Using phylogenetic diversity to identify ancient rain forest refugia and diversification zones in a biodiversity hotspot

Diversity and Distributions

Volumn 21, Issue 3, 2015, Pages 279-289

  Costion, Craig M ^a,b   Edwards, Will ^a   Ford, Andrew J ^c   Metcalfe, Daniel J ^c   Cross, Hugh B ^d   Harrington, Mark G ^a   Richardson, James E ^e,f   Hilbert, David W ^c   Lowe, Andrew J ^b,d   Crayn, Darren M ^a  

^a JAMES COOK UNIVERSITY   (Australia)

^b UNIVERSITY OF ADELAIDE   (Australia)

^c CSIRO   (Australia)

^d State Herbarium of South Australia   (Australia)

^e ROYAL BOTANIC GARDEN EDINBURGH   (United Kingdom)

^f UNIVERSIDAD DE LOS ANDES   (Colombia)

Author keywords

Biome assembly; Conservation prioritization; Gondwanan; Relict species; Sahul; Sunda

Indexed keywords

BIODIVERSITY; BIOGEOGRAPHY; BIOME; LAST GLACIAL; PHYLOGENETICS; PRIORITIZATION; RAINFOREST; REFUGIUM; SPECIES RICHNESS;

ASIA; AUSTRALIA; QUEENSLAND;

EID: 84922537381     PISSN: 13669516     EISSN: 14724642     Source Type: Journal    
DOI: 10.1111/ddi.12266     Document Type: Article

References (47)

1. Adam, P. (1992) Australian rainforests. Clarendon Press, Oxford.
2. Bremer, B., Bremer, K., Chase, M.W., Fay, M.F., Reveal, J.L., Soltis, D.E., Soltis, P.S., Stevens, P.F., Anderberg, A.A., Moore, M.J., Olmstead, R.G., Rudall, P.J., Sytsma, K.J., Tank, D.C., Wurdack, K., Xiang, J.Q.Y., Zmarzty, S. & Angiosperm Phylogeny, G. (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. Burnham, K.P. & Anderson, D.R. (1998) Model selection and inference: a practical information-theoretic approach. Springer-Verlag, New York, 353 p.
4. Byrne, M., Steane, D.A., Joseph, L., Yeates, D.K., Jordan, G.J., Crayn, D., Aplin, K., Cantrill, D.J., Cook, L.G., Crisp, M.D., Keogh, J.S., Melville, J., Moritz, C., Porch, N., Sniderman, J.M.K., Sunnucks, P. & Weston, P.H. (2011) Decline of a biome: evolution, contraction, fragmentation, extinction and invasion of the Australian mesic zone biota. Journal of Biogeography, 38, 1635-1656.
5. Cadotte, M.W. & Davies, T.J. (2010) Rarest of the rare: advances in combining evolutionary distinctiveness and scarcity to inform conservation at biogeographical scales. Diversity and Distributions, 16, 376-385.
6. CBOL Plant Working Group (2009) A DNA barcode for land plants. Proceedings of the National Academy of Sciences USA, 106, 12794-12797.
7. Christophel, D.C. (1981) Tertiary megafossil floras as indicators of floristic associations and paleoclimate. Ecological biogeography of Australia (ed. by A. Keast ), pp. 379-390. Junk, The Hague.
8. Christophel, D.C. (1994) The early tertiary macrofloras of continental Australia. History of the Australian vegetation, cretaceous to recent (ed. by R.S. Hill ), pp. 262-275. Cambridge University Press, New York.
9. Crayn, D.M., Costion, C., Harrington, M.G. (2014) The Sahul-Sunda floristic exchange: dated molecular phylogenies document Cenozoic intercontinental dispersal dynamics. Journal of Biogeography, Early View published 9 September 2014, DOI 10.1111/jbi.12405.
10. Crisp, M.D., Laffan, S., Linder, H.P. & Monro, A. (2001) Endemism in the Australian flora. Journal of Biogeography, 28, 183-198.
11. Crisp, M.D., Isagi, Y., Kato, Y., Cook, L.G. & Bowman, D. (2010) Livistona palms in Australia: ancient relics or opportunistic immigrants? Molecular Phylogenetics and Evolution, 54, 512-523.
12. Davies, T.J. & Buckley, L.B. (2011) Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals. Philosophical Transactions of the Royal Society B, 366, 2414-2425.
13. Davies, T.J., Fritz, S.A., Grenyer, R., Orme, C.D.L., Bielby, J., Bininda-Emonds, O.R.P., Cardillo, M., Jones, K.E., Gittleman, J.L., Mace, G.M. & Purvis, A. (2008) Phylogenetic trees and the future of mammalian biodiversity. Proceedings of the National Academy of Sciences USA, 105, 11556-11563.
14. Dettmann, M.E. (1994) Cretaceous vegetation, the microfossil record. History of the Australian vegetation. Cretaceous to recent (ed. by R.S. Hill ), pp. 143-170. Cambridge University Press, New York.
15. Diniz-Filho, J.A.F. & Bini, L.M. (2005) Modelling geographical patterns in species richness using eigenvector-based spatial filters. Global Ecology and Biogeography, 14, 177-185.
16. Drummond, A.J. & Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
17. Endress, P.K. (1986) Tropical rainforests of North Queensland. Their conservation significance. Special Australian Heritage Publication Series, 3, 1-195.
18. Erwin, T.L. (1991) An evolutionary basis for conservation strategies. Science, 253, 750-752.
19. Faith, D.P. (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation, 61, 1-10.
20. Forest, F., Grenyer, R., Rouget, M., Davies, T.J., Cowling, R.M., Faith, D.P., Balmford, A., Manning, J.C., Proches, S., van der Bank, M., Reeves, G., Hedderson, T.A.J. & Savolainen, V. (2007) Preserving the evolutionary potential of floras in biodiversity hotspots. Nature, 445, 757-760.
21. Fritz, S.A. & Rahbek, C. (2012) Global patterns of amphibian phylogenetic diversity. Journal of Biogeography, 39, 1373-1382.
22. Greenwood, D.R. & Christophel, D.C. (2005) The Origins and Tertiary History of Australian "Tropical" Rainforests. Tropical Rainforests: past, present, and future (ed. by E. Bermingham, C.W. Dick and C. Moritz ), pp. 336-373. University of Chicago Press, Chicago, IL.
23. Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W. & Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic Biology, 59, 307-321.
24. Hijmans, R.J., Guarino, L., Cruz, M. & Rojas, E. (2001) Computer tools for spatial analysis of plant genetic resources data: 1. DIVA-GIS. Plant Genetics Resources Newsletter, 127, 15-19.
25. Hilbert, D.W., Graham, A. & Hopkins, M.S. (2007) Glacial and interglacial refugia within a long-term rainforest refugium: the wet tropics bioregion of NE Queensland, Australia. Palaeogeography Palaeoclimatology Palaeoecology, 251, 104-118.
26. Hill, R.S. (1994) History of the Australian vegetation. Cretaceous to recent. Cambridge University Press, New York.
27. Huang, Y., Dai, Q., Chen, Y., Wan, H., Li, J. & Wang, Y. (2011) Lizard species richness patterns in China and its environmental associations. Biodiversity and Conservation, 20, 1399-1414.
28. Kershaw, A.P. (1988) Australasia. Vegetation history (ed. by B. Huntely and T. Webb III), pp. 237-306. Kluwer academic publishers, Dordrecht.
29. Kershaw, A.P., Moss, P.T. & Wild, R. (2005). Patterns and causes of vegetation change in the Australian Wet Tropics region over the last 10 million years. Tropical rainforests, past, present, and future (ed. by E. Bermingham, C.W. Dick and C. Moritz ), pp. 374-400. University of Chicago Press, Chicago, IL.
30. Kissling, W.D., Eiserhardt, W.L., Baker, W.J., Borchsenius, F., Couvreur, T.L.P., Balslev, H. & Svenning, J.-C. (2012) Cenozoic imprints on the phylogenetic structure of palm species assemblages worldwide. Proceedings of the National Academy of Sciences USA, 109, 7379-7384.
31. Laffan, S.W., Lubarsky, E. & Rosauer, D.F. (2010) Biodiverse, a tool for the spatial analysis of biological and related diversity. Ecography, 33, 643-647.
32. Mace, G.M., Gittleman, J.L. & Purvis, A. (2003) Preserving the tree of life. Science, 300, 1707-1709.
33. May, R.M. (1990) Taxonomy as destiny. Nature, 347, 129-130.
34. Metcalfe, D.J. & Ford, A.J. (2008) Floristics and plant biodiversity of the rainforests of the Wet Tropics. Living in a dynamic tropical forest landscape (ed. by N.E. Stork and S.M. Turton ), pp. 123-132. Blackwell Publishing, Oxford.
35. Polasky, S., Csuti, B., Vossler, C.A. & Meyers, S.M. (2001) A comparison of taxonomic distinctness versus richness as criteria for setting conservation priorities for North American birds. Biological Conservation, 97, 99-105.
36. Rangel, T.F., Diniz-Filho, J.A.F. & Bini, L.M. (2010) SAM: a comprehensive application for Spatial Analysis in Macroecology. Ecography, 33, 46-50.
37. Ratnasingham, S. & Hebert, P.D.N. (2007) BOLD: The Barcode of Life Data System (www.barcodinglife.org). Molecular Ecology Notes, 7, 355-364.
38. Richardson, J.E., Costion, C.M. & Muellner, A.N. (2012) The Malaysian floristic interchange. Biotic evolution and environmental change in Southeast Asia (ed. by D. J Gower, J.E. Richardson, B.R. Rosen, L. Rüber and S.T. Williams ), pp. 138-163. Cambridge University Press, Cambridge.
39. Rodrigues, A.S.L. & Gaston, K.J. (2002) Maximising phylogenetic diversity in the selection of networks of conservation areas. Biological Conservation, 105, 103-111.
40. Rodrigues, A.S.L., Brooks, T.M. & Gaston, K.J. (2005) Integrating phylogenetic diversity in the selection of priority areas for conservation: does it make a difference? Phylogeny and Conservation, 8, 101-119.
41. Sechrest, W., Brooks, T.M., da Fonseca, G.A.B., Konstant, W.R., Mittermeier, R.A., Purvis, A., Rylands, A.B. & Gittleman, J.L. (2002) Hotspots and the conservation of evolutionary history. Proceedings of the National Academy of Sciences USA, 99, 2067-2071.
42. Silvestro, D. & Michalak, I. (2012) raxmlGUI: a graphical front-end for RAxML. Organisms Diversity & Evolution, 12, 335-337.
43. Sniderman, J.M.K. & Jordan, G.J. (2011) Extent and timing of floristic exchange between Australian and Asian rain forests. Journal of Biogeography, 38, 1445-1455.
44. Truswell, E.M., Kershaw, A.P. & Sluiter, I.R. (1987) The Australian-Southeast Asian connection, evidence from the palaeobotanical record. Biogeographical evolution of the Malay archipelago (ed. by T.C. Whitmore ), pp. 32-49. Oxford University Press, Oxford.
45. UNESCO (1988) Decision - 12COM XIV. A - Inscription: Wet Tropics of Queensland. World Heritage List. Available at: http://whc.unesco.org/en/list/486 (accessed 15 July 2012).
46. Webb, C.O. & Donoghue, M.J. (2005) Phylomatic: tree assembly for applied phylogenetics. Molecular Ecology Notes, 5, 181-183.
47. Webb, L.J. & Tracey, J.G. (1981) Australian rainforests, patterns and change. Ecological biogeography of Australia (ed. by A. Keast ), pp. 605-694. Junk, The Hague.