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Professor Alan Cooper
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Prof. Alan Cooper has been an Australian Research Council Federation and Future Fellow (2005-2010, 2011-2014), during which time he has specialized in the genetic analysis of evolution, biodiversity, climate change, paleoecology and microbiomes. He built his first research group as a postdoc at the University of Oxford where he also established his first large research facility, the Henry Wellcome Ancient Biomolecules Centre, through a $3M grant from the UK Joint Infrastructure Fund (UK Government/Wellcome Trust). He directed the HWABC as the Professor of Ancient Biomolecules from 2001-2005 during which time it published a series of ground-breaking studies in ancient population genetics and evolutionary research. He was awarded a prestigious ARC Federation Fellowship in 2004, and moved to the University of Adelaide to establish the Australian Centre for Ancient DNA (ACAD), the first largescale ancient DNA research centre in the Southern Hemisphere. This international standard research facility was formally opened by the Premier, Mike Rann in August 2006, and provides the specialist equipment and ultra-sterile working environment required for the study of minute traces of preserved genetic material from hundreds to hundreds of thousands of years.
ACAD has been designed to provide a centre for evolutionary research in Australia and the Southern Hemisphere, particularly the impacts and timing of environmental change (eg climate, humans) on animals, plants and microbes. ACAD specialises in recovering and analyzing genetic records preserved in ancient bones, teeth, leaves and seeds, coprolites, and other remains from caves, museums as well as sediment cores from lakes, rivers and marine sites. Prof. Cooper’s work focuses on the use of ancient DNA to record and study evolutionary processes in real time, especially those associated with environmental change. His work ranges over timescales of hundreds of years old (eg museum specimens) to material well beyond the ca. 60 kyr range of carbon-dating, such as permafrost-preserved bones of mammals and sediment dating to >300 kyr. His research is characterised by multi-disciplinary approaches involving the combination of information from areas such as geology, archaeology, anthropology, and mathematics, bioinformatics and phylogenetics to provide novel views of evolution, population genetics and palaeoecology. Recent research highlights include the use of Ice Age mammal populations to record the effects of environmental change, the first analysis of ancient human microbiomes, and human evolutionary history around thw world.
Prof. Cooper's current research features studies of Australian megafaunal species, permafrost preserved material from the Arctic and Antarctic, ancient human DNA (modern humans, Neandertals Denisovans, and Flores hobbits), and DNA from environmental deposits (sediments, stalactites, marine, terrestrial and freshwater samples). He is also heavily involved in developing new molecular biology techniques to both improve the ability to recover DNA from the past (eg nuclear genomes and metagenomic approaches), and to analyse the authenticity of aDNA data. A further major research theme concerns the use of molecular clocks to estimate the timing of past evolutionary events from genetic data. He has led studies showing that evolutionary rates appear to change according to the time period over which they are measured, which has major implications for our ability to date recent evolutionary events.
Current fieldwork areas include Australia, Beringia and North America, South America, Europe, China and New Zealand, and involve cave deposits, permafrost sites, many dark and dingy backrooms of museums around the world, and active archaeological sites. His main job for the latter is to convince archaeologists to use gloves and masks, and not wash valuable specimens, to prevent contamination with modern human DNA.
Ancient DNA, evolution, palaeoecology, molecular evolution (human/mammalian/avian), molecular clocks, mass extinctions/palaeontology, biogeography, bioinformatics, forensics, microbiome evolution, molecular clocks.
Visit this link for a full listing on Google Scholar, including current h and m indices, and citation statistics.
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. (accepted March 2014).
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 (accepted March 2014).
Young JM, Rawlence NJ, Weyrich LS, Cooper A. Limitations and recommendations for successful DNA extraction from forensic soil samples. Science and Justice (accepted February 2014).
Weyrich L, Llamas B, Cooper A. Was luxS isolated from bacteria in 25- to 40-million-year-old amber? FEMS Microbiol. Lett. (accepted February 2014).
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 (accepted February 2014).
Clarke LJ, Czechowski P, Soubrier J, Stevens MI, Cooper A. Modular tagging of amplicons using a single PCR for high-throughput sequencing. Molecular Ecology Notes 14:117-121 (2014).
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 (online version doi: 10.1073/pnas.1320412111, 2014).
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 (2014).
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, (2014): doi: 10.1098/rspb.2013.2782
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 recxent Eurasian history of the spotted hyena, Crocuta crocuta. Molecular Ecology. 23:522-533 (2014). Cover article.
Der Sarkissian C, Brotherton P, Balanovsky O, Templeton J, Llamas B, Soubrier J, Moiseyev V, Khartanovich V, Cooper A, Haak W, The Genographic Consortium. Mitochondrial Genome Sequencing in Mesolithic North East Europe Unearths a New Sub-clade Within the Broadly Distributed Human Haplogroup C1. PLoS One 9: e87612. doi:10.1371/journal.pone.0087612 (2014).
Clarke AC, Prost S, Stanton JL, White WT, Kaplan ME, Matisoo-Smith EA, The Genographic Consortium. From cheek swabs to consensus sequences: an A to Z protocol for DNA sequencing of complete human mitochondrial genomes. BMC Genomics 15:68 (2014).
Mitchell KJ, Wood JR, Scofield RP, Llamas B, Cooper A. Ancient mitochondrial genome reveals unsuspected taxonomic affinity of the extinct Chatham Islands duck (Pachyanas chathamica) and resolves divergence times for New Zealand and sub-Antarctic brown teals. Molecular Phylogenetics and Evolution 70:420-428 (2013).
Brandt G, Haak W, Adler CJ, Roth C, Szécsényi-Nagy A, Karimnia S, Moller-Rieker S, Meller H, Ganslmeier R, Friederich S, Dresely V, Nickllisch N, Pickrell JK, Sirocko F, Reich D, Cooper A, Alt, KW. Ancient DNA Reveals Key Stages in the Formation of Central European Mitochondrial Genetic Diversity. Science 342:257-261 (2013). Co-senior author.
Cooper A, Stringer CB. Did the Denisovans cross Wallace’s Line? Science 342: 321-323 (2013).
Wood, JR, Wilmshurst JM, Richardson SJ, Rawlence NJ, Wagstaff SJ, Worthy TH, Cooper A. Resolving lost herbivore community structure using coprolites of four sympatric moa species (Aves: Dinornithiformes). Proc Natl Acad Sci USA 110:16910-16915 (2013).
Johnson CN, Bradshaw CJA, Cooper A, Gillespie R, Brook BW. Rapid megafaunal extinction following human arrival throughout the New World. Quaternary International 308: 273-277 (2013).
Brook BW, Bradshaw CJA, Cooper A, Johnson CN, Worthy TH, Bird M, Gillespie R, Roberts RG. Lack of chronological support for stepwise prehuman extinctions of Australian megafauna. Proc Natl Acad Sci USA 110:e3368 (2013).
Brotherton P, Haak W, Templeton J, Brandt G, Soubrier J, Adler CJ, Richards SM, Der Sarkissian C, Ganslmeier R, Friederich S, Dresely V, van Oven M, Kenyon R, Van der Hoek MB, Korlach J, Luong K, Ho SWY, Quintana-Murci L, Behar DM, Meller H, Alt KW, Cooper A & The Genographic Consortium. Neolithic mitochondrial genomes and the genetic origins of Europeans. Nature Communications 4:e1764 (2013).
Wood JR, Wilmshurst JM, Rawlence NJ, Boot K, Worthy TH, Kinsella JM, Cooper A. A megafauna’s microfauna: gastrointestinal parasites of New Zealand’s extinct moa (Aves: Dinornithiformes). PLoS One 8:e57315 (2013).
Der Sarkissian C, Balanivsky O, Brandt G, Khartanovich V, Buzhilova A, Koshel S, Zaporozhchenko V, Gronenborn D, Moiseyev V, Kolpakov E, Shumkin V, Alt KW, Balanovska E, Cooper A, Haak W, Genographic Consortium. Ancient DNA reveals prehistoric gene-flow from Siberia in the complex human populations history of north east Europe. PLoS Genetics 9:e1003296 (2013).
Adler CJ, Dobney K, Weyrich L, Kaidonis J, Walker AW, Haak W, Bradshaw CJA, Townsend G, Soltysiak A, Alt KW, Parkhill J, Cooper A. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial Revolutions. Nature Genetics 45:450-455 (2013).
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. Mitochondrial Phylogenomics of Modern and Ancient Equids. PLoS ONE 8: e55950 (2013).
Edson J, Brooks EM, McLaren C, Robertson J, McNevin D, Cooper A, Austin JJ. A quantitative assessment of a reliable screening technique for the STR analysis of telogen hair roots. Forensic Sci. International 7:180-188 (2013).
Austin JJ, Soubrier J, Prevosti FJ, Prates L, Trejo V, Mena F, Cooper A. The origins of the enigmatic Falkland Islands wolf. Nature Communications 4:e1552 (2013).
Badro DA, Douaihy B, Haber M, Youhanna SC, Salloum A, Ghassibe-Sabbagh M, Johnsrud B, Khazen G, Matisoo-Smith E, Soria-Hernanz DF, Wells RS, Tyler-Smith C, Platt DE, Zalloua PA, The Genographic Consortium. Y chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations. PLoS One 8:e54616 (2013).
Nguyen LV, Warren-Smith SC, Cooper A, Monro TM. Molecular beacon immobilized within suspended core fiber for specific DNA detection. Optics Express 20:29378-29385 (2012). [Also selected for publication in the Virtual Journal of Biomedical Optics].
Wood JR, Wilmshurst JM, Worthy TH, Holzapfel AS, Cooper A. A lost link between a flightless parrot and a parasitic plant and the potential role of coprolites in conservation paleobiology. Conservation Biology 26:1091-1099 (2012).
Bray SCE, Austin JJ, Østbye K, Østbye E, Lauritzen S-E, Aaris-Sørensen K, Valdiosera C, Adler CJ, Metcalf JL, Cooper A. Ancient DNA identifies post-glacial recolonisation, not recent bottlenecks, as the primary driver of contemporary mtDNA phylogeography and diversity in Scandinavian brown bears. Diversity and distributions 19:245-256 (2012).
Rawlence NJ, Cooper A. Youngest reported radiocarbon age of a moa (Aves: Dinornithiformes) dated from a natural site in New Zealand. J. Roy. Soc. New Zeal. 43:100-107 (2012).
Soubrier J, Steel M, Lee M, Der Sarkissian C, Guindon S, Ho SYW, Cooper A, The Genographic Consortium. The influence of rate heterogeneity among sites on the time dependence of molecular rates. Mol Biol Evol. 29:3345-3358 (2012).
Rawlence N, Metcalf JL, Wood JR, Worthy TH, Austin JJ, Cooper A. The effect of climate and environmental change on the megafaunal moa of New Zealand in the absence of humans. Quaternary Science Reviews 50:141-153 (2012).
Metcalf J, Love Stowell S, Kennedy C, Rogers K, McDonald D, Keepers K, Epp J, Cooper A, Austin J, Martin A. Historical stocking data and 19th century DNA reveal human-induced changes to native diversity and distribution of cutthroat trout. Molecular Ecology 21:5194-5207 (2012).
Wood JR, Wilmshurst JM, Worthy TH, Cooper A. High-Resolution Coproecology: Using Coprolites to Reconstruct the Habits and Habitats of New Zealand's Extinct Upland Moa (Megalapteryx didinus). PLoS One. 7:e40025 (2012).
Wood JR, Wilmshurst JM, Worthy TH, Cooper A. First coprolite evidence for the diet of Anomalopteryx didiformis, an extinct forest ratite from New Zealand. NZ J Ecology 36:164-170 (2012).
Gillespie R, Camens AB, Worthy TH, Rawlence NJ, Reid C, Bertuch F, Levchenko V, Cooper A. Man and megafauna in Tasmania: closing the gap. Quaternary Science Reviews 37:38-47 (2012).
Llamas B, Holland ML, Chen K, Cropley JE, Cooper A, Suter CM. High-resolution analysis of cytosine methylation in ancient DNA. PLoS One, 7:e30226 (2012).
Bradshaw CJA, Cooper A, Turney CSM, Brook BW. Robust estimates of extinction time in the geological record. Quaternary Science Reviews, 33:14-19 (2012).
Rębała K, Martínez-Cruz B, Tönjes A, Kovacs P, Stumvoll M, Lindner I, Büttner A, Wichmann HE, Siváková D, Soták M, Quintana-Murci L, Szczerkowska Z, Comas D, The Genographic Consortium. Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements. European Journal of Human Genetics. Sep 12 (2012). doi: 10.1038/ejhg.2012.190.
Martinez-Cruz B, Ioana M, Calafell F, Arauna LR, Sanz P, Ionescu R, Boengiu S, Kalaydjieva L, Pamjav H, Makukh H, Plantinga T, van der Meer JW, Comas D, Netea MG, The Genographic Consortium. Y-Chromosome Analysis in Individuals Bearing the Basarab Name of the First Dynasty of Wallachian Kings. PLoS One 7: e41803 (2012).
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. Evidence of Pre-Roman Tribal Genetic Structure in Basques from Uniparentally Inherited Markers. Molecular Biology & Evolution 29: 2211-2222 (2012).
Schurr TG, Dulik MC, Owings AC, Zhadanov SI, Gaieski JB, Vilar MG, Ramos J, Moss MB, Natkong F, The Genographic Consortium. Clan, language, and migration history has shaped genetic diversity in Haida and Tlingit populations from Southeast Alaska. American Journal of Physical Anthropology 148: 422-35 (2012).
Kang L, Lu Y, Wang C, Hu K, Chen F, Liu K, Li S, Jin L, Li H, The Genographic Consortium. Y-chromosome O3 haplogroup diversity in Sino-Tibetan populations reveals two migration routes into the eastern Himalayas. Annuals of Human Genetics 76: 92-9 (2012).
Javed A, Melé M, Pybus M, Zalloua P, Haber M, Comas D, Netea MG, Balanovsky O, Balanovska E, Jin L, Yang Y, Arunkumar G, Pitchappan R, Bertranpetit J, Calafell F, Parida L, The Genographic Consortium. Recombination networks as genetic markers in a human variation study of the Old World. Human Genetics 131(4): 601-13 (2012).
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, The Genographic Consortium. The Basque paradigm: genetic evidence of a maternal continuity in the Franco-Cantabrian Region since the Late Paleolithic. American Journal of Human Genetics 90 (3): 486-493 (2012).
Arunkumar G, Soria-Hernanz DF, Kavitha VJ, Arun VS, Syama A, Ashokan KS, Gandhirajan KT, Vijayakumar K, Narayanan M, Jayalakshmi M, Ziegle JS, Royyuru AK, Parida L, Wells RS, Renfrew C, Schurr TG, Smith CT, Platt DE, Pitchappan R, The Genographic Consortium. Population differentiation of southern Indian male lineages correlates with agricultural expansions predating the caste system. PLoS One 7(11): e50269 (2012).
Melé M, Javed A, Pybus M, Zalloua P, Haber M, Comas D, Netea MG, Balanovsky O, Balanovska E, Jin L, Yang Y, Pitchappan RM, Arunkumar G, Parida L, Calafell F, Bertranpetit J, and The Genographic Consortium. Recombination gives a new insight in the effective population size and the history of the Old World human populations. Molecular Biology and Evolution 29:25-30 (2012).
Dulik MC, Owings AC, Gaieski JB, Vilar MG, Andre A, Lennie C, Mackenzie MA, Kritsch I, Snowshoe S, Wright R, Martin J, Gibson N, Andrews TD, Schurr TG, The Genographic Consortium. Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan- speaking populations. Proc Natl Acad Sci USA 109: 8471-8476 (2012).
Haber M, Platt DE, Bonab MA, Youhanna SC, Soria-Hernanz DF, Martinez-Cruz B, Douaihy B, Ghassibe-Sabbagh M, Rafatpanah H, Ghanbari M, Whale J, Balanovsky O, Wells RS, Comas D, Tyler-Smith C, Zalloua PZ, The Genographic Consortium. Afghanistan’s ethnic groups share a Y-chromosomal heritage structured by historical events. PLoS One 7:e34288 (2012).
Lu Y, Wang C, Qin Z, Wen B, Farina SE, Jin L, Li H, The Genographic Consortium. Mitochondrial origin of the matrilocal Mosuo people in China. Mitochondrial DNA. 23:13-9 (2012).
Aplin KP, Hitoshi S, Alejandro A, Chinen R, Chesser T, ten Have J, Donnellan SC, Austin J, Frost A, Gonzalez JP, Herbreteau V, Catzeflis F, Soubrier J, Fang Y-P, Robins J, Matisoo-Smith E, Bastos ADS, Maryanto I, Sinaga MH, Denys C, Yap G, Van Den Bussche RA, Chris Conroy C, Rowe K, Cooper A. Multiple geographic origins of commensalism and complex dispersal history of Black Rats. PLoS One, 6:e26357 (2011).
Lorenzen ED, Nogues-Bravo D, Orlando L, Weinstock J, Binladen J, Marske KA, Ugan A, Borregaard MK, Gilbert MTP, Nielsen R, Ho SYW, Goebel T, Graf KE, Byers D, Stenderup JT, Rasmussen M, Campos PF, Leonard JA, Koepfli K-P, Froese D, Zazula G, Stafford TW, Aaris-Sorensen K, Batra P, Haywood AM, Singarayer JS, Valdes PJ, Boeskorov G, Burns JA, Davydov SP, Haile J, Jenkins DL, Kosintsev P, Kuznetsova T, Lai X, Martin LD, McDonald HG, Mol D, Meldgaard M, Munch K, Stephan E, Sablin M, Sommer RS, Sipko T, Scott E, Suchard MA, Tikhonov A, Willerslev R, Wayne RK, Cooper A, Hofreiter M, Sher A, Shapiro B, Rahbek C, Willerslev E. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 479:359-364 (2011).
Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A. Time dependent rates of molecular evolution. Molecular Ecology 20:3087-3101 (2011).
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. Discovery of lost diversity of paternal horse lineages using ancient DNA, Nature Communications 2:450 (2011).
Wood JR, Wilmshurst JM, Worthy TH, Cooper A. Sporormiella as a proxy for non-mammalian herbivores in island ecosystems. Quaternary Science Reviews. 30:915-920 (2011).
Yuan Y, Shen TJ, Gupta P, Ho N, Simplaceanu V, Tam T-C, Hofreiter M, Cooper A, Campbell K, Ho, C. A Biochemical-Biophysical Study of Hemoglobins from Woolly Mammoth, Asian Elephant, and Humans. Biochemistry 50:7350-7360 (2011).
Adler CJ, Haak W, Donlon D, Cooper A, The Genographic Consortium. Survival and recovery of DNA from ancient teeth and bones. J Archaeological Science. 38:956-964 (2011).
Davidson J, Ho SYW, Bray S, Korsten M, Vulla E, Hindrikson M, Ostbye K, Ostbye E, Lauritzen S-E, Austin J, Cooper A, Saarma U. Late-Quaternary biogeographic scenarios for the brown bear (Ursus arctos), a wild mammal model species. Quaternary Science Reviews, 30:418-430 (2011).
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. The complete mitochondrial genome of an 11,300-year-old aurochsen (Bos primigenius) from Central Italy. BMC Evolutionary Biology 11:32-42 (2011).
Martínez-Cruz B, Ziegle J, Sanz P, Sotelo G, Anglada R, Plaza S, Comas D, and The Genographic Consortium1. Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes. Investigative Genetics 2:13 (2011).
Balanovsky O, Dibirova K, Dybo A, Mudrak O, Frolova S, Pocheshkhova E, Haber M, Platt D, Schurr T, Haak W, Kuznetsova M, Radzhabov M, Balaganskaya, Romanov A, Zakharova T, Hernanz DF, Zalloua P, Koshei S, Ruhlen M, Renfrew C, Wells RS, Tyler-Smith C, Balanovska E, The Genographic Consortium. Parallel evolution of genes and languages in the Caucasus region. Molecular Biology Evolution 28:2905-2920 (2011).
Haber M, Platt DE, Badro DA, Xue Y, El-Sibai M, Bonab MA, Youhanna SC, Saade S, Soria-Hernanz DF, Royyuru A, Wells RS, Tyler-Smith C, Zalloua PA, The Genographic Consortium. Influences of history, geography, and religion on genetic structure: The Maronites in Lebanon. European J Human Genetics 19: 334-340 (2011).
Yan S, Wang C-C, Li H, Li S-L, Jin L, The Genographic Consortium. An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4. Eur J Human Genetics 19:1013-1015 (2011).
Jota MS, Lacerda DR, Sandoval J., Vieira PPR, Santos-Lopes SS, Bisso-Machado R, Paixão-Cortes VR, Revollo S, Paz-y-Miño C, Fujita R, Salzano FM, Bonatto SL, Bortolini MC, Tyler-Smith C, Santos FR, and The Genographic Consortium1. A new sub-haplogroup of Native American Y-chromosomes from the Andes. American Journal of Physical Anthropology 146: 553-559 (2011).
Yang K, Zheng H, Qin Z, Lu Y, Farina SE, Li S, Jin L, Li D, Li H, and The Genographic Consortium1. Positive selection on mitochondrial M7 lineages among the Gelong people in Hainan. Journal of Human Genetics 56: 253–256 (2011).
Gaieski JB, Owings AC, Vilar MG, Dulik MC, Gaieski DF, Gittelman RM, Lindo J, Gau L, Schurr TG, The Genographic Consortium1. Genetic ancestry and indigenous heritage in a Native American Descendant Community in Bermuda. American Journal of Physical Anthropology 146 (3): 392-405 (2011).
Cai X, Qin Z, Wen B, Xu S, Wang Y, Lu Y, Wei L, Wang C, Li S, Huang X, Jin L, Li H, The Genographic Consortium1. Human migration through bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum revealed by Y chromosomes. PLoS One 6 (8): e24282 (2011).
Haak W, Balanovsky O, Sanchez JJ, Koshei S, Zaporozhchenko V, Adler CJ, Der Sarkissian CS, Brandt G, Schwarz C, Nicklisch N, Dresely V, Fritsch B, Balanovska E, Villems R, Meller H, Alt KW, Cooper A, The Genographic Consortium. Ancient DNA from European Early Neolithic Farmers reveals their Near Eastern Affinities. PLoS Biology 8:e1000536 (2010).
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. Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance. Nature Genetics, 42:536-540 (2010).
Brotherton P, Sanchez JJ, Cooper A, Endicott P. Preferential access to genetic information from endogenous ancient DNA and quantitative SNP-typing from ancient hominin samples via SPEX. Nucleic Acids Research. 38:e7 (2010).
Zhadanov SI, Dulik MC, Markley M, Jennings GW, Gaieski JB, Elias G, Schurr TG, The Genographic Consortium. Genetic heritage and native identity of the Seaconke Wampanoag tribe of Massachusetts. Am J Phys Anthropol, 142:579-89 (2010).
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. A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the last Glacial Maximum. Am J Phys Anthropol 143:555-569 (2010).
Melé M, Javed A, Pybus M, Calafell F, Parida L, Bertranpetit J, The Genographic Consortium1. A New Method to Reconstruct Recombination Events at a Genomic Scale. PLoS Computational Biology 6(11): e1001010 (2010).
Bunce M, Worthy TH, Phillips MJ, Holdaway RN, Willerslev E, Haile J, Shapiro B, Scofield P, Drummond A, Kamp P, Cooper A. The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. Proc Natl Acad Sci USA 106:20646-20651 (2009).
Haile J, Froese D, MacPhee RDE, Roberts RG, Arnold LJ, Rasmussen M, Nielsen R, Brook BW, Robinson S, Demuro M, Gilbert MTP, Munch K, Reyes AV, Austin JJ, Cooper A, Barnes I, Möller P Willerslev E. Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proc Natl Acad Sci USA 106:22352-22357 (2009).
Orlando L, Metcalf J, Alberdi MT, Telles-Antunes M, Bonjean D, Otte M, Martin F, Eisenmann V, Mashkour M, Morello F, Prado JL, Salas-Gismondi R, Shockey BJ, Wrinn PJ, Vasil’ev SK, Ovodov ND, Cherry MI, Hopwood B, Male D, Austin JJ, Hänni C, Cooper A. Revising the recent evolutionary history of equids using ancient DNA. Proc Natl Acad Sci USA 106:21754-21759 (2009).
Slater GJ, Thalmann O, Leonard JA, Schweizer RM, Koepfli K, Pollinger JP, Rawlence NJ, Austin JJ, Cooper A, Wayne RK. Solving a Darwinian mystery: Evolutionary history of the Falkland Island Wolf. Current Biology, 19:R937 - R938 (2009).
Decker JE, Pires JC, Conant GC, McKay SD, Heaton MP, Chen KC, Cooper A, Vilkki J, Seabury CM, Caetano AR, Johnson GS, Brenneman RA, Hanotte O, Eggert LS, Wiener P, Kim J-J, Kim KS, Sonstegard TS, Van Tassell CP, Neibergs HL, McEwan JC, Brauning R, Coutinho LL, Babar ME, Wilson GA, McClure MC, Rolf MM, Kim JW, Schnabel RD, Taylor JF. Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics. Proc Natl Acad Sci USA 106:18644-18649 (2009).
Endicott P, Sanchez JJ, Pichler I, Brotherton P, Brooks J, Egarter-Vigl E, Cooper A, Pramstaller P. Genotyping human ancient mtDNA control and coding region polymorphisms with a multiplexed Single-Base-Extension assay: the singular maternal history of the Tyrolean Iceman. BMC Genetics 10:29 (2009).
Rawlence NJ, Wood JR, Armstrong KN, Cooper A. DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct taxa. Proc Roy Soc B 276:3395-402 (2009).
Boessenkool S, Austin JJ, Worthy TH, Scofield P, Cooper A, Seddon PJ, Waters JM. Relict or colonizer? Extinction and range expansion of penguins in southern New Zealand. Proc Roy Soc B 276:815-821 (2009).
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National Geographic 'Genographic Project', Ancient DNA Node Leader 2006-2011
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