Publications

2023

  • Alexander, J. B., Marnane, M. J., Elsdon, T. S., Bunce, M., Sitaworawet, P., Songploy, S., Chaiyakul, S., & Harvey, E. S. (2023). Using environmental DNA to better inform decision making around decommissioning alternatives for offshore oil and gas infrastructure. Science of The Total Environment, 901, 165991. https://doi.org/10.1016/j.scitotenv.2023.165991
  • Alexander, J. B., Marnane, M. J., McDonald, J. I., Lukehurst, S. S., Elsdon, T. S., Simpson, T., Hinz, S., Bunce, M., & Harvey, E. S. (2023). Comparing environmental DNA collection methods for sampling community composition on marine infrastructure. Estuarine Coastal and Shelf Science, 283, 108283. https://doi.org/10.1016/j.ecss.2023.108283
  • Berry, T. E., Coghlan, M. L., Saunders, B. J., Richardson, A. J., Power, M., Harvey, E., Jarman, S., Berry, O., Davies, C. H., & Bunce, M. (2023). A 3-year plankton DNA metabarcoding survey reveals marine biodiversity patterns in Australian coastal waters. Diversity and Distributions, 29(7), 862–878. https://doi.org/10.1111/ddi.13699
  • Campbell, M. A., Laini, A., White, N. E., Allentoft, M. E., & Saccò, M. (2023). When nets meet environmental DNA metabarcoding: Integrative approach to unveil invertebrate community patterns of hypersaline lakes. Journal of Oceanology and Limnology, 41(4), 1331–1340. https://doi.org/10.1007/s00343-022-2151-9
  • Dhami, N. K., Greenwood, P. F., Poropat, S. F., Tripp, M., Elson, A., Vijay, H., Brosnan, L., Holman, A. I., Campbell, M., Hopper, P., Smith, L., Jian, A., & Grice, K. (2023). Microbially mediated fossil concretions and their characterization by the latest methodologies: A review. Frontiers in Microbiology, 14. https://www.frontiersin.org/articles/10.3389/fmicb.2023.1225411
  • Fernandes, K., Bateman, P. W., Saunders, B. J., Bunce, M., Bohmann, K., & Nevill, P. (n.d.). Use of carrion fly iDNA metabarcoding to monitor invasive and native mammals. Conservation Biology, n/a(n/a), e14098. https://doi.org/10.1111/cobi.14098
  • Grealy, A., Miller, G. H., Phillips, M. J., Clarke, S. J., Fogel, M., Patalwala, D., Rigby, P., Hubbard, A., Demarchi, B., Collins, M., Mackie, M., Sakalauskaite, J., Stiller, J., Clarke, J. A., Legendre, L. J., Douglass, K., Hansford, J., Haile, J., & Bunce, M. (2023). Molecular exploration of fossil eggshell uncovers hidden lineage of giant extinct bird. Nature Communications, 14(1), Article 1. https://doi.org/10.1038/s41467-023-36405-3
  • Griebler, C., Hahn, H. J., Mammola, S., Niemiller, M. L., Weaver, L., Saccò, M., Bichuette, M. E., & Hose, G. C. (2023). Chapter 24—Legal frameworks for the conservation and sustainable management of groundwater ecosystems. In F. Malard, C. Griebler, & S. Rétaux (Eds.), Groundwater Ecology and Evolution (Second Edition) (pp. 551–571). Academic Press. https://doi.org/10.1016/B978-0-12-819119-4.15005-X
  • Harvey, M. S., Burger, M. a. A., Abrams, K. M., Finston, T. L., Huey, J. A., & Perina, G. (2023). The systematics of the pseudoscorpion genus Indohya (Pseudoscorpiones: Hyidae) in Australia. Zootaxa, 5342(1), Article 1. https://doi.org/10.11646/zootaxa.5342.1.1
  • Kestel, J. H., Bateman, P. W., Field, D. L., White, N. E., Lines, R., & Nevill, P. (2023). eDNA metabarcoding of avocado flowers: ‘Hass’ it got potential to survey arthropods in food production systems? Molecular Ecology Resources, 23(7), 1540–1555. https://doi.org/10.1111/1755-0998.13814
  • Laini, A., Stubbington, R., Beermann, A. J., Burgazzi, G., Datry, T., Viaroli, P., Wilkes, M., Zizka, V. M. A., Saccò, M., & Leese, F. (2023). Dissecting biodiversity: Assessing the taxonomic, functional and phylogenetic structure of an insect metacommunity in a river network using morphological and metabarcoding data. The European Zoological Journal, 90(1), 320–332. https://doi.org/10.1080/24750263.2023.2197924
  • McDonald, R., Bateman, P. W., Cooper, C., van der Heyde, M., Mousavi-Derazmahalleh, M., Hedges, B. A., Guzik, M. T., & Nevill, P. (2023). Detection of vertebrates from natural and artificial inland water bodies in a semi-arid habitat using eDNA from filtered, swept, and sediment samples. Ecology and Evolution, 13(4), e10014. https://doi.org/10.1002/ece3.10014
  • Mousavi-Derazmahalleh, M., Ellis, R. J., D’Rozario, B. L., Berry, T. E., Peverley, G., Dawkins, K. L., Campbell, M., White, N. E., & Allentoft, M. E. (2023). Rock pools as a source of environmental DNA for the detection of the threatened Pilbara olive python (Liasis olivaceus barroni). Frontiers in Environmental Science, 11. https://www.frontiersin.org/articles/10.3389/fenvs.2023.1187545
  • Simpson, T. J., Wellington, C. M., Lukehurst, S. S., Huerlimann, R., Veilleux, H., Snow, M., Dias, J., & McDonald, J. I. (2023). Development of a real-time PCR (qPCR) method for the identification of the invasive paddle crab Charybdis japonica (Crustacea, Portunidae). PeerJ, 11, e15522. https://doi.org/10.7717/peerj.15522
  • van der Heyde, M., White, N. E., Nevill, P., Austin, A. D., Stevens, N., Jones, M., & Guzik, M. T. (2023). Taking eDNA underground: Factors affecting eDNA detection of subterranean fauna in groundwater. Molecular Ecology Resources, 23(6), 1257–1274. https://doi.org/10.1111/1755-0998.13792
  • Venarsky, M., Simon, K. S., Saccò, M., François, C., Simon, L., & Griebler, C. (2023). Chapter 10—Groundwater food webs. In F. Malard, C. Griebler, & S. Rétaux (Eds.), Groundwater Ecology and Evolution (Second Edition) (pp. 241–261). Academic Press. https://doi.org/10.1016/B978-0-12-819119-4.00010-X
  • Corriveau, A., Klaassen, M., Garnett, S. T., Kaestli, M., Power, M. W., Mousavi-Derazmahalleh, M., Coghlan, M. L., Christian, K., Bunce, M., & Campbell, H. A. (2022). Using dietary metabarcoding analyses to characterise waterbirds–agriculture interactions. Journal of Applied Ecology, 59(11), 2756–2766. https://doi.org/10.1111/1365-2664.14272
  • Kjær, K. H., Winther Pedersen, M., De Sanctis, B., De Cahsan, B., Korneliussen, T. S., Michelsen, C. S., Sand, K. K., Jelavić, S., Ruter, A. H., Schmidt, A. M. A., Kjeldsen, K. K., Tesakov, A. S., Snowball, I., Gosse, J. C., Alsos, I. G., Wang, Y., Dockter, C., Rasmussen, M., Jørgensen, M. E., Willerslev, E. (2022). A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature, 612(7939), Article 7939. https://doi.org/10.1038/s41586-022-05453-y
  • Muir, P. R., Obura, D. O., Hoeksema, B. W., Sheppard, C., Pichon, M., & Richards, Z. T. (2022). Conclusions of low extinction risk for most species of reef-building corals are premature. Nature Ecology & Evolution, 6(4), Article 4. https://doi.org/10.1038/s41559-022-01659-5
  • Nester, G. M., Heydenrych, M. J., Berry, T. E., Richards, Z., Wasserman, J., White, N. E., De Brauwer, M., Bunce, M., Takahashi, M., & Claassens, L. (2023). Characterizing the distribution of the critically endangered estuarine pipefish (Syngnathus watermeyeri) across its range using environmental DNA. Environmental DNA, 5(1), 132–145. https://doi.org/10.1002/edn3.365
  • Newton, J. P., Bateman, P. W., Heydenrych, M. J., Kestel, J. H., Dixon, K. W., Prendergast, K. S., White, N. E., & Nevill, P. (2023). Monitoring the birds and the bees: Environmental DNA metabarcoding of flowers detects plant–animal interactions. Environmental DNA. https://doi.org/10.1002/edn3.399
  • Perina, G., Camacho, A., Cooper, S. J. B., Floeckner, S., Blyth, A. J., & Saccò, M. (2023). An integrated approach to explore the monophyletic status of the cosmopolitan genus Hexabathynella (Crustacea, Bathynellacea, Parabathynellidae): Two new species from Rottnest Island (Wadjemup), Western Australia. Systematics and Biodiversity, 21(1), 2151662. https://doi.org/10.1080/14772000.2022.2151662
  • Perina, G., Camacho, A. I., Danks, M., White, N., & Guzik, M. T. (2023). Two new species of Atopobathynella (Parabathynellidae, Bathynellacea) from the Pilbara region, Australia. Systematics and Biodiversity, 21(1), 2228326. https://doi.org/10.1080/14772000.2023.2228326
  • Suter, L., Wotherspoon, S., Kawaguchi, S., King, R., MacDonald, A. J., Nester, G. M., Polanowski, A. M., Raymond, B., & Deagle, B. E. (2023). Environmental DNA of Antarctic krill (Euphausia superba): Measuring DNA fragmentation adds a temporal aspect to quantitative surveys. Environmental DNA. https://doi.org/10.1002/edn3.394
  • Takahashi, M., Saccò, M., Kestel, J. H., Nester, G., Campbell, M. A., van der Heyde, M., Heydenrych, M. J., Juszkiewicz, D. J., Nevill, P., Dawkins, K. L., Bessey, C., Fernandes, K., Miller, H., Power, M., Mousavi-Derazmahalleh, M., Newton, J. P., White, N. E., Richards, Z. T., & Allentoft, M. E. (2023). Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution. Science of The Total Environment, 873, 162322. https://doi.org/10.1016/j.scitotenv.2023.162322
  • Thomas, L., Underwood, J. N., Rose, N. H., Fuller, Z. L., Richards, Z. T., Dugal, L., Grimaldi, C. M., Cooke, I. R., Palumbi, S. R., & Gilmour, J. P. (2022). Spatially varying selection between habitats drives physiological shifts and local adaptation in a broadcast spawning coral on a remote atoll in Western Australia. Science Advances, 8(17), eabl9185. https://doi.org/10.1126/sciadv.abl9185
  • Zhang, J., Richards, Z. T., Adam, A. A. S., Chan, C. X., Shinzato, C., Gilmour, J., Thomas, L., Strugnell, J. M., Miller, D. J., & Cooke, I. (2022). Evolutionary Responses of a Reef-building Coral to Climate Change at the End of the Last Glacial Maximum. Molecular Biology and Evolution, 39(10), msac201. https://doi.org/10.1093/molbev/msac201

2022

  • Alexander, J. B., Marnane, M. J., Elsdon, T. S., Bunce, M., Songploy, S., Sitaworawet, P., & Harvey, E. S. (2022). Complementary molecular and visual sampling of fish on oil and gas platforms provides superior biodiversity characterisation. Marine Environmental Research, 179, 105692. https://doi.org/10.1016/j.marenvres.2022.105692
  • D’Agui, H. M., van der Heyde, M. E., Nevill, P. G., Mousavi-Derazmahalleh, M., Dixon, K. W., Moreira-Grez, B., & Valliere, J. M. (2022). Evaluating biological properties of topsoil for post-mining ecological restoration: Different assessment methods give different results. Restoration Ecology, 30(S1), e13738. https://doi.org/10.1111/rec.13738
  • Fernandes, K., Prendergast, K., Bateman, P. W., Saunders, B. J., Gibberd, M., Bunce, M., & Nevill, P. (2022). DNA metabarcoding identifies urban foraging patterns of oligolectic and polylectic cavity-nesting bees. Oecologia, 200(3–4), 323–337. https://doi.org/10.1007/s00442-022-05254-0
  • Kestel, J. H., Field, D. L., Bateman, P. W., White, N. E., Allentoft, M. E., Hopkins, A. J. M., Gibberd, M., & Nevill, P. (2022). Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects. The Science of the Total Environment, 847, 157556. https://doi.org/10.1016/j.scitotenv.2022.157556
  • Ryan, E., Bateman, P., Fernandes, K., van der Heyde, M., & Nevill, P. (2022). EDNA metabarcoding of log hollow sediments and soils highlights the importance of substrate type, frequency of sampling and animal size, for vertebrate species detection. Environmental DNA, 4(4), 940–953. https://doi.org/10.1002/edn3.306
  • Shen, Z., D’Agui, H., Walden, L., Zhang, M., Yiu, T. M., Dixon, K., Nevill, P., Cross, A., Matangulu, M., Hu, Y., & Viscarra Rossel, R. A. (2022). Miniaturised visible and near-infrared spectrometers for assessing soil health indicators in mine site rehabilitation. SOIL, 8(2), 467–486. https://doi.org/10.5194/soil-8-467-2022
  • van der Heyde, M., Bunce, M., & Nevill, P. (2022). Key factors to consider in the use of environmental DNA metabarcoding to monitor terrestrial ecological restoration. Science of The Total Environment, 848, 157617. https://doi.org/10.1016/j.scitotenv.2022.157617
  • Walters, S. J., Robinson, T. P., Byrne, M., & Nevill, P. (2022). Seed sourcing in the genomics era: Multispecies provenance delineation for current and future climates. Restoration Ecology, 30(S1), e13718. https://doi.org/10.1111/rec.13718
  • Wanniarachchi, S., Swan, M., Nevil, P., & York, A. (2022). Using eDNA metabarcoding to understand the effect of fire on the diet of small mammals in a woodland ecosystem. Ecology and Evolution, 12(11), e9457. https://doi.org/10.1002/ece3.9457
  • Adam, A. A., Thomas, L., Underwood, J., Gilmour, J., & Richards, Z. T. (2022). Population connectivity and genetic offset in the spawning coral Acropora digitifera in Western Australia. Molecular Ecology, 31, 3533-3547. https://doi.org/10.1111/mec.16498
  • Bohmann, K., Elbrecht, V., Carøe, C., Bista, I., Leese, F., Bunce, M., … & Creer, S. (2022). Strategies for sample labelling and library preparation in DNA metabarcoding studies. Molecular Ecology Resources. 22(4), 1231-1246.
  • Demarchi, B., Stiller, J., Grealy, A., Mackie, M., Deng, Y., … & Miller, G. (2022). Ancient proteins resolve controversy over the identity of Genyornis eggshell. PNAS. https://doi.org/10.1073/pnas.2109326119
  • DiBattista, J. D., Berumen, M. L., Priest, M. A., De Brauwer, M., Coker, D. J., Sinclair‐Taylor, T. H., . . . Marshell, A. (2022). Environmental DNA reveals a multi‐taxa biogeographic break across the Arabian Sea and Sea of Oman. Environmental DNA, 4(1), 206-221.
  • Elbourne, L. D. H., Sutcliffe, B., Humphreys, W., Focardi, A., Saccò, M., Campbell, M. A., Paulsen, I. T., & Tetu, S. G. (2022). Unravelling Stratified Microbial Assemblages in Australia’s Only Deep Anchialine System, The Bundera Sinkhole. Frontiers in Marine Science, 0, 679. https://doi.org/10.3389/FMARS.2022.872082
  • Espino, M. M., Mychajliw, A. M., Almonte, J. N., Allentoft, M. E., Van Dam, A. R. (2022). Raptor roosts as invasion archives: insights from the first black rat mitochondrial genome sequenced from the Caribbean. Biol Invasions. 24, 17–25. https://doi.org/10.1007/s10530-021-02636-y
  • Ferreira, R. L., Bernard, E., da Cruz Júnior, F. W., Piló, L. B., Calux, A., Souza-Silva, M., … & Frick, W. F. (2022). Brazilian cave heritage under siege. Science, 375(6586), 1238-1239.
  • Jones, J., Reinke, S. N., Mousavi-Derazmahalleh, M., Palmer, D. J., & Christophersen, C. T. (2022). Changes to the Gut Microbiome in Young Children Showing Early Behavioral Signs of Autism. Frontiers in Microbiology, 13, 905901. https://doi.org/10.3389/fmicb.2022.905901
  • Juszkiewicz, D. J., White, N. E., Stolarski, J., Benzoni, F., Arrigoni, R., Hoeksema, B. W., … & Richards, Z. T. (2022). Phylogeography of recent Plesiastrea (Scleractinia: Plesiastreidae) based on an integrated taxonomic approach. Molecular Phylogenetics and Evolution, 172, 107469. https://doi.org/10.1016/j.ympev.2022.107469
  • Latino, C., Gianatti, E.J., Mehta, S., Lo, J., Devine, A. & Christophersen, C.T. (2022). Does a high dietary intake of resistant starch affect glycaemic control and alter the gut microbiome in women with gestational diabetes? A randomised control trial protocol. BMC Pregnancy and Childbirth, 22:46, https://doi.org/10.1186/s12884-021-04366-4
  • Newton, P. J., Bateman, P. W., Heydenrych, M. J., Mousavi-Derazmahalleh, M., Nevill, P. (2022). Home is where the hollow is: Revealing vertebrate tree hollow user biodiversity with eDNA metabarcoding. Environmental DNA. https://doi.org/10.1002/edn3.313
  • Rao, W-Q., Kalogeropoulos, K., Allentoft, M.E., Gopalakrishnan, Sh., Zhao, W-N., Workman, K.T., … Laustsen, A.H. (2022). The rise of genomics in snake venom research: recent advances and future perspectives, GigaScience, 11. https://doi.org/10.1093/gigascience/giac024
  • Rees, J., Fu, S.C., Lo, J.,Sambell, R., Lewis, J.R., Christophersen, C.T., Byrne, M.F., Newton, R.U., Boyle, S., & Devine, A. (2022). How a 7-week food literacy cooking program affects cooking confidence and mental health: Findings of a quasi-experimental controlled intervention trial. Frontiers in Nutrition.
  • Saccò, M., Humphreys, W. F., Stevens, N., Jones, M. R., Takulis, F., Thomas, E., & Blyth, A. J. (2022). Subterranean carbon flows from source to stygofauna: a case study on the atyid shrimp Stygiocaris stylifera (Holthuis, 1960) from Barrow Island (WA). Isotopes in Environmental and Health Studies, 1-11.
  • Saccò, M., Blyth, A. J., Venarsky, M., & Humphreys, W. F. (2022). Trophic Interactions in Subterranean Environments. Reference Module in Earth Systems and Environmental Sciences. Amsterdam: Elsevier. doi: 10.1016/B978-0-12-819166-8.00064-5.
  • Saccò, M., Guzik, M. T., van der Heyde, M., Nevill, P., Cooper, S. J., Austin, A. D., …  White, N. E. (2022). eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects. Science of The Total Environment, 153223.
  • Saccò, M., Campbell, M. A., Nevill, P., Humphreys, W. F., Blyth, A. J., Grierson, P. F., & White, N.E. (2022). Getting to the root of organic inputs in groundwaters: stygofaunal plant consumption in a calcrete aquifer. Frontiers in Ecology and Evolution, 10, 854591.
  • Valliere, J.M., D’Agui, H.M., Dixon, K.W. et al (2022). Stockpiling disrupts the biological integrity of topsoil for ecological restoration. Plant Soil. 471, 409–426. https://doi.org/10.1007/s11104-021-05217-z
  • van der Heyde, M., Bunce, M., Dixon, K.W., Fernandes, K., Majer, J., Wardell-Johnson, G., White, N.E., & Nevill, P. (2022). Evaluating restoration trajectories using DNA metabarcoding of ground-dwelling and airborne invertebrates and associated plant communities. Mol. Ecol. 1–17. https://doi.org/10.1111/mec.16375
  • Wong, W.S., Morald, T.K., Whiteley, A.S., Nevill, P.G., Trengove, R.D., Yong, J.W., Dixon, K.W., Valliere, J.M., Stevens, J.C. and Veneklaas, E.J. (2022). Microbial inoculation to improve plant performance in mine‐waste substrates: A test using pigeon pea (Cajanus cajan). Land Degradation & Development, 33(3), 497-511.

2021

  • Adam, A. A. S., Garcia R., Galaiduk R., Tomlinson S., Radford B., Thomas L., & Richards Z. T. (2021). Diminishing potential for tropical reefs to function as coral diversity strongholds under climate change conditions. Diversity and Distributions, 00, 1-17.
  • Ali, A., Christophersen C.T. & Keelan J.A. (2021). Vaginal microbial profiling in a preterm birth high-risk cohort using shallow shotgun metagenomics. Microbiology Australia, 42, 69-74. https://doi.org/10.1071/MA21023
  • Arrigoni, R., Huang, D., Berumen, M.L., Budd, A.F., Montano, S., Richards, Z., Terraneo, T.I. & Benzoni, F. (2021). Integrative systematics of the scleractinian coral genera Caulastraea, Erythrastrea and Oulophyllia. Zoologica Scripta. 50(4), 509-527.
  • Bessey, C., Jarman, S.N., Simpson, T., Miller, H., Stewart, T., Keesing, J.K. & Berry, O. (2021). Passive eDNA collection enhances aquatic biodiversity analysis. Communications Biology, 4: 236.
  • Bohmann, K., Elbrecht, V., Carøe, Ch., . . ., Bunce, M., . . . Creer, S. (2021). Strategies for sample labelling and library preparation in DNA metabarcoding studies. Authorea. DOI: 10.22541/au.162141261.10649593/v1
  • Cross, S. L., Cross, A. T., Tomlinson, S., Clark-Ioannou, S. M., Nevill, P. G., & Bateman, P. W. (2021). Mitigation and management plans should consider all anthropogenic disturbances to fauna. Global Ecology and Conservation, 26. e01500
    s://doi.org/10.1038/s42003-021-01760-8
  • Crump, S.E., Frechette, B., Power, M.W.P., Cutler, S., de Wet, G., Raynolds, M.K., Raberg, J., Briner, J.P., Thomas, E.K., Sepulveda, J., Shapiro, B., Bunce, M., Miller, G.H. (2021). Ancient plant DNA reveals High Arctic greening during the Last Interglacial. Proceedings of the National Academy of Sciences of the United States of America, 118(13), 1-9. https://doi.org/10.1073/pnas.2019069118
  • Cvitanovic, C., Mackay, M., Kelly, R., Wilson, S.K., Waples, K., . . . Mathews, D. (2021). Thirty critical research needs for managing an ecologically and culturally unique remote marine environment: The Kimberley region of Western Australia. Ocean & Coastal Management, 212, p.105771.
  • De Jong, E., Lauzon-Joset, J., Leffler, J., Serralha, M., Larcombe, A., Christophersen, C.T., . . . Bosco, A. (2021). IRF7-associated immunophenotypes have dichotomous responses to virus/allergen co-exposure and OM-85-induced reprogramming. Frontiers in Immunology, 12, 2961. https://doi.org/10.3389/fimmu.2021.699633
  • Dias, P.J., Lukehurst, S.S., Simpson, T., Rocha, R.M., Tovar-Hernandez, M.A., Wellington, C., McDonald, J.I., Snow, M. & Kennington, W.J. (2021). Multiple introductions and regional spread shape the distribution of the cryptic ascidian Didemnum perlucidum in Australia: an important baseline for management under climate change. Aquatic Invasions, 16, 297-313.
  • DiBattista J.D., Berumen M.L., Priest M.A., De Brauwer, M., Coker, D.J., Sinclair-Taylor, T.H., Hay, A., Bruss, G., Mansour, S., Bunce, M., Goatley, C.H.R., Power, M.W.P., Marshell, A. (2021). Environmental DNA reveals a multi-taxa biogeographic break across the Arabian Sea and Sea of Oman. Environmental DNA, 1, 1-16. https://doi.org/10.1002/edn3.252
  • Dugal, L., Thomas, L., Jensen, M.R., Sigsgaard, E.E., Simpson, T., Jarman, S., Thomsen, P.F. & Meekan, M. (2021) Individual haplotyping of whale sharks from seawater environmental DNA. Molecular Ecology Resources. DOI: 10.1111/1755-0998.13451
  • Dugal, L., Thomas, L., Wilkinson, S. P., Richards, Z. T., Alexander, J. B., Adam, A. A., . . . Gilmour, P. (2021). Coral monitoring in northwest Australia with environmental DNA metabarcoding using a curated reference database for optimized detection. Environmental DNA
  • Egfjord AF-H, Margaryan A, Fischer A, Sjögren K-G, Price TD, Johannsen NN,…, Allentoft ME. (2021). Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture in Denmark. PLoS ONE. 16(1): e0244872. https://doi.org/10.1371/journal.pone.0244872
  • Evans, R.D., Thomas, L., Kennington, W.J., Ryan, N.M., Wilson, N.G., Richards, Z., Lowe, R.J. & Tuckett, C. (2021). Population genetic structure of a broadcast‐spawning coral across a tropical–temperate transition zone reveals regional differentiation and high‐latitude reef isolation. Journal of Biogeography. 48(12).3185-3195. https://doi.org/10.1111/jbi.14280
  • Fujise, L., Suggett, D. J., Stat, M., Kahlke, T., Bunce, M., Gardner, S. G., . . . Nitschke, M. R. (2021). Unlocking the phylogenetic diversity, primary habitats, and abundances of free‐living Symbiodiniaceae on a coral reef. Molecular Ecology, 30(1), 343-360.
  • Gajdzik, L., DeCarlo, T., Koziol, A., Mousavi-Derazmahalleh M., Coghlan, M., Power, M.W.P., Bunce, M., Fairclough, D.V., Travers, M.J., Moore, G.I. & Dibattista, J.D. (2021). Climate-assisted persistence of tropical fish vagrants in temperate marine ecosysyems. Communications Biology, 4(1), 1231-1240. https://doi.org/10.1038/s42003-021-02733-7
  • Harvey, ES., Watts, SL., Saunders, BJ., Driessen, D., Fullwood, LAF., Bunce, M., Songploy, S., Kettratad, J., Sitaworawet, P., Chaiyakul, S., Elsdon, TS. and Marnane, MJ. (2021). Fish Assemblages Associated With Oil and Gas Platforms in the Gulf of Thailand. Front. Mar. Sci. 8:664014. doi: 10.3389/fmars.2021.664014
  • Heydenrych, M. J., Saunders, B. J., Bunce, M. & Jarman, S. N. (2021). Epigenetic Measurement of Key Vertebrate Population Biology Parameters. Frontiers in Ecology and Evolution, 9, 617376. https://doi.org/10.3389/fevo.2021.61737
  • Hobbs, J.P.A., Richards, Z.T., Popovic, I., Lei, C., Staeudle, T.M., Montanari, S.R. & DiBattista, J.D., (2021). Hybridisation and the evolution of coral reef biodiversity. Coral Reefs. 1-15.
  • Jones, K.K., Humphreys, W.F., Saccò, M., Bertozzi, T., Austin, A.D. & Cooper, S. J. (2021). The critical thermal maximum of diving beetles (Coleoptera: Dytiscidae): a comparison of subterranean and surface-dwelling species. Current Research in Insect Science, 1, 100019. https://doi.org/10.1016/j.cris.2021.100019
  • Jones, J., Reinke, S. N., Ali, A., Palmer, D. J., & Christophersen, C. T. (2021). Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations. Scientific Reports, 11(1), 1-13. https://doi.org/10.1038/s41598-021-93031-z
  • Librado, P., Khan, N., Fages, A.,…Allentoft M.E, et al. (2021). The origins and spread of domestic horses from the Western Eurasian steppes. Nature. 598, 634–640. https://doi.org/10.1038/s41586-021-04018-9
  • Milazzo, C., Zulak, K.G., Muria-Gonzalez, M.J., Jones, D., Power, M.W.P., Bransgrove, K., Bunce, M., Lopez-Ruiz, F.J. (2021) High-Throughput Metabarcoding Characterizes Fungal Endophyte Diversity in the Phyllosphere of a Barley Crop. (2021). Phytobiomes Journal, 5, 316-325. https://doi:10.1094/pbiomes-09-20-0066-r
  • Milla, L., Sniderman, K., Lines, R., Mousavi-Derazmahalleh, M., & Encinas‐Viso, F. (2021). Pollen DNA metabarcoding identifies regional provenance and high plant diversity in Australian honey. Ecology and Evolution. 11(13), 8683-8698.
  • Mousavi‐Derazmahalleh, M., Stott, A., Lines, R., Peverley, G., Nester, G., Simpson, T., . . . Christophersen, C. T. (2021). eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity. Molecular Ecology Resources. 21(5), 1697-1704. https://doi.org/10.1111/1755-0998.13356
  • Nester, GM, De Brauwer, M, Koziol, A, . . . Bunce, M. (2020). Development and evaluation of fish eDNA metabarcoding assays facilitate the detection of cryptic seahorse taxa (family: Syngnathidae). Environmental DNA. 2: 614– 626. https://doi.org/10.1002/edn3.93
  • Nielsen, T.G., Nielsen, S.H., Gravlund, P., Moyer, D., Galatius, A., & Allentoft, M.E. (2021). A can of worms: Identification issues and morphological conservatism in a large sample of African Green and Bush Snakes (Colubridae: Philothamnus) from Minziro Forest, Tanzania. African Journal of Herpetology, DOI: 10.1080/21564574.2021.1976289
  • Parkin, K., Christophersen, C.T., Verhasselt, V., Cooper, M.N. & Martino, D. (2021). Risk Factors for Gut Dysbiosis in Early Life. Microorganisms, 9, 2066. https://doi.org/10.3390/microorganisms9102066
  • Rees, J., Bagatini, S.R., Lo, L., Hodgson, J.M., Christophersen, C.T., Daly, R.M, . . . Devine, A. (2021). Association between Fruit and Vegetable Intakes and Mental Health in the Australian Diabetes Obesity and Lifestyle Cohort. Nutrients, 13, 1447. https://doi.org/10.3390/nu13051447
  • Richards, Z.T., Juszkiewicz, D.J. & Hoggett, A. (2021). Spatio-temporal persistence of scleractinian coral species at Lizard Island, Great Barrier Reef. Coral Reefs. 40, 1369–1378. https://doi.org/10.1007/s00338-021-02144-4
  • Saccò, M., Blyth, A.J., Humphreys, W.F., Cooper, S.J., White, N.E., Campbell, M., . . . and Grice, K. (2021). Rainfall as a trigger of ecological cascade effects in an Australian groundwater ecosystem. Scientific Reports, 11(1), 1-15. https://doi.org/10.1038/s41598-021-83286-x
  • Saccò, M., White, N.E., Campbell, M., Allard, S., Humphreys, W.F., Pringle, P., . . . Allentoft, M.E. (2021). Metabarcoding under brine: microbial ecology of five hypersaline lakes at Rottnest Island (WA, Australia). Water, 13(14), 1899. https://doi.org/10.3390/w13141899
  • Saccò, M., White, N.E., Harrod, C., Salazar, G., Aguilar, P., Cubillos, C. F., . . . Allentoft, M.E. (2021). Salt to conserve: a review on the ecology and preservation of hypersaline ecosystems. Biological reviews of the Cambridge Philosophical Society, 96(6), 2828-2850. https://doi.org/10.1111/brv.12780
  • Seersholm, F., Grealy, A., McDowell, M.C., Cole, T.L., Arnold, L.J., Prideaux, G.J., Bunce, M. (2021). Ancient DNA from bulk bone reveals past genetic diversity of vertebrate fauna on Kangaroo Island, Australia. Quaternary Science Reviews. 262, P.106962
  • Seersholm, F., Lykke Hansen, K., Heydenrych, M., Hansen, A. J., Bunce, M., & Allentoft, M. E. (2021). Ancient DNA preserved in small bone fragments from the P.W. Lund collection. Ecology and Evolution, 11(5), 2064-2071. https://doi.org/10.1002/ece3.7162
  • Segawa T, Yonezawa T, Mori H, Akiyoshi A, Allentoft ME et al. (2021). Ancient DNA reveals multiple origins and migration waves of extinct Japanese brown bear lineages. Royal Society Open Science. 8(8). http://doi.org/10.1098/rsos.210518
  • Shafaei, A., Rees, J., Christophersen, C.T., Devine, A., Broadhurst, D., & Boyce, M.C. (2021). Data supporting development and validation of liquid chromatography tandem mass spectrometry method for the quantitative determination of bile acids in feces. Data in Brief. https://doi.org/10.1016/j.dib.2021.107091
  • Staikou, V., Sianis, PD., Vassou, D., Psonis, N., Allentoft, ME., & Iliopoulos., G. (2021). Middle Helladic Tombs at Nydri Plain, Lefkas Island. An Archaeological and Paleoanthropological Study. Journal of Greek Archaeology, 6, 43-60
  • Taninaka H, Maggioni D, Seveso D, Huang D, Townsend A, Richards Z.T. et al. (2021). Phylogeography of blue corals (genus Heliopora) across the Indo-West Pacific. Frontiers in Marine Science. 8, 714662 https://doi.org/10.3389/fmars.2021.714662
  • van der Heyde, M., Bateman, P. W., Bunce, M., Wardell-Johnson, G., White, N. E., & Nevill, P. (2021). Scat DNA provides important data for effective monitoring of mammal and bird biodiversity. Biodiversity and Conservation, 30(12), 3585-3602. https://doi.org/10.1007/s10531-021-02264-x
  • Walters, S. J., Robinson, T. P., Byrne, M., Wardell‐Johnson, G. W., & Nevill, P. (2021). Association of putatively adaptive genetic variation with climatic variables differs between a parasite and its host. Evolutionary Applications. 14(7). 1732-1746.
  • Wepfer, P.H., Nakajima, Y., Sutthacheep, M., Radice, V.Z., Richards, Z., Ang, P., Terraneo, T., Fujimura, A., Toonen, R.J., Mikheyev, A.S. & Mitarai, S. (2021). Inclusivity is key to progressing coral biodiversity research: Reply to comment by Bonito et al. Molecular Phylogenetics and Evolution, 162, p.107135.
  • West, K.M., Adam, A.A., White, N., Robbins, W.D., Barrow, D., Lane, A. & Richards, Z. (2021). The applicability of eDNA metabarcoding approaches for sessile benthic surveying in the Kimberley region, north‐western Australia. Environmental DNA.
  • West K.M., Heydenrych, M., Lines, R., Tucker, T., Fossette, S., Whiting, S., Bunce, M. (2021) Development of a 16S metabarcoding assay for the environmental DNA (eDNA) detection of aquatic reptiles across northern Australia. Marine and Freshwater Research. https://doi.org/10.1071/MF20288
  • West, K., Travers, M.J., Stat, M., Harvey, E.S., Richards, Z.T., DiBattista, J.D., Newman, S.J., Harry, A., Skepper, C.L., Heydenrych, M. & Bunce, M. (2021). Large‐scale eDNA metabarcoding survey reveals marine biogeographic break and transitions over tropical north‐western Australia. Diversity and Distributions. 27(10), 1942-1957. https://doi.org/10.1111/ddi.13228
  • Yan, R., Andrew, L., Marlow, E., Kunaratnam, K., Devine, A., Dunican, I.C. & Christophersen, C.T. (2021). Dietary Fibre Intervention for Gut Microbiota, Sleep and Mental Health in Adults with Irritable Bowel Syndrome: A Scoping Review. Nutrients, 13, doi:10.3390/nu13072159
  • Zacho CM, Bager MA, Margaryan A, Gravlund P, Galatius A, Rasmussen AR, & Allentoft ME. (2021). Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes. PLoS ONE 16(8): e0256353. https://doi.org/10.1371/journal.pone.0256353
  • Zaiko, A., Greenfield, P., Abbott, C., von Ammon, U., Bilewitch, J., Bunce, M., Cristescu, M.E., Chariton, A., Dowle, E., Geller J., . . . Pochon, X. (2021). Towards reproducible metabarcoding data: Lessons from an international cross-laboratory experiment. Molecular Ecology Resources. DOI: 10.1111/1755-0998.13485

2020

  • Adams, L.A., Wang, Z., Liddle, C., Melton, P.E., Ariff, A., Chandraratna, H., Tan, J., Ching, H., Coulter, S., de Boer, B., Christophersen, C.T., O’Sullivan, T.A., Morrison, M. and Jeffrey, G.P. (2020). Bile acids associate with specific gut microbiota, low level alcohol consumption and liver fibrosis in patients with non-alcoholic fatty liver disease. Liver International. 40(6), 1356-1365. DOI: http://dx.doi.org/10.1111/liv.14453
  • Ball, J. W., Robinson, T. P., Wardell-Johnson, G. W., Bovill, J., Byrne, M., & Nevill, P. G. (2020). Fine-scale species distribution modelling and genotyping by sequencing to examine hybridisation between two narrow endemic plant species. Scientific reports, 10(1), 1-12.
  • Beger, M., Wendt, H., Sullivan, J., Mason, C., LeGrand, J., Davey, K., . . . Fernandes, L. (2020). National-scale marine bioregions for the Southwest Pacific. Marine Pollution Bulletin, 150, 110710.
  • Bessey, C., Jarman, S. N., Berry, O., Olsen, Y. S., Bunce, M., Simpson, T., . . . Keesing, J. (2020). Maximizing fish detection with eDNA metabarcoding. Environmental DNA, 2(4), 493-504.
  • Deering, K.E., Devine, A., O’Sullivan, T.A., Lo, J., Boyce, M.C., Christophersen, C.T. (2020). Characterizing the composition of the pediatric gut microbiome: A systematic review. Nutrients, 12 (16). DOI:10.3390/nu12010016
  • DiBattista, J. D., Reimer, J. D., Stat, M., Masucci, G. D., Biondi, P., De Brauwer, M., . . . Bunce, M. (2020). Environmental DNA can act as a biodiversity barometer of anthropogenic pressures in coastal ecosystems. Scientific Reports, 10(1), 1-15.
  • Durack, J., Christophersen, C.T. (2020). Human respiratory and gut microbiomes – do they really contribute to respiratory health? Frontiers in Pediatrics (Review), 8. DOI:10.3389/fped.2020.00528
  • Gakuhari, T., Nakagome, S., Rasmussen, S., Allentoft, M. E., Sato, T., Korneliussen, T., . . . Oota, H. (2020). Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations. Communications biology, 3(1), 1-10.
  • Gatej, S.M., Bright, R., Weyrich, L.S., Marino, V., Christophersen, C.T., Gibson, R.J., Gully, N., Zilm, P. and Bartold, P.M. (2020). Probiotic Lactobacillus Rhamnosus GG Protects Against P. Gingivalis And F. Nucleatum Gut Dysbiosis. Journal of the International Academy of Periodontology. 22(2), 18-27.
  • Grealy, A., McDowell, M., Retallick, C., Bunce, M., & Peacock, D. (2020). Novel mitochondrial haplotype of spotted-tailed quoll (Dasyurus maculatus) present on Kangaroo Island (South Australia) prior to extirpation. The Holocene, 30(1), 136-144.
  • Grosse, C.S.J., Christophersen, C.T., Devine A., & Lawrance, I.C. (2020): The role of a plant-based diet in the pathogenesis, etiology and management of the inflammatory bowel diseases. Expert Review of Gastroenterology & Hepatology. 14(3), 137-145. DOI: 10.1080/17474124.2020.1733413
  • Hart, M. M., Cross, A. T., D’Agui, H. M., Dixon, K. W., Van der Heyde, M., Mickan, B., … & Nevill, P. (2020). Examining assumptions of soil microbial ecology in the monitoring of ecological restoration. Ecological Solutions and Evidence, 1(2), e12031.
  • Hoban, C. L., Musgrave, I. F., Byard, R. W., Nash, C., Farrington, R., Maker, G., . . . Coghlan, M. (2020). Combined liquid Chromatography-mass Spectrometry and Next-generation DNA sequencing detection of adulterants and contaminants in analgesic and Anti-inflammatory herbal Medicines. Pharmaceutical Medicine, 34(1), 49-61.
  • Huhn, M., Madduppa, H.H., Khair, M., Sabrian, A., Irawati, Y., Anggraini, N.P., Wilkinson, S.P., Simpson, T., Iwasaki, K., Setiamarga, D.H.E., Dias, P.J. (2020). Keeping up with introduced marine species at a remote biodiversity hotspot: awareness, training and collaboration across different sectors is key. Biological Invasions, 22, 749-771
  • Margaryan, A., Lawson, D. J., Sikora, M., Racimo, F., Rasmussen, S., Moltke, I., . . . Willerslev, E. (2020). Population genomics of the Viking world. Nature, 585(7825), 390-396.
  • McLean, D. L., Parsons, M. J., Gates, A. R., Benfield, M. C., Bond, T., Booth, D. J., . . . Jones, D. O. B. (2020). Enhancing the scientific value of industry remotely operated vehicles (ROVs) in our oceans. Frontiers in Marine Science, 7, 220.
  • Michael, P. J., Jones, D., White, N., Hane, J. K., Bunce, M., & Gibberd, M. (2020). Crop-zone weed mycobiomes of the south-western Australian grain belt. Frontiers in microbiology, 11.
  • Mühlemann, B., Vinner, L., Margaryan, A., Wilhelmson, H., de la Fuente Castro, C., Allentoft, M. E., . . . Sikora, M. (2020). Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age. Science, 369(6502).
  • Nester, G. M., De Brauwer, M., Koziol, A., West, K. M., DiBattista, J. D., White, N. E., . . . Bunce, M. (2020). Development and evaluation of fish eDNA metabarcoding assays facilitate the detection of cryptic seahorse taxa (family: Syngnathidae). Environmental DNA, 2(4), 614-626.
  • Nevill, P. G., Zhong, X., Tonti-Filippini, J., Byrne, M., Hislop, M., Thiele, K., … & Small, I. (2020). Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics. BMC Plant Methods, 16(1), 1-8.
  • Preston, S., & Richards, Z. (2020). Biological consequences of an outbreak of growth anomalies on Isopora palifera at the Cocos (Keeling) Islands. Coral Reefs, 1-13.
  • Ran,Y., Murphy, M., Genoni, A., Marlow, E., Dunican, IC., Lo, J., Andrew, L., Devine, A., Christophersen, C.T. (2020). Does Fibre-fix provided to people with irritable bowel syndrome who are consuming a low FODMAP diet improve their gut health, gut microbiome, sleep and mental health? A double-blinded, randomised controlled trial. BMJ Open Gastroenterology, 7(1), e000448. DOI:http://dx.doi.org/10.1136/bmjgast-2020-000448
  • Rayner, M. J., Van Loenen, A. L., Shepherd, L. D., Cubrinovska, I., Scofield, R. P., Tennyson, A. J., . . . Steeves, T. E (2020). Comprehensive evidence for subspecies designations in Cook’s Petrel Pterodroma cookii with implications for conservation management. Bird Conservation International, 1-13.
  • Rees, J., Christophersen, C.T., Lewis, J.R., Lo, J., Sambell, R., Costello, L., Walker, C., Byrne, M.F., Boyce, M.C., Newton, R.U., and Devine, A. (2020). The study protocol for a pseudo-randomised pre-post designed controlled intervention trial to study the effects of a 7-week cooking program on self-efficacy and biomarkers of health: the ECU lifestyle and biomarkers get connected study (ECULABJMOF) including the Jamie’s Ministry of Food WA participant experience. BMC Public Health, 20(1), 1-13. DOI: https://doi.org/10.1186/s12889-020-09124-3
  • Richards, Z. T., Haines, L., Scaps, P., & Ader, D. (2020). New Records of Heliopora hiberniana from SE Asia and the Central Indian Ocean. Diversity, 12(9), 328.
  • Richards, Z. T., Carvajal, J. I., Wallace, C. C., & Wilson, N. G. (2020). Phylotranscriptomics confirms Alveopora is sister to Montipora within the family Acroporidae. Marine genomics, 50, 100703.
  • Saccò, M., Blyth, A.J., Humphreys, W.F., Middleton, J.A., White, N.E., Campbell, M., Mousavi-Derazmahalleh, M., Laini, A., Hua, Q., Meredith, K., Cooper, S.J.B., Griebler, C., Grierson, P., Grice, K. (2020). Tracking down carbon inputs underground from an arid zone Australian calcrete. PLOS ONE.
  • Saccò, M., Blyth, A. J., Humphreys, W. F., Cooper, S. J., Austin, A. D., Hyde, J., . . . Grice, K. (2020). Refining trophic dynamics through multi‐factor Bayesian mixing models: A case study of subterranean beetles. Ecology and evolution, 10(16), 8815-8826.
  • Seersholm, F. V., Werndly, D. J., Grealy, A., Johnson, T., Early, E. M. K., Lundelius, E. L., . . . Bunce, M. (2020). Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change. Nature Communications, 11(1), 1-10.
  • Sjögren, K.-G., Olalde, I., Carver, S., Allentoft, M. E., Knowles, T., Kroonen, G., . . . Heyd, V. (2020). Kinship and social organization in Copper Age Europe. A cross-disciplinary analysis of archaeology, DNA, isotopes, and anthropology from two Bell Beaker cemeteries. PLoS One, 15(11), e0241278.
  • Seersholm, F. V., Werndly, D. J., Grealy, A., Johnson, T., Early, E. M. K., Lundelius, E. L., . . . Hansen, A. J. (2020). Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change. Nature Communications, 11(1), 1-10.
  • Takahashi, M., DiBattista, J. D., Jarman, S., Newman, S. J., Wakefield, C. B., Harvey, E. S., & Bunce, M. (2020). Partitioning of diet between species and life history stages of sympatric and cryptic snappers (Lutjanidae) based on DNA metabarcoding. Scientific Reports, 10(1), 4319.
  • Thomas, L., Underwood, J. N., Adam, A. A., Richards, Z. T., Dugal, L., Miller, K. J., & Gilmour, J. P. (2020). Contrasting patterns of genetic connectivity in brooding and spawning corals across a remote atoll system in northwest Australia. Coral Reefs, 39(1), 55-60.
  • Underwood, J.N., Richards, Z., Berry, O., Oades, D., Howard, A., Gilmour, J.P. (2020). Extreme seascape drives local recruitment and genetic divergence in brooding and spawning corals in remote northwest Australia. Evolutionary Applications, DOI: 10.1111/eva.13033
  • Valliere, J. M., Wong, W. S., Nevill, P. G., Zhong, H., & Dixon, K. W. (2020). Preparing for the worst: Utilizing stress‐tolerant soil microbial communities to aid ecological restoration in the Anthropocene. Ecological Solutions and Evidence, 1(2), e12027.
  • van der Heyde, M., Bunce, M., Dixon, K., Wardell-Johnson, G., White, N.E. and Nevill, P., 2020. Changes in soil microbial communities in post mine ecological restoration: Implications for monitoring using high throughput DNA sequencing. Science of The Total Environment, p.142262.
  • van der Heyde, M., Bunce M., Wardell-Johnson G., Fernandes K., White N.E., Nevill, P. (2020). Testing multiple substrates for terrestrial biodiversity monitoring using environmental DNA (eDNA) metabarcoding. Molecular Ecology Resources. 20(3).
  • Walters, S. J., Robinson, T. P., Byrne, M., Wardell‐Johnson, G. W., & Nevill, P. (2020). Contrasting patterns of local adaptation along climatic gradients between a sympatric parasitic and autotrophic tree species. Molecular Ecology, 29(16), 3022-3037.
  • Wepfer, P. H., Nakajima, Y., Sutthacheep, M., Radice, V. Z., Richards, Z., Ang, P., … & Mikheyev, A. S. (2020). Evolutionary biogeography of the reef-building coral genus Galaxea across the Indo-Pacific ocean. Molecular Phylogenetics and Evolution, 151, 106905.
  • West, K.M., Stat, M., Harvey, E.S., Skepper, C.L., DiBattista, J.D., Richards, Z.T., Travers, M.J., Newman, S.J., Bunce, M. (2020). eDNA metabarcoding survey reveals fine-scale coral reef community variation across a remote, tropical island ecosystem. Molecular Ecology
  • West, K. M., Richards, Z. T., Harvey, E. S., Susac, R., Grealy, A., & Bunce, M. (2020). Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia. Scientific Reports, 10(1), 1-15.
  • White, N.E., Guzik, M.T., Austin, A.D., Moore, G.I., Humphreys, W.F., Alexander, J., Bunce, M. (2020). Detection of the rare Australian endemic blind cave eel (Ophisternon candidum) with environmental DNA: implications for threatened species management in subterranean environments. Hydrobiologia, Vol.847(15), p.3201-3211.

2019

  • Adams C.I., Knapp, M., Gemmell, N.J., Jeunen, G.J., Bunce, M., Lamare, M.D., Taylor, H.R. (2019). Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool? Genes. Mar;10(3):192.
  • Alexander, J.B., Bunce, M., White, N., Wilkinson, S.P., Adam, A.A.S., Berry, T., Stat, M., Thomas, L., Newman, S.J., Dugal, L., Richards, Z.T. (2019). Development of a multi-assay approach for monitoring coral diversity using eDNA metabarcoding. Coral Reefs. Nov 22:1-3.
  • Anderson, B., Thiele, K., Grierson, P., Krauss, S., Nevill, PG., & Small, I., Zhong, X., & Barrett, M. (2019). Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing. AoB PLANTS, 11, https://doi.org/10.1093/aobpla/plz017.
  • Antonosyan, M., Seersholm, F. V., Grealy, A. C., Barham, M., Werndly, D., Margaryan, A., . . . Bunce, M. (2019). Ancient DNA shows high faunal diversity in the Lesser Caucasus during the Late Pleistocene. Quaternary Science Reviews, 219, 102-111.
  • Berry, T.E., Saunders, B.J., Coghlan, M.L., Stat, M., Jarman, S., Richardson, A.J., Davies, C.H., Berry, O., Harvey, E.S., Bunce, M. (2019). Marine environmental DNA biomonitoring reveals seasonal patterns in biodiversity and identifies ecosystem responses to anomalous climatic events. PLoS genetics. Feb 8;15(2):e1007943.
  • Berry, O., Richards, Z., Moore, G., Hernawan, U., Travers, M., & Gruber, B. (2019). Oceanic and coastal populations of a harvested macroinvertebrate Rochia nilotica in north-western Australia are isolated and may be locally adapted. Marine and Freshwater Research.
  • Bessey, C., Jarman, S.N., Stat, M., Rohner, C.A., Bunce, M., Koziol, A., Power, M., Rambahiniarison, J.M., Ponzo, A., Richardson, A.J., Berry, O. (2019). DNA metabarcoding assays reveal a diverse prey assemblage for Mobula rays in the Bohol Sea, Philippines. Ecology and evolution. Mar;9(5):2459-74.
  • Boast, A. P., Chapman, B., Herrera, M. B., Worthy, T. H., Scofield, R. P., Tennyson, A. J., . . . Mitchell, K. J. (2019). Mitochondrial genomes from New Zealand’s extinct Adzebills (Aves: Aptornithidae: Aptornis) support a sister-taxon relationship with the Afro-Madagascan Sarothruridae. Diversity, 11(2), 24.
  • Bohu, T., Anand, R., Noble, R., Lintern, M., Kaksonen, A. H., Mei, Y., . . . Bunce, M. (2019). Evidence for fungi and gold redox interaction under Earth surface conditions. Nature Communications, 10(1), 1-13.
  • Byrne, M., et al., (2019). Persistence and stochasticity are key determinants of genetic diversity in plants associated with banded iron formation inselbergs. Biological Reviews, 94, 753-772.
  • Claramunt, A.A., White, N.E., Bunce, M., O’Connell, M., Bullen, R., Mawson, P. (2019). Determination of the diet of the ghost bat (Macroderma gigas) in the Pilbara region of Western Australia from dried prey remains and DNA metabarcoding. Australian Journal of Zoology.
  • Crighton, E., Coghlan, M. L., Farrington, R., Hoban, C. L., Power, M. W., Nash, C., . . . Musgrave, I. F. (2019). Toxicological screening and DNA sequencing detects contamination and adulteration in regulated herbal medicines and supplements for diet, weight loss and cardiovascular health. Journal of pharmaceutical and biomedical analysis, 176, 112834.
  • Cross, A.T., Nevill, P.G., Dixon, K.W. and Aronson, J. (2019). Time for a paradigm shift toward a restorative culture. Restoration Ecology, 27(5), pp.924-928.
  • Crump, S. E., Miller, G. H., Power, M., Sepúlveda, J., Dildar, N., Coghlan, M., & Bunce, M. (2019). Arctic shrub colonization lagged peak postglacial warmth: Molecular evidence in lake sediment from Arctic Canada. Global change biology, 25(12), 4244-4256.
  • Darling, E. S., McClanahan, T. R., Maina, J., Gurney, G. G., Graham, N. A., Januchowski-Hartley, F., … & Puotinen, M. (2019). Social–environmental drivers inform strategic management of coral reefs in the Anthropocene. Nature ecology & evolution, 3(9), 1341-1350.
  • DiBattista, J.D., Reimer, J.D., Stat, M., Masucci, G.D., Biondi, P., De Brauwer, M., Bunce, M. (2019). Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient. PeerJ. Feb 6;7:e6379.
  • Fernandes, K., van der Heyde, M., Coghlan, M., Wardell‐Johnson, G., Bunce, M., Harris, R. and Nevill, P. (2019). Invertebrate DNA metabarcoding reveals changes in communities across mine site restoration chronosequences. Restoration Ecology, 27(5), pp.1177-1186.
  • Fromont, J., Richards, Z., & Wilson, N. (2019). First report of the coral-killing sponge Terpios hoshinota Ritzier and Muzik, 1993 in Western Australia: A new threat to Kimberley coral reefs? Diversity, 11(184), 1-9.
  • Funnekotter, AV., Millar, MA., Krauss, SL., & Nevill, PG. (2019). Phylogeographic analyses of Acacia karina (Fabaceae) support long term persistence of populations both on and off banded iron formations. Australian Journal of Botany, 67, 194-204.
  • Genoni, A., Christophersen, C.T., Lo, J., Coghlan, M., Boyce, M.C., Bird, A.R., Lyons-Wall P., and Devine, A. (2019) Longterm Paleolithic diet is associated with lower resistant starch intake, different gut microbiota composition and increased serum TMAO concentrations. European Journal of Nutrition. 59(5), 1845-1858. DOI: https://doi.org/10.1007/s00394-019-02036-y
  • Genoni, A., Lo, J., Lyons-Wall, P., Boyce, M.C., Christophersen, C.T., Bird, A., Devine, A. (2019). A Paleolithic diet lowers resistant starch intake but does not affect serum trimethylamine-N-oxide concentrations in healthy women. British Journal of Nutrition, 121 (3): 322-329. DOI:10.1017/S000711451800329X.
  • Gilmour, J., Cook, K., Ryan, N., Puotinen, M., Green, R., Shedrawi, G., … & Foster, T. (2019). The state of Western Australia’s coral reefs. Coral Reefs, 1-16.
  • Gopalsamy, G., Mortimer, E., Greenfield, P., Bird, A.R., Young G.P., and Christophersen C.T. (2019). Resistant Starch is Actively Fermented by Infant Faecal Microbiota and Increases Microbial Diversity. Nutrients, 11(6), 1345. DOI: https://doi.org/10.3390/nu11061345.
  • Grealy, A., Bunce, M., & Holleley, C. E. (2019). Avian mitochondrial genomes retrieved from museum eggshell. Molecular Ecology Resources, 19(4), 1052-1062.
  • Hammer, T.A., Zhong, X., Colas des Francs‐Small, C., Nevill, PG., Small, I.D. and Thiele, K.R., (2019). Resolving intergeneric relationships in the aervoid clade and the backbone of Ptilotus (Amaranthaceae): evidence from whole plastid genomes and morphology. Taxon, 68(2), pp.297-314.
  • Hart, M., Gorzelak, M.A., McAmmond, B.M., Van Hamme, J.D., Stevens, J., Abbott, L., Whiteley, A.S. and Nevill, P., (2019). Fungal Communities Resist Recovery in Sand Mine Restoration. Frontiers in Forests Global Change, 2, p.78.
  • Jeunen, G.J., Knapp, M., Spencer, H.G., Taylor, H.R., Lamare, M.D., Stat, M., Bunce, M., Gemmell, N.J. (2019). Species‐level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization. Ecology and evolution. Feb;9(3):1323-35.
  • Jeunen, G.J., Knapp, M., Spencer, H.G., Lamare, M.D., Taylor, H.R., Stat, M., Bunce, M., Gemmell, N.J. (2019). Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement. Molecular ecology resources. Mar;19(2):426-38.
  • Jeunen, G.J., Lamare, M.D., Knapp, M., Spencer, H.G., Taylor, H.R., Stat, M., Bunce, M., Gemmell, N.J. (2019). Water stratification in the marine biome restricts vertical environmental DNA (eDNA) signal dispersal. Environmental DNA
  • Khalil Suleiman, M., et al., (2019) Assessment of the Diversity of Fungal Community Composition Associated with Vachellia pachyceras and its Rhizosphere Soil from Kuwait Desert. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2019.00063.
  • Kirkendale, L., Hosie, A.M., Richards, Z. (2019). Defining biodiversity gaps for North West Shelf marine invertebrates. Journal of the Royal Society of Western Australia, 102, 1-9.
  • Knapp, M., Thomas, J. E., Haile, J., Prost, S., Ho, S. Y., Dussex, N., . . . Bunce, M. (2019). Mitogenomic evidence of close relationships between New Zealand’s extinct giant raptors and small-sized Australian sister-taxa. Molecular phylogenetics and evolution, 134, 122-128.
  • Koziol, A., Stat, M., Simpson, T., Jarman, S., DiBattista, J.D., Harvey, E.S., Marnane, M., McDonald, J., Bunce, M. (2019). Environmental DNA metabarcoding studies are critically affected by substrate selection. Molecular ecology resources. Mar;19(2):366-76.
  • Le, T.T., Shafaei, A., Genoni, A., Christophersen, C.T., Devine, A., Lo, J., Lyons-Wall, P., Boyce, M.C. (2019). Development and validation of a simple LC-MS/MS method for the simultaneous quantitative determination of trimethylamine N-oxide and the branched chain amino acids in human serum. Analytical and Bioanalytical Chemistry, 411(5):1019-1028. DOI: 10.1007/s00216-018-1522-8.
  • Moreira-Grez, B., Tam, K., Cross, A.T., Yong, J.W., Kumaresan, D., Nevill, PG., Farrell, M. and Whiteley, A.S., (2019). The Bacterial Microbiome Associated With Arid Biocrusts and the Biogeochemical Influence of Biocrusts Upon the Underlying Soil. Frontiers in Microbiology, 10, p.2143.
  • Nevill, PG., Howell, KA., Cross, AT., Williams, AV., Zhong, X., Tonti-Filippini, J., Boykin, LM., & Small, I. (2019). Plastome-wide rearrangements and gene losses in carnivorous Droseraceae, Genome Biology and Evolution, 11, 472–485. https://doi.org/10.1093/gbe/evz005.
  • Nevill, PG., Robinson, T., Di Virgilio, G., & Wardell-Johnson, G. (2019). Beyond isolation by distance: what best explains functional connectivity among populations of three sympatric plant species in an ancient terrestrial island system? Diversity and Distributions.
  • Newton, R., Christophersen, C.T., Fairman, C., Hart, N., Taaffe, D., Broadhurst, D., Devine, A., Chee, R., Tang, C., Spry, N., and Galvao, D. (2019). Does exercise impact gut microbiota composition in men receiving androgen deprivation therapy for prostate cancer? A single-blinded, two-armed, randomised controlled trial. BMJ Open, 9(4), e024872, DOI: http://dx.doi.org/10.1136/bmjopen-2018-024872.
  • Ng, S. H., Stat, M., Bunce, M., Simpson, S. J., & Simmons, L. W. (2019). Protein and carbohydrate intakes alter gut microbial community structure in crickets: a Geometric Framework approach. FEMS microbiology ecology, 95(8), fiz106.
  • Richards, Z.T., Garcia, R., Moore, G., Fromont, J., Kirkendale, L., Bryce, M., … & Whisson, C. (2019). A tropical Australian refuge for photosymbiotic benthic fauna. Coral Reefs, 38(4), 669-676.
  • Richards, Z., & Newman, S. J. (2019). Outbreak of growth anomalies in Isopora palifera at Cocos (Keeling) Islands. Marine Biodiversity, 49(3), 1071-1072.
  • Ritchie, AL., Dyer, RJ., Nevill, PG., Sinclair, EA., & Krauss, SL. (2019). Wide outcrossing provides functional connectivity for new and old Banksia populations within a fragmented landscape. Oecologia. https://doi.org/10.1007/s00442-019-04387-z.
  • Saccò, M., Blyth, A., Bateman, P.W., Hua, Q., Mazumder, D., White, N., Humphreys, W.F.,  Laini, A., Griebler, C., Grice, K. (2019). New light in the dark – a proposed multidisciplinary framework for studying functional ecology of groundwater fauna. Science of the Total Environment, Vol 660, 963-977.
  • Saccò, M., Blyth, A.J., Humphreys, W.F., Cooper, S., White, N.E., Campbell, M., Mousavi-Derazmahalleh, M., Hua, Q., Mazumder, D., Smith, C., Grice, K. (2019). What’s going on down (under) there? Unravelling biochemical flows under differential rainfall periods in a Western Australian calcrete. Australasian Groundwater Conference (AGC) 2019.
  • Sanchez-Puerta, MV., Edera, A., Gandini, CL., Williams, AV., Howell, K., Nevill, PG., & Small, I. (2019). Genome-scale transfer of mitochondrial DNA from legume hosts to the holoparasite Lophophytum mirabile (Balanophoraceae). Molecular Phylogenetics and Evolution, 132, 243250.
  • Stat, M., John, J., DiBattista, J.D., Newman, S.J., Bunce, M., Harvey, E.S. (2019). Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity. Conservation biology. Feb;33(1):196-205.
  • Suleiman, MK., et al., (2019). Evaluating the diversity and composition of bacterial communities associated with Acacia gerrardii-the only existing native tree species in Kuwait desert. Canadian Journal of Microbiology, 65, 235-251. doi: 10.1139/cjm-2018-0421.
  • Swift, J. A., Bunce, M., Dortch, J., Douglass, K., Faith, J. T., Fellows Yates, J. A., . . . Johnson, C. N. (2019). Micro methods for megafauna: novel approaches to late quaternary extinctions and their contributions to faunal conservation in the anthropocene. BioScience, 69(11), 877-887.
  • Wang, Y., Mortimer, E.K., Katundu, K. G.H., Kalanga, N., Leong, L. E.X., Gopalsamy, G.L., Christophersen, C.T., Richard, A.C., Shivasami, A., Abell, G. C.J., Young, G.P., and Rogers G.B. (2019). The capacity of the faecal microbiota from Malawian infants to ferment resistant starch. Frontiers in Microbiology. , 10, 1459. DOI: https://doi.org/10.3389/fmicb.2019.01459

2018

  • DiBattista, J. D., Wakefield, C. B., Moore, G. I., Bunce, M., Williams, A. J., O’Malley, J. M., . . . Green, M. A. (2018). Genomic and life-history discontinuity reveals a precinctive lineage for a deep-water grouper with gene flow from tropical to temperate waters on the west coast of Australia. Ecological Genetics and Genomics, 9, 23-33.
  • Dormontt, EE., Van Dijk, KJ., Bell, KL., Biffin, E., Breed, MF., Byrne, M., Caddy-Retalic, S., Encinas-Viso, F., Nevill, PG., Shapcott, A. & Young, JM. (2018). Advancing DNA metabarcoding applications for plants requires systematic analysis of herbarium collectionsan Australian perspective. Frontiers in Ecology and Evolution, 6, 134.
  • Douglass, K., Antonites, A. R., Morales, E. M. Q., Grealy, A., Bunce, M., Bruwer, C., & Gough, C. (2018). Multi-analytical approach to zooarchaeological assemblages elucidates Late Holocene coastal lifeways in southwest Madagascar. Quaternary International, 471, 111-131.
  • Fernandes, K., van der Heyde, M., Bunce, M., Dixon, K., Harris, R.J., Wardell‐Johnson, G., Nevill, P.G. (2018). DNA metabarcoding-a new approach to fauna monitoring in mine site restoration. Restoration ecology. Nov;26(6):1098-107.
  • Hoban, C. L., Musgrave, I. F., Coghlan, M. L., Power, M. W., Byard, R. W., Nash, C., . . . Trengove, R. (2018). Adulterants and contaminants in psychotropic herbal medicines detected with mass spectrometry and next-generation DNA sequencing. Pharmaceutical Medicine, 32(6), 429-444.
  • Jarman, S.N., Berry, O., Bunce, M. (2018) The value of environmental DNA biobanking for long-term biomonitoring. Nature ecology & evolution. Aug;2(8):1192.
  • Jones, J., DiBattista, J. D., Stat, M., Bunce, M., Boyce, M. C., Fairclough, D. V., . . . Huggett, M. J. (2018). The microbiome of the gastrointestinal tract of a range-shifting marine herbivorous fish. Frontiers in microbiology, 9, 2000. 
  • Mendoza, M. L. Z., Xiong, Z., Escalera-Zamudio, M., Runge, A. K., Thézé, J., Streicker, D., . . . Ryder, O. A. (2018). Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. Nature ecology & evolution, 2(4), 659-668.
  • Ng, S. H., Stat, M., Bunce, M., & Simmons, L. W. (2018). The influence of diet and environment on the gut microbial community of field crickets. Ecology and evolution, 8(9), 4704-4720.
  • Rey‐Iglesia, A., Gopalakrishan, S., Carøe, C., Alquezar‐Planas, D. E., Ahlmann Nielsen, A., Röder, T., . . . Fredensborg Rath, M. (2018). MobiSeq: De novo SNP discovery in model and non‐model species through sequencing the flanking region of transposable elements. Molecular Ecology Resources, 19(2), 512-525.
  • Richards, Z.T., Yasuda, N., Kikuchi, T., Foster, T., Mitsuyuki, C., Stat, M., … & Wilson, N. G. (2018). Integrated evidence reveals a new species in the ancient blue coral genus Heliopora (Octocorallia). NatSR, 8, 15875.
  • Richards, Z., Bryce, M., & Bryce, C. (2018). The composition and structure of shallow benthic reef communities in the Kimberley, north-west Australia. Records of the Western Australian Museum Supplement, 85, 103.
  • Richards, Z.T., & Day, J.C. (2018). Biodiversity of the Great Barrier Reef—how adequately is it protected? PeerJ, 6, e4747.
  • Schnell, I. B., Bohmann, K., Schultze, S. E., Richter, S. R., Murray, D. C., Sinding, M. H. S., . . . Dolch, R. (2018). Debugging diversity–a pan‐continental exploration of the potential of terrestrial blood‐feeding leeches as a vertebrate monitoring tool. Molecular Ecology Resources, 18(6), 1282-1298.
  • Seersholm, F. V., Cole, T. L., Grealy, A., Rawlence, N. J., Greig, K., Knapp, M., . . . Shepherd, L. (2018). Subsistence practices, past biodiversity, and anthropogenic impacts revealed by New Zealand-wide ancient DNA survey. Proceedings of the National Academy of Sciences, 115(30), 7771-7776.
  • Turpin, J.M., White, N.E., Dunlop, J.A., & Bamford, M.J. (2018). New populations of the black-flanked rock-wallaby (Petrogale lateralis) from the Little Sandy Desert and Murchison, Western Australia. Australian Mammalogy, 40(2), 234-242. doi:10.1071/AM14043.
  • Underwood, J.N., Richards, Z.T., Miller, K.J., Puotinen, M.L., & Gilmour, J.P. (2018). Genetic signatures through space, time and multiple disturbances in a ubiquitous brooding coral. Molecular ecology.
  • Zinke, J., Gilmour, J.P., Fisher, R., Puotinen, M., Maina, J., Darling, E. … & Hobbs, J.P.A. (2018). Gradients of disturbance, environmental conditions and coral community. Biodiversity research

2017

  • Berry, T.E., Osterrieder, S.K., Murray, D.C., Coghlan, M.L., Richardson, A.J., Grealy, A.K., Stat, M., Bejder, L., Bunce, M. (2017). DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea). Ecology and Evolution. Jul;7(14):5435-53.
  • Byard, R. W., Musgrave, I., Maker, G., & Bunce, M. (2017). What risks do herbal products pose to the Australian community? Medical Journal of Australia, 206(2), 86-90.
  • Clark, A.L., King, C.L., Buckley, H., Collins, C., Dhavale, N., Elliot, G., … & West, K. (2017). Biological Anthropology in the Indo-Pacific Region: New Approaches to Age-Old Questions. Journal of Indo-Pacific Archaeology, 41, 78-94.
  • DiBattista, J.D., Coker, D.J., Sinclair-Taylor, T.H., Stat, M., Berumen, M.L., Bunce M. (2017). Assessing the utility of eDNA as a tool to survey reef-fish communities in the Red Sea. Coral Reefs. Dec 1;36(4):1245-52.
  • Grealy, A., Phillips, M., Miller, G., Gilbert, M. T. P., Rouillard, J.-M., Lambert, D., . . . Haile, J. (2017). Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell. Molecular phylogenetics and evolution, 109, 151-163.
  • Grealy, A., Rawlence, N. J., & Bunce, M. (2017). Time to spread your wings: a review of the avian ancient DNA field. Genes, 8(7), 184.
  • Hardy, N., Berry, T., Kelaher, B.P., Goldsworthy, S.D., Bunce, M., Coleman, M.A., Gillanders, B.M., Connell, S.D., Blewitt, M., Figueira, W. (2017). Assessing the trophic ecology of top predators across a recolonisation frontier using DNA metabarcoding of diets. Marine Ecology Progress Series. Jun 21;573:237-54.
  • Rosser, N.L., Thomas, L., Stankowski, S., Richards, Z.T., Kennington, W.J., & Johnson, M.S. (2017). Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus Acropora. Proceedings of the Royal Society B: Biological Sciences, 284(1846).
  • Stat, M., Huggett, M.J., Bernasconi, R., DiBattista, J.D., Berry, T.E., Newman, S.J., Harvey, E.S., Bunce, M. (2017). Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment. Scientific Reports. Sep 25;7(1):12240.
  • Tridico, S. R., Murray, D. C., Bunce, M., & Kirkbride, K. P. (2017). DNA profiling of bacteria from human hair: Potential and pitfalls. Forensic Microbiology, 358. 
  • West, K., Collins, C., Kardailsky, O., Kahn, J., Hunt, T. L., Burley, D., & Matisoo-Smith, E. (2017). The Pacific rat race to Easter Island: tracking the prehistoric dispersal of Rattus exulans using ancient mitochondrial genomes. Frontiers in Ecology and Evolution, 5, 52.