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In Southern South America, Evidence from AFLP and ITS Sequence Data Author(S): Alexandra M

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Molecular Analyses of the Genus Ilex (Aquifoliaceae) in Southern South America, Evidence from AFLP and ITS Sequence Data Author(s): Alexandra M. Gottlieb, Gustavo C. Giberti and Lidia Poggio Source: American Journal of Botany, Vol. 92, No. 2 (Feb., 2005), pp. 352-369 Published by: Botanical Society of America, Inc. Stable URL: https://www.jstor.org/stable/4123880 Accessed: 18-12-2018 17:13 UTC REFERENCES Linked references are available on JSTOR for this article: https://www.jstor.org/stable/4123880?seq=1&cid=pdf-reference#references_tab_contents You may need to log in to JSTOR to access the linked references. JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact [email protected]. Your use of the JSTOR archive indicates your acceptance of the Terms & Conditions of Use, available at https://about.jstor.org/terms Botanical Society of America, Inc. is collaborating with JSTOR to digitize, preserve and extend access to American Journal of Botany This content downloaded from 157.92.6.34 on Tue, 18 Dec 2018 17:13:49 UTC All use subject to https://about.jstor.org/terms American Journal of Botany 92(2): 352-369. 2005. MOLECULAR ANALYSES OF THE GENUS ILEX (AQUIFOLIACEAE) IN SOUTHERN SOUTH AMERICA, EVIDENCE FROM AFLP AND ITS SEQUENCE DATA' ALEXANDRA M. GOTTLIEB,1,3 GUSTAVO C. GIBERTI,2 AND LIDIA POGGIO' 'Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Ciudad Universitaria, Pabell6n II, 4to piso, Departamento de Ecologifa, Gen6tica y Evoluci6n, Lab. 62, C1428EHA, Buenos Aires, Argentina; and 2Instituto de Quifmica y Metabolismo del Ffirmaco (IQUIMEFA), Junin 956, 1113-Buenos Aires, Argentina In order to clarify the relationships among southern South American (sSA) representatives of the genus Ilex, an amplified fragment length polymorphism (AFLP) analysis was accomplished. In addition, the phylogenetic relationships of the species were studied using ribosomal internal transcribed spacer (ITS) sequence data alone and in combination with AFLP data, taking into account the possible existence of paralogous sequences and the influence of alignment parameters. To explore stability of phylogenetic hypotheses, a sensitivity analysis was performed using 15 indel-substitution models. Within each species assayed, the AFLPs allowed the recognition of several diagnostic bands. Furthermore, the AFLP analysis revealed that individuals belonging to the same morpho-species formed coherent clades. In addition, some cases of geographical association were noted. Studies on ITS sequences revealed divergence between data obtained herein and sequence data downloaded from GenBank. The sensitivity analyses yielded different interspecific hypotheses of relationships. Notwithstanding, analyses of the ITS data alone and in combination with AFLPs, rendered clades stable to variation in the analytical parameters. Topologies obtained for the AFLPs, the ITS data alone and the combined analyses, demonstrated the existence of a group formed by I. argentina, I. brasiliensis, I. brevicuspis, L integerrima, and L theezans, and that L dumosa and I. paraguariensis were distantly related to the former. Incongruence with traditional taxonomical treatments was found. Key words: AFLP; direct optimization; Ilex; ITS; sensitivity analysis. The plant genus Ilex L., which belongs to the holly family, Reissek, L microdonta Reissek, L paraguariensis A. St. Hil., Aquifoliaceae Bartl., comprises deciduous and evergreen I. pseudobuxus Reissek, I. taubertiana Loes., and I theezans bushes or trees with economic importance as crops and C. or- Martius ex Reissek. Of those mentioned, I. paraguariensis namentals. These plants are functionally dioecious; rudimen- is the most relevant from an economic perspective. In Argen- tary pistils in staminate flowers and sterile stamens in pistillate tina, southern Brazil, Paraguay, and Uruguay, the aerial parts flowers are borne on different plants. A remarkable morpho- of this plant are used to prepare a very popular beverage called logical diversity has been described in the genus, including mate, which is highly appreciated for its flavor and stimulating trees to creeping prostrate plants or epiphytic shrubs. It properties has due to its caffeine and theobromine contents (Filip more than 400 species, dispersed mainly in America and Eur-et al., 2001). asia, but also in Oceania and Africa (Giberti, 1994b). About a hundred years after Linnaeus (1753) published the South America is considered one of the main areas of di- diagnosis for the genus Ilex, Gray (1856) attempted to estab- versification of Ilex, together with East Asia (Loesener, lish 1942; an infrageneric classification. In 1861, Reissek published Cuenoud et al., 2000). In southern South America (sSA) the greatestthe species inventory for the time, followed by Hooker species are mostly found in areas with tropical or subtropical (1862) who reported the occurrence of about 145 species climates, mainly in northeastern Argentina, southeastern worldwide. Brazil Loesener (1891, 1901, 1908, 1942) published a and eastern Paraguay. Twelve species have been described series for of seminal studies recording almost 280 species of Ilex, sSA (Loesener, 1901; Lillo, 1911; Edwin and Reitz, 1967; dispersed Gi- globally, and recognizing several subgeneric ranks berti, 1998), namely, Ilex affinis Gardner, I. argentina althoughLillo, L under an unconventional hierarchical arrangement. brasiliensis (Sprengel) Loes., I. brevicuspis Reissek, SinceI. cha- then, several authors have recognized some inaccuracies maedryfolia Reissek, L dumosa Reissek, L integerrima in(Vell.) Loesener's system and proposed emendations in the system- atics of the genus (Rehder, 1927; Hu, 1949, 1950; Krtissmann, 1962; Baas, 1975; Lobreau-Callen, 1975; Martin, 1977). Spe- ' Manuscript received 11 December 2003; revision accepted 17 September cies delimitation in Ilex, based on overall morphological sim- 2004. ilarity, is complicated due to the various concepts used by The authors are indebted to L. D. Belingheri, S. D. Prat Kricun, and R. M. Mayol from EE. INTA Cerro Azul (Misiones, Argentina) who kindly different provided authors to define the taxa and to the lack of complete specimens from living collections; to N. Jouv6 and P. Rubio of University information, of particularly for evergreen species (Galle, 1997). Alcald (Madrid, Spain) who supported the sequencing, to M. E. Rol6n In from order to investigate the relationships among the species the "Establecimiento Las Marias" (Corrientes, Argentina) who facilitatedof Ilex found in sSA, we implemented the amplified fragment commercial lines of "mate," to S. A. Catalano and V. A. Confalonieri for length polymorphism (AFLP) technique (Vos et al., 1995). In their invaluable suggestions. We also want to thank three anonymous review- addition, we studied the phylogenetic relationships of the spe- ers whose suggestions helped to improve this manuscript. This work was supported from grants of the "Agencia Nacional de Investigaciones Cientifi- cies using ribosomal internal transcribed spacer (ITS) se- cas y Tecnicas" (Argentina) (PICT 01-4443) and from CONICET (PIP 0559/ quence data alone and in combination with AFLP data, taking 98). into account the possible existence of paralogous sequences SAuthor for correspondence. E-mail: [email protected]. and the influence of alignment parameters. 352 This content downloaded from 157.92.6.34 on Tue, 18 Dec 2018 17:13:49 UTC All use subject to https://about.jstor.org/terms February 2005] GOTTLIEB ET AL.-MOLECULAR ANALYSES OF SOUTH AMERICAN ILEX 353 Beside the general use of AFLP markers in the estimation ments. Because parameter choice is arbitrary but unavoidable of genetic diversity and differentiation among individuals, when doing algorithmic DNA sequence comparisons, its ex- populations, and plant species, they have also been ploration success- becomes essential (Giribet and Wheeler, 1999; Gi- fully used in phylogenetic analysis between closely ribet related and Ribera, 2000). Herein, we used ITS sequences to species (Cervera et al., 1998; Kardolus et al., 1998; study Mace the et phylogenetic relationships of sSA taxa and to explore al., 1999; Negi et al., 2000; Ren and Timko, 2000; the Koopman influence of applying different insertion/deletion (indel or et al., 2001). Because of the rapidity with which reliable gap) and high substitution models (sensitivity analysis sensu resolution markers can be generated, the AFLP technique Wheeler, is 1995) on phylogenetic inference. Phylogenetic anal- considered a powerful tool for molecular studies (Mueller yses were and accomplished through direct optimization of DNA Wolfenbarger, 1999). In addition, the high ratio of sequencespolymor- (Wheeler, 1996). The sensitivity analysis is a way phism generated per PCR experiment (the multiplex to explore ratio) the data and to discern between stable relationships (Powell et al., 1996) and the random distribution of most (those supported throughout the parameters range) and unsta- AFLP bands across the genome (Zhu et al., 1998) are consid- ble relationships (those appearing only under particular con- ered key features of this technique. Several drawbacks have ditions), allowing the formulation of more robust hypotheses been detected for AFLPs (Robinson and Harris, 1999), which
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