Joe Miller

Ph.D. University of Wisconsin-Madison, 1997.

B.A. University of Minnesota-Minneapolis, 1987.

Joe Miller

Phone: (+61) 6246 5514


Centre for Australian National Biodiversity Research
CSIRO Plant Industry
GPO Box 1600
Canberra ACT 2601


Plant molecular systematics, especially polyploid species complexes, functional genomics of plant-animal interactions, application of new technologies in systematics research.


Miller, J.T. and M. Burd. In Press.  Australia’s Acacia: Unrecognized convergent evolution. In “Invasion Biology and Ecosystem Theory; insights from a continent in transformation”  eds. H. Prins & I. Gordon. Cambridge University Press, Cambridge. (0 citations).

Miller, J.T. and D.M. Seigler The generic status of Acacia sensu lato (Leguminosae:  Mimosoideae). 2012. Australian Systematic Botany. 25: 217–224. (IF=1.0, 0 citations).

González-Orozco, C. E., Brown, A.H.D., Knerr, N., and J.T. Miller. 2012. Centres of diversity of Australian Glycine species. Conservation Genetics. (IF=1.6, 0 citations).

González-Orozco, C. E., S.W. Laffan and J.T. Miller. 2011. Spatial distribution of species richness and endemism of the genus Acacia in Australia. Australian Journal of Botany. 59:600–608. (IF=1.7, 1 citation).

Otero, J.T., P.H. Thrall, M. Clements, J.T. Miller and J.J. Burdon. 2011. Co-diversification of Orchids (Pterostylidinae) and their Associated Mycorrhizal Fungi. Australian Journal of Botany. (IF=1.9, 1 citations).

Miller, J.T., D. M. Murphy, G. K. Brown, D. M. Richardson and C. E. González-Orozco. 2011. The evolution and phylogenetic placement of invasive Acacia speciesDiversity and Distributions. 17: 848–860 .(IF=4.2, 22 citations).

Miller, J.T. and C. Miller. 2011. Acacia seedling morphology: Correlation of juvenile leaf forms and seed weight.  Australian Journal of Botany. 59: 185–196. (IF=1.9, 0 citations).

Miller, J.T., R. Andrew, and R.J. Bayer. 2003. Molecular phylogenetics of the Australian Acacias, Acacia subg. Phyllodineae(Fabaceae: Mimosoideae) based on chloroplast DNA sequences. Australian Journal of Botany 51: 167–177. (IF=0.9, 21 citations).

Maslin, B.R., J.T. Miller and D.S. Seigler. 2003. Overview of the generic status of Acacia (Leguminoseae: Mimosoideae). Australian Systematic Botany 16: 1–18. (IF=1.0, 88 citations).

Miller, J.T. and R.J. Bayer. 2001. Molecular phylogenetics of Acacia (Fabaceae: Mimosoideae) based on chloroplast matK coding sequence and flanking trnK intron spacer regions. American Journal of Botany 88: 697–706. (IF=2.5, 73 citations).

Miller, J.T. and D.M. Spooner. 1999. Collapse of species boundaries in the wild potato Solanum brevicaule complex (Solanaceae, S. sect. Petota): molecular data. Plant Systematics and Evolution 214: 103–130. (IF=1.3, 57 citations).

Miller, J.T., F. Dong, S.A. Jackson, J. Song, and J. Jiang. 1998. Retrotransposon-related DNA sequences in the centromeres of grass chromosomes. Genetics 150: 1615–1623. (IF=4.5, 126 citations).


Acacia evolution: I have developed a 700 species phylogeny of the Australian plant genus Acacia.  With fossil Acacia data we have dated the major lineage diversification and now will trace the evolution of plant morphology and environmental niche.

Ongoing projects include:

Evolution of phyllodes

  • Insect co-diversification
  • Biogeography of Acacia
  • Phylogenetic classification

Phylogenetic Endemism: Over the past year our group has developed novel metrics to identify and quantify areas for evidenced-based conservation planning. Relative Phylogenetic Endemism (RPE) quantitatively differentiates areas of paleo- and neo-endemism.

It is anticipated that these methods will be valuable in the conservation decision-making process; reserve design can be guided by assessment of phylogeny rather than species counts alone and can identify complementary areas of biodiversity that have unique evolutionary histories and traits in need of conservation.

Evolution of Australian flora: As part of our phylogenetic diversity and endemism work my postdoc Andrew Thornhill has generated a phylogeny of 90% of the Australian genera.  This tree has over 2,500 terminals and with the allied spatial data from the AVH we are exploring the big picture of Australian flora.

Endangered orchids: Orchids are famous for its immense diversity in floral morphology but infamous for the taxonomic difficulties. Orchids, such as Caladenia, are some of the most threatened species with this genus representing almost 40% of endangered orchids and approximately 5% of all threatened flora in Australia. 

​We are investigating species boundaries with a combination of molecular, morphological and ecological tools. Our goal is to provide science based recommendations to better understand what is truly endangered.

PhyloJIVE: In collaboration with Garry Jolley-Rogers I developed a web-based tool, PhyloJIVE, that brings information, available online in IdentifyLife, EOL and other biodiversity web-services, and directly annotates it on the branches on the Tree of Life.  This has been a collaboration with the TRIN informatics team and the Atlas of Living Australia.


Updated 27 November, 2012 , webmaster, CANBR (