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Phylogenetic relationships among Myrceugenia, Blepharocalyx, and Luma (Myrtaceae) based on paired-sites models and the secondary structures of ITS and ETS sequences

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Abstract

To establish relationships among the genera Blepharocalyx, Luma, and Myrceugenia, the phylogeny of tribe Myrteae was reconstructed based on secondary structures of the sequences of ITS (ITS1-5.8S-ITS2) and ETS regions from 93 taxa belonging to 29 genera. The DNA sequences were aligned according to their secondary structure and analysed with Bayesian inference (BI) using base substitution models for RNA, which can differentiate between the regions consisting of base pairs (helices) and unpaired bases (loops). The best-fit models were RNA7C for ITS and RNA7B for ETS, which differ in how they predict double substitutions and symmetry of the frequency of base pairs. The phylogenetic hypothesis was compared with results obtained using classical 4-state models, the results of maximum parsimony, and using sequence alignment without considering the secondary structure. Analyses show low support along the backbone of the consensus trees, those using substitution models of paired sites showing more highly supported derived clades than substitution models of independent sites. All tests were consistent and differed in the positioning of certain groups, but they also showed that Blepharocalyx, Luma, and Myrceugenia arise from three independent lineages that are not closely related. The substitution model for RNA shows that Luma is a monophyletic group and sister to the other genera of Myrteae, except for Myrtus communis. Myrceugenia appears as a monophyletic group, except for M. fernandeziana, which is related to Blepharocalyx, a genus that appears to be biphyletic.

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Acknowledgments

This research was funded by the Comisión Nacional de Investigación Científica y Tecnológica, Gobierno de Chile (CONYCIT, 24090098) and the University of Concepción (DIUC 209.111.054-1.0). The herbaria ASU, CONC, K, MO, RB, and the Botanical Garden of the University of Vienna provided material for DNA extraction. We thank Leslie Landrum for cooperation in sending samples for extraction, academic discussions, and critical reading of the manuscript. Eva Lucas and Edith Karpino (Jodrell Laboratory, Royal Botanic Garden, Kew), sent us DNA samples. División de Investigación Bogotá (DIB-Universidad Nacional de Colombia) and B. Matthew, C. Michael, and B. Erin from American Journal Expert for translations into English. We thank to anonymous reviewers for their suggestions and comments on the manuscript. JM received a Grant from the University of Concepción-Programa de Mejoramiento de la Calidad y la Equidad de la Educación Superior (MECESUP, UCO0708) and funding from CONICYT and Universidad Nacional de Colombia for a stay in the Department of Systematic and Evolutionary Botany, University of Vienna. TFS was partially financed by Austrian Science Fund (FWF) Grant No. P21723-B16.

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Authors and Affiliations

  1. Departamento de Botánica, Universidad de Concepción, Casilla 160-C, Concepción, Chile

    José Murillo-A & Eduardo Ruiz

  2. Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, 1030, Vienna, Austria

    Tod F. Stuessy

  3. Instituto de Ciencias Naturales, Universidad Nacional de Colombia, Apartado, 7495, Bogotá, Colombia

    José Murillo-A

Authors
  1. José Murillo-A
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  2. Tod F. Stuessy
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  3. Eduardo Ruiz
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Correspondence to José Murillo-A.

Appendix 1

Appendix 1

Taxon: collector and number (herbarium) (GenBank registration number for ITS, ETS)

Acca sellowiana (O. Berg) Burret: Lucas 205 (K) (AM234067, AM489888). Algrizea macrochlamys (DC.) Proença and Nic Lughadha: Giulietti and Harley 1648 (K) (AM234126, AM489890). Amomyrtus meli (Phil.) D. Legrand and Kausel: RBGE 1996-1083 (E) (AM234069, AM489891). Blepharocalyx cruckshankii (Hook. and Arn.) Nied.: Murillo 4219 (CONC) (JN660907, JN660857). Blepharocalyx salicifolius (Kunth) O. Berg: Landrum 11232 (ASU) (JN660936, JN660886). Blepharocalyx salicifolius (Kunth) O. Berg: Negritto 927 (CONC) (JN660935, JN660885). Calyptranthes concinna DC.: Lucas 74 (K) (AM234103, AM489898). Calyptranthes thomasiana O. Berg: Pollard 1195 (K) (AM234106, AM489901). Campomanesia pubescens O. Berg Brazil: Farinaccio and Costa 1669 (K) (AM234077, AM489903). Campomanesia guazumifolia (Cambess.) O. Berg Cult. RBG Sydney: Belsham M86; K (AM489902, AM234076). Decaspermum humile (G. Don) A.J. Scott: Belsham M82 (OTA) (AM234128, AM489905). Eugenia latifolia Aubl.: Prevost 4707 (K) (AM234091, AM489913). Eugenia stictosephala Kiaersk.: Zappi 406 (K) (AM234086, AM489908). Eugenia uniflora L.: Lucas 207 (K) (AM234088, AM489910). Gomidesia flagellaris (D. Legrand) Sobral: Lucas 83 (K) (AM234113, AM489918). Gomidesia tijucensis (Kiaersk.) D. Legrand: Zappi 305 (K) (AM234110, AM489915). Gossia inophloia (J.F. Bailey and C.T. White) Snow and Guymer: Belsham M79 (OTA) (AM234131, AM489919). Legrandia concinna (Phil.) Kausel: RBGE 1999-0656 (E) (AM234072, AM489921). Lophomyrtus obcordata (Raoul) Burret: Belsham M41 (OTA) (AM234146, AM489924). Luma apiculata (DC.) Burret: Murillo 4205 (CONC) (JN660910, JN660860). Luma chequen (Molina) A. Gray: Landrum 7873 (CONC) (JN660911, JN660861). Marlierea eugeniopsoides (Kausel) D. Legrand: Lucas 61 (K) (AM234107, AM489928). Marlierea obscura O. Berg: Lucas 88 (K) (AM234109, AM489930). Marlierea suaveolens Cambess.: Lucas 85 (K) (AM234108, AM489929). Metrosideros perforata (J.R. and G. Forst.) A. Rich.: Lucas 209 (K) (AM234141, AM489931). Myrceugenia alpigena (DC.) Landrum: Lucas 167 (K) (JN660892, JN660842). Myrceugenia alpigena (DC.) Landrum var. fuliginea (O. Berg) Landrum: G. Hatschbach 59697 (ASU) (JN660891, JN660841). Myrceugenia alpigena (DC.) Landrum var longifolia (Burret) Landrum: R. Harley 26218 (ASU) (JN660893, JN660843). Myrceugenia brevipedicellata (Burret) D. Legrand and Kausel: Landrum 2830 (ASU) (JN660894, JN660844). Myrceugenia campestris (DC.) D. Legrand and Kausel: R. Kummrow 2940 (ASU) (JN660895, JN660845). Myrceugenia chrysocarpa (O. Berg) Kausel: Landrum 8166 (CONC) (JN660896, JN660846). Myrceugenia colchaguensis (Phil.) Navas: Landrum 8033 (CONC) (JN660897, JN660847). Myrceugenia correifolia (Hook. and Arn.) O. Berg; Teillier 5360 (CONC) (JN660901, JN660851). Myrceugenia cucullata D. Legrand: Wasum 105 (ASU) (JN660898, JN660848). Myrceugenia euosma (O. Berg) D. Legrand: Soares 715 (ASU) (JN660899, JN660849). Myrceugenia exsucca (DC.) O. Berg: Murillo 4217 (CONC) (JN660900, JN660850). Myrceugenia fernandeziana (Hook. and Arn.) Johow: Stuessy 15283 (CONC) (JN660903, JN660853). Myrceugenia franciscensis (O. Berg) Landrum: Miyagi 357 (ASU) (JN660902, JN660852). Myrceugenia gertii Landrum: E. Barbosa 948 (ASU) (JN660904, JN660854). Myrceugenia glaucescens (Cambess.) D. Legrand and Kausel: Landrum 11231 (ASU) (JN660905, JN660855). Myrceugenia kleinii D. Legrand and Kausel: Cordeiro 734 (ASU) (JN660906, JN660856). Myrceugenia lanceolata (Juss. ex J. St.-Hil.) Kausel: Mihoc 6220 (CONC) (JN660908, JN660858). Myrceugenia leptospermoides (DC.) Kausel: Murillo 4214 (CONC) (JN660909, JN660859). Myrceugenia miersiana (Gardner) D. Legrand and Kausel: Lucas 164 (K) (JN660912, JN660862). Myrceugenia myrciodes (Cambess.) O. Berg var. acrophylla (O. Berg) D. Legrand: Ribas 229 (ASU) (JN660913, JN660863). Myrceugenia myrcioides (Cambess.) O. Berg: Lucas 503 (K) (JN660915, JN660865). Myrceugenia myrtoides O. Berg: Rossato 47 (MO) (JN660919, JN660869). Myrceugenia obtusa (DC.) O. Berg: Brownless 1227 (CONC) (JN660916, JN660866). Myrceugenia ovalifolia (O. Berg) Landrum: Lucas 259 (K) (JN660917, JN660867). Myrceugenia ovata (Hook. and Arn.) O. Berg var. acutata (D. Legrand) Landrum: Chagas 1979 (ASU) (JN660918, JN660868). Myrceugenia ovata (Hook. and Arn.) O. Berg var. nannophylla (Burret) Landrum: Mihoc 5162 (CONC) (JN660920, JN660870). Myrceugenia ovata (Hook. and Arn.) O. Berg var. ovata: Gardner 19 (CONC) (JN660922, JN660872). Myrceugenia ovata (Hook. and Arn.) O. Berg var. regnelliana (O. Berg) Landrum: Silva 18 (ASU) (JN660921, JN660871). Myrceugenia ovata (Hook. and Arn.) O. Berg var. regnelliana (O. Berg) Landrum: Souza 10621 (ASU) (-, JN660889). Myrceugenia oxysepala (Burret) D. Legrand and Kausel: Ribas 2234 (ASU) (JN660923, JN660873). Myrceugenia parvifolia (DC.) Kausel: Landrum 5916 (CONC) (JN660924, JN660874). Myrceugenia pilotantha (Kiaersk.) Landrum: Lucas 230 (K) (JN660925, JN660875). Myrceugenia pilotantha (Kiaersk.) Landrum: Lohmann 35 (ASU) (JN660926, JN660876). Myrceugenia pinifolia (F. Phil.) Kausel: Gardner 164 (CONC) (JN660927, JN660877). Myrceugenia planipes (Hook. and Arn.) O. Berg: Aedo 7378 (CONC) (JN660928, JN660878). Myrceugenia reitzii D. Legrand and Kausel: Barbosa 945 (ASU) (JN660937, JN660887). Myrceugenia rufa (Colla) Skottsb. ex Kausel: Teillier 150795 (CONC) (JN660929, JN660879). Myrceugenia rufescens (DC.) D. Legrand and Kausel: Lucas 469 (K) (JN660930, JN660880). Myrceugenia schulzei Johow: Ruiz 8266 (CONC) (JN660938, JN660888). Myrceugenia seriatoramosa (Kiaersk.) D. Legrand and Kausel: Silva 2358 (MO) (JN660932, JN660882). Myrceugenia smithii Landrum: García 533 (ASU) (JN660931, JN660881). Myrcia bicarinata (O. Berg) D. Legrand: Lucas 71 (K) (AM234121, AM489945). Myrcia coumeta (Aubl.) DC.: Lucas 107 (K) (AM234123, AM489947). Myrcia laricina (O. Berg) Burret ex Luetzelb.: Mello Silva 1713 (K) (AM234118, AM489942). Myrcia laruotteana Cambess.: Mello Silva 1705 (K) (AM234115, AM489939). Myrcia pubipetala Miq.: Lucas 86 (K) (AM234114, AM489938). Myrcia rostrata DC.: Lucas 73 (K) (AM234122, AM489946). Myrcia saxatilis (Amsh.) McVaugh: Lucas 98 (K) (AM234119, AM489943). Myrcia tomentosa (Aubl.) DC.: Soares 752 (K) (AM234116, AM489940). Myrcia venulosa DC.: Cruz and Cordeiro 195 (K) (AM234125, AM489949). Myrcianthes cisplatensis (Cambess.) O. Berg: Landrum 11233 (ASU) (JN660914, JN660864). Myrcianthes pseudomato (D. Legrand) McVaugh: Beck 9667 (K) (AM234100, AM489951). Myrciaria cauliflora O. Berg: Lucas 210 (K) (AM234093, AM489952). Myrteola nummularia (Lam.) O. Berg: RBGE 1996-1096 € (AM234068, AM489954). Myrtus communis L.: Botanical Garden Austria (JN660890, JN660840). Neomitranthes cordifolia (D. Legrand) D. Legrand: Forster 1011 (ESA) (AM489410, AM489413). Neomyrtus pedunculata (Hook. f.) Burret: Belsham M42 (OTA) (AM234144, AM489956). Pimenta pseudocaryophyllus (Gomes) Landrum: Lucas 161 (K) (AM234083, AM489960). Pimenta racemosa (Mill.) J.W. Moore: Holst 8866 (K) (AM234082, AM489959). Plinia pauciflora M.L. Kawas. and B. Holst: Mazine 957 (ESA) (AM489411, AM489414). Psidium cattleianum Sabine: Lucas 213 (K) (AM234080, AM489962). Psidium cinereum Mart. ex DC.: Da Silva and Farias, 4535 (K) (AM234079, AM489961). Psidium guajava L.: ASU199194 (ASU) (AY487283, AY454126). Rhodamnia rubescens (Benth.) Miq.: Belsham M83 (OTA) (AM234127, AM489963). Rhodomyrtus psidioides (G. Don) Benth.: Belsham M72 (OTA) (AM234134, AM489965). Siphoneugena guilfoyleana C. Proença: Lucas 70 (K) (AM234085, AM489966). Ugni molinae Turcz.: Murillo 4213 (CONC) (JN660933, JN660883). Ugni selkirkii (Hook. and Arn.) O. Berg: F. Gardner 31 (CONC) (JN660934, JN660884). Xanthomyrtus montivaga A.J. Scott: Lucas 16 (K) (AM234147, AM489971).

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Murillo-A, J., Stuessy, T.F. & Ruiz, E. Phylogenetic relationships among Myrceugenia, Blepharocalyx, and Luma (Myrtaceae) based on paired-sites models and the secondary structures of ITS and ETS sequences. Plant Syst Evol 299, 713–729 (2013). https://doi.org/10.1007/s00606-012-0754-x

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