Showing papers by "Lynn Bohs published in 2007"

A Three-Gene Phylogeny of the Genus Solanum (Solanaceae)

Abstract: Solanum, with approximately 1,500 species, is the largest genus in the Solanaceae and includes economically important species such as the tomato, potato, and eggplant. In part due to its large size and tropical center of diversity, resolving evolutionary relationships across Solanum as a whole has been challenging. In order to identify major clades within Solanum and to gain insight into phylogenetic relationships among these clades, we sampled 102 Solanum species and seven outgroup taxa for three DNA sequence regions (chloroplast ndhF and trnT- F, and nuclear waxy) and analyzed the data using parsimony and Bayesian methods. The same major Solanum clades were identified by each data partition, and the combined analysis provided the best resolved hypothesis of relationships within the genus. Our data suggest that most traditionally recognized Solanum subgenera are not monophyletic. The Thelopodium clade is sister to the rest of Solanum, which is split into two large clades. These two large clades are further divided into at least 10 subclades, for which informal names are provided and morphological synapomorphies are proposed. The identification of these subclades provides a framework for directed sampling in further phylogenetic studies, and identifies natural groups for focused revisionary work.

A summary of molecular systematic research in solanaceae: 1982-2006

Abstract: A summary of progress in molecular phylogenetic studies of Solanaceae indicates that with over 50 published studies, more than 90% of genera and 37% of species have been sampled. Circumscription of Solanaceae now includes Nolanaceae, Goetzeaceae, Duckeodendron, and Sclerophylax. Well-sampled groups include Capsicum, Lycium, Nicotiana, Nolana, and Petunia and the clades Anthocercideae, Goetzeoideae, and Iochrominae. A major effort currently underway promises extensive sampling of Solanum. Groups that remain poorly sampled include Cestrum, Brunfelsia, Jaltomata, Lycianthes, and Juanulloeae. INTRODUCTION The beginning of modern (DNA-based) molecular plant systematics can be traced to a study of the tomato and its wild relatives (Palmer and Zamir, 1982). In the quarter century since then, the Solanaceae have remained in the forefront of molecular plant systematics, with innovations in the sources of data and analytical approaches used (e.g., chloroplast rflp analysis: Palmer and Zamir, 1982; Hosaka et al., 1984; chloroplast restriction site mapping: Olmstead and Palmer, 1992; Spooner et al., 1993; chloroplast ndhF and rbcL sequences: Olmstead and Sweere, 1994; Bohs and Olmstead 1997; nuclear ITS and “waxy” sequences: Peralta and Spooner, 2001 Walsh and Hoot, 2001; Levin and Miller, 2005; Whitson and Manos, 2005; Levin et al., 2005; Martine et al., 2006; nuclear SAMT sequences: Martins and Barkman, 2005; AFLP analysis: Mace et al., 1999; Spooner et al., 2005a, b; nuclear retroposon markers: Yuan et al., 2006). Significant advancements have been made in our understanding of relationships of Solanaceae (Olmstead and Palmer, 1992; Olmstead and Sweere, 1994; Olmstead et al. 1999; Gemeinholzer and Wink, 2004; Martins and Barkman, 2005), including its circumscription to include several small groups previously excluded (e.g., Nolanaceae, Goetzeaceae, Duckeodendron, and Sclerophylax). A provisional phylogenetic classification presented at the 1994 Solanaceae Conference in Adelaide (Olmstead et al., 1999) has been revised (Fig. 1; Table 1) following expanded sampling in many groups and inclusion of over 90% of all genera in subsequent molecular studies (Olmstead et al., in prep.). Several clades in Solanaceae have been subject to detailed study, including Nicotiana (Aoki and Ito, 2000; Clarkson et al., 2004), Capsicum (Walsh and Hoot, 2001; E. Dean and L. Bohs, pers. commun.), Lycium (Miller 2002; Levin and Miller, 2005); Goetzeoideae (Santiago-Valentin and Olmstead, 2003), Anthocercideae (Garcia and Olmstead, 2003), Physalinae (Whitson and Manos, 2005), Petunia (Ando et al., 2005; Kulcheski et al., 2006); Iochrominae (Smith and Baum, 2006), Nolana (M. Dillon and J. Wen, pers. commun.), and, of course, Solanum (e.g., Spooner et al., 1993; Bohs, 2005; Levin et al., 2006; Weese and Bohs, 2007). RESULTS AND DISCUSSION In an effort to bring together the accomplishments of the past 25 years and to identify where our knowledge is most complete and where further work is needed, we have compiled a summary of molecular systematic studies in Solanaceae organized in conjunction with the classification in Table 1. In order to quantify the progress, estimates of the number of species in each group were revised from prior compendia (D’Arcy, 1991; Hunziker, 2001) where needed using recent publications and the assistance of authorities in those groups. A new estimate of species number in Solanum was calculated from estimates of the ratio of accepted species names to published species names in recently monographed groups and extrapolated to the rest of the genus (S. Knapp and J. Bennett, pers. commun.). Table 1 provides estimated numbers and percentages of species sampled for each genus and of genera sampled for suprageneric clades compiled from all studies. Studies are referenced to each genus or clade for information on phylogeny within that group or on the placement or the genus or clade within the Solanaceae. Clade names in Figure 1 follow Olmstead et al. (1999) with the exceptions of “Salpichroina,” “Lyciina,” and “Atropina,” which are unranked informal names used here for the first time. The “-ina” ending does not denote a formal taxonomic rank, but is used in accordance with other studies coining informal clade names (Kron, 1997). Sampling at the genus level is nearly complete (94%), with only a few hard-to-get taxa remaining to be sampled. However, sampling is uneven at the species level with a total of ca. 37% sampled. Some large clades, including Cestrum, Brunfelsia, Lycianthes, Jaltomata, and Juanulloeae remain poorly sampled. Solanum, with nearly half the species in the family, is somewhat undersampled at the moment with ca. 31% of species sampled, vs. 37% for the entire Solanaceae (Fig. 2, Table 1). However, there is a major effort underway to understand the global taxonomy and phylogeny of Solanum (Knapp et al., 2004; Solanaceae Source: http://www.nhm.ac.uk/solanaceaesource/) and a molecular phylogeny of Solanum is progressing at a rapid rate (Bohs, 2004, 2005; Levin et al., 2005, 2006; Martine et al., 2006; Weese and Bohs, 2007; Bohs, in press; L. Bohs and D. Spooner, pers. commun.). A primary goal of systematics is to discover and describe biodiversity at all levels in the hierarchy of life. Discovery occurs in the field, the herbarium, and in the lab, where molecular phylogenetic studies enable the discovery of clades thoughout that hierarchy. Having a fully sampled and fully resolved phylogeny for Solanaceae will permit interpretation of patterns of character evolution, biogeography, and genome structure resulting in a fully integrated biology of the Solanaceae. Acknowledgements We thank several scientists who graciously provided summaries of their unpublished research and estimates of species numbers for groups on which they work, including T. Barkman, J. Bennett, M. Dillon, S. Knapp, R. Levin, M. Manoko, T. Mione, E. Moscone, N. Sawyer, S. Smith, D. Spooner, G. van der Weerden, W. Wagner, and J. Wen. L.B. acknowledges the support of NSF grants DEB-023533 and DEB-0316614. Literature Cited Anderson, G.J., Jansen, R.K. and Kim, Y. 1996. The origin and relationships of the pepino, Solanum muricatum (Solanaceae): DNA restriction evidence. Econ. Bot. 5: 369-380. Ando, T., Kokubun, H., Watanabe, H., Tanaka, N., Yukawa, T., Hashimoto, G., Marchesi, E., Suárez, E. and Basualdo, I.L. 2005. Phylogenetic analysis of Petunia sensu Jussieu (Solanaceae) using chloroplast DNA RFLP. Ann. Bot. 96: 289-297. Aoki, S. and Ito, M. 2000. Molecular phylogeny of Nicotiana (Solanaceae) based on the nucleotide sequence of the matK gene. Plant Biol. 2: 316-324. Bohs, L. 2004. A chloroplast DNA phylogeny of Solanum section Lasiocarpa. Syst. Bot. 29: 177-187. Bohs, L. 2005. Major clades in Solanum based on ndhF sequence data. p. 27-49. In: R.C. Keating, V.C. Hollowell and T.B. Croat (eds.), A Festschrift for William G. D’Arcy: The Legacy of a Taxonomist. Missouri Botanical Garden, St. Louis. Bohs, L. 2007. Phylogeny of the Cyphomandra clade of the genus Solanum (Solanaceae) based on ITS sequence data. Taxon 56, in press. Bohs, L. and Olmstead, R.G. 1997. Phylogenetic relationships in Solanum (Solanaceae) based on ndhF sequences. Syst. Bot. 22: 5-17. Bohs, L. and Olmstead, R.G. 1999. Solanum phylogeny inferred from chloroplast DNA sequence data. p. 97-110. In: M. Nee, D. Symon, R.N. Lester, and J. Jessop. (eds.), Solanaceae IV: Advances in Biology and Utilization. Royal Botanic Gardens, Kew. Bohs, L. and Olmstead, R.G. 2001. A reassessment of Normania and Triguera (Solanaceae). Pl. Syst. Evol. 228: 33-48. Castillo T., R. and Spooner, D.M. 1997. Phylogenetic relationships of wild potatoes, Solanum series Conicibaccata (sect. Petota). Syst. Bot. 22: 45-83. Clarkson, J. J., Knapp, S., Aoki, S., Garcia, V.F., Olmstead, R.G. and Chase, M.W.. 2004. Phylogenetic relationships in Nicotiana (Solanaceae) inferred from multiple plastid DNA regions. Mol. Phylogen. Evol. 33: 75-90. D’Arcy, W.G. 1991. The Solanaceae since 1976, with a review of its biogeography. p. 75-138. In: Hawkes, J.G., Lester, R.N., Nee, M. and Estrada, N. (eds.), Solanaceae III: Taxonomy, Chemistry, Evolution. Royal Botanic Gardens, Kew. Fay, M. F., Olmstead, R.G., Richardson, J.E., Santiago, E., Prance, G.T. and Chase, M.W. 1998. Molecular data support the inclusion of Duckeodendron cestroides in Solanaceae. Kew Bulletin 53: 203-212. Fukuda, T., Yokoyama, J. and Ohashi, H. 2001. Phylogeny and biogeography of the genus Lycium (Solanaceae): Inferences from chloroplast DNA sequences. Mol. Phylogenetics Evol. 19: 246-258. Garcia, V.F. and Olmstead. R.G. 2003. Phylogenetics of Tribe Anthocercideae (Solanaceae) based on ndhF and trnL/F sequence data. Syst. Bot. 28: 609-615 Gemeinholzer, B. and Wink, M. 2004. Solanaceae: Occurrence of secondary compounds versus molecular phylogeny. p. 165-177. In: R.G. van den Berg, G.W.M. Barendse, G.M.van der Weerden and C. Mariani (eds.) Solanaceae V: Advances in taxonomy and utilization. Nijmegen U. Press, Nijmegen. Hosaka, K., Ogihara, Y., Matsubayashi, M. and Tsunewaki, K. 1984. Phylogenetic relationship between the tuberous Solanum species as revealed by restriction endonuclease analysis of chloroplast DNA. Jap. J. Genet. 59: 349-369. Hunziker, A.T. 2001. Genera Solanacearum: The genera of Solanaceae illustrated, arranged according to a new system. A.R.G. Gantner Verlag K.-G., Ruggell, Germany. Knapp, S., Persson, V. and Blackmore, S. 1997. A phylogenetic conspectus of the Juanulloeae (Solanaceae). Ann. Missouri Bot. Garden 84: 67-89. Knapp, S., Bohs, L., Nee, M. and Spooner, D.M. 2004. Solanaceae – a model for linking genomics with biodiversity. Comp. Funct. Genomics. 5: 285-291. Kron, K.A. 1997. Exploring alternative systems of classification. Aliso 15: 105-112. Kulcheski, F.R., Muschner, V.C., Lorenz-Lemke, A.P., Stehmann, J.R., Bonatto, S.L., Salzano, F.M. and Freitas, L.B. 2006. Molecular phylogenetic analysis of Petunia Juss. (Solanaceae). Genetica 12

Phylogeny of the Cyphomandra clade of the genus Solanum (Solanaceae) based on ITS sequence data

Abstract: About 13 major clades can be recognized within the genus Solanum (Solanaceae) based on chloroplast DNA sequence data. One of these is the Cyphomandra clade, which includes about 50 neotropical species. These have traditionally been placed into two or three sections: S. section Pachyphylla (formerly recognized as the genus Cyphomandra), S. section Cyphomandropsis, and S. section Glaucophyllum (monotypic and sometimes placed in S. section Cyphomandropsis). Phylogenetic relationships among 61 accessions of 35 species of the Cyphomandra clade are investigated using sequence data from the nuclear ITS region analyzed by parsimony and Bayesian inference. The Cyphomandra clade forms a monophyletic group, but the ITS data are equivocal as to the monophyly of sections Pachyphylla and Cyphomandropsis. Four well-supported groups of species can be recognized within the Cyphomandra clade; these conform in part to species groups proposed on the basis of morphology. The distribution of self-incompatible and self-compatible breeding systems is mapped onto the ITS cladogram, and patterns of evolution of enlarged anther connectives, osmophores, and volatile composition are discussed in light of hypothesized phylogenetic relationships.

Phylogeny of Balsamorhiza and Wyethia (Asteraceae: Heliantheae) Using Its, Ets, and trnK Sequence Data

Abstract: Balsamorhiza and Wyethia together comprise 24 species native to western North America. All species in the two genera are perennial herbs with large taproots and chromosome base numbers of x 5 19. The species of Balsamorhiza have exclusively basal leaves while the species of Wyethia have cauline leaves (in addition to basal leaves in some species). The relationships among the species of Balsamorhiza and Wyethia were examined using sequences from the nuclear internal transcribed spacer and external transcribed spacer regions and the chloroplast 39 trnK intron. Twenty-three species of Balsamorhiza and Wyethia and eight outgroups were sampled. The analyses support the monophyly of the Balsamorhiza/Wyethia clade. Wyethia ovata, a species from southern California and northern Baja California, is sister to the other members of the Balsamorhiza/Wyethia clade. Balsamorhiza is strongly supported as monophyletic and is the sister to the rest of Wyethia. The mostly Californian Wyethia section Agnorhiza, which lacks basal leaves, is not monophyletic. The remainder of the Wyethia species, traditionally placed in sections Alarconia and Wyethia, form a clade in the molecular trees and share synapomorphic large basal leaves.