Prof. Dr. Marcus Koch
For the various research projects we are always seeking for enthusiastic students and co-workers (Bachelor- Master- Dipoma- or Staatsexamens-thesis):
Our research is funded by DFG, EU-Synthesis, DAAD and the Humboldt-foundation, the Tschira-foundation as well as from the excellence initiative I (Federal State and Heidelberg University), and graduate programmes (Landesgraduiertenförderung. HBIGS) and the Naturschutzfond Baden-Württemberg.
Research projects at the Botanical Gardens and Herbarium
Selected other projects
Principles of Crucifer Evolution, DFG-Project: Crucifers (Brassicaceae, Cruciferae) are a large family comprising some 340 genera and approximately 4,000 species. The family includes important crops as well as several model species in various fields of plant research. Meanwhile, we have nearly complete coverage of a molecular-systematic characterization of all genera. And, in addition numerous phylogenetic hypothesis based on various genes from the plastome, nuclear and mitochondrial DNA are available enabling us to provide first robust and reliable family-wide phylogenetic trees. The Brassicaceae are characterized by frequently occurring hybridization and poly-ploidization, which, as a consequence, is greatly affecting genome size and structure, but also any mode of speciation. Nonetheless, it is still unclear if the evolution of the Brassicaceae on the various taxonomic/temporal levels and of its evolutionary lineages is mostly or even best explained by multiple radiation events. A fact that can also account for the difficulties to resolve deep phylogenetic relationships within the family. Herein we are aiming to use the actually available knowledge and phylogenetic data and a phylogenetic backbone to address these principles questions of crucifer evolution by adding genome size data across the whole family.
Adaptation and introgression: Habitat adaptation and the acquisition of adaptive traits via introgression in an Arabidopsis lyrata - arenosa introgression zone (DFG - SSP1529): We here propose to analyze the genetic basis of edaphic adaptation in outcrossing Arabidopsis species and to study a natural hybridization and introgression zone of these species in the north-eastern Limestone Forealps. We have previously characterized introgression from Arabidopsis arenosa (with a broad ecological niche regarding edaphic conditions) into limestone adapted Arabidopsis lyrata (with a very narrow ecological niche in mountainous regions). The introgressed populations were capable to escape from this narrow ecological niche and migrated into lowland areas dominated by siliceous bedrocks northward into the Danube river valley. Within the here proposed project, massive parallel DNA sequencing will be used to identify genomic regions associated with edaphic adaptation in diploid populations of both species. In tetraploid populations we will then analyze the genomic contribution of the Arabidopsis arenosa genome that has introgressed into A. lyrata and allowed the latter to adapt to the new substrate. Specifically, we will ask whether adaptive genes identified in diploid populations have preferentially introgressed in the tetraploid hybridization zone. In parallel, reciprocal cultivation experiments with material from different edaphically adapted populations will be conducted to assess the extend of local adaptation and to study at the transcriptome level genetic differences that have evolved on different substrate types.
Evolutionary Biology and Conservation Genetics of Gingko biloba (Collaboration project, Zhejiang University, Prof. Fu/Prof. Zhao): This long-term projects is aiming to unravel not only the history of this spectacular and mysterious plant species. But since we were able to demonstrate the existence of refuge populations in China, we now aim to understand in depth the population dynamics and genetics of natural populations. This knowledge is important for any future conservation action plan since also these protected regions are under severe threat.
BrassiBase: Tools and biological resources to study characters and traits in the Brassicaceae (DFG - SSP1529) We aim to develop a system of cross-referenced information and resources on Brassicaceae taxonomy, systematics, evolution, chromosome numbers, accurate enumeration of all species, traits and characters and germplasm resources. Biological, molecular and evolutionary knowledge is exponentially increasing in the mustard family (Brassicaceae, Cruciferae). However, because of the complex and overwhelming biological diversity in the family, it is difficult for non-specialists in this plant family to put any research result in a larger evolutionary framework. Many species are remarkable study objects but rarely available. Biological material and resources, either collected directly in the wild or held in germplasm collections, is often taxonomically mis-itentified; and very rarely the material is further characterized and documented. There is also no family-wide and comprehensive survey of character and trait distribution despite the fact that we approached a reliable phylogenetic framework quite recently. In order to close these various gaps and provide the full potential of research focusing on the adaptive characters and character-trait evolution in the Brassicaceae, we will provide a comprehensive documentation of the taxonomy and systematics of the entire family. This will include a database with all the relevant taxonomic, systematic and phylogenetic literature; a comprehensive data collection of characters and traits including all potentially adaptive traits scientists participating in SSP 1529 are interested in; a DNA-based identification tool for genera and species; electronic interactive keys for the identification of genera and species, and a setup of a carefully selected and documented germplasm collection representing the entire family. Basic research will be conducted to provide first and comparative insights into the evolution of characters and traits over the whole family utilizing also the data collected during the project. The results and framework provided herein will be the basis and starting point for other projects focusing in more details on individual characters and traits – inside and outside SSP 1529 “Adaptomics”.
Evolutionary dynamics in a populational network in Arabidopsis lyrata (LGFG). The most important “evolutionary units” is the species in a population context. On the species level new characters, traits and abilities have been manifested and genetic differentiation, mutation, adaptation and selection shaped these new species and, finally, they are separated from closely related sister species. These evolutionary processes take place on the population level and are represented by networks of populations with gradients of geneflow, decreasing “cohesive genetic contact” and, finally, reproductive isolation. Since the introduction of Arabidopsis thaliana, the Thale Cress, to a broader scientific community in 1965, nearly 40 years passed until the phylogenetic position of this species was resolved and its closest relatives were characterized. More and more molecular data is available for Arabidopsis thaliana and it has become the most important model system among dicotyledonous plants. However, Arabidopsis thaliana provides only a limited set of traits and characters. We are now in the position that scientists move into the more diverse relatives of Arabidopsis, transferring knowledge from the model plant to these species. In Arabidopsis thaliana it is hardly possible to analyse past and ongoing evolutionary processes within and between neighbouring populations as outlined above to learn more about general evolutionary principles, because of its short life cycle, high levels of inbreeding and its ability to colonize rapidly. Recently, we characterized in detail the closest relatives (eg. Arabidopsis arenosa and A. lyrata) and provided a comprehensive evolutionary scenario for all speciation of the genus . Within the framework of this study we discovered a 900 km² suture zone in the foothills of the Eastern Austrian Alps between A. arenosa and A. lyrata with genetically stabilized populations indicating that a “new” hybrid species has evolved. However, although all populations have been stabilized genetically and ancestral populations went extinct most likely prior last maximum glaciation gradients of morphological and genetical variation are obvious. This is an indicator that a cohesive geneflow is still in action. We sampled and characterized more than 150 populations with 20-30 individuals in initial screening to measure genetic differentiation and morphological variation. In the herein proposed project we aim to ask the question if the breeding system itself can explain the observed pattern of variation. The Brassicaceae family is characterized by a sporophytic incompatibility (SI) system preventing selfing. This is also true for most Arabidopsis species (except A. thaliana) . The SI system is well characterized genetically and molecularly, and case studies in Brassica (cabbage) elucidated the existence of large set of SI alleles and also demonstrated the possibility of occurrence of inbreeding depending on which alleles are combined during pollination. Within mostly outbreeding populations with large effective population size, and especially when the network of populations arose via hybridization long time ago, we can assume that geneflow across populations is heavily affected. Therefore, we would like to test the hypothesis if restricted geneflow due to varying populational gene pools of SI-alleles can counteract homogenization of a gene pool, a scenario that can explain the observed gradients of morphological and genetical differentiation.
Systematics and Evolution of the tribe Arabideae with special emphasis on the genus Arabis (Brassicaeae). The broadly defined genus Arabis has been revised systematically only in few parts. Some species previously assigned to Arabis are now confined to genera such as Turritis, Pseudoturrits, Boechera or Fourraea. Other genera such as Arabidopsis, Cardaminopsis or Borodinia have been erroneously placed into Arabis in the past. In contrast genera such as Rhammotophyllum, Pachyneurum or Botschantzevia might be best placed in a revised tribe Arabideae. Some of the above mentioned genera are not members of tribe Arabideae, and considering the actual knowledge actually 70 to 140 Arabis species together with approximately 370 species of the genus Draba and its closest relatives might represent the core of tribe Arabideae. Our preliminary work has demonstrated that Draba and its segregates are mostly monophyletic, but in contrast, Arabis species appeared as a largely para- und polyphyletic set of species. Species-rich and widely distributed species complexes such as the Arabis hirsuta-aggregate have been also wrongly interpreted in the past, and it is apparent that hybridization, polyploidization and reticulation play an important role in the evolutionary history of many species. In this project we aim to analyze the systematics and evolution of the currently broadly defined genus Arabis in the context of the whole tribe Arabideae. We reconstruct the phylogeny of the whole tribe with special emphasis on the evolutionary history and phylogeography of the more important and wider distributed species complexes such as the Arabis hirsuta-aggregate, red-flowering North American Arabis and the Arabis alpina group playing an increasing role as model in developmental and evolutionary research. Representatives of the genus Arabis are distributed in all north-hemispherical alpine to montane habitats and provide an ideal system to study the evolution of adaptive characters and traits.
Phylogeography and conservation genetics of the Central European Cochlearia. The genus Cochlearia comprises less than 20 species. There are various polpyloid taxa, but most interestingly are the diploid and ancestral species. Most of them occurr in extreme cold-temperate habitat types (springs, creeks, or high alpine regions) and especially the Central European lowland populations seem to be one of the few examples of cold-adapted plants severely suffering from climate change and global warming. Consequently Cochlearia pyrenaica is one of the most threatend plant species all over Europe. In various countries less then five populations survived. Germany plays an important role in the conservation of this species since most of the populations are found in Bavaria and Baden-Württemberg. We aim to develop a phylogeographic-evolutionary scenario of the whole genus with some particular focus on the conservation genetic status of the species.
Phylogeography and the evolutionary history of Hypericum perforatum L., DFG-PROJECT - HypEvol: The genus Hypericum is a morphologically and ecologically highly diverged and large group of more than 460 species. Several species are wide-spread in Eurasia and dominate in lowland habitats not affected by extreme environmental factors. Hypericum perforatum and H. maculatum are representative examples with a largely overlapping distribution area, but the first one tends to prefer drier habitats, while the second species is distributed even in boreal Eurasian regions. We aim to unravel the evolutionary history of these two wide-spread lowland species during the pleistocene (phylogeography) and to characterize genetical contact zones reflecting actual and past geneflow between both. We would like to test if this evolutionary scenario of the wide-spread lowland species confirm patterns of refuge areas and principle migration routes revealed from the analysis of woody plants, annuals, arctic-alpine representatives and others. It is very likey that hybridization and reticulation played a role in the evolution of different morpho- and cytotypes in H. perforatum as well as in H. maculatum, and it is also obvious, that there is ongoing geneflow between both species groups. This project is embedded in a larger research network focusing on the evolution and systematics of Hypericum in general, but selecting H. perforatum and closest relatives as model to focus on evolutionary important traits and characters. The results from this study are a prerequisite to discuss the evolution of one important trait in Hypericum, namely apomixis, the propagation via seeds produced without sexuality. This study will provide fundamental information about 1) centres of genetic diversity, 2) migration routes and source areas of genetic variation, 3) hybridization and suture zones, and 4) temporal estimates of diversification. All these information can be linked with the trait apomixis within populations actually analysed in detail and should answer questions about 1) multiple origin and constitution of apomixis (in space and time), 2) transmission of the trait via hybrid bridges, and 3) temporal dynamics of adaptation and transition from sexual to asexual propagation and vice versa.
Conservation Biology and Genetics of Cheddar Pink - Artenschutzprogramm Pfingstnelke, Naturschutzfond BW (in coll. with the Federal State BW and NHM STU) The Cheddar Pink (Dianthus gratianopolitanus) is an endemic element of the Central European flora. Its distribution centers are located in the French, Swiss and German Jura mountains. Furthermore, there are numerous relic populations throughout Europe, found in low elevation mountain areas, ranging from France and Belgium to the Czech Republic and Poland in the East. A distribution outpost is found in the UK (Somerset: Mendip Hills). The Cheddar Pink is growing on shallow, humus-poor soils, at habitats with high light intensities, such as margins of acclivities, rocky outcrops and cliffs. The plant is frequently found on limestone (dolomite). In the northeast of its distribution range, populations are frequently found on schistous gravel, sandstone, diabase or greenstone and serpentine. Occasionally the Cheddar Pink manages to penetrate into pine forests adjacent to its rocky habitat. In Brandenburg, Germany, D. gratianopolitanus var. sabulosa is found in pine forest on sandy soils. In France and Switzerland the species is found at elevations between 500 and 1600 m asl. Outside these areas, the species occurs at much lower elevations. It is important to notice, that the habitat type colonized by the Cheddar Pink is almost exclusively highly endangered and characterized by very specific species assemblages. This is especially true for rocky outcrops and cliffs as well as serpentine habitats. It is also important to realize that these rock and cliff habitats are mostly NON-alpine. Consequently, con-sidering the large and native Central European distribution range, the Cheddar Pink can be regarded as a “flagship species” for many of these habitat types. Further investigation is necessary to illucidate the Cheddar Pink’s eligibility to serve as target species in nature conservation and action plans. The Cheddar Pink is endangered troughout its whole distribution area. The different factors causing this severe threat can be roughly categorized as follows: 1) vegetation encroachment, 2) human recreational activities – especially climbing, or hiking close to cliff sides, 3) genetic and autecological effects caused by very small and isolated, populations. Especially factors 1 and 2 are surprising at first, for today, most populations are located in nature reserves. However, especially these habitats suffer largely from successional processes towards closed woodlands. And as a curiosity one population in Lower Saxony (sünteln, Niedersachsen) occurs on rocks surronded by avalanche forest, which is a major conflict of objectives. The distribution pattern demonstrates that Germany and Switzerland share particular responsibility for any longterm preservation and action plans. Populations in Germany are especially noteworthy for they display an exceptionally broad ecological amplitude (e.g. adaptation to a wide range of different soil types). As a consequence, populations in Germany must be regarded as central to any conservation strategy. Although the highly endangered Dianthus gratianopolitanus is neither protected as annex species to the FFH-EU directive nor protected under the Berne convention, in most countries strict national protection guidelines are given. Our project on conservation genetics and evolution of the Cheddar Pink is based on these various aspects. At first glance, the continuous Central European distribution indicates only little differentiation. However, edaphic factors indicate a major geographical split, separating a major area harbouring populations on limestone (Jura mountains in Switzerland, France and Germany), from northeastern populations, with many satellite populations remaining scattered throughout Central Europe. The project aims to answers several open, but important questions regarding genetic diversity, distribution and evolutionary history, but also regarding systematics and taxonomy. These datasets are virtually important to develop effective conservation management strategies for Dianthus gratianopolitanus.
THE WERNER RAUH HERITAGE PROJECT Prof. Werner Rauh (1913–2000) studied Botany, Zoology, Chemistry and Geology at Leipzig, Innsbruck and Halle (Saale). In 1956 he was appointed as associate Professor of Botany at Heidelberg University. In 1960 he became full Professor and Director of the newly established «Institut für systematische Botanik und Pflanzengeographie», until 2010 Heidelberg Institute for Plant Science (HIP), now part of Centre for Organismal Studies (COS Heidelberg). He held this position until he retired in 1981 and beyond that until 1982.
During his time as director and in his retirement until 1994, he made more than 36 expeditions, mainly to South- and Central-America, as well as to the south of Africa and particularly to Madagascar. From these journeys, he took innumerable plants to the Botanical Gardens Heidelberg, especially succulents, bromeliads and orchids, which are a valuable part of today's living collection and of the Herbarium (HEID). During his expeditions he scribed more than 90 booklets with detailed information not only about the plants collected, but on vegetation and geology of the regions he visited. A total of 8.776 hand written pages with more than 19.000 entries, hardly accessible for research, were scanned in 2008 and 2009 and are now being processed within «The Werner Rauh Heritage Project».
The heart of the project is a relational database to store the heterogenous information found in the field books, as well as to link it to a clear taxonomy and to the garden's database. A number of powerful tools are being developed to enable researchers to search the database for information like collected taxa by name, Rauh's field numbers and the place of collection etc. The central parts of the database are a look-up table with the itineraries of Werner Rauh's journeys (all geographical points to be found in his field books, with the taxa collected or observed) and another table with the taxa entries (all taxa with a field number noted in the field books). Tables with synonyms and basionyms and protologue data are included as well as links to other taxonomic databases, e.g. IPNI and TROPICOS.
AFRICAN and GLOBAL PLANT INITIATIVE - API/GPI (Aluka ) is an international, collaborative initiative building an online digital library of scholarly resources from and about Africa. Our name,"Aluka", is derived from a Zulu word meaning"to weave", reflecting Aluka"s mission to connect resources and scholars from around the world. Aluka seeks to attract high-quality scholarly content about Africa from institutions and individuals across the globe. By contributing their collections to the Aluka platform, content owners will have a means of offering access to their collections to an international audience without having to develop and support their own technology platforms.
Aluka"s web-based platform provides powerful tools for research, teaching, collaboration, and knowledge exchange. The Aluka website includes a wide variety of high-quality scholarly materials contributed by Aluka"s partners, ranging from archival documents, periodicals, books, reports, manuscripts, and reference works, to three-dimensional models, maps, oral histories, plant specimens, photographs, and slides. By aggregating these materials online, the Aluka collections link materials that are widely dispersed and difficult to access, opening up new opportunities for research, teaching, and broader public discussion. One of Aluka"s primary objectives is to provide African scholars and students with access to scholarly materials originally from Africa, but now out of their reach. Aluka also works closely with partner organisations in Africa to build capacity in digitisation and the use of online materials for teaching and research. In some cases this includes setting up digital labs and providing technical training in scanning and creating metadata records; in others, Aluka convenes training workshops for librarians, archivists, faculty, and heritage professionals on topics related to digital imaging, preservation, and the use of online tools in the classroom. To demonstrate the potential of Aluka as a scholarly resource, three content areas are currently under development: African Cultural Heritage Sites and Landscapes, Afrian Plants Type Collection, and Struggles for Freedom in Southern Africa. New materials are added to the collections on an ongoing basis. In the longer run, our hope is that Aluka"s work in Africa will be a model for expanding the initiative to other regions of the developing world. The African Plants content area comprises scientific data contributed by the African Plants Initiative (API) [e.g. from Germany Berlin, Munich, Heidelberg, and others], a collaboration among more than 50 institutions
in Africa, Europe, and the United States. Partnering with Aluka, API's long-term goal is to build a comprehensive online research tool aggregating and linking presently scattered scholarly resources about African plants, thereby dramatically improving access for students, scholars, and scientists around the globe. Each plant species in the African Plants digital library is represented by high-resolution digital images of type specimens provided by participating herbaria. When complete, the digital library will include images of more than 250 000 type specimens drawn from the estimated 60 000 plant species in Africa, Madagascar, and the other islands surrounding the African continent. A wide range of related images and data, including photographs, drawings, botanical art, field notes, and reference works, is also included. Examples of other resources include: The Useful Plants of West Tropical Africa, La Flore du Cameroun, Flowering Plants of South Africa, illustrations from Curtis's Botanical Magazine, individual botanists' slide collections, and selected archival materials such as David Livingstone's South Eastern Africa Expedition Papers. By aggregating materials from such a broad array of sources and making them easily accessible online, the African Plants digital library will revolutionise research and teaching about African plants. As an example, in taxonomic research, access to type specimens is essential, but because most African type specimens are located outside of Africa, it is time-consuming and expensive for African scientists to conduct research. Not only does the availability of Aluka greatly reduce the need to travel to faraway herbaria to view type specimens, it also makes possible bringing together for the first time specimens from multiple herbaria, linked to other relevant scientific data. The ability to examine and compare specimens online will expose gaps in current knowledge, stimulate new research, and increase the use of taxonomic data for conservation and sustainable use, resulting in benefits of a possibly global nature. Because of its breadth, the African Plants content is useful not only to botanists, but also to students and scholars in many related academic disciplines, including ecology, ethnobotany, biology, natural products, anthropology, history, economic development, and environmental studies.
Evolution of apomixis in North American Boechera, Kooperation with Tim Sharbel. Over the past years we developed a comprehensive evolutionary model of the diversification of the genus Boechera in space and time. More than 2000 accessions have been analysed and genotyped over the whole North american continent. Additional information was achieved analysing the reproductive mode and the trait apomixis..
Evolution of the genus Draba, Koopearation with Ingrid Jordon. We developed a comprehensive phylogeny of the genus Draba with its more than 350 species. In this collaboration we further focus on biogeographic aspects and unravel the importance of various different modes of the reproductive system triggering the evolution of particular clades within Draba.
Regeneration of limestone grassland in Lower Saxonony. Over the past 25 years we have monitored and evaluated management strategies to restore limestone grasslands in Lower Saxony near Osnabrück. With particular consideration of the soil seed bank these management strategies will be further optimized and developed to guarantee the survival of this unique vegetation type.
Further projects are focusing on the phylogeography and taxonomy of Noccaea caeruelscens agg, the genus genus Aubrieta, terrestrial tillandsia´s, ...