Higher genetic diversity is associated with stable water refugia for a gecko with a wide distribution in arid Australia

Diversity and Distributions

Volumn 19, Issue 8, 2013, Pages 1072-1083

  Duckett, Paul E ^a   Stow, Adam J ^a  

^a MACQUARIE UNIVERSITY   (Australia)

Author keywords

Arid; Australia; Phylogeography; Refugia; Run off; Species distribution modelling

Indexed keywords

ARID REGION; BIODIVERSITY; CONSERVATION GENETICS; CONSERVATION MANAGEMENT; GENETIC VARIATION; LIZARD; MITOCHONDRIAL DNA; NORTHERN HEMISPHERE; PHYLOGEOGRAPHY; PLEISTOCENE; POPULATION DISTRIBUTION; REFUGIUM;

AUSTRALIA;

GEHYRA VARIEGATA; GEKKONIDAE;

EID: 84880131845     PISSN: 13669516     EISSN: 14724642     Source Type: Journal    
DOI: 10.1111/ddi.12089     Document Type: Article

References (75)

1. Arnell, N.W., van Vuuren, D.P. & Isaac, M. (2011) The implications of climate policy for the impacts of climate change on global water resources. Global Environmental Change, 21, 592-603.
2. Arnold, E.N. & Poinar, G. (2008) A 100 million year old gecko with sophisticated adhesive toe pads, preserved in amber from Myanmar. Zootaxa, 1847, 62-68.
3. Australian-Government (2012) Australia's 89 bioregions, Department of Sustainability, Environment, Water, Population and Communities, http://www.environment.gov.au/.
4. Avise, J.C. (2000) Phylogeography: the history and formation of species. Harvard University Press, Cambridge, MA.
5. Barker, W.R. & Greenslade, P.J.M. (1982) Evolution of the flora and fauna of arid Australia. Peacock Publications, Adelaide, SA.
6. Blacket, M.J., Adams, M., Cooper, S.J.B., Krajewski, C. & Westerman, M. (2001) Systematics and evolution of the dasyurid marsupial genus sminthopsis: I. The Macroura species group. Journal of Mammalian Evolution, 8, 149-170.
7. Bowler, J.M., Kotsonis, A. & Lawrence, C.R. (2006) Environmental evolution of the Mallee region, Western Murray Basin. Proceedings of the Royal Society of Victoria, 118, 161-210.
8. Bustard, H.R. (1968) The ecology of the Australian gecko, Gehyra variegata, in northern New South Wales. Journal of Zoology, 154, 113-138.
9. Byrne, M., Tischler, G., Macdonald, B., Coates, D.J. & McComb, J. (2001) Phylogenetic relationships between two rare acacias and their common, widespread relatives in south-western Australia. Conservation Genetics, 2, 157-166.
10. Byrne, M., Yeates, D.K., Joseph, L., Kearney, M., Bowler, J., Williams, M.A.J., Cooper, S., Donnellan, S.C., Keogh, J.S., Leys, R., Melville, J., Murphy, D.J., Porch, N. & Wyrwoll, K.H. (2008) Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota. Molecular Ecology, 17, 4398-4417.
11. Chakraborty, R. (1990) Mitochondrial DNA polymorphism reveals hidden heterogeneity within some Asian populations. American Journal of Human Genetics, 47, 87-94.
12. Chapuis, M.-P. & Estoup, A. (2007) Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution, 24, 621-631.
13. Chapple, D.G., Keogh, J.S. & Hutchinson, M.N. (2004) Molecular phylogeography and systematics of the arid-zone members of the Egernia whitii (Lacertilia: Scincidae) species group. Molecular Phylogenetics and Evolution, 33, 549-561.
14. Clement, M., Posada, D. & Crandall, K.A. (2000) TCS: a computer program to estimate gene genealogies. Molecular Ecology, 10, 1657-1659.
15. Cogger, H.G. (2000) Reptiles and amphibians of Australia. Reed New Holland, Sydney, NSW.
16. Crisp, M. (2006) Biome assembly: what we know and what we need to know. Journal of Biogeography, 33, 1332-1333.
17. Darwin, C. (1859) On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life, 1st edn. John Murray, London.
18. Dempster, A.P., Laird, N.M. & Rubin, D.B. (1977) Maximum likelihood from incomplete data via the EM algorithm. Journal of Royal Statistical Society series B, 39, 1-38.
19. Drummond, A.J. & Rambaut, A. (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7, 214.
20. Drummond, A.J., Ho, S.Y.W., Phillips, M.J. & Rambaut, A. (2006) Relaxed phylogenetics and dating with confidence. PLoS Biology, 4, e88.
21. Duckett, P.E. & Stow, A. (2010) Rapid isolation and characterisation of microsatellite loci from a widespread Australian gecko, the Tree Dtella, Gehyra variegata. Conservation Genetics Resources, 2, 349-351.
22. Duckett, P.E. & Stow, A.J. (2012) Levels of dispersal and tail loss in an Australian gecko (Gehyra variegata) are associated with differences in forest structure. Australian Journal of Zoology, 59, 170-176.
23. Duckett, P.E., Wilson, P.D. & Stow, A.J. (2013) Keeping up with the neighbours: using a genetic measurement of dispersal and species distribution modelling to assess the impact of climate change on an Australian arid zone gecko (Gehyra variegata). Diversity and Distributions, doi: 10.1111/ddi.12071.
24. Elith, J., Kearney, M. & Phillips, S. (2010) The art of modelling range-shifting species. Methods in Ecology and Evolution, 1, 330-342.
25. Excoffier, L., Laval, G. & Scneider, S. (2005) Arlequin version 3.11: an integrated software package for population data analysis. Evolutionary Bioinformatics Online, 1, 47-50.
26. Forstner, M.R.J., Davis, S.K. & Arévalo, E. (1995) Support for the hypothesis of anguimorph ancestry for the suborder serpentes from phylogenetic analysis of mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 4, 93-102.
27. Fu, Y. (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915-925.
28. Fujioka, T., Chappell, J., Honda, M., Yatsevich, I., Fifield, K. & Fabel, D. (2005) Global cooling initiated stony deserts in central Australia 2-4 Ma, dated by cosmogenic 21Ne-10Be. Geology, 33, 993-996.
29. Fujioka, T., Chappell, J., Fifield, L.K. & Rhodes, E.J. (2009) Australian desert dune fields initiated with Pliocene-Pleistocene global climatic shift. Geology, 37, 51-54.
30. Gibbard, P.L., Head, M.J. & Walker, M.J.C. (2010) Formal ratification of the Quaternary System/Period and the Pleistocene Series/Epoch with a base at 2.58 Ma. Journal of Quaternary Science, 25, 96-102.
31. Goudet, J. (2001) FSTAT, a program to estimate an test gene diversities and fixation indices (version 2.9.3), updated from Goudet (1995), Journal of Heredity, 86, 485-486.
32. Guthrie, D.R. (2003) Rapid body size decline in Alaskan Pleistocene horses before extinction. Nature, 426, 169-171.
33. Hamilton, S.K., Bunn, S.E., Thoms, M.C. & Marshall, J.C. (2005) Persistence of aquatic refugia between flow pulses in a dryland river system (Cooper Creek, Australia). Limnology and Oceanography, 50, 743-754.
34. Harpending, H. (1994) Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Human Biology: An International Record of Research, 66, 4.
35. Heads, M. (2005) Dating nodes on molecular phylogenies: a critique of molecular biogeography. Cladistics, 21, 62-78.
36. Heinicke, M.P., Greenbaum, E., Jackman, T.R. & Bauer, A.M. (2011) Phylogeny of a trans-Wallacean radiation (Squamata, Gekkonidae, Gehyra) supports a single early colonization of Australia. Zoologica Scripta, 40, 584-602.
37. Henle, K. (1990) Population ecology and life history of the arboreal gecko Gehyra variegata in arid Australia. Herpetological Monographs, 4, 30-60.
38. Hewitt, G.M. (1996) Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society, 58, 247-276.
39. Hewitt, G.M. (1999) Post-glacial re-colonization of European biota. Biological Journal of the Linnean Society, 68, 87-112.
40. Hewitt, G.M. (2001) Speciation, hybrid zones, and phylogeography- or seeing genes in space and time. Molecular Ecology, 10, 537-549.
41. Hijimans, R.J., Cameron, S.E., Parra, J.L., Jones, P.G. & Jarvis, A. (2005) Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25, 1965-1978.
42. Ho, S.Y.W. & Phillips, M.J. (2009) Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Systematic Biology, 58, 367-380.
43. Hoehn, M. & Sarre, S. (2006) Microsatellite DNA markers for Australian geckos. Conservation Genetics, 7, 795-798.
44. Hughes, L. (2000) Biological consequences of global warming: is the signal already apparent? Trends in Ecology and Evolution, 15, 56-61.
45. IPCC (2007) Summary for policymakers. 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 ), pp. 13-14. Cambridge University Press, Cambridge, UK and New York, NY, USA.
46. King, M. (1979) Karyotypic evolution in Gehyra (Gekkonidae: Reptilia) I. The Gehyra variegata-punctata complex. Australian Journal of Zoology, 27, 373-393.
47. Kitchener, D.J., How, R.A. & Dell, J. (1988) Biology of Oedura reticulata and Gehyra variegata (Gekkonidae) in an isolated woodland of Western Australia. Journal of Herpetology, 22, 401-412.
48. Magee, J.W. & Miller, G.H. (1998) Lake Eyre palaeohydrology from 60 ka to the present: beach ridges and glacial maximum aridity. Palaeogeography, Palaeoclimatology, Palaeoecology, 144, 307-329.
49. McDonald, J.H. & Kreitman, M. (1991) Adaptive protein evolution at the Adh locus in Drosophila. Nature, 351, 652-654.
50. Moritz, C. (1994) Defining 'evolutionary significant units'. Trends in Ecology and Evolution, 9, 373-375.
51. Peakall, R.O.D. & Smouse, P.E. (2006) Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288-295.
52. Phillips, S.J. & Dudík, M. (2008) Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography, 31, 161-175.
53. Phillips, S.J., Anderson, R.P. & Schapire, R.E. (2006) Maximum entropy modeling of species geographic distributions. Ecological Modelling, 190, 231-259.
54. Posada, D. & Crandall, K.A. (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics, 14, 817-818.
55. R Core Development Team (2011) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
56. Rambaut, A. & Drummond, A.J. (2007) Traver v1.5. Available at: http://beast.bio.ed.ac.uk/Tracer (accessed January 2012).
57. Rogers, A.R. & Harpending, H. (1992) Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552-569.
58. Ronquist, F. & Huelsenbeck, J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
59. Rouget, M., Cowling, R.M., Lombard, A.T., Knight, A.T. & Kerley, G.I.H. (2006) Designing large-scale conservation corridors for pattern and process. Conservation Biology, 20, 549-561.
60. Ryder, O.A. (1986) Species conservation and systematics: the dilemma of subspecies. Trends in Ecology and Evolution, 1, 9-10.
61. Sarre, S.D. (1998) Demographics and population persistence of Gehyra variegata (Gekkonidae) following habitat fragmentation. Journal of Herpetology, 32, 153-162.
62. Scoble, J. & Lowe, A.J. (2010) A case for incorporating phylogeography and landscape genetics into species distribution modelling approaches to improve climate adaptation and conservation planning. Diversity and Distributions, 16, 343-353.
63. Sinervo, B., Méndez-de-la-Cruz, F., Miles, D.B., et al. (2010) Erosion of Lizard Diversity by Climate Change and Altered Thermal Niches. Science, 328, 894-899.
64. Sistrom, M., Hutchinson, M., Hutchinson, R. & Donnellan, S. (2009) Molecular phylogeny of Australian Gehyra (Squamata: Gekkonidae) and taxonomic revision of Gehyra variegata in south-eastern Australia. Zootaxa, 2277, 14-32.
65. Slater, M. (1987) Gene flow and the geographic structure of natural populations. Science, 236, 787-792.
66. Stafford Smith, D.M. & Morton, S.R. (1990) A framework for the ecology of arid Australia. Journal of Arid Environments, 18, 255-278.
67. Sunnucks, P. & Hales, D.F. (1996) Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae). Molecular Biology and Evolution, 13, 510-524.
68. Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
69. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011) MEGA 5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28, 2731-2739.
70. Tavare, S. (1986) Some probabilistic and statistical problems in the analysis of DNA sequences. American Mathematical Society, 17, 57-86.
71. Thomas, C.D., Cameron, A., Green, R.E., Bakkenes, M., Beaumont, L.J., Collingham, Y.C., Erasmus, B.F.N., Siqueira, M.F.D, Grainger, A., Hannah, L., Hughes, L., Huntley, B., Jaarsveld, V., Midgley, G.F., Miles, L., Huerta, O., Peterson, A.T., Phillips, O.L. & Williams, S.E. (2004) Extinction risk from climate change. Nature, 427, 145-148.
72. Thuiller, W., Lavorel, S., Araujo, M.B., Sykes, M.T. & Prentice, I.C. (2005) Climate change threats to plant diversity in Europe. Proceedings of the National Academy of Sciences USA, 102, 8245-8250.
73. Vos, C.C., Berry, P., Opdam, P., Baveco, H., Nijhof, B., O'Hanley, J., Bell, C. & Kuipers, H. (2008) Adapting landscapes to climate change: examples of climate-proof ecosystem networks and priority adaptation zones. Journal of Applied Ecology, 45, 1722-1731.
74. Wahlund, S. (1928) Zusammensetzun von Population und Korrelationsercheinung vom Standpunkt der Verbungslehre aus betrachtet. Hereditas, 11, 65-106.
75. Walther, G.-R., Post, E., Convey, P., Menzel, A., Parmesan, C., Beebee, T.J.C., Fromentin, J.-M., Hoegh-Guldberg, O. & Bairlein, F. (2002) Ecological responses to recent climate change. Nature, 416, 389-395.