.g., Oja 1998, 22fc, c). The remaining sectins in Brmus (Bissiera, Nebrmus, Nevskiella, and Triniusia) are individually small, but cntribute substantially t mrphlgical variatin in the genus as a whle (Table 2). Sectin Nebrmus cmprises tw annual hexaplid species native t the Pacific casts f Nrth and Suth America (Matthei 1986; Pavlick 1995). Sectins Nevskiella (diplid; Armstrng 1991) and Bissiera (diplid [Smith 1972] r tetraplid [Oja and Jaaska 1998]) are bth mntypic, while sect. Triniusia cmprises tw diplid species (Schlz 1998); species in these three sectins are all annuals native t Asia and the eastern Mediterranean. Sectins Bissiera and Triniusia were included within sect. Brmus by Smith (197). Bissiera was treated as a subgenus by Stebbins (1981; Table 1), but he included Triniusia in subgen. Brmus. Bth taxa were recgnized as sectins by Smith (1985a) and Schlz (1998), respectively (Table 1). Phylgenetic Relatinships Past attempts t understand phylgenetic relatinships in Brmus amng species and infrageneric taxa have been based largely n data frm mrphlgy (e.g.. Shear 19; Wagnn 1952), karylgy (including chrmsme number, satellite type, chrmsme size, and DNA quantities) and hybridizatin experiments (e.g., Stebbins and Tgby 1944; Stebbins 1947, 1956, 1981; Schulz-Schaeffer 196; Wiltn 1965; Armstrng 1975, 1981, 198; Kzuharv et al. 1981; Naganwska 199a, b), serlgy (Smith 1969, 1972), and allzymes (e.g., Oja 1998, 27; Oja and Jaaska 1998). Chrmsme numbers, plyplidy, genme size, karytypes, c-banding, crss-cmpatibility, and genme hmlgy within Brmus have been summarized by Armstrng (1991). Five systematic studies have been cnducted in Brmus using data frm DNA, althugh the number f species included in each study was relatively limited. Pillay and Hilu (199, 1995) studied chlrplast DNA restrictin site variatin amng 2 Brmus species, and identified tw majr clades: ne cmprising sects. Ceratchla and Nebrmus, the ther cmprising sects. Brmpsis, Brmus, and Genea. Species f sect. Brmpsis ccurred in three different lineages, indicating that this taxn is nt mnphyletic, but the data did nt supprt the New Wrld/Old Wrld split hypthesized by Armstrng (198) n the basis f mrphlgy and chrmsme pairing data. Sectins Brmus and Genea were nt mnphyletic; species frm bth sectins were intermixed in a single clade. Jachimiak et al. (21) used RAPD data t prtray relatinships amng nine species representing fur infrageneric taxa in Brm.us frm the New and Old Wrld. Based n a phenetic analysis, they identified tw distinct clusters: ne cmprising sect. Ceratchla and the ther cmprising sects. Brmpsis, Brmus, and Genea. Hwever, because f the small sample size, and the lw level f mlecular divergence detected, they were unable t make definitive statements regarding relatinships in Brmus. Ainuche and Bayer (1997) and Ainuche et al. (1999) used sequence data frm the internal transcribed spacer (ITS) regin f nuclear ribsmal DNA t study the phylgeny f sect. Brmus. Based n an analysis f 22 species frm sect. Brmus (including sect. Triniusia) and three species frm ther infrageneric grups, they fund sect. Brmus t be mnphyletic. They als studied the rigin f sme tetraplid species in the sectin. Little sequence hetergeneity was detected within tetraplid species, and they fund that the inclusin f alltetraplid taxa with diplid taxa did nt change the underlying tplgy f the trees btained, cmpared t trees btained frm analyses f the diplid taxa alne. T further characterize phylgenetic relatinships in Brmus S.I., we btained new sequence data frm the chlrplast trnl (UAA) intrn, the rapidly evlving '-end f the chlrplast ndhp gene, and the nuclear ribsmal ITS regin, frm 46 exemplar Brmus species that represent a large prprtin f the gegraphical and mrphlgical diversity in the genus. The specific bjectives f this study were t use DNA sequence data t (1) test the mnphyly f the currently recgnized infrageneric grups in Brmus, and (2) determine phylgenetic relatinships amng infrageneric grups and species. Taxn Sampling MATERIALS AND METHODS Exemplars frm each f the currently recgnized sectins in Brmus were included in this study, except fr the tw mntypic sectins, Bissiera and Nevskiella. Attempts t extract DNA frm a herbarium specimen f B. gracillimus Bunge (sect. Nevskiella) were unsuccessful, and material f B. pumili (Trin.) P. M. Sm. (sect. Bissiera) was nt available. Table lists the species sampled (fllwing the classificatin schemes f Smith 197 and Schlz 1998), surces

4 VOLUME 2 Mlecular Phylgenetics f Bimus 45 Table 1. Summary f infrageneric classificatins and generic segregatins f Brmus fllwing Smith (197), Tsvelev (1976), and Stebbins (1981). Equivalent circumscriptins are aligned hrizntally. Indented names were treated by the authr as synnyms f the taxn abve. Sectins (Smith 197) Brmpsis Dumrt. (as sect. Pnigma Dumrt.) Brmus Triniusia (Steud.) Nevski" Bissiera (Höchst, ex Steud.) P. M. Sm.'' Ceratchla (P. Beauv.) Griseb. Genea Dumrt. Nebrmus (Shear) Hitchc. Nevskiella (Krecz. & Vved.) Turnay 'Given sectinal status by Schlz (1998). ' Given sectinal status by Smith (1985a). = Outside gegraphic range f Tsvelev (1976). Subgenera (Stebbins 1981) Festucaria Gren. & Gdr Brmus Triniusia (Steud.) Pénzes Bissiera nm. inval. Ceratchla (P. Beauv.) Hack. Stenbrmus Hack. Nebrmus Shear Nevskiella (Krecz. & Vved.) Krecz. & Vved. Genera (Tsvelev 1976) Brmpsis (Dumrt.) Furr. Brmus L. Triniusia Steud. Bissiera Höchst, ex Steud. Ceratchla P. Beauv. Anisantha C. Kch Trisetbrmus Nevski Nevskiella Krecz. & Vved. f materials, vuchers, and GenBank accessin numbers fr the DNA sequences. One individual f each species was examined, except fr B. madritensis subsp. rubens, fr which three individuals were sampled, and B. anmalus, fr which tw individuals were sampled. Samples were btained frm silica-gel-dried leaf material frm field cllectins, frm plants grwn in the greenhuse frm seed btained frm the Western Reginal Plant Intrductin Statin (United States Department f Agriculture, Pullman, Washingtn, USA) and Plant Gene Resurces f Canada (Saskatn Research Centre, Agriculture and Agri-Fd Canada, Saskatn, Saskatchewan), and frm herbarium specimens. All taxnmic identificatins were cnfirmed using the available wrld taxnmic literature f Brmus. Outgrup taxa frm tribes Triticeae and Peae were chsen based n previus mlecular investigatins f the grasses (see Catalán et al. 1997; GPWG 21). The Brmus and Festuca breviglumis sequences used in this study are new. Sequence data fr Hrdeum vulgäre and Triticum aestivum were btained frm GenBank. DNA Extractin, Amplificatin, and Sequencing Ttal genmic DNA was extracted using a mdified cetyltrimethylammnium brmide (CTAB) methd (Dyle and Table 2. Number f species, mrphlgical characteristics, and native gegraphic distributin f sectins f Brmus. The classificatin fllws Smith (197, 1985a) and Schlz (1998). Sectin 1st 2nd N. glume glume species nerves nerves Spikelet shape Lemmas Native gegraphic distributin Bissiera Brmpsis Brmus Nebrc Nevskiella Triniusia Linear-lancelate t blng; terete ca. 6 1 () (5) Narrw, lancelate; terete Ovate t vate-lancelate; terete t slightly cmpressed Ceratchla Ovate r vate-lancelate; strngly cmpressed Genea 6 1 Cunéate, wider at tp -5 5 Narrwly elliptic Ovate-lancelate t cuneifrm, wider abve; terete t slightly cmpressed 5 9 Ovate t lancelate; cmpressed Oblng; awns 5 9 Runded r slightly keeled; awn single, usually shrter than length f lemma, rarely absent Runded; awn single, equaling r slightly exceeding length f lemma, rarely absent Strngly keeled; awn single, shrt, ften absent Narrw and elngate; awns single, less than times length f lemma Deep apical sinus and 2 lng, narrw teeth; awn single, lnger than length f lemma, geniculate Runded; awn single, 4 6 times length f lemma Runded: upper lemma with awns; irregular apical ntches Asia, E Mediterranean Eurasia, Africa, N and S America Eurpe, Asia N and S America Mediterranean, SW Asia, N Eurpe Pacific casts f N and S America Central Asia, Iran, Afghanistan E Mediterranean, SW Asia

5 454 Saarela, Petersn, Keane, Cayuette, and Graham ALISO s rt rt 55 M C c c ' CO < ci - fû a ci O c C cd ID U O" i>5 < z "El " < Í-I xj 'M c OJ cs Í-I 1 e (U ID tó _2 : a (U c II 1 w ÎJ LH K (U Aá u in ON \Q r ) O O Q \ \ y > rn rn m r m r > >H > Í" >H Í" < < < < < < (N m ID H H H,J, (N (N (N (N (N (N O O O O O O O O O O O O O NO >.D NO > ) MS MS MS MS MS MS > MS \ MS \ MS MS rr\ n n Ci n ri n r", n ri m m ri n r ri n Í" " < < Í" >H Í" < < < >H Í" < < " Í" < < >H < Í" < Í" Í" < < Í" Í" >H Í" < < < < NO ON H r~ (N n un NO t- ON O (N O m m ND un in ND un NO NO NO NO NO ND NO NO l-~ -~ ON ON ON ON ON ON ON ON ON ON ON ON ON ON ON ON ON ON -~ r~ -~ t 1 1 t t 1 t t ND NO ND NO ND ND NO NO NO NO NO NO NO NO NO NO NO NO NO Oi Oi Oi Oi Oi Oi n n n n n n O n n n n n m >i >:i >:i < < < >i >:i >i >:i < < < < >:i >i < < >i >i >i < < < >i >i >i >i >i < < < < < >i < >i < un NO O \ H r (N n 2; un IS ON ON ON Q\ ON ON ON ON S ON ON r r r r~ r-- r r r~ r r r r NO NO NO NO y:; NO NO NO NO NO NO NO n n Oi n (Ti n n n n n ", n Í" Í" " < < < Í" >H Í" Í" < < < < Í" Í" < < Í" Í" Í" < < < nunnotono i-~i-~tiiti ONONONONONONONON ronofnnunnrono QN(N(N(N(NuncN(N(N(N(N(Nnn ONONONONONONONONONONONONONONONONON NDNDNONDNDNONDNDNONDNDNONDNDNONDND r, r, r, r, r r c r r c r r c r, r, r, r, ON (N (N O O NO NO i n m, & ON ON 1 1 NfJ NfJ m, m, >i >i < < un r ON r ON r r NT) NT) m, m, " Í" < < PQ c -a c ca E' cd (U (U C w cd & 1 (U cd CO ' çr's S s 1) Cd Í-I i Td -O r/ (U s-i H P S : (U d a. 1) ö C) II w ph w C) CÄ tó -n C) n cd cd ö. < r m t/) LJ 1) ai> ns (1). Ë S ö r/1 ON C/5 c c ce ce - - iïj,, O Q r/1 (1 ri n < «1 H K Ö ON < ON s; n c tu,<a Ci = a. 5 ON ON.&.& eu 2 (N Ë Ë n (N f2f2!-i a. Ö Ö il) T1 < X X n in (D (U Xi cd cd U cd O n Ö >i (U (N IT) (D Ai f2 t B => ; K Ë. NO Un Q, a. G M Q S S t b > Q K Un \f ON? r K Un K Un S K &> Ä a U Q, ON ON O (N (N (N /, u u la S en Cd '. cd ri 1 S (U 1 U u < cd u L-i C/5 P "a S Q " "ñ >a» tu 5Î Tl K ON K M- ' n 1 n «1 ' n O 8 Un Un IN Un I "-1 " -N Un Un? S" s- tí S" O n en n «j en,> Í" Í" & Í" Q, Q, n fí 'if' < tó < < Td cd i cd < < (/) '6 t/i f n t/i (/) n P P U U P P U HH.2 N O j U pq P C/5 _ 2-2 A OO IN OO < Q i Un S9 ON a 5J 1 S a la < Í < ÍP H u CM H K 5 nsi K K < < OO IN < Un Un Un " = c J c C\»J f5 s fî!ü f5 i 2 ë t s 1 a S,a.>"..>" s,q 1 Q, Ü a. Q, i«; 5 Ü =a rt rt a- S - G _ y < U > - G "ri n < pq p D D S P G M S D, I > f M :: 8 ON <; N un U P : S : n f) ë Td cd u < íá Ë s u s ft se Q D OJ il f-i -n (ij r) 11 f2 (U O 's Ü ) $ X 1 Q & S Í S- c s p- c c J = X, 5 c S Cl c a s -X G -Cj Ü 1) ««cq «CQ a -a " ;S g- -O Pi 5 - "S ', p S a a >a c c a Q a G U N bjo 4' ), - 1A ö es Í - 'Ö O "1 - [/5 Î' G s-s s: y, I D. D: D. D. D. Q, C D CQCqCQ cqcqcakdkdkdkdk CQ G U

6 VOLUME 2 Mlecular Phylgenetics f Bimus 455 ri (N t t O (N, ( -H m >.D m ri (N C<1 ri r r, C<-i m r, C<1 O O O O O O O O O O O O O O O O MS VJ > VJ y >.D \D \D \ \D \ \ \ > MS ri ri r ri m C<1 ri ri r ri ri r ri r r ri r ri í" >H >H >H >H Í" >H í" í" >H í" >H >H í" >H >H í" í" < < < < < < < < < < < < < < < < < < ND S g S n C> >H (N U ON t-~ 1 1 (N -H (N un t NO NO NO ON O \ ON -~ ON ON ON ON ON ON ON ON O \ ON ON ON O ON ON ON ON ON ON ON 1 1 t 1 t- 1 1 t t t 1 t t 1 t -~ NJ ND NO ND NO ND \ NO NO NO NO NO NO NO NO NO n n n i n n i n n i O n i O n i O n n >:i >i >i >i >i >i >:<>:'>:'>:' >:i >i >i >i >i >i >i >i >i < < < < < < < < < < < < < < < < < < < X X \ (N NO O r~ c<i r<i ir n in i n O n lo n Tf (N in Nc r H (N ON ON s \ C\ ON ON ON Ch ON ON ON ON ON ON ON ON ON r r r r r r r r r r r~ r r r~ r~ i-~ r~ r >H >H >H >H í" í" í" í" >H >H >H >H < < < < < < < < < < < < < < < < < < >.D n " \D \ n n \c y ri m >.D n í" O ND n n n n NO n í" NO ND n n NO n í" NO ND n n NO n í" ND n í" (N n ON ON :«9î r -i un >H -H fc <; N <; < in --: G < < H H J J "N < < > rri CN CN S C s< a a ) hi ÍÍ, iïj S < í>í CO 5; si s? Ä s; a Q, CO iïj í>í C/5 a, hi hi t vj t c > c s; < < < H K H H J ON J J 1 < < a Un ". S Cs Q!ü in 5 s: s; S s< a i a Q ) ÜJ 5j îj i a; i i«; à; îj ON D- 5 CO u ON n (N M 1/5 > p< S n 2 vn S < r = Í M pq P S < 8 s P< il ü5 tó ô U P rt- in i> in N O NO U U O. Si C C/5 K < tó L-i O & B r-i 'Z P I S ON?: n -= S «2 " ï cq P< HH (N.2 (N bj (U U u un., c/5., (U U (U Aá tó S 9- S G M C X U c G j= H J -S g g.s Q. a es S ï! >a Ö s a Q. s ü ÍJ CQ D (U CQ cq cq C/5.a S tí K cq cq cq cq > Ü s S cq J s cq -S s _ -Cl O _ = cq cq - M fc. tê

7 456 Saarela, Petersn, Keane, Cayuette, and Graham ALISO Dyle 1987) with 2% ß-mercaptethanl added t each extractin. DNA extracts and PCR amplificatins were purified using a QIAGEN PCR Purificatin Kit (QIAGEN, Santa Clarita, Califrnia, USA) fllwing manufacturer's instructins. The trnl (UAA) intrn was amplified and sequenced with primers develped by Taberlet et al. (1991). The regin we refer t as ITS, which includes tw spacer regins, ITSl and ITS2, and the 5.8S rdna lcus, was amplified and sequenced using primers published by White et al. (199), Hsia et al. (1994), and Blattner (1999). The '-end f ndhf was amplified and sequenced using primers designed by Olmstead and Sweere (1994) and Graham et al. (1998). Amplificatin reactins cnsisted f 26.5 [ú sterile water, 5 ú lox buffer, 4 (ji,l 1 mm dntps, (ji,l 25 mm MgClj, 5 jjul f each 5 pml/(ji,l primer, 1 ú template DNA, and.5 ú Tag DNA plymerase (1 unit). The thermal prfile was: 1 cycle f min at 94 C; 5 cycles f sec at 94 C, 1 min at 42.5 C, and 2 min at 72 C; and 1 cycle f 5 min at 72 C. Sequencing prducts were generated using a BigDye Terminatr Cycle Sequencing Ready Reactin Kit (Applied Bisystems, Fster City, Califrnia, USA) with 5 ng f template DNA and the fllwing thermal prfile: 25 cycles f 1 sec at 96 C, 5 sec at 45 C, and 4 min at 6 C. Fr each sample, ne r several duplicate sequencing reactins were included using a secnd DNA extract frm the same surce material. Sequencing reactins were analyzed using an Applied Bisystems Prism 77 autmated DNA sequencer. Sequence data were assembled and edited using Sequencher vers. 4.1 (Gene Cdes Crpratin, Ann Arbr, Michigan, USA). Cnsensus sequences were exprted fr each sample and aligned manually using Se-Al vers. 1. alpha 1 (Rambaut 1998) accrding t guidelines utlined in Graham et al. (2). Gaps in the final matrix were cded as missing data. Several inferred insertins/deletins (indels) in the /rnl intrn were scred as binary characters. Alignments were imprted int PAUP* vers. 4.bl (Swffrd 22) fr analysis. All sequence data have been submitted t GenBank (Table ). Phylgenetic Analyses Fr the ITS data set, a heuristic search was cnducted with 1 randm starting trees, tree-bisectin-recnnectin (TBR) branch swapping, and all character and character-state changes equally weighted. A tw-tiered apprach was taken fr the heuristic searches f the cmbined plastid data because an upper limit n the number f mst-parsimnius trees was unattainable with the available cmputatinal resurces and time: (1) 1 independent heuristic searches each with a randm starting tree, saving 1 trees each (MaxTrees set t 1), were perfrmed with the parameters nted abve, and (2) anther heuristic search, with the same parameters as abve, was cnducted, except that the shrtest f the 1, trees frm step 1 were used as starting trees, and MaxTrees was set t 5,. We als implemented the parsimny ratchet (Nixn 1999) using PAUPRat (Sikes and Lewis 21) t search fr shrter trees with the cmbined plastid data set. The incngruence length difference (ILD) test (Farris et al. 1994, 1995) was used t test fr cnflict between the plastid and nuclear data partitins, with MaxTrees set t 5. In additin, trees and btstrap values derived frm analyses f the plastid and nuclear data were cmpared visually t assess the rbustness f tplgical incngruence (e.g., Graham et al. 1998). We cmputed strict cnsensus trees frm all f the mst-parsimnius trees fr bth f the data partitins. We present phylgrams f ne randmly chsen tree frm each f these analyses, and indicate which clades n the phylgrams cllapse in the strict cnsensus trees. Branch supprt was assessed using maximum parsimny btstrap analysis (Felsenstein 1985) frm 5 replicates using the heuristic search ptin, with ne randm starting tree, TBR branch swapping, and MaxTrees set t 5 per replicate. We use weak, mderate, and well supprted in reference t clades having btstrap values f <71, 71-9, and 91-1, respectively. Analyses f ITS Sequences The bundaries f ITSl, 5.8S, and ITS2 fllw Eckenrde et al. (1985), Ykta et al. (1989), and Klsha and Fdr (199). Lengths f ITSl and ITS2 were and base pairs (bp), respectively. The 5.8S rrna gene was 16 bp in length. A small regin f 1 bp (psitins ) in ITSl was difficult t align acrss taxa, and was excluded frm all analyses. The ITS data matrix, withut excluded sites, was 66 aligned nucletides in length. Of these characters, 82 were cnstant, 224 were variable, and 125 (2.6%) were parsimny infrmative. Amng the ingrup taxa, 47 characters were cnstant, 169 were variable, and 14 (17.2%) were parsimny infrmative. The heuristic searches f the ITS data set recvered 449 mst-parsimnius trees (tree length = 8 steps; cnsistency index [CI] =.71; retentin index [RI] =.826). Several clades receive gd btstrap supprt (Fig. 1). The mnphyly f the genus Brmus is mderately supprted (btstrap supprt value [BV] = 75%). Sectin Brmpsis is nt mnphyletic. A well-supprted clade (BV = 99%) cnsisting f tw Nrth American Brmpsis species, B. attenuatus and B. dlichcarpus, is the sister grup f the rest f the genus, the latter clade with BV = 1%. The next majr split in Brmus is between a well-supprted clade (BV = 1%) f fur Suth American species f sect. Brmpsis (B. lanatus, B. mdestus, B. pellitus, and B. pflanzii) and all remaining species f Brmus. The latter clade is weakly supprted (BV = 59%). A large and well-supprted clade (BV = 96%) includes five species f sect. Brmpsis f Eurasian rigin (ß. erectus, B. inermis, B. krtkyi, B. pumpellianus [which is als native in the New Wrld], and B. riparius), ne species f sect. Brmpsis frm Suth American (B. brachyanthera), and the mnphyletic sects. Ceratchla, Genea, and Nebrmus (BV = 92%, 1%, and 94%, respectively). The Eurasian representatives f sect. Brmpsis are nt united in a single clade. A secnd large, weakly supprted clade (BV <5%) cntains the remaining Nrth American species f sect. Brmpsis, B. ramsus (a species classified in sect. Brmpsis frm the Old Wrld), and sects. Brmus and Triniusia (Fig. 1). Several well-supprted relatinships are evident amng

8 VOLUME 2 Mlecular Phylgenetics f Bimus , 59 6 I anmalus 1 laevipes ~ ciliatus 81 - kalmii - latiglumis Brmpsis nttwayanus - pubescens " anmalus 2 grandis exaltatus scparius n t- ' apnicus Brmus 1 p2' ifl 5ÖI pectinatus r,.,, danthniae 94 pseuddanthniae Triniusia 51 texensis t: frndsus suksdrfii lanatipes prteri Brmpsis pseudlaevipes r mucrglumis 9V~~ richardsnii ramsas J>rachyanthera Brmpsis 1 marginatus carinatus 75 clratus striatus Ceratchla suhvelutinus cathartic US cebadilla herteranus gunckelli Nebrmus diandrus 1 r ' ' IJ WÍÍ) madritensis subsp. ruhens 1 madritensis subsp. rubens G enea 67 /./ ' madritensis subsp. rubens J erectus riparius inermis Brmpsis 55 ï pumpellianus krtkyi 98 I lanatus 1 I I jt7/za«z// I [~~ mdestus 72" pellitus Brmpsis - attenuatus dlichcarpus Triticum aestivum 5 changes Hrdeum vulgäre Festuca breviglumis Fig. 1. Phylgram f ne f 449 mst-parsimnius (MP) trees fund using data frm the internal transcribed spacer (ITS) regin f nuclear ribsmal DNA. MP trees are each 8 steps, with a CI f.71 and RI f.826. Btstrap supprt values greater than 5% are indicated. Ndes that cllapse in the strict cnsensus tree are indicated with an arrw. Sectins in Brmus (fllwing Smith 197 and Schlz 1998) are indicated t the right f the tree. Native gegraphic distributins f species in sect. Brmpsis are indicated: light shading = New Wrld; dark shading = Old Wrld; bxed species {B. pumpellianus) = New and Old Wrld.

9 458 Saarela, Petersn, Keane, Cayuette, and Graham ALISO sme species f sect. Brmpsis frm Nrth America. Sectin Triniusia is mnphyletic (BV = 94%), and is part f a well-supprted clade (BV = 1%) that therwise nly includes representatives f sect. Brmus. Analyses f Plastid Sequences The sequence data btained fr the '-end f ndhf crrespnd t psitins f ndh in Oryza sativa L. (GenBank accessin n. NC12). The sequenced prtin was 662 bp in length in all taxa, except fr B. grandis, which had a six bp insertin. The unambiguusly aligned ndhb matrix was 668 bp lng; 576 nucletides were cnstant, 92 were variable, and 44 (6.5%) were parsimny infrmative. Amng the ingrup taxa, 616 characters were cnstant, 52 were variable, and 1 (4.6%) were parsimny infrmative. The ir«l intrn ranged in length frm 568 t 586 bp. Several indels were present in the final data matrix; three f these were phylgenetically infrmative and were cded as binary characters in the analysis. Tw regins f 18 bp (psitins ) and 11 bp (psitins ) were hmplymer repeats f variable length that were difficult t align; these regins were excluded frm all analyses. The aligned rr«l intrn matrix (including binary characters but withut excluded sites) cnsisted f 646 characters; 578 were cnstant, 68 were variable, and 28 (4.9%) were parsimny infrmative. Amng the ingrup taxa, 61 characters were cnstant, 6 were variable, and 2 (.5%) were parsimny infrmative. N sequence data were btained frm either plastid lcus fr B. mdestus and B. nttwayanus, and fur species are represented slely by data frm the ir«l intrn (Table ). The heuristic search f the cmbined plastid data recvered 5, mst-parsimnius trees (tree length = 218 steps; CI =.817; RI =.882). In the mst-parsimnius trees there is mderate phylgenetic structure that is supprted by btstrap analysis (Fig. 2). The mnphyly f the genus Brmus is well supprted (BV = 99%). Taxa classified in sects. Brmus, Genea, and Triniusia frm a well-supprted mnphyletic grup (BV = 91%), but nne f the three sectins is mnphyletic. Brmus pectinatus (sect. Brmus) and B. diandrus (sect. Genea) frm a well-supprted clade (BV = 1%) that is weakly supprted (BV = 56%) as the sister grup f B. madritensis subsp. rubens (sect. Genea). The ther species f sect. Brmus and species f sect. Triniusia are mixed in a clade (BV = 86%). Sectin Ceratchla, sect. Nebrmus, and B. brachyanthera (sect. Brmpsis) frm a weakly supprted clade (BV = 62%). Sectin Nebrmus is nt mnphyletic, and the mnphyly f sect. Ceratchla is weakly supprted (BV = 6%). A large clade f 2 New and Old Wrld species f sect. Brmpsis is weakly supprted (BV = 68%). Incngruence Amng Data Partitins The ILD test indicated significant incngruence between the nuclear ribsmal and plastid data partitins (P <.1). Overall, the trees derived frm the nuclear ribsmal data are mre reslved than trees derived frm the plastid data (Fig. 1, 2). There are sme well-supprted clades whse psitins differ substantially amng trees, althugh nt always with strng supprt. Tplgically, the greatest differences between the plastid and nuclear ribsmal trees are the psitins and mnphyly f sects. Brmus, Genea, and Triniusia. In the nuclear trees, species frm sects. Brmus and Triniusia frm a clade, and sect. Genea is well supprted as mnphyletic; a clse relatinship between the tw clades is nt inferred (Fig. 1). In the plastid trees, species frm these three sectins are intermixed in a well-supprted clade (Fig. 2); fr example, B. pectinatus (sect. Brmus) and B. diandrus (sect. Genea) frm a well-supprted clade. Other incngruencies invlve relatinships amng species f sect. Brmpsis (Fig. 2). The plastid trees include species frm the Old Wrld in a weakly supprted clade with sme Nrth American species, while the nuclear ribsmal trees indicate a mre distant relatinship between the Old Wrld (with the exceptin f B. ramsus) and Nrth American species. Because f these pssible instances f intergenmic cnflict, we did nt cnduct analyses f the cmbined nuclear ribsmal and plastid data. DISCUSSION Phylgenetic Utility f the Regins Examined Of the three regins examined, the nuclear ribsmal regin was the mst variable and accunted fr 65.8% f the ttal number f parsimny-infrmative characters (ingrup taxa nly) amng all three data sets. Reslutin (number f bifurcated ndes in the strict cnsensus tree) was greater in the nuclear ribsmal phylgeny cmpared with the plastid phylgeny, prbably because f the greater amunt f variatin in the frmer data set. The least parsimny-infrmative variatin (amng ingrup taxa) was bserved in the ir«l intrn, which accunted fr 14.5% f the ttal number f infrmative characters in all three data sets. Althugh this intrn is cmmnly used fr lwer-level phylgenetic studies, several investigatrs have reprted a paucity f phylgenetically-infrmative characters in it t sufficiently reslve relatinships amng clsely related grass genera and species (e.g., Hdkinsn et al. 22), and a wide variety f ther plant taxa (e.g., Bruneau et al. 21; Klak et al. 2; Shaw et al. 25). The '-end f ndh prvided 19.6% f the ttal parsimny-infrmative variatin (ingrup taxa nly) amng all three data sets, 1.5 times as many parsimny-infrmative characters as the ir«l intrn fr apprximately the same length. The cmplete ndhp regin has been used in several phylgenetic studies f grasses at the familial, subfamilial, tribal, and generic levels (e.g., Clark et al. 1995; Catalán et al. 1997; Spangler et al. 1999; Giussani et al. 21; Ahscini et al. 2). The mre rapidly evlving '-end f ndhv has been used at the genus level in grasses (e.g.. Catalán and Olmstead 2) and ther plants (e.g., Graham et al. 1998; Davis et al. 22; Winkwrth et al. 22; Graham and Barrett 24). The greater level f sequence variatin detected in the '-end f ndh cmpared with the variatin detected in the mre cmmnly used trnl intrn indicates that the frmer warrants cnsideratin fr use in the reslutin f relatinships at similar taxnmic levels in ther grups. Incngruence Between Nuclear Ribsmal and Plastid Data Partitins Significant incngruence was detected between the nuclear ribsmal and plastid data partitins using the ILD test.

10 VOLUME 2 Mlecular Phylgenetics f Bimus V *. 56 N anmalus 1 erectus rrnnrms pubescens anmalus 2 ciliatus pseudlaevipes pumpellianus ramsus xaltatus 95 \j frndsus laevipes I lanatipes Im I grandis ' mucrglumis inermis kalmii latiglumis prteri richardsnii texensis t krtkyi suksdrfii Bwmpsis r scparius 86,_. 6 r japmcus pseuddanthniae danthniae 1 diandrus pflanzü "~ lanatus 85 pellitus ' dlichcarpus attenuatus pectinatus madritensis subsp. rubens 1 madritensis subsp. rubens madritensis subsp. rubens 2 Brmpsis brachyanthera marginatus clratus cebadilla striatus carinatus subvelutinus - catharticus gunckelli berteranus 6 Triticum aestivum ~ Hrdeum vulgäre Brmus Triniusia Genea Brmus Brmpsis Ceratchla Nebrmus Genea 5 changes Festuca breviglumis Fig. 2. Phylgram f ne f 5, mst-parsimnius (MP) trees fund using cmbined plastid data frm the i;«l intrn and the '- end f ndh. MP trees are each 218 steps, with a CI f.817 and RI f.882. Btstrap supprt values greater than 5% are indicated. Ndes that cllapse in the strict cnsensus tree are indicated with an arrw. Sectins in Brmus (fllwing Smith 197 and Schlz 1998) are indicated t the right f the tree. Native gegraphic distributins f species in sect. Brmpsis are indicated: light shading = New Wrld; dark shading = Old Wrld; bxed species {B. pumpellianus) = New and Old Wrld.

11 46 Saarela, Petersn, Keane, Cayuette, and Graham ALISO The ILD test is cmmnly emplyed by systematists t examine cngruence amng data partitins, but there is grwing evidence (e.g., Yder et al. 21; Barker and Lutzni 22) that the test can be misleading and shuld nt be used t determine data cmbinability. Thus, we als visually cmpared trees derived independently frm the plastid and nuclear data partitins fr regins f incngruence, and fund that each cntained sme mderately t well-supprted clades whse cmpsitin and psitin differed. Because f this pssible intergenmic cnflict, we did nt cnduct analyses f the cmbined plastid and nuclear ribsmal data. Incngruence amng trees is nt uncmmn in phylgenetic studies that emply multiple gene regins, particularly when the data are frm different genmes (e.g., Hardig et al. 2; Les et al. 22). Althugh ften viewed as a hindrance t reliable phylgenetic estimatin, incngruence can ptentially prvide insight int past evlutinary events, such as hybridizatin, intrgressin, and lineage srting (Wendel and Dyle 1998). Our data suggest that sme f these phenmena may have been invlved in the evlutinary histry f Brmus. Hwever, it is difficult t infer the exact evlutinary prcesses that have led t the differing gene trees, as reticulate patterns f evlutin are difficult t study in a cladistic framewrk, and gene trees inferred frm mre than tw linkage grups are ideally required. Nnetheless, previus studies have indicated that hybridizatin, allplidy, and intrgressin may have been prminent in the evlutin f many Brmus species and sectins (reviewed by Stebbins 1981 and Armstrng 1991). The implicatins f the different gene histries detected here in understanding the evlutinary histry f infrageneric grups in Brmus are discussed belw. Clarificatin f the cntributin f these prcesses t the evlutinary histry f Brmus will require better-supprted phylgenetic trees frm multiple genetic linkage grups. Phytgeny and Classificatin In all analyses there is mderate t strng supprt fr the mnphyly f the genus Brmus s.l., based n current utgrup and ingrup taxn sampling. These findings agree with Ainuche and Bayer's (1997) study f sect. Brmus, and brader studies f grass phylgeny that included several species OÎ Brmus s.l. (e.g.. Catalán et al. 1997; Hsia et al. 1999), which all identified Brmus s.l. as a mnphyletic taxn. Sectins Brmus, Genea, and Triniusia. The mlecular evidence indicates that species f sect. Triniusia are nested within a clade that includes species f sect. Brmus (Fig. 1, 2). Sectin Triniusia was riginally circumscribed as a mntypic sectin that included B. danthniae, characterized by three awns n each f the uppermst lemmas f the spikelets (Schlz 1998), but mst authrs have included this species in sect. Brmus (e.g.. Smith 197, 1972; Ainuche and Bayer 1997). A clse relatinship between B. danthniae and B. pseuddanthniae was nt hypthesized until Schlz (1998) bserved that the latter species smetimes has three awns n the uppermst lemmas f its spikelets, and that in prtins f their ranges in the Middle East the tw taxa intergrade. As a result, Schlz (1998) treated B. pseuddanthniae as a subspecies f a plymrphic B. danthn- iae, and recircumscribed sect. Triniusia t include tw mrphlgically similar species and several subspecies {B. danthniae subsp. danthniae, B. danthniae subsp. pseuddanthniae (Drbw) H. Schlz, B. danthniae subsp. rgersii C. E. Hubb. ex H. Schlz, and B. turcmanicus H. Schlz). Schlz's (1998) recgnitin f sect. Triniusia is supprted by iszyme data, which shw B. danthniae t be distinct frm diplid members f sect. Brmus (Oja and Jaaska 1998), althugh serlgical evidence shw B. danthniae t be clsely allied t species f sect. Brmus, including B. pumili (classified currently in sect. Bissiera but ften included in sect. Brmus), a species that als has multiple awns n the uppermst lemmas f its spikelets (Smith 1972). We did nt sample B. turcmanicus, thus we were unable t fully test the mnphyly f sect. Triniusia sensu Schlz (1998). Hwever, ur data cnfirm the clse relatinship hypthesized between B. danthniae and B. pseuddanthniae, and indicate that these species are nested phylgenetically within sect. Brmus (Fig. 1) r perhaps a smewhat brader clade (Fig. 2). These data are in accrdance with the findings f Ainuche and Bayer (1997), wh included B. danthniae in their study f sect. Brmus. Recgnitin f sect. Triniusia renders sect. Brmus paraphyletic; it therefre shuld cntinue t be treated as a synnym f sect. Brmus, as has been dne previusly (e.g.. Smith 197, 1972; Ainuche and Bayer 1997). The distinct mrphlgical characters that separate B. danthniae and its clse relatives frm ther species in sect. Brmus arse frm within sect. Brmus. The tw surces f mlecular evidence are in cnflict with regard t the mnphyly f sects. Brmus and Genea, due t the psitin f B. pectinatus. Sectins Brmus (including sect. Triniusia; see abve) and Genea (based n sampling nly tw f the apprximately five species in the sectin) are each rbustly supprted as mnphyletic in the nuclear ribsmal trees (Fig. 1). Hwever, the plastid trees indicate that B. pectinatus (sect. Brmus) is the sister grup f B. diandrus (sect. Genea; Fig. 2). Species f the B. pectinatus cmplex (nly ne species sampled here), a grup f five tetraplid species that range frm suthern Africa t Tibet and classified in sect. Brmus, are mrphlgically similar t species f sect. Genea, with lemmas that taper tward the apex and paleas whse mrphlgy is intermediate between the tw sectins (Smith 1972; Schlz 1981; Stebbins 1981; Sales 199). A clse relatinship between B. pectinatus and sect. Genea is als supprted by data frm iszymes (Oja 27) and embry structure (Ksina 1996). Based n its mrphlgical intermediacy, Stebbins (1956, 1981) suggested that the B. pectinatus cmplex (represented by B. arenarius in his studies) may be an intersectinal amphidiplid that riginated via a hybridizatin event between species f sects. Brmus and Genea. The cnflicting psitins f B. pectinatus in ur plastid and nuclear ribsmal trees lend supprt t this hypthesis, indicating that the genme dnrs in the rigin(s) f the cmplex were likely frm sects. Brmus and Genea. Sampling f additinal species f the B. pectinatus cmplex, and additinal genetic linkage grups, wuld be valuable, and may prvide further insight int their rigin(s). If B. pectinatus is a species f hybrid rigin that arse after sects. Brmus and Genea initially diversified, and it is excluded frm cnsideratin, then sects. Brmus and Genea are mnphyletic. The mrphlgical characteristics

12 VOLUME 2 Mlecular Phylgenetics f Bimus 461 utlined in Table 2, widely emplyed in taxnmic keys t separate these tw lineages (e.g., Pavlick 1995), cnstitute pssible synapmrphies fr these clades; hwever, validatin f these hyptheses will require rigrus recnstructins f character evlutin n rbustly supprted and fully reslved gene trees. The plastid and nuclear ribsmal data sets infer different relatinships between sects. Brmus and Genea. The nuclear ribsmal data d nt infer a clse relatinship between the sectins (Fig. 1), while the plastid data strngly supprt a clade cntaining all taxa frm bth sectins (Fig. 2). The placement f species frm sects. Brmus and Genea tgether in a clade in the plastid trees crrbrates Pillay and Hilu (1995), althugh they did nt detect sufficient chlrplast DNA variatin t separate the sectins int distinct mnphyletic grups. Pillay and Hilu (1995) suggested that the similarity in chlrplast genmes between sects. Brmus and Genea may be the result f chlrplast transfer by hybridizatin and phylgenetic srting. A clse relatinship between the sectins is further supprted by data frm flral micrstructural variatin (Ksina 1999), and by their life histries. Bth include nly annual species (mst ther sectins f Brmus cmprise mstly perennial species), and bth include many weedy species (Stebbins 1981). Stebbins (1981) als hypthesized a clse relatinship between sects. Brmus and Genea, and suggested that their rigins prbably invlved different species f sect. Brmpsis as genme dnrs. Our nuclear ribsmal data are ptentially cnsistent with this hypthesis, as sect. Brmus is nested within a clade that includes species f sect. Brmpsis frm Nrth America and B. ramsus frm the Old Wrld, while sect. Genea is clsely related t species f sect. Brmpsis frm the Old Wrld (excluding B. ramsus). These species grups f sect. Brmpsis, respectively, are ptential candidates fr genme dnrs in the rigins f sects. Brmus and Genea. Within sect. Genea, ur data indicate a fairly substantial amunt f genetic variability amng individuals f B. madritensis subsp. rubens, in line with the results f a previus iszyme study (Kahler et al. 1981). The high genetic variatin bserved here seems t crrespnd with mrphlgical variatin that was high enugh t result in the grss misidentificatin f ne seed bank accessin (see Table ). The genetic variatin bserved in B. madritensis subsp. rubens raises the pssibility that similar high levels f variatin may be present in at least sme ther Brm.us species. Sectin Brmpsis. Sectin Brmpsis, the largest sectin currently recgnized in Brmus, cmprises several independent lineages and is nt mnphyletic in any f ur analyses. These results are cngruent with Pillay and Hilu (1995), wh fund members f the sectin t ccur in three distinct lineages (based n the plastid genme but with less taxn sampling). Based n ur nuclear ribsmal data, B. attenuatus and B. dlichcarpus, tw Nrth American species f sect. Brmpsis native t nrtheastern Mexic and suthern Mexic and Guatemala, respectively (Wagnn 1952; Sderstrm and Beaman 1968), are the sister grup f the rest f Brmus (Fig. 1). Fur Suth American species (ß. lanatus, B. mdestus, B. pellitus, and B. pflanzii) frm a well-supprted clade that is reslved as part f the secnd deepest split in the genus. The plastid data alne d nt supprt these phy- lgenetic placements, pssibly because f insufficient variatin; hwever, the plastid trees d indicate that these species are nt part f the clade that includes ther New and Old Wrld species f sect. Brmpsis (Fig. 2), and they d nt rule ut the relatinships inferred frm the nuclear ribsmal data. The mrphlgical characteristics f the species are nt sufficiently distinct cmpared with ther New Wrld species f sect. Brmpsis fr previus wrkers t have cnsidered them majr evlutinary lineages. Hwever, Wagnn (1952) suspected that B. attenuatus and B. dlichcarpus are clsely related t each ther, and that they are distantly related t ther Nrth American species f sect. Brmpsis. The mlecular data agree with this hypthesis. Further study is necessary t identify pssible mrphlgical and/r anatmical synapmrphies fr a B. attenuatus B. dlichcarpus clade as well as a putative clade f Suth American species that may be part f the secnd deepest split in Brmus. The deep psitins f these tw clades in the nuclear ribsmal trees suggest that the crwn clade f Brmus riginated in the New Wrld. In cntrast, Stebbins (1981) suggested that Brmus riginated in Eurasia, with sects. Brmpsis, Ceratchla, and Nebrmus being the first t differentiate and subsequently spreading t Nrth and Suth America, fllwed by the evlutin f sects. Bissiera, Brmus, and Genea. The mlecular evidence suggests that the remaining Suth American species f sect. Brmpsis sampled, B. brachyanthera (a hexaplid; Schifin and Winge 198), is clsely related t Old Wrld species f sect. Brmpsis and sects. Ceratchla and Nebrmus. In the plastid trees, B. brachyanthera is the sister grup f a clade crrespnding t sect. Ceratchla (Fig. 2), whereas in the nuclear ribsmal trees the species is the sister grup f a clade cmprising sects. Ceratchla and Nebrmus (Fig. 1). Despite the clse mlecular relatinship, B. brachyanthera is mrphlgically distinct frm species in sects. Ceratchla and Nebrmus, having drsiventrally flattened spikelets typical f ther species in sect. Brmpsis, and straight awns. Stebbins (1981) suggested that sme members f sect. Brmpsis may have dnated genmes during the rigin f sect. Ceratchla. In line with this hypthesis, the phylgenetic affinities f B. brachyanthera and the Old Wrld species f sect. Brm.psis with sect. Ceratchla suggest that these species f sect. Brmpsis, their clse relatives, r their immediate ancestrs are amng the mst likely candidates as pssible genme dnrs. In future studies, inclusin f the six unsampled native species f sect. Brmpsis frm Suth America (Planchuel and Petersn 2) shuld prvide further insight int the evlutin and relatinships f this grup f prly understd species. Armstrng (198) hypthesized that the Nrth American and Old Wrld members f sect. Brmpsis may represent distinct evlutinary lineages. Species frm Nrth America are generally diplids (a few are tetraplids), and all have large chrmsmes with pinhead satellites, whereas Old Wrld species are generally plyplids with smaller chrmsmes lacking pinhead satellites (Armstrng 198). Exceptins are B. pumpellianus, which is native in Nrth America and Eurasia and mrphlgically and cytlgically similar t Old Wrld taxa, and the B. ramsus cmplex f the Old Wrld (represented here by B. ramsus), which is

13 462 Saarela, Petersn, Keane, Cayuette, and Graham ALISO mrphlgically and cytlgically similar t Nrth American species f sect. Brmpsis (Armstrng 198). Differences in flral micrstructural variatin further supprt the distinctiveness f these mrphlgically and cytlgically differentiated grups (Ksina 1999). Our nuclear ribsmal data may partly supprt these hyptheses, as species f sect. Brmpsis frm Nrth America (excluding B. attenuatus and B. dlichcarpus) and B. ramsus frm the Old Wrld frm a clade that des nt include the ther Old Wrld species in the sectin (Fig. 1). Old Wrld species f sect. Brmpsis (including B. pumpellianus) ccur in several independent lineages that are part f a well-supprted clade that als includes B. brachyanthera (sect. Brmpsis) and sects. Ceratchla, Genea, and Nebrmus (Fig. 1). These relatinships are cnsistent with the findings f Ksina (1996), wh bserved similarity in the embry structure f species f sect. Ceratchla and Old Wrld species f sect. Brmpsis. In cntrast, the plastid data include Old Wrld species f sect. Brmpsis in a large, weakly supprted clade with many Nrth American species f the sectin (Fig. 2). The gene trees thus indicate that mst Old Wrld and Nrth American lineages f sect. Brmpsis share a similar plastid genme, but have cnflicting nuclear ribsmal histries. The Old Wrld species (mstly plyplids) may have riginated via a hybridizatin event, with a diplid member f sect. Brmpsis cntributing the plastid genme. Additinal Old Wrld representatives f sect. Brmpsis as traditinally circumscribed, and imprved genmic sampling, will be required t prvide further insight int the evlutin and relatinships f these species. If it becmes desirable t frmally recgnize these Old Wrld lineages, the sectinal name Pnigma Dumrt. is available fr the clade that cntains B. inermis (Armstrng 198). Within the clade that includes mst f the Nrth American species f sect. Brmpsis, several weakly t well-supprted clades f tw t five species are evident (Fig. 1, 2). Wagnn (1952) suggested several grupings f the Nrth American species based n gegraphical distributin: (1) an Arctic grup, (2) a Rcky Muntain Mexican Highland grup, () a Pacific Slpe grup, and (4) an East Midwest grup. Our nuclear ribsmal trees are largely cngruent with the East- Midwest grup that Wagnn (1952) defined t include B. ciliatus, B. kalmii, B. nttwayanus, B. pubescens, B. purgans L. (nm. rejic; here treated as B. latiglumis), and B. texensis. All f these species, except B. texensis, make up a mderately supprted clade in these trees; there is insufficient variatin in the plastid data t supprt r reject such clse species relatinships. Wagnn (1952) nted that the placement f B. texensis might seem ut f place in this grup, since its gegraphic range is intermediate between ther members f the East Midwest grup and members f the Rcky Muntain Mexican Highland grup, but he included it because the mrphlgy f its ligule is similar t ther members f the grup. Our data neither supprt nr reject Wagnn's (1952) ther grups, as the phylgenetic relatinships f many f the species are unreslved. The shrt branch lengths and lack f reslutin amng many f the Nrth American species f sect. Brmpsis indicate that the species in this grup likely diversified during a recent rapid radiatin. There has been much cnfusin abut the species status f B. ciliatus and B. richardsnii (Nrth American species f sect. Brmpsis). Brmus richardsnii is ften treated as a synnym f ß. ciliatus (e.g., Hitchcck 1951; Sderstrm and Beaman 1968; Allred 199), althugh recent taxnmic study has indicated that these taxa are sufficiently distinct mrphlgically, cytlgically, and genetically t warrant specific recgnitin (Petersn et al. 22). Our nuclear ribsmal data cnfirm that B. richardsnii is a distinct species, clsely related t B. mucrglumis (althugh the species status f B. mucrglumis is als cntrversial; Wagnn 1952; Petersn et al. 22); these taxa d nt share an immediate cmmn ancestr with B. ciliatus (Fig. 1, 2). It is clear frm bth plastid and nuclear ribsmal data that sect. Brmpsis is an artificial assemblage f species. The mrphlgical characteristics traditinally used t circumscribe the sectin (Table 2) may therefre be a mixture f characters that are hmplasius r that represent symplesimrphies f larger clades. The recgnitin f Brmpsis, in its present circumscriptin, as a distinct sectin, subgenus, r genus (Table 1) is clearly nt apprpriate. Sectins Ceratchla and Nebrmus. Sectin Ceratchla is weakly supprted as mnphyletic in the plastid trees (Fig. 2), and rbustly supprted as mnphyletic in the nuclear ribsmal trees (Fig. 1). Nne f the sequence data is sufficiently variable t reslve relatinships amng species in the sectin, and several species are genetically identical at the lci examined. Similarly, Pillay and Hilu (199, 1995) fund n chlrplast DNA restrictin site variatin amng species f sect. Ceratchla. The plastid and nuclear ribsmal data are in cnflict regarding the mnphyly f sect. Nebrmus. In the plastid trees (Fig. 2), the tw species f sect. Nebrmus cmprise a grade, in which B. berteranus is the sister grup f a clade cmprising B. gunckelli, sect. Ceratchla and B. brachyanthera (sect. Brmpsis). Hwever, sect. Nebrmus is a well-supprted mnphyletic grup in the nuclear ribsmal trees (Fig. 1), a relatinship nt strngly rejected by the plastid data, and clearly the species are clsely related. Bth species are mrphlgically similar, sharing geniculate awns (Table 2), hence their classificatin as a sectin. Brmus berteranus (syn. B. trinii E. Desv.) is mrphlgically similar t ther grass genera because f its large glumes and a lemma that is deeply bilbed apically (Stebbins 1981), and in the past the species has been cnfused as a species f the genus Trisetum Pers. (Luis-Marie 1928), althugh this classificatin has nt been fllwed by recent authrs. Our data cnfirm that B. berteranus is a species f Brmus. The weakly supprted relatinship between sects. Ceratchla and Nebrmus (Fig. 1, 2) agrees with previus hyptheses that these taxa share cmmn ancestry. Stebbins (1981) reprted a weak affinity between ne genme f sects. Ceratchla and Nebrmus, and Pillay and Hilu (1995) fund that these taxa shared eight synapmrphies based n chlrplast DNA restrictin site variatin. Unfrtunately, neither f these studies included representatives f Suth American species f sect. Brmpsis, ne f which appears here t be clsely related t sects. Ceratchla and Nebrmus (Fig. 1, 2). Stebbins (1981) hypthesized that sects. Ceratchla and Nebrmus evlved early within

14 VOLUME 2 Mlecular Phylgenetics f Bimus 46 Brmas, based n their small chrmsme size and spikelets that resemble thse in genera he thught were derived frm the ancestral cmplex that als prduced Brmus (including Littledalea, Megalachne, Metcalfia, and Pseuddanthnid). The plastid data neither reject nr supprt this hypthesis (Fig. 2), but the nuclear ribsmal data indicate that B. attenuatus and B. dlichcarpus (sect. Brmpsis), species that are mrphlgically distinct frm taxa in sects. Ceratchla and Nebrmus, are part f a deep lineage that diverged early in the histry f the genus (see abve; Fig. 1). Sectins Ceratchla and Nebrmus are nested deep within the nuclear ribsmal trees. Current knwledge, favring distant phylgenetic psitins f the mrphlgically similar genera thught previusly t be clsely related t sects. Ceratchla and Nebrmus (e.g., Sreng et al. 2), further discunts Stebbins's (1981) hyptheses. Sectins Bissiera and Nevskiella. Material f B. pumili (sect. Bissiera) was nt available, and sampled material f B. gracillimus (sect. Nevskiella) was recalcitrant t mlecular study, thus the phylgenetic psitins f these taxa remain uncertain. Brmus pumili was riginally classified in its wn genus, Bissiera, but was transferred t Brmus based n serlgical and mrphlgical similarities t ther Brmus species (Smith 1969). It has since been treated either in sect. Brmus (e.g.. Smith 197) r within its wn sectin, Bissiera (Smith 1985a; Table 1), because f its unique mrphlgy, having five t nine awns n each lemma (Table 2). Based n allzyme evidence, Oja and Jaaska (1998) fund B. pumili t be distinct frm members f sect. Brmus, supprting its placement in its wn sectin. The phylgenetic psitin f B. gracillimus, characterized by awns that are fur t six times the length f the lemma (Table 2), remains unknwn. It wuld be valuable t include bth species in future mlecular studies. Cnclusins and Future Directins Our study prvides genus-wide phylgenetic hyptheses f relatinships in Brmus s.l., based n DNA sequence data frm the plastid genme and the nuclear ribsmal internal transcribed spacer regin, and prvides a fundatin fr further phylgenetic study f the genus. Based n the nuclear ribsmal data, sects. Brmus (including sect. Triniusia), Ceratchla, Genea, and Nebrmus are mnphyletic, and sect. Brmpsis cmprises several distinct lineages. Plastid trees indicate that sects. Brmus and Genea are clsely related, and the incngruence detected between the plastid and nuclear ribsmal data supprt a hybrid rigin fr the B. pectinatus cmplex (here represented by a single exemplar) between sects. Brmus and Genea. Plastid trees indicate a clse relatinship between Old Wrld and sme Nrth American species f sect. Brmpsis, and the plastid and nuclear ribsmal data indicate that ne Suth American species f sect. Brmpsis is nt clsely related t Nrth American and Eurasian species traditinally classified in the same sectin. Mst species f Brmus sampled had levels f sequence variatin t lw t allw cmplete reslutin f relatinships amng clse relatives at the species level (e.g., amng Nrth American members f sect. Brmpsis and within sect. Ceratchla). Sequence data frm additinal nuclear lci, such as the granule-bund starch synthase gene {waxy; e.g., Masn-Gamer 21), AFLPs (e.g.. Beardsley et al. 2; Després et al. 2), r micrsatellites (e.g., Alvarez et al. 21) may prvide further insight int specieslevel relatinships in Brmus. Adding data frm the plastid genme (e.g., Shaw et al. 25) and the nuclear ribsmal regin (the external transcribed spacer [ETS] f nuclear rdna; e.g., Baldwin and Marks 1998; Marks and Baldwin 22; Starr et al. 2) wuld als be valuable t imprve reslutin and supprt f trees inferred frm these tw linkage grups. Recgnitin f the brme grasses as ne distinct genus, Brmus, is in agreement with the mlecular data, but current classificatin schemes d nt satisfactrily reflect phylgenetic relatinships within the genus, particularly with respect t the circumscriptin f sect. Brmpsis. Hwever, befre a revised infrageneric classificatin f Brmus is prpsed, we advcate that substantially better sampling shuld be cnducted f (1) DNA sequence regins, t btain better supprt fr phylgenetic relatinships amng taxa, and t further clarify incngruence amng nuclear and plastid data partitins, and (2) taxa, t mre adequately sample the mlecular, mrphlgical, and gegraphical variability in the genus. Althugh this is the largest study f Brmus phylgeny cnducted thus far, all cnclusins are based n a sample f less than ne-third f the recgnized species, mstly with ne individual per taxn, and it is plausible that additin f ther species will further cntribute t and change ur understanding f evlutin and phylgeny in this genus. ACKNOWLEDGMENTS Travis Clumbus, Vanessa Ashwrth, Linda Wrlw, and tw annymus reviewers prvided cmments that have imprved the manuscript. We thank the Western Reginal Plant Intrductin Statin (USDA), Plant Gene Resurces f Canada (Agriculture and Agri-Fd Canada), and Rb Sreng (US) fr prviding seed and leaf material. Hardeep Rai generusly prvided technical assistance. The labratry cmpnent f this research was supprted by a grant frm the Athertn Seidell Endwment Fund t PMP and an NSERC Discvery Grant t SWG. Field cllectins by PMP were supprted by the Smithsnian Institutin's Fellwships and Grants Schlarly Studies Prgram, The Natinal Museum f Natural Histry's Research Opprtunities Fund, and the Department f Btany. Field cllectins by JC were supprted by ECORC, Agriculture and Agri-Fd Canada, Ottawa; Frage Crp Breeding and Genetics, Agriculture and Agri- Fd Canada, Saskatn; and Ducks Unlimited Canada. Field cllectins by RMK were supprted by a Natinal Science Fundatin Graduate Research Fellwship. JMS was supprted by schlarships frm NSERC, Alberta Ingenuity, the University f Alberta, and the University f British Clumbia. Travel supprt t attend the Furth Internatinal Sympsium n Grass Systematics and Evlutin was prvided t JMS by the Natinal Science Fundatin, a Mary Luise Imrie Graduate Student Award (University f Alberta), and the Department f Bilgical Sciences (University f Alberta). LITERATURE CITED ACEDO, C, AND F. LLAMAS Brmus cabrerensis and Brmus nervsus, tw new species frm the Iberian Peninsula. Willdenwia 27:

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18 VOLUME 2 Mlecular Phylgenetics f Bimus 467 mny (*and ther methds), vers. 4.bl. Sinauer Assciates, Inc., Sunderland, Massachusetts, USA. TABERLET, R, L. GIELLY, G. PAUTOU, AND J. BOUVET Universal primers fr amplificatin f three nn-cding regins f chlrplast DNA. PI. Mlec. Bil. 17: TSVELEV, N. N Grasses f the Sviet Unin, Part I. Nauka Publishers, Leningrad, Russia. 788 p The system f grasses (Paceae) and their evlutin. Bt. Rev. (Lancaster) 55: VELDKAMP, J. E, M. ERIKS, AND S. S. SMIT Brmus (Gramineae) in Malesia. Blumea 5: WAGNON, H. K Three new species and ne new frm in Bimus. Leafl. W. Bt. 6: A revisin f the genus Bimus, sectin Brmpsis, f Nrth America. Biittnia 1: WENDEL, J. E, AND J. J. DOYLE Phylgenetic incngruence: windw int genme histry and speciatin, pp In P. S. Sltis, D. E. Sltis, and J. J. Dyle [eds.]. Mlecular systematics f plants. Chapman and Hall, New Yrk, USA. WHITE, T J., T BRUNS, S. LEE, AND J. TAYLOR Amplificatin and direct sequencing f fungal ribsmal RNA genes fr phylgenetics, pp In M. Innis, D. Gelfand, J. Sninsky, and T. White [eds.], PCR prtcls: a guide t methds and applicatins. Academic Press, San Dieg, Califrnia, USA. WILTON, A. C Phylgenetic relatinships f an unknwn tetraplid Bimus, sectin Brmpsis. Canad. J. Bt. 4: WiNKWORTH, R. C, J. GRAU, A. W ROBERTSON, AND P. J. LOCKHART. 22. The rigins and evlutin f the genus Mystis L. (Braginaceae). Mlec. Phylgen. Evl. 24: YDER, A. D., J. A. IRWIN, AND B. A. PAYSEUR. 21. Failure f the ILD t determine data cmbinability fr slw lris phylgeny. Syst. Bil. 5: YKOTA, Y, T KAWATA, Y. IIDA, A. KATO, AND S. TANIFUII Nucletide sequences f the 5.8S rrna gene and internal transcribed spacer regins in carrt and brad bean ribsmal DNA. J. Mlec. Evl. 29: ZAIAC, E. U. 1996a. Kmpleks Brmus mllis (Paceae) w Plsce. Fragm. Flrist. Gebt, Ser. Pln. : è. Interspecies differentiatin f Brmus hrdeaceus (Paceae) in Pland. Fragm. Flrist. Gebt. 41:

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