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Literature related to Taxonomy

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Papers – Part 1

Albert, V.A. (Ed.) 2005. Parsimony, Phylogeny, and Genomics. Oxford University Press, 229 pp

Ariño, A.H. 2010. Approaches to estimating the universe of natural history collections data. Biodiversity Informatics 7: 81– 92

Bacher, S. 2012. Still not enough taxonomists: reply to Joppa et al. Trends in Ecology and Evolution, 27 (2): 65-66. doi:10.1016/j.tree.2011.11.003

Baird, R. 2010. Leveraging the fullest potential of scientific collections through digitization. Biodiversity Informatics 7: 130–136.

Bateman, A. 2010. Curators of the world unite: the International Society of Biocuration. Bioinformatics, 26 (8): 991. doi: 10.1093/bioinformatics/btq101

Beehler, B.M. 2010. The forgotten science: a role for natural history in the twenty-first century? J. Field Ornithol. 81(1):1–4. doi: 10.1111/j.1557-9263.2009.00253.x

Bennetzen, J.L. 2008. Biology and the beasts: individual investigator-driven research in the megaprojects era. Trends in Genetics, 25 (2): 57-59

Berents, P., Hamer, M. & Chavan ,V. 2010. Towards demand-driven publishing: approaches to the prioritization of digitization of natural history collection data. Biodiversity Informatics 7: 113–119

Bertorelle, G., Bruford, M.W., Hauffe, H.C., Rizolli, A. & Vernesi, C. 2009. Population Genetics for Animal Conservation. Conservation Biology. Cambridge University Press, 395 pp

Blackwelder, R.E. 1954. The Open Season on Taxonomists. Systematic Zoology, 3(4): 177-181.

Blaustein, R. 2009. The Encyclopedia of Life: Describing Species, Unifying Biology. BioScience, 59 (7): 551–556. doi: 10.1525/bio.2009.59.7.4

Bonney, R., Cooper, C.B., Dickinson, J., Kelling, S., Phillips, T., Rosenberg, K.V. & Shirk, J. 2009.  Citizen Science: A Developing Tool for Expanding Science Knowledge and Scientific Literacy. BioScience, 59(11):977-984. doi: 10.1525/bio.2009.59.11.9

Brasier, M. 2009. Darwin's Lost World. The hidden history of animal life.  Oxford University Press, 304 pp

Brewer, S., Jackson, S.T. & Williams, J.W. 2012. Paleoecoinformatics: applying geohistorical data to ecological questions. Trends in Ecology and Evolution, 27 (2): 104-112. doi:10.1016/j.tree.2011.09.009

Burguiere, T., Causse, T., Ung, V. & Vignes-Lebbe, R. 2013. IKey+: A New Single-Access Key Generation Web Service. Systematic Biology 62(1): 157–161.

Casas-Marce, M., Revilla, E., Fernandes, M., Rodriguez, A., Delibes, M. & Godoy, J.A. 2012. The Value of Hidden Scientific Resources: Preserved Animal Specimens from Private Collections and Small Museums. BioScience, 62(12): 1077-1082.

Chavan, V. & Krishnan, S. 2003. Natural history collections: A call for national information infrastructure. Current Science, 84 (1): 34-42

Clark, J.Y. 2003. Artificial neural networks for species identification by taxonomists. BioSystems, 72: 131–147. doi: 10.1016/S0303-2647(03)00139-4

Constable, H., Guralnick, R., Wieczorek, J., Spencer, C. & Peterson, A.T. 2010. VertNet: A New Model for Biodiversity Data Sharing. PLoS Biol, 8(2): e1000309. doi: 10.1371/journal.pbio.1000309

Cotterill, F.P.D. & Foissner, W. 2010. A pervasive denigration of natural history misconstrues how biodiversity inventories and taxonomy underpin scientific knowledge. Biodivers. Conserv. 19:291–303. Doi: 10.1007/s10531-009-9721-4

Crisci, J.V., Katinas, L., & Posadas, P. 2003. Historical Bioegeography: An Introduction. Harvard University Press, Cambridge MA. 264 pp

Deans, A.R., Yoder, M.J. & Balhoff, J.P. 2012. Time to change how we describe biodiversity. Trends in Ecology and Evolution, 27 (2): 78-84. doi:10.1016/j.tree.2011.11.007

de Carvalho, M.R., Bockmann, A., Amorim, D.S. & Brandao, C.R.F. 2008. Systematics must Embrace Comparative Biology and Evolution, not Speed and Automation. Evol. Biol. 35:150–157. doi: 10.1007/s11692-008-9018-7

Ebach, M.C. & de Carvalho, M.R. 2010. Anti-intellectualism in the DNA Barcoding Enterprise. Zoologia, 27 (2): 165-178. doi: 10.1590/S1984-46702010000200003

Ebach, M.C., Valdecasas, A.G. & Wheeler, Q.D. 2011. Impediments to taxonomy and users of taxonomy: accessibility and impact evaluation. Cladistics, 27: 550–557. doi:10.1111/j.1096-0031.2011.00348.x

Enghoff, H. & Seberg, O. 2006. A Taxonomy of Taxonomy and Taxonomists. The Systematist, 27: 13–15

Esselstyn, J.A. 2007. Should universal guidelines be applied to taxonomic
research? Biological Journal of the Linnean Society, 90: 761–764

Ginsparg, P. 2011. ArXiv at 20. Nature, 476: 145-147.

Guralnick, R. & Constable, H. 2010. Creating a Data-sharing Community
BioScience, 60 (4):  258-259. doi: 10.1525/bio.2010.60.4.2

Hamilton, A. & Wheeler, Q.D. 2008. Taxonomy and Why History of Science Matters for Science. A Case Study. Isis, 99:331-340

Hawksworth, D. 2010. Terms Used in Bionomenclature. Published by Global Biodiversity Information Facility, Copenhagen. More information and links to the PDF and web versions can be found on the glossary

Heads, M. 2009. Vicariance. In Encyclopedia of Islands(ed. by R. Gillespie and D. Clague), 947-950. University of California Press.

Heads, M. 2009. Inferring biogeographic history from molecular phylogenies. Biological Journal of the Linnean Society, 98: 757–774

Heads, M. 2009. Darwin’s changing views on evolution: from centres of origin and teleology to vicariance and incomplete lineage sorting. Journal of Biogeography, 36 (6): 1018-1026. 1-9. doi: 10.1111/j.1365-2699.2009.02127.x

Hein, J., Schierup, M.H. & Wiuf, C. 2005. Gene Genealogies, Variation and Evolution. A Primer in Coalescent Theory. Oxford University Press, 276 pp

Hine, C., 2008. Systematics as cyberscience : computers, change, and continuity in science. The MIT Press, 307 pp

Hochachka, W.M., Fink, D., Hutchinson, R.A., Sheldon, D., Wong, W.-K. & Kelling, S. 2012. Data-intensive science applied to broad-scale citizen science. Trends in Ecology and Evolution, 27 (2): 130-137. doi:10.1016/j.tree.2011.11.006

Höglund J. 2009. Evolutionary Conservation Genetics. Oxford University Press, 189 pp

Huang, X. & Qiao, G. 2011. Biodiversity databases should gain support from journals. Trends in Ecology & Evolution, 26 (8): 377-378. doi:10.1016/j.tree.2011.05.006

Joppa, L.N., Roberts, D.L. & Pimm, S.L. 2011. The  population  ecology  and  social  behaviour  of taxonomists. Trends in Ecology & Evolution doi:10.1016/j.tree.2011.07.010

Joppa, L.N., Roberts, D.L. & Pimm, S.L. 2012. Taxonomy that matters: response to Bacher. Trends in Ecology and Evolution, 27 (2): 66. doi:10.1016/j.tree.2011.11.015

La Salle, J., Wheeler, Q., Jackway, P., Winterton, S., Hobern, D. & Lovell, D. 2009. Accelerating taxonomic discovery through automated character extraction. Zootaxa, 2217: 43–55

Legendre, P. & Legendre, L. 1998. Numerical ecology. 2nd English edition. Elsevier Science BV, Amsterdam, 853 pp

Lucking, R. 2008. Taxonomy: a discipline on the brink of extinction. Are DNA barcode scanners the future of biodiversity research? Archives des Sciences, 61(2): 75-88

Maddison, D.R., Guralnick, R., Hill, A., Reysenbach, A.-L. & McDade, L.A. 2012. Ramping up biodiversity discovery via online quantum contributions. Trends in Ecology and Evolution, 27 (2): 72-77. doi:10.1016/j.tree.2011.10.010

Mares, M.A. 2009. Natural Science Collections: America’s Irreplaceable Resource. BioScience, 59 (7): 544-545. doi: 10.1525/bio.2009.59.7.2

May, R.M. 2011. Why Worry about How Many Species and Their Loss? PLoS Biology, 9 (8): e1001130. 2 pp. doi:10.1371/journal.pbio.1001130

Mayer, A. 2010. Phenology and Citizen Science. BioScience, 60 (3): 172–175. doi: 10.1525/bio.2010.60.3.3

McNeely, J.A. 2002. The role of taxonomy in conserving biodiversity. J. Nat. Conserv. 10, 145–153

Michener, W.K. & Jones, M.B. 2012. Ecoinformatics: supporting ecology as a data-intensive science. Trends in Ecology and Evolution, 27 (2): 85-93. doi:10.1016/j.tree.2011.11.016

Mindell, D.P., Fisher, B.L., Roopnarine, P., Eisen, J., Mace, G.M., Page, R.D.M. & Pyle, R.L. 2011. Aggregating, Tagging and Integrating Biodiversity Research. PLoS ONE, 6 (8): e19491. 3 pp. doi:10.1371/journal.pone.0019491

Minelli, A. 2013. Zoological nomenclature in the digital era. Frontiers in Zoology 10(4): 1-7.  doi: 10.1186/1742-9994-10-4

Mooi, R.D. & Gill, A.C. 2010. Phylogenies without Synapomorphies—A Crisis in Fish Systematics: Time to Show Some Character. Zootaxa, 2450: 26–40

Mora, C., Tittensor, D.P., Adl, S., Simpson, A.G.B., Worm, B. 2011. How Many Species Are There on Earth and in the Ocean? PLoS Biology, 9 (8): e1001127. 8 pp. doi:10.1371/journal.pbio.1001127

Morrison, W.R., Lohr, J.L., Duchen, P., Wilches, R., Trujillo, D., Mair, M. & Renner, S.S. 2009. The impact of taxonomic change on conservation: Does it kill, can it save, or is it just irrelevant? Biological Conservation, 142: 3201–3206. doi: 10.1016/j.biocon.2009.07.019

New, T.R. 2008. What’s in common names: are they really valuable in insect
conservation? J. Insect Conserv. 12: 447–449. doi: 10.1007/s10841-007-9127-0

O’Connell, A.F. JR., Gilbert, A.T. & Hatfield, J.S. 2004. Contribution of Natural History Collection Data to Biodiversity Assessment in National Parks. Conservation Biology, 18 (5): 1254–1261

Padial, J.M., Miralles, A., De la Riva, I. & Vences, M. 2010.  The integrative future of taxonomy. Frontiers in Zoology, 7:16. doi: 10.1186/1742-9994-7-16

Page, R.D.M. 2012. Space, time, form: viewing the Tree of Life. Trends in Ecology and Evolution, 27 (2): 113-120. doi:10.1016/j.tree.2011.12.002

Paik, IH., Lim, J., Chun, BS., Jin, SD., Yu, JP., Lee, JW., Bhak, J. & Paek, WK. 2009. The Korean Bird Information System (KBIS) through open and public participation. BMC Bioinformatics, 10 (15): S11. doi: 10.1186/1471-2105-10-S15-S11

Paradis, E. 2006. Analysis of Phylogenetics and Evolution with R. Springer Science+Business Media B.V., 211 pp

Parr, C.S., Guralnick, R., Cellinese, N. & Page, R.D.M. 2012. Evolutionary informatics: unifying knowledge about the diversity of life. Trends in Ecology and Evolution, 27 (2): 94-103. doi:10.1016/j.tree.2011.11.001

Porter, J.H., Hanson, P.C. & Lin, C.-C. 2012. Staying afloat in the sensor data deluge. Trends in Ecology and Evolution, 27 (2): 121-129. doi:10.1016/j.tree.2011.11.009

Pyke, G.H. & Ehrlich, P.R. 2010. Biological collections and ecological/environmental research: a review, some observations and a look to the future. Biol. Rev. 85: 247–266. doi: 10.1111/j.1469-185X.2009.00098.x

Rieseberg, L.H. & Wood, T.E. 2006. Plant Species Evolution. The Systematist, 27: 3-8

Robinson, P.N. & Bauer, S. 2011. Introduction to Bio-Ontologies. CRC Press, 488 pp

Rodman, J.E. 2007. Reflections on PEET, the Partnerships for Enhancing Expertise in Taxonomy. Zootaxa, 1668: 41–46

Santos, L.M. & Faria, L.R.R. 2011. The taxonomy’s new clothes: a little more about the DNA-based taxonomy. Zootaxa 3025: 66-68.

Scoble, M.J. 2010. Natural history collections digitization: rationale and value. Biodiversity Informatics 7: 77–80

Smith, G.F. & Figueiredo, E. 2011. Responsible species description: A change of attitude is needed to facilitate and improve access to biological material. TAXON, 60 (6): 1549–1551

Soberon, J. & Peterson, A.T. 2004. Biodiversity informatics: managing and applying primary biodiversity data. Phil. Trans. R. Soc. Lond. B, 359: 689–698. doi: 10.1098/rstb.2003.1439

Stork, N.E. 2010. Re-assessing current extinction rates. Biodivers. Conserv. 19: 357–371. doi: 10.1007/s10531-009-9761-9

Strain, D. 2011. 8.7 Million: A New Estimate for All the Complex Species on Earth. Science, 333 (6046): 1083. doi:10.1126/science.333.6046.1083

Szwedo, J. 2007. Taxonomy and EDIT – Toward of European Distributed Institute of Taxonomy. Proceedings of the 8th Conference of the Polish Taxonomical Society, Wiechlice 18-20 (V): 11-33.

Tenopir, C., Allard, S., Douglass, K., Aydinoglu, A.U., Wu, L., Read, E., Manoff, M. & Frame, M. 2011. Data Sharing by Scientists: Practices and Perceptions. PLoS ONE 6(6): e21101. 21 pp. doi:10.1371/journal.pone.0021101

Ung, V., Dubus, G., Zaragüeta-Bagils, R. & Vignes-Lebbe, R. 2010. Databases and ontologies. Xper2: introducing e-taxonomy. Bioinformatics, 26 (5): 703–704. doi: 10.1093/bioinformatics/btp715

Vernon, K. 1993. Desperately Seeking Status: Evolutionary Systematics and the Taxonomists' Search for Respectability 1940-60. The British Journal for the History of Science, 26 (2): 207-227

Vollmarr, A., Macklin, J.A. & Ford, L.S. 2010. Natural history specimen digitization: challenges and concerns. Biodiversity Informatics, 7: 93–112

Wägele, H., Klussmann-Kolb, A., Kuhlmann, M., Haszprunar, G., Lindberg, D., Koch, A. & Wolfgang, J.W. 2011. The taxonomist - an endangered race. A practical proposal for its survival. Frontiers in Zoology, 8: 25. doi:10.1186/1742-9994-8-25

Wheeler, Q.D. 2007. Invertebrate systematics or spineless taxonomy? Zootaxa, 1668: 11–18

Whitfield, J. 2011. Species spellchecker fixes plant glitches. Nature, 474: 263. 

Wiley, E.O., Siegel-Causey, D. Brooks, D.R. & V. A. Funk, V.A. 1991. The Compleat Cladist: A Primer of Phylogenetic Procedures. The University of Kansas Museum of Natural History, Special Publication, 19, 158 pp

Winston, J.E. 1999. Describing Species: Practical Taxonomic Procedure for Biologists. Columbia University Press, 512 pp

Winston, J.E. 2007. Archives of a small planet: The significance of museum collections and museum-based research in invertebrate taxonomy. Zootaxa, 1668: 47–54

Yang, Z. 2006. Computational Molecular Evolution. Oxford University Press, 376 pp

Yeates, D. 2009. Viva La Revolución! Designing the digital renaissance in zoological
Taxonomy. Australian Journal of Entomology, 48: 189–193.
doi: 10.1111/j.1440-6055.2009.00703.x

Zachos, F.E. 2013. Species splitting puts conservation at risk. Nature 494: 35. doi: 10.1038/494035c

Zauner, H. 2009. Evolving e-taxonomy. BMC Evolutionary Biology, 9: 141. doi: 10.1186/1471-2148-9-141

 

Papers – Part 2

 

Assis, L.C.S. & de Carvalho, M.R. 2010. Key Innovations: Further Remarks on the Importance of Morphology in Elucidating Systematic Relationships and Adaptive Radiations. Evol Biol  37:247–254. doi 10.1007/s11692-010-9098-z

Bawa, K.S. 2010. Cataloguing life in India: the taxonomic imperative. Current Science, 98 (2): 151-153

Bernstein, A. S. & Ludwig, D.S. 2008. The Importance of Biodiversity to Medicine. JAMA, 300(19) 2297-2299

Béthoux, O. 2010. Alternative nomenclatural procedures as a potential benefit to natural history collections. Organisms, Diversity & Evolution, 10:341–342
doi: 10.1007/s13127-010-0029-8

Blagoderov, V., Brake, I., Georgiev, T., Penev, L., Roberts, D., Rycroft, S., Scott, B., Agosti, D., Catapano, T. & Smith, V. 2010. Streamlining taxonomic publication: a working example with Scratchpads and ZooKeys. Zookeys, 50: 17-28. doi: 10.3897/zookeys.50.539

Carbayo, F. & Marques, A.C. 2011. The costs of describing the entire animal kingdom. Trends in Ecology and Evolution, 26(4): 154-155. doi: 10.1016/j.tree.2010.12.009

Coleman, C.O., Lowry, J.K. & Macfarlane, T. 2010. DELTA for Beginners: An introduction into the taxonomy software package DELTA. ZooKeys, 45: 1-75. doi: 10.3897/zookeys.45.263
http://pensoftonline.net/zookeys/index.php/journal/article/viewArticle/263

Derraik, J.G.B., Early, J.W., Closs, J.P. & Dickinson, K.J.M. 2009. Morphospecies and taxonomic species comparison for Hymenoptera. Journal of Insect Science, 10:108

Dickinson, J.L., Zuckerberg, B. & Bonter, D.N.  2010. Citizen Science as an Ecological Research Tool: Challenges and Bene?ts.  Annu. Rev. Ecol. Evol. Syst.  41:149–172. doi:10.1146/annurev-ecolsys-102209-144636

Dubois, A. 1988. The genus in zoology: a contribution to the theory of evolutionary systematics. Mém. Mus. natn. Hist. nat. (A) 140: 1-123

Dubois, A. 2008. Phylogenetic hypotheses, taxa and nomina in zoology. In: A. Minelli, L. Bonato & G. Fusco (ed.), Updating the Linnaean heritage: names as tools for thinking about animals and plants, Zootaxa, 1950: 51-86

Dubois, A. 2009. Endangered species and endangered knowledge. Zootaxa, 2201: 26-29.

Dubois, A. 2009. Incorporation of nomina of higher-ranked taxa into the International Code of Zoological Nomenclature: the nomenclatural status of class-series zoological nomina published in a non-latinized form. Zootaxa, 2106: 1-12

Dubois, A. 2010. La liaison organique taxinomie-collections-bibliothèques. Biosystema 26 – Systématique et collections: 21-44

Dubois, A., 2010. Zoological nomenclature in the century of extinctions: priority vs. “usage”. Organisms, Diversity & Evolution, 10: 259–274

Dubois, A. 2010. Nomenclatural rules in zoology as a potential threat against natural history museums. Organisms, Diversity & Evolution, 10: 81-90

Dubois, A. 2010. Contributions to the discussion on electronic publication IV. (6) Registration as a fourth floor of the nomenclatural process. Bulletin of zoological Nomenclature, 67 (1): 11-23

Dubois, A. 2010. Retroactive changes should be introduced in the Code only with great care: problems related to the spellings of nomina. Zootaxa, 2426: 1-42

Dubois, A. 2010. Taxonomy in the century of extinctions: taxonomic gap, taxonomic impediment, taxonomic urgency. Taprobanica, 02 (01): 1-5

Dubois, A. 2010. Describing new species. Taprobanica, 02(01): 6-24

Dubois, A. 2011. The international Code of Zoological Nomenclature must be drastically improved before it is too late. Bionomina, 2: 1-104 www.mapress.com/bionomina/

Dubois, A. 2011. Species and strange species in zoology: Do we need a “unified concept of species”?. Comptes Rendus de l'Académie des Sciences . C.R. Palevol 10: 77-94. Doi: 10.1016/j-crpv2011.010.002. www.sciencesdirect.com

Ebach, M.C. 2011. Taxonomy and the DNA Barcoding Enterprise. Zootaxa, 2742: 67–68

Ejnavarzala, H. 2010.  DNA barcoding: access to biodiversity and benefit-sharing policy issues in the Indiancontext. Current Science, 99 (5): 594-600.

Evenhuis, N.L. 2008. A Compendium of Zoological Type Nomenclature:  a Reference Source. Bishop Museum Technical Report, 41: 1-23

Fisher, J.R. & Dowling, A.P.G. 2010. Modern methods and technology for doing classical taxonomy. Acarologia, 50(3): 395–409. doi: 10.1051/acarologia/20101981

Fontaine, B. 2010. European bounty for taxonomist. Nature, 468: 377

Keller, R.P., Lodge, D.M., Lewis, M.A. & Shogren, J.F. (Ed.) 2009. Bioeconomics of invasive species. Integrating, Ecology, Economics, Policy and Management. Oxford University Press, 315 pp

Kim, D. & Yu, H. 2011. Figure Text Extraction in Biomedical Literature. PLoS ONE 6(1): e15338. 11 pp. doi: 10.1371/journal.pone.0015338

Kontolea, A., Pascual, U. & Swanson, T. (Ed.) 2007. Biodiversity Economics. Principles, Methods and Applications. Cambridge University Press, 2297-2299

Lister, A.M. & Climate Change Research Group. 2011. Natural history collections as sources of long-term datasets. Trends in Ecology & Evolution, 26(4): 153-154. doi: 10.1016/j.tree.2010.12.009

Maclaurin, J. & Sterelny, K. 2008. What is biodiversity. The university of Chicago Press, 231 pp

MacLeod, N., Benfield, M. & Culverhouse, P. 2010. Time to automate identification. Nature, 467/9: 154-155.

Magurran, A.E. 2010. Q&A What is biodiversity? BMC Biology, 8:145, 4 pp. doi: 10.1186/1741-7007-8-145

McBirney, A. & Cook, S. 2009. The Philosophy of Zoology Before Darwin: A translated and annotated version of the original French text by Edmond Perrier. Springer Dordrecht Heidelberg London New YorkDordrecht, The Netherlands: Springer, 266 pp. ISBN 978-90-481-3008-5

Nimis, P.L. & Vignes Lebbe, R. (Ed.) 2010. Tools for identifying Biodiversity: Progress and Problems. Proceedings of the International Congress, 480 pp 

Numbers, R.L. (Ed.) 2009. Galileo goes to jail and other myths about science and religion.  Harvard University Press, 317 pp. ISBN: 978-0-674-05741 

Packer, L., Grixti, J.C., Roughley, R.E. & Hanner, R. 2009. The status of taxonomy in Canada and the impact of DNA barcoding. Can. J. Zool. 87: 1097-1110. doi: 10.1139/Z09-100.  

Pearson, D.L., Hamilton, A.L., & Erwin, T.L. 2011. Recovery Plan for the Endangered Taxonomy Profession. BioScience, 61(1): 58-63

Penev, L. et al. 2010. Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples. ZooKeys, 50: 1-16. doi: 10.3897/zookeys.50.538

Perrings, Ch. 2010. The economics of biodiversity: the evolving agenda. Environment and Development Economics 15: 721–746. Cambridge University Press. doi:10.1017/S1355770X10000343

Queenborough, S.A., Cooke, I.R. & Schildhauer, M.P. 2010. Methods in ecology: Do we need an EcoBank? The ecology of data-sharing. British Ecological Society Bulletin, 41(3): 32-35

Richards, R.A. 2010. The Species Problem: A Philosophical Analysis. Cambridge University Press, 236 pp

Russell, N. 2010. Communicating Science  Professional, Popular, Literary. Cambridge University Press, 350 pp

Schlick-Steiner, B.C., Steiner, F. M., Seifert, B., Stauffer, Ch., Christian, E., & Crozier, R.H. 2010. Integrative Taxonomy: A Multisource Approach to Exploring Biodiversity. Ann. Rev. Entomol.  55:421–438. doi:  10.1146/annurev-ento-112408-085432

Schuh, R.T. & Brower, A.V.Z. 2009. Biological Systematics. Principles and Applications. Cornell University Press, 2nd ed., 311 pp

Simonite, T. & Le Page, M. 2010. Digital doomsday: the end of knowledge. New Scientist, 2745: 36-39

Smith, G.F. &  Figueiredo, E. 2010. E-taxonomy: an affordable tool to fill the biodiversity knowledge gap. Biodivers. Conserv. 19:829-836. doi: 10.1007/s10531-009-9738-8

Stafford, R., Hart, A.G., Collins, L., Kirkhope, C.L., Williams, R.L., Rees, S.G., Lloyd, J.R. & Goodenough, A.E. 2010. Eu-Social Science: The Role of Internet Social Networks in the Collection of Bee. Biodiversity Data. PLoS ONE 5(12): e14381. 7 pp. doi: 10.1371/journal.pone.0014381 

Tancoigne, E., Bole, C., Sigogneau, A. & Dubois, A. 2011. Insights from Zootaxa on potential trends in zoological taxonomic activity. Frontiers in Zoology 8:5.

The Expert Panel on Biodiversity Science. 2010. Canadian Taxonomy: Exploring Biodiversity, Creating opportunity. The Council of Canadian Academies. 142 pp 

Vision, T.J. 2010. Open Data and the Social Contract of Scientific Publishing. BioScience, 60(5): 330-331. doi:10.1525/bio.2010.60.5.2 

Whitlock, M.C. 2011. Data archiving in ecology and evolution: best practices. Trends Ecology & Evolution, 26 (2): 61-65

Wilkins, J. S. 2010. What is a species? Essences and generation. Theory Biosci. 129:141–148. doi: 10.1007/s12064-010-0090-z

Wilkins, J.S. 2010.  Species A history of the idea. Species and Systematics, 1. University of California Press, 320 pp

Williams, K.A. 2010. Museum collections - resources for biological monitoring. African Invertebrates, 51 (1): 219-221

Woodwell, G. M. 2010. The Biodiversity Blunder. BioScience, 60(11):870-871

 

e-Library topics

• Taxonomy databases
• Networks, Organisations , Projects and Societies
• Software
• Identification keys
• Training manuals

 

Taxonomy databases

GBIF Data Portal - Access millions of data records shared via the GBIF network. Explore species, countries and datasets: http://data.gbif.org/welcome.htm

Taxonomy and online databases: http://www.eti.uva.nl/tools/links/taxonomy.php

• World Biodiversity Database - The WBD currently consists of 21 separate projects, each with its own interface and feature set. These projects cover a total of 25493 unique taxa, plus an additional 4149 synonyms/ http://www.eti.uva.nl/tools/wbd.php

Additional links to databases:

• Catalogue of Life: http://www.catalogueoflife.org/
• Euro+Med Plantbase (E+M): http://www.emplantbase.org/home.html
• European Register of Marine Species (ERMS): http://www.marbef.org/data/erms.php
• Encyclopedia of Life: http://www.eol.org/
• Espèces de Belgique/Belgische soortenlijst : http://www.species.be
• Fauna Europaea’s other relevant on-line databases within the Kingdom Animalia: http://www.faunaeur.org/external_databases.php
• SoortenBank.nl: http://www.soortenbank.nl/
• World Register of Marine Species (WoRMS): www.marinespecies.org

 

Networks, Organisations, Projects and Societies

• A Long-Term Biodiversity, Ecosystem and Awareness Research Network: http://www.alter-net.info/
• Biodiversity Information Networks Database: http://www.tdwg.org/biodiv-networks/networks-database/
• Biodiversity Information Projects of the World: http://www.tdwg.org/biodiv-projects/projects-database/
• Biodiversity Information Standards (TDWG) is an international not-for-profit group that develops standards and protocols for sharing biodiversity data: http://www.tdwg.org/
• Biodiversity links: http://www.eti.uva.nl/tools/links/biodiversity.php
• Creating a taxonomic e-science (CATE): http://www.cate-project.org/
• Comisión Nacional para el conocimiento y uso de la Biodiversidad (CONABIO): http://www.conabio.gob.mx/
• Consortium for the Barcode of life (CBoL): http://www.barcoding.si.edu/
• Convention on Biological Diversity: http://www.biodiv.org/default.shtml
• Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES): http://www.cites.org/
• European Consortium for the Barcode of Life (ECBoL): http://www.ecbol.org/
• European Network of Palm Scientists (EUNOPS): http://eunops.org/
• European Platform for Biodiversity Research Strategy: http://www.epbrs.org/
• European Strategy Forum on Research Infrastructures (ESFRI):: http://cordis.europa.eu/esfri/
• Global Biodiversity Information Facility (GBIF): http://www.gbif.org/
• Global Environment Facility (GEF): http://www.gefweb.org/
• Group on Earth Observations Biodiversity Observation Network (GEO-BON): http://www.earthobservations.org/geobon.shtml
• International Barcode of Life (iBOL): http://www.ibolproject.org/home.html
• International Commission on Zoological Nomenclature: http://www.iczn.org/
• International Society of Arachnology: http://www.arachnology.org/
• LifeWatch: e-science and technology infrastructure for biodiversity data and observatories: http://www.lifewatch.eu/
• Marine Biodiversity and Ecosystem Functioning: http://www.marbef.org/
• National Center for Biotechnology Information (NCBI): http://www.ncbi.nlm.nih.gov/
• National Geographic Society: http://www.nationalgeographic.com/research/
• Society for the Preservation of Natural History Collections: http://www.spnhc.org/
• Society of Systematic Biologists: http://systbiol.org/
• Species Survival Commission, IUCN: http://www.iucn.org/themes/ssc/
• Systematics Association: http://www.systass.org/
• Willi Hennig Society: http://www.cladistics.org/
• World Conservation Union (IUCN): http://www.iucn.org/
• World Taxonomist Database - You can search for a person, an institute, a specific country, a taxonomic group, etc.: http://www.eti.uva.nl/tools/wtd.php
• World Wide Fund for Nature (WWF): http://www.panda.org/index.cfm; http://www.worldwildlife.org 

 

Software

Biodiversity and Biological Collections Software

• BIOTA: The Biodiversity Database Manager: http://viceroy.eeb.uconn.edu/biota
• DeltaAccess: http://www.bgbm.fu-berlin.de/Projects/DeltaAccess/
• DELTA/Intkey: http://delta-intkey.com/
• EDIT Biodiversity Service & Application Tracker - Collection of links to software, tools and resources useful to taxonomists: http://www.bdtracker.net/
• EDIT Platform Cybergate - The EDIT Platform for Cybertaxonomy is a collection of tools and services which together cover all aspects of the taxonomic workflow: taxonomic editing; publishing of edited data; data storage and exchange; collections and specimens; descriptions; fieldwork; literature; and geography: http://dev.e-taxonomy.eu/platform/
• EndNote: http://www.endnote.com/
• Freezerworks, Dataworks Development, Inc.: http://www.freezerworks.com/
• Iowa State Entomology Index of Software Internet Resources: http://www.ent.iastate.edu/list/directory/104/vid/4
• LucID 3: http://www.lucidcentral.com/
• Papyrus: http://www.researchsoftwaredesign.com/
• Platypus: http://www.deh.gov.au/biodiversity/abrs/online-resources/software/platyp...
• TDWG Subgroup on Biological Collection Data - Software for Biological Collection Management: http://www.bgbm.org/TDWG/acc/Software.htm

Morphology and Imaging Hardware and Software

• Auto-montage: http://www.syncroscopy.com/syncroscopy/automontageshort.asp
• CombineZ5: http://www.hadleyweb.pwp.blueyonder.co.uk/CZ5/combinez5.htm
• Digital Morphology: http://digimorph.org/
• HeliconFocus: http://helicon.com.ua/heliconfocus/
• Microptics: http://www.microptics-usa.com/
• Morphometrics at SUNY Stony Brook: http://life.bio.sunysb.edu/morph/
• Syncroscopy: http://www.syncroscopy.com/syncroscopy/

 
Phylogenetics Software

• Evolutionary Biology Group, University of Oxford, Department of Zoology: http://evolve.zps.ox.ac.uk/
• Felsenstein’s list of Phylogeny Programs: http://evolution.genetics.washington.edu/phylip/software.html
• Page’s software programs: http://taxonomy.zoology.gla.ac.uk/software/index.html
• Page’s software list: http://taxonomy.zoology.gla.ac.uk/software/software.html
• POY (Phylogeny Reconstruction via Optimization of DNA and other Data): http://research.amnh.org/scicomp/projects/poy.php
• Winclada/Nona/TNT: http://www.cladistics.com/

 

Identification keys

• Key to nature:  www.keytonature.eu
  http://dbiodbs.units.it/dryades/tools.html

• Discover Life ID guides: http://www.discoverlife.org/mp/20q

Training manuals

GBIF manuals: http://www.gbif.org/participation/training/resources/gbif-training-manuals/

• Digitisation of Natural History Collections Data
• A practical hands-on tutorial
• Uses of Primary Species-Occurrence Data
• Initiating a Collection Digitisation Project
• Principles of Data Quality
• Principles and Methods of Data Cleaning
• Biogeomancer, Guide to Best Practices in Georeferencing
• Guide to Best Practices for Generalising Sensitive Species Occurrence Data