Anne Bruneau, A.,  L.M. Borges, R. Allkin, A.N. Egan, M. de la Estrella, F. Javadi, B. Klitgård, J.T. Miller, D.J. Murphy, C. Sinou, M. Vatanparas, R. Zhang. In Press. Towards a new online species information system for legumes. Australian Systematic Botany.

Murphy, D.J., M.C. Ebach, J.T. Miller, S.W. Laffan, G. Cassis, V. Ung, A.H. Thornhill, N. Kerr, M.L. Tursky. 2019. Do phytogeographic patterns reveal biomes or biotic regions? Cladistics. 10.1111/cla.12381

Thornhill, A.H., M.D. Crisp, C. Külheim, K.E. Lam, L.A. Nelson D.K. Yeates, and J.T. Miller. 2019. A dated molecular perspective of eucalypt taxonomy, evolution, and diversification. Australian Systematic Botany.

Gallien, L., A.H. Thornhill, D. Zurella, J.T. Miller, D.M. Richardson. In Press. Global predictors of alien plant establishment success: combining niche and trait proxies. Proceedings of the Royal Society B

Miller, J.T., R. Pirzl, D. Rosauer, G. Jolley-Rogers, and T. Varghese.  2018. Phylolink: Phylogenetically-based profiling, visualisations and metrics for biodiversity. Bioinformatics. doi: 10.1093/bioinformatics/xxxxx

Miller, J.T., G. Jolley-Rogers, B.D. Mishler, and A.H. Thornhill. 2018. Phylogenetic Diversity is a Better Measure of Biodiversity than Taxon Counting. Journal of Systematics and Evolution.  doi: 10.1111/jse.12436

Lu, L., L. Mao, T. Yang, J. Ye, B. Liu, H. Li, M. Sun, J.T. Miller, S. Mathews, H. Hu, Y. Niu, D. Peng, Y. Chen, M. Chen, K. Xiang, C.T. Le, V.C. Dang, A. Lu, P.S. Soltis, D.E. Soltis, J. Li and Z. Chen. 2018. Accepted. Evolutionary history of the angiosperm flora of China—cradle vs. museum? Nature. 554(7691):234-238. doi: 10.1038/nature25485

Marsh K.J., C. Kulheim, S.P. Blomberg, A.T. Thornhill, J.T. Miller, I.R. Wallis, D. Nicolle, J.P. Salminen and W.J. Foley. 2017. Genus-wide variation in foliar polyphenolics in eucalypts. Phytochemistry. 144:197–207. doi:10.1016/j.phytochem.2017.09.014. PMID: 28957714.

Bush, A., R.A. Catullo, K. Mokany, A.H. Thornhill, J.T. Miller and S. Ferrier. 2017. Truncation of Thermal Tolerance Niches among Australian Plants. Global Ecology and Biogeography. DOI: 10.1111/geb.12637

Prentice, E., N. Knerr, A.N. Schmidt-Lebuhn, C.E. González-Orozco, E.N. Bui, S.W. Laffan and J.T. Miller. 2016. Soil and climate properties drive biogeography of the Australian Proteaceae. Plant and Soil. doi:10.1007/s11104-017-3261-6

J.T. Miller, V. Terra, C.W. Riggins, J.E. Ebinger, and D.S. Seigler. 2017. Molecular Phylogenetics of Parasenegalia and Pseudosenegalia (Fabaceae: Mimosoideae). Systematic Botany

Terra, V., C.P Flávia. Garcia, L.P. de Queiroz, M. van der Bank, and J.T. Miller. 2017. Phylogenetic Relationships in Senegalia (Leguminosae-Mimosoideae) Emphasizing the South American Lineages. Systematic Botany

Bui, E.N., A.H. Thornhill, C.E. González-Orozco, and J.T. Miller. 2017. Eucalypts, climate, and geochemistry in Australia. Geobiology 15:427-440. doi: 10.1111/gbi.12235.

The Legume Phylogeny Working Group.  2017. A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny. Taxon. 66: 44-77. https://doi.org/10.12705/661.3The Legume Phylogeny Working Group.  2017. A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny. Taxon. 66: 44-77. https://doi.org/10.12705/661.3.

Miller J.T., C. Hui, A.H. Thornhill, L. Gallien, J.J. Le Roux, and D.M. Richardson. 2017. The role of phylogenetic history and native range size in mediating the invasion success of exotic. AoB PLANTS. 9 (1): plw080. https://doi.org/10.1093/aobpla/plw080.

Laffan, S.W., A.H. Thornhill, J.T. Miller, N. Knerr, C.E. González-Orozco, and B.D. Mishler. 2016.  Understanding spatial patterns of biodiversity: How sensitive is phylogenetic endemism to the randomisation model? GIScinece. In press.

Seigler, D.S., J.E. Ebinger, C.W. Riggins, V. Terra dos Santos, and J.T. Miller. 2017. Parasenegalia and Pseudosenegalia (Fabaceae: Mimosoideae): New genera of the Mimosoideae. Novon.

McLeish, M.J., C.E. González-Orozco, and Miller, J.T.  2016. Spatial correspondence between the specialist galling insect genus Kladothrips (Thysanoptera: Tubulifera: Phlaeothripidae) and its Acacia host: ecological and evolutionary constraints on host use. Austral Entomology.  doi:10.1111/aen.12256

González-Orozco C.E., L.J. Pollock, A.H. Thornhil, B.D. Mishler, N. Knerr, S.W. Laffan, J.T. Miller, D.F. Rosauer, D.P. Faith, and D.A. Nipperess. 2016, Phylogenetic approaches reveal biodiversity threats under climate change. Nature Climate Change. 537: 453  http://dx.doi.org/10.1038/nclimate3126

Laffan, S.W., D.F. Rosauer, G. Di Virgilio, J.T. Miller, González-Orozco, C.E, A. H. Thornhill, A.H., and B.D. Mishler, 2016. Range-weighted metrics of species and phylogenetic turnover can better resolve biogeographic transition zones. Methods in Ecology and Evolution 7: 580–588. http://dx.doi.org/10.1111/2041-210X.12513

Thornhill, A.H., B.D. Mishler, N.J. Knerr, González-Orozco, C.E, C.M. Costion, D.M. Crayn, S.W. Laffan, and J.T. Miller. 2016. Continental scale spatial phylogenetics of Australian angiosperms provides insights into ecology, evolution and conservation. Journal of Biogeography. 43: 2085–2309 doi:10.1111/jbi.12797

Barrett, L.G., P.C. Zee, J.D. Bever, J.T. Miller, and P.H. Thrall. 2016. Evolutionary history shapes patterns of mutualistic benefit in Acacia\rhizobial interactions. Evolution 70:1473-C85. doi: 10.1111/evo.12966.

Williams A.V., J.T. Miller, I. Small, P.G. Nevill, and L.M. Boykin. 2016. Integration of complete chloroplast genome sequences with small amplicon datasets improves phylogenetic resolution in Acacia. Molecular Phylogenetics and Evolution. DOI: 10.1016/j.ympev.2015.11.021.

González-Orozco, C.E., B.D. Mishler, J.T. Miller, S.W. Laffan, N.J. Knerr, A.H. Thornhill and B. Gruber. 2015. Phylogenetic diversity, paleo-endemism, and neo-endemism in Acacia and eucalypts in the Murray-Darling Basin, south-eastern Australia: a strategy for conservation prioritization. Biodiversity and Conservation 5: 5177–5192 doi: 10.1002/ece3.1747.

González-Orozco, C.E., B.D. Mishler, J.T. Miller, S.W. Laffan, N.J. Knerr, P. Unmack, A. Georges, A.H. Thornhill, D.F. Rosauer and B. Gruber. 2015. Assessing biodiversity and endemism using phylogenetic methods across multiple taxonomic groups. Ecology and Evolution. DOI: 10.1002/ece3.1747

Ebach, M.C., N. D.J. Murphy, C.E. González-Orozco and J.T. Miller. 2015. A revised area taxonomy of phytogeographical regions within the Australian Bioregionalisation Atlas. Phylotaxa. http://dx.doi.org/10.11646/phytotaxa.00.0.0

Nagalingum, N.S., N. Knerr, S. Laffan, C.E. González-Orozco, A. Thornhill, J.T. Miller, and B.D. Mishler. 2015.  Continental scale patterns and predictors of fern richness and phylogenetic diversity. Frontiers in Genetics. 6: 1–14 http://dx.doi.org/10.3389/fgene.2015.00132.

Clements, M.A., C.G. Howard, and J.T. Miller. 2015. Caladenia (Orchidaceae) revisited: results of molecular phylogenetic analyses of Caladeniinae plastid and nuclear loci. American Journal of Botany. 102: doi: 10.3732/ajb.1500021.

Laity T., S.W. Laffan, C.E. González-Orozco, D.P. Faith, D.F. Rosauer, M. Byrne, J.T. Miller, D. Crayn, C. Costion, C.C. Moritz, and K. Newport. 2015. Phylodiversity to inform conservation policy: An Australian example. Sci Total Environ. 534: 131–43. doi: 10.1016/j.scitotenv.2015.04.113

Schmidt-Lebuhn, A.N., N.J. Knerr, J.T. Miller and B.D. Mishler. 2015. Phylogenetic diversity and endemism of Australian daisies (Asteraceae). Journal of Biogeography. 42: 1114-1122. DOI: 10.1111/jbi.12488

Pollock, L., J.D. Rosauer, A.H. Thornhill, H. Kujala, M. D. Crisp, J.T. Miller and M.A. McCarthy. 2015. Phylogenetic diversity meets conservation policy: small areas are key to preserving eucalypt lineages. Philosophical Transactions of the Royal Society. DOI: 10.1098/rstb.2014.0007

Miller, J.T., D. Seigler and B.D. Mishler. 2014. A phylogenetic solution to the Acacia problem. Taxon. 59: 7–19.

Miller, J.T. and M.A. Clements. 2014. Molecular phylogenetic analyses of Drakaeinae: Diurideae (Orchidaceae) based on ITS. Australian Systematic Botany. 27: 3–22.

Miller, J.T. and G. Jolley-Rogers. 2014. Correcting the disconnect between phylogenetics and biodiversity informatics Zootaxa 3754 (2): 195–200.

Miller, J.T. and M. Burd. 2014. 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.

Mishler, B.D., N.J. Knerr, C.E González-Orozco, A.H. Thornhill, S.W. Laffan and J.T Miller. 2014.   Phylogenetic measures of biodiversity and neo- and paleo-endemism in Australian Acacia. Nature Communications DOI: 10.1038/ncomms5473

Bui, E.N., A.H. Thornhill and J.T. Miller. 2014.  Salt- and alkaline-tolerance are linked in Acacia. Biology Letters 10: 20140278

Bui, E.N., C.E. González-Orozco and J.T. Miller. 2014. Acacia, climate, and geochemistry in Australia. Plant Soil. DOI 10.1007/s11104-014-2113-x

González-Orozco, C.E. , M.C. Ebach, S.W. Laffan, A.H. Thornhill, N.J. Knerr, A.N. Schmidt-Lebuhn, C.C. Cargill, M.A. Clements, N.S. Nagalingum, B.D. Mishler and J.T. Miller. 2014. Quantifying Phytogeographical Regions of Australia Using Geospatial Turnover in Species Composition. PlosOne 10.1371/journal.pone.0092558.

Jolley-Rogers, G., T. Varghese, P. Harvey, N. dos Remedios and J.T. Miller. 2014 PhyloJIVE: Integrating biodiversity data with the Tree of Life. Bioinformatics. 10.1093/bioinformatics/btu024

Swarts N.D, M.A Clements, C.C. Bower and J.T. Miller. 2014. Defining conservation units in a complex of morphologically similar, sexually deceptive highly endangered orchids.  Biological Conservation. 171: 55–64.

González-Orozco, C.E., A.H. Thornhill, S.W. Laffan, N.J. Knerr and J.T. Miller. 2014.  Biogeographical regions and phytogeography of the eucalypts. Diversity and Distributions. 20: 46–58.

Joseph, L., D. Yeates, J.T. Miller, D. Spratt, D. Gledhill and A. Butler. 2014. Australia's biodiversity – major features. Chapter 2, pp 13–37, in Biodiversity, Morton, S. (ed.). CSIRO Publishing: Melbourne.

McLeish, M.J., Miller, J.T. and L.A. Mound. 2013. Delayed colonisation of Acacia by thrips and the timing of host-conservatism and behavioural specialisation. BMC Evolutionary Biology. 13: 188 doi:10.1186/1471-2148-13-188.

Miller, J.T., D. Murphy, S. Y.W.Ho, D.J. Cantrill and D. Seigler. 2013. Comparative dating of Acacia: combining fossils and multiple phylogenies to infer ages of clades with poor fossil records. Australian Journal of Botany 61: 436–445.

Cargill, D.C., N. G. F. Vella, I. Sharma and J.T. Miller. 2013.  Cryptic speciation and species diversity among Australian and New Zealand hornwort taxa of Megaceros campb. (dendrocerotaceae). Australian Systematic Botany 26: 356-377.

The Legume Phylogeny Working Group.  (2013) Towards a new classification system for legumes: progress report from the ILC6. South African Journal of Botany. 89: 3–9. DOI: 10.1016/j.sajb.2013.07.02

González-Orozco, C.E., S.W. Laffan, N. Knerr and J.T. Miller. 2013. A biogeographical regionalisation of Australian Acacia species. Journal of Biogeography. 40: 2156–2166. DOI: 10.1111/jbi.12153

The Legume Phylogeny Working Group  (2013) Legume phylogeny and classification in the 21st century: progress, prospects and lessons for other species-rich clades. Taxon. 62: 217–248.

Joseph, S., M. Bhave, J.T. Miller and D.J. Murphy. 2013. Rapid Identification of Acacia Species With Potential Salt Tolerance by Using Nuclear Ribosomal DNA Markers. Sustainable Agriculture Research. 2: 77–86.

Joseph, S., D.J. Murphy, J.T. Miller and M. Bhave. 2013. Application of Molecular Markers for Identification of Potential Salt Tolerant Plant Species for Use in Agroforestry and Saline Land Reclamation. APCBEE Procedia. 5: 514–519.

Bessega, C., C. Pometti, J.T. Miller, R. Watts, B.O. Saidman and J.C. Vilardi. 2013. New Microsatellite loci for Prosopis alba and P. chilensis (Leguminosae). American Journal of Botany Primer Notes. 1: 1200324.

Neville, P.G., M.J Wallace, S.K Krauss and J.T. Miller. 2013. DNA barcoding for conservation and ecological restoration of Acacia in the Midwest of Western Australia. Molecular Ecology Resources. 13: 1033–1042.

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

González-Orozco, C.E., A.H.D Brown, N. Knerr and J.T. Miller. 2012. Centres of diversity of Australian Glycine species. Conservation Genetics. 13: 1269–1281.

Maslin, B.R., M. O’Leary, J.E. Reid and J.T. Miller. 2012. The type of Acacia aneura (Mulga) and ambiguities concerning the application of this name. Nuytsia. 22: 269–294.

Stevenson, L., C.E. González-Orozco, N. Knerr, C. Cargill and J.T. Miller. 2012. Spatial distribution and analysis of species richness and endemism of liverworts, hornworts and mosses in Australia. Journal of Bryology. 34: 101–107.

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.

Richardson, D.M., J. Carruthers, C. Hui, F.A.C. Impson, J.T. Miller, M.P Robertson, M. Rouget, J.J. Le Roux and J.R.U Wilson. 2011. Human-mediated introductions of Australian Acacia species—a global experiment in biogeography. Diversity and Distributions.17: 771–787.

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. 59: 480–497.

Miller, J.T., D. J. Murphy, G. K. Brown, D. M. Richardson and C. E. González-Orozco. 2011. The evolution and phylogenetic placement of invasive Acacia species Diversity and Distributions. 17: 848–860.

Gallagher, R., M.R. Leishman, J.T. Miller, C. Hui, D.M. Richardson, J. Suda and P. Trávníček . 2011. Genome size as a predictor of invasion success and trait variation in Australian acacias. Diversity and Distributions. 17: 884–897.

Gibson M.R., D.M. Richardson, E. Marchante, H. Marchante, J.G. Rodger, G.N. Stone, M. Byrne, A. Fuentes-Ramírez, N. George, C. Harris, S.D. Johnson, J.J. Le Roux, J.T. Miller, D.J. Murphy, A. Pauw, M.N. Prescott, E.M. Wandrag and J.R.U Wilson. 2011. Reproductive biology of Australian Acacia species: important mediator of invasiveness? Diversity and Distributions. 17: 911–933.

Clements, M.A., J. Tupac-Otero and J.T Miller. 2011. Phylogenetic relationships in Pterostylidinae (Cranichideae: Orchidaceae): combined evidence from nuclear and plastid DNA sequences. Australian Journal of Botany. 59: 99–117.

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.

Neiman, M., G. Hehman, J.T. Miller, J.M. Logsdon, Jr and D.R. Taylor. 2010. Accelerated mutation accumulation in asexual lineages of a freshwater snail. Molecular Biology and Evolution. 27: 954–963.

Murphy, D.J., G. K. Brown, J. T. Miller and P. Y. Ladiges. 2010. Molecular phylogeny of Acacia s.s. (Mimosoideae: Leguminosae) – evidence for major clades and informal classification. Taxon. 59: 7–19.

Brown, G.K., D.J. Murphy, J.T. Miller and P.Y. Ladiges. 2008. Acacia s.s. and its relationships among tropical legumes, tribe Ingeae (Leguminosae: Mimosoideae). Systematic Botany 33: 739–751.

Ruiz Guajardo, J.C., A. Otero-Arnaiz, T. Taylor, G. Stone, T.C. Glenn, J.T. Miller, and A. Schnabel. 2007. Isolation of polymorphic microsatellite markers in the sub-Saharan tree, Acacia (Senegalia) mellifera (Fabaceae: Mimosoideae). Molecular Ecology Notes 7: 1138–1140.

Ahn, Y.O., M. Zheng, B. Winkel, D.R. Bevan, A. Esen, S-H. Shiu, J. Benson, H.P. Peng, J.T. Miller, C.L. Cheng, J.P. Poulton and M.-C. Shih. (2007). Functional genomic analysis of Arabidopsis thaliana glycoside hydrolase family 35. Phytochem. 68: 1510–20.

Ballard, J.W.O., R.G. Melvin, J.T. Miller and S.D. Katewa, 2007. Sex differences in survival and disparity of mitochondrial bioenergetics in Drosophila simulans. Aging Cell 6: 699–708.

Seigler, D.S., J.E. Ebinger and J.T. Miller. 2007. Mariosousa: A new segregate genus from Acacia sensu lato (Fabacese: Mimosoideae) from North America. Novon 16: 413–420.

Brown, G.K., S.R Ariati, D.J. Murphy, J.T. Miller and P.Y. Ladiges. 2006. Bipinnate acacias (Acacia subg. Phyllodineae sect. Botrycephalae) of eastern Australia are polyphyletic based on DNA sequence data. Australian Systematic Botany 19: 315–326.

Seigler, D.S., J.E. Ebinger and J.T. Miller. 2006. The genus Senegalia (Fabaceae: Mimosoideae) from the New World. Phytologia 88: 38–93.

Miller, J.T., D. Murphy, J. Grimes, P. Ladiges and R.J. Bayer. 2003. Chloroplast DNA evidence for non-monophlyly of derived tribes of the legume subfamily Mimosoideae. Systematic Botany 38: 558–564.

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.

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.

Murphy, D.J., J.T. Miller, R.J. Bayer and P.Y. Ladiges. 2003. Molecular phylogeny of Acacia subgenus Phyllodineae (Mimosoideae: Leguminoseae) based on DNA sequences of the internal transcribed spacer region. Australian Systematic Botany 16: 19–26.

Miller, J.T. and R.J. Bayer. 2003. Molecular Phylogenetics of Acacia subgenera Acacia and Aculeiferum (Fabaceae: Mimosoideae) based on the chloroplast matK coding sequence and flanking trnK intron spacer regions. Australian Systematic Botany 16: 27–33.

Andrew R.A., J.T. Miller, R. Peakall, M.D. Crisp and R.J. Bayer. 2003. Genetic, cytogenetic and morphological patterns in a mixed mulga population: evidence for apomixis. Australian Systematic Botany. 16: 69–80.

Luckow, M, J.T. Miller, D.J. Murphy and T. Livshultz. 2003. A phylogenetic analysis of the Mimosoideae (Leguminosae) based on chloroplast DNA sequence data. In: B. Klitgaard and A. Bruneau (editors). Advances in Legume Systematics, pp 197–220. Royal Botanic Gardens Kew.

Miller, J.T., R.A. Andrew and B.R. Maslin. 2002. Towards an understanding of variation in the Mulga complex (Acacia aneura and relatives). Conservation Science Western Australia 4: 19–35.

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.

Spooner, D.M., R.G. van den Berg and J.T. Miller. 2001. Species and series boundaries of Solanum series Longipedicellata and phenetically similar species in ser. Demissa and ser. Tuberosa: Implications for a practical taxonomy of Section Petota. American Journal of Botany 88: 113–130.

Miller, J.T. and R.J. Bayer. 2000. Molecular phylogenetics of Acacia (Fabaceae: Mimosoideae) based on chloroplast matK/trnK and nuclear Histone H3-D DNA sequences. In: P.S. Herendeen and A. Bruneau (editors) Advances in legume systematics , part 9, pp 181–200. Royal Botanic Gardens, Kew.

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.

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.

Miller, J.T., S.A. Jackson, S. Nasuda, B.S. Gill, R.A. Wing and J. Jiang. 1998. Cloning and characterization of a centromere-specific repetitive DNA element from Sorghum bicolor. Theoretical and Applied Genetics 96: 832–839.

Dong, F., J.T. Miller, S.A. Jackson, G. Wang, P.C. Ronald and J. Jiang. 1998. Rice (Oryza sativa) centromeric region consists of complex DNA. Proceedings of the National Academy of Sciences USA 95: 8135–8140.

van den Berg, R.G., J.T. Miller, J. Kardolas, M.L. Ugarte, J. Villand, J. Nienhuis and D.M. Spooner. 1998. Collapse of morphological species in the wild potato Solanum brevicaule complex (Solanum sect. Petota). American Journal of Botany 85: 92–107.

Miller, J.T. and D. M. Spooner. 1996. Introgression of Solanum chacoense (Solanum sect. Petota) upland populations reexamined. Systematic Botany. 21: 461–475.

Spooner, D.M., J. Tivang, J. Nienhuis, J.T. Miller, D.S. Douches and A. Contreras-M. 1996. Comparison of four molecular markers in measuring relationships among the wild potato relatives Solanum section Etuberosum (subgenus Potatoe). Theoretical and Applied Genetics 92: 532–540.