Congruence between phylogeographic patterns in cpDNA variation in Eucalyptus marginata (Myrtaceae) and geomorphology of the Darling Plateau, south-west of Western Australia
M. A. Wheeler A and M. Byrne B CA School of Biology and Biotechnology, Murdoch University, South Street Murdoch, WA 6150, Australia.
B Science Division, Department of Conservation and Land Management, Locked Bag 104, Bentley Delivery Centre, WA 6983, Australia.
C Corresponding author. Present Address: PO Box 65, Rosebank, NSW 2480, Australia. Email: margaretb@calm.wa.gov.au
Australian Journal of Botany 54(1) 17-26 https://doi.org/10.1071/BT05086
Submitted: 13 May 2005 Accepted: 8 September 2005 Published: 22 February 2006
Abstract
Phylogeographic patterns in the cp genome of Eucalyptus marginata Don ex Sm., a species common in the mesic region of south-western Australia, were investigated by using RFLP analysis. The chloroplast diversity was structured into two geographically distinct lineages and nested clade analysis inferred historical fragmentation as the major influence on the phylogeographic pattern. The lineages were separated along the geomorphological boundary of the Darling Scarp, which separates the Coastal Plain from the Darling Plateau. The divergence between the lineages is consistent with uplifting of the Darling Plateau in the late Neogene. Further geographic structuring in haplotype distributions was evident in the forest lineage on the Darling Plateau, where one sublineage was present in the central forest region and another was restricted to the south-eastern region. The level of divergence between these sublineages was similar to that between divergent lineages that have been identified in comparative phylogeographic studies of cpDNA variation in three species widespread throughout south-western Australia. In these species, divergence was attributed to the influence of significant changes in climatic oscillations across the semi-arid region during the mid-Pleistocene. The divergence identified in this study indicates that the influence of climatic change was widespread throughout south-western Australia, including the mesic, higher-rainfall region.
Acknowledgments
We thank Bronwyn Macdonald for technical assistance and M. French for assistance with field identification. M. A. W. was in receipt of an APA(I) scholarship while undertaking this work.
Avise, JC (2000).
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: Frewville, SA)
Brooker MIH, Hopper SD
(1993) New series, subseries, species and subspecies of Eucalyptus (Myrtaceae) from Western Australia and from South Australia. Nuytsia 9, 1–68.
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, 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,
Moran GF, Tibbits WN
(1993) Restriction map and maternal inheritance of chloroplast DNA in Eucalyptus nitens. The Journal of Heredity 84, 218–220.
Byrne M,
Parrish TL, Moran GF
(1998) Nuclear RFLP diversity in Eucalyptus nitens. Heredity 81, 225–233.
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 |
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
(2003) Phylogeography and divergence in the chloroplast genome of Western Australian Sandalwood (Santalum spicatum). Heredity 91, 389–395.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
PubMed |
Churchill DM
(1968) The distribution and prehistory of Eucalyptus diversicolor F.Muell., E. marginata Donn. ex Sm., and E. calophylla R.Br. in relation to rainfall. Australian Journal of Botany 16, 125–151.
| Crossref |
Crossref |
Coates DJ
(2000) Defining conservation units in a rich and fragmented flora: implications for management of genetic resources and evolutionary processes in south-west Australian plants. Australian Journal of Botany 48, 329–339.
| Crossref | GoogleScholarGoogle Scholar |
Demesure B,
Comp B, Petit RJ
(1996) Chloroplast DNA phylogeography of the common beech (Fagus sylvatica L.) in Europe. Evolution 50, 2515–2520.
Dodson, JR (1994). Quarternary vegetation history. In ‘Australian vegetation’. pp. 37–56. (Cambridge University Press: Cambridge, UK)
Dodson JR, Kershaw AP
(1994) Evolution and history of Mediterranean vegetation types in Australia. In ‘Ecology and biogeography of Mediterranean ecosystems in Chile, California and Australia’. (Eds MT Kalin Arroyo, PH Zedler, MD Fox)
pp. 21–40. (Springer: New York)
Doebley J,
Durbin M,
Golenberg EM,
Clegg M, Ma DP
(1990) Evolutionary analysis of the large subunit of carboxylase (rbcl) nucleotide sequence among the grasses (Gramineae). Evolution 44, 1097–1108.
Dumolin-Lapègue S,
Demesure B,
Fineschi S,
Le Corre V, Petit RJ
(1997) Phylogeographic structure of white oaks throughout the European continent. Genetics 146, 1475–1487.
| PubMed |
| PubMed |
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)
Ferris C,
Oliver RP,
Davy AJ, Hewitt GM
(1993) Native oak chloroplasts reveal an ancient divide across Europe. Molecular Ecology 2, 337–344.
| PubMed |
| PubMed |
Ferris C,
King RA,
Väinölä R, Hewitt GM
(1998) Chloroplast DNA recognizes three refugia sources of European oaks and suggests independent eastern and western immigrations to Finland. Heredity 80, 584–593.
| Crossref |
Crossref |
PubMed |
PubMed |
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 |
Kendrick GW,
Wyrwoll KH, Szabo BJ
(1991) Pliocene–Pleistocene coastal events and history along the western margin of Australia. Quaternary Science Reviews 10, 419–439.
| Crossref | GoogleScholarGoogle Scholar |
King RA, Ferris C
(1998) Chloroplast DNA phylogeography of Alnus glutinosa (L.) Gaertn. Molecular Ecology 7, 1151–1161.
| Crossref | GoogleScholarGoogle Scholar |
Ladiges PY,
Humphries CJ, Brooker MIH
(1987) Cladistic and biogeographic analysis of Western Australian species of Eucalyptus L’Hérit., informal subgenus Monocalyptus Pryor & Johnson. Australian Journal of Botany 35, 251–281.
| Crossref |
Crossref |
Lynch M, Crease TJ
(1990) The analysis of population survey data on DNA sequence variation. Molecular Biology and Evolution 7, 377–394.
| PubMed |
| 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 |
Crossref |
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 |
PubMed |
Nei M
(1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583–590.
Playford, PE ,
Cockbain, AE ,
and
Low, GH (1976).
Posada D,
Crandall KA, Templeton AR
(2000) GeoDis, a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Molecular Ecology 9, 487–488.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
PubMed |
Posada, D ,
and
Templeton, AR (2004).
Quilty PG
(1974) Cainozoic structure in the Perth area. Journal of the Royal Society of Western Australia 57, 16–31.
Rieseberg LH,
Beckstrom-Sternberg SM,
Liston A, Arias DM
(1991) Phylogenetics and systematic inferences from chloroplast DNA and isozyme variation in Helianthus sect. Helianthus (Asteraceae). Systematic Botany 16, 50–76.
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 |
Soltis DE,
Mayer MS,
Soltis PS, Edgerton M
(1991) Chloroplast-DNA variation in Tellima grandiflora (Saxifragaceae). American Journal of Botany 78, 1379–1390.
Soltis DE,
Gitzendanner MA,
Strenge DD, Soltis PE
(1997) Chloroplast DNA intraspecific phylogeography of plants from the Pacific Northwest of North America. Plant Systematics and Evolution 206, 353–373.
| Crossref | GoogleScholarGoogle Scholar |
Sugiura M,
Shinozaki K,
Zaita N,
Kusuda M, Kumano M
(1986) Clone bank of the tobacco (Nicotiana tabacum) chloroplast genome as a set of overlapping restriction endonuclease fragments, mapping of eleven ribosomal protein genes. Plant Science 44, 211–216.
| Crossref | GoogleScholarGoogle Scholar |
Swofford, DL (1991).
Sytsma KJ, Gottlieb LD
(1986) Chloroplast DNA evolution and phylogenetic relationships in Clarkia sect. Peripetasma (Onagraceae). Evolution 40, 1248–1261.
Templeton AR
(1998) Nested clade analysis of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology 7, 381–397.
| Crossref | GoogleScholarGoogle Scholar | PubMed |
PubMed |
Templeton AR,
Crandall KA, Sing CF
(1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction mapping and DNA sequence data. III. Cladogram estimation. Genetics 132, 619–633.
| PubMed |
| PubMed |
| PubMed |
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 |
| PubMed |
| PubMed |
Wendel JF, Doyle JJ
(1998) Phylogenetic incongruence: window into genome history and molecular evolution. In ‘Molecular systematics of plants II: DNA sequencing’. (Eds DE Soltis, P Soltis, JJ Doyle)
pp. 265–296. (Kluwer Academic Publishers: Norwell, MA)
Wheeler MA,
Byrne M, McComb JA
(2003) Little genetic differentiation within the dominant forest tree, Eucalyptus marginata (Myrtaceae) of south-western Australia. Silvae Genetica 52, 254–259.
Zurawski G, Clegg MT
(1987) Evolution of higher-plant chloroplast DNA-encoded genes: implications for structure-function and phylogenetic studies. Annual Review of Plant Physiology 38, 391–418.
| 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.
