Phylogeography provides an evolutionary context for the conservation of a diverse and ancient flora

I thank Bronwyn Macdonald for ongoing technical support, and David Coates and Stephen Hopper for valuable discussions of historical impacts on the Western Australian flora.

Avise JC (1998) The history and purview of phylogeography: a personal reflection. Molecular Ecology 7, 371–379.
| Crossref | GoogleScholarGoogle Scholar |

Avise JC (2000) ‘Phylogeography. The history and formation of species.’ (Harvard University Press: Cambridge, MA)

Avise JC, Walker D (1999) Species realities and numbers in sexual vertebrates: perspectives from an asexually transmitted genome. Proceedings of the National Academy of Sciences, USA 96, 992–995.
| Crossref | GoogleScholarGoogle Scholar |

Avise JC, Arnold J, Ball RM, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18, 489–522.

Balme J, Merrilees D, Porter JK (1978) Late Quaternary mammal remains spanning about 30 000 years from excavations in Devils Lair, WA. Journal of the Royal Society of Western Australia 61, 33–65.

Beard JS (1982) Late Pleistocene aridity and Aeolian landforms. In ‘Evolution of the flora and fauna of arid Australia’. (Eds WR Barker, PJM Greenslade) pp. 101–106. (Peacock Publications: Adelaide)

Bint AN (1981) An early Pliocene pollen assemblage from Lake Tay, south-western Australia, and its phylogeographical implications. Australian Journal of Botany 29, 277–291.
| Crossref | GoogleScholarGoogle Scholar |

Bowen DQ (1978) ‘Quaternary geology.’ (Pergamon Press: Oxford, UK)

Bowler JM (1982) Aridity in the late Tertiary and Quaternary of Australia. In ‘Evolution of the flora and fauna of arid Australia’. (Eds WR Barker, PJM Greenslade) pp. 35–45. (Peacock Publications: Adelaide)

Brewer R, Bettenay E (1973) Further evidence concerning the origins of the Western Australian sand plains. Journal of the Geological Society of Australia 19, 533–541.

Broadhurst LM, Coates DJ (2002) Genetic diversity within and divergence between rare and geographically widespread taxa of the Acacia acuminata (Mimosaceae) complex. Heredity 88, 250–257.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

Buist ML (2003) Comparative ecology and conservation biology of two critically endangered acacias (Acacia lobulata and A. sciophanes) and two common, widespread relatives (Acacia verricula and A. anfractuosa) from the south-west of Western Australia. PhD Thesis, The University of Western Australia, Perth.

Bush M (1996) Amazonian conservation in a changing world. Biological Conservation 76, 219–228.
| Crossref | GoogleScholarGoogle Scholar |

Butcher PA, Byrne M, Moran GF (1995) Variation within and among the chloroplast genomes of Melaleuca alternifolia and M. linariifolia (Myrtaceae). Plant Systematics and Evolution 194, 69–81.
| Crossref | GoogleScholarGoogle Scholar |

Butt CRM (1985) Granite weathering and silcrete formation on the Yilgarn Block, Western Australia. Australian Journal of Earth Sciences 32, 425–433.

Byrne M (2003) Phylogenetics and the conservation of a diverse and ancient flora. Comptes Rendues Biologies 326, S73–S79.
| Crossref | GoogleScholarGoogle Scholar |

Byrne M, Hines B (2004) Phylogeographic analysis of cpDNA variation in Eucalyptus loxophleba (Myrtaceae). Australian Journal of Botany 52, 459–470.
| Crossref | GoogleScholarGoogle Scholar |

Byrne M, Hopper SD (2007) 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 in press ,

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.
| Crossref | GoogleScholarGoogle Scholar |

Byrne M, Moran GF (1994) Population divergence in the chloroplast genome of Eucalyptus nitens. Heredity 73, 18–28.

Byrne M, Macdonald B, Coates DJ (1999) Divergence in the chloroplast genome and nuclear rDNA of the rare Western Australian plant Lambertia orbifolia Gardner (Proteaceae). Molecular Ecology 8, 1789–1796.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

Byrne M, Tischler G, Macdonald B, Coates DJ, McComb J (2001) Phylogenetic relationships between two rare acacias and their common, widespread relatives in south-western Australia. Conservation Genetics 2, 157–166.
| Crossref | GoogleScholarGoogle Scholar |

Byrne M, Macdonald B, Coates DJ (2002) Phylogeographical patterns in chloroplast DNA variation within the Acacia acuminata (Leguminosae: Mimosoideae) complex in Western Australia. Journal of Evolutionary Biology 15, 576–587.
| Crossref | GoogleScholarGoogle Scholar |

Byrne M, Macdonald B, Brand J (2003a) Phylogeography and divergence in the chloroplast genome of Western Australian sandalwood (Santalum spicatum). Heredity 91, 389–395.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

Byrne M, Macdonald B, Broadhurst L, Brand J (2003b) Genetic diversity in Western Australia Sandalwood (Santalum spicatum) as revealed by nuclear RFLP analysis. Theoretical and Applied Genetics 107, 1208–1214.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

Clarke JDA (1994) Lake Lefroy, a palaeodrainage playa in Western Australia. Australian Journal of Earth Sciences 41, 417–427.

Coates DJ (2000) Defining conservation units in a rich and fragmented flora: implications for the management of genetic resources and evolutionary processes in south-west Australian plants. Australian Journal of Botany 48, 329–339.
| Crossref | GoogleScholarGoogle Scholar |

Coates DJ, Hamley VL (1999) Genetic divergence and the mating system in the endangered and geographically restricted species Lambertia orbifolia Gardner (Proteaceae). Heredity 83, 418–427.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

Comes HP, Kadereit JW (1998) The effect of Quaternary climatic changes on plant distribution and evolution. Trends in Plant Science 3, 432–438.
| Crossref | GoogleScholarGoogle Scholar |

Dodson JR (1994) Quaternary vegetation history. In ‘Australian vegetation’. (Ed. RH Groves) pp. 37–56. (Cambridge University Press: Cambridge, UK)

Dodson JR , Kershaw AP (1995) Evolution and history of Mediterranean vegetation types in Australia. In ‘Ecology and biogeography of Mediteranean ecosystems in Chile, California and Australia’. (Eds MT Kalin Arroyo, PH Zedler, MD Fox) pp. 21–40. (Springer: New York)

Dodson JR, Macphail MK (2004) Palynological evidence for aridity events and vegetation change during the Middle Pliocene, a warm period in southwestern Australia. Global and Planetary Change 41, 285–307.
| Crossref | GoogleScholarGoogle Scholar |

Ennos RA , Sinclair WT , Hu X-S , Langdon A (1999) Using organelle markers to elucidate the history, ecology and evolution of plant populations. In ‘Molecular systematics and plant evolution’. (Eds PM Hollingsworth, RM Bateman, RJ Gornall) pp. 1–19. (Taylor and Francis: London)

Faith DP (1992) Conservation evaluation and phylogenetic diversity. Biological Conservation 61, 1–10.
| Crossref | GoogleScholarGoogle Scholar |

Fiedler PL , Ahouse JJ (1992) Hierarchies of cause: towards an understanding of rarity in vascular plant species. In ‘Conservation biology: the theory and practice of nature conservation preservation and management’. (Eds PL Fiedler, SK Jain) pp. 23–47. (Chapman and Hall: New York)

Frankham R , Ballou JD , Briscoe DA (2002) ‘Introduction to conservation genetics.’ (Cambridge University Press: Cambridge, UK)

Freeman JS, Jackson HD, Steane DA, McKinnon GE, Dutkowski GW, Potts BM, Vaillancourt RE (2001) Chloroplast DNA phylogeography of Eucalyptus globulus. Australian Journal of Botany 49, 585–596.
| Crossref | GoogleScholarGoogle Scholar |

Gentilli J (1971) Dynamics of the Australian troposphere. In ‘Climates of Australia and New Zealand’. (Ed. J Gentilli) pp. 53–117. (Elsevier Publishing Company: Amsterdam)

Hays JD, Imbrie J, Shackleton NJ (1976) Variations in the Earth’s orbit: pacemaker of the ice ages. Science 194, 1121–1132.
| Crossref | GoogleScholarGoogle Scholar |

Hewitt GM (2001) Speciation, hybrid zones and phylogeography—or seeing genes in space and time. Molecular Ecology 10, 537–549.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

Hewitt GM (2004) Genetic consequences of climatic oscillations in the Quaternary. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 359, 183–195.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

Hines B, Byrne M (2001) Genetic differentiation between mallee and tree forms in the Eucalyptus loxophleba complex. Heredity 87, 566–572.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

Hopkins AJM, Keighery GJ, Marchant NG (1983) Species rich uplands of south-western Australia. Proceedings of the Ecological Society of Australia 12, 15–26.

Hopper SD (1979) Biogeographical aspects of speciation in the southwest Australian flora. Annual Review of Ecology and Systematics 10, 399–422.
| Crossref | GoogleScholarGoogle Scholar |

Hopper SD (2000) Creation of conservation reserves and managing fire on granite outcrops—a case study of Chiddarcooping Nature Reserve in the Western Australian wheatbelt. Journal of the Royal Society of Western Australia 83, 173–186.

Hopper SD, Maslin BR (1978) Phytogeography of Acacia in Western Australia. Australian Journal of Botany 26, 63–78.
| Crossref | GoogleScholarGoogle Scholar |

Hopper SD , Harvey MS , Chappill JA , Main AR , Main B (1996) The Western Australian biota as Gondwanan heritage—a review. In ‘Gondwanan heritage. Past, present and future of the Western Australian biota’. (Eds SD Hopper, JA Chappill, MS Harvey, AS George) pp. 1–46. (Surrey Beatty: Sydney)

Hopper SD, Brown AP, Marchant NG (1997) Plants of Western Australia granite outcrops. Journal of the Royal Society of Western Australia 80, 141–158.

Humphries CJ, Williams PH, Vane-Wright RI (1995) Measuring biodiversity value for conservation. Annual Review of Ecology and Systematics 26, 93–111.
| Crossref | GoogleScholarGoogle Scholar |

Jackson HD, Steane DA, Potts BM, Vaillancourt RE (1999) Chloroplast DNA evidence for reticulate evolution in Eucalyptus (Myrtaceae). Molecular Ecology 8, 739–751.
| Crossref | GoogleScholarGoogle Scholar |

Jordan GJ (1997) Evidence of Pleistocene plant extinction and diversity from Regatta Point, western Tasmania, Australia. Botanical Journal of the Linnean Society 123, 45–71.
| Crossref | GoogleScholarGoogle Scholar |

Kershaw AP , Martin HA , McEwen Mason JRC (1994) The Neogene: a period of transition. In ‘History of the Australian vegetation: Cretaceous to Recent’. (Ed. RS Hill) pp. 299–327. (Cambridge University Press: Cambridge, UK)

Knowles LL (2001) Did the Pleistocene glaciations promote divergence? Tests of explicit refugial models in montane grasshoppers. Molecular Ecology 10, 691–701.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

Knowles LL, Maddison WP (2002) Statistical phylogeography. Molecular Ecology 11, 2623–2635.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

Macphail MK, Jordan GJ, Hill RS (1993) Key periods in the evolution of the flora and vegetation in Western Tasmania I. The Early–Middle Pleistocene. Australian Journal of Botany 41, 673–677.
| Crossref | GoogleScholarGoogle Scholar |

Masta SE, Laurent M, Routman EJ (2003) Population genetic structure of the toad Bufo woodhousii: an empirical assessment of the effects of haplotype extinction on nested clade analysis. Molecular Ecology 12, 1541–1554.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

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.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

Merrilees D (1979) The prehistoric environment in Western Australia. Journal of the Royal Society of Western Australia 62, 109–142.

Moritz C (1994) Defining ‘evolutionarily significant units’ for conservation. Trends in Evolution and Ecology 9, 373–375.
| Crossref | GoogleScholarGoogle Scholar |

Moritz C, Faith D (1998) Comparative phylogeography and the identification of genetically divergent areas for conservation. Molecular Ecology 7, 419–429.
| Crossref | GoogleScholarGoogle Scholar |

Moritz C, Patton JL, Schneider CJ, Smith TB (2000) Diversification of rainforest faunas: an integrated molecular approach. Annual Review of Ecology and Systematics 31, 533–563.
| Crossref | GoogleScholarGoogle Scholar |

Palmer JD (1992) Mitochondrial DNA in plant systematics: applications and limitations. In ‘Molecular systematics of plants’. (Eds PS Soltis, DE Soltis, JJ Doyle) pp. 36–49. (Chapman and Hall: New York)

Playford PE , Cockbain AE , Low GH (1976) ‘Geology of the Perth Basin, Western Australia.’ (Geological Survey of Western Australia: Perth)

Ryder OA (1986) Species conservation and systematics: the dilemma of subspecies. Trends in Evolution and Ecology 1, 9–10.
| Crossref | GoogleScholarGoogle Scholar |

Ryder OA , Kumamoto AT , Durrant BS , Benirschke K (1989) Chromosomal divergence and reproductive isolation in dik-diks. In ‘Speciation and its consequences’. (Eds D Otte, JA Endler) pp. 208–255. (Sinauer Associates Inc.: Sunderland, MA)

Schaal BA, Olsen KM (2000) Gene genealogies and population variation in plants. Proceedings of the National Academy of Sciences, USA 97, 7024–7029.
| Crossref | GoogleScholarGoogle Scholar |

Schaal BA, Haywood DA, Olsen KM, Rauscher JT, Smith WA (1998) Phylogeographic studies in plants: problems and prospects. Molecular Ecology 7, 465–474.
| Crossref | GoogleScholarGoogle Scholar |

Schneider CJ, Cunningham M, Moritz C (1998) Comparative phylogeography and the history of endemic vertebrates in the wet tropics rainforests of Australia. Molecular Ecology 7, 487–498.
| Crossref | GoogleScholarGoogle Scholar |

Seddon JM, Santucci F, Reeve NJ, Hewitt GM (2001) DNA footprints of European hedgehogs, Erinaceus europaeus and E. concolor: Pleistocene refugia, postglacial expansion and colonization routes. Molecular Ecology 10, 2187–2198.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

Soltis DE , Soltis PS , Milligan BG (1992) Intraspecific chloroplast DNA variation: systematic and phylogenetic implications. In ‘Molecular systematics of plants’. (Eds PS Soltis, D Soltis, JJ Doyle) pp. 151–176. (Chapman and Hall: New York)

Steane DA, Byrne M, Vaillancourt RE, Potts BM (1998) Chloroplast DNA polymorphisms signal complex inter-specific interactions in Eucalyptus (Myrtaceae). Australian Systematic Botany 11, 25–40.
| Crossref | GoogleScholarGoogle Scholar |

Templeton AR (1986) Coadaptation and outbreeding depression. In ‘Conservation biology. The science of scarcity and diversity’. (Ed. ME Soule) pp. 105–116. (Sinauer Associates Inc.: Sunderland, MA)

Templeton AR (2001) Using phylogeographic analyses of gene trees to test species status and processes. Molecular Ecolology 10, 779–791.
| Crossref | GoogleScholarGoogle Scholar |

Templeton AR, Shaw K, Routman E, Davis SK (1990) The genetic consequences of habitat fragmentation. Annals of the Missouri Botanic Garden 77, 13–27.
| Crossref | GoogleScholarGoogle Scholar |

Templeton AR, Routman E, Phillips CA (1995) Separating population structure from population history. A cladistic analysis of the geographical distribution of mitochondrial haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics 140, 767–782.
| PubMed |


Vane-Wright RI, Humphries CJ, Williams PH (1991) What to protect? Systematics and the agony of choice. Biological Conservation 55, 235–254.
| Crossref | GoogleScholarGoogle Scholar |

Wagstaff BE, Kershaw AP, O’Sullivan PB, Harle KJ, Edwards J (2001) An early to middle Pleistocene palynological record from the volcanic crater of Pejark Marsh, Western Plains of Victoria, southeastern Australia. Quaternary International 83–85, 211–232.
| Crossref | GoogleScholarGoogle Scholar |

Wheeler M, Byrne M (2006) Congruence between phylogeographic patterns in cpDNA variation in Eucalyptus marginata (Myrtaceae) and geomorphology of the Darling Plateau. Australian Journal of Botany 54, 17–26.
| Crossref | GoogleScholarGoogle Scholar |

Wheeler M, Byrne M, McComb J (2003) Little genetic differentiation within the dominant forest tree, Eucalyptus marginata (Myrtaceae) of south-western Australia. Silvae Genetica 52, 254–259.

Williams D , Dunkerley D , DeDecker P , Kershaw P , Chappell M (1998) ‘Quaternary environments.’ (Arnold: London)

Willis KJ, Niklas KJ (2004) The role of Quaternary environmental change in plant macroevolution: the exception or the rule. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 359, 159–172.
| Crossref | GoogleScholarGoogle Scholar | PubMed |

Wyrwoll K-H (1979) Late Quaternary climates of Western Australia: evidence and mechanisms. Journal of the Royal Society of Western Australia 62, 129–142.

Yates CP, Ladd PG, Coates DJ, McArthur S (2007) Hierarchies of cause: understanding rarity in an endemic shrub with a highly restricted distribution. Australian Journal of Botany 55, 194–205.

Zheng H, Wyrwoll K-H, Li Z, Powell C (1998) Onset of aridity in southern Western Australia—a preliminary palaeomagnetic appraisal. Global and Planetary Change 18, 175–187.
| Crossref | GoogleScholarGoogle Scholar |

Zink RM, Kale HW (1995) Conservation genetics of the extinct dusky seaside sparrow Ammodramus maritimus nigrescens. Biological Conservation 74, 69–71.
| Crossref | GoogleScholarGoogle Scholar |

Zurawski G, Clegg MT, Brown AHD (1984) The nature of nucleotide sequence divergence between barley and maize chloroplast DNA. Genetics 106, 735–749.
| PubMed |