Daniel Murphy

Senior Research Scientist (Molecular Systematist)

Daniel Murphy is a molecular systematist (systematic botanist) whose research primarily involves the use of molecular data (DNA sequencing) to investigate questions about the systematics, taxonomy, classification and biogeography of flowering plants. Dan is Editor-in-Chief of Australian Systematic Botany, Australia's major scientific journal in his field of research. Dan has a particular interest in the evolutionary history of Australia's flora and the historical connections of this flora to other parts of the world. He has focussed much of his research on Acacia (the largest genus of plants in Australia) and related legumes in the Mimosoideae subfamily. Together with staff at the Royal Botanic Gardens Victoria and researchers in tertiary institutions, Dan is involved in a range of research projects, including the biogeography of Persoonia; plant movements of Adansonia and Vachellia (Acacia) farnesiana; grass phylogenetics and DNA barcoding; salinity tolerance research in Acacia; and pollination biology and plant–animal interactions.

Much of Dan's work uses the Royal Botanic Gardens Victoria's living and herbarium collections for molecular research with an overarching aim of integrating systematics and taxonomic research into practical tools. This has resulted in the development of applications of systematics to the areas of plant identification (DNA barcoding), biosecurity, invasive plant studies, and sustainable agriculture.

Publications

Book Chapters

Luckow, M., Miller, J.T., Murphy, D.J. and Livshultz, T. (2003). A phylogenetic analysis of the Mimosoideae (Leguminosae) based on chloroplast DNA sequence data. In B. Klitgaard and A. Bruneau (eds), Advances in Legume Systematics,part 10, pp. 197–220. Royal Botanic Gardens, Kew.

Refereed journal articles

Ebach, M.C., Michaelis, M., Shaw, W., Goff, J., Murphy, D.J. and Matthews, S., 2016. Big Data and the Historical Sciences: A Critique. Geoforum, 71, 1–4.

Birch, J.L., Berwick, F., Walsh, N.G., Cantrill, D.J. and Murphy, D.J. (accepted 2015). Distribution of morphological diversity within widespread Australian species of Poa (Poaceae, tribe Poeae) and implications for taxonomy of the genus. Australian Systematic Botany.

Joseph, S., Murphy, D.J. and Bhave, M. (2015). Identification of salt tolerant Acacia species for saline land utilisation. Biologia 70, 174–182. DOI: 10.1515/biolog-2015-0032.

Martínez-Bauer, A.E., Martínez, G.C., Murphy, D.J. and Burd, M. (2015). Multitasking in a plant-ant interaction: how does Acacia myrtifolia manage both ants and pollinators? Oecologia. DOI 10.1007/s00442-014-3215-0

Bell, K.L., Rangan, H., Fowler, R., Kull, C.A., Pettigrew, J.D., Vickers, C.E. and Murphy, D.J. (2014). Genetic diversity and biogeography of the boab Adansonia gregorii (Malvaceae: Bombacoideae). Australian Journal of Botany 62, 164–174.

Birch, J.L., Cantrill, D.J., Walsh, N.G. and Murphy, D.J. (2014). Phylogenetic investigation and divergence dating of Poa (Poaceae tribe Poeae) in the Australasian Region. Botanical Journal of the Linnean Society 175, 523–552. DOI: 10.1111/boj.12185.

Bell, K.L., Murphy, D.J. and Gardner, M.G. (2013). Isolation, via 454 Sequencing, and characterization of microsatellites for Vachellia farnesiana (Fabaceae: Mimosoideae). Applications in Plant Sciences 1(10): 1300035. doi:http://dx.doi.org/10.3732/apps.1300035

Joseph, S., Bhave, M., Miller J.T. and Murphy, D.J. (2013). Rapid identification of Acacia species with potential salt tolerance by using nuclear ribosomal DNA markers. Sustainable Agriculture Research 2, 77–86.

Joseph, S., Murphy, D.J. and Bhave, M. (2013). Glycine betaine biosynthesis in saltbushes (Atriplex spp.) under salinity stress. Biologia 68, 879–895.

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

Ebach, M.C., Gill, A.C., Kwan, A. Ahyong, S.T., Murphy, D.J. and Cassis, G. (2013). Towards an Australian Bioregionalisation Atlas: a provisional area taxonomy of Australia's biogeographical regions. Zootaxa 3619, 315–342. 

Joseph, S., Murphy, D.J., Miller, J.T. and Bhave, M. (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.

Syme, A.E., Udovicic, F., Stajsic, V. and Murphy, D.J. (2013). A test of sequence-matching algorithms for a DNA barcode database of invasive grasses. DNA Barcodes 1, 19–26. doi:10.2478/dna-2012-0002

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.

Brown, G.K., Murphy, D.J., Kidman, J. and Ladiges, P.Y. (2012). Phylogenetic connections of phyllodinous species of Acacia outside Australia are explained by geological history and human-mediated dispersal. Australian Systematic Botany 25, 390–403.

Hurry, C.R., Walsh, N.G. and Murphy, D.J. (2012). A taxonomic review of Triodia bunicola and T. scariosa (Poaceae: Chloridoideae), based on morphological and molecular data. Australian Systematic Botany 25, 304–312.   

Sauquet, H., Ho, S.Y.W., Gandolfo, M.A., Jordan, G.J., Wilf, P., Cantrill, D.J., Bayly, M.J., Bromham, L., Brown, G.K., Carpenter, R.J., Lee, D.M., Murphy, D.J., Sniderman, J.M.K. and Udovicic, F. (2012). Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case ofNothofagus (Fagales). Systematic Biology 61(2), 289–313.  

Syme, A.E., Murphy, D.J., Holmes, G.D., Gardner, S., Fowler, R. and Cantrill, D.J. (2012). An expanded phylogenetic analysis of Austrostipa (Poaceae: Stipeae) to test infrageneric relationships. Australian Systematic Botany 25, 1–10. 

Brown, G.K., Murphy, D.J. and Ladiges, P.Y. (2011). Relationships of the Australo-Malesian genus Paraserianthes ( Mimosoideae: Leguminosae) identifies the sister group of Acacia sensu stricto and two biogeographical tracks.Cladistics 27, 380–390.

Gibson, M.R., Richardson, D.M., Marchante, E., Marchante, H., Rodger, J.G., Stone, G.N., Byrne, M., Fuentes-Ramírez, A., George, N., Harris, C., Johnson, S.D., Roux, J.J.L., Miller, J.T., Murphy, D.J., Pauw, A., Prescott, M.N., Wandrag, E.M. and Wilson, J.R.U. (2011). Reproductive biology of Australian acacias: important mediator of invasiveness? Diversity and Distributions 17(5), 911–933.

Miller, J.T., Murphy, D.J., Brown, G.K., Richardson, D.M. and González-Orozco, C.E. (2011). The evolution and phylogenetic placement of invasive AustralianAcacia species. Diversity and Distributions 17(5), 848–860.

Wilson, J.R.U., Gairifo, C., Gibson, M.R., Arianoutsou, M., Bakar, B.B., Baret, S., Celesti-Grapow, L., DiTomaso, J.M., Dufour-Dror, J.-M., Kueffer, C., Kull, C.A., Hoffmann, J.H., Impson, F.A.C., Loope, L.L., Marchante, E., Marchante, H., Moore, J.L., Murphy, D.J., Tassin, J., Witt, A., Zenni, R.D. and Richardson, D.M. (2011) Risk assessment, eradication, and biological control: global efforts to limit Australian acacia invasions. Diversity and Distributions 17(5), 1030–1046.

Brown, G.K., Clowes, C., Murphy, D.J. and Ladiges, P.Y. (2010). Phylogenetic analysis based on nuclear DNA and morphology defines a clade of eastern Australian species of Acacia s.s. (section Juliflorae): the 'Acacia longifoliagroup'. Australian Systematic Botany 23, 162–172.

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

Maslin, B.R. and Murphy, D.J. (2009). A taxonomic revision of Acacia verniciflua and A. leprosa (Leguminosae: Mimosoideae) in Australia. Muelleria27, 183–223.

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

Byrne, M., Yeates, D.K., Joseph, L., Kearney, M., Bowler, J., Williams, M.A.J., Cooper, S., Donnellan, S.C., Keogh, J.S., Leys, R., Melville, J., Murphy, D.J., Porch, N. and Wyrwoll, K.-H. (2008). Birth of a biome: insights into the assembly and maintenance of the Australian arid zone biota. Molecular Ecology17, 4398– 4417.

Reid, J.C. and Murphy, D.J. (2008). Some case studies of Acacia as weeds and implications for herbaria. Muelleria 26(1), 57–66.

Murphy, D.J. (2008). A review of the classification of Acacia (Leguminosae, Mimosoideae). Muelleria 26(1), 10–26.

Ariati, S.R., Murphy, D.J., Gardner, S. and Ladiges, P.Y. (2007). Morphological and genetic variation within the widespread species Acacia victoriae(Mimosaceae). Australian Systematic Botany 20, 54–62.

Ariati, S.R., Murphy, D.J., Udovicic, F. and Ladiges, P.Y. (2006). Molecular phylogeny of three groups of acacias (Acacia subgenus Phyllodineae) in arid Australia based on the internal and external transcribed spacer regions of nrDNA. Systematics and Biodiversity b, 417–426.

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

Ladiges, P.Y., Ariati, S.R. and Murphy, D.J. (2006). Biogeography of the Acacia victoriae, pyrifolia and murrayana species groups in arid Australia. Journal of Arid Environments 66, 462–476.

Gardner, S.K., Murphy, D.J., Newbigin, E., Drinnan, A.N. and Ladiges, P.Y. (2005). An investigation of phyllode variation in Acacia verniciflua and A. leprosa (Mimosaceae), and implications for taxonomy. Australian Systematic Botany 8, 383–398.

Smith Z.F., Murphy D.J., James E.A. and McLean C.B. (2005). Molecular investigation of the Diuris 'punctata' group in south eastern Australia. Selbyana26, 217–228.

Hunter, A.M., Orlovich, D.A., Lloyd, K.M., Lee, W.G. and Murphy, D.J. (2004). The generic position of Austrofestuca littoralis and the reinstatement ofHookerochloa and Festucella (Poaceae) based on evidence from nuclear (ITS) and chloroplast (trnL-trnF) DNA sequences. New Zealand Journal of Botany 42, 253–262.

Piccinin, R.C., Murphy, D.J. and Ladiges, P.Y. (2004). Morphometric study of a hybrid population of Acacia verniciflua and A. aspera (Acacia subgenusPhyllodineae). Muelleria 19, 9–18.

Miller, J.T., Grimes, J., Murphy, D.J., Bayer, R.J. and Ladiges, P.Y. (2003). Molecular phylogenetics of the tribes Acacieae and Ingeae (Mimosoideae) based on chloroplast DNA sequences. Systematic Botany 28, 558–566.

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

Nelson, G., Murphy, D.J. and Ladiges, P.Y. (2003). Brummitt on paraphyly: a response. Taxon 52, 295–298.

Udovicic, F. and Murphy, D.J. (2002). Successful DNA amplification from Acacia(Leguminosae) and other refractory Australian plants and fungi using a nested/semi-nested PCR protocol. Muelleria 16, 47–53.

Murphy, D.J., Udovicic, F. and Ladiges, P.Y. (2000). Phylogenetic analysis of Australian Acacia (Leguminosae: Mimosoideae) using sequence variations of an intron and two intergenic spacers of chloroplast DNA. Australian Systematic Botany 13, 745–754

Other

Other articles

Murphy, D.J. (2008). Acacia 2006: Knowing and growing Australian wattles.Muelleria 26(1), 3–6.

Murphy, D.J. (2006). Book Review: Nitrogen fixation in Acacias. Australian Systematic Botany Society Newsletter 126, 40–41.

Murphy, D.J. and Reid, J.C. (2006). Wattles as weeds: some case studies from western Victoria. In Australian Plants Society Inc. Maroondah Group (ed.),Proceedings, Acacia 2006: knowing and growing Australian wattles, pp. 55–60. Australian Plants Society Inc. and National Herbarium of Victoria, Melbourne.