Drawbacks to palaeodistribution modelling: The case of South American seasonally dry forests

Journal of Biogeography

Volumn 40, Issue 2, 2013, Pages 345-358

  Collevatti, Rosane G ^a   Terribile, Levi Carina ^a   de Oliveira, Guilherme ^a   Lima Ribeiro, Matheus S ^a   Nabout, João C ^b   Rangel, Thiago F ^a   Diniz Filho, Jose Alexandre F ^a  

^a FEDERAL UNIVERSITY OF GOIÁS   (Brazil)

^b UNIVERSIDADE ESTADUAL DE GOIÁS   (Brazil)

Author keywords

Cerrado biome; Dry forests; Palaeodistribution models; Pleistocene arc; Pleistocene refugia; Quaternary climatic change; South America; Species distribution modelling

Indexed keywords

BIOME; CERRADO; CLIMATE VARIATION; DRY FOREST; ECOLOGICAL MODELING; FOSSIL RECORD; GENERAL CIRCULATION MODEL; GEOGRAPHICAL DISTRIBUTION; HYPOTHESIS TESTING; MOLECULAR ANALYSIS; PALEOCLIMATE; PHYLOGENY; PHYLOGEOGRAPHY; PHYTOGEOGRAPHY; PLEISTOCENE; REFUGIUM; SEASONALITY; VEGETATION HISTORY;

SOUTH AMERICA;

EID: 84872611344     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/jbi.12005     Document Type: Article

References (85)

1. Allouche, O., Tsoar, A. & Kadmon, R. (2006) Assessing the accuracy of species distribution models: prevalence, Kappa and the true skill statistic (TSS). Journal of Applied Ecology, 43, 1223-1232.
2. Angiosperm Phylogeny Group (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society, 161, 105-121.
3. Araújo, M.B. & New, M. (2007) Ensemble forecasting of species distributions. Trends in Ecology and Evolution, 22, 42-47.
4. Becerra, J.X. (2005) Timing the origin and expansion of the Mexican tropical dry forest. Proceedings of the National Academy of Sciences USA, 102, 10919-10923.
5. Behling, H. & Hooghiemstra, H. (2000) Neotropical savanna environments in space and time: late Quaternary. Interhemispheric climate linkages (ed. by V. Markgraf), pp. 307-323. Academic Press, Oxford.
6. Braconnot, P., Otto-Bliesner, B., Harrison, S. et al. (2007a) Results of PMIP2 coupled simulations of the Mid-Holocene and Last Glacial Maximum - part 1: experiments and large-scale features. Climate of the Past, 3, 261-277.
7. Braconnot, P., Otto-Bliesner, B., Harrison, S. et al. (2007b) Results of PMIP2 coupled simulations of the Mid-Holocene and Last Glacial Maximum - part 2: feedbacks with emphasis on the location of the ITCZ and mid- and high latitudes heat budget. Climate of the Past, 3, 279-296.
8. Braconnot, P., Harrison, S.P., Kageyama, M., Bartlein, P.J., Masson-Delmotte, V., Abe-Ouchi, A., Otto-Bliesner, B. & Zhao, Y. (2012) Evaluation of climate models using palaepclimatic data. Nature Climate Change, 2, 417-424.
9. Brown, K.S. & Ab'Saber, A.N. (1979) Ice-age refuges and evolution in the Neotropics: correlation of paleoclimatical, geomorphological and pedological data with modern biological endemism. Paleoclimas, 5, 1-30.
10. Brunes, T.O., Sequeira, F., Haddad, C.F.B. & Alexandrino, J. (2010) Gene and species trees of a Neotropical group of treefrogs: genetic diversification in the Brazilian Atlantic Forest and the origin of a polyploid species. Molecular Phylogenetics and Evolution, 57, 1120-1133.
11. Buisson, L., Thuiller, W., Casajus, N., Lek, S. & Grenouillet, G. (2010) Uncertainty in ensemble forecasting of species distribution. Global Change Biology, 16, 1145-1157.
12. Burnham, K.P & Anderson, D.R. (2002) Model selection and multimodel inference: a practical information-theoretic approach. Springer, New York.
13. Burnham, R.J. & Graham, A. (1999) The history of Neotropical vegetation: new developments and status. Annals of the Missouri Botanical Garden, 86, 546-589.
14. Burnham, R.J. & Johnson, K.R. (2004) South American palaeobotany and the origins of Neotropical rainforests. Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 1595-1610.
15. Carnaval, A.C. & Moritz, C. (2008) Historical climate modelling predicts patterns of current biodiversity in the Brazilian Atlantic forest. Journal of Biogeography, 35, 1187-1201.
16. Carnaval, A.C., Hickerson, M.J., Haddad, C.F.B., Rodrigues, M.T. & Moritz, C. (2009) Stability predicts genetic diversity in the Brazilian Atlantic forest hotspot. Science, 323, 785-789.
17. Carstens, B.C. & Richards, C.L. (2007) Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution, 61, 1439-1454.
18. Chan, L.M., Brown, J.L. & Yoder, A.D. (2011) Integrating statistical genetic and geospatial methods brings new power to phylogeography. Molecular Phylogenetics and Evolution, 59, 523-537.
19. Colinvaux, P.A., de Oliveira, P.E., Moreno, J.E., Miller, M.C. & Bush, M.B. (1996) A long pollen record from lowland Amazonia: forest and cooling in glacial times. Science, 274, 85-88.
20. Colinvaux, P.A., De Oliveira, P.E. & Bush, M.B. (2000) Amazonian and Neotropical plant communities on glacial time-scales: the failure of the aridity and refuge hypothesis. Quaternary Science Reviews, 19, 141-169.
21. Contoux, C., Ramstein, G. & Jost, A. (2012) Modelling the mid-Pliocene Warm Period climate with the IPSL coupled model and its atmospheric component LMDZ4. Geoscentific Model Development Discussions, 5, 515-548.
22. Cowling, S.A., Maslin, M.A. & Sykes, M.T. (2001) Paleovegetation simulations of lowland Amazonia and implications for Neotropical allopatry and speciation. Quaternary Research, 55, 140-149.
23. Cowling, S.A., Betts, R.A., Cox, P.M., Ettwein, V.J., Jones, C.D., Maslin, M.A. & Spall, S.A. (2004) Contrasting simulated past and future responses of the Amazonian forest to atmospheric change. Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 539-547.
24. Cowling, S.A., Cox, P.M., Jones, C.D., Maslin, M.A., Peros, M. & Spall, S.A. (2008) Simulated glacial and interglacial vegetation across Africa: implications for species phylogenies and trans-African migration of plants and animals. Global Change Biology, 14, 827-840.
25. Diniz-Filho, J.A.F., Bini, L.M., Rangel, T.F., Loyola, R.D., Hof, C., Nogués-Bravo, D. & Araújo, M.B. (2009) Partitioning and mapping uncertainties in ensembles of forecasts of species turnover under climate change. Ecography, 32, 897-906.
26. Diniz-Filho, J.A.F., Nabout, J.C., Bini, L.M., Loyola, R.D., Rangel, T.F., Nogués-Bravo, D. & Araújo, M.B. (2010) Ensemble forecasting shifts in climatically suitable areas for Tropidacris cristata (Orthoptera: Acridoidea: Romaleidae). Insect Conservation and Diversity, 3, 213-221.
27. Dormann, C.F., Purschke, O., García Márquez, J.R., Lautenbach, S. & Schröder, B. (2008) Components of uncertainty in species distribution analysis: a case study of the great grey shrike. Ecology, 89, 3371-3386.
28. Elith, J. & Leathwick, J.R. (2009) Species distribution models: ecological explanation and prediction across space and time. Annual Review of Ecology, Evolution, and Systematics, 40, 677-697.
29. Elith, J., Kearney, M. & Phillips, S. (2011) The art of modelling range-shifting species. Methods in Ecology and Evolution, 1, 330-342.
30. Fitzpatrick, M.C. & Hargrove, W.W. (2009) The projection of species distribution models and the problem of non-analog climate. Biodiversity and Conservation, 18, 2255-2261.
31. Franklin, J. (2009) Mapping species distribution: spatial inference and prediction. Cambridge University Press, Cambridge.
32. Furley, P.A. & Ratter, J.A. (1988) Soil resources and plant communities of the central Brazilian cerrado and their development. Journal of Biogeography, 15, 97-108.
33. Giovanni, R., Bernacci, L.C., Siqueira, M.F. & Rocha, F.S. (2012) The real task of selecting records for ecological niche modeling. Natureza & Conservação, 10, in press.
34. Haberle, S.G. & Maslin, M.A. (1999) Late Quaternary vegetation and climate change in the Amazon basin based on a 50 000 year pollen record from the Amazon fan, PDP site 932. Quaternary Research, 51, 27-38.
35. Haffer, J. (1969) Speciation in Amazonian forest birds. Science, 165, 131-137.
36. van der Hammen, T. (1974) The Pleistocene changes of vegetation and climate in tropical South America. Journal of Biogeography, 1, 3-26.
37. van der Hammen, T. & Absy, M.L. (1994) Amazonia during the last glacial. Palaeogeography, Palaeoclimatology, Palaeoecology, 109, 247-261.
38. Hijmans, R.J. & Graham, C.H. (2006) The ability of climate envelope models to predict the effect of climate change on species distributions. Global Change Biology, 12, 2272-2281.
39. IBGE (2011) Mapas iterativos. Instituto Brasileiro de Geografia e Estatística. Available at: http://www.ibge.gov.br/mapas_ibge/ (accessed 18 October 2011).
40. JBRJ (2011) Jabot - Banco de Dados da Flora Brasileira. Instituto de Pesquisas Jardim Botânico do Rio de Janeiro. Available at: http://www.jbrj.gov.br (accessed 5 May 2011).
41. Kageyama, M., Braconnot, P., Bopp, L., Caubel, A., Foujols, M.-A., Guilyardi, E., Khodri, M., Lloyd, J., Lombard, F., Mariotti, V., Marti, O., Roy, T. & Woillez, M.-N. (2012) Mid-Holocene and Last Glacial Maximum climate simulations with the IPSL model: new features with the IPSL_CM-5A version. Climate Dynamics, in press.
42. Knowles, L.L., Carstens, B.C. & Keat, M.L. (2007) Coupling genetic and ecological-niche models to examine how past population distributions contribute to divergence. Current Biology, 17, 940-946.
43. Lorenzen, E.D., Nogués-Bravo, D., Orlando, L. et al. (2011) Species-specific responses of Late Quaternary megafauna to climate and humans. Nature, 479, 359-365.
44. Marske, K.A., Leschen, R.A.B. & Buckley, T.R. (2011) Reconciling phylogeography and ecological niche models for New Zealand beetles: looking beyond glacial refugia. Molecular Phylogenetics and Evolution, 59, 89-102.
45. Martínez-Meyer, E. & Peterson, A.T. (2006) Conservatism of ecological niche characteristics in North American plant species over the Pleistocene-to-Recent transition. Journal of Biogeography, 33, 1779-1789.
46. Martínez-Meyer, E., Peterson, A.T. & Hargrove, W.W. (2004) Ecological niches as stable distributional constraints on mammal species, with implications for Pleistocene extinctions and climate change projections for biodiversity. Global Ecology and Biogeography, 13, 305-314.
47. Mayle, F.E. (2004) Assessment of the Neotropical dry forest refugia hypothesis in the light of palaeoecological data and vegetation model simulations. Journal of Quaternary Science, 19, 713-720.
48. Mayle, F.E. (2006) The Late Quaternary biogeography history of South American seasonally dry forests: insights from paleo-ecological data. Neotropical savannas and seasonally dry forests - plant diversity, biogeography, and conservation (ed. by R.T. Pennington, G.P. Lewis and J.A. Ratter), 395-416. CRC Taylor and Francis, New York.
49. Mayle, F.E., Beerling, D.J., Gosling, W.D. & Bush, M.B. (2004) Responses of Amazonian ecosystems to climatic and atmospheric carbon dioxide changes since the Last Glacial Maximum. Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 499-514.
50. Mayle, F.E., Langstroth, R.P., Fisher, R.A. & Meir, P. (2007) Long-term forest-savannah dynamics in the Bolivian Amazon: implications for conservation. Philosophical Transactions of the Royal Society B: Biological Sciences, 362, 291-307.
51. McPherson, J.M. & Jetz, W. (2007) Effect of species' ecology on the accuracy of distribution models. Ecography, 30, 135-151.
52. Mooney, H.A., Bullock, S.H. & Medina, E. (1995) Introduction. Seasonally dry tropical forests (ed. by S.H. Bullock, H.A. Mooney and E. Medina), pp. 1-8. Cambridge University Press, Cambridge.
53. Nogués-Bravo, D. (2009) Predicting the past distribution of species climatic niches. Global Ecology and Biogeography, 18, 521-531.
54. Nogués-Bravo, D., Rodríguez, J., Hortal, J., Batra, P. & Araújo, M.B. (2008) Climate change, humans, and the extinction of the woolly mammoth. PLoS Biology, 6, e79.
55. Oliveira-Filho, A.T. & Ratter, J.A. (1995) A study of the origin of central Brazilian forests by the analysis of plant species distribution patterns. Edinburgh Journal of Botany, 52, 141-194.
56. Oliveira-Filho, A.T. & Ratter, J.A. (2002) Vegetation physionomies and woody flora of the cerrado biome. The cerrados of Brazil: ecology and natural history of a Neotropical savanna (ed. by P.S. Oliveira and R.J. Marquis), pp. 91-120. Columbia University Press, New York.
57. Oliveira-Filho, A.T., Jarenkow, J.A. & Rodal, M.J.N. (2006) Floristic relationships of seasonally dry forests of eastern South America based on tree species distribution patterns. Neotropical savannas and seasonally dry forests: plant diversity, biogeography, and conservation (ed. by R.T. Pennington, G.P. Lewis and J.A. Ratter), pp. 159-192. CRC Press, London.
58. Pennington, R.T., Prado, D.E. & Pendry, C.A. (2000) Neotropical seasonally dry forests and Quaternary vegetation changes. Journal of Biogeography, 27, 261-273.
59. Pennington, R.T., Lewis, G.P. & Ratter, J.A. (2006) An overview of the plant diversity, biogeography and conservation of Neotropical savannas and seasonally dry forests. Neotropical savannas and seasonally dry forests: plant diversity, biogeography, and conservation (ed. by R.T. Pennington, G.P. Lewis and J.A. Ratter), pp. 193-211. CRC Press, London.
60. Peterson, A.T., Soberón, J., Pearson, R.G., Anderson, R.P., Martínez-Meyer, E., Nakamura, M. & Araújo, M.B. (2011) Ecological niches and geographic distributions. Princeton University Press, Princeton, NJ.
61. Pires, J.M. & Prance, G.T. (1984) The Amazon Forest. The Amazon - limnology and landscape ecology of mighty tropical river and its basin (ed. by H. Sioli), pp. 581-602. Junk, Dordrecht.
62. Prado, D.E. (1993a) What is the Gran Chaco vegetation in South America? I. A review Candollea, 48, 145-172.
63. Prado, D.E. (1993b) What is the Gran Chaco vegetation in South America? II. A redefinition Candollea, 48, 615-629.
64. Prado, D.E. (2000) Seasonally dry forests of tropical South America: from forgotten ecosystems to a new phytogeographic unit. Edinburgh Journal of Botany, 57, 437-461.
65. Prado, D.E. & Gibbs, P.E. (1993) Patterns of species distributions in the dry seasonal forests of South America. Annals of the Missouri Botanical Garden, 80, 902-927.
66. Prance, G.T. (1973) Phytogeographic support for the theory of Pleistocene forest refuges in the Amazon Basin, based upon evidence from distribution patterns in Caryocaraceae, Chrysobalanaceae, Dichapetalaceae and Lecythidaceae. Acta Amazonica, 3, 5-28.
67. Queiroz, L.P. (2006) The Brazilian caatinga: phytogeographical patterns inferred from distribution data of the Leguminosae. Neotropical savannas and seasonally dry forests: plant diversity, biogeography, and conservation (ed. by R.T. Pennington, G.P. Lewis and J.A. Ratter), pp. 121-158. CRC Press, London.
68. Randall, D.A., Wood, R.A., Bony, S., Colman, R., Fichefet, T., Fyfe, J., Kattsov, V., Pitman, A., Shukla, J., Srinivasan, J., Stouffer, R.J., Sumi, A. & Taylor, K.E. (2007). Climate models and their evaluation. Climate Change 2007: the physical science basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change (ed. by S. Solomon, D. Qin, M. Manning, Z. Chen, M. Marquis, K.B. Averyt, M. Tignor and H.L. Miller). Cambridge University Press, Cambridge.
69. Richards, C.L., Carstens, B.C. & Knowles, L.L. (2007) Distribution modelling and statistical phylogeography: an integrative framework for generating and testing alternative biogeographical hypotheses. Journal of Biogeography, 34, 1833-1845.
70. Salgado-Labouriau, M.L. (1997) Late Quaternary paleoclimate in the savannas of South America. Journal of Quaternary Science, 12, 371-379.
71. Santika, T. (2011) Assessing the effect of prevalence on predictive performance of species distribution models using simulated data. Global Ecology and Biogeography, 20, 181-192.
72. Sokal, R.R. & Rohlf, F.J. (1995) Biometry: the principles and practice of statistics in biological research, 3rd edn. W. H. Freeman and Company, New York.
73. Spichiger, R., Bise, B., Calenge, C. & Chatelain, C. (2006) Biogeography of the forests of the Paraguay-Paraná basin. Neotropical savannas and seasonally dry forests: plant diversity, biogeography, and conservation (ed. by R.T. Pennington, G.P. Lewis and J.A. Ratter), pp. 193-211. CRC Press, London.
74. Svenning, J.-C., Fløjgaard, C., Marske, K.A. & Nógues-Bravo, D. (2011) Applications of species distribution modeling to paleobiology. Quaternary Science Reviews, 30, 21-22.
75. Taylor, K.E., Stouffer, R.J. & Meehl, G.A. (2012) An overview of CMIP5 and the experiment design. Bulletin of the American Meteorological Society, 93, 485-498.
76. Thuiller, W. (2003) BIOMOD - optimizing predictions of species distributions and projecting potential future shifts under global change. Global Change Biology, 9, 1353-1362.
77. Thuiller, W., Lafourcade, B., Engler, R. & Araújo, M.B. (2009) BIOMOD - a platform for ensemble forecasting of species distributions. Ecography, 32, 369-373.
78. Vanzolini, P.E. (1963) Problemas faunísticos do cerrado. Simpósio sobre o cerrado (ed. by M.G. Ferri), pp. 307-320. University of São Paulo Press, São Paulo.
79. Varela, S., Lobo, J.M., Rodríguez, J. & Batra, P. (2010) Were the Late Pleistocene climatic changes responsible for the disappearance of the European spotted hyena populations? Hindcasting a species geographic distribution across time. Quaternary Science Reviews, 29, 2027-2035.
80. Varela, S., Lobo, J.M. & Hortal, J. (2011) Using species distribution models in paleobiogeography: a matter of data, predictors and concepts. Palaeogeography, Palaeoclimatology, Palaeoecology, 310, 451-463.
81. Waltari, E., Hijmans, R.J., Peterson, A.T., Nyári, A.S., Perkins, S.L. & Guralnick, R.P. (2007) Locating Pleistocene refugia: comparing phylogeographic and ecological niche model predictions. PLoS ONE, 7, e563.
82. Webber, B.L., Yates, C.J., Le Maitre, D.C., Scott, J.K., Kriticos, D.J., Ota, N., McNeill, A., Le Roux, J.J. & Midgley, G.F. (2011) Modelling horses for novel climate courses: insights from projecting potential distributions of native and alien Australian acacias with correlative and mechanistic models. Diversity and Distributions, 17, 978-1000.
83. Werneck, F.P., Costa, G.C., Colli, G.R., Prado, D.E. & Sites, J.W. (2011) Revisiting the historical distribution of seasonally dry tropical forests: new insights based on palaeodistribution modelling and palynological evidence. Global Ecology and Biogeography, 20, 272-288.
84. Werneck, F.P., Nogueira, C., Colli, G.R., Sites, J.W. & Costa, G.C. (2012) Climatic stability in the Brazilian Cerrado: implications for biogeographical connections of South American savannas, species richness and conservation in a biodiversity hotspot. Journal of Biogeography, 39, 1695-1706.
85. Woodward, F.I., Lomas, M.R. & Kelly, C.K. (2004) Global climate and the distribution of plant biomes. Philosophical Transactions of the Royal Society B: Biological Sciences, 359, 1465-1476.