Large-Scale Syntheses
Background
Taxonomic and nomenclatural syntheses
For more than 150 years RBG Kew scientists have maintained a balance between regionally and systematically focused research programmes and broader projects encompassing most of the plant kingdom. One of the earliest of these global-scale surveys produced at Kew was Bentham and Hooker's Genera Plantarum. This multi-volume work, begun in 1862 and completed in 1883, was made possible by the collections and knowledge assembled as a result of W.J. Hooker's Colonial Floras scheme first proposed in 1857.
Another major project, at Charles Darwin's instigation and with his financial support, was the production of Index Kewensis (1885): the first attempt to list all scientific names of plants and their place of publication. Although this list contains only limited linkages between accepted names and synonymy, and minimal geographic information, it now contains almost 1,000,000 scientific names for plant species and thousands more above and below species level. New names are added as they first appear in the literature, and the database grows at a steady rate of some 6,000 entries per year, of which more than 2,000 are species new to science. Applying modern software has revolutionized the preparation and dissemination of Index Kewensis, and it is now available free online as part of the International Plant Names Index (IPNI), a collaborative venture between the Royal Botanic Gardens, Kew, Harvard University, and the Centre for Plant Diversity Research, Canberra. On average, users around the world access IPNI 10,000 times per day.
In addition, Kew produces the Kew Record of Taxonomic Literature, which provides bibliographic details of taxonomic literature dating from 1971. However, neither IPNI nor the Kew Record make taxonomic decisions or identify the correct name of a taxon.
Major reference works on Vascular Plant Families and Genera (1992) and Authors of Plant Names (1992) have continued Kew's traditional role of providing a comprehensive overview of particular aspects of plant diversity developed over the last hundred and fifty years. The database of vascular plant families and genera was supplemented with distributions for all accepted genera of vascular plants, based on herbarium specimens. This distributional data provides an ability to investigate global patterns of plant diversity and distribution using comprehensive and auditable data.
At species level, Kew has developed a programme of producing global plant checklists for selected families (www.kew.org/wcsp/). Typically these global checklists provide information on accepted scientific names, synonyms, distributions and life forms. They are compiled using diverse published sources and personal communications from taxonomic specialists that are then reconciled to produce a consensus listing for a particular taxonomic group.
The production of global checklists gained greater impetus with the adoption of the Global Strategy for Plant Conservation (GSPC) by the Conference of Parties to the Convention on Biological Diversity in April 2002. Target 1 of the GSPC is the production of a widely accessible working list of known plant species as a step towards a complete world flora. The GSPC recognises the role of such a list in underpinning and monitoring progress towards the other Targets.
Molecular systematics and the new angiosperm classification
Since 1992, Kew has been a leader involved in a major collaborative programme of research in molecular systematics. The aim was to develop a broadly based hypothesis of angiosperm phylogeny that in turn could form the basis for a new comprehensive global classification of flowering plants.
The new classification proposed by the Angiosperm Phylogeny Group (APG) in 1998, and updated in 2003, developed an all-purpose picture of what is known about the interrelationships of major groups of flowering plants. The APG classification had as one of its major goals the portrayal of evolutionary relationships that are as accurate as possible. This also included identifying groups for which the information base or hypotheses of relationship were either speculative or unknown.
To date, the history of this collaborative endeavour has been largely one of corroboration rather than refutation as the classification has been compared with existing and newly developed data from both molecular and non-molecular sources. This is what would be predicted if the classification were an accurate record of evolutionary patterns.
Much progress has been made since the initial publication of the APG classification in 1998. A further update will be published in 2007-8. Family and ordinal-level relationships in the angiosperms are now reasonably well characterised, and the changes in the final update are anticipated to be only minor.This process is now drawing to its logical conclusion, and the APG classification at this level should remain stable for years to come.
Attention is now being focused increasingly on relationships within families at the level of genera and species. Many “complete species” phylogenetic studies are in progress for some of the smaller clades.
Evolutionary biology and biodiversity analyses
Evolution is driven by natural selection, but its power to modify organisms is limited by patterns of heritable variation, which in part are dictated by their history (i.e. what they have inherited from their predecessors). Distinguishing between the effects of history and natural selection is perhaps the most basic challenge addressed by evolutionary biologists. Evolution is a contingent process and so establishing the pattern of evolution by developing robust phylogenetic trees is essential for addressing many of the most important questions in evolutionary biology. Some of these questions are: 1) how do speciation rates and extinction rates differ among different angiosperm clades and what are the bases of those differences? 2) which patterns of character evolution have occurred repeatedly in different angiosperm groups and what processes underlie these iterative patterns? 3) how do patterns of flowering plant evolution compare with those for animal groups and is there evidence for pervasive co-evolution? and 4) are the patterns of evolution predicted for key features from evolutionary theory consistent with the results of phylogenetic studies?
Major future challenges also include addressing several apparent paradoxes: 1) why if evolution can be so rapid (e.g. as demonstrated in laboratory experiments) is it often so slow (stasis has been amply documented in the fossil record)? 2) although there is a continuum of variation, why are there discrete entities that we call species? 3) why are some morphological or anatomical traits fixed within higher taxa, whereas the same characters are labile even within populations in other groups?
Because of the dramatic acceleration in data gathering that has taken place over the last five years, we face new challenges and exciting opportunities. The development of new computing technologies and faster phylogenetic algorithms have also improved our analytical power so that large scale biodiversity analyses are now feasible and can integrate taxonomic, genetic, ecological and evolutionary data. Although the production of a classification (and the underlying phylogenetic tree) has sometimes been viewed as an end-point, it is in fact a springboard for further studies.
Evolutionary biology is an implicit component of Kew’s mission; Kew is one of the world leaders in plant phylogenetics, has numerous large taxonomic data sets, and therefore is better placed than ever before to make cutting-edge advances in plant evolutionary biology. Biodiversity analyses also have the potential to link profitably with conservation (e.g. in the recognition of so-called biodiversity hotspots, and in the use of phylogenetic diversity indices for conservation planning) although the problem of the loss of biodiversity is obviously so complex that it needs to involve a wider range of disciplines. Finally, new genetic tools of and for global application are also being rapidly developed, such as ‘DNA barcoding’. Although still controversial, the scientific benefits of DNA barcoding include: 1) enabling species identification; 2) facilitating species discoveries based on cluster analyses of gene sequences; 3) promoting the development of handheld DNA sequencing technology that can be applied in the field for biodiversity inventories and in evolutionary ecology; and 4) providing insight into the diversity of life.
Kew has used empirical and simulated data to study the molecular evolution of the plastid genome, which is commonly used in phylogenetic work by systematic botanists. We have specified in which context (quantity of data) and for what type of genes (quality of data) it is appropriate to use simple tree-building methods despite criticisms of their use on large data sets. As a result we can now conduct even larger-scale analyses. For cases in which combinable data are not yet available, we have investigated the use of supertrees (composite phylogenetic trees) to study evolutionary patterns.
We have made use of broad-scale phylogenetic trees (e.g. a complete family-level supertree of the angiosperms) to look for correlates of species diversification, age of clades and general patterns of evolution and geographic distribution. Phylogenetic trees are not only networks exhibiting evolutionary affinity, they include branch lengths that can be translated into rates of change at both genotypic and phenotypic levels. Relative time or absolute dates (e.g. after calibration using tectonic or volcanic events) can then be inferred from molecular data, which is particularly useful when the fossil record is incomplete. The shape of phylogenetic trees also retains important information on the sequence of radiations/extinctions. Finally, since complete species-level analyses for extant taxa represent the best opportunity to unravel a direct record of speciation/extinction processes, they also allow more accurate hypotheses of the causes of diversification.
Several detailed phylogenetic analyses have been produced that focus on groups of interest in terms of evolution (e.g. high diversity of pollination systems, unusual species richness), geographic distribution (e.g. occurring in biodiversity hotspots or remote oceanic islands), and ecology (e.g. epiphytic orchids). Speciation processes have been studied for these targeted genera to explain some of the key questions in evolutionary biology, e.g. sympatric speciation, pollinator-driven plant diversification, mimicry and adaptive radiations. These studies have been published in the top-journals for biodiversity analyses, including Nature, Science, PNAS, Systematic Biology, Evolution, Molecular Phylogenetics and Evolution, The American Naturalist and the Royal Society publications.
Genomics
The APG classification of flowering plants was made possible by a combination of advances, including new molecular and computer techniques. Rapid progress has depended fundamentally on an ability to sequence and compare small, selected DNA regions from nuclear and organellar genomes. These advances have had a significant impact on genomic research as genomic diversity includes striking variation in nuclear and organellar DNA at many levels ranging from base sequences within and between genes, the number of chromosomes per genome, the number of genomes (ploidy) and the amount of DNA per genome. It was once assumed that variation in coding genes explained all biodiversity. Recent advances have shown that gene content and order are surprisingly highly conserved within families, whereas amount and organisation of repetitive sequences differ considerably between even closely related species. Variation in DNA amount has profound phenotypic consequences. Describing diversity requires attention being paid to genomic variation at all levels, whereas understanding its origins and significance demands a synthetic, unifying approach.
Kew makes a unique range of contributions to describing and understanding plant genome diversity. Besides undertaking DNA sequencing to create a fundamental overview of flowering plant phylogeny, Kew is also a leading centre undertaking and co-ordinating work on genome size evolution in plants and its significance. RBG Kew continues to publish the world’s central reference for plant DNA C-values in both hard and electronic forms (link to project Plant DNA C-values database). In 2003 RBG Kew hosted the second Plant Genome Size Workshop and Discussion Meeting. The workshop (attended by 17 scientists from eight countries) reviewed progress against targets set at the first workshop in 1997, and agreed new goals for the next five years. The discussion meeting (attended by 67 scientists from 17 countries) addressed aspects of genome size, including its evolution, ecological and conservation significance, and the molecular mechanisms responsible for variation. A special issue of Annals of Botany containing papers from the discussion meeting was published in 2005.
Other fundamental genomic research at RBG Kew concerns the nature and significance of polyploidy, the most widespread and distinctive cytogenetic process affecting the evolution of higher plants. In 2003 Kew co-hosted an international meeting on polyploidy with the Linnean Society and in 2004 co-edited a special issue of the Biological Journal of the Linnean Society containing key papers arising from the meeting. Recent molecular research has cast serious doubt on our ability to recognise individual polyploids and, 85 years after polyploidy was discovered, the precise proportion of polyploid angiosperms remains unknown, as are the implications of polyploidy for patterns of extinction and diversification. A better understanding of polyploidy in plants is needed. A combined molecular and cytological approach, that includes multicoloured fluorescent chromosome painting, is emerging as one of the best ways to study this key component of plant diversity.
RBG Kew’s approach to genomic diversity combines a range of strengths that are probably unique at an international scale. Research on DNA sequences is combined with a strong capability for work at the chromosomal level. For example, RBG Kew played a pioneering role in developing molecular painting techniques as powerful new tools in plant biosystematic research, including identification of hybrids and allopolyploids and visualising introgression, recombination and intergenomic rearrangements. As predicted, the use of these tools has become ubiquitous. Since 1996 we have evaluated them in studies of practical and theoretical interest focused on polyploidy in monocots (including Andropogon, Dupontia, Miscanthus and Poa). They were also used in a study showing that the ‘typical’ Arabidopsis-type telomeric sequence (TTTAGGG)n was replaced once in an early progenitor of most families of Asparagales. About 6,300 species, corresponding to about 2.5% of angiosperms, are now predicted to lack ‘typical’ Arabidopsis type telomeres.
Evolutionary genomics research was initiated in the Genetics section of the Jodrell Laboratory, RBG Kew in 2003. This work is focused on Populus, the first tree to have its entire genome sequenced and an ideal genus from which to explore phylogenomic relationships in Malpighiales. The first steps of this research program involve ‘genomic scans’ for departures from neutral gene introgression in hybrid zones of European poplars and aspens, and funding for this work has been secured from NERC, the Royal Society, and the Austrian Science Foundation. In addition, this research has also benefited from a collaboration with researchers in the United States on genetics of species differences in Helianthus (sunflowers), and from reviews of the literature covering model organisms in both animals and plants. The work has resulted in 10 papers in journals with CIF >2 since 2003.
Together these different approaches encourage an holistic approach to genomic research, which makes RBG Kew an ideal place and/or partner for new developments in plant genomics.
Evolutionary developmental genetics
Evolutionary developmental genetics (evo-devo) combines various areas of comparative biology in order to understand the nature and expression of the genes controlling development, and in doing so to answer 'big questions' about homology and evolution of key plant organs and functional developmental changes in seeds as they germinate. The success and location of evo-devo projects at Kew are dependent on the stategic appointment of a new staff member to set up and run an evo-devo laboratory. Collaborative projects remain important in this field, but a comparative evolutionary approach of wide taxonomic scope is of limited appeal to University-based researchers that rely on highly competitive funding centred on model organisms. Thus, a Kew-based programme focused on Kew's unique collections and resources would help to consolidate some current areas of research.
A primary Kew evo-devo focus is on floral morphology/anatomy. Four PhD students are currently working on collaborative floral studies (Floral Evolution project-) that combine developmental genetics with micromorphology, ontogeny and phylogenetics. These projects involve collaborations with Cambridge University, Reading University, Imperial College and the Natural History Museum. In addition, Kew plans to utilize developmental-genetics to address questions of floral homologies and evolution in the monocot order Pandanales, in collaboration with researchers in Mexico, the rosid eudicot order Malpighiales in collaboration with researchers in Austria and the asterid eudicot order Lamiales in collaboration with RBG Edinburgh. These projects will ultimately address questions about the homology and evolution of the flower.
A further Kew evo-devo focus is on genes controlling dormancy, and germination using microarray technology, supported by Defra and in collaboration with HRI-Warwick and Wageningen University. This global analysis of gene transcription has identified a core set of 442 genes with higher expression in the dormant state and 778 genes associated with germination. Ongoing work has revealed more detail with regards to breaking of dormancy, and, uniquely, a quantitative measure of the depth of dormancy. Kew plans to use gene markers for dormancy elucidation in Brassicaceae to facilitate improved germination testing in support of sustainable use. The work is accepted for a high impact publication (CIF 6)
Evolution of plant form
Several decades of monographic research have generated considerable data on the anatomy and pollen morphology of seed plants, especially angiosperms. This empirical basis, together with specialist expertise on plant anatomy and pollen morphology, unique collections and other Kew resources, facilitate a series of research projects that utilize both traditional and novel micromorphological methods to examine the evolution of plant form. These projects interface with other disciplines, including molecular phylogenetics, developmental genetics and plant physiology. They are underpinned by the Plant Micromorphology Bibliographic Database (PMBD), a unique online database that provides probably the most comprehensive index to angiosperm and gymnosperm plant structure. The PMBD covers vegetative plant anatomy and reproductive and pollen/spore morphology, and is regularly updated with new literature.
The advent of DNA-based systematics in the early 1990's, augmented by a new understanding of the genetic bases for morphological features in a limited range of model organisms, has stimulated studies on the evolution of flowers, pollen and wood. An explicitly phylogenetic approach is employed to evalute a range of hypotheses in these areas. Some of these projects have an interface with the planned programme of evolutionary developmental-genetics ("evo-devo"). They seek to determine the origin and homologies of these structures in angiosperms and their sister groups.
Work on floral evolution currently focuses on monocots, Fabales and Malpighiales. These are supplemented by studies that concentrate on conceptual issues such as the role of determinacy in the evolution of the flower, and the significance of flower-like terminal structures as a tool in morphogenetic and evolutionary research. Studies on pollen evolution are centred on monocots, magnoliids, early-divergent eudicots and Fabales. They aim to review pollen and anther characters of systematic significance throughout the angiosperms, and target specific groups for more detailed study, including ultrastructure. Ultrastuctural techniques using both Scanning and Transmission Electron Microscopes (SEM, TEM) are also a focus of studies on non-protoplasmic contents in plant cells (cell inclusions), such as starch granules, calcium oxalate crystals and opaline silica bodies, especially in selected monocots (Poales and Araceae).
Two long-term projects that were initiated in the mid-twentieth century, Anatomy of the Dicotyledons and Anatomy of the Monocotyledons have provided the best available synthesis of plant anatomical characteristics across all flowering plants, and are due to be concluded in the next ten years.
Research on xylem function and evolution in woody plants uses a phylogenetic approach to study ecological adaptations and physiological functions, especially the structure and function of pits and pit membranes, in collaboration with project partners from different research fields. This is underpinned by empirical systematic studies in wood anatomy that focus on groups of strategic importance to Kew, such as Leguminosae, Myrtaceae and Rubiaceae. This programme, together with the Anatomy of the Dicotyledons volume series, form the basis for work on wood identification (including the Insidewood interactive online program), and applied projects such as CITES-listed timbers and Fuelwoods. The goal of the CITES-listed timbers project is to aid identification of timber that is protected in international trade by CITES regulations. An applied project on the structure and biology of woods used for fuel in under-resourced areas aims to help conservation of the biologically complex and over-exploited caatinga vegetation in northeast Brazil.
Comparative seed biology
Whilst research on aspects of seed biology has been carried out within Seed Conservation over many years, the Millennium Seed Bank Project has enabled Kew to maximise the opportunities to undertake large-scale synthesis in this research area.
In order to better predict seed behaviour in the large number of diverse species collected in the MSBP we rely on comparative analyses of several seed biological traits. To enable these analyses we are accumulating large, global datasets of seed characteristics, for example mass, desiccation sensitivity, seed chemistry, seed morphology, germination and dormancy, both from our own collections and from the literature. This compilation constitutes the Seed Information Database (SID) which, as well as being a vital internal resource, since 2001 has been delivered to external scientists via the web, and is also searchable under ePIC.
Where appropriate our analyses attempt to identify evolutionary trends in seed biology and are carried out in the context of the latest phylogenetic classification of seed plants. As well as providing decision support for our seed conservation operations, we take every opportunity to improve the general understanding of the evolution of seed biology, for example desiccation tolerance, longevity, and dormancy.
Sustainable uses of plants
Kew has a long tradition of studying the economic uses of plants and this is reflected in the diversity of information about their uses in archives and in the 80,000 objects in the Economic Botany Collection. Data in these collections can provide a focus not only for research based projects but also for the dissemination of information about the economic and social uses of plants on the web as illustrated by the development of the website Plant Cultures (www.plantcultures.org.uk), a project funded by Culture OnLine (Department of Culture Media and Sports). In 2005, the website was nominated for two British Interactive Media Awards (BIMA) in the class of a) Information and b) Culture and Art as well as a British Environment Media Award (BEMA) for the best environmental website. The website is currently focused on 25 species of Asian plants but it is planned to collate traditional information about species from Africa, the Middle East and Britain and disseminate this information on an expanded version of the website.
The over-arching aim of many of the sustainable uses of plants projects is to document the traditional uses of plants as well as identify more species of plants that need to be used sustainably for economic and social needs. The results of the projects contribute to meeting objectives of the Global Strategy for Plant Conservation as well as supporting the United Nations Millennium Development Goals. We are also investigating how our data and expertise could contribute to the challenges associated with climate change. For example, by furthering our understanding of species used as fuelwoods in Africa and S America, communities in these countries can make better sustainable uses of their flora. Similarly, by conserving nutritional and medicinal species the same communities can improve their health and fight infections. Kew has identified over 1,700 species of plants used traditionally to treat diabetes and is currently working with collaborators at Kings College, University of London, to study the active compounds in a selection of these species. Kew’s research on anti-tuberculosis species is currently targeted on furthering our understanding of the active compounds in some African and British plants traditionally used to treat infections. Information about the traditional uses of species of plants together with laboratory-based evaluation of these traditional uses can contribute to more effective utilisation of genetic resources and thus help to reduce poverty and improve health. Projects that involve using indigenous knowledge about the traditional uses of plants are undertaken once agreements are in place with institutes in the source countries to ensure that any use of this knowledge by third parties involves benefit-sharing arrangements with the source country. These projects follow the Convention on Biological Diversity principles.
Over 20 years research into different aspects of plant chemistry, especially chemosystematics and the role of plant-derived compounds in insect-plant interactions have provided data about the distribution of compounds among different species and families as well as their role in insect host selection (Insect-plant project link). Data from testing the role of different groups of compounds on insect feeding behaviour and the new DNA-based phylogenies provide a framework to test different hypotheses about insect-plant interactions. Information about chemical diversity has been used not only to further our understanding about the role of plant-derived compounds in different aspects of insect ecology but also to identify chemical markers that can be used to authenticate different species of plants or fungi entering the trade.
In recent years there has been an increase in the use of plant-based products for making cosmetics, unlicensed herbal medicines, functional foods, potpourri, colouring agents and pet products. Kew has been researching these products using a range of morphological as well as chemical and DNA fingerprinting methods to identify the species of plants being traded and whether they are being produced from sustainable sources. To date, over 600 different species have been authenticated. Specific emphasis has been placed on species used in traditional Chinese medicine. In most cases the correct species have been traded, although incidents have occurred when the incorrect species or poor quality substitutes have been used, sometimes resulting in human cases of adverse reaction, sometimes of life-threatening severity. Other issues relate to the over-exploitation of some species, especially those that are wild harvested where there is a need to develop sustainable harvesting practises to avoid adulterants or poor quality material entering the trade. The outputs of the projects are published in high impact journals, trade journals and books, and are being used to write monographs for the European and British Pharmacopoeias. Development of the DNA-barcoding research will have significant impact on the ability to support the monitoring of plants entering the trade, especially endangered species that are obtained from non-sustainable sources.