Limited sampling hampers "big data" estimation of species richness in a tropical biodiversity hotspot

Ecology and Evolution

Volumn 5, Issue 3, 2015, Pages 807-820

  Engemann, Kristine ^a   Enquist, Brian J ^b   Sandel, Brody ^a   Boyle, Brad ^b   Jørgensen, Peter M ^c   Morueta Holme, Naia ^d   Peet, Robert K ^e   Violle, Cyrille ^f   Svenning, Jens Christian ^a  

^a AARHUS UNIVERSITY   (Denmark)

^b UNIVERSITY OF ARIZONA   (United States)

^c MISSOURI BOTANICAL GARDEN   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF NORTH CAROLINA   (United States)

^f UNIV MONTPELLIER   (France)

Author keywords

Ecuador; Rarefaction; Resampling; Richness estimation; Sampling effort

Indexed keywords

EID: 84922756988     PISSN: None     EISSN: 20457758     Source Type: Journal    
DOI: 10.1002/ece3.1405     Document Type: Article

References (62)

1. Balslev, H. 1988. Distribution patterns of Ecuadorean plant species. Taxon 37:567-577.
2. Bass, M. S., M. Finer, C. N. Jenkins, H. Kreft, D. F. Cisneros-Heredia, S. F. McCracken, et al. 2010. Global conservation significance of Ecuador's Yasuní National Park. PLoS ONE 5:e8767.
3. Bebber, D. P., M. A. Carine, G. Davidse, D. J. Harris, E. M. Haston, M. G. Penn, et al. 2012. Big hitting collectors make massive and disproportionate contribution to the discovery of plant species. Proc. R. Soc. B Biol. Sci. 279:2269-2274.
4. Beck, J., L. Ballesteros-Mejia, C. M. Buchmann, J. Dengler, S. A. Fritz, B. Gruber, et al. 2012. What's on the horizon for macroecology? Ecography 35:673-683.
5. BIEN. 2013. Available at http://bien.nceas.ucsb.edu/bien/ (accessed May 30, 2013).
6. Botkin, D. B., H. Saxe, M. B. Araújo, R. Betts, R. H. W. Bradshaw, T. Cedhagen, et al. 2007. Forecasting the effects of global warming on biodiversity. Bioscience 57:227-236.
7. Boyle, B., N. Hopkins, Z. Lu, J. A. Raygoza Garay, D. Mozzherin, T. Rees, et al. 2013. The taxonomic name resolution service: an online tool for automated standardization of plant names. BMC Bioinformatics 14:16.
8. Chao, A. 1984. Non-parametric estimation of the number of classes in a population. Scand. J. Stat. 11:265-270.
9. Chao, A., N. J. Gotelli, T. C. Hsieh, E. L. Sander, K. H. Ma, R. K. Colwell, et al. 2014. Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. Ecol. Monogr. 84:45-67.
10. Colwell, R. K., A. Chao, N. J. Gotelli, S.-Y. Lin, C. X. Mao, R. L. Chazdon, et al. 2012. Models and estimators linking individual-based and sample-based rarefaction, extrapolation and comparison of assemblages. J. Plant Ecol. 5:3-21.
11. Conservation International. 2007. Available at: http://www.conservation.org/where/priority_areas/hotspots/Pages/hotspots_main.aspx (accessed August 25, 2014).
12. Distler, T., P. M. Jørgensen, P. M. Jørgensen, A. Graham, G. Davidse, and I. Jiménez. 2009. Determinants and prediction of broad-scale plant richness across the Western Neotropics 1. Ann. Mo. Bot. Gard. 96:470-491.
13. Dodson, C. H., and A. H. Gentry. 1991. Biological extinction in western Ecuador. Ann. Mo. Bot. Gard. 78:273-295.
14. Dubuis, A., J. Pottier, V. Rion, L. Pellissier, J.-P. Theurillat, and A. Guisan. 2011. Predicting spatial patterns of plant species richness: a comparison of direct macroecological and species stacking modelling approaches. Divers. Distrib. 17:1122-1131.
15. Efron, B. 1981. Nonparametric estimates of standard error: the jackknife, the bootstrap and other methods. Biometrika 68:589-599.
16. Elith, J., C. H. Graham, R. P. Anderson, M. Dudík, S. Ferrier, A. Guisan, et al. 2006. Novel methods improve prediction of species' distributions from occurrence data. Ecography 29:129-151.
17. Enquist, B. J., R. Condit, B. Peet, M. Schildhauer, B. Thiers, and BIEN working group. 2009. The Botanical and Information Ecology Network (BIEN): Cyberinfrastructure for an integrated botanical information network to investigate the ecological impacts of global climate change on plant biodiversity. Available at http://www.iplantcollaborative.org/sites/default/files/BIEN_White_Paper.pdf (accessed 25 August 2014).
18. Ferrier, S. 2002. Mapping spatial pattern in biodiversity for regional conservation planning: where to from here? Syst. Biol. 51:331-363.
19. Field, R., B. A. Hawkins, H. V. Cornell, D. J. Currie, J. A. F. Diniz-Filho, J.-F. Guégan, et al. 2009. Spatial species-richness gradients across scales: a meta-analysis. J. Biogeogr. 36:132-147.
20. Fisher, R. A., A. S. Corbet, and C. B. Williams. 1943. The relation between the number of species and the number of individuals in a random sample of an animal population. J. Anim. Ecol. 12:42-58.
21. Gamito, S. 2010. Caution is needed when applying Margalef diversity index. Ecol. Ind. 10:550-551.
22. Gentry, A. H. 1982. Neotropical floristic diversity: phytogeographical connections between Central and South America, Pleistocene climatic fluctations, or an accident of the Andean origeny? Ann. Mo. Bot. Gard. 69:557-593.
23. Gentry, A. H. 1988. Changes in plant community diversity and floristic composition on environmental and geographical gradients. Ann. Mo. Bot. Gard. 75:1-34.
24. Gotelli, N. J., and R. K. Colwell. 2001. Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness. Ecol. Lett. 4:379-391.
25. Green, J. L., A. Hastings, P. Arzberger, F. J. Ayala, K. L. Cottingham, K. Cuddington, et al. 2005. Complexity in ecology and conservation: mathematical, statistical, and computational challenges. Bioscience 55:501-510.
26. Hawkins, B. A., R. Field, H. V. Cornell, D. J. Currie, J.-F. Guégan, D. M. Kaufman, et al. 2003. Energy, water, and broad-scale geographic patterns of species richness. Ecology 84:3105-3117.
27. Hellmann, J. J., and G. W. Fowler. 1999. Bias, precision, and accuracy of four measures of species richness. Ecol. Appl. 9:824-834.
28. Heltshe, J. F., and N. E. Forrester. 1983. Estimating species richness using the jackknife procedure. Biometrics 39:1-11.
29. Hijmans, R. J., S. E. Cameron, J. L. Parra, P. G. Jones, and A. Jarvis. 2005. Very high resolution interpolated climate surfaces for global land areas. Int. J. Climatol. 25:1965-1978.
30. Hurlbert, S. H. 1971. The nonconcept of species diversity: a critique and alternative parameters. Ecology 52:577.
31. Ibáñez, I., J. S. Clark, M. C. Dietze, K. Feeley, M. Hersh, S. LaDeau, et al. 2006. Predicting biodiversity change: outside the climate envelope, beyond the species-area curve. Ecology 87:1896-1906.
32. Jiménez, I., T. Distler, and P. M. Jørgensen. 2009. Estimated plant richness pattern across northwest South America provides similar support for the species-energy and spatial heterogeneity hypotheses. Ecography 32:433-448.
33. Jørgensen, P. M., and S. León-Yánez. 1999. Catalogue of the vascular plants of Ecuador. Monogr. Syst. Bot. Missouri Bot. Gard. 75:1-1182.
34. Kadmon, R., O. Farber, and A. Danin. 2004. Effect of roadside bias on the accuracy of predictive maps produced by bioclimatic models. Ecol. Appl. 14:401-413.
35. Kreft, H., and W. Jetz. 2007. Global patterns and determinants of vascular plant diversity. Proc. Natl Acad. Sci. USA 104:5925-5930.
36. Lavoie, C. 2013. Biological collections in an ever changing world: herbaria as tools for biogeographical and environmental studies. Perspect. Plant Ecol. Evol. Syst. 15:68-76.
37. Loiselle, B. A., P. M. Jørgensen, T. Consiglio, I. Jiménez, J. G. Blake, L. G. Lohmann, et al. 2007. Predicting species distributions from herbarium collections: does climate bias in collection sampling influence model outcomes? J. Biogeogr. 35:105-116.
38. Malcolm, J. R., C. Liu, R. P. Neilson, L. Hansen, and L. Hannah. 2006. Global warming and extinctions of endemic species from biodiversity hotspots. Conserv. Biol. 20:538-548.
39. Margalef, R. 1958. Information theory in ecology. Gen. Syst. 3:36-71.
40. Margules, C. R., and R. L. Pressey. 2000. Systematic conservation planning. Nature 405:243-253.
41. Mateo, R. G., M. de la Estrella, Á. M. Felicísimo, J. Muñoz, and A. Guisan. 2013. A new spin on a compositionalist predictive modelling framework for conservation planning: a tropical case study in Ecuador. Biol. Conserv. 160:150-161.
42. McGill, B. J. 2010. Matters of scale. Science 328:575-576.
43. Myers, N., R. A. Mittermeier, C. G. Mittermeier, G. A. da Fonseca, and J. Kent. 2000. Biodiversity hotspots for conservation priorities. Nature 403:853-858.
44. Nagelkerke, N. J. D. 1991. A note on a general definition of the coefficient of determination. Biometrika 78:691-692.
45. Peet, R. K. 1974. The measurement of species diversity. Annu. Rev. Ecol. Syst. 5:285-307.
46. Plotkin, J. B., M. D. Potts, D. W. Yu, S. Bunyavejchewin, R. Condit, R. Foster, et al. 2000. Predicting species diversity in tropical forests. Proc. Natl Acad. Sci. 97:10850-10854.
47. Quinn, G. P., and M. J. Keough. 2002. Experimental design and data analysis for biologists. Cambridge University Press, Cambridge.
48. R Core Team. 2013. R: A language end environment for statistical computing.
49. Rahbek, C. 1995. The elevational gradient of species richness: a uniform pattern? Ecography 18:200-205.
50. Reddy, S., and L. M. Da. 2003. Geographical sampling bias and its implications for conservation priorities in Africa. J. Biogeogr. 30:1719-1727.
51. Schulman, L., T. Toivonen, and K. Ruokolainen. 2007. Analysing botanical collecting effort in Amazonia and correcting for it in species range estimation. J. Biogeogr. 34:1388-1399.
52. Shaffer, H. B., R. N. Fisher, and C. Davidson. 1998. The role of natural history collections in documenting species declines. Trends Ecol. Evol. 13:27-30.
53. Sheth, S. N., L. G. Lohmann, T. Distler, and I. Jiménez. 2012. Understanding bias in geographic range size estimates. Glob. Ecol. Biogeogr. 21:732-742.
54. Skov, F., and F. Borchsenius. 1997. Predicting plant species distribution patterns using simple climatic parameters: a case study of Ecuadorian palms. Ecography 20:347-355.
55. Smith, E. P., and G. Van Belle. 1984. Nonparametric estimation of species richness. Biometrics 40:119-129.
56. Svenning, J.-C., M. C. Fitzpatrick, S. Normand, C. H. Graham, P. B. Pearman, L. R. Iverson, et al. 2010. Geography, topography, and history affect realized-to-potential tree species richness patterns in Europe. Ecography 33:1070-1080.
57. Ter Steege, H., N. C. A. Pitman, D. Sabatier, C. Baraloto, R. P. Salomão, J. E. Guevara, et al. 2013. Hyperdominance in the Amazonian tree flora. Science 342:1243092.
58. Ugland, K. I., and J. S. Gray. 2004. Estimation of species richness : analysis of the methods developed by Chao and Karakassis. Mar. Ecol. Prog. Ser. 284:1-8.
59. Ulloa, C. U., B. León, S. León-Yánez, S. G. Beck, M. Nee, J. L. Zarucchi, et al. 2011. Regional patterns of vascular plant diversity and endemism. Pp. 192-203 in Climate change and biodiversity in the tropical Andes. São José dos Campos, IAI for Climate Change Research-SCOPE. Available at http://www.iai.int/files/communications/publications/scientific/Climate_Change_and_Biodiversity_in_the_Tropical_Andes/chapter13.pdf. (accessed 24 September 2014).
60. Valencia, R., R. B. Foster, G. Villa, R. Condit, J. C. Svenning, C. Hernández, et al. 2004. Tree species distributions and local habitat variation in the Amazon: large forest plot in eastern Ecuador. J. Ecol. 92:214-229.
61. Whittaker, R. J., M. B. Araújo, P. Jepson, R. J. Ladle, J. E. M. Watson, and K. J. Willis. 2005. Conservation biogeography: assessment and prospect. Divers. Distrib. 11:3-23.
62. Yang, W., K. Ma, and H. Kreft. 2013. Geographical sampling bias in a large distributional database and its effects on species richness-environment models. J. Biogeogr. 40:1415-1426.