Genetic and palaeo-climatic evidence for widespread persistence of the coastal tree species Eucalyptus gomphocephala (Myrtaceae) during the Last Glacial Maximum

Annals of Botany

Volumn 113, Issue 1, 2014, Pages 55-67

  Nevill, Paul G ^a,b   Bradbury, Donna ^a,b   Williams, Anna ^a,b   Tomlinson, Sean ^a,b   Krauss, Siegfried L ^a,b  

^a BOTANIC GARDENS AND PARKS AUTHORITY   (Australia)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

Australian biogeography; climate change; coastal geomorphology; Eucalyptus gomphocephala; founder effects; Last Glacial Maximum; LGM; microsatellites; Myrtaceae; palaeodistribution modelling; phylogeography; south western Australia; southern hemisphere; tuart

Indexed keywords

CHLOROPLAST; COASTAL ZONE; GENETIC VARIATION; GEOMORPHOLOGICAL RESPONSE; LAST GLACIAL MAXIMUM; PALEOCLIMATE; PALEOGEOGRAPHY; PERSISTENCE; POPULATION DISTRIBUTION; POPULATION SIZE; TREE;

MICROSATELLITE DNA;

ARTICLE; AUSTRALIA; AUSTRALIAN BIOGEOGRAPHY; CELL NUCLEUS; CHLOROPLAST; CLIMATE CHANGE; COASTAL GEOMORPHOLOGY; EUCALYPTUS; EUCALYPTUS GOMPHOCEPHALA; FOUNDER EFFECTS; GENETIC VARIABILITY; GENETICS; HAPLOTYPE; ICE COVER; LAST GLACIAL MAXIMUM; LGM; MICROSATELLITES; MYRTACEAE; PALAEODISTRIBUTION MODELLING; PALEONTOLOGY; PHYLOGEOGRAPHY; POPULATION GENETICS; SOUTH-WESTERN AUSTRALIA; SOUTHERN HEMISPHERE; TUART;

AUSTRALIAN BIOGEOGRAPHY; CLIMATE CHANGE; COASTAL GEOMORPHOLOGY; EUCALYPTUS GOMPHOCEPHALA; FOUNDER EFFECTS; LAST GLACIAL MAXIMUM; LGM; MICROSATELLITES; MYRTACEAE; PALAEODISTRIBUTION MODELLING; PHYLOGEOGRAPHY; SOUTH-WESTERN AUSTRALIA; SOUTHERN HEMISPHERE; TUART;

CELL NUCLEUS; CHLOROPLASTS; CLIMATE CHANGE; EUCALYPTUS; GENETIC VARIATION; GENETICS, POPULATION; HAPLOTYPES; ICE COVER; MICROSATELLITE REPEATS; PALEONTOLOGY; PHYLOGEOGRAPHY; SOUTH AUSTRALIA;

EID: 84891515686     PISSN: 03057364     EISSN: 10958290     Source Type: Journal    
DOI: 10.1093/aob/mct253     Document Type: Article

References (99)

1. Arafeh R, Kadreit JW. 2006. Long-distance seed dispersal, clone longevity and lack of phylogeographical structure in the European distributional range of the coastal Calystegia soldanella (L) R. Br (Convolvulaceae). Journal of Biogeography 33: 1461-1469
2. Austerlitz F, Mariette S, Machon N, Gouyon PH, Godelle B. 2000. Effects of colonization processes on genetic diversity: Differences between annual plants and tree species. Genetics 154: 1309-1321
3. Bandelt HJ, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37-48
4. Beaumont LJ, Pitman A, Poulsen M, Hughes L. 2007. Where will species gö Incorporating newadvances in climate modelling into projections of species distributions. Global Change Biology 13: 1368-1385
5. Beheregaray LB. 2008. Twenty years of phylogeography: The state of the field and the challenges for the Southern Hemisphere. Molecular Ecology 17: 3754-3774
6. Bloomfield JA, Nevill P, Potts BM, Vaillancourt RE, Steane DA. 2011. Molecular genetic variation in a widespread forest tree species Eucalyptus obliqua (Myrtaceae) on the island of Tasmania. Australian Journal of Botany 59: 226-237
7. Bradbury D, Krauss SL. 2013. Limited impact of fragmentation and disturbance on the mating system of tuart (Eucalyptus gomphocephala, Myrtaceae): Implications for seed-source quality in ecological restoration. Australian Journal of Botany 61: 148-160
8. Brondani R, Brondani C, Tarchini R, Grattapaglia D. 1998. Development, characterization and mapping of microsatellite markers in Eucalyptus grandis and E. urophylla. Theoretical and Applied Genetics 97: 816-827
9. Byrne M, Hines B. 2004. Phylogeographical analysis of cpDNA variation in Eucalyptus loxophleba (Myrtaceae). Australian Journal of Botany 52: 459-470
10. Byrne M, Hopper S. 2008. Granite outcrops as ancient islands in old landscapes: Evidence from the phylogeography and population genetics of Eucalyptus caesia (Myrtaceae) in Western Australia. Biological Journal of the Linnean Society 93: 177-188
11. Byrne M, Macdonald B. 2000. Phylogeography and conservation of three oil mallee taxa, Eucalyptus kochii ssp kochii, ssp plenissima and E. horistes. Australian Journal of Botany 48: 305-312
12. Byrne M, Moran G, Tibbits W. 1993.Restriction map and maternal inheritance of chloroplastDNAin Eucalyptus nitens. Journal of Heredity 84: 218-220
13. Byrne M, MacDonald B, Coates D. 2002. Phylogeographical patterns in chloroplast DNA variation within the Acacia acuminata (Leguminosae: Mimosoideae) complex in Western Australia. Journal of Evolutionary Biology 15: 576-587
14. Byrne M, Macdonald B, Brand J. 2003. Phylogeography and divergence in the chloroplast genome of Western Australian Sandalwood (Santalum spicatum). Heredity 91: 389-395
15. Byrne M, Elliot CP, Yates CJ, Coates DJ. 2008. Maintenance of high pollen dispersal in Eucalyptus wandoo, a dominant tree of the fragmented agricultural region inWestern Australia. Conservation Genetics 9: 97-105
16. Churchill DM. 1959. Late Quaternary eustatic changes in the Swan River district. Journal of the Royal Society of Western Australia 42: 53-55
17. Coates D, Keighery G, Broadhurst L. 2002. Genetic and morphological variation, and the mating system in Tuart. In: Keighery B, Longman V, eds. Tuart (Eucalyptus gomphocephala) and Tuart communities. Perth Branch Wildlife Society of Western Australia (Inc): Nedlands, Western Australia, 89-107
18. Collins WD, Bitz CM, Blackmon ML, et al. 2006. The Community Climate System Model version 3 (CCSM3). Journal of Climate 19: 2122-2143
19. Cornuet J, Luikart G. 1997. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144: 2001-2014
20. CremerKW. 1977. Distance of seed dispersal in eucalypts estimated from seed weights. Australian Forest Research 7: 225-228
21. Di Rienzo A, Peterson AC, Garza JC, Valdes AM, Slatkin M. 1994. Mutational processes of simple sequence repeat loci in human populations. Proceedings of the National Academy of Sciences, USA 91: 3166-3170
22. Earl DA, von Holdt BM. 2012. Structure harvester: A website and program for visualizing structure output and implementing the evanno method. Conservation Genetic Resources 4: 359-361
23. El Mousadik A, Petit R. 1996. High level of genetic differentiation for allelic richness among populations of the argan tree (Argania spinosa L. Skeels) endemic to Morocco. Theoretical and Applied Genetics 92: 832-839
24. Ennos RA. 1994. Estimating the relative rates of pollen and seed migration among plant populations. Heredity 72: 250-259
25. Evanno G, Regnaut S, Goudet J. 2005. Detecting the numberof clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology 14: 2611-2620
26. Falush D, Stephens M, Pritchard K. 2003. Inference of population structure: Extensions to linked loci and correlated allele frequencies. Genetics 164: 1567-1587
27. Freeman JS, Jackson HD, Steane DA, et al. 2001. ChloroplastDNAphylogeography of Eucalyptus globulus. Australian Journal of Botany 49: 585-596
28. Gilbert KJ, Andrew RL, Bock DG, et al. 2012. Recommendations for utilizing and reporting population genetic analyses: The reproducibility of genetic clustering using the program STRUCTURE. Molecular Ecology 21: 4925-4930
29. Goudet J. 2002. FSTAT version 2.9.3.2. Department of Ecology and Evolution, Lausanne University, Lausanne, Switzerland
30. Hasumi H, Emori S. 2004. K-1 coupledGCM (MIROC) description. Center for Climate System Research, University of Tokyo
31. Hewitt GM. 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society 58: 247-276
32. Hewitt GM. 2000. The genetic legacy of the Quaternary ice ages. Nature 405: 907-913
33. Hewitt GM. 2004. Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society B: Biological Sciences 359: 183-195
34. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25: 1965-1978
35. Hopkins AJM, Coker J, Beeston GR, Bowan P, Harvey JM. 1996. Conservation status of vegetation types throughout Western Australia: Final Report. Australian Nature Conservation Agency National Reserves System Co-operative Research Program
36. Hopper SD, Gioia P. 2004.TheSouthwestAustralian FloristicRegion: Evolution and conservation of a global hotspot of biodiversity. Annual Review of Ecology and Systematics 35: 623-650
37. Hubbard NN. 1995. In search of regional palaeoclimates-Australia, 18,000 Yr BP. Palaeogeography, Palaeoclimatology, Palaeoecology 116: 167-188
38. Hubisz MJ, Falush D, Stephens M, Pritchard JK. 2009. Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources 9: 1322-1332
39. Hundertmark KJ, Van Daele LJ. 2010. Founder effect and bottleneck signatures in an introduced, insular population of elk. Conservation Genetics 11: 139-147
40. Jackson HD, Steane DA, Potts BM, Vaillancourt RE. 1999. Chloroplast DNA evidence for reticulate evolution in Eucalyptus (Myrtaceae). Molecular Ecology 8: 739-751
41. Jackson S, Overpeck J. 2000. Responses of plant populations and communities to environmental changes of the late Quaternary. Palaeobiology 26: 194-220
42. Kadreit JW, Arafeh R, Somogyi G, Westbridge E. 2005.Terrestrial growth and marine dispersal?Comparative phylogeography of five coastal plant species at a European scale. Taxon 54: 861-876
43. Katz RW. 2002. Techniques for estimating uncertainty in climate change scenarios and impact studies. Climate Research 20: 167-185
44. Keighery B, Keighery G, Shepherd D. 2002. The distribution and conservation ofTuart and the community with which it lives. In: Keighery B, Longman V, eds. Tuart (Eucalyptus gomphocephala) and tuart communities. Perth Branch Wildflower Society of Western Australia (Inc): Nedland, Western Australia, 6-86
45. Klein C, Wilson K, Watts M, et al. 2009. Incorporating ecological and evolutionary processes into continental-scale conservation planning. Evolutionary Applications 19: 206-217
46. Lewis PO, Zaykin D. 2001. Genetic Data Analysis Software, version 1.1
47. Linder HP, Eldenas P, Briggs BG. 2003. Contrasting patterns of radiation in African and Australian Restionaceae. Evolution 57: 2688-2702
48. Mantel N. 1967. The detection of disease clustering and a generalized regression approach. Cancer Research 27: 209-220
49. Margules CR, Pressey RL. 2000. Systematic conservation planning. Nature 405: 243-253
50. Marshall JC, Kingsbury BA, Minchella DJ. 2009. Microsatellite variation, population structure, and bottlenecks in the threatened copperbelly water snake. Conservation Genetics 10: 465-476
51. McKinnon GE, Steane DA, Potts BM, Vaillancourt RE. 1999. Incongruence between chloroplast and species phylogenies in Eucalyptus subgenus Monocalyptus (Myrtaceae). American Journal of Botany 86: 1038-1046
52. McKinnon GE, Vaillancourt RE, Jackson HD, Potts BM. 2001. Chloroplast sharing in the Tasmanian eucalypts. Evolution 55: 703-711
53. McKinnon GE, Jordan GJ, Vaillancourt RE, Steane DA, Potts BM. 2004. Glacial refugia and reticulate evolution: The case of the Tasmanian eucalypts. Philosophical Transactions of the Royal Society B: Biological Sciences 359: 275-284
54. Meadows ME, Sugden JM. 1993. The late quaternary palaeoecology of a floristic kingdom: The southwestern Cape South Africa. Palaeogeography, Palaeoclimatology, Palaeoecology 101: 271-281
55. Mercer JH. 1968. Antarctic ice and Sangamon sea level. International Association of Scientific Hydrology 79: 217-225
56. Mimura M, Barbour RC, Potts BM, Vaillancourt RE, Watanabe KN. 2009. Comparison of contemporarymating patterns in continuous and fragmented Eucalyptus globulus native forests. Molecular Ecology 18: 4180-4192
57. Mittermeier RA, Robles Gil P, Hoffman M, et al. 2004. Hotspots revisited. CEMEX: Garza Garcia N.L. Mexico
58. Molins A, Mayol M, Rosselló JA. 2009. Phylogeographical structure in the coastal species Senecio rodriguezii (Asteraceae), a narrowly distributed endemic Mediterranean plant. Journal of Biogeography 36: 1372-1383
59. Morueta-Holme N, Fløjgaard C, Svenning JC. 2010. Climate change risks and conservation implications for a threatened small-range mammal species. PloS One 5: Pe10360
60. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GA, Kent J. 2000. Biodiversity hotspots for conservation priorities. Nature 403: 853-858
61. Nei M. 1972. Genetic distance between populations. American Naturalist 106: 283-292
62. Nevill P, Bossinger G, Ades P. 2010. Phylogeography of the world́s tallest angiosperm Eucalyptus regnans: Evidence for multiple isolated quaternary refugia. Journal of Biogeography 37: 179-192
63. Oberle B, Schaal BA. 2011.Responses to historical climate change identify contemporary threats to diversity in Dodecatheon. Proceedings of the National Academy of Sciences, USA 108: 5655-5660
64. Ottewell KM, Donnellan SC, Moran GF, Paton DC. 2005. Multiplexed microsatellite markers for the genetic analysis of Eucalyptus leucoxylon (Myrtaceae) and their utility for ecological and breeding studies in other Eucalyptus species. Journal of Heredity 96: 445-451
65. Pannell JR, Dorken ME.2006.Colonisations as acommondemoninator in plant metapopulations and range expansions: Effects on genetic diversity and sexual systems. Landscape Ecology 21: 837-848
66. Peakall R, Smouse PE. 2006. GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288-295
67. Phillips SJ, Anderson RP, Schapire RE. 2006. Maximum entropy modelling of species geographic distributions. Ecological Modelling 190: 231-259
68. Phillips SJ., Dudík M. 2008. Modelling of species distributions with Maxent: New extensions and a comprehensive evaluation. Ecography 31: 161-175
69. Phillips SJ. 2008. Transferability, sample selection bias and background data in presence-only modelling: A response to Peterson et al. (2007). Ecography 31: 272-278
70. Pickett EJ, Newsome JC. 1997. Eucalyptus (Myrtaceae) pollen and its potential role in investigations of Holocene environments in southwestern Australia. Review of Palaeobotany and Palynology 98: 187-205
71. Playford PE, Cockbain AE, Low GH.1976. Geologyof thePerth BasinWestern Australia. Geological Society of Western Australia, Bulletin 124
72. Pollock LJ, Bayly MJ, Nevill PG, Vesk PA. 2013. Chloroplast DNA diversity associated with protected slopes and valleys for hybridizing Eucalyptus species on isolated ranges in south-eastern Australia. Journal of Biogeography 40: 155-167
73. Pons O, Petit R. 1996. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics 144: 1237-1245
74. Pritchard JK, Stephens M, DonnellyP. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959
75. Provan J, Soranzo N, Wilson NJ, Goldstein DB, PowellW. 1999. A low mutation rate for chloroplast microsatellites. Genetics 153: 943-947
76. Provan J, Powell W, Hollingsworth PM.2001. Chloroplast microsatellites: New tools for studies in plant ecology and evolution. Trends in Ecology and Evolution 16: 142-147
77. Raymo ME, Mitrovica JX, ÓLeary MJ, DeConto RM, Hearty PJ. 2011. Departures from eustasy in Pliocene sea-level records. Nature Geoscience 4: 328-332
78. Raymond M, Rousset F. 1995. GENEPOP (version 1.2): Population genetics software for exact tests and ecumenicism. Journal of Heredity 86: 248-249
79. Remington CL. 1968. Suture-zones of hybrid interaction between recently joined biotas. In: Dobzhansky T, Hecht MK, Steere WC, eds. Evolutionary biology. New York: Plenum, 321-428
80. Rojas M, Moreno P, Kageyama M, et al. 2009. The SouthernWesterlies during the Last Glacial Maximum in PMIP2 simulations. Climate Dynamics 32: P525e548
81. Ruthrof KX, Yates CJ, Loneragan WA. 2002. The biology of Tuart. In: Keighery BJ, Longman VM. eds. Tuart (Eucalyptus gomphocephala) and Tuart communities. Perth BranchWildflower Society ofWestern Australia (Inc): Nedlands, Western Australia, 108-121
82. Seddon G. 2004. Sense of place: A response to an environment. The Swan coastal plain, Western Australia. Bloomings Books: Melbourne
83. Semeniuk V. 1995. New Pleistocene and Holocene stratigraphic units in the Yalgorup Plain area, southern Swan Coastal Plain. Royal Society of Western Australia 78: 67-79
84. Semeniuk V. 1997. Pleistocene coastal palaeogeography in Southwestern Australia-carbonate and quartz sand sedimentation in cuspate forelands, barriers and ribbon shoreline deposits. Journal of Coastal Research 13: 468-489
85. Skabo S, Vaillancourt R, Potts B. 1998. Fine-scale genetic structure of Eucalyptus globulus ssp. globulus forest revealed by RAPDS. Australian Journal of Botany 46: 583-594
86. Slatkin M. 1985. Rare alleles as indicators of gene flow. Evolution 39: 53-65
87. Speck NH.1953. Atmospheric pollen in the city of Perth and environs. Journal of the Royal Society of Western Australia 37: 119-125
88. Spooner MI, De Deckker P, Barrows TT, Fifield LK. 2010. The behaviour of the Leeuwin Current offshore NWAustralia during the last five glacial-interglacial cycles. Global and Planetary Change 75: 119-132
89. Steane DA, Byrne M, Vaillancourt RE, Potts BM. 1998. Chloroplast DNA polymorphism signals complex interspecific interactions in Eucalyptus (Myrtaceae). Australian Systematic Botany 11: 25-40
90. Steane D, Vaillancourt R, Russell J, Powell W, Marshall D, Potts B. 2001. Development and characterisation of microsatellite loci in Eucalyptus globulus (Myrtaceae). Silvae Genetica 50: 89-91
91. Steane DA, Jones RC, Vaillancourt RE. 2005. A set of chloroplast microsatellite primers for Eucalyptus (Myrtaceae). Molecular Ecology Notes 5: 538-541
92. Svenning JC., Fløjgaard C, Marske KA, Nógues-Bravo D, Normand S. 2011. Applications of species distribution modelling to palaeobiology. Quaternary Science Reviews 30: 2930-2947
93. Szpiech ZA, Jakobsson M, Rossenberg NA. 2008. ADZE: A rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24: 2498-2504
94. TuartResponse Group. 2003. An atlas of Tuart woodlands on the SwanCoastal Plain in Western Australia. Government of Western Australia, Perth, Australia
95. Wheeler MA, Byrne M.2006.Congruencebetween phylogeographic patterns in cpDNAvariation in Eucalyptus marginata (Myrtaceae) and geomorphology of the Darling Plateau, south-west ofWestern Australia. Australian Journal of Botany 54: 17-26
96. Williamson-Natesan EG. 2005. Comparison of methods for detecting bottlenecks from microsatellite loci. Conservation Genetics 6: 551-562
97. Wright S. 1931. Evolution in Mendelian populations. Genetics 16: 97-159
98. Wyrwoll KH, Dong B, Valdes P. 2000. On the position of the southern hemispherewesterlies at the Last Glacial Maximum: An outline of AGCM simulation results and evaluation of their implication. Quaternary Science Reviews 19: 881-898
99. Zaneto A, Kremer A. 1995. Geographical structure of gene diversity inQuercus petraea (Matt) Liebl. 1. Monolocus patterns of variation. Heredity 75: 506-517