Publications

The Australian Centre for Ancient DNA's world-class research is published in various scientific journals.

We invite you to browse our publications which highlight the many scientific discoveries by our researchers and collaborators. ACAD members are marked in bold.

Year Title Authors Publication
2024 Shrouded in history: Unveiling the ways of life of an early Muslim population in Santarém, Portugal (8th– 10th century AD) Rebecca Anne MacRoberts, Marco Liberato, Xavier Roca-Rada, Maria João Valente, Claudia Relvado, Teresa Matos Fernandes, Cristina Barrocas Dias, Bastien Llamas, Hermínia Vasconcelos Vilar, Bernd R Schöne, Sara Ribeiro, José Francisco Santos, João C Teixeira, Anne-France Maurer Plos one
2024

Optimised in-solution enrichment of over a million ancient human SNPs

 Roberta Davidson, Xavier Roca-Rada, Shyamsundar Ravishankar, Leonard Taufik, Christian Haarkötter, Evelyn Collen, Peter Webb, Matthew P Williams, M Irfan Mahmud, Erlin Novita Idje Djami, Gludhug A Purnomo... João C Teixeira, Raymond Tobler, Lars Fehren-Schmitz, Bastien Llamas bioRxiv
2024 Biological sex estimation using ancient DNA in Classic Maya contexts: some findings from Naachtun (Guatemala) Hemmamuthé Goudiaby, Xavier Roca-Rada, Kalina Kassdjikova, Lars Fehren-Schmitz, Bastien Llamas Bulletins et mémoires de la Société d’Anthropologie de Paris
2024 Cases of trisomy 21 and trisomy 18 among historic and prehistoric individuals discovered from ancient DNA Adam Benjamin Rohrlach, Maïté Rivollat, Patxuka de-Miguel-Ibáñez, Ulla Moilanen, Anne-Mari Liira, João C Teixeira, Xavier Roca-Rada, Javier Armendáriz-Martija, Kamen Boyadzhiev, Yavor Boyadzhiev, Bastien Llamas... Wolfgang Haak, Kay Prüfer Nature Communications
2023 Millennial processes of population decline, range contraction and near extinction of the European bison July A Pilowsky, Stuart C Brown, Bastien Llamas, Ayla L van Loenen, Rafał Kowalczyk, Emilia Hofman-Kamińska, Ninna H Manaseryan, Viorelia Rusu, Matija Križnar, Carsten Rahbek, Damien A Fordham Proceedings of the Royal Society B
2023 The landscape of genomic structural variation in Indigenous Australians Andre LM Reis, Melissa Rapadas, Jillian M Hammond, Hasindu Gamaarachchi, Igor Stevanovski, Meutia Ayuputeri Kumaheri, Sanjog R Chintalaphani, Duminda SB Dissanayake, Owen M Siggs, Alex W Hewitt, Bastien Llamas...  Hardip R Patel, Ira W Deveson Nature
2023 Allelic bias when performing in‐solution enrichment of ancient human DNA Roberta Davidson, Matthew P Williams, Xavier Roca‐Rada, Kalina Kassadjikova, Raymond Tobler, Lars Fehren‐Schmitz, Bastien Llamas Molecular Ecology Resources 
2023 Equity, diversity, and inclusion at the Global Alliance for Genomics and Health Neerjah Skantharajah, Shakuntala Baichoo, Tiffany F Boughtwood, Esmeralda Casas-Silva, Subhashini Chandrasekharan, Sanjay M Dave, Khalid A Fakhro, Aida B Falcon de Vargas, Sylvia S Gayle, Vivek K Gupta, Rachele Hendricks-Sturrup, Ashley E Hobb, Stephanie Li, Bastien Llamas... Manuel Corpas  Cell Genomics
2023 Paleogenomic study of the Mexican past Bastien Llamas, Xavier Roca-Rada Science
2023 Deep FASTQ and BAM co-compression in Genozip 15 Divon Mordechai Lan, Daniel ST Hughes, Bastien Llamas bioRxiv 

2023

 Developing Loop Mediated Isothermal Amplification (LAMP) assays for rapid, presumptive DNA detection of an invasive reptile (Boa constrictor) Nathan Deliveyne, Jeremy J Austin, Phillip Cassey Wildlife Research
2023 Ecological dynamics of moa extinctions reveal convergent refugia that today harbor flightless birds. Sean Tomlinson, Mark Lomolino, Jamie Wood, Atholl Anderson, Stuart Brown, Sean Haythorne, George Perry, Janet Wilmshurst, Jeremy Austin, Damien Fordham Research Square
2023 From clean spaces to crime scenes: Exploring trace DNA recovery from titania-coated self-cleaning substrates Dan Nana Osei Bonsu, Denice Higgins, Jeremy J Austin Science & Justice
2023 Metal–DNA interactions: Exploring the impact of metal ions on key stages of forensic DNA analysis Dan Nana Osei Bonsu, Denice Higgins, Claire Simon, Julianne M Henry, Jeremy J Austin Electrophoresis
2023 Quantitative PCR overestimation of DNA in samples contaminated with tin Dan Nana Osei Bonsu, Denice Higgins, Claire Simon, Corey S Goodwin, Julianne M Henry, Jeremy J Austin Journal of Forensic Sciences
2023 Umbrella terms conceal the sale of threatened shark species: A DNA barcoding approach Ashleigh E Sharrad, Patrick Reis-Santos, Jeremy Austin, Bronwyn M Gillanders Food Control
2023 A custom hybridisation enrichment forensic intelligence panel to infer biogeographic ancestry, hair and eye colour, and Y chromosome lineage Felicia Bardan, Denice Higgins, Jeremy J Austin Forensic Science International: Genetics 
2023 Methods guides based on dogma not science: an example from microbiota restoration Jessica Stanhope, Jeremy J Austin, Emily Skelly, Philip Weinstein Restoration Ecology
2023 Diagnosing a synchronous extinction Lauren White, Frederik Saltre, Corey Bradshaw, Jeremy Austin Book: Thylacine: The History, Ecology and Loss of the Tasmanian Tiger
2023  Shining a LAMP on the applications of isothermal amplification for monitoring environmental biosecurity Nathan Deliveyne, Jennifer M Young, Jeremy J Austin, Phillip Cassey Neobiota
2023 Reconstructing colonization dynamics to establish how human activities transformed island biodiversity Sean Tomlinson, Mark Lomolino, Sean Haythorne, Atholl Anderson, Jeremy Austin, Stuart C Brown, George Perry, Janet Wilmshurst, Jamie Wood, Damien A Fordham bioRxiv
2023 Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects Leonard Taufik, João C Teixeira, Bastien Llamas, Herawati Sudoyo, Raymond Tobler, Gludhug A Purnomo Genes 
2022 More than dirt: Sedimentary ancient DNA and Indigenous Australia Dawn A Lewis, Rebecca Simpson, Azure Hermes, Alex Brown, Bastien Llamas Molecular Ecology Resources 
2022 Individuals with Inflammatory Bowel Disease Have an Altered Gut Microbiome Composition of Fungi and Protozoa Gina L Guzzo, Murthy N Mittinty, Bastien Llamas, Jane M Andrews, Laura S Weyrich Microorganisms
2022 A 1000-year-old case of Klinefelter's syndrome diagnosed by integrating morphology, osteology, and genetics Xavier Roca-Rada, Sofia Tereso, Adam B Rohrlach, André Brito, Matthew P Williams, Cláudia Umbelino, Francisco Curate, Ira W Deveson, Yassine Souilmi, António Amorim, Pedro C Carvalho, Bastien Llamas, João C Teixeira The Lancet 
2022 The immunogenetic impact of European colonization in the Americas Evelyn Jane Collen, Angad Singh Johar, João C Teixeira, Bastien Llamas Frontiers in Genetics
2022 Genozip 14-advances in compression of BAM and CRAM files Divon Mordechai Lan, Bastien Llamas bioRxiv
2022 Genozip Dual-Coordinate VCF format enables efficient genomic analyses and alleviates liftover limitations Divon Mordechai Lan, Gludhug Purnomo, Raymond Tobler, Yassine Souilmi, Bastien Llamas bioRxiv
2021 Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment Adrien Oliva, Raymond Tobler, Bastien Llamas, Yassine Souilmi Ecology and Evolution
2021 Ethics of DNA research on human remains: five globally applicable guidelines Songül Alpaslan-Roodenberg, David Anthony, Hiba Babiker, Eszter Bánffy, Thomas Booth, Patricia Capone, Arati Deshpande-Mukherjee, Stefanie Eisenmann, Lars Fehren-Schmitz, Michael Frachetti, Ricardo Fujita, Catherine J Frieman, Qiaomei Fu, Victoria Gibbon, Wolfgang Haak, Mateja Hajdinjak, Kerstin P Hofmann, Brian Holguin, Takeshi Inomata, Hideaki Kanzawa-Kiriyama, William Keegan, Janet Kelso, Johannes Krause, Ganesan Kumaresan, Chapurukha Kusimba, Sibel Kusimba, Carles Lalueza-Fox, Bastien Llamas... Muhammad Zahir Nature 
2021 Ten millennia of hepatitis B virus evolution Arthur Kocher, Luka Papac, Rodrigo Barquera, Felix M Key, Maria A Spyrou...Ken Massy, Marcello Mannino, Vyacheslav Moiseyev Science
2021 Systematic benchmark of ancient DNA read mapping Adrien Oliva, Raymond Tobler, Alan Cooper, Bastien Llamas, Yassine Souilmi Briefings in Bioinformatics
2021 Genozip: a universal extensible genomic data compressor Divon Lan, Ray Tobler, Yassine Souilmi, Bastien Llamas Bioinformatics
2021 Mitogenomes Reveal Two Major Influxes of Papuan Ancestry across Wallacea Following the Last Glacial Maximum and Austronesian Contact Gludhug A Purnomo, Kieren J Mitchell, Sue O’Connor, Shimona Kealy, Leonard Taufik, Sophie Schiller, Adam Rohrlach, Alan Cooper, Bastien Llamas, Herawati Sudoyo, João C Teixeira, Raymond Tobler Genes 
2021 Ancient mitochondrial genomes from the Argentinian Pampas inform the early peopling of the Southern Cone of South America Xavier Roca-Rada, Gustavo Politis, Pablo G Messineo, Nahuel Scheifler, Clara Scabuzzo, Mariela González, Kelly M Harkins, David Reich, Yassine Souilmi, João C Teixeira, Bastien Llamas, Lars Fehren-Schmitz iScience
2021 Stochastic models support rapid peopling of Late Pleistocene Sahul Corey JA Bradshaw, Kasih Norman, Sean Ulm, Alan N Williams, Chris Clarkson, Joël Chadœuf, Sam C Lin, Zenobia Jacobs, Richard G Roberts, Michael I Bird, Laura S Weyrich, Simon G Haberle, Sue O’connor, Bastien Llamas, Tim J Cohen, Tobias Friedrich, Peter Veth, Matthew Leavesley, Frédérik Saltré Nature Communications
2021 Runes from Lány (Czech Republic)-The oldest inscription among Slavs. A new standard for multidisciplinary analysis of runic bones Jiří Macháček, Robert Nedoma, Petr Dresler, Ilektra Schulz, Elias Lagonik, Stephen M Johnson, Ludmila Kaňáková, Alena Slámová, Bastien Llamas, Daniel Wegmann, Zuzana Hofmanová Journal of Archaeological Science 
2021 A Multidisciplinary Review of the Inka Imperial Resettlement Policy and Implications for Future Investigations Roberta Davidson, Lars Fehren-Schmitz, Bastien Llamas Genes
2020 An optimized method for the extraction of ancient eukaryote DNA from marine sediments Ambrecht L, Herrando‐Pérez S, Eisenhofer R, Gustaaf M Hallegraeff, Christopher JS Bolch, Cooper A. Molecular Ecology Resources
2020 Binding affinities of 438 HLA proteins to complete proteomes of seven pandemic viruses and distributions of strongest and weakest HLA peptide binders in populations worldwide Barquera R, Collen E, Di D, Buhler S, Teixeira J, Llamas B, Manuel Nunes J, Sanchez‐Maza A. HLA
2020 Forensic touch DNA recovery from metal surfaces–A review Bonsu DOM, Higgins D, Austin JJ. Science & Justice
2020 Ancient DNA from an extinct Mediterranean micromammal-Hypnomys morpheus (Rodentia: Gliridae) - Provides insight into the biogeographic history of insular dormice Bover P, Mitchell KJ, Torres‐Roig E, Llamas B, Thomson VA,  Alcover JA, Agustí J,  Cooper A, Joan Pons. Journal of Zoological Systematics and Evolutionary Research
2020 Spatiotemporal landscape genetics: Investigating ecology and evolution through space and time Fenderson LE, Kovach AI, Llamas B. Molecular Ecology
2019 Widespread male sex bias in mammal fossil and museum collections Gower G, Fenderson LE,  Salis AT, Helgen KM, van Loenen AL, Heiniger H, Hofman-Kamińska E, Kowalczyk R, Mitchell KJ, Llamas B, Cooper A. PNAS
2020 European and Asian contribution to the genetic diversity of mainland South American chickens Herrera MB, Kraitsek S, Alcalde JA, Quiroz D, Revelo H, Alvarez LA, Rosario MF, Thomson V, Jianlin H, Austin JJ, Gongora J. Royal Society Open Science
2020 Genozip: a fast and efficient compression tool for VCF files Lan D, Tobler R, Souilmi Y, Llamas B. Bioinformatics
2020 More arrows in the ancient DNA quiver: Use of paleoepigenomes and paleomicrobiomes to investigate animal adaptation to environmen Liu Y, Weyrich LS, Llamas B. Molecular Biology and Evolution
2020 Ancient DNA helps trace the peopling of the world Llamas B, Roca Rada S, Collen E. The Biochemist
2020 Using ancient DNA and radiocarbon dating to determine the provenance of an unusual whaling artifact Mudge C, Dallwitz R, Llamas B, Austin JJ Frontiers in Ecology and Evolution
2020 Oligocene divergence of frogmouth birds (Podargidae) across Wallace's Line Paul M Oliver, Holly Heiniger, Andrew F Hugall, Leo Joseph, Kieren J Mitchell. Biology Letters
2020 Ancient DNA studies in Pre-Columbian Mesoamerica.  Roca-Rada X, Souilmi Y, Teixeira JC, Llamas B  Genes
2020 Microbiome applications for pathology: challenges of low microbial biomass samples during diagnostic testing Selway CA, Eisenhofer R, Weyrich LS. The Journal of Pathology: Clinical Research
2020 Ancient DNA of northern China Hystricidae sub-fossils reveals the evolutionary history of old world porcupines in the Late Pleistocene Sheng G, Hu J, Tong H, Llamas B, Yuan J, Hou X, Chen S, Xiao B, Lai X BMC Evolutionary Biology
2020 PolyLinkR: A linkage-sensitive gene set enrichment R package Tobler T, Johar A, Huber C, Souilmi Y. arXIV preprint arXIV:2004.03224
2019 Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation. Armbrecht LH, Coolen MJL, Lejzerowicz F, George SC, Negandhi K, Suzuki Y, Young J, Foster NR, Armand LK, Cooper A, Ostrowski M, Focardi A, Stat M, Moreau JW, Weyrich LS. Earth Science Reviews
2019 Mitochondrial genomes from New Zealand's extinct Adzebills (Aves: Aptornithidae: Aptornis) support a sister-taxon relationship with the Afro-Madagascan Sarothruridae Boast AP, Chapman B, Herrera MB, Worthy TH, Scofield RP, Tennyson AJD, Houde P, Bunce M, Cooper A, Mitchell KJ. Diversity 
2019 Unraveling the phylogenetic relationships of the extinct bovid Myotragus balearicus Bate 1909 from the Balearic Islands  Bover P, Llamas B, Mitchell KJ, Thomson VA, Alcover JA, Lalueza-Fox C, Cooper A, Pons J. Quaternary Science Reviews
2019 Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA  Carmen Gomez Cabrera M del, Young JM, Roff G, Staples T, Ortiz JC, Pandolfi JM, Cooper A. Molecular Ecology 
2019 Mitogenomes uncover extinct penguin taxa and reveal island formation as a key driver of speciation   Cole TL, Ksepka DT, Mitchell KJ, Tennyson AJD, Thomas DB, Pan H, Zhang G, Rawlence NJ, Wood JR, Bover P, Bouzat JL, Cooper A, Fiddaman S, Hart T, Miller G, Ryan PG, Shepherd L, Wilmshurst JM, Waters JM. Molecular Biology and Evolution
2019 Ancient microbial DNA in dental calculus: A new method for studying rapid human migration events   Eisenhofer R, Anderson A, Dobney K, Cooper A, Weyrich LS. Journal of Island and Coastal Archaeology
2019 Widespread male sex bias in mammal fossil and museum collections Gower G, Fenderson LE, Salis AT, Helgen KM, van Loenen AL, Heiniger H, Hofman-Kamińska E, Kowalczyk R, Mitchell KJ, Llamas B, Cooper A. PNAS
2019 The dogma of dingoes - Taxonomic status of the dingo: A reply to Smith et al.  Jackson SM, Fleming PJs, Eldridge MDb, Ingleby S, Flannery T, Johnson RN, Cooper SJb, Mitchell KJ, Souilmi Y, Cooper A, Wilson DE, Helgen KM. Zootaxa
2019 Race in a genome: Long read sequencing, ethnicity-specific reference genomes and the shifting horizon of race Kowal E, Llamas B  Journal of Anthropological Sciences
2019 A microbial sea of possibilities: current knowledge and prospects for an improved understanding of the fish microbiome Legrand TPRA, Wynne JW, Weyrich LS, Oxley APA. Reviews in Aquaculture
2019 A strategy for building and using a human reference pangenome Llamas B, Narzisi G, Schneider V...Busby B F1000Research
2019 Recombinase polymerase amplification (RPA) versus PCR for ancient DNA library amplification   Richards SM, Mitchell KJ, Tobler R, Cooper A. Peer J Preprints
2019 Low-cost cross-taxon enrichment of mitochondrial DNA using in-house synthesised RNA probes  Richards SM, Hovhannisyan N, Gilliham M, Ingram J, Skadhauge B, Heiniger H, Llamas B, Mitchell KJ, Meachen J, Fincher JB, Austin JJ, Cooper A. PloS One 
2019 Retrospective eDNA assessment of potentially harmful algae in historical ship ballast tank and marine port sediments   Shaw JLA, Weyrich LS, Hallegraeff G, Cooper A. Molecular Ecology
2019 Laboratory contamination over time during low-biomass sample analysis  Weyrich LW, Farrer AG, Eisenhofer R, Arriola LA, Young J, Selway CA, Handsley‐Davis M, Adler CJ, Breen J, Cooper A. Molecular Ecology Resources
2019 Soil DNA: advances in DNA technology offers a powerful new tool for forensic science   Young JM, Higgins D, JJ Austin. Geological Society, London, Special Publications
2018

Coprolites reveal ecological interactions lost with the extinction of New Zealand birds 

 Boast AP, Weyrich LS, Wood RJ, Metcalf JL, Knight R, Cooper A. PNAS 
2018 A mini-multiplex SNaPshot assay for the triage of degraded human DNA   Bardan F, Higgins D, Austin JJ. Forensic Science International Genetics
2018 Genetic diversity through time and space: diversity and demographic history from natual history specimens and serially sampled contemporary populations of the threatened Gouldian finch (Erythrura gouldiae) Bolton PE, Rollins LA, Brazill-Boast J, Maute KL, Legge S, Austin JJ, Griffith SC. Conservation Genetics
2018 Molecular phylogenetics supports the origin of an endemic Balearic shrew lineage (Nesiotites) coincident with the Messinian Salinity Crisis   Bover P, Mitchell KJ, Llamas B, Rofes J, Thomson VA, Cuenca-Bescós G, Alcover JA, Cooper A, Pons J. Molecular Phylogenetics and Evolution
2018 Molecular resolution to a morphological controversy: the case of North American fossil muskoxen Bootherium and Symbos  Bover P, Llamas B, Thomson VA, Pons J, Cooper A, Mitchell KJ. Molecular Phylogenetics and Evolution
2018 Ancient DNA tracks the mainland extinction and island survival of the Tasmanian devil   Brüniche–Olsen A, Jones ME, Burridge CP, Murchison EP, Holland BR, Austin JJ. Journal of Biogeography
2018 Reconstructing the evolution of giant extinct kangaroos: Comparing the utility of DNA, morpholgy and total evidence Cascini M, Mitchell KJ, Cooper A, Phillips MJ. Systematic Biology
2018 Contamination in low microbial biomass microbiome studies: Issues and recommendations   Eisenhofer E, Minich JJ, Marotz C, Cooper A, Knight R, Weyrich LS. Trends in Microbiology
2018 Assessing alignment-based taxonomic classification of ancient microbial DNA Eisenhofer E, Weyrich LS. Peer J Preprints
2018 Biological and cultural drivers of oral microbiota in Medieval and Post-Medieval London, UK  Farrer AG, Bekvalac J, Redfern R, Gully N, Dobney K, Cooper A, Weyrich LS. bioRxiv p343889
2018 Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore Feigin CY, Newton AH, Doronina L, Schmitz J, Hipsley CA, Mitchell KJ, Gower G, Llamas B, Soubrier J, Heider TN, Menzies BR, Cooper A, O’Neill RJ, Pask AJ. Nature Ecology & Evolution
2018 Singleplex quantitative real-time PCR for the assessment of human mitochondrial DNA quantity and quality Goodwin C, Higgins D, Tobe SS, Austin JJ, Wotherspoon A, Gahan ME, McNevin D. Forensic Science, Medicine and Pathology
2018 Consequences of colonialism: A microbioal perspective to contemporary Indigenous health. 167(2) pp 423-437 Skelly, E, Kapellas K, Cooper A, Weyrich LS. American Journal of Physical Anthropology
2018 Ancient DNA from Giant Panda (Ailuropoda melanoleuca) of South-Western China Reveals Genetic Diversity Loss during the Holocene. 9(4), 198. Sheng G-L, Barlow A, Cooper A, Hou X-D, Ji X-P, Jablonski NG, Zhong B-J, Liu H, Flynn LJ, Yuan J-X, Wang LR, Basler N, Westbury MV, Hofreiter M and Lai X-L. Genes 
2018 Genetic diversity and drivers of dwarfism in extinct island emu populations Thomson VA, Mitchell KJ, Eberhard R, Dortch J, Austin JJ, Cooper A. Biology Letters 
2018 Early Last interglacial ocean warming drove substantial ice mass loss from Antarctica  Turney C, Fogwill C, Golledge N,... Weyrich LS, Young J, Cooper A. EarthArXiv
2018 Laboratory contamination over time during low-biomass sample analysis  Weyrich LS, Farrer AG, Eisenhofer R, Arriola LA, Young J, Selway CA, Handsley-Davis M, Adler C, Breen J, Cooper A. BioRxiv p460212
2018 Long-term genetic consequences of mammal reintroductions into an Australian conservation reserve  White LC, Moseby KE, Thomson VA, Donnellan SC Austin JJ. Biological Conservation
2018 High-qulity fossil dates support a synchronous, Late Holocene extinction of devils and thylacines in mainland Australia  White LC, Saltre F, Bradshaw CJA, Austin JJ. Biology Letters 
2018 Ancient mitochondrial genomes reveal the demographic history and phylogeography of the extinct, enigmatic thylacine (Thylacinus cynocephalus)  White LC, Mitchell KJ, Austin JJ. Journal of Biogeography
2017

A case for realigning species limits in the southern Australian shipbirds long recognised as the Western Whipbird (Psophodes nigrogularis) 

 Burbidge AH, Joseph L, Toon A, White LC, McGuire A, Austin JJ. Emu-Austral Ornithology 
2017 Experimental conditions improving in-solution target enrichment for ancient DNA Cruz‐Dávalos DI, Llamas B, Gaunitz C, Fages A, Gamba C, Soubrier J,...  Cooper A, Willerslev E, Orlando L. Molecular Ecology Resources
2017 Ground-truthing Phylotype Assignments for Antarctic Invertebrates   Czechowski P, Clarke L, Cooper A, Stevens M. DNA Barcodes
2017 A primer to metabarcoding surveys of Antarctic terrestrial biodiversity Czechowski P, Clarke LJ, Cooper A, Stevens M. Antarctic Science
2017 Ancient Microbioal DNA in Dental Calculus: A new m.ethod for studying rapid human migration events Eisenhofer R, Anderson A, Dobney K, Cooper A, Weyrich LS. Journal of Island and Coastal Archaeology
2017 Reply to Santiago-Rodriguez et al.: proper authentication of ancient DNA is essential Eisenhofer R, Cooper A, Weyrich LS. FEMS Microbiology Ecology
2017 A palaeogenetic perspective on the early population history of the high altitude Andes Fehren-Scmitz L, Harkins KM, Llamas B. Quaternary International 
2017  Antarctic ice sheet discharge driven by atmosphere-ocean feedbacks at the Last Glacial Termination Fogwill CJ, Turney CSM, Golledge NR,... Cooper A. Scientific Reports
2017 The influence of Antarctic subglacial volcanism on the global iron cycle during the Last Glacial Maximum Frisia S, Weyrich LS, Hellstrom J, Borsato A, Golledge NR, Anesio AM, Bajo P, Drysdale RN, Augustinus PC, Rivard C, Cooper A.  Nature Communications
2017 Consent: Data-sharing for indigenous peoples   Kowal E, Llamas B, Tishkoff S. Nature
2017 Intrinsic factors drive spatial genetic variation in a highly vagile species, the wedge-tailed eagle (Aquila audax), in Tasmania Kozakiewicz CP, Carver S, Austin JJ, Shephard JM, Burridge CP. Avian Biology
2017 Parallel palaeogenomic transects reveal complex genetic history of early European farmers Lipson M, Szécsényi-Nagy A, Mallick S, ... Reich D. Nature
2017 From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era  Llamas B, Valverde G, Fehren-Schmitz L, Weyrich LS Cooper, Haak W. STAR: Science & Technology of Archaeological Research
2017 Genetic studies of the peopling of the Americas: What insights do diachronic mitochondrial genome datasets provide Llamas B, Harkins KM, Fehren-Schmitz. Quaternary International
2017 Human evolution: A tale from ancient genomes  Llamas B. Willerslev E, Orlando E. The Royal Society
2017 Urban habitat restoration provides a human health benefit through microbiome rewilding: The Microbiome Rewilding Hypothesis Mills JG, Weinstein P. Gellie NJC, Weyrich LS, Lowe AJ, Breed M. Restoration Ecology 
2017 Observations on breeding Night Parrots (Pezoporus occidentalis) in western Queensland  Murphy SA, Austin JJ, Murphy RK, Silcock J. Joseph L, Garnett ST, Leseberg NP, Watson JEM, Burbidge AH. Emu - Austral Ornithology 1
2017 Movements and habitat use of the night parrot Pezoporus occidentalis in south-western Queensland   Murphy SA, Silcock J, Murphy R, Reid J, Austin JJ. Austral Ecology
2017 Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania  Nagle N, Ballantyne KN... Genographic Consortium. Journal of Human Genetics
2017 Did the historical range of the European bison (Bison bonasus L.) extend further south? - a new finding from the Yenikapi Metro and Marmaray excavation,Turkey   Onar V, Soubrier J, Toker NY, van Loenen A, Llamas B, Siddiq AB, Pasicka E, Tokarska M. Mammal Research
2017 Ancient DNA analysis of the extinct North American flat-headed peccary (Platygonus compressus) Perry T, van Loenen AL, Heiniger H, Lee C, Gongora J, Cooper A, Mitchell KJ. Molecular Phylogenetics and Evolution
2017 Corrigendum: Megafaunal isotopes reveal role of increased moisture on rangeland during late Pleistocene extinctions  Rabanus-Wallace MT, Wooller MJ, Zazula GD, Shute E, Jahren H, Kosintsev P, Burns JA, Breen J, Llamas B, Cooper A. Nature Ecology & Evolution
2017 Megafaunal isotopes reveal role of increased moisture on rangeland during late Pleistocene extinctions Rabanus-Wallace MT, Wooller MJ, Zazula GD, Shute E, Jahren AH, Kosintsev P, Burns JA, Breen J, Llamas B, Cooper A. Nature Ecology & Evolution
2017 The origin and phylogenetic relationships of the new Zealand ravens Scofield RP, Mitchell KJ, Wood JR , De Pietri VL, Jarvie S, Llamas B, Cooper A. Molecular Phylogenetics and Evolution
2017 Using environmental (e) DNA sequencing for aquatic biodiversity surveys: a beginner's guide Shaw JLA, Weyrich, Cooper A. Marine and Freshwater Research
2017  Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia   Tobler R, Rohrlach A, Soubrier J, Bover P, Llamas B, ... Richards SM, Mitchell RJ, Kowal E, Stephen JR, Williams L, Haak W, Cooper A. Nature
2017 Embracing the gut microbiota: the new frontier for inflammatory and infectiousdisease Van Den Elsen LWJ, Poyntz HC, Weyrich LS, Young W, Forbes‐Blom EE. Clinical & translational immunology
2017 Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus   Weyrich LS, Duchene S, Soubrier J, Arriola L, Llamas B, Breen J,... Dobney K, Cooper A. Nature
2017 Soil DNA metaboarcoding and high-throughput sequencing as a forensic tool: considerations, potential limitations and recommendations Young J. Austin JJ, Weyrich LS. FEMS Microbiology Ecology 
2016

Exploring relationships between host genome and microbiome: new insights from genome-wide association studies

 Abdul-Aziz, Cooper A, Weyrich LS. Frontiers in microbiology.
2016 Detecting Selection on Temporal and Spatial Scales: A Genomic Time-Series Assessment of Selective Responses to Devil Facial Tumor Disease  Brüniche-Olsen A, Austin JJ, Jones ME, Holland BR, Burridge CP. PloS One
2016 Experimental conditions improving in solution target enrichment for ancient DNA Cruz‐Dávalos DI, Llamas B, Gaunitz D, Fages A, Gamba C, Soubrier J, Librado P, Seguin‐Orlando A, Pruvost M, Alfarhan AH, Alquraishi SA, Al‐Rasheid KAS, Scheu A, Beneke N, Ludwig A, Cooper A, Willerslev E, Orlando L. Molecular Ecology Resources 
2016 Age-related environmental gradients influence invertebrate distribution in the Prince Charles Mountains, East Antarctica   Czechowski P, White, D, Clarke L, McKay A, Cooper A, Stevens M. Royal Society Open Science
2016 Isolating viable ancient bacteria: what you put in is what you get out   Eisenhofer R, Cooper A, Weyrich LS. Microbiology Resource Announcements
2016 Ancient DNA reveals complexity in the evolutionary history and taxonomy of the endangered Australian brush-tailed bettongs Haouchar D, Pacioni C, Haile J, McDowell MC, Baynes A, Phillips MJ, Austin JJ, Pope LC, Bunce M. Biodiversity and Conservation
2016 Nucleic Acid sample preparation from teeth/dental remains  Higgins D, Austin JJ. Sample Preparation Techniques for Soil, Plant and Animal Samples
2016 Ancient DNA resolves the subspecific identity of the holotype of the Galah Eolophus roseicapilla, a widespread Australian cockatoo  Joseph L, Boussès P, Wilke T, Austin JJ.  Emu
2016 Norfolk Island Robins are a distinct endangered species: ancient DNA unlocks surprising relationships and phenotypic discordance within the Australo-Pacific Robins Kearns AM, Joseph L, White LC, Austin JJ, Baker C, Driskell AC, Malloy JF, Omland KE. Conservation Genetics
2016 Ancient mitochondrial DNA provides high-resolution timescale of the peopling of the Americas Llamas B*, Fehren-Schmitz L*, Valverde G, Soubrier J,...Ho SYW, Cooper A, Haak W. Science Advances
2016 Synergistic roles of climate warming and human occupataion in Patagonian megafaunal extinctions during the Last Deglaciation   Metcalf JL, Turney C, Barnett R,... Austin JJ, Cooper A.  Science Advances
2016 Ancient mitochonddrial DNA reveals convergent evolution of giant short-faced bears (Tremarctinae) in North and South America   Mitchell KM, Bray SC, Bover P, Soibelzon L, Schubert BW, Prevosti F, Prieto A, Martin F, Austin JJ, Cooper A. Biology Letters
2016 Iron Age and Anglo-Saxon genomes from East England reveal British migration history.   Schiffels S, Haak W, Paajanen P, Llamas B, Popescu E, Loe L, Clarke R, Lyons A, Mortimer R, Sayer D, Tyler-Smith C, Cooper A, Durbin R. Nature Communications
2016 The origin and phylogenetic relationships of the New Zealand ravens Scofield RP, Mitchell KJ, Wood JR,De Pietri VL, Jarvie S, Llamas B, Cooper A. Molecular Phylogenetics and Evolution
2016 Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system Shaw JLA, Clarke LJ, Wedderburn SD, Barnes TC, Weyrich LS, Cooper A.  Biological Conversation 
2016  Early cave art and ancient DNA record the origin of European bison   Soubrier J, Gower G [...] Shapiro B, Cooper A. Nature Communications
2016 Ancient DNA analysis suggests negligible impact of the Wari Empire expansion in Peru's central coast during the Middle Horizon  Valverde G, Romero MIB, Espinoza IF, Cooper A, Fehren-Schmitz L, Llamas B, Haak W. PloS One
2016 High-throughput sequencing of trace quantities of soil provides reproducible and discriminative fungal DNA profiles   Young JM, Weyrich LS, Cooper A. Journal of Forensic Sciences
2015 Abrupt warming events drove Late Pleistocene Holarctic megafaunal turnover  Cooper A, Turney C, Hughen KA, Brook BW, McDonald HG, Bradshaw CJA. Science 
2015 Reintroduction of locally extinct vertebrates impacts arid soil fungal communities Clarke LJ, Weyrich LS, Cooper A. Molecular Ecology
2015 The relevance of ancient DNA to contemporary disease   Cooper A, Weyrich LS, Farrer AG. Pathology-Journal of the RCPA
2015 A Re-appraisal of the early andean human remains from Iauricocha in Peru  Fehren-Schmitz L, Llamas B, Lindauer S,... Cooper A, Reich D, Haak W. PloS One
2015 Genome-wide data from ancient Peruvian highlanders and the Population History of South America   Fehren-Schmitz L, Skoglund P, Llamas B, Lindauer S, Tomasto E, Kuzminsky S, Rohland N, Nordenfelt S, Mallick S, Cooper A, Patterson N, Haak W, Reich D. American Journal of Physical Anthropology
2015 Massive migration from the steppe was a source for Indo-European languages in Europe  Haak W, Lazaridis I, Patterson N,... Cooper A, Werner Alt K & Reich D. Nature
2015 Differential Nuclear and Mitochondrial DNA Preservation in Post-Mortem Teeth with Implications for Forensic and Ancient DNA Studies   Higgins D, Rohrlach AB, Kaidonis J, Townsend G, Austin JJ. PloS One
2015 Late Pleistocene australian marsupial DNA clarifies the affinities of extinct megafaunal kangaroos and wallabies Llamas B, Brotherton P, Mitchell KJ, Templeton JEL, Thomson VA, Metcalf JL, Armstrong KN, Kasper M, Richards SM, Camens AB, Lee MSY, Cooper, A. Molecular Biology and Evolution
2015 Eight thousand years of natural selection in Europe   Mathieson I, Lazaridis I, Rohland N, Mallick S, Llamas B, Pickrell J, Meller H, Rojo Guerra MA, Krause J, Anthony D, Brown D, Lalueza Fox C, Cooper A, Alt KW, Haak W, Patterson N, Reich D. bioRxiv
2015 Phenotypic inference from ancient DNA Mathieson I, Haak W, Patterson N, Mallick S, Llamas B, Rohland N, Harney E, Nordenfeldt S, Stewardson K, Lazaridis I, Pickrell J, Cooper A, Brandt G, Nicklisch N, Meller H, Alt KW, Reich D. American Journal of Physical Anthropology
2015 Reduced reactions volumes and increased Taq DNA polymerase concentration improve STR profiling outcomes from a real-world low template DNA source: telogen hairs  McNevin D, Edson J, Robertson J, Austin JJ. Forensic Science, Medicine and Pathology
2015 Radiocarbon-dating and ancient DNA reveal rapid replacement of extinct prehistoric penguins Rawlence NJ, Perry GLW, Smith IWG, Scofield RP, Tennyson AJD, Matisoo-Smith EA, Boessenkool S, Austin JJ, Waters JM. Quaternary Science Reviews
2015 Uncertainties in dating constrain model choice for inferring extinction time from fossil records  Saltré F, Brook BW, Rodríguez-Rey M, Cooper A, Johnson CN, Turney CSM, Bradshaw CJA. Quaternary Science Reviews 
2015 Amplification of TruSeq ancient DNA libraries with AccuPrime Pfx: consequences on nucleotide misincorporation and methylation patterns  Seguin-Orlando A, Hoover CA, Vasiliev SK, Ovodov ND, Shapiro B, Cooper A, Rubin EM, Willerslev E, Orlando L. Science & Technology of Archaeological Research
2015 Using amplicon sequencing to characterize and monitor bacterial diversity in drinking water distribution systems   Shaw JLA, Monis P, Weyrich LS, Sawade E, Drikas M, Cooper A. Applied and Environmental Microbiology
2015 The skin microbiome: Associations between altered microbial communities and disease Weyrich LS, Dixit, Farrer AG, Cooper A. Australasian Journal of Dermatology
2015 Predicting the origin of soil evidence: High throughput eukaryote sequencing and MIR spectroscopy applied to a crime scene scenario   Young JM, Weyrich LS, Breen J, MacDonald LM, Cooper A. Forensic Science International
2015 Residual soil DNA extraction increases the discriminatory power between samples  Young JM, Weyrich LS, Clarke LJ, Cooper A. Forensic Science, Medicine and Pathology
2014

Twenty microsatellite loci for population and conservation genetic studies of the wedge-tailed eagle (Aquila audax) 

 Austin JJ, Oliver L, Nankervis D, Brown WE, Gardner MG, Burridge CP. Australian Journal of Zoology 
2014 Human paeogenetics of Europe - The known knowns and the known unknowns  Brandt G. Szecseryi-Nagy AS, Roth CR, Alt KW, Haak W. Journal of Human Evolution
2014 Extensive population decline in the Tasmanian devil predates European settlement and devil facial tumour disease  Brüniche-Olsen A, Jones ME, Austin JJ, Burridge CP, Holland BR. Biology Letters 
2014 AmericaPlex26: A SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas   Coutinho A, Valverde G, Fehren-Schmitz L, Cooper A, Barreto Romero MI, Flores Espinoza I, Llamas B, Haak W. PLoS One
2014 Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias. . Vol 14(6). Clark, LJ, Soubrier J, Weyrich LS, Cooper A. Molecular Ecology Resources
2014 Modular tagging of amplicons using a single PCR for high-throughput sequencing Clarke LJ, Czechowski P, Soubrier J, Stevens MI, Cooper A. Molecular Ecology Resources
2014 From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes Clarke AC, Prost S, Stanton JAL, White WT, Kaplan ME, Matisoo-Smith EA, The Genographic Consortium . BMC genomics
2014 Mitochondrial Genome Sequencing in Mesolithic North East Europe Unearths a New Sub-clade Within the Broadly Distributed Human Haplogroup C1 Der Sarkissian C, Brotherton P, Balanovsky O, Templeton J, Llamas B, Soubrier J, Moiseyev V, Khartanovich V, Cooper A, Haak W, The Genographic Consortium PLoS ONE
2014 Climate change underlies global demographic, genetic, and cultural transitions in pre-Columbian southern Peru Fehren-Schmitz L., Haak W, Mächtle B, Masch F, Llamas B, Tomasto Cagigao E, Sossna V, Schittek K, Isla Cuadrado, Eitel B, Reindel M. PNAS 
2014 Ancient DNA and the early population history of western South America: what have we learned so far and where do we go from here?  Fehren-Schmitz L, Llamas B, Tomasto-Cagigao E, Haak W. Boletin Arqueologia PUCP [Spanish].
2014 Evaluation of carrier RNA and low volume demineralization for recovery of nuclear DNA from human teeth Higgins D, Kaidonis J, Townsend G, Austin JJ. Forensic Science Medicine and Pathology
2014 Distinctiveness of Pacific Robin subspecies in Vanuatu revealed from disparate patterns of sexual dichromatism, plumage colour, morphometrics and ancient DNA Kearns A, White L, Austin JJ, Omland K. Emu
2014 Ancient DNA reveals elephant birds and kiwis are sister taxa and clarifies ratite bird evolution Mitchell K, Llamas B, Soubrier J, Rawlence NJ, Worthy TH, Wood J, Lee MSY, Cooper A. Science [For non subscribers to the journal, click here for abstract, here for reprint and here for full text.] 
2014 Molecular phylogeny, biogeography, and ancestral habitat preference of marsupials Mitchell KJ, Pratt RC, Watson LN, Gibb GC, Llamas B, Kasper M, Edson J, Hopwood B, Male D, Armstrong K, Meyer M, Hofreiter M, Austin JJ, Donnellan SC, Lee MSY, Phillips MJ, Cooper A. Molecular Biology and Evolution
2014 Ancient mitochondrial genome reveals unsuspected taxonomic affinity of the extinct Chatham duck (Pachyanas chathamica) and resolves divergence times for New Zealand and sub-Antarctic brown teals Mitchell KJ, Wood JR, Scofield PR, Llamas B, Cooper A. Molecular Phylogenetics and Evolution
2014 Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects Rawlence NJ, Lowe DJ, Wood JR, Young JM, Churchman G, Huang YT, Cooper A. Journal of Quaternary Science
2014 Assessing the impact of water treatment on bacterial biofilms in drinking water distribution systems using high-throughput DNA sequencing  Shaw JLA, Monis P, Fabris R, Ho L, Braun K, Drikas M, Cooper A. Chemosphere 
2014 Pleistocene chinese cave hyenas and the recent Eurasian history of the spotted hyena, Crocuta crocuta Sheng GL, Soubrier J, Liu JY, Werdelin L, Llamas B, Thomson VA, Tuke J, Wu LJ, Hou XD, Chen QJ, Lai XL, Cooper A. Molecular Ecology
2014 Using ancient DNA to study the origins and dispersal of ancestral Plynesian chickens across the Pacific Thomson VA, Lebrasseur O, Austin JJ, Hunt TL, Burney DA, Denham T, USA.Rawlence NJ, Wood JR, Gongora J, Firdi LF, Linderhalm A, Dobney K, Larson G, Cooper A.  Proceedings of the National Academy of Sciences
2014 Reply to Beavan, Bryant, and Storey and Matisoo-Smith: Ancestral Polynesian “D” haplotypes reflect authentic Pacific chicken lineages Thomson VA, Lebrasseur O, Austin JJ, Hunt TL, Burney DA, Denham T, Nicolas JR, Wood JR, Gongora J, Fink LG, Linderholm A, Dobney K. Larson G, Cooper A. Proceedings of the National Academy of Sciences
2014 Limitations and recommendations for successful DNA extraction from forensic soil samples: A Review Young J, Rawlence N, Weyrich LS, and Cooper A.  Science and Justice
2014 Forensic soil DNA analysis using high-throughput sequencing. A comparison of four molecular markers. Forensics Science International: Young JM, Weyrich LS, Cooper A. Genetics 
2014 Limitations and recommendations for successful DNA extraction from forensic soil samples: A review Young JM, Rawlence NJ, Weyrich LS, Cooper A. Science & Justice
2014 Genetic inference as a method for modelling occurrence: A Viable alternative to visual surveys. Wadley JJ, Austin JJ, Fordham DA. Austral Ecology
2014 Fifteen microsatellite loci for use in non-invasive sampling studies of the antilopine wallaroo (Macropus antilopinus)  Wadley JJ, Austin JJ, Gardner, Fordham DA. Australian Journal of Zoology
2014 Reply to Santiago-Rodriquez et al: Was luxS really isolated from 25- to 40-million-year-old bacteria? Weyrich L, Llamas B, and Cooper A. FEMS Microbiology Letters
2014 Ancient DNA analysis of dental calculus.   Weyrich LS, Dobney K. Cooper A. Journal of Human Evolution
2014 Improving genetic monitoring of the northern hairy-nosed wombat (Lasiorhinus krefftii) White LC, Horsup A, Taylor AC, Austin JJ. Australian Journal of Zoology
2014 An extinct nestorine parrot (Aves, Psittaciformes, Stripopidae, Nestorinae) from the Chatham Islands, New Zealand Wood JR, Mitchell KJ, Scofield RP, Tennyson AJD, Fidler AE, Wilmshurst JM, Llamas B, Cooper A. Zoological Journal of the Linnean Society
2013

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

 Adler CJ, Dobney K, Weyrich LS, Kaidonis J, Walker AW, Haak W, Bradshaw CJA, Townsend G, Soltysiak A, Alt KW, Parkhill J and Cooper A. Nature Genetics
2013 Uncovering cryptic evolutionary diversity in extant and extinct populations of the southern Australian arid zone Western and Thick-billed Grasswrens (Passeriformes: Maluridae: Amytornis) Austin JJ, Joseph L, Pedler LP, Black AB. Conservation Genetics
2013 The origins or the enigmatic Falkland Islands Wolf Austin JJ, Soubrier J, Prevosti FJ, Prates L, Trejo V, Mena F, Cooper A. Nature Communications
2013 Y chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations. Badro DA, Douaihy B, Haber M,...The Genographic Consortium.  PLoS One
2013 Ancient DNA reveals key stages in the formation of Central European mitochondrial genetic diversity Brandt G, Haak W, Adler CJ,... Cooper A, Alt KW, The Genographic Consortium. Science 
2013 Neolithic mitochondrial genomes and the genetic origins of Europeans Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, Adler CJ, Richards SM, Der Sarkissian C,...Cooper A, The Genographic Consortium. Nature Communications
2013 Disease induced changes in gene flow patterns among Tasmanian devil populations Bruniche-Olsen A, Burridge CP, Austin JJ, Jones ME. Biological Conservation
2013 Did postglacial sea-level changes initiate the evolutionary divergence of a Tasmanian endemic raptor from its mainland relative? Burridge CP, Brown WE, Wadley J, Nankervis DL, Olivier L, Gardner MG, Hull C, Barbour R and Austin JJ. Proceedings of The Royal Society
2013 Modular tagging of amplicons using a single PCR for high-throughput sequencing Clarke LJ, Czechowski P, Soubrier J, Stevens MI, Cooper A. Molecular Ecology Resources
2013  Did the Denisovans Cross Wallace’s Line?   Cooper A and Stringer CB. Science
2013 Antarctic Tardigrada: a first step in understanding molecular operational taxonomic units (MOTUs) and biogeography of cryptic meiofauna Czechowski P, Sands CJ, Adams BJ, D'Haese CA, Gibson JAE, McInnes SJ, Stevens MI. Invertebrate Systematics
2013 Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe Der Sarkissian C, Balanovsky O, Brandt G, Khartanovich V, Buzhilova A, Koshel S, Zaporozhchenko V, Gronenbom D, Moiseyev V, Kolpakov E, Shumkin V, Alt KW, Balanovska E, Cooper A, Haak W and The Genographic Consortium. PloS Genetics
2013 Mitochondrial Genome Sequencing in Mesolithic North East Europe Unearths a New Sub-Clade within the Broadly Distributed Human Haplogroup C1 Der Sarkissian C, Brotherton P, Balanovsky O, Templeton JEL, Llamas B, Soubrier J, Moiseyev V, Khartanovich V, Cooper A, Haak W, the Genographic Consortium. PLoS One
2013 Rapid megafaunal extinction following human arrival throughout the New World Johnson CN, Bradshaw CJA, Cooper A, Gillespie R, Brook BW. Quaternary International
2013 Teeth as a source of DNA for forensic identification of human remains: A Review Higgins D, Austin JJ. Science and Justice
2013 Targeted sampling of cementum for recovery of nuclear DNA from human teeth and the impact of common decontamination measures Higgins D, Kaidonis J, Townsend G, Hughes T, Austin JJ. Investigative Genetics
2013 Rates of Phenotypic and Genomic Evolution during the Cambrian Explosion Lee MSY, Soubrier J, Edgecombe GD. Current Biology
2013 Ancient mitochondrial genome reveals unsuspected taxonomic affinity of the extinct Chatham duck (Pachyanas chathamica) and resolves divergence times for New Zealand and sub-Antarctic brown teals Mitchell KJ, Wood JR, Scofield RP, Llamas B, Cooper, A. Molecular Phylogenetics and Evolution
2013 Perched at the mito-nuclear crossroads: Divergent mitochondrial lineages correlate with environment in the face of ongoing nuclear gene flow in an Australian bird Pavlova A, Amos JN, Joseph L, Loynes K, Austin JJ, Keogh JS, Stone GN, Nichols JA, Sunnucks P. Evolution
2013 Spatio-Temporal changes in the structure of an Australian Frog Hybrid zone: A 40-year perspective Smith Kl, Hale JM, Gray L, Kearney M, Austin JJ, Parris KM, Melville J. Evolution
2013 DNA Capture and next-Generation Sequencing Can Recover Whole Mitochondrial Genomes from Highly Degraded Samples for Human Identification Templeton JEl, Brotherton PM, Llamas B, Soubrier J, Haak W, Cooper A, and Austin JJ. Investigative Genetics
2013 Mitochondrial Phylogenomics of Modern and Ancient Equids Vilstrup JT, Seguin-Orlando A, Stiller M, Ginolhac A, Raghavan M, Nielsen SCA, Weinstock J, Froese D, Vasiliev SK, Ovodov ND, Clary J, Helgen KM, Fleischer RC, Cooper A, Shapiro B, Orlando L. PLoS One 
2013 Rapid species identification of eight sympathic northern Australian macropods from faecal-pellet DNA  Wadley JJ, Austin JJ and Fordham D. Wildlife Research
2013 A megafauna's microfauna: gastrointestinal parasites of New Zealand's extinct moa (Aves: Dinornithiformes) Wood JR, Wilmshurst JM, Rawlence NJ, Boot K, Worthy TH, Kinsella JM, Cooper A. PloS One
2013 Resolving lost herbivore community structure using coprolites of four sympatric moa species (Aves: Dinornithiformes) Wood JR, Wilmshurst JM, Richardson SJ, Rawlence NJ, Wagstaff SJ, Worthy TH, Cooper A. PNAS
2012

Ancient DNA identifies post-glacial recolonisation, not recent bottlenecks, as the primary driver of contemporary mtDNA phylogeography and diversity in Scandinavian brown bears 

 Bray SCE, Austin JJ, Metcalf JL, Østbye K, Østbye E, Lauritzen S-E, Aaris-Sørensen K, Valdiosera C, Adler CJ, Cooper A. Diversity and Distributions
2012 The Basque paradigm: genetic evidence of a maternal continuity in the Franco-Cantabrian region since pre-Neolithic times Behar DM, Harmant C, Manry J, van Oven M, Haak W, Martinez-Cruz B, Salaberria J, Oyharçabal B, Bauduer F, Comas D, Quintana-Murci L, Genographic Consortium. American Journal Human Genetics
2012 Robust estimates of extinction time in the geological record Bradshaw CJA, Cooper A, Turney CSM, and Brook BW. Quaternary Science Reviews
2012 A quantitative assessment of a reliable screening technique for the STR analysis of telogen hair roots Edson J, Brooks EM, McLaren C, Robertson J, McNevin D, Cooper A, Austin JJ. Forensic Science International: Genetics
2012 Man and megafauna in Tasmania: closing the gap Gillespie R, Camens AB, Worthy TH, Rawlence NJ, Reid C, Bertuch F, Levchenko V, Cooper A. Quaternary Science Reviews
2012 Afghanistan's ethnic groups share a Y-chromosomal heritage structured by historical events Haber M, Platt DE, Ashrafian Bonab M, ... The Genographic Consortium. PLoS One
2012 Structure and Fragmentation of growling grass frog metapopulations Hale JM, Heard GW, Smith KL, Parris JM, Austin JJ, Kearney M, Melville J. Conservation Genetics
2012 Recombination networks as genetic markers in a human variation study of the Old World Javed A, Melé M, Pybus M,... The Genographic Consortium. Human Genetics
2012 Y-chromosome O3 haplogroup diversity in Sino-Tibetan populations reveals two migration routes into the eastern Himalayas Kang L, Lu Y, Wang C, Hu K, Chen F, Liu K, Li S, Jin L, Li H; The Genographic Consortium. American Human Genetics
2012 High-Resolution Analysis of Cytosine Methylation in Ancient DNA Llamas B, Holland ML, Chen K, Cropley JE, Cooper A, Suter CM. Plos One
2012 Mitochondrial origin of the matrilocal Mosuo people in China Lu Y, Wang C, Qin Z, Wen B, Farina SE, Jin L, Li H; The Genographic Consortium. Mitochondrial DNA
2012 Evidence of Pre-Roman Tribal Genetic Structure in Basques from Uniparentally Inherited Markers Martínez-Cruz B, Harmant C, Platt DE, Haak W, Manry J, Ramos-Luis E, Soria-Hernanz DF, Bauduer F, Salaberria J, Oyharçabal B, Quintana-Murci L, Comas D; the Genographic Consortium. Molecular Biology and Evolution
2012 Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout Metcalf J, Love SS, Kennedy C, Rogers K, McDonald D, Keepers K, Epp J, Cooper A, Austin J, Martin A. Molecular Ecology
2012 Low MHC diversity in the Tasmanian devil pre-dates European settlement and may explain susceptibility to disease epidemics Morris K, Austin JJ, Belov K. Biology Letters
2012 Molecular beacon immobolized within suspended core fibre for specific DNA detection Nguyen LV, Warren-Smith SC, Cooper A, Monro TM. Optics Express
2012 The effect of climate and environmental change on the megafaunal moa of New Zealand in the absence of human Rawlence N, Metcalf JL, Wood JR, Worthy TH, Austin JJ, Cooper A. Quaternary Science Reviews
2012 Youngest reported radiocarbon age of a moa ( Aves: Dinornithiformes) dated from a natural site in New Zealand Rawlence NJ, Cooper A. Journal of the Royal Society of New Zealand.
2012 The influence of rate heterogeneity among sites on the time dependence of molecular rates Soubrier J, Steel M. Lee M. Der Sarkissian C, Guindon S, Ho SYW, Cooper A and The Genographic Consortium. Molecular Biology Evolution
2012 A lost link between a flightless parrot and a parasitic plant and the potential role of coprolites in conservation paleobiology Wood JR, Wilmshurst JM, Worthy TH, Holzapfel AS, Cooper A. Conservation Biology.
2012 High-Resolution Coproecology: Using Coprolites to Reconstruct the Habits and Habitats of New Zealand's Extinct Upland Moa (Megalapteryx didinus) Wood JR, Wilmshurst JM, Worthy TH, Cooper A. PLoS One
2012 First coprolite evidence for the diet of Anomalopteryx didiformis, an extinct forest ratite from New Zealand Wood JR, Wilmshurst JM, Worthy TH, Cooper A. NZ J Ecology
2011

Survival and recovery of DNA from ancient teeth and bones. 

 Adler CJ, Haak W, Donlon D, Cooper A, The Genographic Consortium. Journal of Archaeological Science
2011 Multiple geographic origins of commensalism and complex dispersal history of Black Rats Aplin KP, Hitoshi S, Alejandro A,...Rowe K, Cooper A.  PLoS One
2011 Parallel evolution of genes and languages in the Caucasus region Balanovsky O, Dibirova K, Dybo A,...The Genographic Consortium. Molecular Biology Evolution
2011 A New Dolphin Species, the Burrunan Dolphin Tursiops australis sp. nov., Endemic to Southern Australian Coastal Waters.  Charlton-Robb K, Gershwin, LA, Thompson R, Austin JJ, Owen K, McKenchnie, S. PLoS One
2011 Late-Quaternary biogeographic scenarios for the brown bear (Ursus arctos), a wild mammal model species Davidson J, Ho SYW, Bray S, Korsten M, Vulla E, Hindrikson M, Ostbye K, Ostbye E, Lauritzen S-E, Austin JJ, Cooper A, Saarma U. Quaternary Science Reviews
2011 Influences of history, geography, and religion on genetic structure: The Maronites in Lebanon.  19: 334-340. Haber M, Platt DE, Badro DA,... The Genographic Consortium. European Journal of Human Genetics
2011 Microsatellite loci for the endangered growling grass frog (litoria raniformis), with cross amplification in other Australian frog species Hale JM, Heard GW, Smith KL, Blacket MJ, Austin JJ, Melville J. Conservation Genetics Resources
2011 Dentine and cementum as sources of nuclear DNA for use in human identification Higgins D., Kaidonis J., Austin JJ, Townsend G., James H., Huighes, T. Australian Journal of Forensic Sciences
2011 Time dependent rates of molecular evolution Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A. Molecular Ecology
2011 Cryptic grey-bellied dunnart (Sminthopsis griseoventer) discovered in South Australia: genetic, morphological and subfossil analyses show the value of collecting voucher material  Kemper C, Cooper SJB, Medlin GC, Adams M, Stemmer D, Saint KM, McDowell MC, Austin JJ. Australian Journal of Zoology
2011 The Complete Mitochondrial Genome of an 11,450-year-old Aurochsen (Bos primigenius) from Central Italy Lari, M., Rizzi, E., Mona, S., Corti, G., Catalano, G., Chen, K., Vernesi, C., Larson, G., Boscato, P., De Bellis, G., Cooper, A., Caramelli, D., Bertorelle, G. BMC Evolutionary Biology
2011 Discovery of lost diversity of paternal horse lineages using ancient DNA  Lippold S, Knapp M, Kuznetsova T, Leonard JA, Benecke N, Ludwig A, Rasmussen M, Cooper A, Weinstock J, Willerslev E, Shapiro B and Hofreiter M. Nature Communications
2011 Species-specific responses of Late Quaternary megafauna to climate and humans   Lorenzen ED, Nogues-Bravo D, Orlando L, ..., Cooper A, Hofreiter M, Sher A, Shapiro B, Rahbek C, Willerslev E. Nature
2011 Phylogeography of the pademelons (Macropodidae: Thylogale) in New Guinea reflects both geological and climatic events during the Plio-Pleistocence   Macqueen P, Goldizen AW, Austin JJ, Seddon JM. Journal of Biogeography
2011 A cryptic and critically endangered species revealed by mitochondrial DNA analyses: the Western Ground Parrot Murphy SA, Joseph L, Burbidge AH, Austin JJ.  Conservation Genetics
2011 Using DNA from museum specimens to preserve the integrity of Evolutionary Significant Unit boundaries in threatened species Paplinska JZ, Taggart DA, Corrigan T, Eldridge MDB, Austin JJ. Biological Conservation
2011 Isolation and characterization of microsatellite markers for the Litoria ewingii complex and their use in conservation and hybridization studies   Smith KL, Hale JM, Austin JJ, Melville J. Conservation Genetics Resources
2011 Evolution of arid zone birds in Australia: leapfrog distribution patterns and mesic-arid connections in quail-thrush (Cinclosoma, Cinclosomatidae)  Toon A, Austin JJ, Dolman G, Pedler L, Joseph LG. Molecular Phylogenetics and Evolution
2011 Sporormiella as a proxy for non-mammalian herbivores in island ecosystems Wood JR, Wilmshurst JM, Worthy TH, Cooper A. Quaternary Science Reviews
2011 A Biochemical-Biophysical Study of Hemoglobins from Woolly Mammoth, Asian Elephant, and Humans   Yuan Y, Shen TJ, Gupta P, Ho N, Simplaceanu V, Tam T-C, Hofreiter M, Cooper A, Campbell K, Ho, C. Biochemistry
2010 Sexual dimorphism in deciduous crown traits of a European derived Australian sample Adler CJ, Donlon D. Forensic Science International
2010 Preferential access to genetic information from endogenous ancient DNA and quantitative SNP-typing from ancient hominin samples via SPEX  Brotherton P, Sanchez JJ, Cooper A, Endicott P. Nucleic Acids Research
2010 Assessing morphological and DNA-based diet analysis techniques in a generalist predator, the arrow squid Nototodarus gouldi   Braley M, Goldsworthy SD, Page B, Steer M, Austin JJ. Molecular Ecology Resources
2010 Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance Campbell KL, Roberts JEE, Watson LN, Stetefeld J, Sloan AM, Signore AV, Howatt JW, Tame JRH, Rohland N, Shen T-J, Austin JJ, Hofreiter M, Ho C, Weber RE, Cooper A. Nature Genetics
2010 Ancient DNA from European early Neolithic farmers reveals their near eastern affinities  Haak W, Balanovsky O, Sanchez JJ, Koshel S, Zaporozhchenko V, Adler CJ, Der Sarkissian CSI, Brandt G, Schwarz C, Nicklisch N, Dresely V, Fritsch B, Balanovska E, Villems R, Meller H, Alt KW, Cooper A, The Genographic Consortium. PLoS Biology
2010 Phylogenetics of the pademelons (Macropodidae: Thylogale) and historical biogeography of the Australo-Papuan region.   Macqueen P, Seddon JM, Austin JJ, Hamilton S, Goldizen AQ. Molecular Phylogenetics and Evolution
2010 A New Method to Reconstruct Recombination Events at a Genomic Scale.   Melé M, Javed A, Pybus M, Calafell F, Parida L, Bertranpetit J, The Genographic Consortium. PLoS Computational Biology
2010 A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the last glacial maximum Qin Z, Yang Y, Kang L, Yan S, Cho K, Cai X, Lu Y, Zheng H, Zhu D, Fei D, Li S, Jin L, Li H. The Genographic Consortium. American Journal Physical Anthropology
2010 Biogeographical and phylogenetic implications of an Early Miocene wren (Aves: Passeriformes: Acanthisittidae) from New Zealand   Worthy, T.H., S.J. Hand, J.M.T. Nguyen, A.J.D. Tennyson, J.P. Worthy, R.P. Scofield W.E. Boles & M. Archer. Journal of Vertebrate Paleontology
2010 Genetic heritage and native identity of the Seaconke Wampanoag tribe of Massachusetts   Zhadanov SI, Dulik MC, Markley M, Jennings GW, Gaieski JB, Elias G, Schurr TG; The Genographic Project Consortium. American Journal of Physical Anthropology