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Phylogenetic Analysis of the <I>Calamus Javensis</I>

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Phylogenetic Analysis of the <I>Calamus Javensis</I> Blumea 65, 2020: 205–211 www.ingentaconnect.com/content/nhn/blumea RESEARCH ARTICLE https://doi.org/10.3767/blumea.2020.65.03.04 Phylogenetic analysis of the Calamus javensis complex (Arecaceae: Calamoideae) in Malesia M. Atria1,2,3,*, M. Eurlings1, W.J. Baker 4, J. Dransfield4, P.C. van Welzen1,3 Key words Abstract A phylogenetic analysis on specimen level was made in possible support of a multivariate analysis of the Calamus javensis complex. Nine species, at some time recognized within the complex, and several recognisable Calamoideae forms were included. The phylogenetic markers used were the nuclear 5S spacer (5S nrDNA) and the chloroplast Calamus javensis Maturase K (matK). The Bayesian analysis showed that only 5S provided some resolution. The 50 % majority rule chloroplast DNA consensus showed one major polytomy with a few supported groups, which were mainly morphologically unsup- intraspecific variation ported pairs of specimens. However, one group, the form C. tenompokensis (the only distinct group in a multivariate matK analysis) is morphologically distinct and phylogenetically monophyletic and can be recognized as a species. Of all molecular phylogeny other recognizable forms, we only consider C. acuminatus to be regarded as a variety as it was not supported in nuclear DNA the morphometric analysis. paraphyletic rattan Citation: Atria M, Eurlings M, Baker WJ, et al. 2020. Phylogenetic analysis of the Calamus javensis complex (Arecaceae: Calamoideae) in Malesia. Blumea 65 (3): 205–211. https://doi.org/10.3767/blumea.2020.65.03.04. Effectively published online: 22 December 2020. INTRODUCTION be found in Barfod & Dransfield 2013). The distribution of the species complex ranges from Southern Thailand and Peninsular Calamus L. is the largest genus among the climbing palms, Malaysia to Sumatra, Java, Borneo and Palawan (Dransfield also called rattans (http://www.fao.org/3/Y2783E/y2783e05. 1992, Barfod & Dransfield 2013). The greatest morphological di- htm; Sreekumar & Renuka 2008), and is classified in subtribe versity is in north Borneo. Typical for all forms is a stem dia meter Calaminae. The generic subdivision of the subtribe appeared of 2–6 mm without leaf sheaths and to 10 mm with sheaths; to be as difficult as the C. javensis complex. The phylogeny internodes up to 30 cm long (usually shorter); a distinct ocrea, of the rattans by Kramadibrata (1992) suggested Calamus to deep crimson when young; pinnate, ecrirrate leaves to 40 cm be paraphyletic. This was confirmed by Baker et al. (2000b) in long, flabellate terminal leaflets and the lowermost pair often their phylogenetic study based on the 5S nrDNA spacer. They swept back across the stem; a flagellum to 75 cm long, long found four major lineages within the genus (Baker et al. 2000b), inflorescences with red rachillae and ripe fruits ovoid in shape. whereby the other genera of the Calaminae are nested within The morphological variation within C. javensis is complex and Calamus. Baker (2015): “A revised classification is proposed in large and there are hardly constant differences among the enti- which [the genera] Ceratolobus [Blume ex Schult. & Schult.f.], ties. As a result, traditional morphological observations did not Daemonorops [Blume], Pogonotium [J.Dransf.] and Retispa- provide a satisfactory solution (Dransfield 1992, Dransfield et tha [J.Dransf.] are placed in synonymy with Calamus. This is al. 2008, Atria et al. 2017). A recent morphometric study by Atria presented as a stable, alternative and pragmatic taxonomic et al. (2017) showed that within the complex only two clearly solution for this problematic group”. defined taxa could be circumscribed, C. javensis with a broad Calamus javensis Blume (Arecaceae: Calamoideae) is a slen- range of variation and a far less variable C. tenompokensis. der rattan common in southeast Asian tropical rainforests. The Calamus tenompokensis can easily be distinguished from other species is very polymorphic and includes some taxonomically taxa within the C. javensis complex by its short stem, angular non-recognized, but morphologically distinct forms, next to a petiole and rachis, a very different leaf sheath appearance range of species that were ever split off: C. acuminatus Becc., (the sheaths being massive and robust), and the number and C. amplijugus J.Dransf., C. congestiflorus J.Dransf., C. corruga- arrangement of the leaflets. Calamus tenompokensis has tus Becc., C. elopurensis J.Dransf., C. hypertrichosus Becc., 9 pairs of large, lanceolate leaflets, which are almost always C. impar Becc. and C. tenompokensis Furtado (synonyms can regularly arranged, while in the rest of the complex the leaflets are smaller, 6 or 7, and ovate to broadly ovate. The staminate 1 Naturalis Biodiversity Center, Research Group Tropical Botany, P.O. Box flowers resemble those of C. javensis, but the base of the calyx 9517, 2300 RA Leiden, The Netherlands; corresponding author e-mail: [email protected]. is swollen (vs not swollen in C. javensis). The pistillate inflo- 2 Departemen Biologi, Fakultas Matematika dan Ilmu Pengetahuan Alam, rescences have rachilla bracts that are different in the broadly Universitas Indonesia (UI), Depok 16424, Indonesia. cupuliform limb (vs bracts tightly sheathing in C. javensis). 3 Institute of Biology Leiden, University of Leiden, P.O. Box 9505, 2300 RA Leiden, The Netherlands. In this study we conduct a phylogenetic analysis of the C. javen- 4 Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, United King- sis complex based on two different regions, 5S nrDNA and dom. matK (formerly used by Baker et al. 2000a, b). Aim is to see if © 2020 Naturalis Biodiversity Center You are free to share - to copy, distribute and transmit the work, under the following conditions: Attribution: You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). Non-commercial: You may not use this work for commercial purposes. No derivative works: You may not alter, transform, or build upon this work. For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights. 206 Blumea – Volume 65 / 3, 2020 the complex can be subdivided in monophyletic, recognisable Alignment of sequences and phylogenetic analysis units, which may corroborate the morphometric study (Atria The alignment of the forward and reverse sequences were et al. 2017). checked manually with Sequencher 4.1.4. The 5S nrDNA se- quences showed in most cases little ambiguity in the align- MATERIALS AND METHODS ments. Refined sequences or multiple sequence alignments were made using CLUSTAL W option of the program Bioedit Taxon sampling v. 7.0.9 (Hall 1999), which was also used for the matK se- About 52 samples of silica gel-dried leaf fragments and her- quences. barium specimens were used for DNA sequencing. One silica sample of C. flabellatus was included as outgroup. One of the Phylogenetic analysis syntypes, from West Java (Blume s.n. (L, sheet 900.182-94) and Sequences with indels are included to provide as much phylo- silica gel-dried material from the type locality were included. All genetic information as possible (Baum et al. 1994). 5S and samples cover the distribution area of the C. javensis complex. matK were analysed both as separate datasets and combined. A list of voucher specimens can be found in Appendix 1. A parsimony analysis was performed with PAUP* v. 4.0a157 (Swofford 2002), but because of the low variability many clado- DNA extraction, amplification and sequencing grams were possible and the program had to be terminated as DNA extraction from the silica gel-dried leaves and herbarium the swapping ran too long. An analysis of the two markers via vouchers was done using the magnetic bead-based isolation Bayesian inference using Markov Chain Monte Carlo algorithms procedure (NucleoMag® 96 Plant kit, Macherey-Nagel; https:// (MCMC) as implemented in MrBayes v. 3.2.6 (Ronquist et al. www.mn-net.com), carried out on an automated KingFisher 2012) with 10 000 000 generations gave better results. Most extractor (https://www.thermofisher.com/nl/en/home.html). default values were used: 4 chains of which 1 cold and 3 heated Two DNA regions were amplified, the nuclear 5S spacer and the in two simultaneous runs, the markov chain was sampled chloroplast marker matK. Primers (Table 1) for this study were every 1 000th generation whereby the first 25 % of the samples designed specifically for the group based on the work of Baker were discarded as burnin. We ran MrBayes in XSEDE via the et al. (2000b) using Geneious v. 10.1.3 (http://www.geneious. CIPRES science gateway (http://www.phylo.org/; Miller et al. com). Primers for the 5S spacer (Table 1) were M13-R435R 2015). The substitution model used is GTR (generalized time- (R2) and M13F-ITS103F (F2). The matK sequences were reversible) (Ronquist et al. 2012, De Salle & Rosenfeld 2013). amplified from total genomic DNA using the designed primers We checked the Potential Scale Reduction Factors (PSRF) in M13R-831RmatK3 (M3) and M13F-578FmatK3 (F3). M13 tails the MrBayes SUMP output, the values were 1 or close to 1, (M13F TGTAAAACGACGGCCAGT, M13R CAGGAAACAGC- which also indicates correct convergence of the chains. The TATGAC) used are from Messing (1983). two tree files of the combined markers were then combined using LogCombiner v. 1.10.3 (in BEAST v. 1.10.3; http://tree. Table 1 Primers designed for this study oriented 5’–3’, m13 tails not in- bio.ed.ac.uk; Drummond et al. 2002, Drummond & Rambaut cluded. 2007, Suchard et al.
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