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Diversity and Evolution of Vitaceae in the Philippines

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Diversity and Evolution of Vitaceae in the Philippines Philippine Journal of Science 142: 223-244, Special Issue ISSN 0031 - 7683 Date Received: ?? ???????? 2013 Diversity and Evolution of Vitaceae in the Philippines Jun Wen1, Limin Lu2, and John K. Boggan1 1 Department of Botany, MRC-166, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, U.S.A. 2 State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China Vitaceae is economically well-known for grapes and ecologically important as major lianas in tropical and temperate forests. This study analyzes the assembly of taxa of Vitaceae in the Philippines in the phylogenetic framework using five chloroplast DNA markers and enumerates the taxonomy of Vitaceae in the Philippines. The results suggest active floristic exchanges between the Philippines and other parts of Asia and Australia in the Miocene and Pliocene with some elements in the Oligocene. The taxonomic study recognizes seven genera and 55 species. Two new species are validly published and four new combinations are made: Ampelocissus sinuosa (Merr.) J. Wen & Boggan, comb. nov.; Causonis corniculata (Benth.) J. Wen & L.M. Lu, comb. nov.; Causonis pterita (Merr.) J. Wen & L.M. Lu, comb. nov.; Tetrastigma simplicifolia (Merr.) J. Wen & Boggan, comb. nov.; Tetrastigma silvestrei Elmer ex J. Wen & Boggan, sp. nov., and Cayratia coi J. Wen & Boggan, sp. nov. The last species is named in honor of Leonardo Co. Key Words: Vitaceae, Philippines, phylogeny, taxonomy, Ampelocissus, Ampelopsis, Causonis, Cayratia, Cissus, Cyphostemma, Parthenocissus, Pterisanthes, Rafflesia, Nothocissus, Tetrastigma, Vitis INTRODUCTION have suggested the need to redefine several genera. Cayratia Juss., Cyphostemma (Planch.) Alston and Tetrastigma were Vitaceae (the grape family) consists of about 14 genera and supported to form a clade by all these analyses and the 900 species primarily distributed in tropical regions (Wen monophyly of Cyphostemma and Tetrastigma was each 2007a). The family is well-known for grapes (species of Vitis strongly supported. Cayratia was, however, found to be L.) and is ecologically important because many species are paraphyletic with Tetrastigma and Cyphostemma nested major climbers in tropical and temperate forests. The genus within it (Lu et al. 2013), rendering the need for redefining Tetrastigma (Miq.) Planch. of Vitaceae is also famous in the generic limits of Cayratia. The phylogenetic analyses southeast Asia for being the host plants of the holoparasitic also supported a clade of the grape genus Vitis and its close Rafflesiaceae, which includes Rafflesia R. Br. ex Gray, the relatives Ampelocissus Planch., Pterisanthes Blume and genus producing the largest flower of the world (Wen 2007a). Nothocissus (Miq.) Latiff from the tropics (hereafter referred Vitaceae has been subjected to recent phylogenetic studies to as the Vitis-Ampelocissus clade, see Ren et al. 2011). (e.g., Soejima & Wen 2006, Rossetto et al. 2007, Wen et al. Pterisanthes was found to be nested within Ampelocissus 2007, Ren et al. 2011, Nie et al. 2012, Trias-Blasi et al. 2012, (Ren et al. 2011). A clade of Ampelopsis and its close Lu et al. 2013, Wen et al. 2013). The phylogenetic analyses relatives (the African Rhoicissus Planch., the Australian Clematicissus Planch. and a small clade of about five species Corresponding Author: [email protected] of Cissus L. from South America) has been resolved as 223 Philippine Journal of Science Wen et al.: Vitaceae in the Philippines… Vol. 142: Special Issue the first diverged lineage within Vitaceae, but the genus the Philippines and Asia overall, with a global sampling Ampelopsis is paraphyletic (Nie et al. 2012). scheme (Appendix 1). Sequences of five plastid markers including atpB-rbcL, rps16, trnC-petN, trnH-psbA, and The Malesian region is an important center of diversity of trnL-F were mostly obtained from GenBank based on Vitaceae with nine of the 14 recognized genera and 165 studies from the senior author’s lab (e.g., Soejima & Wen of the 900 species in the family: Ampelocissus (35 spp.), 2006, Nie et al. 2010, 2012, Chen et al. 2011a, b, Ren et Ampelopsis (2 spp.), Cayratia (20 spp.), Cissus (31 spp.), al. 2011, Lu et al. 2012, 2013, Liu et al. 2013), with 52 Nothocissus (6 spp.), Parthenocissus (1 sp.), Pterisanthes new sequences (including nine atpB-rbcL, nine rps16, (20 spp.), Tetrastigma (50 spp.), and Vitis (1 sp. native 15 trnC-petN, 11 trnH-psbA, and eight trnL-F) generated and 1 sp. cultivated). for the current study following the protocols in Ren et al. Vitaceae of the Philippines was treated initially by Blanco (2011) and Lu et al. (2013). The program Sequencher 5.0 (1837, 1845, 1877), who recognized seven species of (Gene Codes Co., Ann Arbor, Michigan, USA) was used to Cissus, belonging to four currently recognized genera evaluate chromatograms for base confirmation and to edit of Vitaceae (Causonis Raf., Cayratia, Cissus and contiguous sequences. Sequences were initially aligned Tetrastigma), and one genus Melicope Forster & Forster f. using MUSCLE 3.8.31 (Edgar 2004), and the alignment of Rutaceae (Hartley 2001; also see Merrill 1905, 1918b). was then adjusted manually in Geneious 6.1.4 (created by Merrill treated Vitaceae in a series of publications (Merrill Biomatters, available from http://www.geneious.com/). 1907, 1912a, b, 1916, 1918a, 1920, 1923). Elmer (1915, 1939) described a few species of the family. Quisumbing Phylogenetic Analyses & Merrill (1924) and Quisumbing (1944) further Phylogenetic analyses were initially conducted for documented Philippine Vitaceae, described new taxa, and individual DNA regions with maximum likelihood made nomenclatural changes in the family. Nevertheless, (ML) method using RAxML 7.2.6 with 1,000 bootstrap the family has not been revised taxonomically and replicates (Stamatakis 2006). Preliminary analyses for systematically for the Philippines in many decades since. each region indicated no significant topological conflicts The objectives in this study are to: (1) discuss the (BS > 70%; Hillis & Bull 1993) among individual evolutionary assembly of Vitaceae in the Philippines based markers. Furthermore, because the chloroplast genome on a broad phylogenetic framework of the grape family; is generally considered as one unit without recombination and (2) enumerate the taxonomic diversity of Vitaceae in in angiosperms (Whitfeld & Bottomley 1983), sequences the Philippines. of the five plastid markers were thus combined and were analysed with maximum parsimony (MP) and Bayesian In memory of Leonardo Co, the senior author Jun Wen felt inference (BI). that it would be most meaningful to provide an updated treatment of Vitaceae in the Philippines and discuss its Maximum parsimony analyses were conducted using evolutionary assembly, in light of recent phylogenetic PAUP*4.0b10 (Swofford 2003) with a heuristic search evidence. Wen first met Leonardo Co in 1991 at the Harvard strategy followed by 100 random-addition-sequence University Herbaria where Wen was a postdoctoral fellow replicates with tree bisection and reconnection (TBR) and Co was visiting. Wen communicated with Leonardo branch swapping. Bootstrap values (BS) were estimated Co on Vitaceae, Leeaceae and Araliaceae treatments for with 1,000 bootstrap replicates (Felsenstein 1985) the Philippines in several different occasions. After the 6th using heuristic searched as described above, but with International Flora Malesiana Symposium in Los Baños branch swapping limited to 10,000,000 rearrangements in 2004, Wen joined the post-symposium excursion led by per replicate due to memory constraints. A partitioned Leonardo to various areas in Luzon. During the trip, Wen Bayesian analysis was conducted using MrBayes 3.2.1 and Co also discussed the taxonomy and identification of (Ronquist & Huelsenbeck 2003, 2012). The data set a number of Vitaceae specimens encountered during the was partitioned into five subsets corresponding to five trip and examined many images of Vitaceae specimens plastid regions with unlinked substitution models. Two they both had. independent runs were simultaneously performed with each run consisting of one cold chain and three heated chains. Each run was conducted with 15,000,000 generations and sampled one tree every 1,500 generations. MATERIALS AND METHODS Analyses were run until the average standard deviation of the split frequencies approached 0.01, indicating that two runs converged onto a stationary distribution. A 50% Taxon Sampling majority-rule consensus tree and the posterior probabilities The study sampled 163 accessions of Vitaceae and its (PP) were calculated after discarding the first 25% trees sister family Leeaceae (Ridsdale 1974), emphasizing as burn-in. The generalized time reversible model (GTR) 224 Philippine Journal of Science Wen et al.: Vitaceae in the Philippines… Vol. 142: Special Issue with a gamma-distributed rate variation was selected as the research. In this study, we excluded Leea from Vitaceae, best-fit models for each partition as well as the combined following Ridsdale (1974) and Wen (2007b). data set as determined by MrModeltest 2.3 (Nylander 2004) under the Akaike Information Criterion (AIC). Divergence Time Estimation RESULTS We estimated the divergence time of clades using The parsimony analysis generated more than 100,000 most the combined 5-marker data set with BEAST 1.7.4 parsimonious trees (MPTs) with a length of 4,025 steps, a (Drummond & Rambaut 2007). The strict molecular consistency index (CI) of 0.65,
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