Publications 2015 – University of Copenhagen

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Publications 2015

Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L, Zhang F, Zhang L, Cui L, He W, Yang J, Yao X, Zhou L, Han L, Li J, Sun S, Xie X, Lai B, Su Y, Lu Y, Yang H, Huang T, Deng W, Nielsen R, Ren J, Huang L. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nature genetics 47 (3), 217-225, 2015.

Alberdi A, Gilbert MTP, Razgour O, Aizpurua O, Aihartza J, Garin I. Contrasting population-level responses to Pleistocene climatic oscillations in an alpine bat revealed by complete mitochondrial genomes and evolutionary history inference. J Biogeography 9:1689-1700, 2015. (PR)

Alfaro-Núñez A, Jensen MP and Abreu-Grobois FP (2015). Does polyandry really pay off?: The effects of multiple mating and number of fathers on morphological traits and survival of nesting green turtles at Tortuguero. PeerJ (IF: 2.1) 3:e880; DOI 10.7717/peerj.880. (PR, OA)

Allendorf FW, Bassham S, Cresko WA, Limborg MT, Seeb LW, Seeb JE (2015). Effects of crossovers between homeologs on inheritance and population genomics in polyploid-derived salmonid fishes. Journal of Heredity 106:217-227. (PR)

Allendorf FW, Bassham S, Cresko WA, Limborg MT, Seeb LW, Seeb JE (2015). Response to May and Delany: We Never Said Wright was Wrong. Journal of Heredity,  106: 767-768. (PR)

Allentoft MA, Sikora M, Sjogren KG, Rasmussen S, Rasmussen M, Stenderup J, Damgaard PB, Schroeder H, Ahlstrom T, Vinner L,  Malaspinas A-S, Margaryan A, Higham T, Chivall D, Lynnerup N,  Harvig L, Baron J, Della Casa P, Dabrowski P, Duffy PR, Ebel AV, Epimakhov A, Frei K, Furmanek M, Gralak T, Gromov A, Gronkiewicz S, Grupe G, Hajdu T, Jarysz R, Khartanovich V, Khokhlov A, Kiss V,  Kolar J, Kriiska A, Lasak I, Longhi K, McGlynn G, Merkevicius A, Merkyte I, Metspalu M, Mkrtchyan M, Moiseyev V, Paja L, Palfi G,  Pokutta D, Pospieszny L, Price TD, Saag L, Sablin M, Shishlina N, Smrcka V, Soenov VI, Szeverenyi V, Toth G, Trifanova SV, Varul L, Vicze M, Yepiskoposyan L, Zhitenev V, Orlando L, Sicheritz-Ponten T, Brunak S, Nielsen R, Kristiansen K & Willerslev E. (2015) Population genomics of Bronze Age Eurasia. Nature, Volume:522, Pages:167–172. 11 June 2015. DOI:doi:10.1038/nature14507. PR

Allentoft et al. Ancient DNA microsatellite analyses of the extinct New Zealand giant moa (Dinornis robustus) identify relatives within a single fossil site. Heredity, Vol. 115, 481-487, 2015. PR

Alsos IG, Sjögren P, Edwards ME, Landvik JY, Gielly L, Forwick M, Coissac E, Brown AG, Jakobsen LV, Føreid MK, Pedersen MW. Sedimentary ancient DNA from Lake Skartjørna, Svalbard: Assessing the resilience of arctic flora to Holocene climate change. The Holocene. November 11, 2015, doi: 10.1177/0959683615612563

Andrews J, Bjørk AA, Eberl D, Jennings A, Verplanck E. Significant differences in late Quaternary bedrock erosion and transport: East versus West Greenland 70°N – evidence from the mineralogy of offshore glacial marine sediments. I: Journal of Quaternary Science, Vol. 30/5, 05.2015, s. 452-463.

Avila-Arcos MC, Lalueza-Fox C, Gilbert MTP. Neanderthal DNA Sequenced. In: Trefil J (ed) Discoveries in Modern Science: Exploration, Invention, Technology. Farmington Hills: Macmillan pp. 732-735. 2015.

Ávila-Arcos MC, Sandoval-Velasco M, Schroeder H, Carpenter ML, Malaspinas A-S, Wales N, Peñaloza F, Bustamante CD, & Gilbert MTP. Comparative Performance of Two Whole Genome Capture Methodologies on Ancient DNA Illumina Libraries. Methods in Ecology and Evolution, 6, 725-734. 2015. PR

Bangsgaard P. Animal Bones. In: J. Strange (ed.): Tall-el-Fukhar, Result from the Excavations in 1990-93 and 2002, vol. I  Text. Proceedings of the Danish Institute in Damascus vol. 9, pp. 378-397, 2015.

Bangsgaard P. An Additional Note to Kent V. Flannery’s Chapter on Animal Domestication at Tepe Guran. In: P. Mortensen, Excavations at Tepe Guran, The Neolithic Period, Acta Iranica 55. Peeters Publishers, pp. 107-114, 2015. PR

Benediktsson ÍÖ, Schomacker A, Johnson MD, Geiger AJ, Ingólfsson Ó & Guðmundsdóttir ER. Architecture and structural evolution of an early Little Ice Age terminal moraine at Múlajökull, surge-type glacier, Iceland. Journal of Geophysical Research, 120, 16 pp, 2015. doi:10.1002/2015JF003514. PR, CO

Bjørk AA, Kruse LM & Michaelsen PB. Getting Greenland’s glaciers right – a new dataset of all official Greenlandic glacier names. The Cryosphere vol. 9, p. 2215-2218, 2015.

Bleicher N, Kelstrup C, Olsen JV, Cappellini E. Molecular evidence of use of hide glue in 4th millennium BC Europe. J. of Archaeological Science, 2015. DOI:10.1016/j.jas.2015.08.012.

Borges R, Khan I, Johnson WE, Gilbert MTP, Zhang G, Jarvis ED, O’Brien SJ, Antunes A.  Gene loss, adaptive evolution, and the co-evolution of plumage coloration genes with opsins in birds. BMC Genomics 16:751, 2015. (OA)

Brown TA, Cappellini E, Kistler L, Lister DL, Oliveira HR, Wales N, Schlumbaum A (2015). Recent advances in ancient DNA research and their implications for archaeobotany. Vegetation History and Archaeobotany 24: 207-214. (PR)

Bruhn CAW, Nielsen SCA, Samaniego JA, Wadsworth J, Knowles N, Gilbert MTP. Viral meningitis epidemics and a single, recent, recombinant and anthroponotic origin of Swine Vesicular Disease Virus. Evolution, Medicine and Public Health 1:289-303. 2015. (OA)

Brynjólfsson S, Schomacker A, Guðmundsdóttir ER & Ingólfsson Ó. A 300-year surge history of the Drangajökull ice cap, northwest Iceland, and its maximum during the ‘Little Ice Age’. The Holocene, 25 (7), 1076-1092, 2015. PR, CO

Brynjólfsson S, Schomacker A, Ingólfsson Ó & Keiding JK. Cosmogenic 36Cl exposure ages reveal a 9.3 ka BP glacier advance and the Late Weichselian-Early Holocene glacial history of the Drangajökull region, northwest Iceland. Quaternary Science Reviews, 126, 140-157, 2015. PR, CO

Cao H, Wu H, Luo R, Huang S, Sun Y, Tong X, Xie Y, Liu B, Yang H, Zheng H, Li J, Li B, Wang Y, Yang F, Sun P, Liu S, Gao P, Huang H, Sun J, Chen D, He G, Huang W, Huang Z, Li Y, Tellier LCAM, Liu X, Feng Q, Xu X, Zhang X, Bolund L, Krogh A, Kristiansen K, Drmanac R, Drmanac S, Nielsen R, Li S, Wang J, Yang H, Li Y, Wong GK-S, Wang J. De novo assembly of a haplotype-resolved human genome. Nature biotechnology 33 (6), 617-622. 2015.

Cracraft J, Houde P, Ho SYW, Mindell DP, Fjeldså J, Lindow B, Edwards SV, Rahbek C, Mirarab S, Warnow T, Gilbert MTP, Zhang G, Braun EL, Jarvis ED. Response to Comment on "Whole-genome Analyses Resolve Early Branches in the Tree of Life of Modern Birds". Science 349:1460, 2015.

Crawford JE, Riehle MM, Wamdaogo M Guelbeogo, Awa Gneme, N'Fale Sagnon, Kenneth D Vernick, Rasmus Nielsen, Brian P Lazzaro. Reticulate Speciation and Barriers to Introgression in the Anopheles gambiae Species Complex. Genome biology and evolution 7 (11), 3116-3131, 2015.

Damgaard PB, Margaryan A, Schroeder H, Orlando L, Willerslev E, Allentoft ME. Improving access to endogenous DNA in ancient bones and teeth. Scientific Reports 5, Article no. 11184, doi:10.1038/srep11184. 17. June 2015. PR

DeGiorgio M, Huber CD, Hubisz MJ, Hellmann I, Nielsen R. User Manual for SweepFinder2. 2015.

DeGiorgio M, Huber CD, Hubisz MJ, Hellmann I, Nielsen R. SWEEPFINDER2: Increased sensitivity, robustness, and flexibility arXiv. arXiv:1505.07142. 2015.

Der Sarkissian C, Allentoft ME, Vila-Arcos MCA, Barnett R, Campos PF, Cappellini E, Ermini L, Fernandez R, da Fonseca R, Ginolhac A, Hansen AJ, Jonsson H, Korneliussen T, Margaryan A, Martin MD, Moreno-Mayar JV, Raghavan M, Rasmussen M, Velasco MS, Schroeder H, Schubert M, Seguin-Orlando A, Wales N, Gilbert MTP, Willerslev E, Orlando L (2015). Ancient genomics. Phil. Trans. B. Article Number: UNSP 20130387. (PR)

Der Sarkissian C, Ermini L, Schubert M, Yang MA, Librado P, Fumagalli M, Jónsson H, Bar-Gal GK, Albrechtsen A, Vieira FG, Petersen B, Ginolhac A, Seguin-Orlando A,  Magnussen K, Fages A, Gamba C, Lorente B, Polani S, Steiner C,  Neuditschko M, Jagannathan V, Feh C, Greenblatt CL, Ludwig A, Abramson N, Zimmermann W, Schafberg R, Tikhonov A, Sicheritz-Ponten T, Willerslev E, Marques-Bonet T, Ryder OA, McCue M, Rieder S, Leeb T, Slatkin M, Orlando L. Evolutionary genomics and conservation of the endangered Przewalski’s horses. Current Biology 25:2577–2583. Current Biology, Available online 24 September 2015. (PR, CO)

Der Sarkissian C, Vilstrup JT, Schubert M, Seguin-Orlando A, Eme D, Weinstock J, Alberdi MT, Martin F, Lopez PM, Prado JL, Prieto A, Douady CJ, Stafford TW, Willerslev E, Orlando L (2015). Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids. Biology Letters, 11. doi: 10.1098/rsbl.2014.1058. (PR, CO)

Dong Y, Zhang X, Xie M, Arefnezhad B, Wang Z, Wang W, Feng S, Huang G, Guan R, Shen W, Bunch R, McCulloch R, Li Q, Li B, Zhang G, Xu X, Kijas JW, Salekdeh GH, Jiang Y. Reference genome of wild goat (Capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication. BMC Genomics 2015, 16:431. (PR, OA)

Enghoff IB & Ediger V. Snapshots of past fish faunas: paleooceanographic perspectives from the Baltic and Black Seas. Environmental Archaeology, 2015.

Ermini L, Der Sarkissian C, Willerslev E, Orlando L (2015). Major transitions in human evolution revisited: a tribute to ancient DNA. Journal of Human Evolution, 79, 4–20. doi:10.1016/j.jhevol.2014.06.015. (PR)

Eöry L, Gilbert MTP, Li C, Li B, Archibald A, Aken BL, Zhang G, Jarvis ED, Flicek P, Burt DW. Avianbase: a community resource for bird genomics. Genome Biology 16:21, 2015.

Fernández R, Schubert M, Vargas-Velázquez AM, Brownlow A, Víkingsson GA, Siebert U, Jensen LF, Øien N, Wall D, Rogan E, Mikkelsen B, Dabin W, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Guillot G, Orlando L. A genomewide catalogue of single nucleotide polymorphisms in white-beaked and Atlantic white-sided dolphins.  Mol. Ecol. Res. 29 May 2015. DOI: 10.1111/1755-0998.12427. (PR, CO)

da Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P, Fumagalli M, Samaniego AJ, Carøe C, Ávila-Arcos MC, Hufnagel DE, Korneliussen TS, Vieira FG, Jakobsson M, Arriaza B, Willerslev E, Nielsen R, Hufford MB, Albrechtsen A, Ross-Ibarra J, Gilbert MTP. The origin and evolution of maize in the Southwestern United States. Nature Plants, (2015). DOI:10.1038/nplants.2014.3. PR, CO

da Fonseca RR, Smith BD, Wales N, Cappellini E, Skoglund P, Fumagalli M, Samaniego AJ, Carøe C, Ávila-Arcos MC, Hufnagel DE, Korneliussen TS, Vieira FG, Jakobsson M, Arriaza B, Willerslev E, Nielsen R, Hufford MB, Albrechtsen A, Ross-Ibarra J, Gilbert MTP. Erratum: The origin and evolution of maize in the Southwestern United States. Nature Plants, 15007, 2015.

Foote AD, Liu Y, Thomas GWC, Vinař T, Alföldi J, Deng J, Dugan S, van Elk CE, Joshi V, Khan Z, Kovar C, Lee SL, Lindblad-Toh K, Mancia A, Nielsen R, Qin X, Qu J Raney BJ, Vijay N, Wolf JBW, Hahn MW, Muzny DM, Worley KC, Gilbert MTP, Gibbs RA. Convergent evolution of the genomes of marine mammals. Nature Genetics 47:272–275, 2015.

Frei et al. Tracing the life story of a Bronze Age Female. Scientific Reports, 5:10431, DOI: 10.1038/srep10431. 2015. PR

Fumagalli M, Moltke I, Grarup N, Racimo F, Bjerregaard P, Jørgensen ME, Korneliussen TS, Gerbault P, Skotte L, Linneberg A, Christensen C, Brandslund I, Jørgensen T, Huerta-Sánchez E, Schmidt EB, Pedersen O, Hansen T, Albrechtsen A, Nielsen R. Greenlandic Inuit show genetic signatures of diet and climate adaptation. Science 349 (6254), 1343-1347, 2015.

Gamba C, Hanghøj K, Gaunitz C, Alfarhan AH, Alquraishi SA, Rasheid KAS Al-, Bradley D, Orlando L. 2015. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing. Mol. Ecol. Resour. [Epub ahead of print]. Available from:

Genome10K Consortium of Scientists. The Genome 10K Project – A way forward. Annual Review of Animal Biosciences 3:57-111, 2015.

Georges A, Li Q, Lian J, O'Meally D, Deakin J, Wang Z, Zhang P, Fujita M, Patel HR, Holleley CE, Zhou Y, Zhang X, Matsubara K, Waters P, Graves JA, Sarre SD,
Zhang G. High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps. Gigascience 2015, 4:45. (PR, OA)

Grayson DK and Meltzer DJ. Revisiting Paleoindian exploitation of extinct North American mammals. Journal of Archaeological Science 56:177-193., 2015. DOI: 10.1016/j.jas.2015.02.009. PR

Gusfield D, Nielsen R. Association Mapping for Compound Heterozygous Traits Using Phenotypic Distance and Integer Programming. Algorithms in Bioinformatics, 136-147, 2015.

Hansen TA, Fridholm H, Frøslev TG, Kjartansdóttir KR, Willerslev E, Nielsen LP, et al. (2015). New Type of Papillomavirus and Novel Circular Single Stranded DNA Virus Discovered in Urban Rattus norvegicus Using Circular DNA Enrichment and Metagenomics. PLoS ONE 10(11): e0141952. doi:10.1371/journal.pone.0141952

Harris K, Nielsen R. The genetic cost of Neanderthal introgression. bioRxiv, 030387. 2015.

Hestand MS, Kalbfleisch TS, Coleman SJ, Zeng Z, Liu J, Orlando L, MacLeod JN. 2015. Annotation of the Protein Coding Regions of the Equine Genome. PLoS One 10:e0124375

Jayalath K, RF Gunst & Meltzer DJ. Spatial point process identification of an apparent Ice Age house structure. Spatial Statistics 14:563-580. 2015. DOI: 10.1016/j.spasta.2015.09.003. PR

Jeffares DC, Rallis C, Rieux A, Speed D, Převorovský M, Mourier T, Marsellach FX, Iqbal Z, Lau W, Cheng TM, Pracana R, Mülleder M, Lawson JL, Chessel A, Bala S, Hellenthal G, O'Fallon B, Keane T, Simpson JT, Bischof L, Tomiczek B, Bitton DA, Sideri T, Codlin S, Hellberg JE, van Trigt L, Jeffery L, Li JJ, Atkinson S, Thodberg M, Febrer M, McLay K, Drou N, Brown W, Hayles J, Salas RE, Ralser M, Maniatis N, Balding DJ, Balloux F, Durbin R, Bähler J. The genomic and phenotypic diversity of Schizosaccharomyces pombe. Nat Genet. 2015 Feb 9. doi: 10.1038/ng.3215. [Epub ahead of print]

Jensen JF, Appelt M, Myrup M, Haack H, Taube M. Himmelsk og jordisk jern i Grønlands forhistorie. Nationalmuseets Arbejdsmark 2015. pp 116-131. 2015. PR

Jensen JF. Qajaa Excavations 1981 and 1982 - a West Greenland Saqqaq site with preserved wood and bone. Sila Arktisk Center ved Etnografisk Samling Nationalmuseet, feltrapport 36, 88 p., 2015

Jensen RH, Mollerup S, Mourier T, HansenTA, Fridholm H, Nielsen LP et al. (2015). Target-Dependent Enrichment of Virions Determines the Reduction of High-Throughput Sequencing in Virus Discovery. PLoS ONE, 10(4). OA

Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME, Venkat A, Fischman BJ, Hernandez A, Yandell M, Ence D, Holt C, Yocum GD, Kemp WP, Bosch J, Waterhouse RM, Zdobnov EM, Stolle E, Kraus FB, Helbing S, Moritz RF, Glastad KM, Hunt BG, Goodisman MA, Hauser F, Grimmelikhuijzen CJ, Pinheiro DG, Nunes FM, Soares MP, Tanaka ED, Simoes ZL, Hartfelder K, Evans JD, Barribeau SM, Johnson RM, Massey JH, Southey BR, Hasselmann M, Hamacher D, Biewer M, Kent CF, Zayed A, Blatti C, 3rd, Sinha S, Johnston JS, Hanrahan SJ, Kocher SD, Wang J, Robinson GE, Zhang G (2015). Social evolution. Genomic signatures of evolutionary transitions from solitary to group living. Science 348:1139-1143. (PR)

Karmin M, Saag L, Vicente M et al. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome research 25 (4), 459-466, 2015. OA

Kerner S, Dann R and Bangsgaard P (eds.), 2015: Climate Change in Ancient Societies. Copenhagen: Museum Tusculanum Press, 341 pages

Khan I, Yang Z, Maldonado E, Li C, Zhang G, Gilbert MTP, Jarvis ED, O’Brien SJ, Johnson WE, Antunes A. Olfactory receptor subgenomes linked with broad ecological adaptations in Sauropsida. Molecular Biology and Evolution 32:2 832-2843, 2015. OA

Khan SA, Aschwanden A, Bjørk AA, Wahr J, Kjeldsen KK, Kjær KH. Greenland ice sheet mass balance: a review. I: Reports on Progress in Physics, Vol. 78, 2015.

Kjartansdóttir KR, Friis-Nielsen J, Asplund M, Mollerup S, Mourier T, Jensen RH et al. (2015). Traces of ATCV-1 associated with laboratory component contamination. Proceedings of the National Academy of Sciences, 201423756.

Kjeldsen KK, Korsgaard NJ, Bjørk AA, Khan SA, Box JE, Funder S, Larsen NK, Bamber JL, Colgan W, van den Broeke M, Siggaard-Andersen ML, Nuth C, Schomacker A, Andresen CS, Willerslev E & Kjær KH. Spatial and temporal distribution of mass loss from the Greenland Ice Sheet since AD 1900. Nature, 528, 396-400. doi:10.1038/nature16183. 2015. (PR, CO)

Korb J, Poulsen M, Hu H, Li C, Boomsma JJ, Zhang G, Liebig J (2015). A genomic comparison of two termites with different social complexity. Frontiers in genetics 6:9. (PR, OA)

Korneliussen TS, Moltke I. NgsRelate: a software tool for estimating pairwise relatedness from next-generation sequencing data. Bioinformatics. 2015 Dec 15;31(24):4009-11. doi:10.1093/bioinformatics/btv509. Epub 2015 Aug 30. PR, OA

Korsgaard NJ, Schomacker A, Benediktsson ÍÖ, Larsen NK, Ingólfsson Ó & Kjær KH. Spatial distribution of erosion and deposition during a glacier surge: Brúarjökull, Iceland. Geomorphology, 250, 258-270, 2015. PR, CO

Larsen NK, Kjær KH, Lecavalier B, Bjørk AA, Colding S, Huybrechts P, Jakobsen K, Kjeldsen KK, Knudsen KL, Odgaard B, Olsen J. The response of the southern Greenland ice sheet to the Holocene thermal maximum. I: GEOLOGY, Vol. 43, Nr. 4, 2015, s. 291-294.

Librado P*, Der Sarkissian C*, Ermini L, Schubert M, Jónsson H, Albrechtsen A, Fummagalli M, Yang MA, Gamba C, Ginolhac A, Seguin-Orlando A, Mortensen CD, Petersen B, Hoover C, Lorente B, Nedoluzhko A, Boulougina E, Neuditschko M, Jagannathan V, Thèves C, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Sicheritz-Ponten T, Popov R, Alekseev AN, Rubin E, McCue M, Rieder S, Leeb T, Tikhonov A, Crubézy E, Slatkin M, Marques-Bonet T, Nielsen R, Willerslev E,  Kantanen J, Prokhortchouk E, Orlando L. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments. Proceedings of the National Academy of Sciences. Doi:10.1073/pnas.1513696112. (PR, CO)

Malmström H, Linderholm A, Skoglund P, Storå J, Sjödin P, Gilbert MTP, Holmlund G, Willerslev E, Jakobsson M, Lidén K, Götherström A (2015). Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process. Phil. Trans. B. 370.

Martin M D, Vieira F G, Ho S Y W, Wales N, Schubert M, Seguin-Orlando A, Ristaino J B, & Gilbert M T P. Genomic Characterization of a South American Phytophthora Hybrid Mandates Reassessment of the Geographic Origins of Phytophthora infestans. Molecular Biology and Evolution. 33:478-491, 2015. (OA, PR, CO)

Meltzer DJ. Kennewick Man: coming to closure. Antiquity 89:1485-1493. 2015. DOI: 10.15184/aqy.2015.160. PR

Meltzer DJ. Pleistocene overkill and North American mammalian extinctions. Annual Review of Anthropology 44:33-53. 2015. DOI: 10.1146/annurev-anthro-102214-013854. PR

Mendoza LMZ, Sicheritz-Ponten T, Gilbert MTP. Environmental genes and genomes: Understanding the differences and challenges in the approaches and software for their analyses. Briefings in Bioinformatics doi: 10.1093/bib/bbv001. 2015. (OA)

Moltke I, Fumagalli M, Korneliussen TS, Crawford JE, Bjerregaard P, Jørgensen ME, Grarup N, Gulløv HC, Linneberg A, Pedersen O, Hansen T, Nielsen R, Albrechtsen A. Uncovering the genetic history of the present-day Greenlandic population. The American Journal of Human Genetics 96 (1), 54-69, 2015.

Moon S, Kim T-H, Lee K-T, Kwak W, Lee T, Lee S-W, Kim M-J, Cho K, Kim N, Chung W-H, Sung S, Park T, Cho S, Groenen MAM, Nielsen R, Kim Y, Kim H. A genome-wide scan for signatures of directional selection in domesticated pigs. BMC genomics 16 (1), 2015.

Morin PA, Parsons KM, Archer FI, Ávila-Arcos MC, Barrett-Lennard LG, Dalla Rosa L, Duchêne S, Durban JW, Ellis G, Ferguson SH, Ford JK, Ford M, Garilao C, Gilbert MTP, Kaschner K, Matkin CO, Petersen SD, Robertson KM, Visser IN, Wade PR, Ho SYW, Foote AD. Geographical and temporal dynamics of a global radiation and diversification in the killer whale. Molecular Ecology 24:3964-3979, 2015.

Mourier T, Mollerup S, Vinner L, Hansen TA, Kjartansdóttir KR, Frøslev TG, Boutrup TS, Nielsen LP, Willerslev E & Hansen AJ. Characterizing novel endogenous retroviruses from genetic variation inferred from short sequence reads. Scientific Reports, 5:15644, DOi: 10.1038/srep15644, 2015

Nadachowska-Brzyska K, Li C, Smeds L, Zhang G, Ellegren H (2015). Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences. Current biology 25:1375-1380. (PR)

Odumosu T & Schroeder H. Memorializing Contested Landscapes. Journal of African Diaspora Archaeology and Heritage. 4:3, 189-194, 2015. DOI: 10.1080/21619441.2015.1124592

Olalde I, Schroeder H, Sandoval-Velasco M, Vinner L, Lobón I, Ramírez O et al. A Common Genetic Origin for Early Farmers from Mediterranean Cardial and Central European LBK Cultures. Molecular Biology and Evolution, 32(12), msv181–11. 2015. PR

Orlando L, Gilbert MT, Willerslev E. Reconstructing ancient genomes and epigenomes. Nat Rev Genet. 2015 Jun 9. doi: 10.1038/nrg3935.

Pacioni et al. Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial. Molecular Ecology, vol. 24, 5813-5828. 2015. PR

Pedersen MW, Overballe-Petersen S, Ermini L, Der Sarkissian C, Haile J, Hellstrom M, Spens J, Thomsen KPF, Bohmann K, Cappellini E, Schnell IB, Wales NA, Carøe C, Campos PF, Schmidt AMZ, Gilbert MTP, Hansen AJH, Orlando L, and Willerslev E (2015). Ancient and modern environmental DNA. Phil. Trans. B. 370, Article Number 20130383. PR

Pereira RJ, Wake DB. Ring species as demonstrations of the continuum of species formation. Molecular Ecology, 28 October 2015. DOI: 10.1111/mec.13412. PR, OA

Racimo F, Gokhman D, Fumagalli M, Hansen T, Moltke I, Albrechtsen A, Carmel L, Huerta-Sanchez E, Nielsen R. Archaic adaptive introgression in TBX15/WARS2. bioRxiv, 033928, 2015.

Racimo F, Sankararaman S, Nielsen R, Huerta-Sánchez E. Evidence for archaic adaptive introgression in humans. Nature Reviews Genetics 16 (6), 359-371, 2015.

Raghavan M, Steinrücken M, Harris K, Schiffels S, Rasmussen S, DeGiorgio M, Albrechtsen A, Valdiosera C, Ávila-Arcos MC, Malaspinas A-S, Eriksson A, Moltke I, Metspalu M, Homburger JR, Wall J, Cornejo OE, Moreno-Mayar JV, Korneliussen TS, Pierre T, Rasmussen M, Campos PF, de Barros Damgaard P, Allentoft ME, Lindo J, Metspalu E, Rodríguez-Varela R, Mansilla J, Henrickson C,  Seguin-Orlando A, Malmström H, Stafford Jr. T, Shringarpure SS, Moreno-Estrada A, Karmin M,  Tambets K, Bergström A, Xue Y, Warmuth V, Friend AD, Singarayer J, Valdes P, Balloux F, Leboreiro I, Vera JL, Rangel-Villalobos H, Pettener D, Luiselli D, Davis LG, Heyer E, Zollikofer CPE, Ponce de León MS, Smith CI, Grimes V, Pike K-A, Deal M, Fuller BT, Arriaza B, Standen V, Luz MF,  Ricaut F, Guidon N, Osipova L, Voevoda MI, Posukh OL, Balanovsky O, Lavryashina M, Bogunov Y, Khusnutdinova E, Gubina M, Balanovska E, Fedorova S, Litvinov S, Malyarchuk B, Derenko M, Mosher MJ, Archer D, Cybulski J, Petzelt B, Mitchell J, Worl R, Norman PJ, Parham P, Kemp BM, Kivisild T, Tyler-Smith C, Sandhu MS, Crawford M, Villems R, Smith DG, Waters MR, Goebel T, Johnson JR, Malhi RS, Jakobsson M, Meltzer DJ, Manica A, Durbin R, Bustamante CD, Song YS, Nielsen R, Willerslev E. Genomic evidence for the Pleistocene and recent population history of Native Americans. Science 21 August 2015:aab3884 Published online 21 July 2015. PR

Rasmussen et al. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. Cell, vol. 163, 571-582. 2015. (PR, CO)

Rasmussen M, Sikora M, Albrechtsen A, Korneliussen TS, Moreno-Mayar JV, Poznik GD, Zollikofer CPE, Ponce de León M, Allentoft ME, Moltke I, Jónsson H, Valdiosera C, Malhi RS, Orlando L, Bustamante CD, Stafford Jr. TW, Meltzer DJ, Nielsen R, and Willerslev E. The Ancestry and Affiliations of Kennewick Man. Nature, 18. June 2015. PR, CO

Rebolledo-Mendez J, Hestand MS, Coleman SJ, Zeng Z, Orlando L, MacLeod JN, KalbfleischT. 2015. Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads. PLoS One 10:e0126852.

Reynard L, Meltzer DJ, Emslie SD and Tuross N. Stable isotopes in yellow-bellied marmot (Marmota flaviventris) fossils reveal environmental stability in the late Quaternary of the Colorado Rocky Mountains. Quaternary Research 83:345-354. 2015. DOI: 10.1016/j.yqres.2014.12.006. PR

Ribeiro AM, Zepeda-Mendoza ML, Bertelsen MF, Kristensen AT, Jarvis ED, Gilbert MTP, da Fonseca RR. A refined model of the genomic basis for phenotypic variation in vertebrate hemostasis. BMC Evolutionary Biology 15:124, 2015. OA

Rohlfs RV, Aguiar VRC, Lohmueller KE, Castro AM, Ferreira ASC, Almeida VCO, Louro ID, Nielsen R. Fitting the Balding–Nichols model to forensic databases. Forensic Science International: Genetics 19, 86-91, 2015.

Rohlfs RV, Nielsen R. Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution. Systematic biology 64 (5), 695-708, 2015. OA

Samaniego Castruita JA, Zepeda Mendoza ML, Barnett R, Wales N & Gilbert MTP. Odintifier - A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing. BMC Bioinformatics, 16, 232. 2015. PR

Schnell IB, Sollman R, Calvignac-Spencer S, Siddall M, Yu D, Wilting A, Gilbert MTP. iDNA from terrestrial haematophagous leeches as a wildlife surveying and monitoring tool - prospects, pitfalls and avenues to be developed. Frontiers in Zoology 12:24, 2015. OA

Schnell IB, Bohmann K, Gilbert MTP. Tag jumps illuminated – reducing sequence-to-sample misidentifications in metabarcoding studies. Molecular Ecology Resources 15:1289-1303, 2015.

Schroeder H, Ávila-Arcos MC, Malaspinas AS, Poznik GD, Sandoval-Velasco M, Carpenter ML et al. (2015). Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean. PNAS USA 112(12), 3669–3673. (PR)

Seersholm FV, Fischer A, Heller M, Jores J, Sachse K, Mourier T & Hansen AJ (2015). Draft Genome Sequence of the First Human Isolate of the Ruminant Pathogen Mycoplasma capricolum subsp. capricolum. Genome Announc. May/June 2015 vol. 3 no. 3 e00583-15. OA

Seguin-Orlando A, Gamba C, Der Sarkissian C, Ermini L, Louvel G, Boulygina E, Sokolov A, Nedoluzhko A, Lorenzen E, Lopez P, McDonald HG, Scott E, Tikhonov A, Stafford TW, Shapiro B, Willerslev E, Prokhortchouk E, Orlando L. 2015. Pros and cons of methylation-based enrichment methods for ancient DNA. Scientific Reports 5, Article number: 11826 doi:10.1038/srep11826. (PR, CO)

Sigsgaard EE, Carl H, Møller PR, Thomsen PF (2015). Monitoring the near-extinct European weather loach Misgurnus fossilis in Denmark by combining traditional fishing surveys and environmental DNA from water samples. Biological Conservation 183, 46-52. (PR)

Sinding, M. H. S. (2015). Den grønlandske slædehunde genetiske oprindelse og båndet til ulven. Tidsskriftet GRØNLAND. Det Grønlandske Selskab. Årgang 63(4), 188-191. (In Danish).

Sinding M-HS, Arneborg J, Nyegaard G, Gilbert MTP. Ancient DNA unravels the truth behind the controversial GUS Greenlandic Norse fur samples: the bison was a horse, and the muskox and bears were goats. Journal of archaeological science, V.53, pp.297-303, (2015) 0305-4403.

Sonne C, Dyck M, Riget F, Bech-Jensen J-E, Hyldstrup L, Letcher R, Gustavson K, Gilbert T, Dietz R. Globally used chemicals and penile density in Canadian and Greenland polar bears. Environmental Research 137:287-291, 2015.

Sveegaard S, Galatius A, Dietz R, Kyhn L, Koblitz JC, Amundin M, Nabe-Nielsen J, Sinding M-HS,  Andersen LW, Teilmann J. Defining management units for cetaceans by combining genetics, morphology, acoustics and satellite tracking. Global Ecology and Conservation. Volume 3, January 2015, Pages 839–850.

Thomsen PF, Willerslev E (2015). Environmental DNA – an emerging tool in conservation for monitoring past and present biodiversity. Biological Conservation 183, 4-18. PR

Valentini A, Taberlet P, Miaud C, Civade R, Herder J, Thomsen PF, Bellemain E, Besnard A, Coissac E, Boyer F, Gaboriaud C, Jean P, Poulet N, Roset N, Copp GH, Geniez P, Pont D, Argillier C, Baudoin J-M, Peroux T, Crivelli AJ, Olivier A, Acqueberge M, Le Brun M, Møller PR, Willerslev E, Dejeanet T. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology. doi:10.1111/mec.13428. 2015. PR

Vestergaard JS, Twomey E, Larsen R, Summers K, Nielsen R. Number of genes controlling a quantitative trait in a hybrid zone of the aposematic frog Ranitomeya imitator. Proceedings of the Royal Society of London B: Biological Sciences 282 (1807), pages 20141950, 2015.

Vieira FG, Lassale F, Korneliussen TS, Fumagalli M (2015). Improving the estimation of genetic distances from Next-Generation Sequencing data. Biological Journal
of the Linnean Society 117:139-149. (PR)

Vinner L, Mourier T, Friis-Nielsen J, Gniadecki R, Dybkaer K, Rosenberg J et al. (2015). Investigation of Human Cancers for Retrovirus by Low-Stringency Target Enrichment and High-Throughput Sequencing. Scientific Reports, 5.

Wales N, Carøe C, Sandoval-Velasco M, Gamba C, Barnett R, Samaniego JA, Ramos Madrigal J, Orlando L, Gilbert MTP. New insights on single-stranded DNA library preparation. BioTechniques 59 (6):368-371. 2015. PR

Welker F, Collins MJ, Thomas JA, Wadsley M, Brace S, Capellini E, Turvey ST, Reguero M, Gelfo J, Kramarz A, Burger J, Thomas-Oates J, Ashford DA, Ashton P, Rowsell K, DM Porter, Kessler B, Fisher R, Baessmann C, Kaspar S, Olsen J, Kelstrup C, Mullin V, Hofreiter M, Willerslev E, Hublin J-J, Orlando O, Southon J, Barnes I, MacPhee RDE. Ancient proteins resolve the evolutionary history of Darwin’s South American ungulates. Nature, Volume:522, Pages: 81–84. 04 June 2015. DOI:doi:10.1038/nature14249

Winther RG, Giordano R, Edge MD, Nielsen R. The mind, the lab, and the field: Three kinds of populations in scientific practice. Studies in History and Philosophy of Science. Part C: Studies in History and Philosophy of Biological and Biomedical Sciences. Vol. 52, pp. 12-21, 2015.

Winther RG, Millstein RL, Nielsen R. Introduction: Genomics and philosophy of race. 2015.

Zepeda Mendoza LM, Sicheritz-Ponten T, Gilbert MTP (2015). Environmental genes and genomes: Understanding the differences and challenges in the approaches and software for their analyses. Briefings in Bioinformatics doi: 10.1093/bib/bbv001. (PR, OA)

Ziesemer KA, Mann AE, Sankaranarayanan K, Schroeder H, Ozga AT, Brandt BW et al.  Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. Scientific Reports, 516498–19. 2015. (PR, OA)