Collections-based systematics: Opportunities and outlook for 2050

Journal of Systematics and Evolution

Volumn 53, Issue 6, 2015, Pages 477-488

  Wen, Jun ^a   Ickert Bond, Stefanie M ^b   Appelhans, Marc S ^a,c   Dorr, Laurence J ^a   Funk, Vicki A ^a  

^a SMITHSONIAN INSTITUTION   (United States)

^b UNIVERSITY OF ALASKA MUSEUM   (United States)

^c UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

Biodiversity CyberBank; collections based systematics; e monograph; Systematics Agenda 2050; World Organization of Systematic Biology

Indexed keywords

EID: 84945300384     PISSN: 16744918     EISSN: 17596831     Source Type: Journal    
DOI: 10.1111/jse.12181     Document Type: Review

References (84)

1. Anderson RP., 2012. Harnessing the world's biodiversity data: Promise and peril in ecological niche modeling of species distributions. Annals of the New York Academy of Sciences 1260: 66-80.
2. Barkworth ME, Murrell ZE., 2012. The US Virtual Herbarium: Working with individual herbaria to build a national resource. ZooKeys 209: 55-73.
3. Barnosky AD, Hadly EA, Bascompte J, Berlow EL, Brown JH, Fortelius M, Getz WM, Harte J, Hastings A, Marquet PA, Martinez ND, Mooers A, Roopnarine P, Vermeij G, Williams JW, Gillespie R, Kitzes J, Marshall C, Matzke N, Mindell DP, Revilla E, Smith AB., 2012. Approaching a state shift in Earth's biosphere. Nature 486: 52-58.
4. Barnosky AD, Matzke N, Tomiya S, Wogan GOU, Swartz B, Quental TB, Marshall C, McGuire JL, Lindsey EL, Maguire KC, Mersey B, Ferrer EA., 2011. Has the Earth's sixth mass extinction already arrived? Nature 471: 51-57.
5. Beaman RS, Cellinese N., 2012. Mass digitization of scientific collections: New opportunities to transform the use of biological specimens and underwrite biodiversity science. ZooKeys 209: 7-17.
6. Blagoderov V, Kitching IJ, Livermore L, Simonsen TJ, Smith VS., 2012. No specimen left behind: Industrial scale digitization of natural history collections. ZooKeys 209: 133-146.
7. Borer ET, Hosseini PR, Seabloom EW, Dobson AP., 2007. Pathogen-induced reversal of native dominance in a grassland community. Proceedings of the National Academy of Sciences USA 104: 5473-5478.
8. Carvalho AF, Filer D, Renner SS., 2015. Taxonomy in the electronic age and an e-monograph of the papaya family (Caricaceae) as an example. Cladistics 31: 321-329.
9. Christenhusz MJM, Chase MW, Fay MF, Lumbsch T, Monro A, Vorontsova M, Zhang Z-Q., 2009. A new international journal for rapid publication of botanical taxonomy. Phytotaxa 1: 1-2.
10. Claridge MF., 1995. Introducing Systematics Agenda 2000. Biodiversity and Conservation 4: 451-454.
11. Council of Heads of Australasian Herbaria. 2010. Australian plant census. Available at http://www.anbg.gov.au/chah/apc/index.html.
12. Council of Heads of Australasian Herbaria. 2013. Australia's Virtual Herbarium. Available at http://avh.chah.org.au/.
13. Croft J, Cross N, Hinchcliffe S, Lughadha EN, Stevens PF, West JG, Whitbread G., 1999. Plant names for the 21st century: The International Plant Names Index, a distributed data source of general accessibility. Taxon 48: 317-324.
14. Daly M, Herendeen PS, Guralnick RP, Westneat MW, McDade L., 2012. Systematics Agenda 2020: The mission evolves. Systematic Biology 61: 549-552.
15. de Candolle AP., 1867. Lois de la nomenclature botanique adoptées par le congrès international de botanique tenu à Paris en aoÛt 1867. Paris: J.-B. Baillière.
16. de Candolle AP, de Candolle ALPP., 1824 -1873. Prodromus Systematis Naturalis Regni Vegetabilis, 17 vols. Paris: Sumptibus Sociorum Treuttel et Würtz.
17. 4 grasses. Proceedings of the National Academy of Sciences USA 107: 2532-2537.
18. Ellis EC, Antill EC, Kreft H., 2012. All is not loss: Plant biodiversity in the Anthropocene. PLoS ONE 7 (1): e30535. doi: 10.1371/journal.pone.0030535.
19. Emshwiller E, Theim T, Grau A, Nina V, Terrazas F., 2009. Origins of domestication and polyploidy in oca (Oxalis tuberosa; Oxalidaceae). 3. AFLP data of oca and four wild, tuber-bearing taxa. American Journal of Botany 96: 1839-1848.
20. Feeley KJ., 2012. Distributional migrations, expansions, and contractions of tropical plant species as revealed in dated herbarium records. Global Change Biology 18: 1335-1341.
21. Flann C., 2011. BioCode: Third time lucky? Zootaxa 2874: 38-40.
22. Frodin DG., 2001. Guide to standard floras of the world. 2nd ed. Cambridge: Cambridge University Press.
23. Funk VA., 2003a. The importance of herbaria. Plant Science Bulletin 49: 94-95.
24. Funk VA., 2003b. 100 uses for an herbarium (well at least 72). ASPT Newsletter 17: 17-19.
25. Funk VA., 2006. Floras: A model for biodiversity studies or a thing of the past? Taxon 55: 581-588.
26. Garcia-Milagros E, Funk VA., 2010. Improving the use of information from museum specimens: Using Google Earth to georeference Guiana Shield specimens in the US National Herbarium. Frontiers of Biogeography 2.3: 71-77.
27. Greuter W, Garrity G, Hawksworth DL, Jahn R, Kirk PM, Knapp S, McNeill J, Michel E, Patterson DJ, Pyle R, Tindall BJ., 2011. Draft BioCode (2011): Principles and rules regulating the naming of organisms. Taxon 60: 201-212.
28. Greuter W, Hawksworth DL, McNeill J, Mayo MA, Minelli A, Sneath PHA, Tindall BJ, Trehane P, Tubbs P, IUBS/IUMS International Committee for Bionomenclature. 1996. Draft BioCode: The prospective international rules for the scientific names of organisms. Taxon 45: 349-372.
29. Haston El, Cubey R, Pullan M, Atkins H, Harris DJ., 2012. Developing integrated workflows for the digitisation of herbarium specimens using a modular and scalable approach. ZooKeys 209: 93-102.
30. Hoek WZ., 2008. The last glacial-interglacial transition. Episodes 31: 226-229.
31. th ed. London: The International Trust for Zoological Nomenclature.
32. Jablonski D., 1994. Extinctions in the fossil record. Philosophical Transactions of the Royal Society B: Biological Sciences 34: 11-17.
33. Johnson KG, Brooks SJ, Fenberg PB, Glover AG, James KE, Lister AM, Michel E, Spencer M, Todd JA, Valsami-Jones E, Young JR, Stewart JR., 2011. Climate change and biosphere response: Unlocking the collections vault. BioScience 61: 147-153.
34. Johnson KR., 2015. Surrounded by science: Tracing the evolution of modern museums of science and natural history. Science 347: 618.
35. Kress WJ., 2004. Paper floras: How long will they last? A review of flowering plants of the neotropics. American Journal of Botany 91: 2124-2127.
36. Kress WJ, Penev L., 2011. Innovative electronic publication in plant systematics: PhytoKeys and the changes to the "Botanical Code" accepted at the XVIII International Botanical Congress in Melbourne. PhytoKeys 6: 1-4.
37. Lane MA., 1996. Roles of natural history collections. Annals of the Missouri Botanical Garden 83: 536-545.
38. Lapage SP, Sneath PHA, Lessel EF, eds. 1992. International code of nomenclature of bacteria: Bacteriological code. 1990 Revision. Washington, D.C.: ASM Press.
39. Lavoie C., 2013. Biological collections in an ever changing world: Herbaria as tools for biogeographical and environmental studies. Perspectives in Plant Ecology, Evolution and Systematics 15: 68-76.
40. Lenton TM., 2011. Early warning of climate tipping points. Nature Climate Change 1: 201-209.
41. Loarie SR, Carter BE, Hayhoe K, McMahon S, Moe R, Knight CA, Ackerly DD., 2008. Climate change and the future of California's endemic flora. PLoS ONE 3: e2502. doi: 10.1371/journal.pone.0002502.
42. Lughadha E., 2004. Towards a working list of all known plant species. Philosophical Transactions of the Royal Society B: Biological Sciences 359: 681-687.
43. Lujan NK, Page LM., 2015. Libraries of life. New York Times 27 February page A25. [online]. Available from http://www.nytimes.com/2015/02/27/opinion/libraries-of-life.html?-r=0 [accessed 1 May 2015].
44. Lumbsch T, Miller AN, Begerow D, Penev L., 2011. MycoKeys, or why we need a new journal in mycology? MycoKeys 1: 1-6.
45. Malmstrom CM, Shu R, Linton EW, Newton LA, Cook MA., 2007. Barley yellow dwarf viruses (BYDVs) preserved in herbarium specimens illuminate historical disease ecology of invasive and native grasses. Journal of Ecology 95: 1153-1166.
46. Marhold K, Stuessy T, Agababian M, Agosti D, Alford MH, Crespo A, Crisci JV, Dorr LJ, Ferencová Z, Frodin D, Geltman DV, Kilian N, Linder HP, Lohmann LG, Oberprieler C, Penev L, Smith GF, Thomas W, Tulig M, Turland N, Zhang XC., 2013. The future of botanical monography: Report from an international workshop, 12-16 March 2012, Smolenice, Slovak Republic. Taxon 62: 4-20.
47. Marshall CR., 2006. Explaining the Cambrian "explosion" of animals. Annual Review of Earth and Planetary Sciences 34: 355-384.
48. McElwain JC, Chaloner WG., 1995. Stomatal density and index of fossil plants track atmospheric carbon dioxide in the Paleozoic. Annals of Botany 76: 389-395.
49. McNeill J, Barrie FR, Buck WR, Demoulin V, Greuter W, Hawksworth DL, Herendeen PS, Knapp S, Marhold K, Prado J, Prud'homme Van Reine WF, Smith GF, Wiersema JH, Turland NJ., 2012. International code of nomenclature for algae, fungi, and plants (Melbourne code) adopted by the 18th International Botanical Congress, Melbourne, Australia, July 2011. Regnum Vegetabile 154. Ruggell: ARG Gantner Verlag KG.
50. Meier R, Dikow T., 2004. Significance of specimen databases from taxonomic revisions for estimating and mapping the global species diversity of invertebrates and repatriating reliable specimen data. Conservation Biology 18: 478-488.
51. Miller J, Dikow T, Agosti D, Sautter G, Catapano T, Penev L, Zhang ZQ, Pentcheff D, Pyle R, Blum S, Parr C, Freeland C, Garnett T, Ford LS, Muller B, Smith L, Strader G, Georgiev T, Bénichou L., 2012. From taxonomic literature to cybertaxonomic content. BMC Biology 10: 87. doi: 10.1186/1741-7007-10-87.
52. Miller JS, Funk VA, Wagner WL, Barrie F, Hoch PC, Herendeen P., 2011. Outcomes of the 2011 Botanical Nomenclature Section at the XVIII International Botanical Congress. PhytoKeys 5: 1-3.
53. O'Connell AF, Gilbert AT, Hatfield JS., 2004. Contribution of natural history collection data to biodiversity assessment in national parks. Conservation Biology 18: 1254-1261.
54. Panchen ZA, Primack RB, Anis̈ko T, Lyons RE., 2012. Herbarium specimens, photographs, and field observations show Philadelphia area plants are responding to climate change. American Journal of Botany 99: 751-756.
55. Penev L, Agosti D, Georgiev T, Catapano T, Miller J, Blagoderov V, Roberts D, Smith VS, Brake I, Ryrcroft S, Scott B, Johnson NF, Morris RA, Sautter G, Chavan V, Robertson T, Remsen D, Stoev P, Parr C, Knapp S, Kress WJ, Thompson CF, Erwin T., 2010a. Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples. ZooKeys 50: 1-16.
56. Penev L, Kress W, Knapp S, Li DZ, Renner S., 2010b. Fast, linked, and open---the future of taxonomic publishing for plants: Launching the journal PhytoKeys. PhytoKeys 1: 1-14.
57. Powers KE, Prather AL, Cook JA, Wooley J, Bart HL Jr, Monfils AK, Sierwald P., 2014. Revolutionizing the use of natural history collections in education. Science Education Reviews 13: 24-33.
58. Primack D, Imbres C, Primack RB, Miller-Rushing AJ, Del Tredici P., 2004. Herbarium specimens demonstrate earlier flowering times in response to warming in Boston. American Journal of Botany 91: 1260-1264.
59. Robbirt KM, Davy AJ, Hutchings MJ, Roberts DL., 2011. Validation of biological collections as a source of phenological data for use in climate change studies: A case study with the Orchid Ophrys sphegodes. Journal of Ecology 99: 235-241.
60. SA2000 (Systematics Agenda 2000). 1994. Charting the biosphere: A global initiative to discover, describe and classify the world's species. Technical report. New York: American Society of Plant Taxonomists, Society of Systematic Biologists, and the Willi Hennig Society.
61. Schilthuizen M, Vairappan CS, Slade EM, Mann DJ, Miller JA., 2015. Specimens as primary data: Museums and 'open science'. Trends in Ecology and Evolution 30: 237-238.
62. Schmid R, Dorr LJ., 2009. TL2/TL2S done!: 15 volumes 1976-2009, 11,227 pages, about 37,600 entries. Taxon 58: 689-691.
63. Scotland RW, Wood JRI., 2012. Accelerating the pace of taxonomy. Trends in Ecology and Evolution 27: 415-416.
64. Spooner DM, Rodriguez F, Polgar Z, Ballard HE, Jansky SH., 2008. Genomic origins of potato polyploids: GBSSI gene sequencing data. Crop Science 48 (S1): S27-S36.
65. Stuessy TF., 1993. The role of creative monography in the biodiversity crisis. Taxon 42: 313-321.
66. Stuessy TF, Lack HW, eds. 2011. Monographic plant systematics: Fundamental assessment of plant biodiversity. Regnum Vegetabile 153. Ruggell: ARG Gantner Verlag KG.
67. Suarez AV, Tsutsui ND., 2004. The value of museum collections for research and society. BioScience 54: 66-74.
68. Thomson KS., 2005. Natural history museum collections in the 21st Century. actionbioscience [online]. Available from http://www.actionbioscience.org/evolution/thomson.html [accessed March 15, 2015].
69. Tripp EA, Hoagland KE., 2013. Typifying an era in biology through synthesis of biodiversity information: Achievements and impediments. Taxon 62: 899-911.
70. Tulig M, Tarnowsky N, Bevans M, Anthony Kirchgessner, Thiers BM,. 2012. Increasing the efficiency of digitization workflows for herbarium specimens. Zookeys 209: 103-113.
71. Turland N., 2013. The code decoded. A user's guide to the International Code of Nomenclature for algae, fungi, and plants. Regnum Vegetabile 155. Königstein, Germany: Koeltz Scientific Books.
72. Vollmar A, Macklin JA, Ford LS., 2010. Natural history specimen digitization: Challenges and concerns. Biodiversity Informatics 7: 93-112.
73. Wen J., 2011. Systematics and biogeography of Aralia L. (Araliaceae): Revision of Aralia sects. Aralia, Humiles, Nanae, and Sciadodendron. Contributions from the United States National Herbarium 57: 1-172.
74. Wen J, Ree RH, Ickert-Bond S, Nie Z-L, Funk VA., 2013. Biogeography: Where do we go from here? Taxon 62: 912-927.
75. Wen J, Shi W., 2012. Revision of the Maddenia clade of Prunus (Rosaceae). PhytoKeys 11: 39-59.
76. Wheeler QD, ed. 2008. The new taxonomy. (The systematics association special volumes series; 76). Boca Raton, FL: CRC Press.
77. Wheeler QD., 2010. What would NASA do? Mission-critical infrastructure for species exploration. Systematics and Biodiversity 8: 11-15.
78. Wheeler QD, Knapp S, Stevenson DW, Stevenson J, Blum SD, Boom BM, Borisy GG, Buizer JL, De Carvalho MR, Cibrian A, Donoghue MJ, Doyle V, Gerson EM, Graham CH, Graves P, Graves SJ, Guralnick RP, Hamilton AL, Hanken J, Law W, Lipscomb DL, Lovejoy TE, Miller H, Miller JS, Naeem S, Novacek MJ, Page LM, Platnick NI, Porter-Morgan H, Raven PH, Solis MA, Valdecasas AG, Van Der Leeuw S, Vasco A, Vermeulen N, Vogel J, Walls RL, Wilson EO, Woolley JB., 2012. Mapping the biosphere: Exploring species to understand the origin, organization and sustainability of biodiversity. Systematics and Biodiversity 10: 1-20.
79. Wilson EO., 1992. The diversity of life. Cambridge: Harvard University Press.
80. 2 from pre-industrial levels. Nature 327: 617-618.
81. Yesson C, Brewer PW, Sutton T, Caithness N, Pahwa JS, Burgess M, Gray WA, White RJ, Jones AC, Bisby FA, Culham A., 2007. How global is the Global Biodiversity Information Facility? PLoS ONE 2 (11): e1124. doi: 10.1371/journal.pone.0001124.
82. Zalasiewicz J, Williams M, Haywood A, Ellis M., 2011. The Anthropocene: A new epoch of geological time? Philosophical Transactions of the Royal Society A 369: 835-841.
83. Zhang Z-Q., 2006. The first five years of Zootaxa. Zootaxa 1111: 68.
84. Zhang Z-Q., 2008. Contributing to the progress of descriptive taxonomy. Zootaxa 1968: 65-68.