TY - JOUR AU - Ekblom, R. AU - Galindo, J. PY - 2011 DA - 2011// TI - Applications of next generation sequencing in molecular ecology of non-model organisms JO - Heredity VL - 107 UR - https://doi.org/10.1038/hdy.2010.152 DO - 10.1038/hdy.2010.152 ID - Ekblom2011 ER - TY - JOUR AU - Koboldt, D. C. AU - Steinberg, K. M. AU - Larson, D. E. AU - Wilson, R. K. AU - Mardis, E. R. PY - 2013 DA - 2013// TI - The next-generation sequencing revolution and its impact on genomics JO - Cell VL - 155 UR - https://doi.org/10.1016/j.cell.2013.09.006 DO - 10.1016/j.cell.2013.09.006 ID - Koboldt2013 ER - TY - JOUR AU - Allentoft, M. E. AU - Sikora, M. AU - Sjögren, K. -. G. AU - Rasmussen, S. AU - Rasmussen, M. AU - Stenderup, J. PY - 2015 DA - 2015// TI - Population genomics of bronze age Eurasia JO - Nature VL - 522 UR - https://doi.org/10.1038/nature14507 DO - 10.1038/nature14507 ID - Allentoft2015 ER - TY - JOUR AU - Orlando, L. AU - Gilbert, M. T. P. AU - Willerslev, E. PY - 2015 DA - 2015// TI - Reconstructing ancient genomes and epigenomes JO - Nat Publ Group VL - 16 ID - Orlando2015 ER - TY - JOUR AU - Raghavan, M. AU - DeGiorgio, M. AU - Albrechtsen, A. AU - Moltke, I. AU - Skoglund, P. AU - Korneliussen, T. S. PY - 2014 DA - 2014// TI - The genetic prehistory of the new world Arctic JO - Sci Am Assoc Adv Sci VL - 345 ID - Raghavan2014 ER - TY - JOUR AU - Fonseca, R. R. AU - Smith, B. D. AU - Wales, N. AU - Cappellini, E. AU - Skoglund, P. AU - Fumagalli, M. PY - 2015 DA - 2015// TI - The origin and evolution of maize in the Southwestern United States JO - Nat Plants Nat Publishing Group VL - 1 ID - Fonseca2015 ER - TY - JOUR AU - Skoglund, P. AU - Malmström, H. AU - Raghavan, M. AU - Stora, J. AU - Hall, P. AU - Willerslev, E. PY - 2012 DA - 2012// TI - Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe JO - Sci Am Assoc Adv Sci VL - 336 ID - Skoglund2012 ER - TY - JOUR AU - Paper, A. L. PY - 2015 DA - 2015// TI - Of AATAA at TE of T. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature JO - Nat Publ Group VL - 513 ID - Paper2015 ER - TY - JOUR AU - Sousa, V. AU - Hey, J. PY - 2013 DA - 2013// TI - Understanding the origin of species with genome-scale data: modelling gene flow JO - Nat Rev Genet VL - 14 UR - https://doi.org/10.1038/nrg3446 DO - 10.1038/nrg3446 ID - Sousa2013 ER - TY - JOUR AU - Degner, J. F. AU - Marioni, J. C. AU - Pai, A. A. AU - Pickrell, J. K. AU - Nkadori, E. AU - Gilad, Y. PY - 2009 DA - 2009// TI - Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp579 DO - 10.1093/bioinformatics/btp579 ID - Degner2009 ER - TY - JOUR AU - Brandt, D. Y. C. AU - Aguiar, V. R. C. AU - Bitarello, B. D. AU - Nunes, K. AU - Goudet, J. AU - Meyer, D. PY - 2015 DA - 2015// TI - Mapping bias overestimates reference allele frequencies at the HLA genes in the 1000 genomes project phase I data JO - G3 VL - 5 UR - https://doi.org/10.1534/g3.114.015784 DO - 10.1534/g3.114.015784 ID - Brandt2015 ER - TY - JOUR AU - Huang, L. AU - Popic, V. AU - Batzoglou, S. PY - 2013 DA - 2013// TI - Short read alignment with populations of genomes JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/btt215 DO - 10.1093/bioinformatics/btt215 ID - Huang2013 ER - TY - JOUR AU - Li, R. AU - Zhu, H. AU - Ruan, J. AU - Qian, W. AU - Fang, X. AU - Shi, Z. PY - 2010 DA - 2010// TI - De novo assembly of human genomes with massively parallel short read sequencing JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.097261.109 DO - 10.1101/gr.097261.109 ID - Li2010 ER - TY - JOUR AU - Li, Y. AU - Zheng, H. AU - Luo, R. AU - Wu, H. AU - Zhu, H. AU - Li, R. PY - 2011 DA - 2011// TI - Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly JO - Nat Biotechnol VL - 29 UR - https://doi.org/10.1038/nbt.1904 DO - 10.1038/nbt.1904 ID - Li2011 ER - TY - JOUR AU - Rasmussen, M. AU - Guo, X. AU - Wang, Y. AU - Lohmueller, K. E. AU - Rasmussen, S. AU - Albrechtsen, A. PY - 2011 DA - 2011// TI - An aboriginal Australian genome reveals separate human dispersals into Asia JO - Sci Am Assoc Adv Sci VL - 334 ID - Rasmussen2011 ER - TY - JOUR AU - Hufford, M. B. AU - Xu, X. AU - Heerwaarden, J. AU - Rvi, T. P. A. PY - 2012 DA - 2012// TI - J. A, Chia J-M, Cartwright RA, et al. comparative population genomics of maize domestication and improvement JO - Nat Genet Nat Publishing Group VL - 44 UR - https://doi.org/10.1038/ng.2309 DO - 10.1038/ng.2309 ID - Hufford2012 ER - TY - JOUR AU - Kopaliani, N. AU - Shakarashvili, M. AU - Gurielidze, Z. AU - Qurkhuli, T. AU - Tarkhnishvili, D. PY - 2014 DA - 2014// TI - Gene flow between wolf and shepherd dog populations in Georgia (Caucasus) JO - J Hered VL - 105 UR - https://doi.org/10.1093/jhered/esu014 DO - 10.1093/jhered/esu014 ID - Kopaliani2014 ER - TY - JOUR AU - Randi, E. AU - Lucchini, V. PY - 2002 DA - 2002// TI - Detecting rare introgression of domestic dog genes into wild wolf (Canis lupus) populations by Bayesian admixture analyses of microsatellite variation JO - Conserv Genet Kluwer Acad Publishers VL - 3 UR - https://doi.org/10.1023/A:1014229610646 DO - 10.1023/A:1014229610646 ID - Randi2002 ER - TY - STD TI - Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, et al. Recalibrating Equus evolution using the genome sequence of an early middle Pleistocene horse. Nat Nat Publishing Group. 2013:1–8. ID - ref19 ER - TY - JOUR AU - Schubert, M. AU - Jónsson, H. AU - Chang, D. AU - Sarkissian, C. AU - Ermini, L. AU - Ginolhac, A. PY - 2014 DA - 2014// TI - Prehistoric genomes reveal the genetic foundation and cost of horse domestication. Proceedings of the National Academy of Sciences JO - National Acad Sci VL - 111 UR - https://doi.org/10.1073/pnas.1416991111 DO - 10.1073/pnas.1416991111 ID - Schubert2014 ER - TY - JOUR AU - Frantz, L. A. F. AU - Mullin, V. E. AU - Pionnier-Capitan, M. AU - Lebrasseur, O. AU - Ollivier, M. AU - Perri, A. PY - 2016 DA - 2016// TI - Genomic and archaeological evidence suggest a dual origin of domestic dogs JO - Science VL - 352 UR - https://doi.org/10.1126/science.aaf3161 DO - 10.1126/science.aaf3161 ID - Frantz2016 ER - TY - STD TI - Ramos-Madrigal J, Smith BD, Víctor Moreno-Mayar J, Gopalakrishnan S, Ross-Ibarra J, Gilbert MTP, et al. Genome Sequence of a 5,310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication. Curr Biol. 2016;26:3195–3201. ID - ref22 ER - TY - STD TI - Park SDE, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, et al. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biol BioMed Central Ltd. 2015:1–15. ID - ref23 ER - TY - JOUR AU - Xia, Q. AU - Guo, Y. AU - Zhang, Z. AU - Li, D. AU - Xuan, Z. AU - Li, Z. PY - 2009 DA - 2009// TI - Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx) JO - Sci Am Assoc Advan Sci VL - 326 ID - Xia2009 ER - TY - JOUR AU - Eriksson, J. AU - Larson, G. AU - Gunnarsson, U. AU - Bed’hom, B. AU - Tixier-Boichard, M. AU - Strömstedt, L. PY - 2008 DA - 2008// TI - Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken JO - PLoS Genet VL - 4 UR - https://doi.org/10.1371/journal.pgen.1000010 DO - 10.1371/journal.pgen.1000010 ID - Eriksson2008 ER - TY - JOUR AU - Kanginakudru, S. AU - Metta, M. AU - Jakati, R. D. AU - Nagaraju, J. PY - 2008 DA - 2008// TI - Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken JO - BMC Evol Biol VL - 8 UR - https://doi.org/10.1186/1471-2148-8-174 DO - 10.1186/1471-2148-8-174 ID - Kanginakudru2008 ER - TY - JOUR AU - Xiang, H. AU - Gao, J. AU - Yu, B. AU - Zhou, H. AU - Cai, D. AU - Zhang, Y. PY - 2014 DA - 2014// TI - Early Holocene chicken domestication in northern China JO - Proc Natl Acad Sci U S A VL - 111 UR - https://doi.org/10.1073/pnas.1411882111 DO - 10.1073/pnas.1411882111 ID - Xiang2014 ER - TY - JOUR AU - Giuffra, E. AU - Kijas, J. M. AU - Amarger, V. AU - Carlborg, O. AU - Jeon, J. T. AU - Andersson, L. PY - 2000 DA - 2000// TI - The origin of the domestic pig: independent domestication and subsequent introgression JO - Genetics VL - 154 ID - Giuffra2000 ER - TY - JOUR AU - Paper, A. L. PY - 2012 DA - 2012// TI - Of AATAA at TE of T. Analyses of pig genomes provide insight into porcine demography and evolution JO - Nat Nat Publishing Group VL - 491 ID - Paper2012 ER - TY - JOUR AU - Wade, C. M. AU - Giulotto, E. AU - Sigurdsson, S. AU - Zoli, M. AU - Gnerre, S. AU - Imsland, F. PY - 2009 DA - 2009// TI - Genome sequence, comparative analysis, and population genetics of the domestic horse JO - Science VL - 326 UR - https://doi.org/10.1126/science.1178158 DO - 10.1126/science.1178158 ID - Wade2009 ER - TY - JOUR AU - Wang, G. -. D. AU - Zhai, W. AU - Yang, H. -. C. AU - Fan, R. -. X. AU - Cao, X. AU - Zhong, L. PY - 2013 DA - 2013// TI - The genomics of selection in dogs and the parallel evolution between dogs and humans JO - Nat Commun Nat Publishing Group VL - 4 UR - https://doi.org/10.1038/ncomms2814 DO - 10.1038/ncomms2814 ID - Wang2013 ER - TY - JOUR AU - Freedman, A. H. AU - Gronau, I. AU - Schweizer, R. M. AU - Ortega-Del Vecchyo, D. AU - Han, E. AU - Silva, P. M. PY - 2014 DA - 2014// TI - Genome sequencing highlights the dynamic early history of dogs JO - PLoS Genet VL - 10 UR - https://doi.org/10.1371/journal.pgen.1004016 DO - 10.1371/journal.pgen.1004016 ID - Freedman2014 ER - TY - JOUR AU - Zhang, W. AU - Fan, Z. AU - Han, E. AU - Hou, R. AU - Zhang, L. AU - Galaverni, M. PY - 2014 DA - 2014// TI - Hypoxia adaptations in the Grey wolf (Canis lupus chanco) from Qinghai-Tibet plateau JO - PLoS Genet VL - 10 UR - https://doi.org/10.1371/journal.pgen.1004466 DO - 10.1371/journal.pgen.1004466 ID - Zhang2014 ER - TY - STD TI - Skoglund P, Ersmark E, Palkopoulou E, Dalén L. Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds. Curr Biol Elsevier Ltd. 2015:1–6. ID - ref34 ER - TY - JOUR AU - Lindblad-Toh, K. AU - Wade, C. M. AU - Mikkelsen, T. S. AU - Karlsson, E. K. AU - Jaffe, D. B. AU - Kamal, M. PY - 2005 DA - 2005// TI - Genome sequence, comparative analysis and haplotype structure of the domestic dog JO - Nat Nat Publishing Group VL - 438 ID - Lindblad-Toh2005 ER - TY - JOUR AU - Vonholdt, B. M. AU - Pollinger, J. P. AU - Lohmueller, K. E. AU - Han, E. AU - Parker, H. G. AU - Quignon, P. PY - 2010 DA - 2010// TI - Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication JO - Nat Nat Publishing Group VL - 464 ID - Vonholdt2010 ER - TY - JOUR AU - Holdt, B. M. AU - Pollinger, J. P. AU - Earl, D. A. AU - Knowles, J. C. AU - Boyko, A. R. AU - Parker, H. PY - 2011 DA - 2011// TI - A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.116301.110 DO - 10.1101/gr.116301.110 ID - Holdt2011 ER - TY - JOUR AU - Savolainen, P. AU - Zhang, Y. -. P. AU - Luo, J. AU - Lundeberg, J. AU - Leitner, T. PY - 2002 DA - 2002// TI - Genetic evidence for an east Asian origin of domestic dogs JO - Sci Am Assoc Adv Sci VL - 298 ID - Savolainen2002 ER - TY - JOUR AU - Thalmann, O. AU - Shapiro, B. AU - Cui, P. AU - Schuenemann, V. J. AU - Sawyer, S. K. AU - Greenfield, D. L. PY - 2013 DA - 2013// TI - Complete mitochondrial genomes of ancient Canids suggest a European origin of domestic dogs JO - Sci Am Assoc Adv Sci VL - 342 ID - Thalmann2013 ER - TY - JOUR AU - Gnerre, S. AU - Maccallum, I. AU - Przybylski, D. AU - Ribeiro, F. J. AU - Burton, J. N. AU - Walker, B. J. PY - 2011 DA - 2011// TI - High-quality draft assemblies of mammalian genomes from massively parallel sequence data JO - Proc Natl Acad Sci U S A VL - 108 UR - https://doi.org/10.1073/pnas.1017351108 DO - 10.1073/pnas.1017351108 ID - Gnerre2011 ER - TY - JOUR AU - Li, H. AU - Durbin, R. PY - 2011 DA - 2011// TI - Inference of human population history from individual whole-genome sequences JO - Nature VL - 475 UR - https://doi.org/10.1038/nature10231 DO - 10.1038/nature10231 ID - Li2011 ER - TY - JOUR AU - Stamatakis, A. PY - 2014 DA - 2014// TI - RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu033 DO - 10.1093/bioinformatics/btu033 ID - Stamatakis2014 ER - TY - JOUR AU - Kozlov, A. M. AU - Aberer, A. J. AU - Stamatakis, A. PY - 2015 DA - 2015// TI - ExaML version 3: a tool for phylogenomic analyses on supercomputers JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv184 DO - 10.1093/bioinformatics/btv184 ID - Kozlov2015 ER - TY - JOUR AU - Skotte, L. AU - Korneliussen, T. S. AU - Albrechtsen, A. PY - 2013 DA - 2013// TI - Estimating individual admixture proportions from next generation sequencing data JO - Genetics VL - 195 UR - https://doi.org/10.1534/genetics.113.154138 DO - 10.1534/genetics.113.154138 ID - Skotte2013 ER - TY - STD TI - Svensson L, Åkesson M. Licensjakt varg 2011: DNA-analyser och inventeringsdata [Internet]. 2011. Available from: http://pub.epsilon.slu.se/13681/7/svensson_s_akesson_m_160928.pdf. UR - http://pub.epsilon.slu.se/13681/7/svensson_s_akesson_m_160928.pdf ID - ref45 ER - TY - STD TI - Åkesson, M, Svensson, L. 2015. Sammanställning av släktträdet över den skandinaviska vargstammen fram till 2014. Available from: http://www.viltskadecenter.se/images/stories/Publikationer/sammanstallning-slakttrad-skand-varg-2014-webb.pdf. UR - http://www.viltskadecenter.se/images/stories/Publikationer/sammanstallning-slakttrad-skand-varg-2014-webb.pdf ID - ref46 ER - TY - STD TI - Smit AFA, Hubley R, Green P. RepeatMasker Open-3.0. 1996. http://www.repeatmasker.org/faq.html. UR - http://www.repeatmasker.org/faq.html ID - ref47 ER - TY - JOUR AU - Schubert, M. AU - Ermini, L. AU - Sarkissian, C. AU - Nsson, H. A. K. J. O. AU - Ginolhac, A. E. L. AU - Schaefer, R. PY - 2014 DA - 2014// TI - Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX JO - Nat Protoc Nat Publishing Group VL - 9 UR - https://doi.org/10.1038/nprot.2014.063 DO - 10.1038/nprot.2014.063 ID - Schubert2014 ER - TY - JOUR AU - Li, H. AU - Handsaker, B. AU - Wysoker, A. AU - Fennell, T. AU - Ruan, J. AU - Homer, N. PY - 2009 DA - 2009// TI - The sequence alignment/map format and SAMtools JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp352 DO - 10.1093/bioinformatics/btp352 ID - Li2009 ER - TY - JOUR AU - McKenna, A. AU - Hanna, M. AU - Banks, E. AU - Sivachenko, A. AU - Cibulskis, K. AU - Kernytsky, A. PY - 2010 DA - 2010// TI - The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data JO - Genome Res VL - 20 UR - https://doi.org/10.1101/gr.107524.110 DO - 10.1101/gr.107524.110 ID - McKenna2010 ER - TY - JOUR AU - Li, H. PY - 2011 DA - 2011// TI - A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr509 DO - 10.1093/bioinformatics/btr509 ID - Li2011 ER - TY - JOUR AU - Fumagalli, M. AU - Vieira, F. G. AU - Linderoth, T. AU - Nielsen, R. PY - 2014 DA - 2014// TI - ngsTools: methods for population genetics analyses from next-generation sequencing data JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu041 DO - 10.1093/bioinformatics/btu041 ID - Fumagalli2014 ER - TY - JOUR AU - Purcell, S. AU - Neale, B. AU - Todd-Brown, K. AU - Thomas, L. AU - Ferreira, M. A. R. AU - Bender, D. PY - 2007 DA - 2007// TI - PLINK: a tool set for whole-genome association and population-based linkage analyses JO - Am J Hum Genet VL - 81 UR - https://doi.org/10.1086/519795 DO - 10.1086/519795 ID - Purcell2007 ER -