The systematic position of the monocotyledons inferred from 26S RNA gene DNA sequences.
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).
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).
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]
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.
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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Department of Biological and Environmental Sciences, P.O. Box 92000, McNeese State University, Lake Charles, Louisiana 70609-2000 U.S.A.
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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|Publication:||Journal of the Alabama Academy of Science|
|Date:||Jul 1, 2007|
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