Molecular Phylogenetics of Calamus (Palmae) and Related Rattan Genera Based on 5S nrDNA Spacer Sequence Data

Baker, William J.; Hedderson, Terry A.; Dransfield, John

doi:10.1006/mpev.1999.0697

Cited by 66 publications

(40 citation statements)

References 35 publications

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“…In the current classification of palms , Calamus is placed in subtribe Calaminae (Calameae: Calamoideae) along with four other rattan genera, Ceratolobus Blume (in Schultes & Schultes 1830: lxxx), Daemonorops Blume (in Schultes & Schultes 1830: 1333, Pogonotium Dransfield (1980a: 763) and Retispatha Dransfield (1980b: 529). Subtribe Calaminae is a strongly supported monophyletic group, whereas all available molecular and morphological phylogenetic evidence indicates that Calamus is not, and that the four other genera in the subtribe are variously nested within it (Baker et al 2000a, Baker et al 2000b, c, Baker et al 2009). These studies also indicate that Daemonorops, the second largest genus of Calaminae with ca.…”

Section: Introductionmentioning

confidence: 99%

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A revised delimitation of the rattan genus Calamus (Arecaceae)

Baker

2015

Phytotaxa

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All available phylogenetic evidence indicates that the rattan genus Calamus, the largest of all palm (Arecaceae) genera, is non-monophyletic and that the four remaining genera of subtribe Calaminae (Calameae: Calamoideae), Ceratolobus, Daemonorops, Pogonotium and Retispatha, are nested within it. This issue has not yet been adequately addressed in palm classifications, with recent authors preferring to wait for further phylogenetic evidence before revising the limits of the genera. Here, an alternative solution is proposed that is both pragmatic and phylogenetically robust. An expanded Calamus is recognised into which Ceratolobus, Daemonorops, Pogonotium and Retispatha are subsumed. This broad generic concept, which includes ca. 520 species, has practical advantages as it is more clearly defined by morphological and anatomical characters, and resolves potential biases introduced to recent eco-evolutionary research on palms by the non-monophyly of critical genera. Future phylogenetic research may yet provide an alternative means of delimiting these genera, but the broad sense Calamus proposed here is a justifiable alternative that can be adopted immediately. Nomenclatural synopses transferring currently accepted species of Ceratolobus, Daemonorops and Pogonotium to Calamus are provided, including 70 new combinations and 12 replacement names.

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Section: Introductionmentioning

confidence: 99%

“…110 species, may not be monophyletic. In the current classification of palms, Dransfield et al (2008) highlighted these systematic issues, but followed Baker et al (2000b) in maintaining the prevailing generic limits, while acknowledging that further phylogenetic research would lead to changes in the future.…”

Section: Introductionmentioning

confidence: 99%

A revised delimitation of the rattan genus Calamus (Arecaceae)

Baker

2015

Phytotaxa

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“…The 120 bp 5S-rRNA gene sequence is highly conserved across species, while the NTS region exhibits variation in base composition and length (in the range 100-800 bp) from species to species, [9] since it is apparently not under the same rigorous selection pressure as in the coding region. [10][11][12] The high level of conservation of the 5S-rRNA gene is associated with the precise function of 5S-rRNA as a component of the large ribosomal subunit in all eukaryotic organisms. Some regions of the gene are more conserved than others, which is explained by the regulation of 5S-rRNA transcription.…”

Section: Introductionmentioning

confidence: 99%

“…[7,13] Based on these assumptions, variation in the NTS region has been used in a number of plant species for studying intraspecifi c variation, mapping 5S-rDNA arrays, genome evolution and phylogenetic reconstruction. [9,10,14] …”

Section: Introductionmentioning

confidence: 99%

PCR, sequencing and PCR–RFLP of the 5S‐rRNA‐NTS region as a tool for the DNA fingerprinting of medicinal and aromatic plants

Varese

Bertea

Maffei

2010

Flavour & Fragrance J

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Molecular genetic methods have several advantages over classical morphological and chemical analyses. For instance, the genetic method requires genotype instead of phenotype, therefore DNA-based techniques have been widely used for rapid identifi cation of herbal medicine and aromatic plants. Using PCR approaches, nanogram quantities of DNA are required to amplify and yield suffi cient amounts of template DNA for molecular genetic analysis. Recently, the molecular discrimination of some higher plant species has been evaluated using sequences of a 5S-rRNA gene spacer region. The variation in the non-transcribed sequence (NTS) region has been used in a number of plant species for studying intraspecifi c variation, mapping 5S rDNA arrays, genome evolution and phylogenetic reconstruction. In this minireview we summarize the potential use of the 5S-rRNA-NTS region as a tool for the DNA fi ngerprinting of medicinal and aromatic plants.

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“…In the palm family, a range of molecular data types from plastid DNA restriction fragment length polymorphisms (RFLPs) (Uhl et al 1995, Wilson et al 1990, plastid DNA coding and noncoding sequence data (Asmussen 1999, Asmussen et al 2000, Asmussen and Chase 2001, Baker et al 2000a, 2000c, Hahn 2002a, 2002b, and nuclear DNA sequence data (Barrow 1999, Baker et al 2000a, 2000b, Hahn 2002a, Loo et al 2006 have been employed.…”

Section: Molecular Phylogeny Of Pinanga (Palmae) Based On Internal Trmentioning

confidence: 99%

Molecular phylogeny of Pinanga (Palmae) based on internal transcribed spacers (ITS) sequence data

Witono

Kondo

2007

Chromosome Botany

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ABSTRACT. Molecular phylogeny of 52 species of Pinanga (Palmae) were investigated using the internal transcribed spacer (ITS) sequence data of nuclear ribosomal DNA. Polymorphic sequence data were identified in the ITS region of Pinanga, indicating that concerted evolution is not completely homogenizing ITS repeats in the nuclear genome. The strict consensus of Pinanga used in the study showed that the genus is monophyletic. Pinanga rivularis and P. aristata formed the basal clade; followed by P. albescens, P. brevipes, P. veitchii, P. sessilifolia and P. crassipes as sister taxa; and P. disticha, P. watanaiana, and P. pulchella were sister taxa to the clade containing the sampled species of Pinanga used in the study. In general, two major clades were recognized: first, Pinanga from Wallacea, East Malesia and adjacent region clade and second, Pinanga from West Malesia and adjacent region clade. The clade separation was strongly correspond with geographical distribution and it did not support infrageneric classification based on distichous and sprirally triads flower described by Beccari (1886). Conforming phylogenetic tree generated by ITS sequence data and morphological observations appear that habit, size and form of stem, leaf and inflorescence were not useful characters for infrageneric classification of Pinanga. Examination of phylogenetic relationships using combination of morphological characters including pollen morphology, cytological data, nuclear genome size and DNA sequence data are necessary for providing a more accurate picture of phylogenetic relationships and affords the opportunity to garner insights into evolutionary process of Pinanga.

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Molecular Phylogenetics of Calamus (Palmae) and Related Rattan Genera Based on 5S nrDNA Spacer Sequence Data

Cited by 66 publications

References 35 publications

A revised delimitation of the rattan genus Calamus (Arecaceae)

A revised delimitation of the rattan genus Calamus (Arecaceae)

PCR, sequencing and PCR–RFLP of the 5S‐rRNA‐NTS region as a tool for the DNA fingerprinting of medicinal and aromatic plants

Molecular phylogeny of Pinanga (Palmae) based on internal transcribed spacers (ITS) sequence data

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