Publications – University of Copenhagen

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GeoGenetics > Publications

Publications

(Updated 07.08.2017)

Publications 2017

Bendtsen J, Mortensen J, Lennert K, Ehn JK, Boone W, Galindo V, Hu Y, Dmitrenko IA, Kirillov SA, Kjeldsen KK, Kristoffersen Y, Barber DG & Rysgaard S. Sea ice breakup and marine melt of a retreating tidewater outlet glacier in northeast Greenland (81°N). Scientific Reports 7, Article number: 4941 (2017). doi:10.1038/s41598-017-05089-3

Bush A, Sollmann R, Wilting A, Bohmann K, Cole B, Balzter H, Martius C, Zlinszky A, Calvignac-Spencer S, Cobbold CA, Dawson TP, Emerson BC, Ferrier S, Gilbert MTP, Herold M, Jones L, Leendertz FH, Matthews L, Millington JDA, Olson JR, Ovaskainen O, Raffaelli D, Reeve R, Rödel M-O, Rodgers TW, Snape S, Visseren-Hamakers I, Vogler AP, White PCL, Wooster MJ and Yu D. (2017). Connecting Earth Observation to High-Throughput Biodiversity Data. Nature Ecology & Evolution. ISSN 2397-334X (In press)

Jensen JF, Andreasen C, Fleischer-Lyberth P, Løgstrup L, Holt Poulsen H, Ólafson OR, Løventoft-Jessen A-C, Barr S, Meldgaard M. Nomination of Aasivissuit - Nipisat, Inuit hunting ground between Ice and Sea, for inclusion on the world heritage list. pp.192. http://snm.ku.dk/SNMnyheder/alle_nyheder/2017/2017.1/levende-groenlandsk-kulturlandskab-nomineret-til-verdensarv/Aasivissuit-Nipisat_web.pdf.

Jensen JF and Grønnow B: 3.2 Qajaa revisited: Integrating technology studies and spatial analysis in archaeology. In: Sørensen M and Pedersen KB: Problems in Palaeolithic and Mesolithic research, Arkæologiske Studier, vol. 12. Pp. 189-204. http://www.academicbooks.dk/search/apachesolr_search/9788789500270

Kampmann M-L, Schnell IB, Jensen RH, Axtner J, Sander AF, Hansen AJ, Bertelsen MF, Greenwood AD, Gilbert MTP, Wilting A. Leeches as a source of mammalian viral DNA and RNA—a study in medicinal leeches. European Journal of Wildlife Research. Short Communication. April 2017, 63:36. DOI: 10.1007/s10344-017-1093-6

Kristiansen K, Allentoft ME, Frei KM, Iversen R, Johannsen NN, Kroonen G, Pospieszny L, Price TD, Rasmussen S, Sjögren K-G, Sikora M and Willerslev E. Re-theorising mobility and the formation of culture and language among the Corded Ware Culture in Europe. Antiquity,  Vol. 91, Issue 356, April 2017, pp. 334-347. (OA)(PR)

Larsen NK, Strunk A, Levy LB, Olsen J, Bjørk AA, Lauridsen TL, Jeppesen E, Davidson TA. Strong altitudinal control on local glacier response to Holocene climate change in southwest Greenland. Quaternary Science Reviews. 168 p.69-78. https://doi.org/10.1016/j.quascirev.2017.05.008

Larson WA, Limborg MT, McKinney GJ, Schindler DE, Seeb JE, Seeb LW (2017). Genomic islands of divergence linked to ecotypic variation in sockeye salmon. Molecular Ecology 26: 554–570. doi: 10.1111/mec.13933. (PR)

Librado P, Cristina G, Gaunitz C, Der Sarkissian C, PruvostM, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK, Povolotskaya IS, Seguin-Orlando A, Lepetz S, Neuditschko M, Thèves C, Alquraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort H-P, Benecke N, Hofreiter M, Ludwig A, Keyser C, Marques-Bonet T, Ludes B, Crubézy E, Leeb T, Willerslev E, Orlando L. Ancient genomic changes associated with domestication of the horse. Science 28 Apr 2017:
Vol. 356, Issue 6336, pp. 442-445. DOI: 10.1126/science.aam5298 (OA, PR)

Marcer MPA, Stentoft E, Bjerre E, Cimoli E, Bjørk AA, Stenseng L and Maguth H. Three Decades of Volume Change of a Small Greenlandic Glacier Using Ground Penetrating Radar, Structure from Motion and Aerial Photogrammetry. Arctic, Antarctic, and Alpine Research (in print).

Mollerup S, Fridholm H, Vinner L, Kjartansdóttir K, Friis-Nielsen J, Asplund M, et al. Cutavirus in Cutaneous Malignant Melanoma. Emerg Infect Dis. 2017;23(2):363-365. https://wwwnc.cdc.gov/eid/article/23/2/16-1564_article

Morard R, Lejzerowicz F, Darling KF, Lecroq-Bennet B, Pedersen MW, Orlando L, Pawlowski J, Mulitza S, de Vargas C and Kucera M. 2017. Plankton-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology. Biogeosciences, bg-2016-486. http://www.biogeosciences-discuss.net/bg-2016-486/

Motyka RJ, Cassotto R, Truffer M, Kjeldsen KK, van As D, Korsgaard NJ, Fahnestock M, Howat I, Langen PL, Mortensen J, Lennert K, Rysgaard S. Asynchronous behavior of outlet glaciers feeding Godthåbsfjord (Nuup Kangerlua) and the triggering of Narsap Sermia's retreat in SW Greenland. In: Journal of Glaciology, Vol. 63, No. 238, 04.2017, p. 288-308.

Nielsen R, Akey JM, Jakobsson M, Pritchard JK, Tishkoff S, Willerslev E. Tracing the peopling of the world through genomics. Nature 541, 302–310 (19 January 2017). doi:10.1038/nature21347. (PR)

Parducci L, Bennett KD, Ficetola GF, Greve Alsos I, Suyama Y, Wood JR and Pedersen MW. 2017. Ancient plant DNA in lake sediments. The New phytologist, 214(3), pp.924–942. http://onlinelibrary.wiley.com/doi/10.1111/nph.14470/full

Pereira RJ, Sasaki MC, Burton RS. Adaptation to a latitudinal thermal gradient within a widespread copepod species: the contributions of genetic divergence and phenotypic plasticity. Published 26 April 2017.DOI: 10.1098/rspb.2017.0236. http://rspb.royalsocietypublishing.org/content/284/1853/20170236

Sawafuji R, Cappellini E, Nagaoka T, Fotakis AK, Jersie-Christensen RR, Olsen JV, Hirata K, Ueda S. 2017. Proteomic profiling of archaeological human bone. R. Soc. open sci. 4: 161004. http://dx.doi.org/10.1098/rsos.161004

Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar-Gal GK, Brem G, Brooks SA, Distl O, Fries R, Finno CJ, Gerber V, Haase B, Jagannathan V, Kalbfleisch T, Leeb T, Lindgren G, Lopes MS, Mach N, da Câmara Machado A, MacLeod JN, McCoy A, Metzger J, Penedo C, Polani S, Rieder S, Tammen I, Tetens J, Thaller G, Verini-Supplizi A, Wade CM, Wallner B, Orlando L, Mickelson JR and McCue ME: Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. BMC Genomics 201718:565, 2017. https://doi.org/10.1186/s12864-017-3943-8

Schubert M, Mashkour M, Gaunitz C, Fagesa A, Seguin-Orlandoa A, Sheikhi S, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS,  Chuang R, Ermini L, Gamba C, Weinstock J, Vedat O, Orlando L. Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages. Journal of Archaeological Science. Volume 78, February 2017, Pages 147–157. http://dx.doi.org/10.1016/j.jas.2016.12.005. (PR, CO)

Sigsgaard EE, Nielsen IB, Carl H, Krag MA, Knudsen SW, Xing Y, Holm‑Hansen TH, Møller PR, Thomsen PF. Seawater environmental DNA reflects seasonality of a coastal fish community. Marine Biology, (2017) 164:128. DOI 10.1007/s00227-017-3147-4

Ullah I, Olofsson JK, Margaryan A, Ilardo M, Ahmad H, Sikora M, Hansen AJ, Nadeem MS, Fazal N, Ali M, Buchard A, Hemphill BE, Willerslev E and Allentoft ME. High Y-chromosomal Differentiation Among Ethnic Groups of Dir and Swat Districts, Pakistan. Annals of Human Genetics (2017), 1–15

Publications 2016

Aizpurua O, Alberdi A, Aihartza J, Garin I (2016). Fishing Technique of Long-Fingered Bats Was Developed from a Primary Reaction to Disappearing Target Stimuli. PLoS ONE 11(12): e0167164. doi:10.1371/journal.pone.0167164. (PR, OA)

Alberdi, O Aizpurua, J Aihartza, I Garin (2016). Ecology, biogeography and evolutionary history of the alpine long-eared bat Plecotus macrobullaris. Galemys. (OA)

Alberdi A, Aizpurua O, Bohmann K, Zepeda-Mendoza ML, Gilbert MTP (in press). Do vertebrate gut metagenomes confer rapid ecological adapataion? Trends in Ecology and Evolution

Alfaro-Núñez A, Bojesen AM, Bertelsen MF, Wales N, Balazs GH, and Gilbert MTP. Further evidence of Chelonid herpesvirus 5 (ChHV5) latency: high levels of ChHV5 DNA detected in clinically healthy marine turtles. PeerJ 4:e2274, 2016.

Almeida D, Maldonado E, Khan I, Silva L, Gilbert MTP, Zhang G, Jarvis ED, O’Brien S, Johnson W, Antunes A (in press). Whole genome identification, phylogeny and evolution of the cytochrome P450 family 2 (CYP2) sub-families in birds. Genome Biology and Evolution

Bangsgaard P, Yeomans L. Zooarchaeological perspectives on rural economy and landscape use in the 18th century Qatar. In: S McPhillips and P. Woodsworth (eds.), The Materiality of the Rural Islamic World: archaeological and historical approaches. Philadelphia: University of Pennsylvania Press, chapter 5. 2016. (CO)

Bangsgaard P. Fauna through the Ages, a view from the Aitolian Heartland. In: S. Dietz and L. Kolonas (eds.):Chalkis Aitolias III, The Emporion. Fortification systems at Aghia Triada and the Late Classical and Hellenistic habitation in area III. The fortifications at Pangali, Monographs of the Danish Institute at Athens, vol. 7.3, Århus: Århus University Press, pp. 239-252. 2016.

Barnes CJ. Unexpectedly high beta-diversity of root-associated fungal communities in the Bolivian Andes. Frontiers in Microbiology. (2016). doi:10.3389/fmicb.2016.01377

Barnes CJ, van der Gast CJ, Burns CA, McNamara NP & Bending GD. Temporally variable geographical distance effects contribute to the assembly of root-associated fungal communities. Frontiers in Microbiology 195 (2016), doi:10.3389/fmicb.2016.00195

Barnett R, Zepeda Mendoza ML, Soares AER, Ho SYW, Zazula G, Yamaguchi N, Shapiro B, Kirillova IV, Larson G, Gilbert MTP (in press). Mitogenomics of the extinct cave lion, Pathera spelaea (Goldfuss, 1810) resolve its position within the Pathera cats. Open Quaternary

Bayerova Z, Janova E, Matiasovic J, Orlando L, Horin P. (2016). Positive selection in the SLC11A1 gene in the family Equidae. Immunogenetics 68:353-64.

Boessenkool S, Hanghøj K, Nistelberger HM, Der Sarkissian C, Gondek A, Orlando L, Barrett JH, Star B. Combining bleach and mild pre-digestion improves ancient DNA recovery from bones. Mol Ecol Resour. 2016 Oct 28. DOI: 10.1111/1755-0998.12623, (PR, CO)

Cammen KM, Andrews KR, Carroll EL, Foote AD, Humble E, Khudyakov JI, Louis M, Mcgowen MR, Olsen MT & Cise AMV 2016. Genomic Methods Take the Plunge: Recent Advances in High-Throughput Sequencing of Marine Mammals. Journal of Heredity, s. 1-15. DOI: 10.1093/jhered/esw044

Chaverri G, Garin I, Alberdi A, Jimenez L, Castillo-Salazar C, Aihartza J (2016). Unveiling the Hidden Bat Diversity of a Neotropical Montane Forest. PLoS ONE, e0162712. (PR, OA).

Christensen EAF, Skovrind M, Olsen MT, Carl H, Nielsen PG & Møller PR. 2016. Hatching success in brackish water of Perca fluviatilis eggs obtained from the western Baltic Sea. Cybium, vol 40(2), s. 133-138.

Crawford JE, Riehle MM, Markianos K, Bischoff E, Guelbeogo WM, Gneme A, Sagnon N'F, Vernick KD, Nielsen R, Lazzaro BP. Evolution of GOUNDRY, a cryptic subgroup of Anopheles gambiae sl, and its impact on susceptibility to Plasmodium infection. Molecular ecology, 2016. doi: 10.1111/mec.13572. (OA)

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 KA, Scheu A, Beneke N, Ludwig A, Cooper A, Willerslev E, Orlando L. Experimental conditions improving in-solution target enrichment for ancient DNA. Mol Ecol Resour. 2016 Aug 27.

Demarchi B, Hall S, Roncal-Herrero T, Freeman CL, Woolley J, Crisp MK, Wilson J, Fotakis A, Fischer R, Kessler BM, Jersie-Christensen RR, Olsen JV, Haile J, Thomas J, Marean CW, Parkington J, Presslee S, Lee-Thorp J, Ditchfield P, Hamilton JF, Ward MW, Wang CM, Shaw MD, Harrison T, Domínguez-Rodrigo M, MacPhee RDE, Kwekason A, Ecker M,
Horwitz LK, Chazan M, Kröger R, Thomas-Oates J, Harding JH, Cappellini E, Penkman K,
& Collins MJ. Protein sequences bound to mineral surfaces persist into deep time. eLife 2016;5:e17092 (published 27. September 2016).

Derst C, Dircksen H, Meusemann K, Zhou X, Liu S, & Predel R (2016). Evolution of neuropeptides in non-pterygote hexapods. BMC Evolutionary Biology, 16(1), 51. http://doi.org/10.1186/s12862-016-0621-4. (PR)

Ersmark E, Klütsch CFC, Chan YL, Sinding M-HS, Fain SR, Illarionova NA, Oskarsson M, Uhlén M,  Zhang Y-p, Dalén L, Savolainen P. From the Past to the Present: Wolf Phylogeography and Demographic History Based on the Mitochondrial Control Region. Front. Ecol. Evol., 02 December 2016. http://dx.doi.org/10.3389/fevo.2016.00134

Fernandez R, Schubert M, Vargas AM, Brownlow A, Vikingsson 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. 2016. A genome-wide catalogue of single nucleotide polymorphisms in white-beaked and atlantic white-sided dolphins. Mol Ecol Resour, Volume 16, Issue 1, pages 266–276, January 2016. Article first published online 29 May 2015, DOI: 10.1111/1755-0998.12427.

Fietz K, Galatius A, Teilmann J, Dietz R, Frie AK, Klimova A, Palsbøll PJ, Jensen LF, Graves J, Hoffman JI & Olsen MT. Shift of grey seal subspecies boundaries in response to climate, culling and conservation. Molecular Ecology, vol 25, nr. 17, s. 4097–4112. 2016. DOI: 10.1111/mec.13748.

Finch BW, Hunter ND, Winkelmann I, Manzano-Vargas K, Njoroge P, Fjeldå J, Gilbert MTP (2016). Redefining the taxonomy of the all-black and pied boubous (Lanarius spp.) in coastal Kenya and Somalia. Bull B.O.C 136:74-85

Flensted KK, Ejrnæs R, Eskildsen A, Bruun HH, Thomsen PF, Heilmann-Clausen J (2016). Red-listed species and forest continuity - A multi-taxon approach to conservation in temperate forests. Forest Ecology and Management 378, 144-159. (PR)

da Fonseca RR, Albrechtsen A, Themudo GE, Ramos-Madrigal J, Sibbesen JA, Maretty L, Zepeda-Mendoza ML, Campos PF, Heller R, Pereira RJ. Next-generation biology: Sequencing and data analysis approaches for non-model organisms. Marine Genomics, Available online 13 May 2016, ISSN 1874-7787, http://dx.doi.org/10.1016/j.margen.2016.04.012. (PR, OA)

Foote AD, Nagarjun V, Avila-Arcos MC, Baird R, Durban J, Morin P, Fumagalli M, Gibbs R, Hanson B, Korneliussen T, Martin MD, Robertson K, Sousa V, Vieira F, Vinar T, Wade P, Worley K, Excoffier L, Gilbert MTP, Wolf J (in press). Genome-culture coevolution promotes rapid divergence in the killer whale. Nature Communications

Friis-Nielsen J, Kjartansdóttir KR, Mollerup S, Asplund M, Mourier T, Jensen RH, Hansen TA, Rey-Iglesia A, Richter SR, Nielsen IB, Alquezar-Planas DE, Olsen PV, Vinner L, Fridholm H, Nielsen LP, Willerslev E, Sicheritz-Pontén T, Lund O, Hansen AJ, Izarzugaza JM, Brunak S. Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers. Viruses. 2016 Feb 19;8(2). pii: E53. doi: 10.3390/v8020053.

Gamba C, Hanghøj K, Gaunitz C, Alfarhan A, Alquraishi S, Al-Rashed K, Bradley D, Orlando L. 2015. Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing. Molecular Ecology Resources, Volume 16,  Issue 2, pages 459–469, March 2016. Article first published online: 15 Oct 2015, DOI: 10.1111/1755-0998.12470

Gelabert P, Sandoval-Velasco M, Olalde I, Fregel R, Rieux A, Escosa R, Aranda C, Paaijmans K, Mueller I, Gilbert MTP, Lalueza-Fox X (in press). Mitochondrial DNA from the eradicated European Plasmodium vivax and P. falciparum from 70-year–old slides from the Ebro Delta in Spain. PNAS. 113(41), 11495–11500, doi: 10.1073/pnas.1611017113. (PR, OA)

Gilbert MTP (in press). Documenting DNA from the dust. Molecular Ecology

Goldberg CS, Turner CR, Deiner K, Klymus KE, Thomsen PF, Murphy MA, Spear SF, McKee A, Oyler-McCance SJ, Cornman RS, Laramie MB, Mahon AR, Lance RF, Pilliod DS, Strickler KM, Waits LP, Fremier AF, Takahara T, Herder J, Taberlet P (2016). Critical considerations for the application of environmental DNA methods to detect aquatic species. Methods in Ecology and Evolution 7, 1299–1307. (PR)

Grealy A, Macken A, Allentoft ME, Rawlence NJ, Reed E, Bunce M. An assessment of ancient DNA preservation in Holocene–Pleistocene fossil bone excavated from the world heritage Naracoorte Caves, South Australia. Journal of Quaternary Science, 2016. DOI: 10.1002/jqs.2830. (OA)

Grealy A, Phillips M, Miller G, Gilbert MTP, Rouillard J-M, Lambert D, Bunce M, Haile J (in press). Eggshell palaeogenomics: palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshells. Molecular Phylogenetics and Evolution. (PR)

Guillot G, Jónsson H, Hinge A, Manchih N, Orlando L. Accurate continuous
geographic assignment from low- to high-density SNP data. Bioinformatics. 2016
Apr 1;32(7):1106-8. doi: 10.1093/bioinformatics/btv703. PubMed PMID: 26615214.

Hanghøj K, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E, Orlando L. Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX. Mol Biol Evol. 2016 Sep 13. pii: msw184. (PR, CO)

Hansen TA, Joshi T, Larsen AR, Andersen PS, Harms K, Mollerup S, Willerslev E, Fuursted K, Nielsen LP, Hansen AJ. Vancomycin gene selection in the microbiome of urban Rattus norvegicus from hospital environment. Evolution, Medicine and Public Health, 12. July 2016. doi:10.1093/emph/eow021

Hansen TA, Mollerup S, Nguyen N-p, White NE, Coghlan M, Alquezar-Planas DE, Joshi T, Jensen RH, Fridholm H, Kjartansdóttir KR,  Mourier T, Warnow T, Belsham GJ, Bunce M, Willerslev E, Nielsen LP, Vinner L and Hansen AJ. High diversity of picornaviruses in rats from different continents revealed by deep sequencing. Emerging Microbes & Infections (2016) 5, e90; doi:10.1038/emi.2016.90. Published online 17 August 2016.

Heide-Jørgensen MP, Sinding MHS, Nielsen NH, Rosing-Asvid A & Hansen RG. (2016). Large numbers of marine mammals winter in the North Water polynya. Polar Biology, 1-10. DOI:10.1007/s00300-015-1885-7. (PR)

Hervella M, Svensson E, Alberdi A, Gunther T, Izagirre N, Munters A, Alonso S, Ioana M, Ridiche F, Soficaru A, Jakobsson M, Netea M, De la Rua C (2016). The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa. Scientific Reports, 6:25501. (PR, OA)

Houmark-Nielsen M, Bennike O, Lemdahl G & Luthgens C. Evidence of ameliorated Middle Weichselian climate and sub-arctic environment in the western Baltic region: coring lake sediments at Klintholm, Møn, Denmark. Boreas, Vol. 45, pp. 347-359. 10.1111/bor.12159.

Huber CD, DeGiorgio M, Hellmann I, Nielsen R. Detecting recent selective sweeps while controlling for mutation rate and background selection. Molecular ecology 25 (1), 142-156, 2016. (OA)

Imsland F, McGowan K, Rubin CJ, Henegar C, Sundström E, Berglund J, Schwochow D, Gustafson U, Imsland P, Lindblad-Toh K, Lindgren G, Mikko S, Millon L, Wade C, Schubert M, Orlando L, Penedo MC, Barsh GS, Andersson L. (2016). Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses. Nat Genet. 48:152-8.

Ingólfsson Ó, Benediktsson ÍÖ, Schomacker A, Kjær KH, Brynjólfsson S, Jónsson SA, Korsgaard NJ & Johnson MD. 2016. Glacial geological studies of surge-type glaciers in Iceland — Research status and future challenges. Earth-Science Reviews, 152, 37-69. http://dx.doi.org/10.1016/j.earscirev.2015.11.008. (PR, CO)

Jensen JF. Greenlandic Dorset. The Oxford Handbook of the Prehistoric Arctic. Edited by Max Friesen and Owen Mason. P. 31 DOI: 10.1093/oxfordhb/9780199766956.013.56

Jensen JF, Gulløv HC, Appelt M. 3.1. Les premiers hommes du Groenland: des paléoesquimaux aux Inuit. In: Valérie Masson-Delmotte, Émilie Gauthier, David Grémillet, Jean-Michel Huctin, Didier Swingedouw (eds.): Le Groenland, Climat, écologie, société, CNRS Editions. pp. 201-206. 2016.

Khan SA, Sasgen I, Bevis M, van Dam T, Bamber JL, Wahr J, Willis M, Kjær KH, Wouters B, Helm V, Csatho B, Flemming K, Bjørk AA, Aschwanden A, Knudsen P &  Kuipers Munneke P. Geodetic measurements reveal similarities between Last Glacial Maximum and present-day mass loss from the Greenland ice sheet. Science Advances, vol. 2, no. 9. 2016.

Korsgaard, NJ, Nuth C, Khan SA, Kjeldsen KK, Bjørk AA, Schomacker A & Kjær KH. Digital elevation model and orthophotographs of Greenland based on aerial photographs from 1978–1987. 10 May 2016 In : Scientific Data. 3, 160032, 160032

Larsen NK, Find J, Kristensen A, Bjørk AA, Kjeldsen KK, Odgaard BV, Olsen J, Kjær KH. Holocene ice marginal fluctuations of the Qassimiut lobe in South Greenland. Nature Scientific Reports Vol 6, 22362, p. 1-11, 2016. (OA)

Larsen NK, Funder S, Linge H, Möller P, Schomacker A, Fabel D, Xu S & Kjær KH. (2016). A Younger Dryas re-advance of local glaciers in North Greenland. Quaternary Science Reviews 147, 47-58. http://dx.doi.org/10.1016/j.quascirev.2015.10.036. (PR, CO)

Larson WA, McKinney GJ, Limborg MT, Everett MV, Seeb LW, Seeb JE. (2016) Identification of multiple QTL hotspots in sockeye salmon (Oncorhynchus nerka) using genotyping-by-sequencing and a dense linkage map. Journal of Heredity 107: 122-133. https://academic.oup.com/jhered/article/107/2/122/2622865/Identification-of-Multiple-QTL-Hotspots-in-Sockeye (PR)

Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E and Orlando L.  Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol, (2016). doi:10.1093/sysbio/syw059. First published online July 5, 2016. (PR, CO)

Librado P, Fages A, Gaunitz C, Leonardi M, Wagner S, Khan N, Hanghøj K, Alquraishi SA, Alfarhan AH, Al-Rasheid KA, Der Sarkissian C, Schubert M, Orlando L. The Evolutionary Origin and Genetic Makeup of Domestic Horses. Genetics. 2016 Oct;204(2):423-434. DOI: 10.1534/genetics.116.194860. (PR, CO)

Limborg MT et al. (2016). Sorting duplicated loci disentangles complexities of polyploid genomes masked by genotyping by sequencing. Molecular Ecology doi:10.1111/mec.13601. (PR)

Limborg MT, Waples RK, Allendorf FW, Seeb JE (2015). Linkage mapping reveals strong chiasma interference in sockeye salmon: Implications for interpreting genomic data. G3: GENES, GENOMES, GENETICS 5:2463-2473. http://www.g3journal.org/content/5/11/2463.full   (PR)

Limborg MT, McKinney GJ, Seeb LW, Seeb JE (2016). Recombination patterns reveal information about centromere location on linkage maps. Molecular Ecology Resources 16: 655–661. http://onlinelibrary.wiley.com/doi/10.1111/1755-0998.12484/abstract (PR, OA)

Liu S, Wang X, Xie L, Tan M, Li Z, Su X, … Zhou X (2016). Mitochondrial capture enriches mito-DNA 100 fold, enabling PCR-free mitogenomic biodiversity analysis. Molecular Ecology Resource,16(2), 470–479. http://doi.org/10.1111/1755-0998.12472. (PR, OA)

Louvel G, Der Sarkissian C, Hanghøj K, Orlando L. metaBIT, an integrative and automated metagenomic pipeline for analysing microbial profiles from high-throughput sequencing shotgun data. Mol Ecol Resour. 2016 Nov;16(6):1415-1427. DOI: 10.1111/1755-0998.12546. (PR)

Machado JM, Johnson WE, Gilbert MTP, Zhang G, Jarvis ED, O’Brien S, Antunues A (in press). Bone-associated gene evolution and the origin of flight in birds. BMC Genomics.

Machguth H, Thomsen HH, Weidick A, Abermann J, Ahlstrøm AP, Andersen ML, Andersen SB, van As D, Bjørk AA, Box A, Braithwaite RJ, Bøggild CE, Citterio M, Clement P, Colgan W, Fausto RS, Gleie K, Hasholt B, Hynek B, Knudsen NT, Larsen SH, Mernild SH, Oerter H, Olesen OB, Steffen K, Stober M, Sugiyama S & van de Wal RS. Database of Greenland surface mass balance observations from the ice sheet ablation area and the local glaciers. Journal of Glaciology (in press).

MacHugh DE, Larson G, Orlando L. Taming the Past: Ancient DNA and the Study of Animal Domestication. Annu Rev Anim Biosci. 2016 Oct 28.

Malaspinas A-S, Westaway MC, Muller C, Sousa VC, Lao O, Alves I, Bergström A, Athanasiadis G, Cheng JY, Crawford JE, Heupink TH, Macholdt E, Peisch S, Rasmussen S, Schiffels S, Subramanian S, Wright JL, Albrechtsen A, Barbieri C, Dupanloup I, Eriksson A, Margaryan A, Moltke I, Pugach I, Korneliussen TS, Levkivskyi IP, Moreno-Mayar JV, Ni S, Racimo F, Sikora M, Xue Y, Aghakhanian FA, Brucato N, Brunak S, Campos PF, Clark W, Ellingvåg S, Fourmile G, Gerbault P, Injie D, Koki G, Leavesley M, Logan B, Lynch A, Matisoo-Smith EA, McAllister PJ, Mentzer AJ, Metspalu M, Migliano AB, Murgha L, Phipps ME, Pomat W, Reynolds D, Ricaut F-X, Siba P, Thomas MG, Wales T, Wall CM,  Oppenheimer SJ, Tyler-Smith C, Durbin R, Dortch J, Manica A, Schierup MH, Foley RA, Lahr MM, Bowern C, Wall JD, Mailund T, Stoneking M,  Nielsen R, Sandhu MS, Excoffier L, Lambert DM, & Willerslev E. A genomic history of Aboriginal Australia. Nature, 22. September 2016.

Martin MD, Olsen MT, Samaniego JA, Zimmer EA, Gilbert MTP (in press). The population genomic basis of geographic differentiation in North American common ragweed (Ambrosia artemisiifolia L). Ecology and Evolution

Martin MD, Vieira FG, Ho SYW, Wales N, Schubert M, Seguin-Orlando A, Ristaino JB, Gilbert MTP (2016). Genomic characterization of a South American Phytophthora hybrid mandates reassessment of the geographic origins of Phytophthora infestans. Molecular Biology and Evolution 33:478-491. DOI:10.1093/molbev/msv241. (PR, CO)

McKinney GJ, Seeb LW, Larson WA, Gomez-Uchida D, Limborg MT, Brieuc MSO, Everett MV, Naish KA, Waples RK, Seeb JE (2016). An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha). Molecular Ecology Resources 16: 769–783. (PR)

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 CJ, Wheeler JC, Borrero L, Austin JJ, Cooper A. Synergistic roles of climate warming and human occupation in Patagonian megafaunal extinctions during the Last Deglaciation. Sci Adv. 2016 Jun 17;2(6):e1501682.

Mollerup S, Friis-Nielsen J, Vinner L, Hansen TA, Richter SR, Fridholm H, Herrera JA, Lund O, Brunak S, Izarzugaza JM, Mourier T, Nielsen LP, Hansen AJ. Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing. J Clin Microbiol. 2016 Apr;54(4):980-7. doi: 10.1128/JCM.02723-15. Epub 2016 Jan 27.

Monadjem A, Joubert C, Richards L, Nielsen IB, Nielsen M, Kjartansdóttir KR, Bohmann K, Mourier T & Hansen AJ (2016). First record of Vespertilio murinus from the Arabian Peninsula. Vespertilio 18, xx-xx. In press.

Muresan IS, Khan SA, Aschwanden A, Khroulev C, van Dam T, Bamber J, van den Broeke M, Wouters B, Munneke PK, Kjær KH. Modelled glacier dynamics over the last quarter of a century at Jakobshavn Isbræ. The Cryosphere vol. 10, p. 597-611 2016. (PR)

Neves JMM, Lima SMQ, Mendes LF, Torres RA, Pereira RJ, Mott T. Population Structure of the Rockpool Blenny Entomacrodus vomerinus Shows Source-Sink Dynamics among Ecoregions in the Tropical Southwestern Atlantic. Laudet V, ed. PLoS ONE. 2016;11(6):e0157472. doi:10.1371/journal.pone.0157472. (PR, OA)

Newbold LK, Burthe SJ, Oliver AE, Gweon HS, Barnes CJ, Daunt F and van der Gast CJ. Helminth burden and ecological factors associated with alterations in wild host gastrointestinal microbiota. The ISME Journal. (2016).

Nielsen SA & Sandoval-Velasco M (2016). Crossing disciplinary lines: reconciling social and genomic perspectives on the histories and legacies of the transatlantic trade in enslaved Africans. New Genetics and Society. 35(2), 149-185, DOI:10.1080/14636778.2016.1197109. (PR)

Odumosu, T., & Schroeder, H (2015). Memorializing Contested Landscapes. Journal of African Diaspora Archaeology and Heritage, 4(3), 189–194. http://doi.org/10.1080/21619441.2015.1124592. (PR)

Olsen MT, Galatius A, Biard V, Gregersen K & Kinze CC. The forgotten type specimen of the grey seal [Halichoerus grypus (Fabricius, 1791)] from the island of Amager, Denmark. Zoological Journal of the Linnean Society, 2016. DOI: 10.1111/zoj.12426

Orlando L. Back to the roots and routes of dromedary domestication. Proc Natl Acad Sci USA. 2016 Jun 14;113(24):6588-90.

Pagani L et al. Genomic analyses inform on migration events during the peopling of Eurasia. Nature  538, 238–242 (13 October 2016) doi:10.1038/nature19792.

Parker CC, Gopalakrishnan S, Carbonetto P, Gonzales NM, Leung E, Park YJ, Aryee E,  Davis J, Blizard DA, Ackert-Bicknell CL, Lionikas A, Pritchard JK, Palmer AA. Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice. Nature Genetics:48. (PR)

Pauli T, Vedder L, Dowling D, Petersen M, Meusemann K, Donath A, Liu S, … Niehuis O (2016). Transcriptomic data from panarthropods shed new light on the evolution of insulator binding proteins in insects. BMC Genomics, 17(1), 861.http://doi.org/10.1186/s12864-016-3205-1. (PR, OA)

Pedersen MW, Ruter A, Schweger C, Friebe H, Staff RA, Kjeldsen KK, Mendoza MLZ, Beaudoin AB, Zutter C, Larsen NK, Potter BA, Nielsen R, Rainville RA, Orlando L, Meltzer DJ, Kjær KH, Willerslev E. Postglacial viability and colonization in North America’s ice-free corridor. Nature (2016), doi:10.1038/nature19085. Published online  10 August 2016.

Pereira RJ, Barreto FS, Pierce NT, Carneiro M, Burton RS (2016). Transcriptome-wide patterns of divergence during allopatric evolution. Molecular Ecology 25 (7): 1478-1493. (PR)

Pereira RJ, Martínez-Solano I, Buckley D. Hybridization during altitudinal range shifts: nuclear introgression leads to extensive cyto-nuclear discordance in the fire salamander. 6 February 2016. Mol. Ecol. DOI:10.1111/mec.13575. (PR)

Ramos-Madrigal J, Smith BD, Moreno-Mayar JV, Gopalakrishnan S, Ross-Ibarra J, Gilbert MTP, Wales N. Genome sequence of a 5,310-yaer-old maize cob provides insights into the early stages of maize domestication. Current Biology 26, 1–7. December 5, 2016.

Renaud G, Hanghøj K, Willerslev E, Orlando L. gargammel: a sequence simulator for ancient DNA. Bioinformatics. 2016 Oct 29.

Ribeiro ÂM, Foote AD, Kupczok A, Frazão B, Limborg MT, Piñeiro R, Abalde S, Rocha S,  da Fonseca RR 2016. Marine Genomics: News and Views. Marine Genomics, in press.

Richmond DJ, Sinding MHS, Gilbert MTP. The potential and pitfalls of de-extinction. Zoologica Scripta, 45(S1), 22-36. DOI:10.1111/zsc.12212. (PR, OA, CO)

Sanchez-Barreiro F, Vieira F, Martin MD, Haile J, Gilbert MTP, Wales N (in press). Characterizing restriction enzyme-associated loci in historic ragweed (Ambrosia artemisiifolia) voucher specimens using custom-designed RNAprobes. Molecular Ecology Resources.

Schubert M, Lindgreen S, Orlando L. (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes. 9:88. (PR, CO)

Seersholm FV, Pedersen MW, Søe MJ, Shokry H, Mak SST, Ruter A, Raghavan M, Fitzhugh W, Kjær KH, Willerslev E, Meldgaard M, Kapel CMO, Hansen AJ. DNA evidence of bowhead whale exploitation by Greenlandic Paleo-Inuit 4,000 years ago. Nature communications, 7, pp.1–9, 2016. (PR, OA)

Seki R, Li C, Fang Q, Hayashi S, Ewaga S, Hu J, Xu L, Pan H, Kondo M, Sato T, Matsubara H, Kamiyama N, Kijajima K, Saito D, Liu Y, Gilbert MTP, Zhou Q, Xu X, Shiroishi T, Irie N, Tamura K, Zhang G (in press). Functional roles of Aves class specific cis-regulatory elements on macroevolution of bird-specific features. Nature Communications.

Sigsgaard EE, Nielsen IB, Bach SS, Lorenzen ED, Robinson DP, Knudsen SW, Pedersen MW, Al Jaidah M, Orlando L, Willerslev E, Møller PR, Thomsen PF. Population characteristics of a large whale shark (Rhincodon typus) aggregation inferred from seawater environmental DNA. Nature Ecology & Evolution 1, Article number: 0004 (2016). (PR), (OA)

Sinding MHS, Gilbert MTP. The draft genome of extinct European aurochs and its implications for de-extinction. Open Quaternary, 2, p.7. DOI:http://doi.org/10.5334/oq.25.

Sinding M-HS, Tervo OM, Grønnow B, Gulløv HC, Toft PA, Bachmann L, Fietz K, Rekdal SL, Christoffersen MF, Heide-Jørgensen MP, Olsen MT & Foote AD. Sex determination of baleen whale artefacts: Implications for ancient DNA use in zooarchaeology. Journal of Archaeological Science: Reports, vol 10, s. 345-349, 2016. DOI:10.1016/j.jasrep.2016.11.001

Skovrind M, Olsen MT, Vieira F, Pacheco G, Carl H, Gilbert MTP, Møller PR (2016). Genomic population structure of freshwater resident and anadromous ide (Leuciscus idus) in north-western Europe. Ecology and Evolution 6:1064-1074.

Soares AER, Novak BJ, Haile J, Heupink T, Fjeldså J, Gilbert MTP, Poinar H, Church GM, Shapiro B (in press). Complete mitochondrial genomes of living and extinct pigeons revise the timing of the Columbiform radiation. BMC Evolutionary Biology.

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. Nat Commun. 2016 Oct 18;7:13158. doi: 10.1038/ncomms13158.

Spens J, Evans AR, Halfmaerten D, Knudsen SW, Sengupta ME, Mak SST, Sigsgaard EE, Hellström M (2016). Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol - Advantage of enclosed filter. Methods in Ecology and Evolution DOI: 10.1111/2041-210X.12683. (PR)

Thomsen PF, Jørgensen PS, Bruun HHK, Pedersen J, Riis-Nielsen T, Jonko K, Słowińska I, Rahbek C, Karsholt O. Resource specialists lead local insect community turnover associated with temperature – analysis of an 18-year full-seasonal record of moths and beetles. Journal of Animal Ecology 85, 251-261. 2016. (PR)

Thomsen PF, Møller PR, Sigsgaard EE, Knudsen SW, Jørgensen OA, Willerslev E: Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes. PLOS ONE, November 16, 2016,  http://dx.doi.org/10.1371/journal.pone.0165252. (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, Dejean T. Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, Vol. 25, No. 4, 2016, p. 929-942. (PR)

Vieira FG, Albrechtsen A, Nielsen R. Estimating IBD tracts from low coverage NGS data. Bioinformatics, Volume 32, Issue 14, Pp. 2096-2102.

Vieira FG, Lassalle F, Korneliussen TS, Fumagalli M. Improving the estimation of genetic distances from Next‐Generation Sequencing data. Biological Journal of the Linnean Society 117 (1), 139-149.

Wales N, Madrigal JR, Cappellini E, Baez AC, Castruita JAS, Romero-Navarro JA, Carøe C, Ávila-Arcos MC et al. The limits and potential of paleogenomic techniques for reconstructing grapevine domestication. Journal of Archaeological Science 72:57-70, 2016.

Wutke S, Andersson L, Benecke N, Sandoval-Castellanos E, Gonzalez J, Hallsson JH, Lõugas L, Magnell O, Morales-Muniz A, Orlando L, Pálsdóttir AH, Reissmann M, Muñoz-Rodríguez MB, Ruttkay M, Trinks A, Hofreiter M, Ludwig A. The origin of ambling horses. Curr Biol. 2016 Aug 8;26(15):R697-9.

Zepeda Mendoza ML, Bohmann K, Baez AC, Gilbert MTP (in press). DAMe: A toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses. BMC Research Notes.Til toppen