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Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales 1 PDF

33 Pages·2010·28.3 MB·English
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ASSEMBLING THE TREE OF THE Thomas Gwnish? Mercedes Arm, J. MONOCOTYLEDONS: PLASTOME 1 1 i . i i PHYLOGENY AND SEQUENCE EVOLUTION OF POALES 1 Wendy Zo Melvin B. G. Briggs,* 9 10 R. Duvall, Michael Moore, Michael J. J. 11 Heaney, Douglas E. Soltis, Kevin 13 and James H. Leebens-Mack3 Thiele, ..' ' . . : . . '. .- ommelinid orders with n i ( allies) are well supported as siste a xyrid clade (Erioc :s s 1 This research was sup] ience Foundation (NSF) g the Mcii .> 1.1' provided access to data " 11 ! >>' -..r.i ',". ! '.•'. .,,! .!.! I : , ! i i i I ' '. ii !!.,! in I :i • i c U.S.A. 0()()2, : ..:. r,\ " . 5 Department of Biology, Pennsyh an 6802, U .S.A. 1 :»,. ^ :<:,' , 8 Botanic Gardens ulh Wales 2000, Australia. J III i , I i ! '"Derailment of Iholo^. OIm-jIjii olle e. Ohe.lm. Ohio 11071. U.S.\. ( S 1 ' 12 Museum Florida of "Western Australian Herharium. Perth. Western Australia 6983. Australia. 72010023 , Bot. Card. 97: 584-616. Published on 27 December 2010. ri i i '! Key words: Commelinids, — Monocots V with ca. ! 'I •' ' . ! ! !"': " ' Ill • : . . Phylogen >erm onships each other that remain to most dherse, inn ried, ecologically included the validation, to a large degree, economically ind i angio<-permr.. Since l"l 'I I" I i I .1 i I .il.il ;i in i I InI II . : ill I I " / , li-; ...'.?; ill ; . i 2000, 2006; Zomlefer, 195 ia, b, of the aquatic la ma 1976; Dahlgren a n IN, mm. et al., i I !l li urn l i ill i I I ill I 111 I I III II III i I I I evolutionary biologists. :: : : Over the past 18 years, molecular systematics has !' ,'l -ill V i- , , ' . i 2000, 2006; b, \-. ::" -v-v "., - i nil i li i II in ill v. ' ';. I l: .:i ;i .<!.. .™ 1999, 2005; Brem 2001; s et al., Chase provided the most powerful et al. (2006) .:; ,< ll'i; 'i-iii; :'., II parsimonj (MP) analysis, other ster to all in, . . lid clade (Chase et al, 1993, 1995a) and on Chase their allies). et al. !i':i ' ' ' ' ' ri,...:l .:: 2009, here reco ships within orders ), nmelmid- plastid genes (rbcL and nuitK) for repieM and \spar- n' . i i I ca. 2400 monoeot geneui. he-e efloit- aie eomple- .juenced included members of I > while the Europeans link our backbone phylogeny to .-'iigle lamilies in We Arecales and Dasypogonales (Dasypogonaceae sensu are jImi ollabo- .a. c Angiosperm Phylogeny Group, Nonmonocot w 2009). We sendix used 1). amount leled of gr AToL Moore plant genomes obtained in our projecl et al., 2007; et al, 2007) as - ' er>'' '!- ' i ' ' : any major plant group studied to date. we In this paper, present a demonstration of the plastome SEQUENCING focusing on relali, Following methods described by Jansen e ies « Poales is Lh ' - Ho.sta Tratt., I,., quenceofitsinelu ....II ' I. I ' . . vere generated De each novo assemblies sequences for taxon. of ip 1 i :, -lei :' I 2004). Resulting assemblies were in Consed (Gordon an et al, 1998) The 83 taxa include. were anno- 3S Group (Appendix (2009) 1). U ;rver (<http:// .; .. I.'! i : 1 ',: . HI ' ' ' : ' . . (Ratan, 2009; ' and available (Edgar, 2004), to ' M N g file. g concatenated alignment. i.i ill i I . . closel) rela f •' .:> i" IT..'. i; i i genome sequences were used as alternative references v>'- Ms- 1. I 1 ,,, . . , i i , I Gapped were cells treated as missing c1 tated and extracted from the resulting contigs using lands of equally most parsimonious trees DOGMA. DOG\l BLASTX searches seeded through o acid sequences iploying tree sequencing rare i t i . . I " . ' ' / , ; , I I In.. i 1 ii . il>i ... ihli-lllll ! ir i. ii:' . & homoplas) in the data (Givnish Sytsma, 1997). '. Hi r- .'II II. ' •: ;i;.-;i.!|.:-v • I- " IIMili'- -I. '• I".'. : ' . A was modeled 2004). single; as i ii! ' ^ . i I i . i ' was modeled using the discrete a & Ucata (Hook, Newell B. C. Stone f.) mry direct sequencing. All gene . - I i . . i i with a total of } ! .'.i:;i i'.) ,ii & son Maddison, 1992) to infer an.-. n i we ecologies, separated -Live i n ii I and sampled alignn (a suJ PACCMAD-BEP + the clade I i - :!-.( .,:..: Centothecoideae, Mi- loideae, DOGMA from lences extracted multitaxon fasta files ) MUSCLE gene sequences using -.:::' lign -i .. . , ' van der 1979; Regal, 1982; Cox, 1991; Linder, Pijl, : 1998; Weller 1998; Givnish 1999; Cully et al., et al., To ii evaluate ,11 )08). in ' Clark et al.. I9«; son 2007a, Bouche- et al., b; tests of correlate* drained or (In ) ,,!(! ' I ii i Iclirr : - ' : |( i: I' >, : . (1985), Givnish (1999, 2000, 2004, 2007), el al. <,:: IDMH..;. oil . I i : ingroups as iied ii I ; & models Meade, 2006 (Pagel u\ i i iii . I! , U: II., il . , ^ . . . -Till hi"!' I i ',v, i : i ii I i 1 & Moore al, 2007; al, 2007; Whitfield et et I I 'i ' '-:.( , " ML : ' H .11,1111 I >' all laxa in the tree (see 2000. al, et > i I i 'I' ' ,, i I I I ". ', I' I ll Hill i,i I, I ' I i (Appendix es within those families 2). V' 111 III V, 1 lh. nV plants via Henderson (1971, 1979), (1986), Stiitzel (1986, 1990), ListabarthllO"! ,. ihere were 25,107 -ps (Fig. ()\erall, 2). : ,..,... ,.i ;-i :,i Appendix et (2009) al. (sec; 8 MP Hordeum plastome phylogeny graminids Triticum Agrostis = Length 152,366 steps Bambusa Oryza = CI 0.384, CI' 0.31 WrSaccharum Mf Poaceae Sorghum 83 taxa (68 monocots) 100 100 Zea Eieusine 109,1 34 aligned bases 100 Pueiia Anomochioa 25,107 informative characters 94 — Streptochaeta Ecde'tocoiea 100 100 "| Ecdeiocoleaceae { GeorgeanthaA n Joinvillea piicata 100| — Joinvilleaceae ascendens Joinviflea Fiageilaria Flagellariaceae Poales Thamnochortus 100 Restionaceae restiids i Centrofep/s Centrolepidaceae Mayaca Mayacaceae xyrids { byngonan thus Eriocaulaceae Abolbodo Xyridaceae Cyperus Cyperaceae 100 - r cyperids Juncus Juncaceae Thurnia Thurniaceae Potarophytum Rapateaceae Spargan/um Typh Typha ] Neoregelia Oft- l mv-Puya Jr Pttcairnia 00 1 Bromeliaceae Fosterella Novia Brocchinia — Chamaedorea 81i 1» fElaeis Arecaceae Arecales Li Ravenea Belosynapsis 100 Commelinaceae Commelinales ~\ ] Tradescantia Musa Mu5aceae Zingiberales Reneaimia J Zingiberaceae Dasypogon Dasypogonaceae Dasypogonales ] King/a ] Hesperafoe 8&- .M- Yucca M\-Hosta m loon Chlorophytum Asparagaceae Albuca Asparagus Lomandra Nolina Asparagales Agapanthus Amaryllidaceae 52 Phormium Xanthorrhoeaceae Iris Iridaceae Curcuiigo Hypoxidaceae Neoasteiia Asteliaceae 100 Apostasia 00 1 j Orchidaceae ] Phaiaenopsis - 100 Dioscorea Dioscoreaceae Dioscorea es I Pandanus Pandanaceae - Pandanales Hum - 100 Li Liliaceae Liliales Lemna - Araceae Alismatales Acorus americanus 100 I — Acoraceae Acorales A corns calam us ] ] ' Anethum Panax Heiianthus 94 Coffea Spinacia Cucumis Eudicots Medicago Populus 100 Buxus Piatanus Nandina 100 Calycanthus Laura es I Liriodendron Magnoliales 94 Drimys Canellales Piper Piperales lliicium Austrobaileyal Nuphar Nymphaeales Amboreiia Amborellales 1000 changes I 100% Mayaca Mayacace bootstrap support; of ! ;'-:^l |.:i f :, .,. »! i i' ii i i i i i i , . ; < 1 1 i I I i B. Sm., B. melanacra L. B. I ,. 100% 94% bootstrap sister (with , IW7. iMi al. 2007) Low-nutrient et ACCTRAN. However, infertile soils are more likely than mfened favor (Givnish. 1980). the to fir,- 2000, 2004, 2007), as do sedg ;i..| I, J ± .... unit node, lminch lengths averaged 1734 170 'iv :.,„<.' ' I. ; i . ' ± ± (mean SD) steps for palms, 2112 103 for ± 7821 1102 ids, Fh running from ilka through the 1416 for graminids. Rates of plastid sequence mux <":'! :.- , : ML produced a single, fully resolved, well- '' ii.i i '': iMill'' ' > i :•'!:: .... trap support as being mono- that the ancestral habitat had commelinids in the for both highly infertih >" .' i"' ' - ML the tree was generally higher than that for the from Bromeliaceae Cyperaceae, and Juncaceae e, !/ . S ,, or< n ly,t} 'Villi IK-;, in I. "I i" ;.. '' ... II II II I II ill ' ML more provided a :h strongly !: through Poaceae) typically .... , . i . i ', !':;: . ' in. :. i ' . i 86% sister to Dasypogonales with bootstra -y, ...;',. i'.t : I I i I ' 1 1 'I I I i ill,! ..ill. I I in S3 VI VI Of vj .2 o « t«fl * 2 VI 41 ID A3 VI O a> a 2 E £ c Q. 8 o N 2. r 1 1 1 1 0J ra a m s re m o u OJ I? a? ra 01 HI t ra ra ra aj v .3 t•re tQsJ,<dco* 2aa;. narej> urraa J3^® rurea aar>>e Sk_if?C arurja- "r8fEaaaj ECE afar»>Oo 1V OurHJaIw rau3ai rCOCoam cran ra jl p8 Si rUa <<rlLa>> s<uRqurUja eraurra>oa arOuiaJ 8 c y> Cr> <T5 o s* 'a CL o o =3 c £1 <e ra u 1— N Qra < X < o < >< £3 — r r 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 I I 1 1 1 1 1/1 1/5 n o OJ 2 vi Ml 3 VI in § 5 o uo .£ p u> 9. 8 O c C E E Cl 5 <C CD 0) g 1 i-J c s '^-. -3 5 U s s ^i E 5 fc^^ E 1 G ^ I >n Q QJ JG Q E §1 Q 01 ^J C3 o VI "^ 5 g "g a ^^ \J £ '3 li.J c Jj 3 eg 00 o-. o s ro CO so s r a + ^ s o-. cc E CO 1 0^1 o ij a S Ml' ' II I li the commelinids. ( I ''.... ' ' ' : • been resolved as [hem anew. ;>; habitats. In J relatives, there liate l , V»: ' ': lining the pollin

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