CV / Publications
Alan Cooper BlueSky Genetics
Adelaide, South Australia
alanjcooper42@gmail.com alan.cooper@blueskygenetics.com
Areas of Interest: Specialist in leading large international teams in cross-disciplinary research: Ancient DNA, evolution, climate change, paleogenomics, evolutionary medicine, Aboriginal genetic heritage, palaeontology, astrobiology, solar physics, geomagnetism
Academic History:
University of Adelaide (2005-2019), Founder and Director, Australian Centre for Ancient DNA
· ARC Laureate Fellow (2014-2019)
· ARC Future Fellow (2011-2014)
· ARC Federation Fellow (2005-2010)
· 235 research papers (10 Nature/Science)
· $23M in research grant funding (ARC, NHMRC, NSF, NZ Marsden, NERC)
· South Australian Scientist of the Year 2016/2017
· South Australian Science Excellence Award 2018 – Research Collaboration
· Eureka Prize 2017 – Excellence in Interdisciplinary Research (Aboriginal Heritage Project)
· Fellow of the Royal Society of South Australia 2015
· Royal Society of South Australia Verco Medal 2013
Summary: Built world-leading research group (entirely grant-funded), competitive with Harvard and Max-Planck, through large international collaborative projects published in Nature and Science, ARC Fellowships (9), and Research Grants (19). Designed, established and Directed Australian Centre for Ancient DNA (ACAD) research centre, including largest bioinformatics group within U. Adelaide, generating high profile public and scientific outreach program. 28 PhD graduates, with high proportion of Dean’s Medal/University Medal awards. Funded my position via ARC Fellowships (2005-2019).
Oxford University (1996-2005)
· Founder and Director, Henry Wellcome Ancient Biomolecules Centre (1999-2005)
· Professor of Ancient Biomolecules (2002-2005)
· Wellcome Trust University Fellow, Dept of Zoology (2001-2005)
· University Research Lecturer, Zoology and Biological Anthropology (1999-2002)
· 46 papers (14 Nature/Science)
· £2.3M in research grant funding (NERC, Wellcome Trust, BBSRC, Royal Society, Leverhulme Trust)
· NERC Advanced Fellowship (1999-2001), Wellcome Trust University Award (2002-2005)
· Balliol College Julian Huxley Research Fellow (1998-2001), Senior Research Fellow (2002-2005)
· Phillip Leverhulme Prize (£50,000, 2002)
· Zoological Society of London Medal (2002)
Summary: Postdoc (1995-99), University Research Lecturer (1999-2002), Full Professor (2002-2005) at age 36. Grant funded (Wellcome Trust/UK Govt Joint Infrastructure Fund) and designed world-leading ancient DNA research centre which established many basic operating principles of the ancient DNA field. Multiple Nature and Science papers, generating high public and scientific profile. 12 postdocs and 14 PhD graduates, many of whom now dominate the ancient DNA field.
Scientific service:
National Geographic ‘Genographic Project’ Ancient DNA Node Leader 2006-2011, International Ocean Drilling Program Project team leader U. Adelaide 2007-2011, Science Nation (Australian Science Public Outreach) Panellist 2017-present, Editorial Board: BMC Biology & BMC Evolution 2004-present, mSystems 2017-present: ARC and NZ Marsden Grant reviewer 2004-present, NERC Electoral College 2004-2005
Total Publications: >320 - of which 33 (10%) are in Science (18) or Nature (15).
h index: 93 (Google Scholar); ~35300 citations
Publications are available for fire download via Researchgate or Google Scholar (link way below)
Journals:
2022 (see Google Scholar for latest papers)
2021
1. Lovelace DM, Redman CM, Minckley TA, Schubert BW, Mahan S, Wood JR, McGuire JL, Laden J, Bitterman K, Heiniger H, Fenderson L, Cooper A, Mitchell KJ, Meachen JA. An age-depth model and revised stratigraphy of vertebrate-bearing units in Natural Trap Cave, Wyoming, Quaternary International (2021)
2. Cooper A, Turney CSM, Palmer J, Hogg A, McGlone M, Wilmshurst J, Lorrey AM, Heaton TJ, Russell JM, McCracken K, Anet JG, Rozanov E, Friedel M, Suter I, Peter T, Muscheler R, Adolphi F, Dosseto A, Faith JT, Fogwill CJ, Hughen K, Lipson M, Liu J, Nowaczyk N, Ramsey CB, Sebastianelli P, Souilmi Y, Stevenson J, Thomas Z, Tobler R, Zech R Response to Comment on “A global environmental crisis 42,000 years ago”. Science 374(6570), eabh3655 (2021).10.1126/science.abh3655
3. Cooper A, Turney CSM, Palmer J, Hogg A, McGlone M, Wilmshurst J, Lorrey AM, Heaton TJ, Russell JM, McCracken K, Anet JG, Rozanov E, Friedel M, Suter I, Peter T, Muscheler R, Adolphi F, Dosseto A, Faith JT, Fogwill CJ, Hughen K, Lipson M, Liu J, Nowaczyk N, Ramsey CB, Sebastianelli P, Souilmi Y, Stevenson J, Thomas Z, Tobler R, Zech R. Response to Comment on “A global environmental crisis 42,000 years ago”. Science 374(6570):eabi9756 (2021).10.1126/science.abi9756
4. Salis AT, Bray SC, Lee MS, Heiniger H, Barnett R, Burns JA, Doronichev V, Fedje D, Golovanova L, Harington CR, Hockett B. Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge. Molecular Ecology (2021) 10.1111/mec.16267
5. Huang DY, Lowe DJ, Churchman GJ, Schipper LA, Cooper A, Chen TY, Rawlence NJ. Characterizing porous microaggregates and soil organic matter sequestered in allophanic paleosols on Holocene tephras using synchrotron-based X-ray microscopy and spectroscopy. Scientific Reports 11:1-3. 10.1038/s41598-021-00109-9
6. Kieren J. Mitchell, Pere Bover, Alexander T. Salis, Caitlin Mudge, Holly Heiniger, Mary Thompson, Bryan Hockett, Laura S. Weyrich, Alan Cooper, Julie A. Meachen, Evidence for Pleistocene gene flow through the ice-free corridor from extinct horses and camels from Natural Trap Cave, Wyoming, Quaternary International (2021)10.1016/j.quaint.2021.11.017.
7. De Pietri, Vanesa L, Worthy TH, Scofield RP, Cole TL, Wood JR, Mitchell KJ, Ciboi A, Jansen JJFJ, Cooper A, Feng S, Chen W, Tennyson A, Wragg G (2020). A new extinct species of Polynesian sandpiper (Charadriiformes: Scolopacidae: Prosobonia) from Henderson Island, Pitcairn Group, and the phylogenetic relationships of Prosobonia. Zoological Journal of the Linnean Society, 192:1045-1070 (2021) 10.1093/zoolinnean/zlaa115
8. Liu S, Westbury MV, Dussex N, Mitchell KJ, Sinding M, Heintzman PD, Kapp JD, von Seth J, Heiniger H, Sánchez-Barreiro F, Margaryan A, André-Olsen R, De Cahsan B, Meng G, Yang C, Chen L, der Valk T, Moodley Y, Rookmaaker K, Bruford MW, Ryder O, Steiner C, Bruins-van Sonsbeek LGR, Vartanyan S, Guo C, Cooper A, Kosintsev P, Lister A, Marques-Bonet T, Lorenzen ED, Shapiro B, Antoine P-O, Dalén L, Gilbert MTP, Ancient and modern genomes unravel the evolutionary history of the rhinoceros family, Cell 184(D1) (2021)
9. Oliva A, Tobler R, Cooper A, Llamas B, Souilmi Y, Systematic benchmark of ancient DNA read mapping, Briefings in Bioinformatics, 2021; bbab076 10.1093/bib/bbab076
10. Torres-Roig E, Mitchell KJ, Alcover JA, Martínez-Freiría F, Bailón S, Heiniger H, Williams M, Cooper A, Pons J, Bover P. Origin, extinction and ancient DNA of a new fossil insular viper: molecular clues of overseas immigration. Zool. J. Linnean Soc. 192:144-168 (2021) 10.1093/zoolinnean/zlaa094
11. Teixeira JC, Jacobs GS, Stringer C, Tuke J, Hudjashov G, Purnomo GA, Sudoyo H, Cox MP, Tobler R, Turney CSM, Cooper A, Helgen KM (2021). Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture. Nat Ecol Evol 5:616–624 10.1038/s41559-021-01408-0
12. Armbrecht L, Hallegraeff G, Bolch CJS, Woodward C, Cooper A (2021). Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes. Scientific Reports 11, no. 1: 1-14. 10.1038/s41598-021-82578-6
13. Cooper A, Turney CSM, Palmer J, Hogg A, McGlone M, Wilmshurst J, Lorrey AM, Heaton TJ, Russell JM, McCracken K, Anet JG, Rozanov E, Friedel M, Suter I, Peter T, Muscheler R, Adolphi F, Dosseto A, Faith JT, Fogwill CJ, Hughen K, Lipson M, Liu J, Nowaczyk N, Ramsey CB, Sebastianelli P, Souilmi Y, Stevenson J, Thomas Z, Tobler R, Zech R (2021). A global environmental crisis 42,000 years ago. Science 371:811-818 10.1126/science.abb8677
14. Perri AR, Mitchell KJ, Mouton A, 35 authors…. Cooper A, Frantz LAF (2021). Dire wolves were the last of an ancient New World canid lineage. Nature 591:87–91. 10.1038/s41586-020-03082-x
2020
15. Torres-Roig E, Mitchell K, Alcover J, Martínez-Freiría F, Bailon S, Heiniger H, Williams M, Cooper A, Pons J, Bover P. (2020). Origin, extinction and ancient DNA of a new fossil insular viper: molecular clues of overseas immigration. Zoological Journal of the Linnean Society 10.1093/zoolinnean/zlaa094
16. Fogwill C, Turney C, Menviel L, Baker A, Weber M, Ellis B, Thomas Z, Golledge N, Etheridge D, Rubino M, Thornton D, van Ommen T, Moy A, Curran M, Davies S, Bird M, Munksgaard N, Rootes C, Millman H, Cooper A(2020). Southern Ocean carbon sink enhanced by sea-ice feedbacks at the Antarctic Cold Reversal. Nature Geoscience13:1-9 10.1038/s41561-020-0587-0
17. Nakatsuka N, Lazaridis I, Barbieri C, Skoglund P, Rohland N, Mallick S, Posth C, Harkins-Kinkaid K, Ferry M, Harney É, Michel M, Stewardson K, Capriles J, Alfonso DM, Aranda Alvarez K, Burger RL, Cadwallader L, (24 authors), Kennett DJ, Cooper A, Krause J, Wolfgang H, Llamas B, Reich D, Fehren-Schmitz Lars (2020). A Paleogenomic Reconstruction of the Deep Population History of the Andes. Cell 181 10.1016/j.cell.2020.04.015
18. Armbrecht L, Herrando-Pérez S, Eisenhofer R, Hallegraeff G, Bolch C, Cooper A (2020). An optimized method for the extraction of ancient eukaryote DNA from marine sediments. Molecular Ecology Resources
10.1111/1755-0998.13162
19. Turney CSM, Fogwill CJ, Golledge NR, McKay NP, van Sebille E, Jones RT, Etheridge D, Rubino M, Thornton DP, Davies SM, Bronk Ramsey C, Thomas ZA, Bird MI, Munksgaard NC, Kohno M, Woodward J, Winter K, Weyrich LS, Rootes CM, Millman H, Albert PG, Rivera A, van Ommen T, Curran M, Moy A, Rahmstorf S, Kawamura K, Hillenbrand C-D, Weber ME, Manning CJ, Young J, Cooper A (2020). Early Last Interglacial ocean warming drove substantial ice mass loss from Antarctica. Proc Natl Acad Sciences, 117:3996-4006 10.1073/pnas.1902469117
20. Bover P, Mitchell KJ, Torres‐Roig E, Llamas B, Thomson VA, Alcover JA, Agusti J, Cooper A, Pons J (2020). Ancient DNA from an extinct Mediterranean micromammal—Hypnomys morpheus (Rodentia: Gliridae)—provides insight into the biogeographic history of insular dormice. Journal of Zool Syst and Evol Research 58:428-438 doi.org/10.1111/jzs.12343
21. Arriola L, Cooper A, Weyrich, L (2020). Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation. Frontiers in Ecology and Evolution8:40 doi.org/10.3389/fevo.2020.00040
2019
22. Teixeira JC & Cooper A (2019). Using hominin introgression to trace modern human dispersals. Proc. Natl Acad Sciences 116:15327-15332. doi.org/10.1073/pnas.1904824116
23. Gower G, Fenderson LE, Salis AT, Helgen KM, van Loenen AL, Heiniger H, Hofman-Kamińska E, Kowalczyk R, Mitchell KJ, Llamas B, Cooper A (2019). Widespread male sex bias in mammal fossil and museum collections. Proc. Natl Acad Sciences 116:19019-19024 doi.org/10.1073/pnas.1903275116
24. Bover P, Llamas B, Mitchell KJ, Thomson VA, Alcover JA, Lalueza-Fox C, Cooper A, Pons J (2019). Unraveling the phylogenetic relationships of the extinct bovid Myotragus balearicus Bate 1909 from the Balearic Islands. Quaternary Science Reviews 215:185-195 doi.org/10.1016/j.quascirev.2019.05.005
25. 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 (2019). Ancient DNA from marine sediments: Precautions and considerations for seafloor coring, sample handling and data generation. Earth-Science Reviews, 196:10288 10.1016/j.earscirev.2019.102887
26. Cascini M, KJ Mitchell, Cooper A, MJ Phillips (2019). Reconstructing the evolution of giant extinct kangaroos: comparing the utility of DNA, morphology, and total evidence. Systematic Biology 68:520-537. 10.1093/sysbio/syy080
27. Eisenhofer R, Cooper A (2019). Fossils: A new home for microbes. eLife 8:e484932019. 10.7554/eLife.48493
28. Shaw JL, Weyrich LS, Hallegraeff G, Cooper A (2019). Retrospective eDNA assessment of potentially harmful algae in historical ship ballast tank and marine port sediments. Molecular Ecology, 28: 2476-248. 10.1111/mec.15055
29. Weyrich LS, Farrer AG, Eisenhofer R, Arriola LA, Young J, Selway CA, Handsley-Davis M, Adler C, Breen J, Cooper A. (2019). Laboratory contamination over time during low-biomass sample analysis. Molecular Ecology Resources. 19:982-996 10.1111/1755-0998.13011
30. Cole TL, Ksepka DT, Mitchell KJ, Tennyson AJ, 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 LD, Wilmshurst JM, Waters, JM (2019). Mitogenomes uncover extinct penguin taxa and reveal island formation as a key driver of speciation. Molecular Biology and Evolution 36:784-797 10.1093/molbev/msz017
31. Gomez Cabrera M, Young J, Roff G, Staples T, Ortiz J, Pandolfi JM, Cooper A (2019). Broadening the taxonomic scope of coral reef paleoecological studies using ancient DNA. Molecular Ecology. 28:2636-2652 doi.org/10.1111/mec.15038
32. Eisenhofer R, Anderson A, Dobney K, Cooper A, Weyrich LS (2019). Ancient microbial DNA in dental calculus: a new method for studying rapid human migration events. The Journal of Island and Coastal Archaeology 14:149-162 doi.org/10.1080/15564894.2017.1382620
33. Jackson S, Fleming P, Eldridge M, Ingleby S, Flannery T, Johnson R, Cooper S, Mitchell K, Souilmi Y, Cooper A, Wilson D, Helgen, K (2019). The Dogma of Dingoes - Taxonomic status of the dingo: A reply to Smith et al. Zootaxa4564: 198-212. 10.11646/zootaxa.4564.1.7
34. Richards SM, Mitchell KJ, Tobler R, Cooper A (2019) Recombinase Polymerase Amplification (RPA) versus PCR for ancient DNA library amplification. PeerJ Preprints2019 10.7287/peerj.preprints.27544v1
35. Boast AP, Chapman B, Herrera MB, Worthy TH, Scofield RP, Tennyson AJD, Houde P, Bunce M, Cooper A, Mitchell KJ (2019). Mitochondrial genomes from New Zealand’s extinct Adzebills (Aves: Aptornithidae: Aptornis) support a sister-taxon relationship with the Afro-Madagascan Sarothruridae. Diversity 11: 24 10.3390/d11020024
36. Richards S, Hovhannisyan N, Gilliham M, Ingram J, Skadhauge B, Heiniger H, Llamas B, Mitchell K, Meachen J, Fincher G, Austin J, Cooper A (2019). Low-cost cross-taxon enrichment of mitochondrial DNA using in-house synthesised RNA probes. PLoS ONE, 14:18 10.1371/journal.pone.0209499
37. Kosintsev P, Mitchell K, Devièse T, van der Plicht J, Kuitems M, Petrova E, Tikhonov A, Higham T, Comeskey D, Turney C, Cooper A, van Kolfschoten T, Stuart A, Lister A (2019). Evolution and extinction of the giant rhinoceros Elasmotherium sibiricum sheds light on late Quaternary megafaunal extinctions. Nature Ecology and Evolution, 3:31-38. 10.1038/s41559-018-0722-0
38. Eisenhofer R, Minich J, Marotz C, Cooper A, Knight R, Weyrich L (2019). Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations. Trends in Microbiology, 27:105-117 10.1016/j.tim.2018.11.003
2018
39. Estrada O, Breen J, Richards S, Cooper A (2018). Ancient plant DNA in the genomic era. Nature Plants, 4:394-396. 10.1038/s41477-018-0187-9
40. O Connell J, Allen J, Williams M, Williams A, Turney C, Spooner N, Kamminga J, Brown G, Cooper A (2018). When did homo sapiens first reach Southeast Asia and Sahul? Proc Natl Acad Sci, 115:8482-8490 10.1073/pnas.1808385115
41. Cascini M, Mitchell KJ, Cooper A, Phillips MJ (2018). Reconstructing the Evolution of Giant Extinct Kangaroos: Comparing the Utility of DNA, Morphology, and Total Evidence. Systematic Biology, Online, 1-18 doi.org/10.1093/sysbio/syy080
42. Adamski N, Bertolini E, Broomandkhoshbacht N, Cooper A, Culleton B, Ferraz T, Ferry M, Furtwängler A, Haak W, Harkins K, Harper T, Hünemeier T, Lawson A, Llamas B, Michel M, Nelson E, Oppenheimer J, Patterson N, Schiffels S, Sedig J, Stewardson K, Talamo S, Wang C, Hublin J, Hubbe M, Harvati K, Delaunay A, Beier J, Francken M, Kaulicke P, Centeno H, Rademaker K, Trask W, Robinson M, Gutierrez S, Prufer K, Salazar-García D, Chim E, Müller Gomes L, Alves M, Liryo A, Inglez M, Oliveira R, Bernardo D, Barioni A, Wesolowski V, Scheifler N, Rivera M, Plens C, Messineo P, Figuti L, Corach D, Scabuzzo C, Eggers S, DeBlasis P, Reindel M, Méndez C, Politis G, Tomasto-Cagigao E, Kennett D, Strauss A, Fehren-Schmitz L (2018). Reconstructing the deep population history of Central and South America. Cell, 175:1185-11. doi.org/10.1016/j.cell.2018.10.027
43. Papac L, Llamas B, Cooper A, Pilbrow V, Haak W (2018). Preliminary ancient DNA screening results from first to eighth century AD sites in Samtavro and Tchkantiskedi, Georgia. In A. Batmaz, G. Bedianashvili, A. Michalewicz, & A. Robinson (Eds.), Context and Connection Studies on the Archaeology of the Ancient Near East in Honour of Antonio Sagona (Vol. 268, pp. 783-786). Leuven, CT: Peeters Publishers hdl.handle.net/2440/128690
44. Bird M, Beaman R, Condie S, Cooper A, Ulm S, Veth P (2018). Palaeogeography and voyage modeling indicates early human colonization of Australia was likely from Timor-Roti. Quaternary Science Reviews, 191:431-439 doi.org/10.1016/j.quascirev.2018.04.027
45. Bover P, Llamas B, Thomson V, Pons J, Cooper A, Mitchell K (2018). Molecular resolution to a morphological controversy: the case of North American fossil muskoxen Bootherium and Symbos. Molecular Phylogenetics and Evolution, 129:70-76 10.1016/j.ympev.2018.08.008
46. Bover P, Mitchell K, Llamas B, Rofes J, Thomson V, Cuenca-Bescós G, Alcover J, Cooper A, Pons J (2018). Molecular phylogenetics supports the origin of an endemic Balearic shrew lineage (Nesiotites) coincident with the Messinian Salinity Crisis. Molecular Phylogenetics and Evolution, 125:188-195 10.1016/j.ympev.2018.03.028
47. Feigin C, Newton A, Doronina L, Schmitz J, Hipsley C, Mitchell K, Gower G, Llamas B, Soubrier J, Heider T, Menzies B, Cooper A, O'Neill R, Pask A (2018). Genome of the Tasmanian tiger provides insights into the evolution and demography of an extinct marsupial carnivore. Nature Ecology and Evolution, 2:182-192 doi.org/10.1038/s41559-017-0417-y
48. Thomson V, Mitchell K, Eberhard R, Dortch J, Austin J, Cooper A (2018). Genetic diversity and drivers of dwarfism in extinct island emu populations. Biology Letters, 14:20170617-1-20170617-4. 10.1098/rsbl.2017.0617
49. Boast A, Weyrich L, Wood J, Metcalf J, Knight R, Cooper A (2018). Coprolites reveal ecological interactions lost with the extinction of New Zealand birds. Proc Natl Acad Sci, 115:1546-1551 10.1073/pnas.1712337115
50. Skelly E, Kapellas K, Cooper A, Weyrich L (2018). Consequences of colonialism: A microbial perspective to contemporary Indigenous health. Am J Phys Anth, 167:423-437 10.1002/ajpa.23637
51. Adolphi F, Bronk Ramsey C, Erhardt T, Lawrence Edwards R, Cheng H, Turney C, Cooper A, Svensson A, Rasmussen S, Fischer H, Muscheler R (2018). Connecting the Greenland ice-core and U/Th timescales via cosmogenic radionuclides: testing the synchroneity of Dansgaard-Oeschger events. Climate of the Past, 14:1755-1781. 10.5194/cp-14-1755-2018
52. Sheng G, Barlow A, Cooper A, Hou X, Ji X, Jablonski N, Zhong B, Liu H, Flynn L, Yuan J, Wang L, Basler N, Westbury M, Hofreiter M, Lai X (2018). Ancient DNA from giant panda (Ailuropoda melanoleuca) of south-western China reveals genetic diversity loss during the holocene. Genes 9:198-1-198-16 10.3390/genes9040198
2017
53. Lipson M, Szécsényi-Nagy A, Mallick S, Pósa A, Stégmár B, Keerl V, Rohland N, Stewardson K, Ferry M, Michel M, Oppenheimer J, Broomandkhoshbacht N, Harney E, Nordenfelt S, Llamas B, Gusztáv Mende B, Köhler K, Oross K, Bondár M, Marton T, Osztás A, Jakucs J, Paluch T, Horváth F, Csengeri P, Koós J, Sebők K, Anders A, Raczky P, Regenye J, Barna JP, Fábián S, Serlegi G, Toldi Z, Gyöngyvér Nagy E, Dani J, Molnár E, Pálfi G, Márk L, Melegh B, Bánfai Z, Domboróczki L, Fernández-Eraso J, Antonio Mujika-Alustiza J, Alonso Fernández C, Jiménez Echevarría J, Bollongino R, Orschiedt J, Schierhold K, Meller H, Cooper A, Burger J, Bánffy E, Alt KW, Lalueza-Fox C, Haak W, Reich D. Parallel palaeogenomic transects reveal complex genetic history of early European farmers. Nature 551:368-372 (2017) doi.org/10.1038/nature24476
54. Eisenhofer R, Anderson A, Dobney K, Cooper A, Weyrich L. (2017). Ancient Microbial DNA in Dental Calculus: A New method for Studying Rapid Human Migration Events. Journal of Island and Coastal Archaeology, Online:1-14. doi.org/10.1080/15564894.2017.1382620
55. Frisia S, Weyrich LS, Hellstrom J, Borsato A, Golledge NR, Anesio AM, Bajo P, Drysdale RN, Augustinus PC, Rivard C, Cooper A. (2017). The influence of Antarctic subglacial volcanism on the global iron cycle during the Last Glacial Maximum. Nature Communications, 8:15425 10.1038/ncomms15425
56. Eisenhofer R, Cooper A, & Weyrich L. Reply to Santiago-Rodriguez et al.: Proper authentication of ancient DNA is essential. FEMS Microbiology Ecology, 93:3 pages (2017) 10.1093/femsec/fix042
57. Czechowski P, Clarke L, Cooper A, Stevens M. Ground-truthing phylotype assignments for Antarctic invertebrates. DNA Barcodes, 5:1-13 (2017). doi.org/10.1515/dna-2017-0001
58. Perry T, van Loenen AL, Heiniger H, Lee C, Gongora J, Cooper A, Mitchell KJ. Ancient DNA analysis of the extinct North American flat-headed peccary (Platygonus compressus). Molecular Phylogenetics and Evolution 112:258-267 doi.org/10.1016/j.ympev.2017.03.024
59. Rabanus-Wallace M, Wooller M, Zazula G, Shute E, Jahren A, Kosintsev P, Burns J, Breen J, Llamas B, Cooper A. Megafaunal isotopes reveal role of increased moisture on rangeland during late Pleistocene extinctions. Nature Ecology and Evolution 1:0125 1-5 10.1038/s41559-017-0125
60. Tobler R, Rohrlach A, Soubrier J, Bover P, Llamas B, Tuke J, Bean N, Abdullah-Highfold A, Agius S, O’Donoghue A, O’Loughlin I, Sutton P, Zilio F, Walshe K, Williams AN, Turney C, Williams M, Mitchell RJ, Kowal E, Stephen JR, Williams L, Haak W, Cooper A. Aboriginal mitochondrial genetic lineages reveal founding population movements and regionalism in Australia. Nature, 544:180-184 10.1038/nature21416
61. Weyrich LS, Duchene S, Soubrier J, Arriola L, Llamas B, Breen J, Morris AG, Alt KW, Caramelli D, Farrell M, FarrerAG, Francken M, Gully N, Haak W, Hardy K, Harvati K, Held P, Holmes E, Kaidonis J, Lalueza-Fox C, Rasilla M, Rosas A, Semal P, Soltysiak A, Townsend G, Usai D, Wahl J, Huson DH, Dobney K, Cooper A. Reconstructing Neandertal behavior, diet, and disease using ancient DNA from dental calculus. Nature, 544:357-361 10.1038/nature21674
62. Turney, C., Jones, R., Phipps, S., Thomas, Z., Hogg, A., Kershaw, A., Fogwill C, Palmer J, Bronk Ramsey C, Adolphi F, Muscheler R, Hughen K, Staff R, Grosvenor M, Golledge N, Rasmussen S, Hutchinson D, Haberle S, Lorrey A, Boswijk G, Cooper, A. Rapid global ocean-atmosphere response to Southern Ocean freshening during the last glacial. Nature Communications, 8:520-1-520-9 10.1038/s41467-017-00577-6
63. Llamas, B., Valverde, G., Fehren-Schmitz, L., Weyrich, L. S., Cooper, A., Haak, W. From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era. STAR: Science & Technology of Archaeological Research, 3:1-14 (2017) 10.1080/20548923.2016.1258824
64. Fogwill CJ, Turney CSM, Golledge NR, Etheridge DM, Rubino M, Thornton DP, Baker A, Woodward J, Winter K, Van Ommen TD, Moy AD, Curran MAJ, Davies SM, Weber ME, Bird MI, Munksgaard NC, Menviel L, Rootes CM, Ellis B, Millman H, Vohra J, Rivera A, Cooper A. Antarctic ice sheet discharge driven by atmosphere-ocean feedbacks at the Last Glacial Termination. Scientific Reports 7:39979 (2017). doi.org/10.1038/srep39979
65. Scofield RP, Mitchell KJ, Wood JR, De Pietri VL, Jarvie S, Llamas B, Cooper A. The origin and phylogenetic relationships of the New Zealand ravens. Mol Phylog Evol, 106:136-143 (2017). 10.1016/j.ympev.2016.09.022
66. Shaw JLA, Weyrich L, Cooper A. Using environmental (e)DNA sequencing for aquatic biodiversity surveys: A beginner's guide. Marine and Freshwater Research 68:20-33 (2017). doi.org/10.1071/MF15361
67. Czechowski P, Clarke LJ, Cooper A, Stevens MI. A primer to metabarcoding surveys of Antarctic terrestrial biodiversity. Antarctic Science 29:3-15 (2017). doi:10.1017/S0954102016000389
68. Nagle N, Van Oven M, Wilcox S, Van Holst Pellekaan S, Tyler-Smith C, Xue Y, Ballantyne K, Wilcox L, Papac L, Cooke K,van Oorschot RAH, McAllister P, Williams L, Kayser M, Mitchell RJ, Genographic Consortium (2017). Aboriginal Australian mitochondrial genome variation - An increased understanding of population antiquity and diversity, Scientific Reports 7:43041 10.1038/srep43041 doi.org/10.1038/srep43041
2016
69. Soubrier J, Gower G, Chen K, Richards SM, Llamas B, Mitchell KJ, Ho SY, Kosintsev P, Lee MS, Baryshnikov G, Bollongino R, Bover P, Burger J, Chivall D, Crégut-Bonnoure E, Decker JE, Doronichev VB, Douka K, Fordham DA, Fontana F, Fritz C, Glimmerveen J, Golovanova LV, Groves C, Guerreschi A, Haak W, Higham T, Hofman-Kamińska E, Immel A, Julien MA, Krause J, Krotova O, Langbein F, Larson G, Rohrlach A, Scheu A, Schnabel RD, Taylor JF, Tokarska M, Tosello G, van der Plicht J, van Loenen A, Vigne JD, Wooley O, Orlando L, Kowalczyk R, Shapiro B, Cooper A. Early cave art and ancient DNA record the origin of European bison. Nature Communications 7:13158-1-13158-7 (2016). doi.org/10.1038/ncomms13158
70. Wood JR, Mitchell KJ, Scofield RP, De Pietri VL, Rawlence NJ, Cooper A. Phylogenetic relationships and terrestrial adaptations of the extinct laughing owl, Sceloglaux albifacies (Aves: Strigidae). Zool J Linn Soc(2016). doi.org/10.1111/zoj.12483
71. Cruz-Dávalos DI, Llamas B, Gaunitz C, 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. (2016) Experimental conditions improving in-solution target enrichment for ancient DNA. Molecular Ecology Resources 10.1111/1755-0998.12595
72. Rodríguez-Rey M, Herrando-Pérez S, Brook BW, Saltré F, Alroy J, Beeton N, Bird MI, Cooper A, Gillespie R, Jacobs Z, Johnson CN, Miller GH, Prideaux GJ, Roberts RG, Turney CSM, Bradshaw CJ. A comprehensive database of quality-rated fossil ages for Sahul’s Quaternary vertebrates. Scientific Data 3:160053-1-160053-7 (2016). doi.org/10.1038/sdata.2016.53
73. Valverde G, Romero MIB, Espinoza IF, Cooper A, Fehren-Schmitz L, Llamas B, Haak W. Ancient DNA analysis suggests negligible impact of the Wari Empire expansion in Peru's Central Coast during the Middle Horizon. PLoS ONE 11: e0155508:1-18 (2016). doi.org/10.1371/journal.pone.0155508
74. Abdul-Aziz MA, Cooper A, Weyrich LS. Exploring relationships between host genome and microbiome: new insights from genome-wide association studies. Frontiers in Microbiology 7:1611-1-1611-9 (2016). doi.org/10.3389/fmicb.2016.01611
75. Bover P, Valenzuela A, Torres E, Cooper A, Pons J, Alcover JA. Closing the gap: New data on the last documented Myotragus and the first human evidence on Mallorca (Balearic Islands, Western Mediterranean Sea). The Holocene26:1887-1891 (2016). doi.org/10.1177/0959683616645945
76. Eisenhofer Philipona RA, Cooper A, Weyrich LS. Isolating viable ancient bacteria: what you put in is what you get out. Genome Announcements, 4: e00712-16 (2016). 10.1128/genomeA.00712-16
77. Huang YT, Lowe DJ, Zhang H, Cursons R, Young JM, Churchman GJ, Schipper LA, Rawlence NJ, Wood JR, Cooper A. A new method to extract and purify DNA from allophanic soils and paleosols, and potential for paleoenvironmental reconstruction and other applications. Geoderma 274:114-125 https://doi.org/10.1016/j.geoderma.2016.04.003
78. Mitchell KJ, Scanferla A, Soibelzon E, Bonini R, Ochoa J, Cooper A. Ancient DNA from the extinct South American giant glyptodont Doedicurus (Xenarthra: Glyptodontidae) reveals that glyptodonts evolved from Eocene armadillos. Molecular Ecology 25:3499–3508 (2016). https://doi.org/10.1111/mec.13695
79. Mitchell KJ, Wood JR, Llamas B, McLenachan PA, Kardailsky O, Scofield RP, Worthy TH, Cooper A. Ancient mitochondrial genomes clarify the evolutionary history of New Zealand’s enigmatic Acanthisittid wrens. Molecular Phylogenetics and Evolution 102:295-304 (2016). https://doi.org/10.1016/j.ympev.2016.05.038
80. Metcalf JL, Turney C, Barnett R, Martin F, Bray SC, Vilstrup JT, Orlando L, Salas-Gismondi R, Loponte D, Medina M, De Nigris M, Civalero T, Fernández PM, Gasco A, Duran V, Seymour KL, Otaola C, Gil A, Paunero R, Prevosti FJ, Bradshaw CJA, Wheeler JC, Borrero L, Austin JJ, Cooper A. Synergistic roles of climate warming and human occupation in Patagonian megafaunal extinctions. Science Advances, 2: e1501682 (2016). 10.1126/sciadv.1501682
81. Cooper A, Turney C, Hughen K. Response to Comment on Abrupt warming events drove Late Pleistocene Holarctic megafaunal turnover. Science 351(6276):927c (2016). 10.1126/science.351.6276.927-a
82. Mitchell KJ, Bray SC, Bover P, Soibelzon L, Schubert BW, Prevosti F, Prieto A, Martin F, Austin JJ, Cooper A. Ancient mitochondrial DNA reveals convergent evolution of giant short-faced bears (Tremarctinae) in North and South America. Biology Letters 12(4) (2016). https://doi.org/10.1098/rsbl.2016.0062
83. Shaw JLA, Clarke LJ, Wedderburn SD, Barnes TC, Weyrich LS, Cooper A. Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system. Biological Conservation 197:131-138 (2016).
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84. Llamas B., Fehren-Schmitz L, Valverde G, Soubrier J, Mallick S, Rohland N, Nordenfelt N, Valdiosera C, RichardsSM, Rohrlach A, Romero MIB, Espinoza IF, Cagigao ET, Jiménez LW, Makowski K, Reyna ISL, Lory JM, TorrezJAB, Rivera MA, Burger RL, Ceruti MC, Reinhard J, Wells RS, Politis G, Santoro CM, Standen VG, Smith C, ReichD, Ho SYW, Cooper A, Haak W. Ancient DNA provides high-resolution timescale of the initial peopling of the Americas, Science Advances 2: e1501385 (2016). doi: 10.1126/sciadv.1501385
85. Johnson CN, Alroy J, Beeton N, Bird MI, Brook BW, Cooper A, Gillespie R, Herrando-Pérez S, Jacobs Z, Miller GH, Prideaux GJ, Roberts RG, Rodríguez-Rey M, Saltré F, Turney CSM, Bradshaw CJA. What caused extinction of the Pleistocene megafauna of Sahul? Proc. Roy. Soc. Lon. B, 283:20152399 https://doi.org/10.1098/rspb.2015.2399
86. Saltré F, Rodríguez-Rey M, Brook BW, Johnson CN, Turney CSM, Alroy J, Cooper A, Beeton N, Bird MI, Fordham DA, Gillespie R, Herrando-Pérez S, Jacobs Z, Miller GH, Nogués-Bravo D, Prideaux GJ, Roberts RG, Bradshaw CJA. Climate change not to blame for late Quaternary megafauna extinctions in Australia. Nature Communications7:10511. (2016) 10.1038/ncomms10511
87. 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. Iron Age and Anglo-Saxon genomes from East England reveal British migration history. Nature Communications 7:1040 (2016). https://doi.org/10.1038/ncomms10408
88. Huang YT, Lowe DJ, Churchman GJ, Schipper LA, Cursons R, Zhang H, Chen TY, Cooper A. DNA adsorption by nanocrystalline allophane spherules and nanoaggregates, and implications for carbon sequestration in Andisols. Applied Clay Science 120:40-50 (2016) https://doi.org/10.1016/j.clay.2015.11.009
89. Young JM, Weyrich LS, Cooper A. High-throughput Sequencing of Trace Quantities of Soil Provides Reproducible and Discriminative Fungal DNA Profiles. J. Forensic Sciences 10.1111/1556-4029.12996
90. Czechowski P, Clarke LJ, Breen J, Cooper A, Stevens MI. Antarctic eukaryotic soil diversity of the Prince Charles Mountains revealed by high-throughput sequencing. Soil Biology and Biochemistry. https://doi.org/10.1016/j.soilbio.2015.12.013
91. Sandoval JR, Lacerda DR, Acosta O, Jota MS, Robles-Ruiz P, Salazar-Granara A, Vieira PPR, Paz-y-Miño C, Fujita R, Santos FR, Jin L, Li H, Li S, Swamikrishnan P, Javed A, Parida L, Royyuru AK, Mitchell RJ, Zalloua PA, Adhikarla S, Kumar A, Prasad G, Pitchappan R, Santhakumari AV, Valampuri K, Wells RS, Vilar MG, Soodyall H, Balanovska E, Balanovsky O, Tyler-Smith C, Bertranpetit J, Comas D, Cooper A, Haak W, Kaplan ME, Merchant NC, Renfrew C, Clarke AC, Matisoo-Smith EA, Gaieski JB, Schurr TG. The Genetic History of Peruvian Quechua-Lamistas and Chankas: Uniparental DNA Patterns among Autochthonous Amazonian and Andean Populations. Annals of Human Genetics 80:88-101 (2016). https://doi.org/10.1111/ahg.12145
2015
92. Weyrich LS, Dixit S, Farrer AG, Cooper AJ, Cooper AJ. The skin microbiome: Associations between altered microbial communities and disease. Australasian Journal of Dermatology 56:268-274 (2015). https://doi.org/10.1111/ajd.12253
93. Weyrich LS, Dobney K, Cooper A. Ancient DNA analysis of dental calculus. Journal of Human Evolution 79:119-124 (2015). doi.org/10.1016/j.jhevol.2014.06.018
94. Turney CSM, Thomas Z, Hutchinson DK, Bradshaw CJA, Brook BW, England MH, Fogwill CJ, Jones R, Palmer J, Hughen KA, Cooper A. Obliquity-driven expansion of North Atlantic sea ice during the last glacial. Geophysical Research Letters 42:10382-10390 (2015) doi.org/10.1002/2015GL066344
95. Mathieson I, Lazaridis I, Rohland N, Mallick S, Llamas B, Pickrell J, Meller H, Guerra MAR, Krause J, Anthony D, Dorcas B, Lalueza C, Cooper A, Alt KW, Haak W, Patterson N, Reich D. Genome-wide patterns of selection in 230 ancient Eurasians. Nature. 528:499-503 (2015) doi.org/10.1038/nature16152
96. Gibb GC, England R, Hartig G, McLenachan PA, Taylor Smith BL, McComish BJ, Cooper A, Penny D. New Zealand Passerines Help Clarify the Diversification of Major Songbird Lineages During the Oligocene. Genome Biology and Evolution 7:2983-2995 (2015) https://doi.org/10.1093/gbe/evv196
97. Rodríguez-Rey M, Herrando-Pérez S, Gillespie R, Jacobs Z, Saltré F, Brook BW, Prideaux GJ, Roberts RG, Cooper A, Alroy J, Miller GH, Bird MI, Johnson CN, Beeton N, Turney CSM, Bradshaw CJA. Criteria for assessing the quality of Middle Pleistocene to Holocene vertebrate fossil ages. Quaternary Geochronology, 30, 69-79. https://doi.org/10.1016/j.quageo.2015.08.002
98. Mitchell KJ, Cooper A, Phillips MJ. Comment on "Whole-genome analyses resolve early branches in the tree of life of modern birds". Science, 349:1460 10.1126/science.aab1062
99. Seguin-Orlando A, Hoover CA, Vasiliev SK, Ovodov ND, Shapiro B, Cooper A, Rubin EM, Willerslev E, Orlando L.Amplification of TruSeq ancient DNA libraries with AccuPrime Pfx: consequences on nucleotide misincorporation and methylation patterns. Science and Technology of Archaeological Research 1: STAR2015112054892315Y. 0000000005 (2015). https://doi.org/10.1179/2054892315Y.0000000005
100. Cooper A, Turney C, Hughen KA, Brook BW, McDonald HG, Bradshaw CJ. Abrupt warming events drove Late Pleistocene Holarctic megafaunal turnover. Science, 349:602-606 10.1126/science.aac4315
101. Shaw JL, Monis P, Weyrich LS, Sawade E, Drikas M, Cooper A. Using Amplicon Sequencing To Characterize and Monitor Bacterial Diversity in Drinking Water Distribution Systems. Applied and Environmental Microbiology, 81:6463-6473 (2015) 10.1128/aem.01297-15
102. Fehren-Schmitz L, Llamas B, Lindauer S, Tomasto-Cagigao E, Kuzminsky S, Rohland N, Santos FR, Kaulicke P, Valverde G, Richards SM, Nordenfelt S, Seidenberg V, Mallick S, Cooper A, Reich D, Haak W. A re-appraisal of the early Andean human remains from Lauricocha in Peru. PLoS One, 10: e0127141-1-e0127141-13 doi.org/10.1371/journal.pone.0127141
103. Young JM, Weyrich LS, Breen J, Macdonald LM, Cooper A. Predicting the origin of soil evidence: High throughput eukaryote sequencing and MIR spectroscopy applied to a crime scene scenario. Forensic Science International, 251:22-31 10.1016/j.forsciint.2015.03.008
104. Young JM, Weyrich LS, Clarke LJ, Cooper A. Residual soil DNA extraction increases the discriminatory power between samples. Forensic Science, Medicine, and Pathology 11:268-272 10.1007/s12024-015-9662-z
105. Llamas B, Brotherton P, Mitchell KJ, Templeton JEL, Thomson VA, Metcalf JL, Armstrong KN, Kasper M, Richards SM, Camens AB, Lee MSY, Cooper A. Late Pleistocene Australian Marsupial DNA Clarifies the Affinities of Extinct Megafaunal Kangaroos and Wallabies. Mol Biol Evol 32:574-584 (2015). 10.1093/molbev/msu338
106. Haak W, Lazaridis I, Patterson N, Rohland N, Mallick S, Llamas B, Brandt G, Nordenfelt S, Harney E, Stewardson K, Fu Q, Mittnik A, Ba ́nffy E, Economou C, Francken M, Friederich S, Pena RG, Hallgren F, Khartanovich V, Khokhlov A, Kunst M. Kuznetsov P, Meller H, Mochalov O, Moiseyev V, Nicklisch N, Pichler SL, Risch R, Guerra MAR, Roth C, Szécsényi-Nagy A, Wahl J, Meyer M, Krause J, Brown D, Anthony D, Cooper A, Alt KW, Reich D. Massive migration from the steppe as a source for Indo-European languages in Europe. Nature, 522: 207-211 (2015). https://doi.org/10.1038/nature14317
107. Saltre F, Brook BW, Rodríguez-Rey M, Cooper A, Johnson CN, Turney CS, Bradshaw CJ. Uncertainties in dating constrain model choice for inferring extinction time from fossil records. Quat. Sci. Rev. 112:128-137 (2015).
108. Clarke LJ, Weyrich LS, Cooper A. Reintroduction of locally extinct vertebrates impacts arid soil fungal communities. Molecular Ecology, 24:3194-3205 10.1111/mec.13229
109. Lari M, Vai S, Torres Vilaça S, Romandini M, Benazzo A, Visentini P, Modolo M, Bertolini M, MacQueen P, Austin JJ, Cooper A, Bertorelle G, Caramelli D. The Biarzo case in northern Italy: is the temporal dynamic of swine mitochondrial DNA lineages in Europe related to domestication? Scientific Reports 5:9 ARTN 16514 09 (2015). https://doi.org/10.1038/srep16514
110. Weyrich LS, Dobney K, Cooper A. Ancient DNA analysis of dental calculus. J Human Evolution 79:119-124 (2015). https://doi.org/10.1016/j.jhevol.2014.06.018
111. Arun Kumar GP, Tatarinova TV, Duty J, Rollo D, Syama A, Arun VS, Kavitha VJ, Triska P, Greenspan B, Wells RS, Genographic Consortium. Genome-wide signatures of male-mediated migration shaping the Indian gene pool. Journal of Human Genetics 60:493-499 (2015). https://doi.org/10.1038/jhg.2015.51
2014
112. Orlando L, Cooper A. Using Ancient DNA to understand evolutionary and ecological processes. Annual Review Ecology Evolution and Systematics 45:573-598 (2014).
113. Thomson VA, Lebrasseur O, Austin JJ, Hunt TL, Burney DA, Denham T, Rawlence NJ, Wood JR, Gongora J, Flink LG, Linderholm A, Dobney K, Larson G, Cooper, A. Reply to Beavan, Bryant, and Storey and Matisoo-Smith: Ancestral Polynesian "D" haplotypes reflect authentic Pacific chicken lineages. Proc Nat Acad Sciences USA, 111:E3585-E3586 10.1073/pnas.1411566111
114. Shaw JLA, Monis P, Fabris R, Ho L, Braun K, Drikas M, Cooper A. Assessing the impact of water treatment on bacterial biofilms in drinking water distribution systems using high-throughput DNA sequencing. Chemosphere, 117:185-192 10.1016/j.chemosphere.2014.06.077
115. Linh VN, Giannetti S, Warren-Smith S, Cooper A, Selleri S, Cucinotta A, Monro T (2014). Genotyping single nucleotide polymorphisms using different molecular beacon multiplexed within a suspended core optical fiber. Sensors 14:14488-14499 10.3390/s140814488
116. Rawlence NJ, Lowe DJ, Wood JR, Young JM, Churchman G, Huang Y-T, Cooper A. Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects. J Quaternary Sci 29:610-626
117. Mitchell KJ, Gibb G, Kasper M, Pratt R, Watson L, Edson J, Armstrong K, Hofreiter M, Meyer M, Austin J, Lee MSY, Phillips MJ, Cooper A. Phylogeny and macroevolution of the marsupials. Mol. Biol. Evol. msu176 (2014)
118. Mitchell KJ, Llamas B, Soubrier J, Rawlence NJ, Worthy TH, Lee MSY, Cooper A. Ancient DNA groups elephant birds and kiwi and clarifies ratite evolution. Science 344: 898-900 (2014).
119. Clarke LJ, Soubrier J, Weyrich LS, Cooper A. Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias. Mol Ecol Res 14:1160-1170 (2014).
120. Clarke LJ, Czechowski P, Soubrier J, Stevens MI, Cooper A. Molecular tagging of amplicons using a single PCR for high-throughput sequencing. Molecular Ecology Resources 14:117-121 (2014).
121. Young JM, Weyrich LS, Cooper A. Forensic soil analysis using high-throughput sequencing: a comparison of four molecular markers. Forensic Science International: Genetics 13: 176-184 (2014).
122. Coutinho A, Valverde G, Fehren-Schmitz L, Cooper A, Barreto Romero MI, Flores Espinoza I, Llamas B, Haak W. NewWorldPlex26: A SNaPshot multiplex system for genotyping the main human mitochondrial founder lineages of the Americas, PLoS One 9: e93292 (2014).
123. Wood J, Mitchell KJ, Scofield PR, Tennyson AJD, Fidler AE, Wilmshurst JM, Llamas B, Cooper A. An extinct nestorine parrot (Aves, Psittaciformes, Strigopidae, Nestorinae) from the Chatham Islands, New Zealand. J. Linnean Soc. 172:185-199 (2014).
124. Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Sudmant PH, Schraiber JG, Castellano S, Kirsanow K, Economou C, Bollongino R, Fu Q, Bos K, Nordenfelt S, de Filippo C, Prüfer K, Sawyer S, Posth C, Haak W, Hallgren F, Fornander E, Ayodo G, Babiker HA, Balanovska E, Balanovsky O, Ben-Ami H, Bene J, Berrada F, Brisighelli F, Busby GBJ, Cali F, Churnosov M, Cole DEC, Damba L, Delsate D, van Driem G, Dryomov S, Fedorova SA, Francken M, Romero IG, Gubina M, Guinet J-M, Hammer M, Henn B, Helvig T, Hodoglugil U, Jha AR, Kittles R, Khusnutdinova E, Kivisild T, Kučinskas V, Khusainova R, Kushniarevich A, Laredj L, Litvinov S, Mahley RW, Melegh B, Metspalu E, Mountain J, Nyambo T, Osipova L, Parik J, Platonov F, Posukh OL, Romano V, Rudan I, Ruizbakiev R, Sahakyan H, Salas A, Starikovskaya EB, Tarekegn A, Toncheva D, Turdikulova S, Uktveryte I, Utevska O, Voevoda M, Wahl J, Zalloua P, Yepiskoposyan L, Zemunik T, Cooper A, Capelli C, Thomas MG, Tishkoff SA, Singh L, Thangaraj K, Villems R, Comas D, Sukernik R, Metspalu M, Meyer M, Eichler EE, Burger J, Slatkin M, Pääbo S, Kelso J, Reich D, Krause J. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature 513:409-413 (2014).
125. Young JM, Rawlence NJ, Weyrich LS, Cooper A. Limitations and recommendations for successful DNA extraction from forensic soil samples. Science and Justice 54:238-244 (2014).
126. Weyrich L, Llamas B, Cooper A. Was luxS isolated from bacteria in 25- to 40-million-year-old amber? FEMS Microbiol. Lett. 353:85-86 (2014).
127. Thomson VA, Aplin KP, Cooper A, Hisheh S, Suzuki H, Maryanto I, Yap G, Donnellan SC. Molecular genetic evidence for the place of origin of the Pacific Rat, Rattus exulans. PLoS One 9:e91356 (2014).
128. Thomson VA, Lebrasseur O, Austin JJ, Hunt T, Burney D, Denham T, Rawlence NJ, Wood JR, Gongora J, Flink LG, Linderholm A, Dobney K, Larson G, Cooper A. Using ancient DNA to study the origins and dispersal of ancestral Polynesian chickens across the Pacific. Proc Natl Acad Sci USA 111:4826-4831 (2014).
129. Willerslev E, Davison J, Moora M, Zobel M, Coissac E, Edwards ME, Lorenzen ED, Vestergard M, Gussarova G, Haile J, Craine J, Gielly L, Boessenkool S, Epp LS, Pearman PB, Cheddadi R, Murray D, Brathen KA, Yoccoz N, Binney H, Cruaud C, Wincker P, Goslar T, Alsos IG, Bellemain E, Brysting AK, Elven R, Sonstebo JH, Murton J, Sher A, Rasmussen M, Ronn R, Mourier T, Cooper A, Austin JJ, Moller P, Froese D, Zazula G, Pompanon F, Rioux D, Niderkorn V, Tikhonov A, Savvinov G, Roberts RG, MacPhee RDE, Gilbert MTP, Kjaer KH, Orlando L, Brochmann C, Taberlet P. Fifty thousand years of Arctic vegetation and megafaunal diet. Nature 506: 47-51
130. Metcalf, JL, Prost S, Nogués-Bravo D, DeChaine EG, Anderson C, Batra P, Araújo MB, Cooper A, Guralnick RP. Integrating multiple lines of evidence into historical biogeography hypothesis testing: a Bison bison case study. Proc Roy Soc B: 281, 20132782 (2014).
131. Sheng G-L, Soubrier J, Liu J-Y, Werdelin L, Llamas B, Thomson VA, Tuke J, Wu L-J, Hou X-D, Chen Q-J, Lai X-L, Cooper A. Pleistocene Chinese cave hyenas and the recent Eurasian history of the spotted hyena, Crocuta crocuta. Molecular Ecology. 23:522-533 (2014). Cover article.
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