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FULLTEXT01.Pdf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finns ingen ro i sinnet finns ingen sorg i minnet finns ingen last att bära men så mycket mycket mer att lära himlen blåser upp! Mats Ronander Papers included in this thesis This thesis is based on the following papers, which are referred to in the text by their Roman numerals: I B. Oxelman, M. Backlund & B. Bremer. 1999. Relationships of the Buddlejaceae s.l. investigated using parsimony jackknife and branch support analysis of chloroplast ndhF and rbcL sequence data. Systematic Botany 24(2): 164-182. II M. Backlund, B. Oxelman & B. Bremer. 2000. Phylogenetic relationships within the Gentianales based on ndhF and rbcL se- quences, with particular reference to the Loganiaceae. American Journal of Botany 87(7): 1029-1043. III M. Backlund, B. Bremer & M. Thulin. Manuscript. Paraphyly of Paederieae, recognition of Putorieae and expansion of Plocama (Rubiaceae-Rubioideae). Submitted to Taxon. IV M. Backlund & M. Thulin. Manuscript. Revision of the Mediter- ranean species of Plocama (Rubiaceae). Submitted to Taxon. ______________________________________________________ Published articles were reproduced in this thesis with the kind permis- sion of the publishers. In papers II, III and IV MB was responsible for the writing (with comments and suggestions given by the co-authors), for all analyses, the major part of the labora- tory work and observations of herbarium material. In paper I MB contributed some lab-work, comments and suggestions of the writing. All the papers were planned in co-operation with the co-authors. Important note. Papers III and IV of this thesis are manuscripts that contain new nomenclatural combinations. These papers have been submitted for publication elsewhere. In order to make clear that these names are not validly published in this thesis, the references to the basionyms, necessary according to the International Code of Botanical Nomenclature, are omitted. Contents Introduction.....................................................................................................9 Phylogenetics .............................................................................................9 Molecules and morphology......................................................................10 Aims .........................................................................................................12 Gentianales....................................................................................................14 Traditional and modern views..................................................................14 Relationships of the Buddlejaceae – paper I ............................................16 Interfamilial relationships of the Gentianales – paper II..........................18 Families of the Gentianales ......................................................................20 Loganiaceae .........................................................................................20 Apocynaceae........................................................................................22 Gelsemiaceae .......................................................................................22 Gentianaceae........................................................................................23 Rubiaceae.............................................................................................23 Rubiaceae systematics ..................................................................................24 The tribes Paederieae & Putorieae – paper III .............................................25 Historical outline......................................................................................25 Identifying the problems ..........................................................................26 The Mediterranean Plocama – paper IV.......................................................30 Historical outline......................................................................................30 Identifying the problems ..........................................................................30 Nomenclatural considerations ..................................................................30 Conclusions and future prospects .................................................................32 Realignment and synopsis of the Gentianales..........................................33 Sammanfattning (Swedish summary) ...........................................................34 Acknowledgements.......................................................................................36 References.....................................................................................................38 Introduction The classical botanical systematists created classification systems that were utilistic and practical but not natural in a modern sense. After the introduc- tion of Darwin's ideas in the middle of the 19th century, there was a wide acceptance of evolution as a concept among most of the natural scientists. Many workers attempted to set up classifications that included hypotheses of natural groups, showing how plants were evolutionarily related to each other. However, these classifications were primarily based on personal opin- ions, which were in fact non-testable. As will be pointed out below this prob- lem was prominent in the Gentianales, as understood in the beginning of the 20th century, and forms the basis for many of the issues adressed in this thesis. Phylogenetics Acceptance of a single origin of life on Earth, results in a single, albeit com- plex history reflecting its development and evolution (e.g. Martin & Embley, 2004). To address the evolutionary relationships in a scientific way, one requires a method by which different hypotheses can be tested and com- pared. In the middle of the 20th century this became possible and many sys- tematists focused on these questions to develop computational tools. In the 1950's and 60's Hennig (1950; 1966) and others began to develop the theo- retical framework leading to parsimony analysis. This is based on the princi- ple often attributed to William of Ockham (*1285 †1349?), the so-called Ockham's razor: PLURALITAS NON EST PONENDA SINE NECCESITATE i.e., plurality should not be posited without necessity. In the case of parsi- mony analysis this is fulfilled by searching for the simplest explanation of the data provided, with the result often represented as a branching diagram, commonly referred to as a cladogram. In systematic studies this diagram is subsequently often interpreted as indicative of evolutionary relationships. A number of other methods for phylogenetic reconstruction have been developed with different theoretical backgrounds. Most notable and widely used being neighbor joining (NJ, Kimura, 1983; Nei, 1987), maximum like- 9 lihood (ML, Edwards & Cavalli-Sforza, 1964; Felsenstein, 1973), and Bayesian inference (BI, Li & al., 1996; Mau & Newton., 1997; Yang & Rannala, 1997; Huelsenbeck & Ronquist, 2001). My reasons for the consis- tent use of parsimony analysis throughout this thesis can be summarised in the following points: • use of an explicit optimality criterion (in contrast to NJ) • avoiding a model (not the case in ML and BI) Parsimony analysis works without the use of an evolutionary model. Some people would consider this a problem, but for me it appears un- intuitive to invoke an evolutionary model to study evolutionary relation- ships, a situation resembling circular evidence. • intuitive tree construction In parsimony analysis there is an immediate connection between the data and the result of the analysis, as the branches and nodes of the branching diagram correspond directly to character-state changes in the data matrix. After obtaining trees which then are interpreted as representing a phy- logeny, estimates of reliability, often referred to as support, should be calcu- lated for the different branches in the tree. Different kinds of indices may be calculated for the most parsimonious trees retrieved, as in papers I, II, and III. In paper I jackknife and Bremer support (BS) values were calculated for the trees. In paper II we also chose to include bootstrap values. In paper III only the bootstrap values were included. Molecules and morphology The first parsimony studies were based on morphological characters in a wide sense. Later the ability to perform DNA restriction site analyses and subsequently to obtain nucleotide sequences has resulted in vastly larger data sets. When
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