Publications (most are available if you click on PDF following citations)
2024
Jense C, Adams M, Raadik TA, Waters J, Morgan D, Barmuta L, Hardie SA, Deagle BE, Burridge C (2024) Cryptic diversity within two widespread diadromous freshwater fishes (Teleostei: Galaxiidae). Ecology and Evolution (In press)
Green ME, Hardesty, DB, Deagle BE, Wilcox C (2024) Environmental DNA as a tool to reconstruct catch composition for longline fisheries vessels. Scientific Reports 4: 10188 (PDF)
2023
Deagle BE, Pansu J, McInnes J, Traugott M (2023) Revealing animal diet and food-webs though DNA metabarcoding. In the book: Applied Environmental Genomics. (eds. Berry O, Holleley C, Jarman S). CSIRO Publishing (Chapter PDF or link to google books website).
De Brauwer M, Deagle B, Dunstan P, Berry O (2023). Integrating environmental DNA science into Australia’s marine parks: a roadmap. CSIRO, Hobart. (link to CSIRO website and PDF)
Shao C, Sun S, Liu K, Wang J, Li S, Liu Q, Deagle B, [+ 41 other contributors], Meyer B, Fan G (2023) The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights. Cell 186: 1279-1294 (PDF)
Suter L, Wotherspoon S, Kawaguchi S, King R, MacDonald A, Nester G, Polanowski AM, Raymond B, Deagle BE (2023) Environmental DNA of Antarctic krill (Euphausia superba): measuring DNA fragmentation adds a temporal aspect to quantitative surveys. Environmental DNA Special Issue: "Beyond Species Detection" 5: 945-959 (PDF)
Maschette D, Wotherspoon S, Polanowski A, Deagle B, Welsford D, Ziegler P (2023) Circumpolar sampling reveals high genetic connectivity of Antarctic toothfish across their spatial distribution. Reviews in Fish Biology and Fisheries 33: 295-310 (PDF)
2022
Thomas AC, Deagle BE, Nordstrom C, Majewski S, Nelson BW, Acevedo-Gutiérrez A, Jeffries S, Moore J, Louden A, Allegue H, Pearson S, Schmidt M, Trites A (2022) Data on the diets of Salish Sea harbour seals from DNA metabarcoding. Scientific Data 9: 68 (PDF)
Sow SLS, Brown MV, Clarke LJ, Bissett A, van de Kamp J, Trull TW, Raes EJ, Boyd PW, Deagle BE, Pardo PC, Sloyan BM, Bodrossy L (2022) Biogeography of Southern Ocean prokaryotes: a comparison of the Indian and Pacific sectors. Environmental Microbiology 24: 2449-2466 (PDF)
2021
Radulovici AE, Vieira PE, Duarte S, Marcos AL Teixeira MAL, Borges LMS, Deagle BE, Majaneva S, Redmond N, Schultz JA, Costa FO (2021) Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon. Metabarcoding and Metagenomics 5: 207–217 (PDF)
Clarke LJ, Suter L, Deagle BE, Polanowski AM, Terauds A, Johnstone GJ, Stark JS (2021) Environmental DNA metabarcoding for monitoring metazoan biodiversity in Antarctic nearshore ecosystems. PeerJ 9:e12458 (PDF)
McInnes JC, Bird J, Deagle BE, Polanowski AM, Shaw JD (2021) Using DNA metabarcoding to detect burrowing seabirds in a remote landscape. Conservation Science and Practice e439 (PDF)
Ratcliffe N, Deagle B, Love K, Polanowski A, Fielding S, Wood AG, Hill S, Grant S, Belchier M, Flemming A, Hall J (2021) Changes in prey fields increase the potential for spatial overlap between gentoo penguins and a krill fishery within a marine protected area. Diversity and Distributions 27:552-563 (PDF)
Clarke LJ, Suter L, Rob King R, Bissett A, Bestley S, Deagle BE (2021) Bacterial epibiont communities of panmictic Antarctic krill are spatially structured Molecular Ecology 30:1042-1052 journal link
Suter L, Polanowski AM, Clarke LJ, Kitchener J, Deagle BE (2021) Capturing open ocean biodiversity: comparing environmental DNA metabarcoding to the continuous plankton recorder. Molecular Ecology Special Issue: "Environmental DNA For biodiversity and ecosystem monitoring" 30:3140-3157 (PDF)
2020
Cavallo CR, Chiaradia A, Deagle BE, Hays GC, Jarman SN, McInnes J, Ropert-Coudert Y, Gomez SS, Reina RD (2020) Quantifying prey availability using the foraging plasticity of a marine predator, the little penguin. Functional Ecology 34:1626-1639 (PDF)
Clarke LJ, Deagle BE (2020) Eukaryote plankton assemblages in the southern Kerguelen Axis region: ecological drivers differ between size fractions. Deep-Sea Research Part II Special Issue 174: "Ecosystem drivers of food webs on the Kerguelen Axis of the Southern Ocean" (PDF)
Clarke LJ, Trebilco R, Walter A, Polanowski AM, Deagle BE (2020) DNA-based diet analysis of mesopelagic fish from the southern Kerguelen Axis. Deep-Sea Research Part II Special Issue 174: "Ecosystem drivers of food webs on the Kerguelen Axis of the Southern Ocean" (PDF)
2019
Suter L, Polanowski AM, King R, Romualdi C, Sales G, Kawaguchi S, Jarman SN, Deagle BE (2019) Sex identification from distinctive gene expression patterns in Antarctic krill (Euphausia superba). Polar Biology 42:2205-2217 (Open Access)
Zinger L, Bonin A, Alsos IG, Bálint M, Bik H, Boyer F, Chariton AA, Creer S, Coissac E, Deagle BE, De Barba M, Dickie IA, Dumbrell AJ, Ficetola GF, Fierer N, Fumagalli L, Gilbert MTP, Jarman S, Jumpponen A, Kauserud H, Orlando L, Pansu J, Pawlowski J, Tedersoo L,Thomsen PF, Willerslev E, Taberlet P (2019) DNA metabarcoding - need for robust experimental designs to draw sound ecological conclusions. Molecular Ecology 28:1857-1862 (Open Access)
De Paoli-Iseppi R, Deagle BE, Polanowski AM, McMahon CR, Dickinson JL, Hindell MA Jarman SN (2019) Age estimation in a long-lived seabird (Ardenna tenuirostris) using DNA methylation-based biomarkers. Molecular Ecology Resources 19:411-425 (ReadOnly PDF)
Clarke LJ, Suter L, King R, Bissett A, Deagle BE (2019) Antarctic krill are reservoirs for distinct Southern Ocean microbial communities. Frontiers in Microbiology 9:3226 (PDF)
Clarke LJ, Bestley S, Bissett A, Deagle BE (2019) A globally distributed Syndiniales parasite dominates the Southern Ocean micro-eukaryote community near the sea-ice edge. ISME journal 13:734-737 (ReadOnly PDF)
Deagle BE, Thomas AC, McInnes JC, Clarke LJ, Vesterinen EJ, Clare EL, Kartzinel TR, Eveson JP (2019) Counting with DNA in metabarcoding studies: how should we convert sequence reads to dietary data? Molecular Ecology 28:391-406 Special Issue: "Species interactions, ecological networks and community dynamics" (PDF)
2018
Cavallo CR, Chiaradia A, Deagle BE, McInnes J, Gomez SS, Hays GC, Reina RD (2018) Molecular analysis of predator scats reveals role of salps in temperate inshore food webs. Frontiers in Marine Science 5:381 (PDF)
Deagle BE, Clarke LJ , Kitchener JA, Polanowski AM, Davidson AT (2018) Genetic monitoring of open ocean biodiversity: an evaluation of DNA metabarcoding for processing continuous plankton recorder samples. Molecular Ecology Resources 18:391-406 (PDF)
2017
De Paoli-Iseppi R, Polanowski AM, McMahon CR, Deagle BE, Dickinson JL, Hindell MA, Dickinson JL, Jarman SN (2017) DNA methylation levels in candidate genes associated with chronological age in mammals are not conserved in a long-lived seabird. PLOS ONE 12:e0189181 (PDF)
McInnes JC, Jarman SN, Lea MA, Raymond B, Deagle BE, Phillips RA, Catry P, Stanworth A, Weimerskirch H, Kusch A, Gras M, Cherel Y, Maschette D, Alderman R (2017) DNA metabarcoding as a marine conservation and management tool: a circumpolar examination of fishery discards in the diet of threatened albatross. Frontiers in Marine Science 4:277 (PDF)
De Paoli-Iseppi R, Deagle BE, McMahon CR, Hindell MA, Dickinson JL, Jarman SN (2017) Measuring animal age with DNA methylation: from humans to wild animals. Frontiers in Genetics 8:106 (PDF)
McInnes JC, Alderman R, Lea MA, Raymond B, Deagle BE, Phillips RA, Stanworth A, Thompson DR, Catry P, Weimerskirch H, Suazo CG, Gras M, Jarman SN (2017) High occurrence of jellyfish predation by black-browed and Campbell albatross identified by DNA metabarcoding. Molecular Ecology 26:4831-4845 (PDF)
Sales G, Deagle BE, Calura E, Martini P, Biscontin A, De Pittà C, Kawaguchi S, Romualdi C, Meyer B, Costa R, Jarman SN (2017) KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba). PLOS ONE 12: e0171908 (PDF)
Clarke LJ, Beard JM, Swadling KM, Deagle BE (2017) Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies. Ecology and Evolution 7: 873–883 (PDF)
McInnes JC, Alderman R, Deagle BE, Lea MA, Raymond B, Jarman SN (2017) Optimised scat collection protocols for dietary DNA metabarcoding in vertebrates. Methods in Ecology and Evolution 8: 192–202 (PDF)
Thomas AC, Lance MC, Deagle BE, Nelson BW, Trites AW (2017) Harbour seals target juvenile salmon of conservation concern. Canadian Journal of Fisheries and Aquatic Sciences 74: 907-921 (PDF)
2016
Jarman SN, Deagle BE (2016) Genetics of Antarctic krill. Book Chapter In: Biology and Ecology of Antarctic Krill (ed.Siegel). Springer (Hamburg). Pages 247-277 (Abstract)
Toomey L, Welsford D, Appleyard SA, Polanowski A, Faux C, Deagle BE, Belchier M, Marthick J, Jarman SN (2016) Genetic structure of Patagonian toothfish populations from otolith DNA. Antarctic Science 28: 347–360 (PDF)
Thomas AC, Deagle BE, Eveson JP, Harsch CH, Trites AW (2016) Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material. Molecular Ecology Resources 16: 714–726 (PDF)
2015
Deagle BE, Faux C, Kawaguchi S, Meyer B, Jarman SN (2015) Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddy the water. Molecular Ecology 24: 4943-4959 (PDF)
Jarman SN, Polanowski AM, Faux CE, Robbins J, De Paoli-Iseppi R, Bravington M, Deagle BE (2015) Molecular biomarkers for chronological age in animal ecology. Molecular Ecology 24: 4826-4847 (PDF)
Peters KJ, Ophelkeller K, Bott NJ, Deagle BE, Jarman SN, Goldsworthy SD (2015) Fine-scale diet of the Australian sea lion (Neophoca cinerea) using DNA-based analysis of faeces. Marine Ecology 36: 347-367 (Abstract)
2014
Deagle BE, Jarman SN, Coissac E, Pompanon F, Taberlet P (2014) DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match. Biology Letters 10: e20140562 (PDF)
Thomas AC, Jarman SN, Haman KH, Trites AW, Deagle BE (2014) Improving accuracy of DNA diet estimates using food tissue control materials and an evaluation of proxies for digestion bias. Molecular Ecology 23: 3706–3718 (PDF)
2013
Jarman SN, McInnes JC, Faux C, Polanowski AM, Marthick J, Deagle BE, Southwell C, Emmerson L (2013) Adelie penguin population diet monitoring by analysis of food DNA in scats. PLOS ONE 8: e82227 (PDF)
Deagle BE, Jones FC, Absher DM, Kingsley DM, Reimchen TE (2013) Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide single nucleotide polymorphism genotyping. Molecular Ecology 22: 1917-1932 (PDF)
Deagle BE*, Thomas AC*, Shaffer AK, Trites AW, Jarman SN (2013) Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count? Molecular Ecology Resources 13: 620-633 (PDF) *joint first authors
2012
Deagle BE, Jones FC, Chan YF, Absher DM, Kingsley DM, Reimchen TE (2012) Population genomics of parallel phenotypic evolution in stickleback across stream–lake ecological transitions. Proceedings of the Royal Society B: Biological Sciences 279: 1277-1286 (PDF)
Pompanon F*, Deagle BE*, Symondson WOC*, Brown DS, Jarman SN, Taberlet P (2012) Who is eating what: diet assessment using next generation sequencing. Molecular Ecology 21: 1931–1950 *joint first authors (PDF)
Jones FC, Chan YF, Schmutz J, Grimwood J, Brady SD, Southwick AM, Absher DM, Myers RM, Reimchen TE, Deagle BE, Schluter D, Kingsley DM (2012) A genome-wide SNP genotyping array reveals patterns of global and repeated species-pair divergence in sticklebacks. Current Biology 22: 83-90 (PDF)
2011
Bowles E, Schulte PM, Tollit DJ, Deagle BE, Trites AW (2011) Proportion of prey consumed can be determined from faecal DNA using real‐time PCR. Molecular Ecology Resources 11: 530-540 (PDF)
Vestheim H, Deagle BE, Jarman SN (2011) Application of blocking oligonucleotides to improve signal-to-noise ratio in a PCR. Methods in Molecular Biology 687: 265-74 (PDF)
2010
Deagle BE, Chiaradia A, McInnes J, Jarman SN (2010) Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out? Conservation Genetics 11: 2039-2048 (PDF)
2009
Deagle BE, Kirkwood R, Jarman SN (2009) Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces. Molecular Ecology 18: 2022–2038 (PDF)
2008
Deagle BE, Gales NJ, Hindell MA (2008) Variability in foraging behaviour of chick-rearing macaroni penguins Eudyptes chrysolophus and its relation to diet. Marine Ecology Progress Series 359: 295–309 (PDF)
2007
Deagle BE, Gales NJ, Evans K, Jarman SN, Trebilco R, Robinson S, Hindell MA (2007) Studying seabird diet through genetic analysis of faeces: a case study on macaroni penguins (Eudyptes chrysolophus). PLOS ONE 2: e831 (PDF)
Deagle BE, Tollit DJ (2007) Quantitative analysis of prey DNA in pinniped faeces: potential to estimate diet composition? Conservation Genetics 8: 743–747 (PDF)
Casper RM, Jarman SN, Deagle BE, Gales NJ, Hindell MA (2007) Detecting prey from DNA in predator scats: a comparison with morphological analysis, using Arctocephalus seals fed a known diet. Journal of Experimental Marine Biology and Ecology 347: 144–154 (PDF)
2006
Deagle BE, Eveson JP, Jarman SN (2006) Quantification of damage in DNA recovered from highly degraded samples — a case study on DNA in faeces. Frontiers in Zoology e3: 11 (PDF)
Tollit DJ, Heaslip SG, Deagle BE, Iverson S, Joy R, Trites AW (2006) Estimating Diet Composition in Sea Lions: What Technique to Choose? In the book: Sea lions of the world. (eds. Trites A, Atkinson S, DeMaster D, Fritz L, Gelatt T, Rea L, Wynne K). Alaska Sea Grant College Program, University of Alaska Fairbanks. (PDF)
2005
Deagle BE, Tollit DJ, Jarman SN, Hindell MA, Trites AW, Gales NJ (2005) Molecular scatology as a tool to study diet: analysis of prey DNA in scats from captive Steller sea lions. Molecular Ecology 14: 1831–1842 (PDF)
Deagle BE, Jarman SN, Pemberton D, Gales NJ (2005) Genetic screening for prey in the gut contents from a giant squid (Architeuthis sp.). Journal of Heredity 96: 417- 423 (PDF)
Patil JG, Gunasekera RM, Deagle BE, Bax NJ (2005) Specific Detection of Pacific Oyster (Crassostrea gigas) Larvae in Plankton Samples Using Nested Polymerase Chain Reaction. Marine Biotechnology 7: 11-20 (PDF)
Patil JG, Gunasekera RM, Deagle BE, Bax NJ, Blackburn SI (2005) Development and Evaluation of a PCR Based Assay for Detection of the Toxic Dinoflagellate, Gymnodinium catenatum (Graham) in Ballast Water and Environmental Samples. Biological Invasions 7: 983-994 (PDF)
2004 and earlier
Jarman SN, Deagle BE, Gales NJ (2004) Group-specific polymerase chain reaction for DNA-based analysis of species diversity and identity in dietary samples. Molecular Ecology 13: 1313–1322 (PDF)
Deagle BE, Bax N, Hewitt CL, Patil JG (2003) Development and evaluation of a PCR-based test for detection of Asterias (Echinodermata: Asteroidea) larvae in Australian plankton samples from ballast water. Marine and Freshwater Research 54: 709-719 (PDF)
Beacham TD, Supernault KJ, Wetklo M, Deagle BE, Labaree K, Irvine JR, Candy JR, Miller KM, Nelson RJ, Withler RE (2003). The geographic basis for population structure in Fraser River Chinook salmon (Oncorhynchus tshawytscha). Fishery Bulletin 101: 229–242 (PDF)
Beacham TD, Candy JR, Supernault KJ, Wetklo M, Deagle BE, Labaree K, Irvine JR, Miller KM, Nelson RJ, Withler RE (2003). Evaluation and application of microsatellites for population identification of Fraser River chinook salmon (Oncorhynchus tshawytscha). Fishery Bulletin 101: 243- 259 (PDF)
Beacham TD, Candy JR, Supernault KJ, Ming T, Deagle BE, Schultz A, Tuck D, Kaukinen K, Irvine JR, Miller KM, Withler RE (2001) Evaluation and application of microsatellite and major histocompatibility complex variation for stock identification of Coho salmon in British Columbia. Transactions of the American Fisheries Society 130: 1116–1155 (PDF)
Deagle BE, Reimchen TE and Levin DB (1996) Origins of endemic stickleback from the Queen Charlotte Islands: mitochondrial and morphological evidence. Canadian Journal of Zoology 74: 1045-1056 (PDF).