In search of a functional flora—towards a greater integration of ecology and taxonomy
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- Pendry, C.A., Dick, J., Pullan, M.R. et al. Plant Ecol (2007) 192: 161. doi:10.1007/s11258-007-9304-y
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Large-scale biodiversity informatics projects will not properly address the needs of one important potential user group. Ecologists do not have ready access to datasets which allow them to assign plant species to functional types. We believe that information technology has developed sufficiently to allow taxonomists and ecologists to work together to address this need and develop specimen databases to combine taxonomic data with ecological and ecophysiological information so that this information will be assigned to the correct taxon in the future. Digital images provide a rapid and economical method of vouchering specimen data, reducing the need to store physical vouchers in herbaria.
KeywordsBioinformaticsTaxonomyDatabasesFunctional ecologyFunctional types
Considerable time, effort and money have been spent in recent years on improving access to biological collection data both at the institutional level (digitisation of museum and herbarium collections and access to this information over the web) and at the international level (e.g. GBIF, the Global Biodiversity Information Facility and BioCASE, the Biological Access Service for Europe). Much of the drive for this increased access has come from taxonomists who have seen it as a way of opening up these enormous historical datasets to analysis by other disciplines, thereby enhancing the ongoing relevance of their collections at a time when financial support for Taxonomy comes under ever increasing pressure. In many cases, however, rather little attention has been paid to exactly who will use these data and what will be done with it (Neale and Pullan 2005; Neale et al. 2005). We believe that another, complementary approach is required, in which biodiversity informatics projects carefully consider the needs of their users and work with those users to develop more focused strategies to address these needs.
Preliminary list of suggested physical and ecophysiological measurements used to assign taxa to functional groups arising from EU funded workshop ‘Functional groupings of tropical trees’ – Edinburgh, 10–13 Dec 2001
Pollen dispersability (mean dispersal distance)
Seed production (fecundity)
Soil seed bank (type, size)
C, num/m2/m (depth)
Tolerance to dessication
Length of reproduction event
Resprouting (ability & type)
Periodicity of flower/fruit production
Size at maturity (1st reproduction)
LAI (Leaf Area index)
Respiration response to temperature
LAR (Leaf Area Ratio)
Minimum leaf water potential (leaf water content)
%, g/g, Pa
Photosynthetic response (Amax)
SLA (Specific Leaf Area)
WUE (Water Use Efficiency) or Delta 13C
dry mass gain/unit water transpired
Leaf quality (C/N, N contents, 15N)
Flammability of residues
Resistance to embolism
Rooting depth (seedling in particular)
Plant architecture (e.g. slope DBH to Height curve)
Growth rate (max or 95%)
%, m/year, g/year
Growth response to CO2
%, m/year, g/year
Growth response to light
%, m/year, g/year
Growth response to nutrients
%, m/year, g/year
Growth response to water
%, m/year, g/year
Abiotic stress tolerance (temperature, flooding, light, low nutrients)
Resistance to herbivory/defense allocation (e.g. leaf palatability, spines)
Resistance to pathogens
genetic distance, C
Specificity of mutualism (e.g. specialised pollination/dispersal, myrmecophily)
The approach of grouping species by their function within the ecosystem has been used to investigate both fundamental ecological issues (Whitfield 2006) and more applied ecological questions including climate change and habitat restoration (Boutin and Keddy 1993; Skarpe 1996; Brooks et al. 1997; Smith et al. 1997; Diaz et al. 2004). For some aspects of ecosystem performance it is not the diversity of species which matters, but the diversity of functional types. Certain ecosystem models require information not (only) about the presence of species, but (also) about their functionality, and such information may be difficult to locate, particularly in botanically less well-known areas such as the wet tropics (Picard and Franc 2003; Gourlet-Fleury et al. 2005). Although functional ecologists are interested not in what an organism is called but what it can do, without using names it is impossible to organise and communicate this information in a meaningful and reproducible way. We therefore advocate reinforcing the links between Functional Ecology and Taxonomy, to their mutual benefit.
Floras are the primary data source about the plants of an area, and may contain not only keys and descriptions, but also information on the distribution and ecology of those plants. As primary data sources, Floras must address many audiences and are the basic tool for all who need to identify plants, from ecologists to conservationists, foresters and horticulturists. Traditional Floras may not be easy to use and their format is inflexible, so there have been attempts to modernise them by using multi-access keys, computer aided identification, multimedia formats, but in the end, all these products supply the same sort of information.
An integrated approach
the underlying data is captured at the specimen level not the taxon level;
the taxon level assertions are in reality synthetic constructions from the underlying specimen level data;
storing just the taxon level information results in the loss of the raw data used to create the syntheses and preclude re-examination or re-working of the product; and
since the raw data is missing it is very difficult to make cross comparisons to other taxon level data without making some major assumptions regarding the congruence of the underlying taxon concepts.
These problems largely arise, because the information systems are not seen as an integrated part of the taxonomic process. We advocate the use of databases which encourage the gathering and storage of data at the specimen level and which can generate taxon level syntheses of the underlying data. These synthetic views can then be regenerated at any time to accommodate changes and additions to the underlying specimen level data.
Functional types can be thought of as analogous to taxa, in that they are both ways of arranging biodiversity. However, while assignment to a particular functional type is made to answer a specific question, taxonomic classifications act as a multi-purpose method of storing data for addressing numerous questions. When relating functional types to taxa we are in fact looking at mapping between two different classification systems. There are problems when both classification schemes develop independently – unless the mappings between the classifications are rigorously maintained, inaccuracies will develop progressively as taxon names inevitably change due to either refinements in taxonomic concepts or for nomenclatural reasons.
Specimens are the link between functional types and taxa. The same relationship between identification and classification exists in functional types as exists in taxa since one set of the physical characteristics of a specimen is used to assign the specimen to a taxon whilst another more or less different set determines its functional type. The ideal situation is therefore to collect specimen level physical data to assign specimens to taxa and within the same system to categorise these taxa as functional types (Fig. 1). Thus, data are collected and stored at the specimen level, but communicated at the taxon level. Within any taxon, there may be considerable physical variation among individuals, so it is important that data on all physical attributes are collected from numerous individuals from across the range of the taxon. Concentrating the management of functional data at the specimen level greatly simplifies the issues related to storing data for use in classifying functional types. Databases which operate at the specimen rather than the taxon level can accommodate extra fields in accordance with type of functional data required. Storing data at the specimen level is also amenable to taxonomic revisions as required and is a more neutral, and therefore a more appropriate method of storing information about plant diversity. Although much of the data used to assign taxa to functional groups could be collected by the non-specialist, taxonomists clearly lack the time and expertise to collect the complete spectrum of data used in functional studies. Large data-sets are currently collected by ecologists and physiologists in the course of their research, but because of its volume, much of this data will never be published and therefore is not integrated with other data. We suggest that taxonomists should manage databases containing these specimen-level data, ensuring that the data are assigned to the correct taxon and will continue to be so assigned in the future. Ideally, the ecophysiological data should reside in a single database which manages data for a country level floristic project, and this is one of the aims of the Flora of Nepal Project (www.floraofnepal.org). Maintenance of web-accessible databases at this scale should help ensure that there is no unnecessary duplication of effort in collection of data and that these data are easily accessible by non-taxonomists.
The large number of physical and ecophysiological measurements that are used to categorise species according to functional types and the need to sample numerous individuals will create enormous quantities of data. These vast data-sets are analogous to those which underlie molecular systematics, with GenBank being the sole repository for molecular data. However there is no need to create a parallel system for functional data since in GBIF and BioCASE there are already systems which can give access to diverse data held in different databases.
Problems with matching functional types to taxa may occur because of incorrect identification of the individual sampled and this raises the important issue of vouchering data to ensure that the functional type assigned to a taxon can be re-examined. For example, the Ecological Database of the British Isles (http://www.york.ac.uk/res/ecoflora/cfm/ecofl/) hosts ecological data from bibliographic sources on over 1,770 species of higher plants that occur in the British Isles, but there is no process by which incorrect identification of species could be addressed. At present, we are aware of no study which stores voucher specimens from the individual plants used to collect traits for functional type analysis. Herbaria can be considered as vouchering systems for taxonomic studies and they are coming under increasing pressure due to the need to maintain physical vouchers for molecular data. Cost and space constraints preclude the storage of voucher specimens for functional data, but another possibility also exists. Digital photography could provide a simple and inexpensive way to preserve sufficient information for most organisms to be reliably identified by a specialist, particularly if the specialist has prescribed what structures are most critical to identifications and how they must be photographed. Indeed, in other disciplines, such as ornithology a photograph is already considered adequate as a voucher specimen. Only in a minority of cases would a photograph be insufficient and a physical specimen is required. The images should be stored within the database which hosts the taxonomic and ecophysiological data. A potential way forward can be seen in MorphBank (www.morphbank.net) which may provide a model system for the storage of images linked to taxonomic data.
We believe that the collection and linking of data from diverse sources in the way which we describe could greatly strengthen both Ecology and Taxonomy. Ecology would benefit from the increase in the range and sophistication of data available and Taxonomy would reinforce its central role in biodiversity studies. There would be benefits in many areas including conservation. As habitats alter due to climate change, or land use different species within them will respond in different ways. Including the functional type approach within conservation assessments will permit a more accurate prediction of how a species will respond to its changing environment and whether threats to it will increase or diminish in the future. In the face of the global erosion of biodiversity it is essential that identities of taxa are integral to the discussions of how habitats will change, and this is one way to keep the focus on the species themselves. Information technology has now progressed to the point where full integration of taxonomic and ecological data is possible. If the approach which we outline is to succeed it will require additional investment in resources, and we hope that the ideas presented here will stimulate discussion among ecologists and taxonomists about how to work with national and international funding agencies to develop this integrated approach to tackling some global issues.
We wish to dedicate this paper to the memory of John Proctor, an ecologist with a keen appreciation of Toxonomy, and we hope that he would approve of the ideas expressed here. We would like to thank the anonymous reviewers whose comments were so useful in preparing the final version of this article.