Phylogeny of the Neotropical element of the Randia clade (Gardenieae, Rubiaceae, Gentianales)
Authors/Creators
- 1. Programa de Pós Graduação em Botânica – PPGBOT, Departamento de Biologia, Universidade Estadual de Feira de Santana, Feira de Santana, BA, Feira de Santana, Brazil
- 2. Bergius Botanic Garden, Stockholm, Sweden
- 3. Universidade Federal da Bahia, Salvador, Brazil
- 4. Stockholm University, Stockholm, Sweden
Description
Background and aims – Generic limits of the tropical tribe Gardenieae (Ixoroideae, Rubiaceae) have partly remained unsettled. We produced a new phylogeny of the Randia clade, with emphasis on its Neotropical clade comprising five genera (Casasia, Randia, Rosenbergiodendron, Sphinctanthus, and Tocoyena). The result was subsequently used to evaluate and discuss: a) the respective monophyly of the above-mentioned genera and their interrelationships; b) relationships within Tocoyena and the evolutionary relevance of its subgeneric classification; and c) the monophyly of the morphologically variable T. formosa.
Material and methods – We examined the phylogeny of the Randia clade based on maximum likelihood and Bayesian analyses of sequence data from two nuclear (ETS and Xdh) and two plastid (petB-petD and trnT-F) DNA regions from 59 individuals (including seven representatives from the remaining Ixoroideae).
Key results – The Neotropical clade of the Randia clade comprises three major lineages, the Randia armata subclade, the Randia-Casasia subclade and the Rosenbergiodendron subclade. Neither Casasia nor Randia is monophyletic. Tocoyena is sister to Rosenbergiodendron + Sphinctanthus and is subdivided into three lineages: the Tocoyena pittieri group, the Tocoyena guianensis group, and the core Tocoyena. Tocoyena williamsii is paraphyletic with respect to T. pittieri. Tocoyena formosa is polyphyletic and should be re-circumscribed.
Conclusions – Our results demonstrate the monophyly of each of the relatively species-poor genera Rosenbergiodendron, Sphinctanthus, and Tocoyena, and confirm their close affinity. The serial classification of Tocoyena does not reflect the evolutionary history of the genus. The paraphyly of T. williamsii with respect to T. pittieri, together with their morphological similarities and geographic distributions, support the inclusion of the former in the latter. Our study calls for additional phylogenetic work on Casasia and the more species-rich genus Randia. While the respective monophyly of both genera is rejected here, future work with a broader representation of Randia is needed.
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References
- Alfaro M.E., Zoller S. & Lutzoni F. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Molecular Biology and Evolution 20(2): 255–266. https://doi.org/10.1093/molbev/msg028
- Andreasen K. & Bremer B. 1996. Phylogeny of the subfamily Ixoroideae (Rubiaceae). In: Robbrecht E., Puff C. & Smets E. (eds) Second International Rubiaceae Conference, Proceedings. Opera Botanica Belgica 7: 119–138.
- Andreasen K. & Bremer B. 2000. Combined phylogenetic analysis in the Rubiaceae-Ixoroideae: morphology, nuclear and chloroplast DNA data. American Journal of Botany 87(11): 1731–1748. https://doi.org/10.2307/2656750
- Baldwin B.G. & Markos S. 1998. Phylogenetic utility of the external transcribed spacer (ETS) of 18S–26S rDNA: congruence of ETS and ITS trees of Calycadenia (Compositae). Molecular Phylogenetics and Evolution 10(3): 449–463. https://doi.org/10.1006/mpev.1998.0545
- Bremekamp C.E.B. 1966. Remarks on the position, the delimitation and the subdivision of the Rubiaceae. Acta Botanica Neerlandica 15: 1–33.
- Bremer B., Bremer K., Heidari N., et al. 2002. Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomic levels. Molecular Phylogenetics and Evolution 24(2): 274–301. https://doi.org/10.1016/s1055-7903(02)00240-3
- Davis A.P., Chester M., Maurin O. & Fay M.F. 2007. Searching for the relatives of Coffea (Rubiaceae, Ixoroideae): the circumscription and phylogeny of Coffeeae based on plastid sequence data and morphology. American Journal of Botany 94(3): 313–329. https://doi.org/10.3732/ajb.94.3.313
- De Candolle A.P. 1830. Prodromus systematis naturalis regni vegetabilis, vol. 4. Treuttel & Würz, Paris. Available from https://www.biodiversitylibrary.org/item/7153#page/5/mode/1up [accessed 6 Sep. 2021].
- Delprete P.G. 2008. Revision of Tocoyena (Rubiaceae: Gardenieae) from the states of Goiás and Tocantins and a new species endemic to white-sand areas in the Brazilian cerrado. Journal of the Botanical Research Institute of Texas 2(2): 983–993.
- Delprete P.G. & Persson C. 2013. Sphinctanthus fluvii-dulcis (Rubiaceae: Gardenieae), a new species from the Rio Doce Valley, Atlantic forest of Minas Gerais, Brazil, with detailed observations on ovary morphology. Kew Bulletin 68(1): 173–177. https://doi.org/10.1007/s12225-012-9426-9
- Doyle J.J. 1991. DNA protocols for plants. In: Hewitt G., Johnson A.W.B. & Young J.P.W. (eds) Molecular techniques in taxonomy: 283–293. Springer, Berlin.
- Doyle J.J. & Doyle J.L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19(1): 11–15.
- Dwyer J.D. 1968. Borojoa and Tocoyena (Rubiaceae) in Panama. Phytologia 17: 445–449.
- Edgar R.C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32(5): 1792–1797. https://doi.org/10.1093/nar/gkh340
- Erixon P., Svennblad B., Britton T. & Oxelman B. 2003. Reliability of Bayesian posterior probabilities and bootstrap frequences in phylogenetics. Systematic Biology 52: 665–673. https://doi.org/10.1080/10635150390235485
- Fagerlind F. 1943. Die Sprossfolge in der Gattung Randia und ihre Bedeutung für die Revision den Gattung. Arkiv för Botanik 30(7): 1–57.
- Gottsberger G., Silberbauer-Gottsberger I. & Ehrendorfer F. 2020. The genus Tocoyena (Rubiaceae): revisiting the T. formosa-complex and description of a new endemic species from the cerrado vegetation in Mato Grosso, Brazil. Plant Diversity and Evolution 132(1): 43–56. https://doi.org/10.1127/pde/2019/0132-0088
- Gustafsson C. & Persson C. 2002. Phylogenetic relationships among species of the neotropical genus Randia (Rubiaceae, Gardenieae) inferred from molecular and mophological data. Taxon 51: 661–674. https://doi.org/10.2307/1555021
- Gustafsson C.G.R. 1998. The neotropical Rosenbergiodendron (Rubiaceae, Gardenieae). Brittonia 50(4): 452–466. https://doi.org/10.2307/2807754
- Hooker J.D. 1873. Rubiaceae. In: Bentham G. & Hooker J.D. (eds) Genera plantarum vol. 2: 7–151. Reeve & Co, London.
- Huelsenbeck J.P. & Ronquist F.R. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17(8): 754–755. https://doi.org/10.1093/bioinformatics/17.8.754
- Kainulainen K. & Bremer B. 2014. Phylogeny of Euclinia and allied genera of Gardenieae (Rubiaceae), and description of Melanoxerus, an endemic genus of Madagascar. Taxon 63(4): 819–830. https://doi.org/10.12705/634.2
- Kainulainen K., Razafimandimbison S.G. & Bremer B. 2013. Phylogenetic relationships and new tribal delimitations in subfamily Ixoroideae (Rubiaceae). Botanical Journal of the Linnean Society 173: 387–406. https://doi.org/10.1111/boj.12038
- Keay R.W.J. 1958. Randia and Gardenia in West Africa. Bulletin du Jardin botanique de l'État à Bruxelles 28(1): 15–72. https://doi.org/10.2307/3667018
- Larget B. & Simon D.L. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Molecular Biology and Evolution 16(6): 750–759. https://doi.org/10.1093/oxfordjournals.molbev.a026160
- Larsson A. 2014. AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 30: 3276–3278. https://doi.org/10.1093/bioinformatics/btu531
- Lorence D.H. 1986. Glossostipula (Rubiaceae), a new genus from México and Guatemala. Candollea 41(2): 453–461.
- Lorence D.H. & Dwyer J.D. 1987. New taxa and a new name in Mexican and Central American Randia (Rubiaceae, Gardenieae). Boletin de la Sociedad Botanica de México 47: 37–48.
- Löhne C. & Borsch T. 2004. Molecular evolution and phylogenetic utility of the petD group II intron: a case study in basal angiosperms. Molecular Biology and Evolution 22(2): 317–332. https://doi.org/10.1093/molbev/msi019
- Mau B., Newton M.A. & Larget B. 1999. Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55: 1–12. https://doi.org/10.1111/j.0006-341X.1999.00001.x
- Miller M.A., Pfeiffer W. & Schwartz T. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. In: Proceedings of the gateway computing environments workshop: 1–8. New Orleans, LA. https://doi.org/10.1109/GCE.2010.5676129
- Mouly A., Kainulainen K., Persson C., et al. 2014. Phylogenetic structure and clade circumscriptions in the Gardenieae complex (Rubiaceae). Taxon 63(4): 801–818. https://doi.org/10.12705/634.4
- Negrón-Ortiz V. & Watson L.E. 2002. Molecular phylogeny and biogeography of Erithalis (Rubiaceae), an endemic of the Caribbean Basin. Plant Systematics and Evolution 234(1): 71–83. https://doi.org/10.1007/s00606-002-0192-2
- Nylander J.A.A. 2004. MrModeltest. Version 2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University, Uppsala.
- Persson C. 1993. Pollen morphology of the Gardenieae‐Gardeniinae (Rubiaceae). Nordic Journal of Botany 13(5): 561–582. https://doi.org/10.1111/j.1756-1051.1993.tb00101.x
- Persson C. 2000. Phylogeny of Gardenieae (Rubiaceae) based on chloroplast DNA sequences from the rps16 intron and trnL(UAA)-F(GAA) intergenic spacer. Nordic Journal of Botany 20(3): 257–270. https://doi.org/10.1111/j.1756-1051.2000.tb00742.x
- Prado A.L. 1987. Revisão taxonómica do gènero Tocoyena Aubl. (Rubiaceae) no Brasil. Master's thesis, Universidade Estadual de Campinas, SP, Brazil. Available from http://www.repositorio.unicamp.br/handle/REPOSIP/315265 [accessed 19 Feb. 2021].
- Rambaut A. & Drummond A.J. 2007. Tracer. MCMC trace analysis tool. Version 1.4. Computer program distributed by the authors. Available from https://beast.community/tracer [accessed 1 Sep. 2020].
- Robbrecht E. 1988. Tropical woody Rubiaceae. Opera Botanica Belgica 1: 1–271.
- Robbrecht E. & Puff C. 1986. A survey of the Gardenieae and related tribes (Rubiaceae). Botanische Jahrbücher für Systematik, Pflanzengeschichte und Pflanzengeographie 108: 63–137.
- Ronquist F. & Huelsenbeck J.P. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–1574. https://doi.org/10.1093/bioinformatics/btg180
- Schumann K. 1891. Rubiaceae. In: Engler A. & Prantl K. (eds) Die natürlichen Pflanzenfamilien: 4(4): 1–156. Wilhelm Engelmann, Leipzig.
- Silberbauer-Gottsberger I., Gottsberger G. & Ehrendorfer F. 1992. Hybrid speciation and radiation in the neotropical woody genus Tocoyena (Rubiaceae). Plant Systematics and Evolution 181(3): 143–169. https://doi.org/10.1007/BF00937441
- Staden R. 1996. The Staden sequence analysis package. Molecular Biotechnology 5: 233–241. https://doi.org/10.1007/BF02900361
- Staden R., Beal K.F. & Bonfield J.K. 2000. The Staden Package, 1998. In: Misener S. & Krawets S.A. (eds) Bioinformatics methods and protocols, vol. 132 of Methods in molecular biology: 115–130. Humana Press Inc., New Jersey. https://doi.org/10.1385/1-59259-192-2:115
- Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9): 1312–1313. https://doi.org/10.1093/bioinformatics/btu033
- Standley P.C. 1921. North American flora. New York Botanical Garden, New York.
- Standley P.C. 1928. New plants from Central America. - XI. Journal of the Washington Academy of Sciences 18(6): 160–169. https://www.jstor.org/stable/24522628
- Standley P.C. 1931. Studies of American plants–V. Publications of the Field Museum of Natural History, Botanical Series 8(5): 295–398. https://doi.org/10.5962/bhl.title.3827
- Standley P.C. 1933. The flora of Barro Colorado Island Panama. Contributions from the Arnold Arboretum of Harvard University 5: 1–178. https://doi.org/10.5962/bhl.title.153450
- Steyermark J.A. 1964. Novedades en las Rubiáceas Colombianas de Cuatrecasas. Acta Biologica Venezuelica 4(1): 1–117.
- Steyermark J.A. 1981. New species of Rubiaceae from French Guiana, Brazil, and Colombia. Brittonia 33(3): 385–400. https://doi.org/10.2307/2806429
- Taberlet P., Gielly L., Pautou G. & Bouvet J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17: 1105–1109. https://doi.org/10.1007/BF00037152
- Thiers B. continuously updated. Index Herbariorum: a global directory of public herbaria and associated staff. New York Botanical Garden's Virtual Herbarium. Available from http://sweetgum.nybg.org/ih/ [accessed Mar. 2021].
- Tropicos 2021. Missouri Botanical Garden. Available from http://www.tropicos.org [accessed 27 Apr. 2021].
- Verdcourt B. 1958. Remarks on the classification of the Rubiaceae. Bulletin du Jardin botanique de l'État à Bruxelles 28(3): 209–281. https://doi.org/10.2307/3667090
- WCSP 2021. World checklist of selected plant families. Facilitated by the Royal Botanic Gardens, Kew. Available from http://wcsp.science.kew.org/ [accessed Mar. 2021].
- Wikström N., Kainulainen K., Razafimandimbison S.G., Smedmark J.E.E. & Bremer B. 2015. A revised time tree of the asterids: establishing a temporal framework for evolutionary studies of the coffee family (Rubiaceae). PLoS ONE 10(5): e0126690. https://doi.org/10.1371/journal.pone.0126690
- Yang Z. & Rannala B. 1997. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo method. Molecular Biology and Evolution 14: 717–724. https://doi.org/10.1093/oxfordjournals.molbev.a025811