PHYLOGENETIC STRUCTURE IN THE GRASS FAMILY (POACEAE): EVIDENCE FROM THE NUCLEAR GENE

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1 American Journal of Botany 87(1): PHYLOGENETIC STRUCTURE IN THE GRASS FAMILY (POACEAE): EVIDENCE FROM THE NUCLEAR GENE PHYTOCHROME B 1 SARAH MATHEWS, 2,3 ROCKY C. TSAI, 2,4 AND ELIZABETH A. KELLOGG 5 2 Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, Massachusetts USA; and 5 Department of Biology, University of Missouri-St. Louis, 8001 Natural Bridge Road, St. Louis, Missouri USA Phylogenetic analyses of partial phytochrome B (PHYB) nuclear DNA sequences provide unambiguous resolution of evolutionary relationships within Poaceae. Analysis of PHYB nucleotides from 51 taxa representing seven traditionally recognized subfamilies clearly distinguishes three early-diverging herbaceous bambusoid lineages. First and most basal are Anomochloa and Streptochaeta, second is Pharus, and third is Puelia. The remaining grasses occur in two principal, highly supported clades. The first comprises bambusoid, oryzoid, and pooid genera (the BOP clade); the second comprises panicoid, arundinoid, chloridoid, and centothecoid genera (the PACC clade). The PHYB phylogeny is the first nuclear gene tree to address comprehensively phylogenetic relationships among grasses. It corroborates several inferences made from chloroplast gene trees, including the PACC clade, and the basal position of the herbaceous bamboos Anomochloa, Streptochaeta, and Pharus. However, the clear resolution of the sister group relationship among bambusoids, oryzoids, and pooids in the PHYB tree is novel; the relationship is only weakly supported in ndhf trees and is nonexistent in rbcl and plastid restriction site trees. Nuclear PHYB data support Anomochlooideae, Pharoideae, Pooideae sensu lato, Oryzoideae, Panicoideae, and Chloridoideae, and concur in the polyphyly of both Arundinoideae and Bambusoideae. Key words: gene family; grasses; nuclear gene; phylogeny; phytochrome B; Poaceae. The grasses (Poaceae) have received abundant scientific attention, both phylogenetic and otherwise. The historical prominence of the grasses as an object of botanical research reflects their almost ubiquitous biogeographical presence and their pervasive economic importance since the very beginnings of human civilization. Approximately one-third of the world s dry land is covered by some species of Poaceae, and the majority of the world s human population relies heavily, if not predominantly, on cereal grasses such as rice, corn, or wheat for its daily sustenance. Most taxonomic treatments of the Poaceae recognize six or seven major subfamilies of grasses, Bambusoideae, Oryzoideae, Pooideae, Panicoideae, Arundinoideae, Chloridoideae, and Centothecoideae, which are further subdivided into 40 tribes consisting of genera (Campbell, 1985; Dahlgren, Clifford, and Yeo, 1985; Clayton and Renvoize, 1986; Renvoize and Clayton, 1992; Watson and Dallwitz, 1992). The scientific effort to distinguish properly, and ultimately to classify into natural groups, the species of the grass family began with systematic attempts to group species according to the morphology of characteristic grass structures such as 1 Manuscript received 2 June 1998; revision accepted 4 May The authors thank Matt Lavin, Lynn Clark, Jerry Davis, Weiping Zhang, Barbara Ertter, Roberta Mason-Gamer, Ben Zaitchik and Elizabeth Farnsworth for DNA and plant material, Elisa Freeman for technical assistance, David Swofford for the use of PAUP*4.0, Lynn Clark and an anonymous reviewer for comments on the manuscript, and acknowledge financial support from NSF grants BIR to SM and DEB to EAK. 3 Author for correspondence ( smathews@oeb.harvard.edu). 4 Current address: 5505 HLS Holmes Mail Ctr., Cambridge, Massachusetts USA. 96 the spikelet (Brown, 1810, 1814). Eventually, this classical morphological approach to grass systematics was supplemented and complemented by data consisting of novel characters derived from detailed studies of anatomy (Prat, 1936; Reeder, 1957; Row and Reeder, 1957; Brown, 1958; Tateoka, Inoue, and Kawano, 1959), physiology (Hattersley and Watson, 1992), cytology (Avdulov, 1931), and most recently, DNA sequences. Recent phylogenetic studies of the grass family have led to a family tree that provides a consistent resolution of genealogical relationships and that can ultimately serve as the basis for a taxonomic system that accurately reflects patterns of evolution within the family. Most conclusions regarding grass phylogeny, however, are based on data from the chloroplast genome (rbcl sequence data: Doebley et al., 1990; Barker, Linder, and Harley, 1995; Duvall and Morton, 1996; Barker, 1997; ndhf sequence data: Clark, Zhang, and Wendel, 1995; Catalán, Kellogg, and Olmstead, 1997; chloroplast restriction site variation: Davis and Soreng, 1993; Soreng and Davis, 1998; rpoc2 sequence data: Cummings, King, and Kellogg, 1994; rps4 sequence data: Nadot, Bajon, and Lejeune, 1994). A comparably comprehensive nuclear data set from the grasses is lacking. Only four published studies incorporate data from nuclear genes. The pioneering study of Hamby and Zimmer (1988) included nuclear ribosomal (nr) RNA sequences from nine species representing four subfamilies. Their nrrna phylogeny indicated early the promise of molecular data, but it included too few taxa for a test of plastid gene trees. Hsaio and colleagues sequenced the internal transcribed spacers (ITS) of nrdna, focusing on Pooideae (Hsaio et al., 1995) and on Arundinoideae (Hsaio et al., 1998). They found support for generic relation-

2 January 2000] MATHEWS ET AL. PHYB PHYLOGENY IN GRASSES 97 ships, but support for relationships among tribes was minimal. Moreover, sequences from arundinoids were difficult to align (Hsaio et al., 1998), suggesting that ITS may have limited utility in broader studies in grasses. Mathews and Sharrock (1996) sampled short fragments ( 300 bp) from three phytochrome loci and inferred a phylogeny from the combined data. The phytochrome phylogeny included a taxonomic sample more comparable to chloroplast gene trees. It was strikingly well resolved and corroborated certain results from analyses of chloroplast data. Perhaps the most notable result was the resolution of a well-supported BOP clade consisting of bambusoid, oryzoid, and pooid genera, a clade that was only poorly supported by ndhf data (Clark, Zhang, and Wendel, 1995) and that was not resolved by the other plastid data sets (Doebley et al., 1990; Davis and Soreng, 1993; Cummings, King, and Kellogg, 1994; Nadot, Bajon, and Lejeune, 1994; Barker, Linder, and Harley, 1995; Duvall and Morton, 1996; Soreng and Davis, 1998). Despite the apparent promise of the phytochrome study, it included none of the taxa relevant to early evolution in the family, and only a sparse taxonomic sample of its derived clades. Additionally, the completeness of the data set depended on sampling each of three different phytochrome loci from each taxon. In this paper, we describe results from our study of a single phytochrome paralog, phytochrome B (PHYB), to generate a nuclear data set comprehensive enough to test plastid phylogenies. We sampled partial PHYB sequences (1.2 kb of exon I) from seven major subfamilies of Poaceae, including taxa that potentially bear on early and secondary diversification within the family. We also included several taxa characterized by equivocal placement in chloroplast phylogenies. Low-copy nuclear genes remain underutilized in phylogenetic studies, despite the need for nuclear tests of plastid phylogenies (Doyle, 1992, 1997). The nuclear sequences commonly sampled in phylogenetic studies are from the high-copy ribosomal loci. Low-copy nuclear genes often are avoided as a source of phylogenetic characters because identification of strictly orthologous sequences may be confounded by the presence of multiple related loci in a genome. This concern is valid; paralogy may be mistaken for orthology if related sequences within a genome are evolving in concert (Zimmer et al., 1980; Sanderson and Doyle, 1992) or if we fail to sample all members of a gene family, even if they are evolving independently (but see below). Nevertheless, multigene families have provided phylogenetically useful characters. Examples include genes for alcohol dehydrogenase (e.g., Gaut and Clegg, 1991; Sang, Donoghue, and Zhang, 1997; Small et al., 1998), phosphoglucose isomerase (Gottlieb and Ford, 1996), phytochromes (Mathews and Sharrock, 1996; Mathews, Tsai, and Kellogg, 1997; Lavin et al., 1998; Mathews and Donoghue, 1999), granule-bound starch synthase (Mason-Gamer, Weil, and Kellogg, 1998; R. Evans, University of Maine, personal communication), arginine decarboxylase (Galloway, Malmberg, and Price, 1998), and vicilin (Whitlock and Baum, 1999). A simple way to sample putatively orthologous loci in the phytochrome gene family is to use locus-specific amplification primers. Three of the four major phytochrome gene lineages occurring in angiosperms predate angiosperm origins (Mathews and Sharrock, 1997). They are divergent in function and in sequence (Sharrock and Quail, 1989; Clack, Mathews, and Sharrock, 1994; Quail, 1994) and can be distinguished by amplification primers (Mathews, Tsai, and Kellogg, 1997; Mathews, unpublished data). Thus, they can be sampled as single-copy sequences in taxonomic lineages in which there is no evidence of recent gene duplication events. This may be the case in most grasses, where Southern blot analyses and surveys using the polymerase chain reaction (PCR) have provided evidence that PHYA, PHYB, and PHYC occur singly in genomes of grasses (Mathews and Sharrock, 1996). The known exception is the genome of maize, in which two PHYB have been mapped; however, a single PHYB has been mapped and sequenced in sorghum (Childs et al., 1997). MATERIALS AND METHODS Sampling strategy Fifty-one species of the grass family, representing 29 tribes and seven traditionally recognized subfamilies, were included in the phytochrome B (PHYB) data set. The sampling distribution of taxa is given in Table 1, which is arranged according to the classification of Clayton and Renvoize (1986). The present data set comprises five short PHYB sequences analyzed in Mathews and Sharrock (1996) and 46 newly generated sequences. DNA cloning and sequencing A 1.2-kilobase (kb) region of exon I of the PHYB gene (Fig. 1a) encompassing the phytochrome chromophore attachment site was amplified from total DNA of 40 newly sampled species of Poaceae (sources of DNA given in Table 1). The five PHYB sequences previously analyzed in Mathews and Sharrock (1996) each comprised 300 base pairs (bp). All newly sampled sequences were amplified using a stepdown polymerase chain reaction (PCR) protocol (Hecker and Roux, 1996) beginning at 70 or 73 C. PHYB-specific primer pairs that were used in the amplification of the novel sequences are listed in Fig. 1b. We used a degenerate primer pair to obtain clones from Aristida, Danthonia, Lolium, Puelia, Streptogyna, and Thysanolaena. The forward degenerate primer sequence is 5-ACIGGITAY- GAYMGIGTIATG-3; the reverse degenerate sequence is 5-GTY- TCDATSARYCKAACCATYTC-3. It amplifies a comparable-sized target, but the forward member of this pair is 153 nucleotides downstream of the forward member of the PHYB-specific pair; these nucleotide sites are thus coded as missing in the final data set. Putative PHYB PCR products were excised after electrophoresis on a 1.2% agarose preparation gel and extracted using the QIAquik TM gel extraction protocol (QIAGEN Inc., Valencia, California, USA). DNA inserts were ligated to pgem -T or pgem -T Easy vectors (Promega, Madison, Wisconsin, USA) during incubation overnight at 4 C. XL1- Blue Epicurian Coli subcloning-grade competent cells (Stratagene, La Jolla, California, USA) were transformed with ligation products and incubated overnight at 37 C. White colonies were cultured overnight in terrific broth, followed by isolation of plasmid DNA via alkaline lysis/ polyethylene glycol minipreparation or QIAprep Spin Miniprep Kits (QIAGEN Inc., Valencia, California, USA). Two plasmid DNAs per taxon were screened by restriction enzyme digestion using PstI and SphI, or EcoRI. ABIPRISM DyeDeoxy terminator cycle sequencing of positive clones was performed in standard extension/termination mixes (Perkin-Elmer, Norwalk, Connecticut, USA) using the universal and internal sequence-specific primer pairs shown in Fig. 1b. Phylogenetic analysis A data matrix of 51 taxa by 1182 nucleotides was obtained by manually adding accumulating sequences to a core alignment from the Multiple Alignment Construction and Analysis

3 98 AMERICAN JOURNAL OF BOTANY [Vol. 87 TABLE 1. Taxa included in the phytochrome B (PHYB) data set. The subfamilial and tribal divisions follow the classification system of Clayton and Renvoize (1986), except for Anomochlooideae and Pharoideae (Clark and Judziewicz, 1996). BZ Ben Zaitchik, EF Elizabeth Farnsworth, EAK Elizabeth A. Kellogg, HPL H. Peter Linder, JD Jerrold Davis, LC Lynn Clark, PP Paul Peterson, RG Roberta Mason-Gamer, RS Robert Soreng, SD Soejatmi Dransfield, SM Sarah Mathews, WZ Weiping Zhang, XL Ximena Londoño, ML Matt Lavin, BBG Berlin Botanic Garden, PI U.S.D.A. Plant Introduction Station (Pullman, Washington). Taxa with asterisks are represented by sequences (306 bp) previously analyzed in Mathews and Sharrock (1996). SUBFAMILY/Tribe/Species ANOMOCHLOOIDEAE Anomochloeae Anomochloa marantoidea Brongn. Streptochaeteae Streptochaeta angustifolia Soderstr. PHAROIDEAE Phareae Pharus lappulaceus Aubl. BAMBUSOIDEAE Parianeae Pariana radiciflora Aubl. Eremitis Doell sp. nov. Streptogyneae Streptogyna americana C. E. Hubbard Puelieae Puelia ciliata Franchet Bambuseae Bambusa (Hackel) Ekman sp.* Chusquea oxylepis Kunth Pseudosasa japonica (Sieb. & Zucc. ex Steud) Makino ex Nakai Olyreae Olyra latifolia L. Buergersiochloa bambusoidea Pilger Lithachne pauciflora Beauv. Ehrharteae Ehrharta erecta Lam. Diarrheneae Diarrhena obovata (Gleason) Brandenburg Oryzeae Oryza sativa L. Zizania aquatica L. POOIDEAE Bromeae Bromus inermis Leyss.* Triticeae Triticum aestivum L. Elymus L. sp. Peridictyon sanctum O. Seberg, S. Frederiksen, & C. Baden Brachypodium pinnatum Beauv. Poeae Poa pratensis L.* Lolium perenne L. Sesleria insularis Sommier Aveneae Ammophila arenaria (L.) Link Phalaris arundinacea L. Stipeae Nassella viridula (Trin.) Barkworth Meliceae Glyceria grandis S. Watson Melica cupanii Guss. Lygeae Lygeum sparteum L. Nardeae Nardus stricta L. CENTOTHECOIDEAE Centotheceae Chasmanthium latifolium Link LC 1299 LC 1304 LC 1329 LC & WZ 1344 LC & WZ 1343 Johnston 433 Voucher Kobayashi et al EAK V6 LC 1069 WZ XL & LC 911 SD 1382 LC 1297 EAK V44 LC & WZ 1216 BZ s.n. RG s.n. EAK s.n. EAK H5575 PI SM 402 PI RS 3389 RS 3427 JD & RS s.n. PI RS 3698 BBG: Royl and Schiers s.n EAK V13 GenBank sequence accession number a GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-U61188 GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-X57563 GBAN-AF GBAN-U61193 GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-U61214 GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF137297

4 January 2000] MATHEWS ET AL. PHYB PHYLOGENY IN GRASSES 99 TABLE 1. Continued. SUBFAMILY/Tribe/Species ARUNDINOIDEAE Arundineae Danthonia spicata Roem. and Schult. Phragmites australis Trin. ex Steud. Hakonechloa macra Honda Molinia caerulea (L.) Moench Anisopogon avenaceus R. Br. Aristideae Aristida longiseta Steud. Thysanolaeneae Thysanolaena maxima (Roxb.) Kuntze CHLORIDOIDEAE Eragrostideae Eragrostis cilianensis (All.) Mosher* Cynodonteae Bouteloua gracilis (Willd. ex H.B.K.) Lag.* Sporoboleae Sporobolus giganteus Nash PANICOIDEAE Andropogoneae Sorghum halepense Pers. Zea mays L. Miscanthus sinensis Anderss. Capillipedium parviflorum Stapf Arundinelleae Arundinella hirta (Thunberg) C. Tanaka Danthoniopsis dinteri C. E. Hubbard Paniceae Panicum capillare L. Pennisetum alopecuroides (L.) Spreng EAK V10 No voucher EAK V21 RS 3305 HPL 5590 SM s.n. EF s.n. PP Voucher PI Arnold Arboretum C PI PI PI EAK s.n. GenBank sequence accession number a GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-U61200 GBAN-U61191 GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF GBAN-AF a The prefix GBAN- has been added to link the online version of American Journal of Botany to GenBank but is not part of the actual GenBank accession number. Workbench (MACAW) software system (Schuler, Altschul, and Lipman, 1991). Phylogenetic analyses were performed using parsimony on PAUP*4.0 (Swofford, 1998). Characters were equally weighted with respect to codon position in all cladistic analyses, and GAPMODE was set to MISSING for the single-codon gap found in all panicoid, arundinoid, chloridoid, and centothecoid taxa. Most parsimonious trees were retained from a heuristic search employing 500 random addition replicates (hold 1000) and the tree-bisection-reconnection (TBR) branch swapping algorithm, with STEEPEST, USENONMIN, ALLSWAP, and MULPARS options invoked. Four alternative topologies were compared with the minimal-length trees by performing additional heuristic searches under the same settings, but with constraints loaded. We used constraint analyses to evaluate conflict with phylogenetic patterns emerging from other molecular data sets rather than to evaluate the many conflicts apparent between most molecular data sets and traditional classifications. To compare levels of support for the monophyly of constituent clades, decay indices (Bremer, 1988; Donoghue et al., 1992) were determined using AutoDecay 4.0 (Eriksson, 1998) and the same heuristic search settings employed to obtain minimal-length trees. In addition, a bootstrap consensus tree from 1000 replicates was generated using an heuristic search strategy employing simple taxon addition and TBR, retaining groups with frequency greater than 50% (Felsenstein, 1985). We used the likelihood ratio test to investigate the assumption that evolution of phytochrome B sequences in grasses is clocklike (Felsenstein, 1993; Huelsenbeck and Rannala, 1997). In order to facilitate computation of log likelihoods, we trimmed the data set so that no column in the data matrix included sites coded as missing. A matrix of 26 taxa and 1141 nucleotide sites resulted. Two maximum likelihood searches of these data using PAUP*4.0 (Swofford, 1998) invoked the evolutionary model of Hasegawa, Kishino, and Yano (1985), but rate heterogeneity across sites was allowed to vary under a discrete approximation to a gamma distribution with four rate categories, and the shape parameter, gamma, was estimated by maximum likelihood. The two searches varied only with respect to whether or not branch lengths were constrained to fit a model of clocklike evolution. Starting trees for NNI branch swapping were obtained from ten random addition replicates. The log likelihoods from the two searches were compared to determine whether the likelihood of the search without a clock had been significantly increased by allowing branch lengths to vary at a unique rate (Felsenstein, 1993). Additionally, the proportions of Jukes-Cantor corrected nonsynonymous differences among taxa were estimated using MEGA (Kumar, Tamura, and Nei, 1993), and pairwise comparisons of evolutionary rates relative to PHYB from Anomochloa marantoidea were estimated by the method of Wu and Li (1985). RESULTS We observed no sequence variation among multiple PHYB from single taxa, consistent with our expectation that PHYB occurs singly in the genomes of most grasses. The final data matrix for parsimony analyses, comprising 1182 bp of the PHYB gene, contained 610 variable sites and 430 informative characters, with 66, 33, and 331 phylogenetically informative sites at the first, second, and third codon positions, respectively. Seven percent of the cells in the matrix were coded as missing. Nongrass sister taxa, Flagellaria and Joinvillea (Campbell and Kellogg, 1987; Doyle et al., 1992), were included as outgroups in our initial analyses, despite their fragmentary nature ( 300 bp) relative to the sequences from grasses (1182 bp). In all trees, Anomochloa and a second grass, Strep-

5 100 AMERICAN JOURNAL OF BOTANY [Vol. 87 Fig. 1. (a) Generalized structure of the PHYB gene (Quail, 1994). (b) Schematic of the PHYB insert and primer sequences. Arrows indicate direction of synthesis from primers. Degeneracy of each sequence is indicated parenthetically. I inosine. tochaeta, are the earliest diverging grasses (not shown), corroborating the results from analyses of ndhf (Clark, Zhang, and Wendel, 1995) and rbcl (Duvall and Morton, 1996). We did not include Flagellaria (GenBank U61203) and Joinvillea (GenBank U61205) in subsequent analyses in order to minimize the amount of missing data; instead, Anomochloa marantoidea was the outgroup. Maximum parsimony analysis of the 51 PHYB sequences from grasses yielded nine equally parsimonious trees (one shown in Fig. 2) in two islands that differ with respect to (1) placement of Molinia as sister either to Phragmites Hakonechloa or to the chloridoids, and (2) placement of Chasmanthium and Thysanolaena as sister either to the panicoids or Phragmites Hakonechloa. Minimal-length trees are 2433 steps and have consistency and retention indices of 0.35 (uninformative characters excluded) and 0.58, respectively. The strict consensus tree, with tribal and subfamilial divisions designated according to Clayton and Renvoize (1986), is given in Fig. 3. The herbaceous bambusoid Streptochaeta occurs in a basal polytomy with Anomochloa (the two are sister taxa in 60% of the bootstrap replicates when Flagellaria and Joinvillea are included; not shown). The monophyly of the rest of the family is supported by 37 base substitutions and bootstrap and decay (d) values of 100% and 18, respectively. The next diverging taxa also are herbaceous bambusoids, first Pharus and then Puelia. The early divergence of Pharus is highly supported: 38 base substitutions and bootstrap and decay values of 100% and 16, respectively, support the monophyly of the grasses exclusive of Pharus. Similarly, the divergence of the rest of the grasses from Puelia is supported by 22 base substitutions and bootstrap and decay values of 93% and 6, respectively. The nonbasal grasses are divided into two major clades, one that includes all sampled panicoid, arundinoid, chloridoid, and centothecoid species and one that includes the rest of the sampled bambusoid, and all the sampled oryzoid and pooid species. The bambusoid oryzoid pooid clade (corresponding with the BOP clade of Clark, Zhang, and Wendel, 1995) is strongly supported as monophyletic in the PHYB phylogeny by 17 base substitutions, a bootstrap value of 96%, and a decay value of 8. Moreover, the internal structure of this clade is completely resolved and 57% of its clades have bootstrap support 90%. For example, the core Bambusoideae (Bambuseae, Olyreae, and Parianeae), the Oryzoideae, and an expanded Pooideae that includes the ex-arundinoid Anisopogon and the ex-bambusoid Diarrhena, occur in 98, 99 and 96% of bootstrap replicates, respectively. There is modest support (15 base substitutions, bootstrap 70%, d 2) for the sistergroup relationship of Pooideae with Oryzoideae. Within Pooideae, nine of the 15 internal branches have bootstrap values of 90%, and six have decay values of 6. A clade of Lygeum Nardus occurs as sister to the remainder of the subfamily in 83% of the bootstrap replicates (d 2). Within Oryzoideae, Oryzeae (monophyletic in 100% of the bootstrap replicates) and Ehrharta are sister taxa. Within Bambusoideae, Parianeae occurs in 100% of the bootstrap replicates and is sister to Olyreae in 83%, but the Bambuseae are poorly supported (bootstrap 70%, d 2). Placement of the herbaceous bambusoid Streptogyna is equivocal. In all nine of the shortest trees, it is sister to the rest of the BOP clade, but there is little support for this arrangement (bootstrap 70%, d 2). Constraint analysis reveals that Streptogyna is placed with the rest of the Bambusoideae of the BOP clade in trees that are just two steps longer than the minimal-length trees from unconstrained analysis. In contrast, constraining Streptogyna to fit the topology of the ndhf tree (Clark, Zhang, and Wendel, 1995), which places it with Oryzoideae, is more costly, adding five steps to minimal-length trees. The clade consisting of the panicoid, arundinoid, chloridoid, and centothecoid grasses (corresponding with the PACC clade of Davis and Soreng, 1993) is strongly resolved as monophyletic in the PHYB phylogeny, supported by 34 base substitutions, a bootstrap value of 100%, and a decay value of 7. However, in comparison with the BOP clade, the internal structure of this clade is less resolved. Two traditionally recognized subfamilies, Panicoideae and Chloridoideae, are well supported with 100 and 94% bootstrap support, respectively. Monophyly of the Centothecoideae remains undetermined because just Chasmanthium was sampled. Chasmanthium and the arundinoid Thysanolaena are sister taxa in 94% of bootstrap replicates. The arundinoids are polyphyletic, as has

6 January 2000] MATHEWS ET AL. PHYB PHYLOGENY IN GRASSES 101 been noted in nearly all other phylogenetic studies. Aristida and Danthonia are sister taxa (bootstrap 91%, d 5), and are sister to the rest of the PACC clade in 81% of the bootstrap replicates (d 3); Phragmites and Hakonechloa are sister taxa in 99% of the bootstrap replicates (d 8), but their relationship with another arundinoid, Molinia, is not retained in the consensus. Among subfamilies, Panicoideae is the best sampled, and displays the most internal structure. Andropogoneae Arundinella and Paniceae are monophyletic in 98 and 100% of the bootstrap replicates, respectively, and are sister taxa in 95% of the bootstrap replicates. Danthoniopsis (Arundinelleae) is sister to the rest of the Panicoideae in 95% of the bootstrap replicates. Constraining Danthonia to a clade with chloridoid taxa, a topology observed in both the rbcl (Barker, Linder, and Harley, 1995) and early chloroplast DNA restriction site (Davis and Soreng, 1993) trees resulted in three equally parsimonious trees requiring 2447 steps, 14 steps longer than the minimallength trees. Constraining Danthonia and Aristida into a trichotomy with Chloridoideae consistent with Barker s (1997) rbcl tree requires ten extra steps. The clock and nonclock searches of the pruned PHYB data set using maximum likelihood resulted in single and identical trees; their topology is identical with a pruned parsimony consensus tree. Comparison of the log likelihoods of the two trees suggests that the log likelihood is significantly increased when branch lengths are allowed to vary at unique rates ( 2 log 89.52, df 24, P 0.005). Thus, evolution of exon I of PHYB in grasses apparently is not clocklike. The Wu and Li (1985) test, however, revealed just a single significant rate difference between the PHYB sequences of Panicum and Phragmites (data not shown). DISCUSSION We found that nucleotide data from the single phytochrome paralog, PHYB, provides strong evidence of phylogenetic structure within the grass family. PHYB data from 51 species resolves a basal grade of herbaceous bambusoids and strongly supports the monophyly of two principal nonbasal clades of the grass family: the first, a panicoid arundinoid chloridoid centothecoid group corresponding with the strongly supported PACC clade of Davis and Soreng (1993); and second, a bambusoid oryzoid pooid group corresponding with the weakly supported BOP clade of Clark, Zhang, and Wendel, In PHYB trees that included Flagellaria and Joinvillea, neotropical Anomochloa and Streptochaeta are the earliest diverging grasses, corroborating the pattern revealed by data from ndhf (Clark, Zhang, and Wendel, 1995), from GBSSI (granule-bound starch synthase I; Mason-Gamer, Weil, and Kellogg, 1998), and from combined chloroplast structural and restriction site characters (Soreng and Davis, 1998), and supporting the placement of Anomochloa as sister to the rest of the grasses by rbcl data (Duvall and Morton, 1996). Similarly, the position of Phareae as the next diverging branch, another feature of the ndhf, GBSSI, and plastid restriction site trees, is strongly corroborated. A third bambusoid element, the West African Puelia, is here resolved as the next diverging branch and sister to the BOP and PACC clades. The basal branches of the grass family tree Members of the subfamily Bambusoideae traditionally have been the focus of speculations concerning the most primitive members of the grass family (e.g., Celakovský, 1889; Arber, 1934; Soderstrom, 1981a). They share apparently plesiomorphic features, such as spikelet-like branches ( pseudospikelets ) and indeterminate inflorescences. The current taxonomic circumscription of the Bambusoideae s.l. (e.g., Clayton and Renvoize, 1986) includes the Bambuseae (mostly woody bamboos, but including Puelia), as well as the herbaceous bambusoid tribes Streptochaeteae, Anomochloeae, Phareae, Streptogyneae, Parianeae, and Olyreae. Molecular data suggest, however, that Bambusoideae s.l. are polyphyletic. For example, data from ndhf (Clark, Zhang, and Wendel, 1995), PHYB (this study), plastid restriction sites (Soreng and Davis, 1998), and GBSSI (Mason-Gamer, Weil, and Kellogg, 1998) establish that the herbaceous bambusoids, Anomochloa, Streptochaeta, and Pharus, are members of the earliest diverging lineages in the grass family, while Parianeae, Olyreae, Streptogyneae, and Bambuseae are nested within the BOP clade. Anomochloa Streptochaeta and the pharoid lineage have been elevated to subfamilial status, in Anomochlooideae and Pharoideae, respectively (Clark and Judziewicz, 1996). The strong resolution in the PHYB phylogeny of another herbaceous bambusoid, Puelia, as the next diverging branch suggests that it also is better placed outside the core Bambusoideae. This West African genus is distinguished by several morphological features, including external ligules, dimorphic florets, and extension of the rachilla. Soderstrom contended that Puelia was ancient (Soderstrom, 1981a), and placed it outside a core Bambusoideae (Soderstrom, 1981a; Soderstrom and Ellis, 1987). Additional molecular data suggest that Puelia and Guaduella, a second West African taxon also segregated from the core Bambusoideae by Soderstrom and Ellis (1987), form a third basal lineage warranting subfamilial rank (GPWG, 1998a, b). Together these findings support the view of Clark, Zhang, and Wendel (1995) that certain presumed synapomorphies of the Bambusoideae s.l., such as the presence of a short mesocotyl internode during embryonic development and the presence of arm cells and fusoid cells, are better considered as synapomorphies of the whole family that are lost from later lineages. Thus, these characters of the embryo and leaf can be added to the long list of morphological characters that distinguish the grasses (Campbell and Kellogg, 1987). Support for the BOP clade The PHYB phylogeny is unique in its highly supported resolution of a BOP clade. The BOP clade is only weakly supported by the ndhf data (6-bp mutations, d 1 in Clark, Zhang, and, Wendel, 1995) and does not occur in other chloroplast gene trees. In rbcl and recent plastid restriction site trees, Pooideae are sister to the PACC clade (Barker, 1997; Barker, Linder, and Harley, 1995; Duvall and Morton, 1996; Soreng and Davis, 1998). Clark and colleagues (1995) hypothesized that the weak support for the BOP group in their ndhf data may have resulted from rapid divergence among its constituent lineages. The absence of this strongly resolved element of the PHYB phylogeny

7 102 AMERICAN JOURNAL OF BOTANY [Vol. 87

8 January 2000] MATHEWS ET AL. PHYB PHYLOGENY IN GRASSES 103 from chloroplast trees, and from trees inferred from combined plastid data sets (L. Clark, J. Davis, and E. Kellogg, unpublished data), is puzzling. It is possible that molecular changes in PHYB coincided with morphological radiation of this clade, while changes in the chloroplast genome did not. Alternatively, ambiguity in the plastid data sets with regard to relationships among the BOP subfamilies might result from patterns of plastid lineage sorting that conflict with the nuclear and/or species phylogeny, or from reticulation. Phylogenetic structure within the BOP clade Oryzoid genera are placed within Bambusoideae s.l. in many classifications (e.g., Clayton and Renvoize, 1986; Soderstrom and Ellis, 1987; Kellogg and Watson, 1993.) In the most comprehensive analysis of morphological data, the oryzoid tribes Oryzeae and Ehrharteae are nested within a monophyletic Bambusoideae s.l. (Kellogg and Watson, 1993), while evidence of their close relationship emerges from analyses of both morphological data (Hilu and Wright, 1982; Kellogg and Campbell, 1987; Kellogg and Watson, 1993) and plastid data (Cummings, King, and Kellogg, 1994; Clark, Zhang, and Wendel, 1995; Soreng and Davis, 1998). In the ndhf consensus tree, Oryzeae Ehrharteae, together with Streptogyna, are one of the trichotomous lineages of the BOP clade (Clark, Zhang, and Wendel, 1995). In contrast, the PHYB phylogeny places the monophyletic oryzoid group in a moderately supported sister-group relationship with Pooideae (70% bootstrap support, d 2), while the core Bambusoideae (Bambuseae, Olyreae, and Parianeae) are resolved as a basal lineage in the BOP clade. Possible morphological synapomorphies of a pooid-oryzoid alliance include lodicule number (2), first seedling internodes that elongate, presence of adventitious roots at the coleoptilar node, a narrow first seedling blade, and absence of the embryonic scutellar cleft. The placement of Streptogyna remains problematic. Based on the amphiatlantic tropical distribution of extant species of Streptogyna, Soderstrom (1981a) included it among taxa he considered archaic. This is not inconsistent with its placement in the PHYB phylogeny, where it is sister to the rest of the BOP clade. However, as noted above, the ndhf phylogeny places Streptogyna as sister to the oryzoids (Clark, Zhang, and Wendel, 1995). Constraining the PHYB phylogeny to this arrangement adds five steps to the length of minimal-length trees, while constraining it to occur with the core Bambusoideae adds just two steps. Our support for a monophyletic pooid group is consistent with a large body of existing morphological and molecular evidence. Kellogg and Campbell (1987), Cummings, King, and Kellogg (1994), and Soreng and Davis (1998) supported a (Nardus Lygeum) group basalmost in a larger pooid clade, a topology that is corroborated by the PHYB phylogeny. The relative order of divergence of the pooid tribes Meliceae and Stipeae has not been resolved unambiguously in any phylogenetic analysis thus far. The PHYB data set unites Meliceae with Stipeae (represented by Nassella), but this topology is not well supported and contradicts other findings (e.g., Hsiao et al., 1995; Catalán, Kellogg, and Olmstead, 1997; Soreng and Davis, 1998); thus, it should be confirmed with additional data from Stipeae. Chloroplast data sets from ndhf and from restriction site morphological characters resolve Diarrhena within the Pooideae (Clark, Zhang, and Wendel, 1995; Catalán, Kellogg, and Olmstead, 1997; Soreng and Davis, 1998), justifying the contention of Kellogg and Campbell (1987) that this bambusoid grass belonged in Pooideae. Similarly, the arundinoid genus Anisopogon is firmly placed in Pooideae by PHYB data, a pattern also noted in analysis of ndhf (J. Davis, Cornell University, personal communication). Thus, the PHYB data concur with other data in supporting a revised circumscription of the Pooideae that is more inclusive than current taxonomic treatments of the subfamily. Phylogenetic structure within the PACC clade Recent chloroplast gene trees and the PHYB phylogeny concur in the strong resolution of a monophyletic PACC group consisting of panicoid, arundinoid, chloridoid, and centothecoid grasses (e.g., Barker, Linder, and Harley, 1995; Clark, Zhang, and Wendel, 1995; Duvall and Morton, 1996; Barker, 1997; Soreng and Davis, 1998). Within this group, the Arundinoideae have long been considered a miscellaneous assemblage of genera, lacking even a single character that would unite its disparate taxa or a subset thereof. Moreover, most comprehensive phylogenetic analyses support the view that the subfamily is paraphyletic or polyphyletic (e.g., Kellogg and Campbell, 1987; Barker, Linder, and Harley, 1995; Clark, Zhang, and Wendel, 1995; Mathews and Sharrock, 1996; Barker, 1997; Soreng and Davis, 1998; but see Hsiao et al., 1998). In the PHYB phylogeny, three reedy Arundineae [Molinia, (Hakonechloa, Phragmites)] are a clade in six of the nine shortest trees, perhaps representing an arundinoid core. The fourth arundinoid, Danthonia, is resolved as the sister to Aristida, (of the Aristideae of Clayton and Renvoize, 1986), and the two are sister to the rest of the PACC clade. Danthonia is our single sample from a sizable group of arundinoid genera (the Danthonieae), all of which apparently share the putative synapomorphy of haustorial synergids in the embryo sac (Verboom, Linder, and Barker, 1994). In the rbcl tree of Barker (1997), separate lineages of reedy arundinoids, danthonioids, and aristidoids are resolved. However, in contrast to the PHYB phylogeny, the latter two are in a clade with Chloridoideae. Constraining the PHYB phylogeny to create a trichotomy of Aristida, Danthonia, and Chloridoideae is costly, requiring ten extra steps. The monophyly of Chloridoideae is supported in analysis of anatomical and physiological characters (including, among other features, the predominance of the C 4 Fig. 2. A phylogeny of PHYB DNA sequences from 51 grasses (1182 nucleotides, 430 informative characters). Heuristic parsimony analysis (500 random addition replicates with TBR swapping in PAUP*4.0; Swofford, 1998) yielded nine most parsimonious trees of 2433 steps; CI 0.35 (autapomorphies excluded); RI Numbers above branches are inferred branch lengths under ACCTRAN optimization.

9 104 AMERICAN JOURNAL OF BOTANY [Vol. 87

10 January 2000] MATHEWS ET AL. PHYB PHYLOGENY IN GRASSES 105 photosynthetic pathway). Recent molecular analyses concur in the monophyly of this subfamily as circumscribed in current taxonomic treatments, as do the PHYB data, which resolve a well-supported chloridoid clade, despite the fragmentary nature of the sequences from Bouteloua and Eragrostis. The monophyly of Panicoideae is supported by morphological features such as paired spikelets with a single female fertile floret (Kellogg and Campbell, 1987). Subsequent phylogenetic analyses have supported the monophyly of the panicoid tribe Andropogoneae and its sistergroup relationship to the Paniceae (e.g., Davis and Soreng, 1993; Barker, Linder, and Harley, 1995; Duvall and Morton, 1996; Mathews and Sharrock, 1996), while the Arundinelleae are polyphyletic (e.g., Barker, Linder, and Harley, 1995; Spangler et al., 1999). Analysis of PHYB data strongly corroborates the polyphyly of Arundinelleae in placing Danthoniopsis as sister to the rest of the panicoids, and Arundinella as sister to the Andropogoneae. The true affinities of centothecoid genera have emerged just recently, having been recognized as a tribe within Bambusoideae (e.g., Watson and Dallwitz, 1992), as a tribe with arundinoid affinities (e.g., Kellogg and Campbell, 1987; Soderstrom and Ellis, 1987), or as a separate subfamily (Soderstrom, 1981b; Clayton and Renvoize, 1986). Chloroplast restriction site data were the first to place the centothecoid Chasmanthium firmly in the PACC clade (Davis and Soreng, 1993), a position confirmed by both rbcl and ndhf data (Barker, Linder, and Harley, 1995; Clark, Zhang, and Wendel, 1995). The plastid data further revealed the relationship of centothecoids with the arundinoid Thysanolaena. Data from PHYB strongly support the relationship of Chasmanthium with Thysanolaena, and six of the nine shortest trees are consistent with the plastid data in placing them as sister to the Panicoideae. The utility of PHYB sequences Our analyses illustrate the power and utility of sampling a single paralog of the phytochrome multigene family for resolving relationships within Poaceae. Phylogenetic structure within Poaceae is well defined by the PHYB data. The basal branches and principle clades are highly supported, 69% of all clades in the phylogeny are supported by bootstrap values of 90%, and structure within the BOP clade is fully resolved and well supported. Thus, the nuclear PHYB phylogeny is a robust test of the plastid phylogenies, which mostly are corroborated. Phytochrome sequences may be especially useful for resolving relationships within Poaceae because of their relatively rapid rate of nucleotide substitution; estimates suggest that they have evolved faster than the plastid sequences from which most molecular phylogenies of Poaceae have been inferred (Mathews, Lavin, and Sharrock, 1995; Olmstead and Reeves, 1995). Although we presented evidence that evolution of the PHYB sequences in grasses is not clocklike, we cannot attribute any conflict observed among the plastid and PHYB phylogenies to this phenomenon. For example, we wondered whether the well-supported resolution of the BOP clade by the PHYB data might result from more rapid nucleotide evolution in this clade relative to evolution in the PACC clade, which also is resolved by the plastid data sets. This is not the case, however; relative rate tests revealed that sequences from BOP taxa are evolving more slowly relative to Anomochloa than sequences from PACC taxa, although the Wu and Li (1985) test does not suggest that the differences are significant (data not shown). Additional points of conflict are the placement of Streptogyna, Danthonia, and Aristida; we did not analyze these conflicts in further detail because they are being investigated in combined analyses of eight data sets from the grasses, of which the PHYB data set is one (GPWG, 1998a, b). LITERATURE CITED ARBER, A The Gramineae: a study of cereal, bamboo, and grass. University Press, Cambridge, UK. AVDULOV, N. P Kario-sistematicheskoye issledovaniye semeystva zlakov. Prilozheniye 44 k Trudy po prikladnoy botanike, genetike I selektsii, 428 pages. Leningrad. [Karyosystematic studies in the grass family. Supplement 44 to the Bulletin of Applied Botany, Genetics and Plant Breeding. Leningrad. Russian text, pages 1 352; German summary, pages ; index, pages English translation (mislabeled as supplement 43) published for the Smithsonian Institution and the National Science Foundation, Washington, D.C., by the Indian National Scientific Documentation Centre, New Delhi, TT ] BARKER, N. P The relationships of Amphipogon, Elytrophorus, and Cyperochloa (Poaceae) as suggested by rbcl sequence data. Telopea 7: , H. P. LINDER, AND E. H. HARLEY Polyphyly of the Arundinoideae (Poaceae): evidence from rbcl sequence data. Systematic Botany 20: BREMER, K The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42: BROWN, R Prodromus Florae Novae Hollandiae et Insulae Van- Diemen, v. 1, viii pages. J. Johnson, London, UK General remarks, geographical and systematical, on the botany of Terra Australis. In M. Flinders, A voyage to Terra Australis, vol. 2, London, UK. BROWN, W. V Leaf anatomy in grass systematics. Botanical Gazette 119: CAMPBELL, C. S The subfamilies and tribes of Gramineae (Poaceae) in the southeastern United States. Journal of the Arnold Arboretum 66: , AND E. A. KELLOGG Sister group relationships of the Poaceae. In T. R. Soderstrom, K. W. Hilu, C. S. Campbell, and M. E. Barkworth [eds.], Grass systematics and evolution, Smithsonian Institution, Washington, DC, USA. CATALÁN, P., E. A. KELLOGG, AND R. G. OLMSTEAD Phylogeny of Poaceae subfamily Pooideae based on chloroplast ndhf gene sequences. Molecular Phylogenetics and Evolution 8: Fig. 3. Strict consensus of the nine most parsimonious trees from parsimony analysis (500 random addition replicates with TBR swapping in PAUP*4.0; Swofford, 1998) of PHYB DNA sequences from 51 grasses (1182 nucleotides, 430 informative characters). All trees are 2433 steps; CI 0.35 (autapomorphies excluded); RI Tribal designation (labels at far right) follows Clayton and Renvoize (1986). BA Bambusoideae, OR Oryzoideae, PO Pooideae, CH Chloridoideae, AR Arundinoideae, PA Panicoideae, CE Centothecoideae. Numbers of above branches are bootstrap percentages 70% from 1000 replicates. Numbers below branches are decay values determined using AutoDecay 4.0 (Eriksson, 1998).

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