Preface. Part I: Molecules and genomes in plant systematics. Chloroplast DNA and the study of plant phylogeny: present status and future prospects - M T Clegg and G Zurawski Use of chloroplast DNA rearrangements in reconstructing plant phylogeny - S R Downie and J D Palmer Mitochondrial DNA in plant systematics: applications and limitations - J D Palmer Ribosomal RNA as a phylogenetic tool in plant systematics - R K Hamby and E A Zimmer Evolution of the NOR and 5S DNA loci in the Triticeae - R Appels and B Baum Part II: Molecular approaches to plant evolution Intraspecific chloroplast DNA variation: systematic and phylogenetic implications - D E Soltis, P S Soltis and B G Milligan Molecular data and polyploid evolution in plants - P S Soltis, J J Doyle and D E Soltis Molecular systematics and crop evolution - J Deobley Part III: Model studies of phylogenetic relationships Contributions of molecular data to polyploid evolution in plants - P S Soltis, J J Doyle and D E Soltis Molecular systematics and crop evolution - J Deobley Contributions of molecular data to papilionoid legume systematics - J J Doyle, M Levin and A Bruneau Chloroplast DNA variation in the asteraceae: phylogenetic and evolutionary implications - R K Jansen, H J Michaels, R S Wallace, K-J Kim, S C Keeley, L E Watson and J D Palmer Chloroplast DNA restriction site variation and the evolution of the annual habit in North American Coreopsis (Asteraceae) - D J Crawford, J D Palmer and M Kobayashi Molecular systematics of onagraceae: examples from Clarkia and Fuschia - K J Systema and J E Smith Floral morphology and chromosome number in the subtribe oncidiinae (Orchidaceae): evolutionary insights from a phylogenetic analysis of the chloroplast DNA restriction site variation - M W Chase and J D Palmer Part IV: Theoretical perspectives The suitability of molecular and morphological evidence in reconstructing plant phylogeny -M J Donaghue and M J Sanderson Character-site weighting for restriction site data in phylogenetic reconstruction, with an example from chloroplast DNA - V A Albert, B D Mishler and M W Chase Polymorphism, hybridization and variable evolutionary rate in molecular phylogenies - K Ritland and J E Eckenwalder Index.

Molecular Systematics of Plants

The Genetics of Corn

The origin and evolution of a hybrid species complex in the genus Brassica (cabbage, turnip, mustard, rapeseed oil) has been explored through mutational analysis of the maternally inherited chloroplast genome. A detailed chloroplast DNA phylogeny enables identification of the maternal parent for most of the amphidiploids examined and permits quantitative resolution of the relative time of hybridization as well as the relative divergence of the diploid parents. Contradictory chloroplast and nuclear phylogenies obtained for two accessions of the amphidiploid B. napus (rapeseed oil) lead to the hypothesis that introgressive hybridization has also figured in their recent evolution.

Chloroplast DNA evolution and the origin of amphidiploid Brassica species.

Summary Harris, S. A. & Ingram, R.: Chloroplast DNA and biosystematics: The effects of intraspecific diversity and plastid transmission. - Taxon 40: 393-412. 1991. - ISSN 0040-0262. The widespread application of chloroplast DNA (cpDNA) to plant biosystematics is usually based on a number of assumptions. The assumption of low levels of intraspecific cpDNA variation is reviewed and the conclusion reached that far from being rare, intraspecific cpDNA variation is relatively common. The evidence for the assumption of predominantly maternal plastid transmission is also reviewed. In both of the cases some of the possible effects on phylogenetic reconstruction are considered.

Chloroplast DNA and biosystematics: The effects of intraspecific diversity and plastid transmission

Chloroplast DNA was purified from 12 accessions that represent most of the species diversity in the genus Lycopersicon (family Solanaceae) and from 3 closely related species in the genus Solanum. Fragment patterns produced by digestion of these DNAs with 25 different restriction endonucleases were analyzed by agarose gel electrophoresis. In all 15 DNAs, a total of only 39 restriction site mutations were detected among 484 restriction sites surveyed, representing 2,800 base pairs of sequence information. This low rate of base sequence change is paralleled by an extremely low rate of convergent change in restriction sites; only 1 of the 39 mutations appears to have occurred independently in two different lineages. Parsimony analysis of shared mutations has allowed the construction of a maternal phylogeny for the 15 accessions. This phylogeny is generally consistent with relationships based on morphology and crossability but provides more detailed resolution at several places. All accessions within Lycopersicon form a coherent group, with two of the three species of Solanum as outside reference points. Chloroplast DNA analysis places S. pennellii firmly within Lycopersicon, confirming recent studies that have removed it from Solanum. Red-orange fruit color is shown to be a monophyletic trait in three species of Lycopersicon, including the cultivated tomato, L. esculentum. Analysis of six accessions within L. peruvianum reveals a limited amount of intraspecific polymorphism which, however, encompasses all the variation observed in L. chilense and L. chmielewskii. It is suggested that these latter two accessions be relegated to positions within the L. peruvianum complex.

https://www.pnas.org/content/pnas/79/16/5006.full.pdf

Chloroplast DNA evolution and phylogenetic relationships in Lycopersicon.

Chloroplast and mitochondrial DNAs from six races of annual teosinte (Guatemala, Huehuetenango, Balsas, Central Plateau, Chalco, and Nobogame), perennial teosinte, and maize were compared and grouped by restriction endonuclease fragment analyses. Three groups of chloroplast DNAs were detected: (i) perennial teosinte and Guatemala; (ii) Balsas and Huehuetenango; and (iii) all other teosintes. Four groups of mitochondrial DNAs were separated: (i) perennial teosinte; (ii) Guatemala; (iii) Nobogame; and (iv) all other teosintes. Separation of the teosinte and maize organelle DNAs into five groups (Guatemala; perennial teosinte; Balsas and Huehuetenango; Central Plateau and Chalco; Nobogame and maize) approximated the biosystematic relationships of the taxa. It was suggested that the evolutions of the chloroplast and mitochondrial DNAs may be independent of each other, that variation of organelle DNA within a species complex of an organism may be the common condition, and that the DNAs of the organelle and nuclear systems evolve in reasonable harmony.

J. L. Kermicle

Papers

Organelle DNA variation and systematic relationships in the genus Zea: Teosinte.