Paul Goetghebeur

Phylogeny of Cyperaceae Based on DNA Sequence Data: Current Progress and Future Prospects

In the last decade, efforts to reconstruct suprageneric phylogeny of the Cyperaceae have intensified. We present an analysis of 262 taxa representing 93 genera in 15 tribes, sequenced for the plastid rbcL and trnL-F (intron and intergenic spacer). Cyperaceae are monophyletic and resolved into two clades, here recognised as Mapanioideae and Cyperoideae, and the overall topology is similar to results from previous studies. Within Cyperoideae, Trilepideae are sister to rest of taxa whereas Cryptangieae, Bisboeckelerieae and Sclerieae are resolved within Schoeneae. Cladium and Rhynchospora (and Pleurostachys) are resolved into clades sister to the rest of Schoeneae, lending support to the recognition of these taxa in separate tribes. However, we retain these taxa in Schoeneae pending broader sampling of the group. The phylogenetic position of 40 species in 21 genera is presented in this study for the first time, elucidating their position in Abildgaardieae (Trachystylis), Cryptangieae (Didymiandrum, Exochogyne), Cypereae (Androtrichum, Volkiella), Eleocharideae (Chillania), and Schoeneae (Calyptrocarya, Morelotia). More sampling effort (more taxa and the use of more rapidly evolving markers) is needed to resolve relationships in Fuireneae and Schoeneae.

AFLP analysis of genetic relationships among papaya and its wild relatives (Caricaceae) from Ecuador

Abstract.The AFLP technique was used to assess the genetic relationships among the cultivated papaya (Carica papaya L.) and related species native to Ecuador. Genetic distances based on AFLP data were estimated for 95 accessions belonging to three genera including C. papaya, at least eight Vasconcella species and two Jacaratia species. Cluster analysis using different methods and principal co-ordinate analysis (PCO), based on the AFLP data from 496 polymorphic bands generated with five primer combinations, was performed. The resulted grouping of accessions of each species corresponds largely with their taxonomic classifications and were found to be consistent with other studies based on RAPD, isozyme and cpDNA data. The AFLP analysis supports the recent rehabilitation of the Vasconcella group as a genus; until recently Vasconcella was considered as a section within the genus Carica. Both cluster and PCO analysis clearly separated the species of the three genera and illustrated the large genetic distance between C. papaya accessions and the Vasconcella group. The specific clustering of the highly diverse group of Vasconcella × heilbornii accessions also suggests that these genotypes may be the result of bi-directional introgression events between Vasconcella stipulata and Vasconcella cundinamarcensis.

Phylogenetic analysis of the highland papayas ( Vasconcellea) and allied genera (Caricaceae) using PCR-RFLP.

The chloroplast and mitochondrial DNA diversity of 61 genotypes belonging to 18 Vasconcellea species, the so-called highland papayas, was studied by PCR-RFLP analysis of two non-coding cpDNA regions (trnM-rbcL and trnK1-trnK2) and one non-coding mtDNA region (nad4/1-nad4/2). This sample set was supplemented with six genotypes belonging to three other Caricaceae genera: the monotypic genus Carica, including only the cultivated papaya, and the genera Jacaratia and Cylicomorpha. Moringa ovalifolia was added as an outgroup species. The PCR-amplified cpDNA regions were digested with 18 restriction endonucleases, the mtDNA region with 11. A total of 22 point mutations and four insertion/deletions were scored in the sample. A higher level of interspecific variation was detected in the two cpDNA regions in comparison to the analysis of the mtDNA. Wagner parsimony and Neighbor-Joining analysis resulted in dendrograms with similar topologies. PCR-RFLP analysis supported the monophyly of Caricaceae, but among the 26 mutations scored, an insufficient number of markers discriminated between the different Caricaceae genera included in this study. Hence the inference of the intergeneric relationships within Caricaceae was impossible. However, some conclusions can be noted at a lower taxonomic level. The Caricaceae species were divided into two lineages. One group included only Vasconcellea spp., whereas the second included the remaining Vasconcellea spp., together with the papaya genotypes and those from the other Caricaceae genera. This may indicate a higher level of inter-fertility for the Vasconcellea species from the latter clade in interspecific crossings with papaya. The putative progenitors of the natural sterile hybrid V. × heilbornii, i.e. V. stipulata and V. cundinamarcensis, were only distantly related to V. × heilbornii. This indicates that probably none of these species was involved as the maternal progenitor in the origin of V. × heilbornii. Surprisingly, V. × heilbornii had organellar genome patterns identical with V. weberbaueri, suggesting a possible involvement of this species in the origin of V. × heilbornii. On the basis of discrepancy between morphological traits and the cpDNA profiles of some pairs of Vasconcellea species, we believe that besides V. × heilbornii, some other species have originated through interspecific hybridization. A reticulate evolution for Vasconcellea has therefore been suggested. Finally, intraspecific cpDNA variation was detected in V. microcarpa, thus providing molecular evidence for the high diversity previously indicated by morphological observations.

The essential oil of Nepeta nuda. Identification of a new nepetalactone diastereoisomer

Abstract The essential oils of nine specimens of N. nuda were prepared by steam distillation, and analysed by GC and GC/MS. Thirty-seven substances were identified, accounting for 91.6–99% of the oils. They all contained varying amounts of 1,8-cineole, a mixture of nepetalactones and germacrene-D as chief components. In seven samples the new 4aβ,7α,7aα-nepetalactone was found. It was isolated, and identified by 1 H and 13 C NMR.

What is a Genus in Cypereae: Phylogeny, Character Homology Assessment and Generic Circumscription in Cypereae

Using a DNA-based tree as the framework, the homology of key taxonomic characters in tribe Cypereae (900 species in 19 genera, the largest of which is Cyperus) is assessed and revisit the question of generic circumscription. Plastid DNA (rbcL gene, rps16 intron, trnL intron and trnL-F intergenic spacer) sequence matrix for 50 species in 19 genera of Cypereae is analysed using the maximum parsimony algorithm of PAUP. Two major groups are observed: the Ficinia and Cyperus clades. The Ficinia clade includes taxa with a center of diversity in the Cape Floristic Region of South Africa. These are predominantly perennial herbs (with exception of Isolepis, which is predominantly annual) having non-Kranz (C3) anatomy and spirally arranged glumes. Species of the Cyperus clade have a predominatly distichous glume arrangement and Kranz anatomy which is either absent (C3) or present (C4). Cyperus is the core genus in the Cyperus clade, in which 13 additional segregate genera are embedded. These segregate genera differ from typical Cyperus in one or more of a few gross morphological characters. There are no unambiguous characters separating C3 and C4Cyperus species. The circumscription of Cypereae is broadened to include all taxa with a Cyperus-type embryo and perianth segments. Three taxa possessing perianth segments, namely Hellmuthia membranacea, Scirpus falsus and S. ficinioides, are supported to be closer to Cyperus than to Scirpus.

Spikelet structure and development in Cyperoideae (Cyperaceae): a monopodial general model based on ontogenetic evidence.

BACKGROUND AND AIMS In Cyperoideae, one of the two subfamilies in Cyperaceae, unresolved homology questions about spikelets remained. This was particularly the case in taxa with distichously organized spikelets and in Cariceae, a tribe with complex compound inflorescences comprising male (co)florescences and deciduous female single-flowered lateral spikelets. Using ontogenetic techniques, a wide range of taxa were investigated, including some controversial ones, in order to find morphological arguments to understand the nature of the spikelet in Cyperoideae. This paper presents a review of both new ontogenetic data and current knowledge, discussing a cyperoid, general, monopodial spikelet model. METHODS Scanning electron microscopy and light microscopy were used to examine spikelets of 106 species from 33 cyperoid genera. RESULTS Ontogenetic data presented allow a consistent cyperoid spikelet model to be defined. Scanning and light microscopic images in controversial taxa such as Schoenus nigricans, Cariceae and Cypereae are interpreted accordingly. CONCLUSIONS Spikelets in all species studied consist of an indeterminate rachilla, and one to many spirally to distichously arranged glumes, each subtending a flower or empty. Lateral spikelets are subtended by a bract and have a spikelet prophyll. In distichously organized spikelets, combined concaulescence of the flowers and epicaulescence (a newly defined metatopic displacement) of the glumes has caused interpretational controversy in the past. In Cariceae, the male (co)florescences are terminal spikelets. Female single-flowered spikelets are positioned proximally on the rachis. To explain both this and the secondary spikelets in some Cypereae, the existence of an ontogenetic switch determining the development of a primordium into flower, or lateral axis is postulated.

Species relationships in the genus Vasconcellea (Caricaceae) based on molecular and morphological evidence

Validity of the taxa currently recognized in the genus Vasconcellea was analyzed by investigating morphological and molecular data from 105 specimens of this genus and six specimens of the related genus Carica. Taxon identification of these specimens was compared with clustering in two phenetic dendrograms generated with 36 morphological characters and 254 amplified fragment length polymorphic (AFLP) markers. Moreover, cytoplasmic haplotypes were assessed using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) of one mitochondrial and two chloroplast DNA regions. Results show that the morphological data set, containing mainly vegetative characteristics, merely reveals external resemblance between specimens, which is not directly associated with genetic relationships and taxon validity. Phenotypic plasticity and intercompatibility between several species are likely to confuse morphological delimitation of the taxa. Based on the results of our study, several specimens that could not be identified with the currently used identification key (1) could be attributed to a known taxon, which should be extended to include a higher range of morphological variability or (2) could be hypothesized to be of hybrid origin. Because of the high intraspecific variation within V. microcarpa and V. × heilbornii, revision of these taxa is recommended.

A Floral Ontogenetic Approach to Questions of Homology within the Cyperoideae (Cyperaceae)

Within the Cyperoideae, which comprise all Cyperaceae except the Mapanioideae, several questions of homology are discussed and reinterpreted based on results of our SEM and LM floral ontogenetic studies. In all species studied, spikelets are interpreted as being indeterminate, with spirally to distichously arranged glumes, each subtending (or not) a flower. Floral development starts with the formation of two lateral stamen primordia, simultaneously with, or followed by the formation of a third, abaxial stamen primordium. Perianth parts, if present, originate only after the formation of the androecium, simultaneously with the appearance of an annular ovary primordium, surrounding a central ovule primordium. Perianth parts vary in number and morphology, and, where present, perianth development follows a general pattern. Three (or two) stigma primordia are formed on the top of the rising ovary wall. In dimerous gynoecia, stigma primordia originate either dorsiventrally, resulting in a laterally flattened ovary/nutlet, or laterally, resulting in a dorsiventrally flattened ovary/nutlet. We conclude that in all species studied the spikelet and floral development occurs according to a general, scirpoid, ontogenetic pattern, which we illustrate using new spikelet and floral ontogenetic results in Eleocharis palustris and other species. Spikelet and floral ontogeny in species with apparently deviating morphologies, can be traced back to the general ontogenetic pattern.ResumenVarias preguntas sobre homología para las Cyperoideae, que incluyen todas las Cyperaceae excepto las Mapanioideae, se discuten e interpretan con base en estudios de ontogenia floral realizados con SEM y LM. En todas las especies estudiadas, las espiguillas son indeterminadas con glumas arregladas en espiral o dicotomicamente, cada una sosteniendo (o no) una flor. El desarrollo floral comienza con la formación de dos primordios estaminales laterales, simultáneamente con o seguido por la formación del tercer primordio estaminal abaxial. Si se desarrollan las partes del perianto, se originan solo después de la formación del androceo, simultáneamente con el desarrollo del primordio anular del ovario que envuelve al primordio central del óvulo. Cuando están presentes las partes del perianto, varían en número y morfología y el desarrollo sigue un patrón general. Se forman tres (o dos) primordios del estigma en el ápice de la pared del ovario en desarrollo. En gineceos dímeros, los primordios de los estigmas se originan dorsiventralmente resultando en una nuececilla/ovario comprimido lateralmente, o se originan lateralmente, resultando en una nuececilla/ovario comprimido dorsiventralmente. Concluimos que, tanto el desarrollo floral, como el de las espiguillas en todas las especies estudiadas, siguen un patrón ontogenético general scirpoide que se ilustra con los resultados obtenidos para Eleocharis palustris y otros especies. La ontogenia floral y de las espiguillas en especies con morfologías aparentemente atípicas, puede estar reducida al patrón ontogenetico general.

Variability in composition of the essential oil of Calamintha nepeta

Abstract C. nepeta ssp. nepeta and C. nepeta ssp. glandulosa are able to produce the same volatiles with the p -menthane skeleton oxygenated in C-3. The compositions of the essential oils range from the very simple, containing almost exclusively piperitone oxide and piperitenone oxide, to the relatively complex, containing the former oxides, pulegone, menthones, menthols and their acetates. As such they cannot be used to distinguish between the two subspecies.

A combined morphometric and AFLP based diversity study challenges the taxonomy of the European members of the complex Prunus L. section Prunus

Multivariate analysis of both endocarp and leaf morphometrics is combined with cluster analysis and Bayesian inference of AFLP markers to assess the morphologic and genetic variation of five European members of Prunus section Prunus (P. cerasifera, P. domestica, P. insititia, P. spinosa, and P. × fruticans). Endocarp morphometrics separate most Prunus taxa studied, but overlap remains between P. domestica and P. cerasifera, and P. spinosa and P. × fruticans. Leaf morphometrics yield better separation of P. domestica and P. cerasifera, but do not allow distinction between P. spinosa and P. × fruticans. Both cluster analysis and PCoA of AFLP markers equally produce three distinct clusters. A first consists of all P. cerasifera samples and the sole P. cocomilia; a second cluster includes all individuals of P. domestica and P. insititia; and a third group comprises all P. spinosa and P. × fruticans samples.