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The systematic position of the monocotyledons inferred from 26S RNA gene DNA sequences.

ABSTRACT

Although there is no consensus concerning the precise phylogenetic position of the monocotyledons within the angiosperms, most studies suggest that the monocotyledons are diverged from a common ancestor with a basally diverged dicotyledon group. In the present study, a high-level angiosperm phylogeny consisting of 92 terminal taxa was inferred from a data set from the first kb segment of the large ribosomal subunit (26S) rRNA gene DNA sequences. Using maximum likelihood methods this analysis recovered a best tree that suggests that the monocots are sister to a clade consisting of the eudicots and the eumagnollids. Sister to this clade is Ceratophyllum L. (Ceratophyllaceae).

INTRODUCTION

Current evidence suggests that the monocotyledons (monocots) are a monophyletic group (Dahlgren, 1980; Duvall et al., 1993; Chase et al., 1993; Parkinson et al., 1999). Although there is no consensus concerning the precise phylogenetic position of the monocots within the angiosperms (Angiosperm Phylogeny Group (APG), 2003), most studies suggest that the monocots are diverged from a common ancestor with a basal dicotyledon (dicot) group. For example, non-molecular-based studies have suggested that the monocots are most closely related to the Ranales (Ranunculales, Nymphaeales, Magnoliales, Ceratophyllum et al.) (Hutchinson, 1959), the Nymphaeales (Cronquist, 1981; Takhtajan, 1969, 1980), the Ariflorae (Thorne, 1976), the Dioscoreales (Huber, 1969), early shrubby dicotyledons (Stebbins, 1974), the Dioscoreales and the Magnoliifloreae (Dahlgren and Clifford, 1982), the Melanthiales (Thorne, 1992) and the paleoherbs (Aristolochiales, Nymphaeales, Piperales) (Behnke, 1969, 1971; Loconte and Stevenson, 1991).

DNA-based studies likewise have failed to reach a consensus as to the phylogenetic position of the monocots. For example, studies have suggested that the monocots are positioned in a clade with Nelumbo and Ceratophyllum (Hamby and Zimmer, 1992), sister to the paleoherbs (Chase et al., 1993), positioned with the Magnoliales, Laurales, Aristolochiales, Piperales, Nymphaeales in an unresolved clade (Qiu et al., 1993), sister to either the Gunneraceae and the Dilleniaceae, the ranunculids or Ceratophyllum (Soltis et al., 1997), positioned with the eudicots Ceratophyllaceae, Laurales, Magnoliales and Piperales in an unresolved polytomy (APG, 1998), basal within the angiosperms (Donoghue and Mathews, 1998), sister to Chloranthus (Mathews and Donoghue, 1999), sister to the Laurales (Parkinson et al., 1999), positioned with the Eumagnoliids (Winterales, Laurales, Magnoliales, Chloranthales, Piperales) in an unresolved polytomy (Soltis et al., 2000), sister to Ceratophyllum (Zanis et al., 2003) and sister to four magnoliid groups (Canellales, Piperales, Magnoliales, Laurales) (Davis et al., 2004).

To date, the primary DNA sequences that have been used to infer higher order angiosperm phylogenies include the mitochondrial genes atpA, cox1, SSU, the chloroplast genes rbcL psaA, psbB and atpB, and the nuclear small ribosomal subunit (18S). Although these gene sequences have been analyzed separately and in various combinations and suggest that the monocots appear to have evolved from a common ancestor with a basally diverged dicot group, there is no consensus concerning the exact phylogenetic position of the monocots within the angiosperms.

The purpose of this study is to construct a high-level phylogeny of the major angiosperm groups with the aim to infer the phyletic position of the monocots. Large ribosomal subunit (26S) DNA gene sequences were used exclusively in a maximum likelihood analysis.

MATERIALS AND METHODS

Scientific name, voucher information, and GenBank accession numbers for the taxa analyzed in this study are listed in Table 1. Following (Chase et al., 1993; Doyle et al., 1994; Soltis et al., 1997; Soltis et al., 2000; Zanis et al., 2003) a set of gymnosperms (specifically Gnetum and Ephedra (Gnetales)) was designated as outgroup. An approximate 1 kb DNA segment of the 26S gene was sequenced for the taxa included in this analysis. This segment, which spans base positions 4-969 in Oryza sativa (Sugiura et al., 1985) is characterized by conserved segments and more variable expansion segments (Kuzoff et al., 1998). Sequences of the 26S gene have been shown to be informative in higher-level plant systematic studies (Kuzoff et al., 1998).

Total DNA was extracted from tissue using the CTAB method of Doyle and Doyle (1987). DNA sequences were amplified via polymerase chain reaction (PCR) (Mullis and Faloona, 1987, Saiki et al., 1988) from DNA extracted for the species listed in Table 1 with combinations of forward and reverse primers referenced in Neyland (2002). Amplification was achieved with Tfl enzyme (Epicentre Technologies, Madison, WI), using the following thermocycling protocol: a hot start at 94[degrees]C for 3 minutes; 30 amplification cycles of 94[degrees]C for 1 minute, 55[degrees]C for 1 minute; 72[degrees]C for 3.5 minutes, a terminal extension phase at 72[degrees]C and an indefinite terminal hold at 4[degrees]C. The double-stranded PCR product was purified with QIAquick (Qiagen, Hilden, Germany) using the manufacturer's protocol. Two [micro]l of each sample was electrophoresed in a 1.0% agarose mini-gel for quantification against a known standard. Automated sequencing was conducted on an ABI Prism 377 Sequencer with XL Upgrade (housed at Louisiana State University, Baton Rouge, LA, USA) using ABI Prism, Big Dye Terminator cycle sequencing protocol (P.E. Applied Biosystems, Foster City, CA, USA). Sequences have been deposited in the GenBank database (Table 1).

A maximum likelihood search of 1000 replicates was performed using the Phylogenetic Analysis Using Parsimony (PAUP) version 4.0b10 software (Swofford, 2002). Maximum likelihood analysis is the most computationally intensive approach to phylogenetic inference and is also one of the most valuable and robust (Stewart et al., 2001). Starting trees were obtained through step-wise addition. In this search, the transition/transversion ratio was estimated at 1.5 based on the value obtained in a preliminary parsimony-based analysis of the same data. Empirical nucleotide frequencies were used and branches less than or equal to one were collapsed.

As a measure of clade stability or robustness, bootstrap support (Felsenstein, 1985; Sanderson, 1989) was calculated. One thousand full heuristic bootstrap replications were employed in this analysis. Transition/transversion rates were calculated using MacClade software (Maddison and Maddison, 2003).

RESULTS

Alignment of sequences required the introduction of gaps that overwhelmingly occurred in the first three 26S expansion segments as defined by Kuzoff et al. (1998). After the introduction of gaps, the total length of the sequenced data set was 1029 bases. Figure 1 illustrates a gap imbedded in a variable region for a subset of sequences for a subset of taxa. Situated between nucleotide positions 125 and 143, this variable region is flanked by conserved sequences. Copies of aligned sequences are available from the author.

From the maximum likelihood analysis, the score of the best tree found had a log likelihood value of -24735.98808. This maximum likelihood tree suggests that the monocots are monophyletic and are sister to a clade composed of the eudicots, and the eumagnoliids Fig. 2). The eumagnoliids are an informal group composed of the Canellales, Laurales, Magnoliales, Piperales and Chloranthales (sensu Soltis et al., 2000). Sister to this clade is Ceratophyllum L. (Ceratophyllaceae). The branch leading to the monocot split received less than 50% bootstrap support and is, therefore, not strongly supported (Fig. 2).

[FIGURE 1 OMITTED]

[FIGURE 2 OMITTED]

DISCUSSION

The best maximum likelihood tree recovered in this study generally agrees with other molecular-based studies that place the monocots within or near the basal dicots. However, as is evident from the above referenced previous molecular-based studies and the present study, there remains no consensus on the exact phylogenetic position of the monocots within the angiosperms. This disparity likely is due to several factors. For example, because the monocots represent an ancient group, there is certainly homoplastic noise in the sequence data due to nucleotide base reversals. Additionally, the use of different genes and genomes and the employment of disparate sequence analysis methods in these studies may have contributed to the variation in the recovered phylogenetic relationships. Inferring phylogenetic relationships from molecular data requires the selection of an appropriate method from an array of techniques (Swofford and Olsen, 1990). Of the existing approaches to inferring phylogenies directly from character data, that of maximum parsimony has been the most widely used. However, parsimony methods may yield inconsistent estimates of the evolutionary tree when amounts of evolutionary change in different lineages are sufficiently unequal (Felsenstein, 1978; Hasegawa and Fujiwara, 1993). When data sets involve moderate to large amounts of change, parsimony methods can fail (Felsenstein, 1985). For example, in their phylogenetic study of seed plants using sequences from all three plant genomes, Soltis et al. (2002) found that maximum likelihood analyses of chloroplast sequences produced topologies highly similar to those produced from mitochondrial sequences. However, parsimony analyses using chloroplast DNA produced similar results only when the more degenerate third codon position was eliminated from the data set. Soltis et al., (2002) concluded that third codon positions in chloroplast DNA genes may be misleading in phylogenetic analyses of seed plants. Because riboso me genes (as used in the present study) are not framed into codons, the elimination of third codon positions to reduce homoplastic noise is not applicable in 26S-based phylogenetic analyses.

Although fossil pollen suggests that a monocot-dicot dichotomy may have occurred as late as 90-112 MYA in the Cretaceous (Cronquist, 1981; Gandolfo et al., 1998). molecular analyses often suggest an older date. An analysis of chloroplast sequences by Wolfe et al. (1989) suggests that the split may have occurred about 190 MYA in the Jurassic. An analysis of GADPH sequences by Martin et al. (1989) suggests that the dichotomy occurred about 300 MYA in the Carboniferous. The oldest date for the monocot-dicot divergence has been estimated at 360 MYA near the Devonian-Carboniferous boundary from an analysis of rRNA gene sequences (Troitsky et al., 1991). Regardless of this disparity, the monocots are an ancient group and a substantial number of homoplastic reversals undoubtedly have occurred in their DNA sequences. Therefore, the use of the maximum likelihood method may recover more reliable phylogenies than that of the parsimony method at this particular level of investigation.

An additional problem in determining the phylogenetic position of the monocots within the angiosperms is designating an appropriate outgroup. Several previously mentioned studies have used various gymnosperm groups (particularly the Gnetales) as outgroup. However, no gymnosperm group has been identified as sister to angiosperms (Stuessy, 2004). Indeed, several recent studies suggest that the Gnetales are sister to other conifers and not the angiosperms (Goremykin et al., 1996; Hansen et al., 1999; Samigullin et al., 1999; Winter at al., 1999; Bowe et al., 2000; Schmidt and Schneider-Poetsch, 2002; Soltis et al., 2002). Therefore, studies that position the Gnetales as sister to the angiosperms may recover misleading phylogenies (including the position of the monocotyledons).

Mathews and Donoghue (1999) noted that the great differences between angiosperms and all other seed plants render homology assessments exceptionally difficult in morphological analyses and may lead to long-branch attraction (sensu Felsenstein, 1978) in molecular analyses. This may result in the spurious attraction among highly diverged sequences. More specifically, distant conifer outgroups might cluster erroneously with the most diverged angiosperms. However, in an attempt to overcome this problem, Mathews and Donoghue (1999) presented an analysis of duplicated phytochrome PHYA and PHYC gene sequences to root the angiosperms. Their results suggested that Amborella is the most basally diverged angiosperm. Furthermore, other molecular-based studies that used conifers to outgroup the angiosperms have also recovered trees that show Amborella as the most basally diverged angiosperm (Parkinson, 1999; Soltis et al., 2000; Zanis et al., 2003 and the present study). If angiosperm trees are to be rooted in molecular-based phylogenetic analyses, then there appear to be few alternatives to using extant conifer sequences as outgroup.

ACKNOWLEDGEMENTS

This project was funded by the Jack V. Doland Professorship and a Shearman Research Initiative Fund granted to the author through McNeese State University. I thank L. Chatelain, T. Guedry and M. Paulissen for their assistance. Additionally, I thank the following individuals and institutions for supplying plant specimens or DNA for sequencing: B. G. Briggs and K. A. Meany, Royal Botanic Garden, Sydney, Australia (NSW); Graham and Barrett, Royal Ontario Museum, Canada (TRT); M. Chase, Royal Botanic Gardens, Kew, U.K (K); Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA (EEB).

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Ray Neyland

Department of Biological and Environmental Sciences, P.O. Box 92000, McNeese State University, Lake Charles, Louisiana 70609-2000 U.S.A.

Correspondence: rneyland@mcneese.edu
Table 1. Sequenced taxa used in this analysis. All specimens with
indicated voucher/accession numbers were sequenced by the author and are
housed at the McNeese State University (MCN) herbarium. DNA sequences
from other sources are indicated in the footnotes below.

 Voucher/ GenBank
 accession accession
Taxon number number

Monocots
Basal
Acoraceae
 Acorus calamus L. EEB 19970056 AF203679
Alismataceae
 Sagittaria graminea Michx. R. Neyland 345 AF203680
Araceae
 Arisaema triphyllum (L.) Schott R. Neyland 500 AF203678
Hydrochartaceae
 Limnobium spongia (Bosc) Steud. R. Neyland 1025 AF203681

Lilioids
Alstroemeriaceae
 Alstroemeria pulchra Sims R. Neyland 1852 AF290586
Amaryllidaceae
 Crinum americanum L. R. Neyland 785 AF293854
Asparagaceae
 Asparagus officinalis L. R. Neyland 1853 AF203683
Asphodelaceae
 Asphodeline lutea (L.) Reichenb. R. Neyland 1895 AF290584
Campynemataceae
 Campynema lineare Labill. R. Neyland 1926 AF364029
Corsiaceae
 Corsia sp. R. Neyland 1834 AF205514
Colchiaceae
 Colchicum autumnale L. R. Neyland 1921 AF331971
Cyclanthaceae
 Carludovica palmata Ruiz. & Pav. R. Neyland 1839 AF205127
Dioscoreaceae
 Dioscorea macrostachya Benth R. Neyland 1887 AF205123
Iridaceae
 Alophia drummondii (Graham) R. C. Foster R. Neyland 1851 AF203685
Liliaceae
 Lilium michauxii Poir. R. Neyland 1822 AF205126
Orchidaceae
 Listera australis Lindl. R. Neyland 1689 AF203686
 Cypripedium kentuckiensis C. F. Reed R. Neyland 1821 AF205119
Smilacaceae
 Smilax bona-nox L. R. Neyland 486 AF293852
Taccaceae
 Tacca chantrieri Andre R. Neyland 1842 AF205124

Commelinoids
Anarthriaceae
 Anarthria humilis R. Br. B. G. Briggs 9476 AF466389
Arecaceae
 Trachycarpus fortunei (Hook.) H. Wendl. R. Neyland 1885 AF290588
 Wodyetia bifurcata A. K. Irvine R. Neyland 1885 AF290588
Cannaceae
 Canna flaccida Salisb. R. Neyland 363 AF205521
Centrolepidaceae
 Centrolepis strigosa Roem. & Schult. B. G. Briggs 9132 AF466388
Commelinaceae
 Commelina virginica L. R. Neyland 901 AF205516
Cyperaceae
 Rhynchospora latifolia (Baldwin) Thomas R. Neyland 301 AF205518
Ecdiocoleaceae
 Ecdeicolea monostachya F. Muell K. A. Meany T20 AF466387
Eriocaulaceae
 Eriocaulon decangulare L. R. Neyland 796 AY079519
Haemodoraceae
 Anigozanthus flavidus DC. R. Neyland 1884 AF290587
Juncaceae
 Juncus effusus L. R. Neyland 453 AF205520
Musaceae
 Musa paradisica L. R. Neyland 1916 AF331972
Philydraceae
 Philydrum lanuginosum Gaertn. Graham & Barrett AF205519
 1
Poaceae
 Oryza sativa L. e M11585
Pontederiaceae
 Pontederia cordata L. R. Neyland 266 AF205517
Restionaceae
 Restio tetraphyllus Labill. M. Chase 560 AF486829
Velloziaceae
 Xerophyta retinervis Bak. EEB 19970041 AF205878
Xyridaceae
 Xyris laxifolia var. iridifolia (Chapm.) R. Neyland 325 AF66386
 Kral
Zingiberaceae
 Zingiber officinalis Roscoe R. Neyland 1840 AF205522

Dicots
Basal
Amborellaceae
 Amborella trichopoda Baill. a AF479238
Austrobaileyaceae
 Austrobaileya scandens C. T. White f AY095452
Canellales
Winteraceae
 Drimys winteri J. R. Forst. & G. Forst. d AF036491
 Tasmannia insipida R. Br. ex DC. f AY095469
Ceratophyllaceae
 Ceratophyllum demersum L. f AY095456
Chloranthales
Chloranthaceae
 Chloranthus multistachys S. J. Pei f AY095457
 Hedyosmum bonplandianum H. B. K. f AY095461
Laurales
Lauraceae
 Sassafras albidum (Nutt.) Nees e AF264140
Monimaceae
 Hortonia floribunda Wight ex Arn. f AF264143
Magnoliales
Annonaceae f AF264140
 Asimina triloba (L.) Dunal f AY095451
Magnoliaceae
 Magnolia denudata Desr. b AF389256
Nymphaeales
Nymphaeaceae
 Nuphar sp. g AY292901
 Nymphaea sp. f AY095465
Piperales
Aristolochiaceae
 Aristolochia macrophylla Lam. f AY095450
Piperaceae
 Piper betle L. f AY095467
Saururaceae
 Saururus cernuus L. f AY095468

Eudicots
Asclepiadaceae
 Asclepias viridis Walt. R. Neyland 1759 AF148280
Asteraceae
 Tragopogon dubius Scop. d AF036493
Boraginaceae
 Heliotropium curvassicum L. R. Neyland 1309 AF148274
Buxaceae
 Buxus sp. f AY292911
 Pachysandra procumbens Michx. b AF389244
Cactaceae
 Pereskia aculeata P. Mill. a AF479092
Campanulaceae
 Lobelia puberula Michx. R. Neyland 1122 AF148276
Caricaceae
 Carica papaya L. a AF479145
Caryophyllaceae
 Stellaria media (L.) Cirillo. a AF479084
Convolvulaceae
 Evolvulus sericeous Sw. R. Neyland 1761 AF148270
 Ipomoea lacunosa L. R. Neyland 1492 AF146016
Cucurbitaceae
 Cucurbita pepo L. a AF479108
Cyrillaceae
 Cyrilla racemiflora L. R. Neyland 856 AY561838
Ericaceae
 Arctostaphylos uva-ursi (L.) Spreng. R. Neyland 2094 AY596455
Euphorbiaceae
 Euphorbia polychroma A. Kerner a AF479125
Hydrophyllaceae
 Phacelia hirsuta Nutt. R. Neyland 480 AF146533
Iteaceae
 Itea virginica L. a AF479216
Lythraceae
 Lythrum salicaria L. a AF479240
Malvaceae
 Sterculia apetala (Jacq.) H. Karst a AF479137
Menispermaceae
 Menispermum canadense L. b AF389257
Menyanthaceae
 Nymphoides aquatica (J. F. Gmel.) Kuntze R. Neyland 1813 AF148283
Nelumbonaceae
 Nelumbo lutea (Willd.) Pers. b AF389259
Oxalidaceae
 Oxalis dillenii Jacq. a AF479230
Plantaginaceae
 Plantago virginica L. R. Neyland 444 AF148277
Platanaceae
 Platanus occidentalis L. c AF274662
Poleminiaceae
 Phlox divaricata L. R. Neyland 1812 AF148281
Ranunculaceae
 Ranunculus recurvatus Poir. h U52631
Rubiaceae
 Mitchella repens L. R. Neyland 276 AF148279
Rutaceae
 Citrus aurantium L. a AY177420
Saxifragaceae
 Saxifraga mertensiana Bong. a AF479224
Scrophulariaceae
 Mazus pumilus (Burm. f.) Steenis R. Neyland 368 AF148278
Solanaceae
 Physalis angulata L. R. Neyland 355 AF148271

Outgroup
Ephedraceae
 Ephedra distachya L. d AF036489
Gnetaceae
 Gnetum gnemon L. d AF036488

Soltis et. al. (2003) = a; Kim et al. (2004) = b; Fishbein et al.
(2001) = c; Kuzoff et al. (1998) = d, Sugiura et al. (1985) = e; Zanis
et al. (2003) = f; Qiu et al. (1993) = g; Ro et al. (1997) = h.
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Author:Neyland, Ray
Publication:Journal of the Alabama Academy of Science
Geographic Code:1USA
Date:Jul 1, 2007
Words:4536
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