Select Committee on Science and Technology Fifth Report

CHAPTER 4: Tools and Technology for the Twenty-First Century


4.1.  According to The NHM, "responses to the biodiversity crisis and to the challenge of climate change require a transformation in the nature and volume of taxonomy …" (p 1). The science of taxonomy is expanding rapidly: new species of plants, animals and microbes are being described daily, new and more powerful analytical and computational methods are constantly under development, and ever-growing amounts of biodiversity informatics data are becoming accessible through the web. The incorporation of new technologies, such as high throughput DNA sequencing and automated digital data-gathering, will be critical to the development of taxonomy.[19] The Committee heard of the exciting opportunities and challenges for systematic biology in the twenty-first century as it develops to meet the need for a more profound understanding of the diversity of life and of the impact of environmental change on that diversity. UK scientists are playing a leading role in developing the vision of taxonomy for the future.

4.2.  Taxonomy is a global enterprise. Its core strength has traditionally been in Europe, North America and Japan, but the balance is changing and the emergence of nations such as Australia, Brazil and China as major contributors serves to emphasise this international dimension. UK national initiatives and the importance of UK resources, such as reference and type collections, are increasingly framed in this wider international context (p 93). The credibility of UK scientists engaged in realising the vision for the future of taxonomy depends in part upon the UK maintaining involvement in major international initiatives, like the Global Biodiversity Information Facility (GBIF) and the Biodiversity Heritage Library (BHL).

Digitisation of collections and the Internet

4.3.  The magnitude of the challenge facing taxonomists as they seek to document biodiversity on a global scale indicates that there will have to be substantial, even radical, changes in how taxonomy is conducted. At our inquiry seminar (see Appendix 4 and also pp 39 and 94), Professor Charles Godfray, Hope Professor of Entomology at Oxford University, described progress towards a web-based taxonomy in the CATE project—Creating a Taxonomic E-science—funded by NERC under their e-science programme. We have no doubt that the Internet will play a crucial role in the evolution of taxonomy and it is clear that further pilot studies in web-based taxonomy involving a wider range of types of organisms should be undertaken urgently by the research community.

4.4.  Essential components of this Internet-based taxonomy will include:

(i)  Internet-based descriptive taxonomy (alpha e-taxonomy);

(ii)  a clearing house mechanism for biodiversity information (for example, the GBIF);

(iii)  access to digital images of specimens;

(iv)  access to specimen-based and collection-based information;

(v)  on-line access to libraries of taxonomic publications (for example, the BHL);

(vi)  databanks of molecular sequence data (for example, GenBank).

All of these components exist already, although some are only small-scale pilots. We believe that a roadmap for the delivery of Internet-based taxonomy should be developed. Furthermore, we encourage the taxonomic community to come together to take the lead in its development since, in our view, it will only be effective if it emerges from the community. The process of developing this roadmap should be funded jointly by the BBSRC and NERC as a high strategic priority.

4.5.  There is no "quick technological fix" for the "taxonomic impediment" (see paragraph 1 above) and the web alone cannot necessarily accelerate the taxonomic enterprise greatly (p 13). Implementation of the roadmap will require long-term commitment by the major UK taxonomic institutions and it will require them to exercise a level of leadership commensurate with the scale and importance of their collections and their expertise in research, curation and informatics. It will, we anticipate, also require substantial additional funding, from Government and other sources.

4.6.  The Committee welcomes the progress of the Linnean Collection digitisation project with its 17,000 images of plants and 27,000 images of insects already available on the web (p 93) and we welcome the success of RBG Kew in obtaining substantial funding from charitable trusts, such as the Andrew W Mellon Foundation, to support digitisation projects for African and Latin American plants (p 20). However, the lack of core funding and the consequent reliance on external charitable sources have resulted in the major UK taxonomic institutions being slow in making collections data available over the Internet. When asked whether UK taxonomists were keeping up with the rest of world in terms of digitisation, the response of Professor Stephen Hopper, Director of RBG Kew, was discouraging: "by no means, way behind" (Q 22 and p 20). Notwithstanding the scale of their collections, the Committee finds the rate of progress by the UK taxonomic institutions in digitising and making collections information available to be disappointingly low. Unless a more strategic view is taken of how they can contribute to the development of the field of biodiversity informatics, there is a significant risk of damage to the international reputation of major institutions such as The NHM (Q 91).

4.7.  More broadly, GBIF suggested that the current rate of data digitisation and dissemination in the UK "hampers the progress of systematics and taxonomy not only in the United Kingdom, but worldwide" (p 251). Given their global scale and historical significance, UK taxonomic collections carry a responsibility to share access to the biodiversity information they house with the country of origin. In the light of the importance of halting biodiversity loss in progressing towards environmental sustainability (one of the Millennium Development Goals), the Committee considers that DFID should take a much stronger interest in promoting benefit-sharing with developing countries through funding digitisation projects.

4.8.  The Committee recommends that those UK taxonomic institutions with major biological collections should develop strategic plans for making biodiversity informatics more readily accessible to users through the Internet, and that DFID should fund selected digitisation projects that focus on the biodiversity conservation and sustainability needs of developing countries.

4.9.  The Research Councils, particularly BBSRC, have played an important role in supporting pilot studies and proof of concept studies in the area of biodiversity informatics (Q 76). Beyond these innovative technological aspects, digitisation of major collections has been viewed as the responsibility of the institutions themselves (Q 91). The Committee, however, recognises that certain kinds of big research questions relating to large-scale biodiversity patterns in space and time can only be addressed using large-scale data. UK researchers addressing such questions should be able to apply for Research Council funding to create large-scale aggregated datasets.


4.10.  Barcoding, the use of a short standard sequence of DNA to identify individual organisms, has been available as a technique since the 1990s. In theory, organisms or fragments of organisms can be identified by comparison to a reference database of barcode sequences. The power of the technique is that it allows accurate identification of previously unidentifiable stages such as larvae, seedlings, and the fungal mycelium. However, the technique is absolutely dependent upon the availability of a searchable databank of reference sequences from accurately identified voucher specimens. Barcoding is a tool of value in addressing many different questions. In the UK there is substantial barcoding effort currently involved with diagnostics—that is, with identification. However, it is apparent that UK research on barcoding has slipped behind progress made elsewhere (pp 18 and 312) and the Wellcome Trust refers to an "apparent lack of collaboration between different barcoding initiatives which makes for significant confusion" (p 322).

4.11.  The evidence we received focused on plant pathogenic fungi, where barcoding effort comes from at least four teams (the Central Science Laboratory (CSL), the Scottish Crops Research Institute, Forest Research and the University of Reading). The CSL is a lead partner in an EU project to barcode statutory plant health pests and diseases (p 56). The development of barcoding technology represents an unprecedented opportunity to tackle the "taxonomic impediment" in mycology but these efforts require close co-ordination (p 270).

4.12.  The Committee is concerned about lack of co-ordination of barcoding effort nationally and about the potential for duplication of effort. The efficiency of barcoding as a diagnostic technique increases in proportion to the number of different species barcodes available for comparison. In the case of plant pathogenic fungi, we recommend that UK BRAG addresses the task of how best to co-ordinate barcoding effort across the UK.

DNA-based taxonomy and the morphological approach

4.13.  Metagenomics, the study of genetic material recovered directly from environmental samples rather than cloned material, and barcoding are immensely powerful techniques for exploring and understanding biodiversity. The European Distributed Institute of Taxonomy (EDIT) Consortium recognises that "there is a danger that DNA-based taxonomies will de-couple from morphologically-derived taxa" (p 236).



In taxonomic studies the two most commonly used types of information about organisms are molecular and morphological. Today, molecular information is usually DNA sequence data and forms the basis of metagenomics techniques and barcoding. In contrast, morphological information is based on external and internal anatomy and is often referred to as traditional or classical taxonomy. In any study, these data types can be used separately or can be combined.

Despite the power of molecular taxonomy "it is important that molecular approach develops alongside the classical [morphological] approach" (p 43). There is considerable concern about the risk of growing "sectoral separation" between professional taxonomists using molecular approaches and the conservation and volunteer communities who require the translation of taxonomic outputs into tailored products such as field guides and keys.

4.14.  The Committee recommends that NERC supports research into developing an effective, functioning interface between rapid taxonomic techniques such as metagenomics and traditional morphological taxonomy.

Keys and handbooks

4.15.  Accurate identification of species is fundamental to conservation in the UK (p 143) and the work of the voluntary sector in particular is heavily dependent on identification tools produced by taxonomists. Handbooks, identification keys and field guides are noted as highly important in the United Kingdom Taxonomic Needs Assessment.[20] However, many species groups have never been covered by an identification guide and many existing guides are out of date due to nomenclatural changes, and to the influx of invasive species (p 313).

4.16.  The production of identification keys and field guides is critical, especially in an environment of increasing numbers of invasive alien species, but in many groups of organisms—about half of all UK insects for example—no field guides are available for the UK (Q 215). There are several established and prestigious series, such as the Synopses of the British Fauna, the Royal Entomological Society handbooks and the Freshwater Biological Association keys, but the production of new guides is slow. The limiting factor is not the funding or marketing of the handbooks but the availability of taxon specialists willing to produce handbooks (pp 90, 294 and 313). We return to this issue in next chapter.

Research collections

4.17.  The three taxonomic tasks of description, identification and phylogeny are supported by key resources, in particular by research collections. The largest national collections, such as those housed at The NHM and RBG Kew, continue to be world-class resources and new developments, such as the Darwin Centre and the Millennium Seed Bank, are world-leading facilities.

4.18.  Regional and university museums represent an important archive providing essential reference material for teaching and housing voucher collections for reference by local recorders. Professor Mace indicated why these collections were valued: "taxonomists, zoologists and botanists, as part of their training need to have access to the specimens themselves"—there was, she said "absolutely no replacement for the real object" (Q 63). These collections are important both for validation of biological records and for training both scientists and new generations of naturalist specialists.

4.19.  Smaller collections are vulnerable and their future appears insecure. In the case of plant collections, of 602 herbaria present in Britain in 1945, 97 have been destroyed or cannot be traced, 230 have been transferred to existing institutions, the whereabouts of 106 are currently unknown, leaving 169 extant (preliminary data from survey by the BSBI, p 88). Adrian Norris, a retired Senior Curator of Natural Sciences at Leeds City Museums, commented that "the development of Regional Museum HUBS and the extra funding from the DCMS has made some difference," but urged that this funding be allocated so that museums can "fund strategic taxonomic tasks by employing trained taxonomists, as well as funding the proper storage of their collections" (p 284). Continued support from Government for regional and university museums, through programmes such as the Renaissance in the Regions programme, is essential.

National Biodiversity Network (NBN)

4.20.  The UK's Biological Records Centre (now hosted by the NERC Centre for Ecology and Hydrology at Wallingford) and many Local Record Centres are connected virtually by the NBN. The NBN provides access to over 27 million species distribution records from 229 different datasets—"the majority of these derive from voluntary recording organisations or from local record centres"—and it makes analytical tools available through its portal, the NBN Gateway (p 146). The NBN functions as a facilitating body and its funding, which is made up from payments from its member organisations, is described as "very fragile" because it is dependent upon individual priorities set by its members (Q 217). The Committee recognises the pivotal role played by the NBN in making datasets available electronically and in facilitating access to a wide range of users.

4.21.  The Committee welcomes the establishment by Defra of the Fund for Innovation in Local Biodiversity Recording. This fund, administered by Natural England, will make £181,000 available during the year 2008-09 for building capacity in Local Record Centres and to increase the geographical scope, quantity and quality of biological information served through the NBN (p 54 and Q 318).

4.22.  In view of the continuing success of the NBN in accessing and serving data, and its importance in engaging with and empowering the large voluntary sector involved in biological recording nationally, the Committee urges Defra to assist the NBN in moving towards a less fragile funding model.

19   Taxonomy in Europe in the 21st Century (Report prepared for the Board of Directors of EDIT). Back

20   A Taylor, United Kingdom Taxonomic Needs Assessment. Natural History Museum/Defra 23/02/2006. Back

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