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Research projects


Phylogenetics, gene evolution, bioinformatics, taxonomy and conservation are all important topics within modern systematics. The evolutionary and phylogenetic aspects of systematics form the core of most research conducted at our department. Our research is mainly approached with DNA sequence data from organellar and nuclear DNA sequences to form gene phylogenies. From these, phylogenetic relationships among taxa, ages and geographical origins of taxa, origins of homoploid and allopolyploid hybrids, and the origins of morphological traits are deduced.

A herbarium sheet A view from our lab Phylogenetic tree
From herbarium sheet to phylogenetic tree. Photos: Elisabeth Långström (left), Magnus Lundberg (middle).

Fundamental systematic/taxonomic research on the biodiversity of plants is focused on club mosses, ferns, many different flowering plant groups, and fungi (especially lichens). Some of these projects contribute to the Swedish Taxonomy Initiative.

Two large Flora projects in East Africa, Flora of Somalia and Flora of Ethiopia and Eritrea, are coordinated and led by researchers at the department. The phylogenetic aspect of conservation is considered. In ethnobotanical research, questions about man's use of plants for medicines, food and phytochemicals are addressed. Botanical historical research is conducted on the life and work of Carl Linnaeus, especially his teaching in Botany.

Tools for displaying information about taxonomy, phylogeny, chorology, DNA sequences, and morphology via an interactive database are being developed, and properties of different support measures for phylogenetic trees are investigated.

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LICHENOLOGY & MYCOLOGY

Taxonomy and phylogeny of lichenized fungi and non-lichenized fungi

Group leader: Leif Tibell
Project description: Molecular data have during the past decade led to a new understanding of the evolution and phylogeny of lichenized fungi. The new insights have revolutionized our knowledge in a way hardly paralleled among other eucaryotic organisms. The main reason for our previously poor knowledge of the phylogeny of lichens are the complex and very often homoplastic character of morphological and anatomical expression during symbiosis. Moreover lichens are very difficult to cultivate and slow-growing which has led to difficulties in experimental genetic work on lichens. The project aims at contributing to the emerging new insights by concentrating on groups where we have an internationally leading competence (calicioid lichens and fungi), on groups containing critical problems (Verrucariales), and on the enigmatic, large and morphologically very variable genus Usnea as a model system for studies on morphological differentiation, speciation and sexual versus asexual strategies for dispersal and evolution. The ecology, cultivation, biography and systematics of Tuber is also being studied. The studies involve both ribosomal, mitochondrial and nuclear genes, depending on the hypothesis investigated. The project is also part of the comprehensive international effort: ’Collaborative research: Assembling the Fungal Tree Of Life’(AFTOL), supported by the US NSF for the forthcoming four years.

Collaborators:

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LAND PLANT SYSTEMATICS

Age and biogeography of major groups of flowering plants

Group leader: Kåre Bremer
Project description: Monocots, eudicots, rosids, and asterids are major groups of flowering plants. Asterids (e.g. sunflowers) and monocots (e.g. lilies), their phylogeny and evolution, have been the main focus of the present project. It will now be expanded to comprise all eudicots, including rosids (e.g. roses) and the phylogenetically basal eudicots (e.g. buttercups), and focused on dating the phylogenies. With dated phylogenies it will be possible to replace the orders and families of classification with groups of the same age as units of comparison in evolutionary research. A dated phylogeny provides answers to questions such as: When did monocots, eudicots, etc. split from other flowering plants? Which extant groups of monocots, eudicots, etc. existed e.g. during the Mid-Cretaceous and at the Cretaceous-Tertiary boundary? – Dated phylogenies increase the possibility of exploring historical biogeography of flowering plants in relation to continental history driven by plate tectonics. During the Cretaceous and the Early Tertiary, major groups of flowering plants evolved and the modern continents separated from Laurasia and Gondwana. These events are related and it should be possible to address questions such as: Which groups of flowering plants evolved in Laurasia and Gondwana, respectively? Is there a difference in life forms, morphological specialisation, etc. in groups with different continental histories?

Collaborators:
Cajsa Anderson, PhD student

land plants | top

Heterogenous DNA - substitution rates (Malvaceae, Asteraceae)

Group leader: Katarina Andreasen
Project description: Comparative studies of molecular data are effective to determine how organisms are related. Certain evolutionary processes like hybridization, however, impact the evolution of organisms genomes and confound the results, especially at lower taxonomic levels. Consequently, it is essential to investigate evolutionary patterns at those levels, not only to correctly reconstruct phylogenies, but also to increase our knowledge about the evolutionary forces acting on different DNA regions. This project aims at understanding the evolutionary processes that lead to heterogeneous copies of nuclear DNA regions in individual organisms and to changes in substitution rates between closely related organisms. Sequences of nuclear low- and multicopy and chloroplast DNA regions and clones of the nuclear DNA regions will be analyzed for three flowering plant genera: Arnica (Asteraceae), Eremalche and Sidalcea (Malvaceae). A major goal is to elucidate effects of life history traits like generation time on substitution rates and of evolutionary processes such as hybridization on the evolution of different DNA regions. Congruent and incongruent patterns between the data sets will be evaluated to determine which evolutionary forces and factors are acting on the genomes of these plants. The phylogenies are also important to evaluate earlier hypotheses about speciation, relationships, and biogeography. Moreover, as the genera contain many endangered taxa the results will have important conservation implications. A PhD project concerns the phylogeny of Arnica but also ethnobotany and phytochemistry as several of the species have medicinal uses.

Collaborators:

land plants | top

Molecular taxonomy of Sileneae (Caryophyllaceae)

Group leader: Bengt Oxelman
Project description:
This project aims at producing a classification of the 7-800 species in Sileneae, which is firmly based on their evolutionary history. A database where information in the form of DNA sequences, gene phylogenies based on these, morphological traits, literature, nomenclature, chorology, and taxonomical treatments is under development.

Collaborators:

land plants | top

Genome evolution of flowering plants as revealed by RNA polymerase gene sequences

Group leader: Bengt Oxelman
 Project description: Nuclear genomes of flowering plants have complex histories characterized for examle by sigle gene duplications, polyploidy, and eneuploidy. Comparative, phylogenetic studies of the RNA polymerase gene families offer great opportunities to understand how the genomes in different taxonomic groups have formed. This project aims at disentangle the evolutionary history of different plant groups, especially those where polyploidy and/or reticulate evolution plays a significant role.

Collaborators:

land plants | top

Properties of resampling methods and other support measures used in phylogenetics

Group leaders: Bengt Oxelman, Tom Britton, Prof, Department of Mathematics, Stockholm University
Project description: The aim is to understand properties of different measures of support on phylogenetic trees, for example resampling methods (bootstrap, jackknife), and Bayesian posterior probabilities obtained from MCMC. We use both simulated and real data to address these questions.

Collaborators:

land plants | top

Taxonomy and Phylogeny of Corydalis (Fumariaceae)

Group leader: Magnus Lidén
Project description: The aim is to produce a systematic monograph of the c 450 species of Corydalis, based on a detailed cpDNA phylogeny, biogeographic studies, nomenclature, etc. Strong focus is put on discovery and description of new species. The genus is most diverse in SE Tibet, NW Yunnan and W Sichuan. Expected outcomes of the project are: - Papers on phylogeny and biogeography of Corydalis - descriptions of new species - A treatment for the "Flora of China" - A treatment for "Species Plantarum" - A web database.

Collaborators:

land plants | top

Plant diversity in the Horn of Africa region

Group leader: Mats Thulin
Project description: Taxonomic/floristic, phylogenetic and biogeographical studies are integrated to investigate the biodiversity in the arid Horn and to put the region in focus for the local and global conservation efforts that it deserves. Three specific but interdependent goals are 1) to complete Flora of Somalia, the core area in the region, by the publishing of the fourth and last volume, 2) to make improved estimates of plant diversity in the region and to map distributions of endemics to be able to pinpoint local biodiversity hotspots, and 3) to analyze biogeographic patterns through molecular biogeographic studies of selected target groups in order to, among other things, investigate the importance of the boreotropic element in the flora.

Collaborators:

land plants | top

Flora of Ethiopia and Eritrea

Group leader: Inga Hedberg
Project description:

Collaborators:

land plants | top

Evolution and diversification of ferns and fern allies

Group leader: Niklas Wikström
Project description: This biodiversity project will investigate patterns in the systematics and diversity of land plants, focusing on groups traditionally classified as "pteridophytes". The project will target issues at different hierarchical levels including: 1) Overall fern relationships; 2) Species level relationships in Schizaeaceae and 3) Species level relationships in Isoetaceae; Resulting phylogenies will be calibrated against the geological time scale by: 1) including information from the fossil record; and 2) using sequence divergence based methods.
Collaborators:
Niklas Wikström

land plants | top

Speciation processes and patterns in Diphasiastrum (Lycopodiaceae): Investigating the genetic and taxonomic impact of homoploid hybrid formation

Group leader: Niklas Wikström
Project description: Several Diphasiastrum (Lycopodiaceae) species have an assumed homoploid hybrid origin and have been described, considered, and included in national biodiversity programs, yet we have very little knowledge as to what these hybrid taxa actually represent. Do they exist? Do they interact with their putative parental taxa, and what consequences do these interactions have? Using DNA sequence, microsattelite and allozyme-based data, this project will investigate the impact with respect to gene flow and taxonomic patterns that the formation of homoploid hybrids has in Diphasiastrum.

Collaborators:

land plants | top

ETHNOBOTANY

Ethnobotany at Uppsala University

Group: Lars Björk , Hugo de Boer , Inga Hedberg , Anneleen Kool

Ethnobotany has a long tradition in Uppsala, starting probably with one of its most prominent scientists Carolus Linnaeus in the middle of the seventeen hundreds, and his research on the use of plants by the Sami people in northern Sweden. Its place in the natural sciences and in botany has not always been very clear, and ethnobotany as it is available and taught today is due to Inga Hedberg's efforts. Inga's interest in ethnobotany is rooted in half a century experience of botanical research in Africa, and the experience that botanical research without people's participation can never lead to biodiversity conservation. In 1995, she taught the first summer course in ethnobotany. A course that has drawn an unexpected average of 25 students per year, and that gives an overview of ethnobotany through a series of presentations, field excursions, and project work. The current high level of research activity was initiated through Lars Björk's professional engagement and project applications. Research in ethnobotany is done by, and under supervision of, the group in Sweden, Laos, Cuba, Bulgaria, Morocco, Tanzania and Ethiopia

ethnobotany | top

Ethnobotany in Bulgaria: Post-communist plant use by elderly people, revival or continued tradition?

Project description: Since 2003 we have been interested in medicinal plant use in Bulgaria, when Lars Björk and Marie Melander carried out an extensive study interviewing mainly elderly people on plant use. During the late spring of 2005, the fieldwork of the 15 ECTS Ethnobotany took place in Bulgaria. Seven groups of two to three students studied different aspects of plant use by local people in Roussenski Lom National Park; Ternichene and Karlovo at the edge of the Central Balkan National Park.

Research was coordinated by the group, with the students writing proposals for their research to us. Research was conducted with the help of Bulgarian botanists and interpreters. Research projects focused on:

The students collected a lot of interesting data, and did some very good preliminary analysis of the data, that we will follow up in a compilation that compares with earlier work.

Collaborators:

ethnobotany | top

Ethnobotany research in Nakai-Nam Theun, Laos

Project description: This project is on: Ethnobotany and Biodiversity research in Nakai-Nam Theun National Biodiversity Conservation Area, Lao PDR. The project is fully funded by Sida-SAREC, and part in a larger collaboration between Uppsala University and the National University of Laos (NUOL). The large project includes one Swedish PhD student in botany and two Lao PhD students, one in botany and one in medical entomology. The part of the project that is carried out by Hugo de Boer consists of three sections:

Collaborators:

ethnobotany | top

Wildlife Trade in the markets of Marrakech, Morocco

Project description: We are collaborating in a project on wildlife trade initiated by The Global Diversity Foundation and Natural History Museum of Marrakech, Cadi Ayyad University, Marrakech. We are developing molecular identification methods to elucidate the composition of species complexes in genera such as Lavandula, Thymus, Ononis, etc.

In May 2006 we will carry out studies in the markets of Marrakech as part of the 15 ECTS Ethnobotany course. Research will focus on morphological determination of species in complexes to estimate trade in rare and endangered species, local species preference, and trade volume. The fieldwork will contribute to a wildlife trade database developed by GDF and MHNM, and to the identification of species complexes that include rare or endangered species that are hard or impossible to identify using morphological characters. These species complexes are to be prioritized for molecular identification to assess trade and endangerment.

Collaborators:

ethnobotany | top

Handbook in Access & Benefit Sharing and Intellectual Property Rights

Project description: Several new laws and international conventions regulate modern research on genetic resources. The awarness among scientists is low and lack of signed contracts like prior informed consent (PIC), Mutually agreed tems (MAT) and material transfer agreements (MTA) have already stopped Swedish scientists from access to their research material. Funding agencies and authorities are informed about obstacles and legal problems which scientists meet when they try to follow the new laws. The project objective is information to all parties involved to facilitate legal research on genetic resources.

Collaborators:

ethnobotany | top

HISTORICAL BOTANY

Linnaeus and his disciples

Group leader: Mariette Manktelow
Project description: The aim of the project "Linné och hans lärjungar" (Linnaeus and his disciples) is to study the relationship between teaching and scientific development, with Swedish naturalist Carolus Linnaeus (ennobled Carl von Linné) and his students serving as the empirical example. In the project we investigate how the various activities of Linnaeus - as teacher, supervisor and researcher - affected each other and how the Linnaean "way of thinking" came to influence his many pupils in their continued careers within and beyond the academic sphere. The point of departure is a cross-disciplinary approach joining together expertise on the theory and practice of botany as well as Swedish rhetoric and the eighteenth century history of Sweden and Europe.

There is a staggering amount of scholarship on Linnaeus and his scientific achievements, but very little is known of his accomplishments as a teacher and research supervisor. This despite the fact that Linnaeus was widely known in his own day as an inspiring lecturer and tutor, and despite the fact that so much has later been written about his disciples and their travels both within Sweden and across the world. No doubt the main contribution of Linnaeus was his scientific system and methodology, but it is questionable whether these ideas would have had such an impact if it had not been for Linnaeus' unusual abilities and innovation as a teacher. His teaching was also closely related to his own research in a manner that was very rare among his contemporaries. Hence, studying Linnaeus and his disciples in their eighteenth century context offers an almost unique opportunity to explore and problematize the interaction between pedagogy and science, between education and cultural development.

The project is carried out during the years 2002-2004 with funding from the Swedish Research Council's Committee for Educational Science. The research team is led by historian Åsa Karlsson, Editor of The Dictionary of Swedish National Biography, and includes two additional historians and a botanist at Uppsala University as well as a specialist in rhetoric and a Latin scholar from Södertörns högskola (University College) in Stockholm.

historical botany | top

 

Research projects
LICHENOLOGY AND MYCOLOGY
LAND PLANT SYSTEMATICS
ETHNOBOTANY
HISTORICAL BOTANY
MEDICAL ENTOMOLOGY