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Phylogenetic Analysis of Nuclear Ribosomal ITS

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Phylogenetic Analysis of Nuclear Ribosomal ITS Phylogenetic Analysis of Nuclear Ribosomal ITS/5.8S Sequences in the Tribe Millettieae (Fabaceae): Poecilanthe-Cyclolobium, the core Millettieae, and the Callerya Group Author(s): Jer-ming Hu, Matt Lavin, Martin F. Wojciechowski, and Michael J. Sanderson Source: Systematic Botany, 27(4):722-733. Published By: The American Society of Plant Taxonomists URL: http://www.bioone.org/doi/full/10.1043/0363-6445-27.4.722 BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/page/terms_of_use. Usage of BioOne content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder. BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. Systematic Botany (2002), 27(4): pp. 722±733 q Copyright 2002 by the American Society of Plant Taxonomists Phylogenetic Analysis of Nuclear Ribosomal ITS/5.8S Sequences in the Tribe Millettieae (Fabaceae): Poecilanthe-Cyclolobium, the core Millettieae, and the Callerya Group JER-MING HU,1,5 MATT LAVIN,2 MARTIN F. W OJCIECHOWSKI,3 and MICHAEL J. SANDERSON4 1Department of Botany, National Taiwan University, Taipei, Taiwan; 2Department of Plant Sciences, Montana State University, Bozeman, Montana 59717; 3Department of Plant Biology, Arizona State University, Tempe, Arizona 85287; 4Section of Evolution and Ecology, University of California, Davis, California 95616 5Author for correspondence ([email protected]) Communicating Editor: Jerrold I. Davis ABSTRACT. The taxonomic composition of three principal and distantly related groups of the former tribe Millettieae, which were ®rst identi®ed from nuclear phytochrome and chloroplast trnK/matK sequences, was more extensively investi- gated with a phylogenetic analysis of nuclear ribosomal DNA ITS/5.8S sequences. The ®rst of these groups includes the neotropical genera Poecilanthe and Cyclolobium, which are resolved as basal lineages in a clade that otherwise includes the neotropical genera Brongniartia and Harpalyce and the Australian Templetonia and Hovea. The second group includes the large millettioid genera, Millettia, Lonchocarpus, Derris,andTephrosia, which are referred to as the ``core Millettieae'' group. Phy- logenetic analysis of nuclear ribosomal DNA ITS/5.8S sequences reveals that Millettia is polyphyletic, and that subclades of the core Millettieae group, such as the New World Lonchocarpus or the pantropical Tephrosia and segregate genera (e.g., Chadsia and Mundulea), each form well supported monophyletic subgroups. The third lineage includes the genera Afgekia, Callerya,andWisteria. These genera are resolved as a basal subclade in the inverted-repeat-lacking clade, which is a large legume group that includes the many well known temperate and herbaceous legumes, such as Astragalus, Medicago and Pisum, but not any other Millettieae. Phylogenetic analyses of trnK/matK DNA sequences morphologically similar to Callerya and Wisteria,such have revealed new and well supported higher level re- as Dewevrea M. Micheli, Endosamara Geesink, Ostry- lationships within Papilionoideae subfamily of Faba- ocarpus Hooker, and Sarcodum Loureiro. ceae (e.g., Hu et al. 2000; Wojciechowski et al. 2000; In order to obtain a more complete phylogeny for Lavin et al. 2001a). In particular, the large tribe Mil- Callerya and other Millettieae, sequence variation from lettieae has been shown to comprise at least three dis- the nuclear ribosomal DNA internal transcribed spacer tantly related lineages: a Poecilanthe-Cyclolobium group, (ITS) region was sampled and analyzed for more of a ``core Millettieae'' group, and a Callerya-Wisteria the relevant species than have been sampled in previ- group (Hu et al. 2000). The genera Callerya and Wis- ous studies of this tribe that involved other loci (Lavin teria, for example, actually belong to the inverted-re- et al. 1998; Hu et al. 2000). This study was motivated peat-lacking clade (IRLC; Wojciechowski et al. 1999), a by the high sequence variability in the ITS region, clade comprising legumes lacking one copy of the 25- which has been shown to provide many informative kb inverted repeat in the chloroplast genome. Notably, sites for phylogenetic analysis and to be amenable to this relationship also has been suggested by studies of exhaustive taxon sampling at and below the genus lev- the chloroplast inverted repeat (Lavin et al. 1990; Lis- el (Baldwin et al. 1995; Wojciechowski et al. 1999; Lavin ton 1995), the nuclear phytochrome gene family, and et al. 2001a, 2001b). the chloroplast rbcL analysis (Doyle et al. 1997). Even chromosome numbers of Millettieae species (Hu MATERIALS AND METHODS 2000a) suggest that Callerya and Wisteria are indeed DNA Extraction and Ampli®cation of the ITS Region. Total ge- distinct from other Millettieae. Whereas the Callerya nomic DNAs were isolated from fresh or dried materials using the and Wisteria taxa examined all have x 5 8 or 16, these standard CTAB extraction method or a protocol designed for rain numbers are uncommon in the other Millettieae genera forest species (Doyle and Doyle 1987; Scott and Playford 1996). such as Millettia, Lonchocarpus,andDerris. Double stranded DNA copies of the ITS region were ampli®ed from genomic DNA using the polymerase chain reaction (PCR) Regardless of the above advances into the higher and used the same reagents and conditions described in Hu et al. level relationships of Millettieae, it remains unclear (2000), but with shorter annealing (1 min) and extension (1 min how many other Millettieae taxa are part of the Caller- 30 sec) time. Ampli®cation and sequencing primers of the ITS re- gion were the same as used by Wojciechowski et al. (1997, 1999). ya-Wisteria group. Furthermore, it is uncertain whether Ven t R DNA Polymerase (New England Biolabs) was used in most all species currently assigned to the genera Callerya of the reactions due to its higher ®delity, but in some recalcitrant and Wisteria group occur within this clade. In addition, samples, Taq polymerase (Promega Corp., Madison, Wisconsin) was used to increase the product yield. Nucleotide sequences of many species of Millettieae have yet to be surveyed for PCR products were determined using automated cycle-sequencing chromosome numbers, especially in genera that are and an ABI 377 DNA Sequencer (PE Applied Biosystems, Foster 722 2002] HU ET AL.: NRDNA ITS PHYLOGENY OF MILLETTIEAE 723 City, California) at the University of California, Davis. To minimize of a clade that otherwise includes Brongniartia, Harpa- errors associated with PCR and sequencing, two or more inde- pendent PCR ampli®cations were employed for each taxon and lyce, Templetonia,andHovea (Fig. 1). This ``Brongniar- sequenced separately for both strands. Ambiguous sites were con- tieae clade'' is very well supported as monophyletic, ®rmed by a third run of PCR and sequencing if there was any whereas the basal branching order of Cyclolobium and con¯ict in the consensus sequences from the ®rst two runs of se- Poecilanthe within the Brongniartieae clade is moder- quencing. The consensus sequences were assembled and edited using Sequenchery 3.0 (Gene Codes Corp., Ann Arbor, Michigan). ately supported. Sequence Alignment and Phylogenetic Analyses. All sequences The data set involving the core Millettieae includes were aligned manually with the aid of Se-Al (Rambaut 1996). The 72 taxa and 398 parsimony-informative sites. Species aligned data set has been deposited in TreeBase (Accession #S760). Missing data represented 6.7% of the data set involving Cyclolob- from the tribe Indigofereae and Phaseoleae were used ium and Poecilanthe (largely because of the missing 5.8S sequence as outgroups in this phylogenetic analysis. The ten from several taxa and the ITS2 sequence of Harpalyce brasiliana), equally most parsimonious trees each have a length of 0% of the core Millettieae data set, and 2.7% of the data set in- 2907, a CI of 0.34, and an RI of 0.65. The best sup- volving Callerya and Wisteria. Parsimony analyses of the individual data sets were performed with PAUP* (Swofford 2001). For all ported of the larger clades involves one that stems analyses, gaps were treated as missing data, no sites containing from the most recent common ancestor of Millettia insertion/deletions were excluded, and search options invoked 100 ichthyochtona and Piscidia mollis (Fig. 2). The core Mil- random addition sequences, tree bisection-reconnection branch- swapping, and retention of multiple parsimonious trees. Bootstrap lettieae clade, which is moderately supported by the analyses (Felsenstein 1985) were used to assess clade stability. ITS analysis, is actually slightly more inclusive than Each of 1,000 bootstrap replicates was analyzed with the heuristic this best supported clade and stems from the most search option invoking one random addition replicate each, and recent common ancestor of Millettia lasianthus and Mil- not invoking the retention
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