Publications 2012 – University of Copenhagen

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Publications 2012

Abel Nielsen SC, Mourier T, Baandrup U, Mangart Søland T, Bertelsen MF, Gilbert MTP, Nielsen LP. Probable Transmission of Coxsackie B3 Virus from Human to Chimpanzee, Denmark. Emerging Infectious Diseases, Volume 18, Number 7 - July 2012

Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, Campos PF, Samaniego JA, Gilbert MTP, Willerslev E, Zhang G, Scofield RP, Holdaway RN, Bunce M. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc. Royal Soc. B 2012 279, 4724-4733, (2012). doi: 10.1098/rspb.2012.1745

Andersen K, Bird KL, Rasmussen M, Haile J, Breuning-Madsen H, Kjær KH, Orlando L, Gilbert MTP, Willerslev E. Meta-barcoding of ‘dirt' DNA from soil reflects vertebrate biodiversity. Mol. Ecol. 21:1966-1979, (2012)

Andresen CS, Straneo F, Ribergaard MH, Bjørk AA, Andersen TJ, Kuijpers A, Nørgaard-Petersen N, Kjær KH, Schjøt F, Weckström K, Ahlstrøm AP. Rapid response of Helheim Glacier in Greenland to climate variability over the past century. Nature Geoscience, vol. 5, pp. 37-41, (2012)

Beck S, Kuningas S, Esteban-Pavo R, Foote AD. The influence of ecology on sociality in the killer whale (Orcinus orca). Behavioral Ecology, 23: 246-253, (2012)

Bengtsson CF, Olsen ME, Brandt LØ, Bertelsen MF, Willerslev E, Tobin DJ, Wilson AS, Gilbert MTP. DNA from keratinous tissue, part I: Hair and nail. Ann Anat 194: 17-25, (2012)

Biagini P, Thèves C, Balaresque P, Géraut A, Cannet C, Keyser C, Nikolaeva D, Gérard P, Duchesne S, Orlando L, Willerslev E, Alekseev AN, de Micco P, Ludes B, Crubézy E. Variola virus in a 300-year-old Siberian mummy. N. Engl. J. Med. 2012 Nov 22;367(21):2057-9. doi: 10.1056/NEJMc1208124

Bjørk AA. Arkivfotos udvider klimaforskernes horisont. Tidsskriftet Grønland, 03/2012, pp. 174-180

Bjørk AA, Kjær KH, Korsgaard NJ, Khan SA, Kjeldsen KK, Andresen CS, Box JE, Larsen NK, Funder S. An aerial view of 80 years of climate-related glacier fluctuations in Southeast Greenland. Nature Geoscience, June 2012 Vol 5 No 6- DOI: 10.1038/NGEO1481 (PR)(CO)

Boessenkool S, Epp LS, Haile J. Bellemain E, Edwards M, Coissac E, Willerslev E, Brochmann C. Blocking human contaminant DNA during PCR allows amplification of rare mammal species in sedimentary ancient DNA. Mol. Ecol. 21, 1806–1815, (2012)

Bray SCE, Austin JJ, Metcalf JL, Østbye K, Østbye E, Lauritzen S-E, Aaris-Sørensen K, Valdiosera C, Adler CJ, 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 2012:1-12

Brüniche-Olsen A, Gravlund P, Lorenzen ED. Impact of genetic drift and restricted gene flow in indigenous cattle breeds: evidence from the Jutland breed. Animal Genetic Resources/Ressources génétiques animales/Recursos genéticos animales, 50, pp.75–85, June 2012Til toppen

Campos PF, Craig OE, Turner-Walker G, Peacock E, Willerslev E, Gilbert MTP. DNA in ancient bone – where is it located and how should we extract it? Ann. Anat. 194: 7-16, (2012)

Campos PF, Gilbert MTP. DNA extraction from formalin-fixed material. In: Shapiro B, Hofreiter M (eds.). Methods in Molecular Biology: Ancient DNA. Springer (2012)

Campos PF, Gilbert MTP. DNA extraction from keratin and chitin. In: Shapiro B, Hofreiter M (eds.) Methods in Molecular Biology: Ancient DNA. Springer (2012)

Cappellini E, Jensen L, Szklarczyk D, Ginolhac A, da Fonseca R, Stafford T, Holven S, Collins M, Orlando L, Willerslev E, Gilbert MTP, Olsen JV. Proteomic analysis of a Pleistocene mammoth femur reveals more than one hundred ancient bone proteins. J. Proteome Res. 11: 917-926, (2012)

Crone SG, Jacobsen A, Federspiel B, Bardram L, Krogh A, Lund AH, Friis- Hansen L. microRNA-146a inhibits G protein-coupled receptor-mediated activation of NF-kappaB by targeting CARD10 and COPS8 in gastric cancer. Mol. cancer, 11(1):71, Sep 2012

Dalén L, Orlando L, Shapiro B, Brandström Durling M, Quam R, Gilbert MTP, Fernández-Lomana JCD, Willerslev E, Arsuaga JL, Götherström A. Partial genetic turnover in neandertals: continuity in the east and population replacement in the west. Mol. Biol. Evol. 29:1893-1897, (2012)

Duchene S, Frey A, Alfaro-Núñez A, Dutton PH, Gilbert MTP, Morin PA. Marine turtle mitogenome phylogenetics and evolution. Mol. Phyl. Evol. Volume 65, Issue 1, October 2012, Pages 241-250

Epp LS, Boessenkool S, Bellemain EP, Haile J, Esposito A, Riaz T, Erséus C, Gusarov VI, Edwards ME, Johnsen A, Stenøien HK, Hassel K, Kauserud H, Yoccoz NG, Bråthen KA, Willerslev E, Taberlet P, Coissac E, Brochmann C. New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Mol. Ecol. Volume 21, Issue 8, April 2012, Pages: 1821–1833, Article first published online : 10 Apr 2012, DOI: 10.1111/j.1365-294X.2012.05537.x

Foote AD. Investigating ecological speciation in non-model organisms: a case study on killer whale ecotypes. Evolutionary Ecology Research 14, 447-465, 2012

Foote AD, Hofreiter M, Morin PA. Ancient DNA and marine mammals: Studying long lived species over ecological and evolutionary timescales. Ann. Anat. 194: 112-120, (2012)

Foote AD, Thomsen PF, Sveegaard S, Wahlberg M, Kielgast J, Kyhn LA, Salling AB, Galatius A, Orlando L, Gilbert MTP. Investigating the Potential Use of Environmental DNA (eDNA) for Genetic Monitoring of Marine Mammals. PLoS ONE, 2012 vol:7 hft.:8 s.:e41781

Foote AD, Vester H, Vikingsson GA, Newton J. Dietary variation within and between populations of northeast Atlantic killer whales Orcinus orca inferred from d13C and d15N analyses. Marine Mammal Science, Volume 28, Issue 4, pages E472–E485, October 2012

Ginolhac A, Vilstrup J, Stenderup J, Rasmussen M, Stiller M, Shapiro B, Zazula G, Froese D, Steinmann KE, Thompson JF, Al-Rasheid KA, Gilbert TM, Willerslev E, Orlando L. Improving the performance of True Single Molecule Sequencing for ancient DNA. BMC Genomics. 2012 May 10;13(1):177

Gotfredsen AB. Book review: Prummel, W., Zeiler, J.T., & Brinkhuizen, D.C. (eds.) 2010. Birds in Archaeology. Proceedings of the 6th Meeting of the ICAZ Bird Working Group in Groningen (23.8 - 27.8 2008). Groningen Archaeological Studies. Volume 12. Barkhuis. Groningen, 284 p., ISBN 978-90-77922-77-4, price: 50 EURO. Praehistorische Zeitschrift 87 (1): 216-221. De Gruyter. Berlin. DOI 10.1515/pz-2012-2013. (2012)

Gotfredsen AB, Møbjerg T. Urokser og bævere fra Midtjylland - nye dateringer af gamle fund. Museum Midtjylland, Midtjyske Fortællinger. 2012: 59-70. (2012)

Gravlund, P, Aaris-Sørensen K, Hofreiter M, Meyer M, Bolbach J, Noe-Nygård N. Ancient DNA extracted from Danish aurochs (Bos primigenius): Genetic diversity and preservation. Ann. Anat. 194 (1):103-111, (2012)

Gregersen LH, Jacobsen A, Frankel LB, Wen J, Krogh A, Lund AH. MicroRNA-143 down-regulates Hexokinase 2 in colon cancer cells. BMC Cancer 12:232, 2012

Hansen KL. E Museo Lundii - Addendum. 26 jun 2012 1. edition udg. Danmark: Statens Naturhistoriske Museum. 104 s. ISBN: 978-87-87519-75-5. 2012

Houmark-Nielsen M, Linge H, Fabel D, Schnabel C, Xu S, Wilcken KM, Binnie S. Cosmogenic surface exposure dating the last deglaciation in Denmark: discrepancies with independent age constraints suggest delayed periglacial landform stabilization. Quaternary Geochronology 13, 1-17, 2012. doi: 10.1016/j.quageo.2012.08.006Til toppen

Jacobsen MW, Hansen MM, Orlando L, Bekkevold D, Willerslev E, Bernatchez L, Gilbert MTP. Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonus spp.). Mol. Ecol. 21:2727-2742, (2012)

Jenkins DL, Davis LG, Stafford Jr TW, Campos PF, Hockett B, Jones GT, Cummings LS, Yost C, Connolly TJ, Yohe II RM, Gibbons SC, Raghavan M, Rasmussen M, Paijmans JLA, Hofreiter M, Kemp BM, Barta JL, Monroe C, Gilbert MTP, Willerslev E. Clovis Age Western Stemmed Projectile Points and Human Coprolites at the Paisley Caves. Science 13 July 2012: Vol. 337 no. 6091 pp. 223-228 DOI:10.1126/science.1218443

Jones EP, Skirnisson K, McGovern TH, Gilbert MTP, Willerslev E, Searle JB. Fellow travellers: a concordance of colonization patterns between mice and men in the North Atlantic region. BMC Evol. Biol. 12, 35. (2012)

Jørgensen T, Haile J, Möller P, Andreev A, Boessenkool S, Rasmussen M, Kielast F, Coissac E, Taberlet P, Brochmann C, Bigelow N, Andersen K, Orlando L, Gilbert MTP, Willerslev E. A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of Northern Siberia reveals long-term vegetational stability. Mol. Ecol. 21:1989-2003, (2012). doi: 10.1111/j.1365-294X.2011.05278.x

Jørgensen T, Kjær K, Haile J, Rasmussen M, Boessenkool S, Andersen K, Coissac E, Taberlet P, Brochmann C, Orlando L, Gilbert MTP, Willerslev E. Islands in the Ice: detecting past vegetation on Greenlandic Nunataks using historical records and sedimentary ancient DNA meta-barcoding. Mol. Ecol. 21:1980-1988, (2012)

Kjær KH, Khan SA, Korsgaard NJ, Wahr J, Bamber JL, Hurkmans R, van den Broeke M, Timm LH, Kjeldsen KK, Bjørk AA, Larsen NK, Jørgensen LT, Færch-Jensen A, Willerslev A. Aerial Photographs Reveal Late–20th-Century Dynamic Ice Loss in Northwestern Greenland. Science 3 August 2012: Vol. 337 no. 6094 pp. 569-573 DOI: 10.1126/science.1220614

Lavstsen T, Turner L, Saguti F, Magistrado P, Rask TS, Jespersen JS, Wang CW, Berger SS, Baraka V, Marquard AM, Seguin-Orlando A, Willerslev E, Gilbert MTP, Lusingu J, Theander TG. Plasmodium falciparum erythrocyte membrane protein 1 domain cassettes 8 and 13 are associated with severe malaria in children. Proc. Natl. Acad. Sci. USA 109:10160-10161

Lorenzen ED, Heller R, Siegismund HR. Comparative phylogeography of African savannah ungulates. Mol. Ecol. 15. June 2012, DOI: 10.1111/j.1365-294X.2012.05650.xTil toppen

Malaspinas AS, Malaspinas O, Evans SN, Slatkin M. Estimating allele age and selection coefficient from time-serial data. GENETICS October 1. 2012 vol. 192 no. 2, 599-607

Malmström H, Vretemark M, Tillmar A, Brandström Durling M, Skoglund P, Gilbert MTP, Willerslev E, Holmlund G, Götherström A. Finding the founder of Stockholm – a kinship study based on Y-chromosomal, autosomal and mitochondrial DNA. Ann. Anat. 194:138-145. (2012)

MacFadden BJ, Barbara A, Purdy, Church K, Stafford Jr TW. Humans were contemporaneous with late Pleistocene mammals in Florida: evidence from rare earth elemental analysis. Journal of Vertebrate Paleontology: 32, 708-716. (2012)

Mourier T, Ho SYW, Gilbert MTP, Willerslev E, Orlando L. Statistical guidelines for detecting past population shifts using ancient DNA. Molecular Biology Evolution 29:2241-2251, (2012)

Murray DC, Pearson SG, Fullagar R, Chase BM, Houston J, Atchison J, White NE, Bellgard MI, Clarke E, Macphail M, Gilbert MTP, Haile J, Bunce M. High-throughput sequencing of ancient plant and mammal DNA preserved in herbivore middens. Quat. Sci. Rev. 58:135-145, (2012)

Nielsen K, Khan SA, Korsgaard NJ, Kjær KH, Wahr J, Bevis M, Stearns LA, Timm LH. Crustal uplift due to ice mass variability on Upernavik Isstrøm, West Greenland. Earth and Planetary Science Letters , vol 353-354, pp. 182-189, (2012)

Noer CL, Dabelsteen T, Bohmann K, Monadjem A. Molossid bats in an African agro-ecosystem select sugarcane fields as foraging habitat. African Zoology 47(1): 1–11(April 2012)

Odumosu, T. Default Positions: African Icons and stereotypes from Georgian print culture. The Ephemerist 158 (Autumn), 10-13

Odumosu T. Abolitionists, African Diplomats and ‘the Black Joke’ in George Cruikshank’s 'New Union Club'. In McGrath, Elizabeth and Jean Michel Massing, eds. The Slave in European Art: From Renaissance Trophy to Abolitionist Emblem. Warburg Institute Colloquia. Vol. 20. (2012). London; Turin: Warburg Institute; Nino Aragno, 333-359. ISBN 978-1-908590-43-5

Olsen J, Kjær KH, Funder S, Larsen NK & Ludikova A, 2012. High-Arctic climate conditions for the last 7,000 years inferred from multi-proxy analysis of the Bliss Lake record, Northern Greenland. Journal of Quaternary Science DOI: 10.1002/jqs.1548 (PR)(CO)

Oonk S, Cappellini E, Collins MC. Soil proteomics: An assessment of its potential for archaeological site interpretation. Organic Geochemistry, Organic Geochemistry, Vol. 50, September 2012, Pp. 57-67

Oskam CL, Allentoft ME, Walter R, Scofield RP, Haile J, Holdaway RN, Bunce M, Jacomb C. Ancient DNA analyses of early archaeological sites in New Zealand reveal extreme exploitation of moa (Aves: Dinornithiformes) at all life stages. Quat. Sci. Rev. 52 (2012) 41e48

Overballe-Petersen S, Orlando L, Willerslev E. Next-generation sequencing offers new insights into DNA degradation. Trends in Biotechnology. 1 July 2012, Vol. 30, Issue 7, pp. 364-368

Paijmans JLA, Gilbert MTP, Hofreiter M. Mitogenomic analyses from ancient DNA. Mol. Phyl. Evol. 22:1494-1499, (2012)

Parducci L, Jørgensen T, Tollefsrud MM, Elverland E, Alm T, Fontana SL, Bennett KD, Haile J, Matetovici I, Suyama Y, Edwards ME, Andersen K, Rasmussen M, Boessenkool S, Coissac E, Brochmann C, Taberlet P, Houmark-Nielsen M, Larsen NK, Orlando L, Gilbert MTP, Kjær KH, Alsos I.G, Willerslev E. Glacial Survival of Boreal Trees in Northern Scandinavia. Science. 2 March 2012: 1083-1086. Supporting online material: 1-16. [DOI:10.1126/science.1216043

Parducci L, Edwards ME, Bennett KD, Alm T, Elverland E, Tollefsrud MM, Jørgensen T, Houmark-Nielsen M, Larsen NK, Kjær KH, Fontana SL, Alsos IG, Willerslev E. Response to Comment on ‘Glacial survival of boreal trees in northern Scandinavia’. Science. 338, 742-743, (2012)

Perren BP, Wolfe AP, Cooke CA, Kjær KH, Mazzucchi D, Steig EJ. Twentieth-century warming revives the world's northernmost lake. Geology. Published online on 18 September 2012 as doi:10.1130/G33621.1

Philip S, Castro LF, da Fonseca RR, Reis-Henriques MA, Vasconcelos V, Santos MM, Antunes A. Adaptive evolution of the Retinoid X receptor in vertebrates. Genomics. 2012 Feb; 99(2):81-9

Reid AJ, Vermont SJ, Cotton JA, Harris D, Hill-Cawthorne GA, Könen-Waisman S, Latham S, Mourier T, Norton R, Quail M, Sanders M, Shanmugam D, Sohal A, Wasmuth J, Brunk B, Grigg M, Howard JC, Parkinson J, Roos D, Trees AJ, Berriman M, Pain A, Wastling JM. Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PLoS Pathogens. 22. March 2012Til toppen

Sánchez-Quinto F, Schroeder H, Ramirez O, Ávila-Arcos MC, Pybus M, Olalde I, Velazquez AMV, Marcos MEP, Encinas JMV, Bertranpetit J, Orlando L, Gilbert MTP, Lalueza-Fox C. Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers. Curr. Biol. 21 August 2012 Vol. 22 Issue 16

Sánchez-Quinto F, Botiguá LR, Civit S, Arenas C, Ávila-Arcos MC et al. North African Populations Carry the Signature of Admixture with Neandertals. PLoS ONE 7(10): e47765. (2012). doi:10.1371/journal.pone.0047765

Schnell IB, Thomsen PF, Wilkinson N, Rasmussen M, Jensen LRD, Willerslev E, Bertelsen MF, Gilbert MTP. Terrestrial mammal biodiversity screening using DNA from Haematophagous leeches. Curr. Biol. 22: R262-263, (2012)

Schomacker A, Benediktsson ÍÖ, Ingólfsson Ó, Friis B, Korsgaard NJ, Kjær KH, Keiding JK. Late Holocene and modern glacier changes in the marginal zone of Sólheimajökull, South Iceland. Jokull, vol 62, pp. 111-130 (2012)

Schubert M, Ginolhac A, Lindgreen S, Thompson JF, Al-Rasheid KA, Willerslev E, Krogh A, Orlando L. Improving ancient DNA read mapping against modern reference genomes. BMC Genomics. 2012 May 10;13(1):178. DOI: 10.1186/1471-2164-13-178. (PR, CO)

Sinding MHS. 4.500 års grønlandshvaler vejer under et gram. Tidsskriftet Grønland, 03/2012, pp. 191-197

Sinding MHS, Gilbert MTP, Grønnow B, Gulløv HC, Toft PA, Foote AD. Minimally destructive DNA extraction from archaeological artefacts made from whale baleen. Journal of Archaeological Science, Vol. 39, Issue 12, December 2012, Pages 3750-3753.

Skoglund P, Malmström H, Raghavan M, Storå J, Hall P, Willerslev E, Gilbert MTP, Götherström A, Jakobsson M. Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science 336:466-469, (2012)

Taberlet P, Coissac E, Brochmann C… E. Willerslev. New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Mol. Ecol. 21(8): 1821-33, (2012)

Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E. Towards next-generation biodiversity assessment using DNA metabarcoding. Mol. Ecol. Volume 21, Issue 8, Pages: 2045–2050, Article first published online : 10 APR 2012, DOI: 10.1111/j.1365-294X.2012.05470.x

Thomsen PF, Kielgast J, Iversen LL, Møller PR, Rasmussen M, Willerslev E. Detection of a Diverse Marine Fish Fauna Using Environmental DNA from Seawater Samples. PLoS One, 29. August 2012

Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MTP, Orlando L, Willerslev E. Monitoring endangered freshwater biodiversity using environmental DNA. Mol. Ecol. 21:2565-2573, (2012)

Tsangaras K, Avila-Arcos MC, Ishida Y, Helgen KM, Roca AL, Greenwood AD. Historically low mitochondrial DNA diversity in koalas (Phascolarctos cinereus). BMC Genetics, Oct. 24; 13:92

Wales N, Romero-Navarro JA, Cappellini E, Gilbert MTP. Choosing the best plant for the job: a cost-effective assay to prescreen plant remains destined for shotgun sequencing. PLoS ONE 20 September 2012

Wang SY, Cappellini E, Zhang HY. Why collagens best survived in fossils? Clues from amino acid thermal stability. Biochemical & Biophysical Research Communications, 422, 5-7, (2012)

Yang MA, Malaspinas AS, Durand EY, Slatkin M. Ancient structure in Africa unlikely to explain neanderthal and non-african genetic similarity. Mol. Biol. Evol. 2012 Oct;29(10):2987-95. Epub 2012 Apr 18

Yoccoz NG, Bråthen NG, Gielly L, Haile J, Edwards ME, Goslar T, von Stedingk H, Brysting AK, Coissac E, Pompanon F, Sønstebø JH, Miquel C, Valentini A, de Bello F, Chave J, Thuiller W, Wincker P, Cruaud C, Gavory F, Rasmussen M, Gilbert MTP, Orlando L, Brochmann C, Willerslev E, Taberlet P. DNA from soil mirrors plant functional and structural diversity. Mol. Ecol. 21:3647-3655, (2012)

Weischenfeldt J, Waage J, Tian G, Zhao J, Damgaard I, Jakobsen JS, Kristiansen K, Krogh A, Wang J, Porse BT. Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns. Genome Biology, 13(5):R35, 2012