Skip to main content

Advertisement

SpringerLink
Log in

Biodiversity inventory and informatics in Southeast Asia

  • Original Paper
  • Published:
Biodiversity and Conservation Aims and scope Submit manuscript

Abstract

Rapidly changing land use in Southeast Asia threatens plant diversity, and reduces the time we have left to document it. Despite over 200 years of scientific plant exploration, many plant species have yet to be discovered. Moreover, we still have a very poor understanding of the distribution of known taxa in this biogeographically complex region. We review the current state of biodiversity exploration, using plants in Indonesia as an example. Traditional methods of collecting and describing species have provided a solid foundation for our understanding of plant biodiversity, but are insufficient for the pragmatic task of rapidly discovering and documenting today’s biodiversity before it is gone, because general collecting expeditions tend to be infrequent, and documentation of most new species must await taxonomic revisions many years in the future. Solutions to this exploration and documentation crisis (i) could use the abundant resource of enthusiastic, networked, national biology students, (ii) should employ biodiversity informatics tools to efficiently engage both specialists and parataxonomists, and (iii) might require adoption of new types of α-taxonomy, utilizing increasingly low-cost molecular methods and high resolution photographs. We describe emerging technologies that will facilitate this taxonomic development. We believe that a new golden age of biodiversity exploration may be dawning, just as biodiversity itself is most threatened, and are hopeful that increasing knowledge of biodiversity will be a positive force to slow its loss.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

Notes

  1. http://www.asianplant.net/.

  2. http://digir.net/.

  3. http://www.tdwg.org/activities/tapir/specification.

  4. http://www.gbif.org/.

  5. http://ibis.biologi.lipi.go.id/.

  6. http://www.biotrop.org/database.php.

  7. http://www.konservasi-laut.net/.

  8. http://rmbr.nus.edu.sg/databases/.

  9. http://dps.plants.ox.ac.uk/bol/singapore.

  10. http://ebird.org/, and http://www.birds.cornell.edu/netcommunity/citsci/.

  11. http://www.usanpn.org/.

  12. http://mushroomobserver.org/.

  13. http://www.greatsunflower.org/.

  14. http://floron.nl/.

  15. http://reefcheck.org/.

  16. See links at: http://citizensci.com/.

  17. http://phylodiversity.net/xmalesia/.

  18. For example, the DiGIR schema: http://digir.net/schema/protocol/2003/1.0/digir.xsd.

  19. http://www.tdwg.org/.

  20. See, e.g., the schema at: http://phylodiversity.net/xmalesia/schema/xmalesia.rnc.

  21. http://www.biodiversitylibrary.org/.

  22. http://drupal.org/.

  23. http://www.mediawiki.org/.

  24. http://recaptcha.net/.

  25. http://semantic-mediawiki.org/.

  26. http://www.mediawiki.org/wiki/Extension:Semantic_Forms.

  27. http://www.bic.nus.edu.sg/, http://www.eijkman.go.id/Research/Bioinformatics.

  28. http://www.cate-project.org/.

  29. http://www.editwebrevisions.info/.

  30. http://scratchpads.eu/.

  31. e.g., http://www.nhm.ac.uk/solanaceaesource/, http://silurus.acnatsci.org/.

References

  • Adamowicz SJ, Purvis A (2005) How many branchiopod crustacean species are there? Quantifying the components of underestimation. Glob Ecol Biogeogr 14(5):455–468

    Article  Google Scholar 

  • Appanah S (1993) Mass flowering of dipterocarp forests in the aseasonal tropics. J Biosci 18(4):457–474

    Article  Google Scholar 

  • Baraloto C, Ferreira E, Rockwell C, Walthier F (2007) Limitations and applications of parataxonomy for community forest management in southwestern Amazonia. Ethnobot Res Appl 5:77–84

    Google Scholar 

  • Baskauf SJ, Kirchoff BK (2008) Digital plant images as specimens: toward standards for photographing living plants. Vulpia 7:16–30

    Google Scholar 

  • Basset Y, Novotny V, Miller SE, Pyle R (2000) Quantifying biodiversity: experience with parataxonomists and digital photography in Papua New Guinea and Guyana. BioScience 50:899–908

    Article  Google Scholar 

  • Berners-Lee T, Fischetti M (1999) Weaving the Web. Harper, San Francisco

    Google Scholar 

  • Bickford D, Howard SD, Ng DJJ, Sheridan JA (2010) Impacts of climate change on the amphibians and reptiles of Southeast Asia. Biodivers Conserv. doi:10.1007/s10531-010-9782-4

  • Blume CL (1827) Bijdragen tot de flora van Nederlandsch Indie. Ter Lands Drukkerij, Batavia, Indonesia

    Google Scholar 

  • Braschler B (2009) Successfully implementing a citizen-scientist approach to insect monitoring in a resource-poor country. BioScience 59(2):103–104

    Article  Google Scholar 

  • Bryant D, Nielsen D, Tangley L (1997) The last frontier forests: ecosystems & economies on the edge. Technical report, World Resources Institute, Forest Frontiers Initiative, Washington, DC

  • Caruana R, Elhawary M, Munson A, Riedewald M, Sorokina D, Fink D, Hochachka W, Kelling S (2006) Mining citizen science data to predict orevalence of wild bird species. In: Proceedings of the 12th ACM SIGKDD international conference on Knowledge discovery and data mining, pp 909–915

  • CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci 106(31):12794–12797

    Google Scholar 

  • Chao A (1984) Nonparametric estimation of the number of classes in a population. Scand J Stat 11: 265–270

    Google Scholar 

  • Chao A (2006) Species estimation and applications. In: Kotz S, Read CB, Balakrishnan N, Vidakovic B (eds) Encyclopedia of statistical sciences. Wiley, New York, pp 7907–7916

    Google Scholar 

  • Chase MW, Salamin N, Wilkinson M, Dunwell JM, Kesanakurthi RP, Haidar N, Savolainen V (2005) Land plants and DNA barcodes: short-term and long-term goals. Phil Trans R Soc B 360(1462):1889–1895

    Article  CAS  PubMed  Google Scholar 

  • Clark B, Godfray H, Kitching I, Mayo S, Scoble M (2009) Taxonomy as an eScience. Phil Trans A 367(1890):953–966

    Article  Google Scholar 

  • Cohn J (2008) Citizen science: can volunteers do real research? BioScience 58(3):192–197

    Article  Google Scholar 

  • Collar N (1998) Extinction by assumption; or, the Romeo Error on Cebu. Oryx 32(4):239–244

    Article  Google Scholar 

  • Couvet D, Jiguet F, Julliard R, Levrel H, Teyssedre A (2008) Enhancing citizen contributions to biodiversity science and public policy. Interdiscip Sci Rev 33(1):95–103

    Article  Google Scholar 

  • de Carvalho M, Bockmann F, Amorim D, de Vivo M, de Toledo-Piza M, Menezes N, de Figueiredo J, Castro R, Gill A, McEachran J et al (2005) Revisiting the taxonomic impediment. Science 307(5708):353–353

    Article  PubMed  Google Scholar 

  • de Wilde WJJO, Duyfjes BEE (2006) Redefinition of Zehneria and four new related genera (Cucurbitaceae), with an enumeration of the Australasian and Pacific species. Blumea 51:1–88

    Google Scholar 

  • Dolphin K, Quicke DLJ (2001) Estimating the global species richness of an incompletely described taxon: an example using parasitoid wasps (Hymenoptera: Braconidae). Biol J Linn Soc 73(3):279–286

    Article  Google Scholar 

  • Erwin TL (1982) Tropical forests: their richness in Coleoptera and other species. Coleopt Bull 36:74–75

    Google Scholar 

  • Frodin DG (1984) Guide to the Standard Floras of the World. Cambridge University Press, Cambridge, UK

    Google Scholar 

  • Gardner RO (2006) Piper (Piperaceae) in the Philippine islands: the climbing species. Blumea 51:569–586

    Google Scholar 

  • Giam X, Ng TH, Yap VB, Tan HTW (2010) The extent of undiscovered species in Southeast Asia. Biodivers Conserv. doi:10.1007/s10531-010-9792-2

  • Godfray HCJ (2002) Challenges for taxonomy. Nature 417:17–19

    Article  CAS  PubMed  Google Scholar 

  • Graham J, Simpson A, Crall A, Jarnevich C, Newman G, Stohlgren T (2008) Vision of a cyberinfrastructure for nonnative, invasive species management. BioScience 58(3):263–268

    Article  Google Scholar 

  • Greenwood JJD (2007) Citizens, science and bird conservation. J Ornithol 148:S77–S124

    Article  Google Scholar 

  • Guralnick R, Hill A (2009) Biodiversity informatics: automated approaches for documenting global biodiversity patterns and processes. Bioinformatics 25(4):421–428

    Article  CAS  PubMed  Google Scholar 

  • Hawksworth DL, Rossman AY (1997) Where are all the undescribed fungi? Phytopathology 87:888–891

    Article  CAS  PubMed  Google Scholar 

  • Hibbett DS, Nilsson RH, Snyder M, Fonseca M, Costanzo J, Shonfeld M (2005) Automated phylogenetic taxonomy: an example in the Homobasidiomycetes (mushroom-forming fungi). Syst Biol 54:660–668

    Article  PubMed  Google Scholar 

  • Hyde K (2003) Mycology in the future in the Asia-Pacific region. Fungal Divers 13:59–68

    Google Scholar 

  • Janzen DH (1986) Blurry catastrophes. Oikos 47:1–2

    Article  Google Scholar 

  • Janzen DH, Hallwachs W, Blandin P, Burns JM, Cadiou J, Chacon I, Dapkey T, Deans AR, Epstein ME, Espinoza B, Franclemont JG, Haber WA, Hajibabaei M, Hall JPW, Hebert PDN, Gauld ID, Harvey DJ, Hausmann A, Kitching IJ, Lafontaine D, Landry J, Lemaire C, Miller JY, Miller JS, Miller L, Miller SE, Montero J, Munroe E, Green SR, Ratnasingham S, Rawlins JE, Robbins RK, Rodriguez JJ, Rougerie R, Sharkey MJ, Smith MA, Solis MA, Sullivan JB, Thiaucourt P, Wahl DB, Weller SJ, Whitfield JB, Willmott KR, Wood DM, Woodley NE, Wilson JJ (2009) Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity. Mol Ecol Resour 9(s1):1–26

    Article  CAS  Google Scholar 

  • Johnson NF (2007) Biodiversity informatics. Annu Rev Entomol 52:421–438

    Article  CAS  PubMed  Google Scholar 

  • Kelling S, Hochachka W, Fink D, Riedewald M, Caruana R, Ballard G, Hooker G (2009) Data-intensive science: a new paradigm for biodiversity studies. BioScience 59(7):613–620

    Article  Google Scholar 

  • Kress W (2004) Paper floras: how long will they last? A review of Flowering Plants of the Neotropics. Am J Bot 91(12):2124–2127

    Article  Google Scholar 

  • Lawrence A (2009) The first cuckoo in winter: phenology, recording, credibility and meaning in Britain. Glob Environ Change 19(2):173–179. Traditional Peoples and Climate Change

    Article  Google Scholar 

  • Lee M (2000) A worrying systematic decline. Trends Ecol Evol 15(8):346–348

    Article  PubMed  Google Scholar 

  • Mace G (2004) The role of taxonomy in species conservation. Philos Trans 359(1444):711–719

    Article  Google Scholar 

  • Mace G, Masundire H, Baillie J et al (2005) Biodiversity. In: Hassan RM, Scholes R, Ash N (eds) Ecosystems and human well-Being: current state and trends. Findings of the Condition and Trends Working Group. Millennium Ecosystem Assessment, Chap. 4. Island Press, Washington, DC

  • May RM (1988) How many species are there on earth? Science 247:1441–1449

    Article  Google Scholar 

  • May R, Lawton J, Stork N (1995) Assessing extinction rates. In: Lawton JH, May RM, Maurer BA (eds) Extinction rates. Oxford University Press, Oxford, pp 1–24

    Google Scholar 

  • Mayo SJ, Allkin R, Baker W, Blagoderov V, Brake I, Clark B, Govaerts R, Godfray C, Haigh A, Hand R, Harman K, Jackson M, Kilian N, Kirkup DW, Kitching I, Knapp S, Lewis GP, Malcolm P, von Raab-Straube E, Roberts DM, Scoble M, Simpson DA, Smith C, Smith V, Villalba S, Walley L, Wilkin P (2008) Alpha e-taxonomy: responses from the systematics community to the biodiversity crisis. Kew Bull 63:1–16

    Article  Google Scholar 

  • 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. Conserv Biol 18:478–488

    Article  Google Scholar 

  • Meier R, Shiyang K, Vaidya G, Ng PKL (2006) DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst Biol 55:715–728

    Article  PubMed  Google Scholar 

  • Miquel FAW (1859) Flora van Nederlandsch Indie. C. G. van der Post, Amsterdam, The Netherlands

    Google Scholar 

  • Nanda M (1997) Against social destruction of science: cautionary tales from the Third World. Monthly Review

  • Novacek M (2008) Engaging the public in biodiversity issues. Proc Natl Acad Sci 105(Suppl 1):11571–11578

    Article  CAS  PubMed  Google Scholar 

  • Novotny V, Basset Y, Miller SE, Weiblen GD, Bremer B, Cizek L, Drozd P (2002) Low host specificity of herbivorous insects in a tropical forest. Nature 416(6883): 841–844

    Article  CAS  PubMed  Google Scholar 

  • Oliver I, Beattie AJ (1993) A possible method for the rapid assessment of biodiversity. Conserv Biol 7:562–568

    Article  Google Scholar 

  • Page RDM (2006) Taxonomic names, metadata, and the semantic web. Biodivers Inform 3:1–15

    Google Scholar 

  • Peh KSH (2010) Invasive species in Southeast Asia: the knowledge so far. Biodivers Conserv (this volume). doi:10.1007/s10531-009-9755-7

  • Pfeiffer J, Uril Y (2003) The role of indigenous parataxonomists in botanical inventory: from Herbarium Amboinense to Herbarium Floresense. Telopea 10:61–72

    Google Scholar 

  • Raczkowski J, Wenzel J (2007) Biodiversity studies and their foundation in taxonomic scholarship. BioScience 57(11):974–979

    Article  Google Scholar 

  • Raes N, Steege H (2007) A null-model for significance testing of presence-only species distribution models. Ecography 30(5):727–736

    Article  Google Scholar 

  • Roos M (2003) Flora Malesiana 1991–2001: what has been achieved: revitalisation, momentum? What next? Telopea 10:1–10

    Google Scholar 

  • Sanderson M, Boss D, Chen D, Cranston K, Wehe A (2008) The PhyLoTA browser: processing GenBank for molecular phylogenetics research. Syst Biol 57(3):335–346

    Article  PubMed  Google Scholar 

  • Scoble MJ (2004) Unitary or unified taxonomy? Phil Trans R Soc B 359(1444):699–710

    Article  PubMed  Google Scholar 

  • Scotland R, Wortley A (2003) How many species of seed plants are there? Taxon 52:101–104

    Article  Google Scholar 

  • Soberón J, Peterson T (2004) Biodiversity informatics: managing and applying primary biodiversity data. Phil Trans R Soc Lond Ser B 359:689–698

    Article  Google Scholar 

  • Sodhi NS, Brooks TM, Koh LP, Acciaioli G, Erb M, Tan AK-J, Curran LM, Brosius P, Lee TM, Patlis JM, Gumal M, Lee RJ (2006) Biodiversity and human livelihood crises in the Malay archipelago. Conserv Biol 20:1811–1813

    Article  PubMed  Google Scholar 

  • Sodhi NS, Lee TM, Koh LP, Brook BW (2009) A meta-analysis of the impact of anthropogenic forest disturbance on Southeast Asias biotas. Biotropica 41:103–109

    Article  Google Scholar 

  • Sohmer SH (1996) The urgency of documenting plant diversity: the Flora of the Philippines Project —a last chance to study the plant diversity of the Philippines. In: Stuessy TF, Sohmer SH (eds) Sampling the green world. Columbia University Press, New York, pp. 28–40

    Google Scholar 

  • Stork N (1997) Measuring global biodiversity and its decline. In: Reaka-Kudla M, Wilson D, Wilson E (eds) Biodiversity II: Understanding and Protecting our Biological Resources. National Academy Press, Washington, DC, pp 41–68

    Google Scholar 

  • Tongsima W, Tongsima S, Palittapongarnpim P (2008), Outlook on Thailands genomics and computational biology research and development. PLoS Comput Biol 4(7):e1000115

    Article  PubMed  Google Scholar 

  • Tummarello G, Morbidoni C (2008) The DBin platform: A complete environment for Semantic Web Communities. J Web Semant 6(4):257–265. Semantic Web Challenge 2006/2007

    Google Scholar 

  • Udell J (2008) A conversation with Janis Dickinson about citizen science. Internet Blog, URL: http://blog.jonudell.net/2008/05/05/a-conversation-with-janis-dickinson-about-citizen-science/

  • van House NA (2002) Digital libraries and practices of trust: networked biodiversity information. Soc Epistemol 16:99–114

    Article  Google Scholar 

  • van Steenis-Kruseman MJ (1950) Cyclopaedia of collectors. Flora Males Ser 1(1):1–639

    Google Scholar 

  • Wee YC, Subaraj R (2009) Citizen science and the gathering of ornithological data in Singapore. Nat Singap 2:27–30

    Google Scholar 

  • Weeks P, Gaston K (1997) Image analysis, neural networks, and the taxonomic impediment to biodiversity studies. Biodivers Conserv 6(2):263–274

    Article  Google Scholar 

  • Wheeler QD (2004) Taxonomic triage and the poverty of phylogeny. Phil Trans R Soc Lond Ser B 359(1444):571–583

    Article  Google Scholar 

  • Wilcove DS, Koh LP (2010) Addressing the threats to biodiversity from oil palm agriculture. Biodivers Conserv. doi:10.1007/s10531-009-9760-x

  • Wortley AH, Scotland RW (2004), Synonymy, sampling and seed plant numbers. Taxon 53: 478–480

    Article  Google Scholar 

  • Zeti AMH, Shamsir MS, Tajul-Arifin K, Merican AF, Mohamed R, Nathan S, Mahadi NM, Napis S, Tan TW (2009) Bioinformatics in Malaysia: hope, initiative, effort, reality, and challenges. PLoS Comput Biol 5(8):e1000457

    Article  PubMed  Google Scholar 

  • Zollinger H (1857) Over het begrip en den omvang eener Flora Malesiana. Natuurkundig Tijdschrift voor Nederlandsch-Indie 13:293–322

    Google Scholar 

Download references

Acknowledgements

Webb would like to thank M. Sanderson, T. Pennington, M. Donoghue, S. Renner, C. Cannon, J. Macklin, L. Lohman and C. Dick for stimulating discussions about these issues, the Government of Indonesia, (MenRisTek FRP, LIPI-PPB, PHKA, and Balai TN Gunung Palung) for assistance and permissions in Indonesia, the Arnold Arboretum and US National Science Foundation for funding, H. Yanto and E. Setiawan for field assistance, and G. Dean and R. Asmarayani for lab assistance. We are grateful to the Leiden herbarium for access to collections data. Finally, we thank the editors of this special issue for the invitation to participate and two anonymous reviewers for their comments.

Author information

Authors and Affiliations

  1. Arnold Arboretum of Harvard University, 22 Divinity Avenue, Cambridge, MA, 02138, USA

    Campbell O. Webb

  2. Herbarium Bogoriense, Bogor, Indonesia

    Campbell O. Webb

  3. Key Laboratory in Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, China

    J. W. Ferry Slik

  4. Herbarium Bogoriense, Research Center for Biology (LIPI), Cibinong Science Center, Cibinong, West Java, Indonesia

    Teguh Triono

Authors
  1. Campbell O. Webb
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. J. W. Ferry Slik
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Teguh Triono
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Campbell O. Webb.

Electronic supplementary material

Below is the link to the electronic supplementary material.

PDF (120 KB)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Webb, C.O., Slik, J.W.F. & Triono, T. Biodiversity inventory and informatics in Southeast Asia. Biodivers Conserv 19, 955–972 (2010). https://doi.org/10.1007/s10531-010-9817-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10531-010-9817-x

Keywords

Search

Navigation