Accelerating the pace of taxonomy

Abstract

In a recent article in TREE [1Maddison D.R. et al.Ramping up biodiversity discovery via online quantum contributions.Trends Ecol. Evol. 2012; 27: 72-77Abstract Full Text Full Text PDF PubMed Scopus (48) Google Scholar], Maddison et al. proposed that taxonomy needs to shift to a model of quantum contributions whereby species hypotheses are published as they are formulated and data as they are collected in web-based repositories and content-management systems. In fact, ‘quantum contributions’ are long-standing practice in paper publications [2Agnew A.D.Q. Wild Flowers of Upland Kenya. Oxford University Press, 1974Google Scholar, 3Collenette S. Wild Flowers of Saudi Arabia. National Commission of Wildlife Conservation and Development, 1999Google Scholar, 4Killeen T.J. et al.Guia de Arboles de Bolivia. Herbario Nacional de Bolivia & Missouri Botanic Garden, 1993Google Scholar, 5Killeen T.J. Schulenberg T. A biological assessment of Parque Nacional Noel Kempff Mercado, Bolivia.RAP Working Papers. 1998; 10: 1-372Google Scholar], going back in botany to at least the 19th century. For example, in Agnew's Wild Flowers of Upland Kenya [2Agnew A.D.Q. Wild Flowers of Upland Kenya. Oxford University Press, 1974Google Scholar], the terms ‘Species A. B. C.’ are extensively used for species identified in the East African herbarium under these letters, which are described and cross-referenced to representative specimens. In their 1993 Guia de Arboles de Bolivia [4Killeen T.J. et al.Guia de Arboles de Bolivia. Herbario Nacional de Bolivia & Missouri Botanic Garden, 1993Google Scholar], Killeen et al. make extensive use of ‘sp. indet #1. sp. indet #2’ and so on (up to 11 in the genus Ocotea for example) for a description and reference collection. Although these and other publications are readily available, we are unaware of any significant use of quantum contributions for subsequent taxonomic work except in the case of Agnew, whose ‘Species A. B. C. etc’ have been taken up in the Flora of Tropical East Africa, which includes the area covered by Agnew's book. Therefore, quantum contributions are not significantly new and there is little evidence that they have made anything other than a minor contribution to advancing systematics and taxonomy. In addition, the central idea ‘that species hypotheses are published as they are formulated and data as they are collected’ does not take into account that, for plants at least, collecting specimens and describing new species are dissociated in time and often carried out by different people. The idea that a biologist is in the field, spotting putative new taxa, certainly happens, but only rarely. Rather, most species hypotheses are generated subsequently after the examination of specimens in reference collections (Figure 1) [6Bebber D.P. et al.Herbaria are a major frontier for species discovery.Proc. Natl. Acad. Sci. U.S.A. 2010; 107: 22169-22171Crossref PubMed Scopus (226) Google Scholar].Another problem, not discussed by the authors, is that many, perhaps the majority, of the plants listed as ‘species A’ or something similar might not be new at all. Many people work to a strict deadline and have no access to good up-to-date floras or experts, and so resort to the ‘species A’ device for an entity they are unable to identify, which is perhaps new but more probably, an existing taxon.If society and policy makers wish to exploit fully the resources available from all species, they need to resource the discovery process. The authors’ initiative [1Maddison D.R. et al.Ramping up biodiversity discovery via online quantum contributions.Trends Ecol. Evol. 2012; 27: 72-77Abstract Full Text Full Text PDF PubMed Scopus (48) Google Scholar], along with other recent proposals to reinvent taxonomy, has at its core the mistaken view that existing taxonomic processes (Figure 1) can readily be bypassed or replaced by an informatics device on the web or technological innovation [1Maddison D.R. et al.Ramping up biodiversity discovery via online quantum contributions.Trends Ecol. Evol. 2012; 27: 72-77Abstract Full Text Full Text PDF PubMed Scopus (48) Google Scholar, 7Deans A.R. et al.Time to change how we describe biodiversity.Trends Ecol. Evol. 2012; 27: 78-84Abstract Full Text Full Text PDF PubMed Scopus (107) Google Scholar, 8Godfray H.C.J. Challenges for taxonomy.Nature. 2002; 417: 17-19Crossref PubMed Scopus (406) Google Scholar]. Despite approximately a decade of DNA barcoding, for example, we are unaware of any new species of flowering plant described during 2010 exclusively using this method. This does not mean that DNA barcoding in plants has no role to play in species identification or even in species discovery in the future, but at the moment it is not integrated into the working practice of specimen-based taxonomy [9Goldstein P.Z. De Salle R. Integrating DNA barcode data and taxonomic practice: determination, discovery, and description.BioEssays. 2010; 33: 135-147Crossref Scopus (250) Google Scholar]. To accelerate the pace of species discovery, we would highlight the importance of: focussed aims (species delimitation); motivation [10Bebber D.P. et al.Big hitting collectors make massive and disproportionate contribution to the discovery of plant species.Proc. R. Soc. B. 2012; 279: 2269-2274Crossref PubMed Scopus (35) Google Scholar, 11Whitfield J.A. Superstars of botany: rare specimens.Nature. 2012; 484: 436-438Crossref PubMed Scopus (6) Google Scholar]; expertise [10Bebber D.P. et al.Big hitting collectors make massive and disproportionate contribution to the discovery of plant species.Proc. R. Soc. B. 2012; 279: 2269-2274Crossref PubMed Scopus (35) Google Scholar, 11Whitfield J.A. Superstars of botany: rare specimens.Nature. 2012; 484: 436-438Crossref PubMed Scopus (6) Google Scholar]; and integrated teamwork but with clear division of roles. Along these lines, we, in collaboration with other colleagues, are producing Foundation Monographs (http://www.leverhulme.ac.uk/news/news_item.cfm/newsid/6/newsid/161): the first, on the genus Convolvulus and containing 200 species, will be completed in approximately 9 months and published in an open access online journal in late 2012, integrating taxonomic decision-making based on comparing specimens, dichotomous keys for identification, descriptions of all species, DNA barcodes for most species and 4000 digitised specimens from a single herbarium. This is only one initiative but it suggests to us that the way to make headway in describing biodiversity is to make use of people who combine taxonomic expertise and motivation with new smart tools, technologies and team work. In a recent article in TREE [1Maddison D.R. et al.Ramping up biodiversity discovery via online quantum contributions.Trends Ecol. Evol. 2012; 27: 72-77Abstract Full Text Full Text PDF PubMed Scopus (48) Google Scholar], Maddison et al. proposed that taxonomy needs to shift to a model of quantum contributions whereby species hypotheses are published as they are formulated and data as they are collected in web-based repositories and content-management systems. In fact, ‘quantum contributions’ are long-standing practice in paper publications [2Agnew A.D.Q. Wild Flowers of Upland Kenya. Oxford University Press, 1974Google Scholar, 3Collenette S. Wild Flowers of Saudi Arabia. National Commission of Wildlife Conservation and Development, 1999Google Scholar, 4Killeen T.J. et al.Guia de Arboles de Bolivia. Herbario Nacional de Bolivia & Missouri Botanic Garden, 1993Google Scholar, 5Killeen T.J. Schulenberg T. A biological assessment of Parque Nacional Noel Kempff Mercado, Bolivia.RAP Working Papers. 1998; 10: 1-372Google Scholar], going back in botany to at least the 19th century. For example, in Agnew's Wild Flowers of Upland Kenya [2Agnew A.D.Q. Wild Flowers of Upland Kenya. Oxford University Press, 1974Google Scholar], the terms ‘Species A. B. C.’ are extensively used for species identified in the East African herbarium under these letters, which are described and cross-referenced to representative specimens. In their 1993 Guia de Arboles de Bolivia [4Killeen T.J. et al.Guia de Arboles de Bolivia. Herbario Nacional de Bolivia & Missouri Botanic Garden, 1993Google Scholar], Killeen et al. make extensive use of ‘sp. indet #1. sp. indet #2’ and so on (up to 11 in the genus Ocotea for example) for a description and reference collection. Although these and other publications are readily available, we are unaware of any significant use of quantum contributions for subsequent taxonomic work except in the case of Agnew, whose ‘Species A. B. C. etc’ have been taken up in the Flora of Tropical East Africa, which includes the area covered by Agnew's book. Therefore, quantum contributions are not significantly new and there is little evidence that they have made anything other than a minor contribution to advancing systematics and taxonomy. In addition, the central idea ‘that species hypotheses are published as they are formulated and data as they are collected’ does not take into account that, for plants at least, collecting specimens and describing new species are dissociated in time and often carried out by different people. The idea that a biologist is in the field, spotting putative new taxa, certainly happens, but only rarely. Rather, most species hypotheses are generated subsequently after the examination of specimens in reference collections (Figure 1) [6Bebber D.P. et al.Herbaria are a major frontier for species discovery.Proc. Natl. Acad. Sci. U.S.A. 2010; 107: 22169-22171Crossref PubMed Scopus (226) Google Scholar]. Another problem, not discussed by the authors, is that many, perhaps the majority, of the plants listed as ‘species A’ or something similar might not be new at all. Many people work to a strict deadline and have no access to good up-to-date floras or experts, and so resort to the ‘species A’ device for an entity they are unable to identify, which is perhaps new but more probably, an existing taxon. If society and policy makers wish to exploit fully the resources available from all species, they need to resource the discovery process. The authors’ initiative [1Maddison D.R. et al.Ramping up biodiversity discovery via online quantum contributions.Trends Ecol. Evol. 2012; 27: 72-77Abstract Full Text Full Text PDF PubMed Scopus (48) Google Scholar], along with other recent proposals to reinvent taxonomy, has at its core the mistaken view that existing taxonomic processes (Figure 1) can readily be bypassed or replaced by an informatics device on the web or technological innovation [1Maddison D.R. et al.Ramping up biodiversity discovery via online quantum contributions.Trends Ecol. Evol. 2012; 27: 72-77Abstract Full Text Full Text PDF PubMed Scopus (48) Google Scholar, 7Deans A.R. et al.Time to change how we describe biodiversity.Trends Ecol. Evol. 2012; 27: 78-84Abstract Full Text Full Text PDF PubMed Scopus (107) Google Scholar, 8Godfray H.C.J. Challenges for taxonomy.Nature. 2002; 417: 17-19Crossref PubMed Scopus (406) Google Scholar]. Despite approximately a decade of DNA barcoding, for example, we are unaware of any new species of flowering plant described during 2010 exclusively using this method. This does not mean that DNA barcoding in plants has no role to play in species identification or even in species discovery in the future, but at the moment it is not integrated into the working practice of specimen-based taxonomy [9Goldstein P.Z. De Salle R. Integrating DNA barcode data and taxonomic practice: determination, discovery, and description.BioEssays. 2010; 33: 135-147Crossref Scopus (250) Google Scholar]. To accelerate the pace of species discovery, we would highlight the importance of: focussed aims (species delimitation); motivation [10Bebber D.P. et al.Big hitting collectors make massive and disproportionate contribution to the discovery of plant species.Proc. R. Soc. B. 2012; 279: 2269-2274Crossref PubMed Scopus (35) Google Scholar, 11Whitfield J.A. Superstars of botany: rare specimens.Nature. 2012; 484: 436-438Crossref PubMed Scopus (6) Google Scholar]; expertise [10Bebber D.P. et al.Big hitting collectors make massive and disproportionate contribution to the discovery of plant species.Proc. R. Soc. B. 2012; 279: 2269-2274Crossref PubMed Scopus (35) Google Scholar, 11Whitfield J.A. Superstars of botany: rare specimens.Nature. 2012; 484: 436-438Crossref PubMed Scopus (6) Google Scholar]; and integrated teamwork but with clear division of roles. Along these lines, we, in collaboration with other colleagues, are producing Foundation Monographs (http://www.leverhulme.ac.uk/news/news_item.cfm/newsid/6/newsid/161): the first, on the genus Convolvulus and containing 200 species, will be completed in approximately 9 months and published in an open access online journal in late 2012, integrating taxonomic decision-making based on comparing specimens, dichotomous keys for identification, descriptions of all species, DNA barcodes for most species and 4000 digitised specimens from a single herbarium. This is only one initiative but it suggests to us that the way to make headway in describing biodiversity is to make use of people who combine taxonomic expertise and motivation with new smart tools, technologies and team work. We thank David Harris and Mark Carine for comments on a draft of this manuscript, and the BBSRC SynTax initiative and the Leverhulme Trust for funding Foundation Monographs of Convolvulus and Ipomoea, respectively.