Large Scale Syntheses: key acheivements 2006 - 2011
The Large-Scale Syntheses Team helps to co-ordinate many over-arching projects that are driven by a variety of more general scientific questions. These projects involve collating data for inventories and bibliographies, studying variation and relationships among plants, and studying underlying processes that generate plant diversity (such as speciation and development). Most projects involve international collaborators, and many focus on dissemination of information via the web, publications and repatriation of data to stakeholders.
An objective of the Large-Scale Syntheses Team is to ensure that data and results obtained from the taxonomic and regional focus teams are collated and synthesised into the broader over-arching projects. Most Team members are also involved in other teams and represent all science Directorates. Outputs from these projects play a vital role in development of predictive classifications to guide future research on plant and fungi. These broad-scale syntheses provide important baselines for documenting and explaining global plant and fungal diversity.
Taxonomic and nomenclatural syntheses
One of the earliest global-scale survey produced at RBG Kew was Bentham and Hooker's Genera Plantarum. 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. 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 taxonomic names, and these are now available free online as part of the International Plant Names Index (IPNI- www.ipni.org ), a collaborative venture between RBG Kew, Harvard University and the Centre for Plant Diversity Research, Canberra. On average, users around the world search IPNI 52,000 times per day. The IPNI team has recently piloted mechanisms to facilitate electronic publication of plant names, providing IPNI identifiers in publication of these names in journals such as PLOS ONE, Phytokeys and Kew Bulletin, and linking the IPNI citation to the source literature via DOI.
Although IPNI is comprehensive for published plant names, it contains little information on synonymy and does not identify the currently accepted name for a particular species. At species level, RBG Kew has developed World Checklists for Selected Plant Families (WCSP - www.kew.org/wcsp/). WCSP currently covers 173 plant families and more than 123,000 species. This effort has involved over 150 collaborators from 22 countries. WCSP includes checklists of families covered by our systematic teams, notably all families of monocotyledons and Rubiaceae, Lamiaceae, Myrtaceae, Euphorbiaceae, and in collaboration with ILDIS, Leguminosae. Data from WCSP are supplied to the Catalogue of Life. Data subsets are also supplied to many collaborators. For example, it provided the initial core of a national list of Brazilian plants published in 2010 by the Rio de Janeiro Botanical Garden following a three-year collaborative initiative including input from many RBG Kew staff.
The 2010 target 1 of the Global Strategy for Plant Conservation (GSPC) was, “A widely accessible working list of known plant species, as a step towards a complete world flora”. That target underpinned the GSPC since without such a list measuring progress towards the other 15 targets of the GSPC reliably would be impossible. RBG Kew played a lead role in developing the GSPC and Target 1 in particular, providing the background documentation and rationale to the Conference of Parties to the Convention on Biological Diversity, which approved the GSPC and its targets in April 2002.
In 2008, it was recognized that the 2010 target was unlikely to be met through traditional checklist compilation by taxonomists. Collaborators at RBG Kew and Missouri Botanical Garden began designing and testing automated processes to merge multiple existing plant name data sets held by RBG Kew, Missouri and by others into a single consistent ‘working list of known plant species”. The resulting database was released on 29 December, 2010, as “The Plant List” (www.theplantlist.org): thus meeting the 2010 Target 1. We are indebted to our collaborators worldwide for making this possible. The Plant List receives over 2000 visits per day.
Digitisation of samples in collections at RBG Kew helps increase their use for scientific, conservation and sustainable use projects. The majority of the digitisation projects have been externally funded.In early 2010, RBG Kew completed its digital contributions to the Latin American Plants Initiative (LAPI) funded by the Andrew W. Mellon Foundation. This international project focused on previously unpublished botanical reference material of relevance to Latin America, which is being digitized and made widely accessible for scholarly research purposes through the JSTOR Plant Science online resourceOver the period 2006-10, RBG Kew’s work within LAPI included the digital capture of label data and high resolution (600 ppi) images of c. 70,000 putative type specimens from the RBG Kew herbarium as well as > 7,400 letters of relevance to Latin America from the RBG Kew archive. Building on LAPI and the African Plants Initiative, the Global Plants Initiative (GPI) expands the geographical coverage of content and the network of partners to all regions of the world (currently 220 participating herbaria from 65 countries). As a founding member and principal partner in the GPI, RBG Kew works closely with other partners, providing equipment and training to institutions joining GPI as well as contributing to the development of standards and protocols now widely adopted by herbarium digitization programmes.
Sampled Red List Index for Plants
The Sampled Red List Index (SRLI) for Plants was established as part of RBG Kew’s response to the 2002 decision by the parties to the Convention on Biological Diversity to reduce the rate of loss of biodiversity by 2010. During Phase 1 (2006-2010) IUCN Red List assessments for the sampled species were based on herbarium specimen data, GIS analysis, published literature and, where available, expert input. Assessments are published on a scratchpad resource to facilitate comments/corrections (http://threatenedplants.myspecies.info/) as well as being submitted to IUCN for inclusion in the Red List. The results of Phase 1 were presented as the First Report of the IUCN Sampled Red List Index for Plants, published to coincide with the tenth Conference of the Parties to the Convention on Biological Diversity in Nagoya. The format was designed to engage national policy-makers and environment correspondents worldwide, and the launch resulted in unprecedented national and international media coverage (c. 300 high profile media articles and > 100,000 blogs). The SRLI was the first study to tackle these headline questions from a globally representative sample of plant species, and it allowed policy-makers to understand which plants are most threatened, where and why to a degree of detail that has so far only been possible for vertebrates. For the first time we are now able to say that plants are more threatened than birds and as threatened as mammals worldwide and to appreciate that conversion of natural habitats to agricultural use directly impacts one in three threatened plant species.
Evolutionary biology and biodiversity analyses
Phylogenetic studies are instrumental to RBG Kew research activities in general and to the Large-Scale Syntheses Team in particular. Several projects produced important phylogenetically-based publications of wide-ranging impact for the scientific community; four are particularly noteworthy. First and foremost is the publication of a second update of the Angiosperm Phylogeny Group classification in 2009 (APGIII, Bot J Linn Soc), which includes the position of previously unplaced families, the recognition of new orders, and new family circumscriptions. Accompanying papers propose a new linear order for APG, subfamilial names for some families in order Asparagales, and a formal supraordinal classification for flowering plants. The second is a study (2006, Nature 441:210) presenting one of the first clear examples of sympatric speciation in plants, in which researchers were able to show that two species of the palm genus Howea, endemic to the remote Lord Howe Island in the South Pacific, present all of the features generally associated with this type of species divergence. In addition, a second publication further develops this topic in other plant groups present on Lord Howe Island (2011; PNAS 108: 13188). This project is ongoing, funded by UK NERC and European Research Council. Thirdly, RBG Kew has been one of the founding members and first chair of the Plant Working Group, for which the main task was to identify an optimal set of markers for DNA barcoding in plants. The group published results of this international collaborative effort in a series of articles, including two in PNAS (2008, 105: 2923; 2009, 106: 12794). Finally, a phylogenetic analysis of the flora of the Cape of South Africa provided evidence that phylogenetic diversity and taxon richness were decoupled and that this situation had important implications for conservation planning (2007; Nature 445: 757).
Other 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, New Phytologist, PNAS, Systematic Biology, Molecular Biology and Evolution, Evolution, Molecular Phylogenetics and Evolution, The American Naturalist and publications of the Royal Society.
Besides undertaking DNA sequencing to create a fundamental overview of flowering plant phylogeny, RBG Kew is also a leading centre undertaking and co-ordinating work on genome size (C-value) evolution in plants and its significance. The database, which is available through the RBG Kew website, provides a user-friendly, ‘one-stop-shop’ of information on genome size diversity across all groups of land plants and algae. The latest update (release 5.0) went live in December 2010, adding data for over 1900 species not previously listed. It currently represents the largest source of genome size data for any group of organisms, with values for 7058 species. Use of the site has more than doubled (from c. 45 hits per day in 2002, to over 100 in 2011). The database is extensively cited in publications and is also used by molecular biologists needing to know the genome size for complete genome and other sequencing projects, and by conservation geneticists who require information on genome size to optimize experiments for assessing genetic diversity within and between populations.
Current projects continue to focus on the evolutionary and biological significance of genome size diversity across broad comparative scales, making extensive use of the Plant DNA C-values database, and new genome size and phylogenetic data generated ‘in house’ and in collaboration with other scientists. RBG Kew continues to embrace new technology to provide deeper insights into the molecular basis of genomic variation across the biodiversity of plants. For example, in recent years huge progress has been made in DNA sequencing following the development of next generation sequencing technologies (e.g. 454 and Illumina). In 2009, RBG, Kew was awarded a three-year NERC grant in collaboration with Queen Mary, University of London, to apply next generation sequencing approaches to investigate the genomic make up of Fritillaria (Liliaceae; Liliales), a monocot genus that contains the largest reported diploid genomes of any plant. Already, the preliminary results are indicating that the genomic processes operating in Fritillaria may be very different from those identified in plants with smaller genomes. Such findings emphasize the importance of conducting studies on genomes of all sizes to uncover the full diversity of genomic processes operating in plants rather than just focusing on the smaller genomes found in model plants and their relatives (as in many universities). In addition, in 2010, researchers in the Jodrell (Pellicier et al.) discovered in Paris japonica (Melanthiaceae; Liliales) the largest genome thus far, more than 15% larger than the previous record.
In addition to ongoing research, RBG Kew continues to disseminate genomic knowledge through publications, lectures, the organization of conferences focused on plant genome diversity and the provision of training courses to develop the skills of future cytogeneticists. For example, in 2007 Genetics staff organized a conference at the Jodrell Laboratory entitled ‘Plant Genome Horizons – vistas and visions’ attended by 80 participants from around the world, with the papers subsequently published in a special issue of Annals of Botany in 2008. In addition, a practical course entitled ‘In situ hybridization to plant chromosomes – a practical introduction to its uses in biosystematics’ was organized and run at the University of Zagreb in Croatia in 2008, attended by 16 participants.
Evolutionary genomics research was initiated in the Genetics Section of the Jodrell Laboratory, RBG Kew in 2003. This work focused on the “model” genus Populus, with funding secured from NERC, the Royal Society and the Austrian Science Foundation (Lexer et al., 2010). More recently, studies of expressed genomes and epigenetic effects (Paun et al., 2010) have been undertaken in the non-model genus Dactylorhiza (with funding from the EU and the Austrian Science Foundation).
Together these different approaches, which have led to numerous papers in high profile journals, have enabled a more holistic view of genomic diversity, and they make RBG Kew an ideal place and/or partner for new developments in plant genomics.
Evolution of plant form
The growing field of evolutionary development (evo-devo) combines comparative morphology/anatomy with two other major disciplines of comparative biology – phylogenetics and developmental genetics – to address 'big questions' about the evolution of key plant structures. Work on several aspects of evo-devo has resulted in papers and research in this area is developing rapidly. RBG Kew has participated in the European Evo-Devo (EED) Society since its first meeting (EED1) in Prague in 2006, organising symposia on Evolution of Plant Form and Origin and diversification of seeds and flowers at EED2 (Ghent 2008), and planning further symposia for EED4 (Lisbon 2012). RBG Kew also organised a symposium on Flower and Inflorescence form at the Society for Experimental Biology (SEB) conference at the University of Canterbury in 2006. We also maintain a training role, not only for students at undergraduate, Masters and PhD levels, but also for professionals who require training in wood identification, an annual course run by the Micromorphology section of the Jodrell Laboratory.
RBG Kew uses targeted comparative ontogenetic studies on a phylogenetically broad range of angiosperms in which the inflorescence–flower boundary is ambiguous, including the monocot order Pandanales, the eudicot family Euphorbiaceae and the early-divergent angiosperm family Hydatellaceae. Some features common to the three case-studies reflect similar developmental constraints and therefore help to develop testable models of floral construction. More than 45 papers have been published on comparative floral structure and evolution since 2006.
A relatively new aspect of research at RBG Kew involves structural colour and iridescence in flowers and fruits. Structural colour, which characterises a significant proportion of flowers, is the generation of a visible colour independently of chemical pigments, using only physical structures. Iridescence occurs when the colour of a surface appears substantially different when that surface is viewed from different angles, and can only be produced using structural methods. This Leverhulme-funded collaborative multidisciplinary research combines studies on comparative plant biology, developmental-genetics and physics to develop comparable models of structural colour and iridescence. Two papers have been published since 2009 in ongoing projects on structural colour and petal spots.
Another RBG Kew research focus is on the early evolution of flowering plants (angiosperms). A priority for future collaborative studies in this project is to establish the early-divergent angiosperm Trithuria (Hydatellaceae) as a model for angiosperm evolution, and to this end RBG Kew organised a symposium on Hydatellaceae and early angiosperm evolution at the 2011 International Botanical Congress (Melbourne). Since 2007, when Hydatellaceae were discovered to occupy a position close to the root of extant angiosperms, a total of 15 papers have been published on seed plant diversification and early angiosperm evolution. In broader collaborations, we compare extant and fossil flowers.
RBG Kew-based studies on pollen evolution aim to review pollen and anther characters of systematic significance throughout the angiosperms and their seed plant outgroups. Large-scale reviews published since 2006 include papers on the tapetum, inaperturate pollen, microsporogenesis and the evolutionary significance of the proximal-distal microspore polarity transition, a key innovation in seed plants. An ongoing collaboration with colleagues in France is investigating the roles of selection pressure and developmental constraints in determining pollen aperture patterns.
Pojects on wood anatomy include Convention on International Trade in Endangered Species (CITES)-listed timbers (related to ongoing anatomical wood identification) and a project on xylem function and evolution. Increased regulation of the international timber trade by CITES has prompted research on timber identification. Since 2006, five research papers and a book were published on this project; also some practical and informative posters on mahogany, afrormosia and ramin woods were produced for UK Customs. The project on xylem function and evolution uses a phylogenetic approach to study ecological adaptations and physiological functions; current collaborative research partly supported by the Royal Society focuses on softwood drought tolerance.
Comparative seed biology
To better predict seed behaviour in the large number of diverse species stores in the Millennium Seed Bank and thus better manage those collections and their sustainable use, we rely on comparative analyses of several seed biological traits. In support of such analyses we continue to compile 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, is delivered free to external scientists via the web. This has led to a number of collaborations with researchers in other institutes, which have led to significant publications, and large elements of the data-set are also shared with two functional trait consortia, ‘TRY’ and ’LEDA-traitbase’. 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.
Over the last five years, the total number of records in SID has increased from around 70,000 thousand to more than 150,000; and the number of taxa covered by around 6,000. During this period we have also added two online tools, based on the data held in SID - seed viability calculations and UK Native Species Toolbox; we collaborate with Sussex University to host their halophyte database (eHALOPH) via SID; and an on-line data submission tool for external contributors to SID is at an advanced stage of development. Future plans include further tools for specific user-groups, and integration with RBG Kew’s Science and Horticulture Systems, as part of the RBG Kew IT and Digital Media Strategy.
Sustainable uses of plants
Community based projects in Ghana have documented the diversity of plants used to treat malaria in order to select those for laboratory based studies to evaluate their efficacy (Asase et al., 2006). The results of this project contribute to the data that RBG Kew has on the uses of over 3,000 species used traditionally to treat fevers associated with malaria. Other ethnobotanical projects have collated information about the plants used to treat diabetes (Simmonds and Howes, 2006) and Alzheimer’s disease (Houghton and Howes, 2006). Support from the Alzheimer’s Trust enabled collaborative research to be undertaken on the efficacy of a range of plants, including Melissa officinalis, and the results of a double-blind placebo-controlled randomised trial have been published in Dementia and Geriatric Cognitive Disorders (2011).
RBG Kew has now gathered data about the influence of over 13,000 species on plant-insect host selection, especially the role compounds plan in modulating the feeding behaviour of insects. These data when combined with the new DNA-based plant analyses provide a robust framework to test different hypotheses about insect-plant interactions and the role plant-derived compounds can play in these interactions. For example, chemical data and information about the susceptibility of species of Aesculus to the horsechestnut leaf minor, Cameraria ohridella, is currently been superimposed onto a DNA-based analysis to evaluate evolution of this specific host-plant interactions and whether this chemical-DNA approach can be used to predict the susceptibility of different species of Aesculus to the leaf minor.
Since 2006, RBG Kew has been involved in providing information about the uses and identification of over 8,000 samples involved in cosmetics and other commonly used plant preparations. This includes work on potpourri (Cook, 2007) and the different dragons blood resins used in paintings (Sousa et al., 2008). The requests have come from academic collaborators as well as customs officers, police, health authorities and companies. In most cases the sample has been correctly identified, although in about 30% of cases samples do not support their intended use, and incidents have occurred when the incorrect species or poor quality substitutes have been used, resulting in adverse reaction, sometimes of life-threatening severity. Analysis of these enquiries also enables us to identify trends in, for example, adulterants. Since 1998, specific emphasis has been placed on the authentication of species used in traditional Chinese medicine (TCM). As part of our work on TCM, we lead the Quality Control work package on an EU F7 funded project (Good practice on Traditional Chinese Medicine (TCM) Research in the Post-genomic Era) that is undertaking a gap-analysis of what scientific data are needed to enable some of the species used in TCM to be used as medicines in Europe. The project involves 150 scientists from 19 countries including China, Australia and USA. The work undertaken by Christine Leon in collaboration with colleagues in China has been published as a two volume book “A colored identification atlas of Chinese material medica and plants as specified in the pharmacopoeia of the People’s Republic of China” (2010). Research on the authentication and quality control of plants being used in cosmetics and health products has been supported by grants from the EPSRC as well as the EU and industry. Results of enquiries formed part of the evidence used in criminal court proceedings (e.g. the use of Aconitum ferox in the murder of a man in Reading (Lancet, 2010)). Solving these enquiries has involved using both the collections at RBG Kew and the botanical, chemical and ethnobotanical expertise of the staff. Data on the poisonous plants growing or entering the horticultural trade in UK was collated for a guide for parents and childcare providers (Dauncey, 2010).
As well as being a key resource for research into plant biochemistry, use and anatomy in RBG Kew’s science programmes, the Economic Botany Collection (EBC) attracts 400 research visitors each year. Collaboration is central to relationships with postgraduate courses at the University of Kent, University College London, the Royal College of Arts and Camberwell, where teaching in the EBC leads to placements and dissertations.
Other examples of uses of plants projects can be found in the reports from other teams, for example, the Millennium Seed Bank Partnership, Leguminosae Team and Drylands: Africa Team.
The Team produces research that contributes heavily to the Breathing Planet Programme strategy 1, but also 4 and 5.
Outputs such as global checklists and provisional conservation assessments are directly relevant to meeting targets of the Global Strategy for Plant Conservation. Outputs of many projects undertaken in collaboration with our overseas partners also contribute to the United Nations Millennium Development Goals to eradicate extreme poverty and hunger (1), combat HIV/AIDS, malaria and other diseases (6) and ensure environmental sustainability (7) by 2015.
Science Team Leader: Monique Simmonds
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