Publications

Below are a selection of publications from lab members for a more up-to-date list check out our google scholar links:

  >Prof. Mike Bunce: http://scholar.google.com.au/citations?user=YPoEsJcAAAAJ&hl

  >Dr Michael Stat: https://scholar.google.com.au/citations?user=dLmx_lEAAAAJ&hl=en

  >Dr Joey DiBattista: https://scholar.google.com.au/citations?user=VSN8cXsAAAAJ&hl=en

  >Dr Nicole White: http://scholar.google.com.au/citations?user=fUfMYoAAAAAJ&hl

  >Dr Megan Coghlan: https://scholar.google.com.au/citations?user=HTutpfcAAAAJ&hl=en

  >Dr Zoe Richards: https://scholar.google.com.au/citations?user=xTpbTPgAAAAJ&hl=en

2017 (so far…)

Berry, Tina; Osterrieder, Sylvia; Murray, Dáithí; Coghlan, Megan; Richardson, Anthony ; Grealy, Alicia; Stat, Michael; Bejder, Lars; Bunce, Michael. DNA metabarcoding for diet analysis and biodiversity: a case study using the endangered Australian sea lion (Neophoca cinerea) (2017) Ecology and Evolution (in press)

Natasha Hardy, Tina Berry, Brendan P. Kelaher, Simon D. Goldsworthy, Michael Bunce, Melinda A. Coleman, Bronwyn M. Gillanders, Sean D. Connell, Michelle Blewitt and Will Figueira. Assessing the trophic ecology of top predators across a recolonisation frontier using DNA metabarcoding of diets. (2017) Marine Ecology Progress Series (in press)

Raina JB, Clode P, Bougoure J, Kilburn M, Reeder A, Foret A, Stat M, Beltran V, Thomas-Hall P, Tapiolas D, Motti CM, Seymour JR, Willis BL, Bourne DG (accepted 2 Feb 2017) Subcellular tracking reveals the location of dimethylsulfoniopropionate in microalgae and visualises its uptake by marine bacteria. eLife 6: e23008

Thomas L, Kennington JW, Evans RD, Kendrick GA, Stat M (accepted 28 Jan 2017) Restricted gene flow and local adaptation highlight the vulnerability of high latitude reefs to rapid environmental change. Global Change Biology DOI 10.1111/gcb.13639

Alicia Grealy, , Matthew Phillips, , Gifford Miller, , M. Thomas P. Gilbert, , Jean-Marie Rouillard, , David Lambert, , Michael Bunce and James Haile. Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell. (2017) Molecular Phylogenetics and Evolution, Volume 109, Pages 151–163.

Newman, Stephen J et al. International workshop on advancing methods to overcome challenges associated with life history and stock assessments of data-poor deep-water snappers and groupers. (2017) Marine Policy 79 (78-83)

Byard, R., Musgrave, I., Maker, G. and Bunce, M. What are the risks to the Australian community from herbal products? (2017). Medical Journal of Australia. 206 (2), 86-90

2016

Crighton, E., Mullaney, I., Trengrove, R., Bunce, M and Marker G. The application of metabolomics for herbal medicine pharmacovigilance: a case study on ginseng (2016) Essays in Biochemistry  - 60 (5), 429-435

Grealy, A., Douglass, K.,  Haile, J., Bruwer, C., Gough, V. and Bunce M. Tropical ancient DNA from bulk archaeological fish bone reveals the subsistence practices of a historic coastal community in southwest Madagascar (2016) Journal of Archaeological Science 75, 82-88

Albornoz, FE., Teste, FP., Lambers, H., Bunce, M., Murray, DC., White, NE. and Laliberté E. Changes in ectomycorrhizal fungal community composition and declining diversity along a 2‐million‐year soil chronosequence (2016) Molecular Ecology 25 (19), 4919-4929

Hansen, TA., Mollerup, S., Nguyen, N., White, NE., Coghlan, M., Alquezar-Planas, DE., Joshi, T., Jensen, RH., Fridholm, H., Kjartansdóttir, KR., Mourier,  T., Warnow, T., Belsham, GJ., Bunce, M., Willerslev, E., Nielsen, LP., Vinner, L. and Hansen, AJ. High diversity of picornaviruses in rats from different continents revealed by deep sequencing  (2016) Emerging Microbes & Infections 5 (8), e90

Haouchar, D., Pacioni, C., Haile, J., McDowell, MC., Baynes, A., Phillips, MJ., Austin, JJ., Pope, LC. and Bunce, M. Ancient DNA reveals complexity in the evolutionary history and taxonomy of the endangered Australian brush-tailed bettongs (Bettongia: Marsupialia: Macropodidae: Potoroinae). (2016) Biodiversity and Conservation, 1-21

Grealy, A.,  Macken, A., Allentoft, ME., Rawlence, NJ., Reed, E. and Bunce, M. An assessment of ancient DNA preservation in Holocene–Pleistocene fossil bone excavated from the world heritage Naracoorte Caves, South Australia (2016) Journal of Quaternary Science 31 (1), 33-45

Harvey E, Bunce M, Stat M, et al. (2016) Science and the Sydney, pgs. 279-303. In: McCarthy M (ed.) From Great Depths
The Wrecks of HMAS Sydney II and HSK Kormoran. UWA Publishing and The Western Australian Museum, Australia.

Lucas MQ, Stat M, Smith MC, Weil E, Schizas NV (2016) Symbiodinium (ITS2) diversity in the coral host Agaricia lamarcki (Cnidaria:Scleractinia) among shallow and mesophotic reefs in the Northern Caribbean (20 – 70 m). Marine Ecology 37: 1079-1087

Thomas L, Stat M, Evans RD, Kennington JW (2016) A fluorescence-based quantitative real-time PCR assay for accurate Pocillopora damicornis species identification. Coral Reefs 35: 895-899

Madin J, Anderson K, Andreasen M, Bridge T, Cairns S, Connolly S, Darling E, Diaz M, Falster D, Franklin E, Gates R, Hoogenboom M, Huang D, Keith S, Kosnik M, Kuo C-Y, Lough J, Lovelock C, Luiz O, Martinelli J, Mizerek T, Pandolfi J, Pochon X, Pratchett MS, Putnam H, Roberts E, Stat M, Wallace C, Widman E, Baird A (2016) The coral trait database, a curated database of trait information for coral species from the global oceans. Scientific Data 3: 160017

2015

Pacioni, C., Hunt, H., Allentoft, M. E., Vaughan, T. G., Wayne, A. F., Baynes, A., Haouchar, D., Dortch, J. and Bunce, M. (2015), Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial. Molecular Ecology. Accepted Author Manuscript. doi:10.1111/mec.13430.

Schoepf V, Stat M, Falter J, McCulloch M (2015) Limits to the thermal tolerance of corals adapted to a highly fluctuating, naturally extreme temperature environment. Scientific Reports 5: 17639

Berry O., Bulman C., Bunce M., Coghlan M., Murray D., Ward  R. (2015) A comparison of morphological and DNA metabarcoding analysis of diets in exploited marine fishes. Marine Ecology Progress Series. doi: 10.3354/meps11524. 

Stat M, Yost D, Gates RD (2015) Geographic structure and host specificity shape the community composition of symbiotic dinoflagellates in corals from the Northwestern Hawaiian Islands. Coral Reefs DOI:10.​1007/​s00338-015-1320-0    

Alicia C. Grealy, Matthew C. McDowell, Paul Scofield, Dáithí C. Murray, Diana A. Fusco, James Haile, Gavin J. Prideaux, Michael Bunce (2015), A critical evaluation of how ancient DNA bulk bone metabarcoding complements traditional morphological analysis of fossil assemblages, Quaternary Science Reviews, Volume 128, Pages 37-47.

 Allentoft ME, Heller R, Holdaway RN, & Bunce M (2015) Ancient DNA microsatellite analyses of the extinct New Zealand giant moa (Dinornis robustus) identify relatives within a single fossil site. Heredity:doi:10.1038/hdy.2015.1048.

Thomas L, Kennington JW, Stat M, Wilkinson SP, Kool JT, Kendrick GA (2015) Isolation by resistance across a complex coral reef seascape. Proceedings of the Royal Society B DOI: 10.1098/rspb.2015.1217

Murray DC, Coghlan ML, & Bunce M (2015) From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows. PLoS one 10(4):e0124671.

Krüger M, et al. (2015) The rise and fall of arbuscular mycorrhizal fungal diversity during ecosystem retrogression. Molecular ecology.

McDowell MC, et al. (2015) Morphological and molecular evidence supports specific recognition of the recently extinct Bettongia anhydra (Marsupialia: Macropodidae). Journal of Mammalogy 96(2):287-296.

Gofton AW, et al. (2015) Inhibition of the endosymbiont Candidatus Midichloria mitochondrii during 16S rRNA gene profiling reveals potential pathogens in Ixodes ticks from Australia. Parasites & vectors 8(1):345.

Cooper C, Clode PL, Thomson DP, Stat M (2015) A flatworm from the genus Waminoa (Acoela: Convolutidae) associated with bleached corals in Western Australia. Zoological Science 32: 465-473    

Paparini A, et al. (2015) Comparison of Sanger and next generation sequencing performance for genotyping Cryptosporidium isolates at the 18S rRNA and actin loci. Experimental parasitology 151:21-27.

2014

Jarvis ED, et al. (2014) Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346(6215):1320-1331.

Zhang G, et al. (2014) Comparative genomics reveals insights into avian genome evolution and adaptation. Science 346(6215):1311-1320.

Allentoft ME, et al. (2014) Extinct New Zealand megafauna were not in decline before human colonization. Proceedings of the National Academy of Sciences 111(13):4922-4927.

Holdaway RN, et al. (2014) An extremely low-density human population exterminated New Zealand moa. Nature communications 5.

Burgar JM, et al. (2014) Who's for dinner? High‐throughput sequencing reveals bat dietary differentiation in a biodiversity hotspot where prey taxonomy is largely undescribed. Molecular ecology 23(15):3605-3617.

Byard RW, Musgrave I, Hoban C, & Bunce M (2014) DNA sequencing and metabolomics: new approaches to the forensic assessment of herbal therapeutic agents. Forensic science, medicine, and pathology 11(1):1-2.

Haouchar D, et al. (2014) Thorough assessment of DNA preservation from fossil bone and sediments excavated from a late Pleistocene–Holocene cave deposit on Kangaroo Island, South Australia. Quaternary Science Reviews 84:56-64.

Jacomb C, et al. (2014) High-precision dating and ancient DNA profiling of moa (Aves: Dinornithiformes) eggshell documents a complex feature at Wairau Bar and refines the chronology of New Zealand settlement by Polynesians. Journal of Archaeological Science 50:24-30.

Tridico SR, et al. (2014) Interpreting biological degradative processes acting on mammalian hair in the living and the dead: which ones are taphonomic? Proceedings of the Royal Society of London B: Biological Sciences 281(1796):20141755.

Tridico SR, Murray DC, Addison J, Kirkbride KP, & Bunce M (2014) Metagenomic analyses of bacteria on human hairs: a qualitative assessment for applications in forensic science. Investigative genetics 5(1):1-13.

Tridico SR, Rigby P, Kirkbride KP, Haile J, & Bunce M (2014) Megafaunal split ends: microscopical characterisation of hair structure and function in extinct woolly mammoth and woolly rhino. Quaternary Science Reviews 83:68-75.

White NE, et al. (2014) Identifying conservation units after large‐scale land clearing: a spatio‐temporal molecular survey of endangered white‐tailed black cockatoos (Calyptorhynchus spp.). Diversity and Distributions 20(10):1208-1220.

2013

Coghlan, M. L., White, N. E., Murray, D. C., Houston, J., Rutherford, W., Bellgard, M. I., Haile, J. & Bunce, M. (2013) Metabarcoding Avian diets at airports: implications for birdstrike hazard management plans. Investigative Genetics 4:27.  OPEN ACCESS

Tridico, S.R., Rigby, B, Kirkbride, K.P, Haile, J and Bunce , M (2013)  Megafaunal split ends: microscopical characterisation of hair structure and function in extinct woolly mammoth and woolly rhino, Quaternary Science Reviews in press, http://dx.doi.org/10.1016/j.quascirev.2013.10.032

Murray, D. C., Haile, J., Dortch, J., White, N., Haouchar, D., Bellgard, M. I., Allcock, R. J., Prideaux, G. J., & Bunce, M. (2013) Scrapheap Challenge: A novel bulk-bone metabarcoding method to investigate ancient DNA in faunal assemblages. Scientific Reports;Scientific Reports 3, Article number: 3371 doi:10.1038/srep03371       OPEN ACCESS

Phillips M, Haouchar D, Pratt R, Gibb G & Bunce, M. (2013) Inferring kangaroo phylogeny from incongruent nuclear and mitochondrial genes. PLoS ONE http://dx.plos.org/10.1371/journal.pone.0057745.

Dáithí C. Murray, Stuart G. Pearson, Richard Fullagar, Brian M. Chase, Jayne Houston, Jenny Atchison, Nicole E. White, Matthew I. Bellgard, Edward Clarke, Mike Macphail, M. Thomas P. Gilbert, James Haile and Michael Bunce. High-throughput Sequencing of Ancient Plant and Mammal DNA in herbivore Middens. Quaternary Science Reviews 2013.

Morten E. Allentoft, Matthew Collins, David Harker, James HaileCharlotte L. Oskam, Marie L. Hale, Paula F. Campos, Jose A. Samaniego, M. Thomas P. Gilbert, Eske Willerslev, Guojie Zhang, R. Paul Scofield, Richard N. Holdaway, and Michael Bunce. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc. R. Soc. B. rspb20121745; published ahead of print October 10, 2012, doi:10.1098/rspb.2012.1745.

Charlotte L. Oskam, Morten E. Allentoft, Richard Walter, R. Paul Scofield, James Haile, Richard N. Holdaway, Michael Bunce and Chris Jacomb. Ancient DNA analyses of early archaeological sites in New Zealand reveal extreme exploitation of moa (Aves: Dinornithiformes) at all life stages. Quaternary Science Reviews. Volume 52, 2 October 2012, Pages 41–48.

Dalal Haouchar, James Haile, Peter Spencer and Michael Bunce. The identity of the Depuch Island rock-wallaby revealed through ancient DNA. Australian Mammalogy.  http://dx.doi.org/ 10.1071/AM11044.

Selected Publications Before 2012

Coghlan, M., Haile, J., Houston, J., Murray, D., White, N., Moolhuijzen, P., Bellgard, M., and Bunce, M., Deep Sequencing of Plant and Animal DNA Contained Within Traditional Chinese Medicines Reveals Legality Issues and Health Safety Concerns. PLoS Genetics - link to paper

M. Rassmussen, et al., An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia. Science, (2011)

D.C. Murray, et al., DNA-Based Faecal Dietary Analysis: A Comparison of qPCR and High Throughput Sequencing Approaches. PLoS ONE, in press (2011).

M.L. Coghlan, et al., Egg forensics: An appraisal of DNA sequencing to assist in species identification of illegally smuggled eggs, Forensic Science International Genetics, doi:10.1016/j.fsigen.2011.06.006, (2011).

N. E. White, et al., The evolutionary history of cockatoos (Aves: Psittaciformes: Cacatuidae). Molecular Phylogenetics and Evolution. 59 , 615–622 (2011).

C. L. Oskam et al.,  Molecular and morphological analyses of avian eggshell excavated from a late thirteenth century earth oven. Journal of Archaeological Science 38, 2589e2595, (2011)

M. E. Allentoft et al., Profiling the Dead: Generating Microsatellite Data from Fossil Bones of Extinct Megafauna-Protocols, Problems, and Prospects. PLoS ONE 6, e16670 (2011).

Oskam, C., Haile, J., McLay, E., Rigby, P., Allentoft, M., Olsen, M., Bengtsson, C., Miller, G., Schwenninger, J., Jacomb, C., Walter, R., Baynes, A., Dortch, J., Parker-Pearson, M., Gilbert, M., Holdaway, R., Willerslev, E., & Bunce, M. (2010). Fossil avian eggshell preserves ancient DNA. Proceedings of the Royal Society B: Biological Sciences (available online from March 15th 2010).

Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MTP, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Gronnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TFG, Ramsey CB, Hansen TvO, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Ponten T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E .Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature, (2010) 463, 757-762.

Morten E. Allentoft , Michael Bunce, R. Paul Scofield, Marie L. Hale and Richard N. Holdaway (2009). Highly skewed sex ratios and biased fossil deposition of moa: ancient DNA provides new insight on New Zealand’s extinct megafauna.  Quaternary Science reviews (2009)  29 (2010) 753–762. 

Bunce, M., Worthy, T.H., Phillips, M.J., Holdaway, R.N., Willerslev, E., Haile, J., Shapiro, B., Scofield, R.P., Drummond, A., Kamp, P.J.J., et al. (2009). The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. Proceedings of the National Academy of Sciences. 10.1073/pnas.0906660106.

Tammy E. Steeves, Richard N. Holdaway, Marie L. Hale, Emma McLay, Ian A. W. McAllan, Margaret Christian, Mark E. Hauber, and Michael Bunce. (2009) Merging ancient and modern DNA: extinct seabird taxon rediscovered in the North Tasman Sea. Biology Letters 2009 : rsbl.2009.0478v1-rsbl20090478.

Hebsgaard, M. B., Gilbert, M. T. P., Arneborg, J., Heyn, P. M. L., Allentoft, M. E., Bunce, M., Schweger, C. and Willerslev, E. An Ancient DNA study from The Farm Beneath the Sand. (2009)  Antiquity, 83 (2009): 430–444. 

Salinas, M., Bunce, M., Cancilla, D., Alpers, D. L. and Spencer, P.B.S Divergent lineages in the heath mouse (Pseudomys shortridgei) are indicative of major contraction to geographically isolated refugia on the eastern and western sides of Australia during the early Pleistocene. (2009) Australian Journal of Zoology (in Press). 

Allentoft, M. E., Schuster, S. C.,, Holdaway, R. N., Hale, M., McLay, E., Oskam, C., Gilbert, M. T. P., Spencer, P., Willerslev, E. and Bunce, M. (2009) Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data. BioTechniques 46, (3): pp 195-200

Worobey, M., Gemmel, M., Teuwen, D. E., Haselkorn, T., Kunstman, K., Bunce, M., Muyembe, J.-J., Kabongo, J.-M. M., Kalengayi, R. M., Van Marck, E., Gilbert, M.T.P. and  Wolinsky, S. M.  (2008) Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960. Nature 455 (7213), 661-664.

Stewart Johnson, S., Hebsgaard, MB., Christensen T., Mastepanov M., Nielsen R., Munch K., Brand T., Gilbert MTP., Zuber MT., Bunce M., Rønn R., Gilichinsky D., Froese D and  Willerslev E. Ancient Bacteria Show Evidence of DNA Repair. Proceeding of the National Academy of Sciences (USA). Accepted for publication 2nd August 2007.

Willerslev, E., Cappellini, E., Boomsma, W., Nielsen, R., Hebsgaard, M. B., Brand, T. B., Hofreiter, M., Bunce, M., Poinar, H. N., Dahl-Jensen, D., Johnsen, S., Steffensen, J. P., Bennike, O., Schwenninger, J.-L., Nathan, R., Armitage, S., de Hoog, C.-J., Alfimov, V., Christl, M., Beer, J., Muscheler, R., Barker, J., Sharp, M., Penkman, K. E. H., Haile, J., Taberlet, P., Gilbert, M. T. P., Casoli, A., Campani, E., and Collins, M. J. (2007). Ancient Biomolecules from Deep Ice Cores Reveal a Forested Southern Greenland. Science 317(5834), 111-114.

Haile J, Holdaway R, Oliver K, Bunce M, Gilbert MTP, et al. 2007. Ancient DNA chronology within sediment deposits: Are paleobiological reconstructions possible and is DNA leaching a factor? Molecular Biology and Evolution 24: 982-9 


Spencer, P. B. S., Cardoso, M., How, R. A., Williams, J., Bunce, M., and Schmitt, L. H. (2007) Cross-species amplification at microsatellite loci in Australian quolls including the description of five new markers from the Chuditch (Dasyurus geoffroii). Molecular Ecology Notes. published online June 2007.

Gilbert MTP, Haselkorn T, Bunce M, Sanchez JJ, Lucas SB, et al. (2007) The Isolation of Nucleic Acids from Fixed, Paraffin-Embedded Tissues–Which Methods Are Useful When?. PLoS ONE 2(6): e537. doi:10.1371/journal.pone.0000537

Vuissoz A, Worobey M, Odegaard N, Bunce M, Machado CA, Lynnerup N, Peacock E, Gilbert MTP (2007) The survival of PCR-amplifiable DNA in cow leather. J Arch Sci 34, 823-829

Bunce, M & Holdaway, RN (2006).  New Zealand 's extinct giant eagle.  Bulletin of the British Ornithologists' Club, 126a, 4-7.

Binladen J, Wiuf C, Gilbert MTP, Bunce M, Barnett R, Larson G, Greenwood AD, Haile J, Ho SYW, Hansen AJ, Willerslev E. 2006 Assessing the fidelity of ancient DNA sequences amplified from nuclear genes. Genetics 172: 733-741

Lister, A. M., Edwards, C. J., Nock, D., Bunce, M., van Pijlen, I, A., Bradley, D. G., Thomas, M. G. and Barnes, I. (2005) The phylogenetic position of the ‘giant deer’ Megaloceros giganteus: congruence of molecular and morphological evidence. Nature 438, 850-853.

Bunce, M., Szulkin, M., Lerner, H.R.L., Barnes, I., Shapiro, B., Cooper, A. and Holdaway, R. N. (2005). Ancient DNA provides new insights into the evolutionary history of New Zealand’s extinct giant eagle. PloS Biology. 3(1): e9. 

Gilbert, M. T.P., Wilson, A. S., Bunce, M., Hansen, A. J., Willerslev, E., Shapiro, B. A., Higham, T. F. G., Richards, M. P., O'Connell, T. C., Tobin, D. J., Janaway, R. C. and Cooper, A. (2004) Ancient mitochondrial DNA from hair. Current Biology 14 (12): R463-464.

Bunce, M., Worthy, T. H., Ford, T., Hoppitt, W., Willerslev, E., Drummond, A., and Cooper, A. (2003). Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis. Nature 425, 172-175. 

Willerslev E, Hansen AJ, Binladen J, Brand TB, Gilbert MTP, Shapiro B, Bunce M, Wiuf C, Gilichinsky DA, Cooper A (2003) Diverse plant and animal genetic records from Holocene and Pleistocene sediments.  Science 300 (5620): 791-795

Worthy, T.H., Bunce, M., Cooper, A. & Scofield, P. 2005. Dinornis– an insular oddity, a taxonomic conundrum reviewed. In Alcover, J.A. & Bover, P. (eds.): Proceedings of the International Symposium “Insular Vertebrate Evolution: the Palaeontological Approach”. Monografies de la Societat d’Història Natural de les Balears, 12: 377-390.

© mike bunce 2015