Publications

2017


72. KA Owers, P Sjödin, CM Schlebusch, P Skoglund, H Soodyall & M Jakobsson. Adaptation to infectious disease exposure in indigenous Southern African populations. (2017). Proceedings of the Royal Society B, 284. Journal website, PDF

71. M Chylenski, A Juras, E Ehler, H Malmstrom, J Piontek, M Jakobsson, A Marciniak & M Dabert. (2017). Late Danubian mitochondrial genomes shed light into the Neolithisation of Central Europe in the 5th millennium BC. BMC Evolutionary Biology, 17:80. Journal website, PDF

70. A Goldberg, T Günther, NA Rosenberg & M Jakobsson. (2017). Ancient X-chromosomes reveal contrasting sex bias in Neolithic and Bronze Age Eurasian migrations. Proceedings of the National Academy of Sciences, Early Edition, Journal website, PDF

69. R Nielsen, JM Akey, M Jakobsson, JK Pritchard, S Tishkoff & E Willerslev. (2017). Tracing the peopling of the world through genomics. Nature 541: 302-310. Journal website, PDF

68. A Juras, M Chyleński, M Krenz-Niedbała, H Malmström, E Ehler, Ł Pospieszny, S Łukasik, J Bednarczyk, J Piontek, M Jakobsson, M Dabert. (2016). Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA. Forensic Science International: Genetics 26: 30-39. Journal websitePDF

2016


67. C Jeong, AT Ozga, D Witonsky, H Malmström, H Edlund, CA Hofman, RW Hagan, M Jakobsson, CM Lewis, Jr., M Aldenderfer, A Di Rienzo & C Warinner. (2016). Long-term genetic stability and a high altitude East Asian origin for the peoples of the high valleys of the Himalayan arc. Proceedings of the National Academy of Sciences USA, 113: 7485-7490. Journal website, PDF

66. S Sten, C Loven, A Kjellstrom, K Liden, M Vretemark, CH Vala, O Ljunggren, M Fjallstrom, A Shalabi, O Duvernoy, M Segelsjo, H Malmström & M Jakobsson. (2016). Erik den heliges skelett. Fornvannen, 111: 27-40. PDF

65. T Günther & M Jakobsson (2016). Genes mirror migrations and cultures in prehistoric Europe – a population genomic perspective. Current Opinion in Genetics and Development 41: 115-123. Journal website, PDF

64. CM Schlebusch, F Prins, M Lombard, M Jakobsson & H Soodyall. (2016). The disappearing San of southeastern Africa and their genetic affinities. Human Genetics 135: 1365-1372. Journal website, PDF, Supplement

63. L Gattepaille, T Günther & M Jakobsson. (2016). Inferring past effective population size from distributions of coalescent times. Genetics. Journal website, PDF

62. G M Kılınç, A Omrak, F Özer, T Günther, A M Büyükkarakaya, E Bıçakçı, D Baird, H M Dönertaş, A Ghalichi, R Yaka, D Koptekin, S C Açan, P Parvizi, M Krzewińska, E A Daskalaki, E Yüncü, N D Dağtaş, A Fairbairn, J Pearson, G Mustafaoğlu, Y S Erdal, Y G Çakan, İ Togan, M Somel, J Storå, M Jakobsson & A Götherström. (2016). The demographic development of the first farmers in Anatolia. Current Biology. Journal website, PDF

61. M Hervella, EM Svensson, A Alberdi, T Günther, N Izagirre, AR Munters, S Alonso, M Ioana, F Ridichi, A Soficaru, M Jakobsson, MG Netea & C de-la-Rua. (2016). The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa. Scientific Reports 6, Article number: 25501. Journal websitePDF

60. A Omrak, T Günther, C Valdiosera, EM SvenssonH Malmström, H Kiesewetter, W Aylward, J StoråM Jakobsson & A Götherström. (2016). Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool. Current Biology 26: 270. Journal websitePDFSupplement

2015


59. T Günther, C Valdiosera, H Malmström, I Ureña, R Rodriguez-Varela, ÓO Sverrisdóttir, EA Daskalaki, Skoglund, Naidoo, EM Svensson, JM Bermúdez de Castro, E Carbonell, M Dunn, J Storå, E Iriarte, JL Arsuaga, J-M Carretero, A Götherström & M Jakobsson. (2015). Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques. Proceedings of the National Academy of Sciences, 112(38): 11917-11922. Journal websitePDFSupplement

58. M Raghavan, M Steinrücken, K Harris, S Schiffels, S Rasmussen, M DeGiorgio, A Albrechtsen, C Valdiosera, M Metspalu, JR Homburger, J Wall, OE Cornejo, JV Moreno-Mayar, TS Korneliussen, T Pierre, M Rasmussen, PE Campos, P de Barros Damgaard, ME Allentoft, J Lindo, E Metspalu, R Rodriguez-Varela, J Mansilla, C Henrickson, A Seguin-Orlando, H Malmström, T Stafford Jr., SS Shringarpure, A Moreno-Estrada, M Karmin, K Tambets, A Bergström, Y XUe, V Warmuth, AD Friend, J Singarayer, P Valdes, F Balloux, I Leboreiro, J Luis Vera, H Rangel-Villalobos, D Pettener, D Luiselli, LG Davis, E Heyer, CPE Zollikofer, MS Ponce de León, CI Smith, V Grimes, K-A Pike, M Deal, BT Fuller, B Arriaza, V Standen, MF Luz, F Ricaut, N Guidon, L Osipova, MI Voevoda, OL Posukh, O Balanovsky, M Lavryashina, Y Bogunov, E Khusnutdinova, M Gubina, E Balanovska, S Federova, S Litvinov, B Malyarchuk, M Derenko, MJ Mosher, D Archer, J Cybulski, B Petzelt, J Mitchell, R Worl, PJ Norman, P Parham, BM Kemp, T Kivisild, C Tyler-Smith, MS Sandhu, M Crawford, R Villems, D Glenn Smith, MR Waters, T Goebel, JR Johnson, RS Mahli, M Jakobsson, DJ Meltzer, A Manica, R Durbin, CD Bustamante, YS Song, R Nielsen & E Willerslev. (2015). Genomic evidence for the Pleistocene and recent population history of Native Americans. Science, 349: 842. Journal websitePDFSupplement

57. CM Schlebusch*, LM Gattepaille*, K Engström, M Vahter, M Jakobsson & K Broberg. (2015). Human Adaptation to Arsenic-Rich Environments. Molecular Biology and Evolution, 32(6): 1544-1555. Journal websitePDFSupplement (chosen by faculty of 1000)

56. H Malmström*, A Linderholm*, P Skoglund, J Storå, P Sjödin, TMP Gilbert, G Holmlund, E Willerslev, M Jakobsson, K Liden & A Götherström. (2015). Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process. Philosophical Transactions of the Royal Society of London B: Biological Sciences, 370: 373. Journal websitePDF

55. NM Kopelman, J Mayzel, M Jakobsson, NA Rosenberg & I Mayrose. (2015). CLUMPAK: A program for identifying clustering modes and packaging population structure inferences across K. Molecular Ecology Resources, 15(5): 1179-1191. Journal websitePDFSupplement

54. N Duforet-Frebourg*, LM Gattepaille*, MGB Blum & M Jakobsson. (2015). HaploPOP: a software that improves population assignment by combining markers into haplotypes. BMC Bioinformatics 16: 242. Journal websitePDF

53. RR daFonseca, BD Smith, N Wales, E Cappellini, P Skoglund, M Fumagalli, JA Samaniego, C Carøe, MC Ávila-Arcos, DE Hufnagel, TS Korneliussen, FG Vieira, M Jakobsson, B Arriaza, E Willerslev, R Nielsen, MB Hufford, A Albrechtsen, J Ross-Ibarra & MTP Gilbert. (2015). The origin and evolution of maize in the Southwestern United States. Nature Plants 1. Journal websitePDFSupplement

2014


52. S Li*, CM Schlebusch*, & M Jakobsson. (2014) Genetic variation reveals large-scale population expansion and migration during the expansion of Bantu-speaking peoples. Proceedings B of the Royal Society, 281: 1448. Journal websitePDFSupplement

51. M Raghavan, M DeGiorgio, A Albrechtsen, I Moltke, P Skoglund, TS Korneliussen, B Gronnøw, M Appelt, HC Gulløv, M Friesen, W Fitzhugh, H Malmström, S Rasmussen, J Olsen, L Melchior, BT Fuller, SM Fahrni, T Stafford Jr. V Grimes, MAP Renouf, J Cybulski, N Lynnerup, MM Lahr, K Britton, R Knecht, J Arneborg, M Metspalu, OE Cornejo, A-S Malaspinas, Y Wang, M Rasmussen, V Raghavan, TVO Hansen, E Khusnutdinova, T Pierre, K Dneprovski, C Andreasen, H Lange, MG Hayes, J Coltrain, VA Spitsyn, A Götherström, L Orlando, T Kivisild, R Villems, M Crawford, FC Nielsen, J Dissing, J Heinemeier, M Meldgaard, C Bustamante, DH O’Rourke, M Jakobsson, MTP Gilbert, R Nielsen & E Willerslev. (2014) The Genetic Prehistory of the New World Arctic. Science, 345: 1255832. Journal websitePDFSupplement

50. P Skoglund, P Sjödin, T Skoglund, M Lascoux & M Jakobsson. (2014) Investigating Population History using Temporal Genetic Differentiation. Molecular Biology and Evolution, 31: 2516-2527. Journal website,  PDFSupplement

49. A Sjöstrand, P Sjödin, & M Jakobsson. (2014) Private haplotypes can reveal local adaptation. BMC Genetics, 15: 61. Journal websitePDFSupplement

48. P Skoglund*, H Malmström*, A Omrak, M Raghavan, C Valdiosera, T Günther, P Hall, K Tambets, J Parik, K-G Sjögren, J Apel, E Willerslev, J Storå, A Götherström & M Jakobsson. (2014) Genomic Diversity and Admixture differs for Stone-Age Scandinavian Foragers and Farmers. Science, 344: 747-750. Journal websitePDFSupplement

47. G Breton*, CM Schlebusch*, M Lombard, H Soodyall, P Sjödin & M Jakobsson. (2014) Lactase Persistence alleles reveal partial East African ancestry of southern African Khoe pastoralists. Current Biology, 24: 852-858. Journal websitePDFSupplement

46. P Sjödin, P Skoglund, & M Jakobsson. (2014). Assessing the maximum contribution from ancient populations. Molecular Biology and Evolution 31(5): 1248-1260. Journal websitePDFSupplement

45. M Rasmussen, SL Anzick, MR Waters, P Skoglund, M DeGiorgio, TW Stafford Jr, S Rasmussen, I Moltke, A Albrechtsen, SM Doyle, GD Poznik, V Gudmundsdottir, R Yadav, A Sapfo, SS White, M Allentoft, OE Cornejo, K Tambets, A Eriksson, P Heintzman, M Meiri, M Karmin, TS Korneliussen, TL Pierre, J Stenderup, L Saag, V Warmuth, MC Lopes, S Brunak, T Sicheritz-Ponten, I Barnes, M Collins, L Orlando, F Balloux, A Manica, R Gupta, M Metspalu, CD Bustamante, M Jakobsson, R Nielsen, & E Willerslev. (2014) The genome of a late Pleistocene human from a Clovis burial site in western Montana. Nature, 506: 225-229. Journal websitePDFSupplement

44. P Skoglund, BH Northoff, MV Shunkov, AP Derevianko, S Pääbo, J Krause & M Jakobsson. (2014) Separating endogenous ancient DNA from modern-day contamination: application to a Siberian Neandertal. Proceedings of the National Academy of Sciences USA, 111: 2229-2234. Journal websitePDFSupplement

43. M Raghavan*, P Skoglund*, K Graf, M Metspalu, A Albrechtsen, I Moltke, S Rasmussen, T Stafford, L Orlando, E Metspalu, M Karmin, K Tambets, S Rootsi, R Mägi, P Campos, E Balanovska, O Balanovsky, E Khusnutdinova, S Litvinov, L Osipova, S Federova, M Voevoda, M DeGiorgio, T Sicheritz-Ponten, S Brunak, S Demeshchenko, T Kivisild, R Villems, R Nielsen, M Jakobsson & E Willerslev. (2014) Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature, 505: 87-91. Journal websitePDFSupplement

2013


42. P Skoglund, J Storå, A Götherström, M Jakobsson. (2013) Accurate sex identification of ancient human remains using DNA shotgun sequencing. Journal of Archaeological Science, 40: 4477–4482. Journal website, PDF, Supplementnews highlight by Nature

41. L Gattepaille, M Jakobsson, & MGB Blum. (2013) Inferring population size changes with sequence and SNP data: lessons from human bottlenecks. Heredity, 110: 409-419 Journal websitePDF

40. M Jakobsson, MD Edge, & NA Rosenberg. (2013) The relationship between FST and the frequency of the most frequent allele. Genetics, 193: 515-528. Journal websitePDF

39. F Jay, P Sjödin, M Jakobsson, & MGB Blum. (2013) Anisotropic isolation by distance: the main orientations of human genetic differentiation. Molecular Biology and Evolution, 30: 513-525. Journal websitePDFSupplement

38. CM Schlebusch, CM Lewis Jr, K Engström, G Concha, RY Tito, AJ Obregn-Tito, D Huerta, SI Polo, AC Medina, TD Brutsaert, M Vahter, M Jakobsson, & K Broberg. Possible Positive Selection for an Arsenic-Protective Haplotype in Humans. Environmental Health Perspectives, 121: 53-58. Journal websitePDFSupplement

37. CM Schlebusch*, P Sjödin*, P Skoglund*, & M Jakobsson. (2013) Stronger signal of recent selection for lactase persistence in Maasai than in Europeans. European Journal of Human Genetics. 21: 550-553. Journal websitePDFSupplement

2012


36. CM Schlebusch*, P Skoglund*, P Sjödin, LM Gattepaille, D Hernandez, F Jay, S Li, M De Jongh, A Singleton, MGB Blum, H Soodyall, & M Jakobsson. (2012) Genomic variation in seven Khoe-San groups reveals adaptation and complex African history. Science, 338: 374-379. Journal website, PDF, SupplementNews article in Nature by M Kaplan, News highlight in Science (chosen by faculty of 1000)

35. P Skoglund, H Malmström, M Raghavan, J Storå, P Hall, E Willerslev, MTP Gilbert, A Götherström & M Jakobsson. (2012) Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe. Science, 336: 466-469. Journal websitePDF, SupplementData,  News & Analysis by M Balter, Science podcast

34. S Li & M Jakobsson (2012) Estimating demographic parameters from large-scale population genomic data using Approximate Bayesian Computation. BMC Genetics 13: 22. Journal websitePDFSupplement(“highly accessed”)

33. V Nyström, J Humphrey, P Skoglund, NJ McKeown, S Vartanyan, PW Shaw, K Liden, M Jakobsson, I Barnes, A Angerbjörn, A Lister, & L Dalen. (2012) Microsatellite genotyping reveals end-Pleistocene shift in mammoth autosomal genetic variation. Molecular Ecology, 21(14): 3391-3402. Journal websitePDFSupplement(“from the cover”)

32. P Sjödin, AE Sjöstrand, M Jakobsson & MGB Blum. (2012) Resequencing Data Provide No Evidence for a Human Bottleneck in Africa during the Penultimate Glacial Period. Molecular Biology and Evolution. 29(7): 1851-1860. Journal websitePDFSupplement

31. P Sjödin & M Jakobsson. (2012) Population genetic properties of Copy Number Variation. Chapter 10 in Genomic Structural Variants: Methods in Molecular Biology vol. 838: 209-223, edited by L. Feuk, Springer, New York, USA.  PDF

30. J Li, H Li, M Jakobsson, S Li, P Sjödin & M Lascoux. (2012) Joint analysis of demography and selection in population genetics: Where do we stand and where could we go? Molecular Ecology, 21: 28-44. Journal websitePDFSupplement

29. LM Gattepaille & M Jakobsson. (2012) Combining markers into haplotypes can improve population structure inference. Genetics, 190: 159-174. Journal websitePDF

28. CM Schlebusch, H Soodyall & M Jakobsson. (2012) Genetic variation of 15 autosomal STR loci in various populations from southern Africa. Forensic Science International: Genetics, 6: e20-e21. Journal websitePDFSupplement

2011


27. L Huang*, M Jakobsson*, TJ Pemberton, JK Pritchard, SA Tishkoff, & NA Rosenberg. (2011) Haplotype variation and genotype imputation in African populations. Genetic Epidemiology, 38: 766-780. Journal website, PDF, Supplement, Data

26. P Skoglund & M Jakobsson. (2011) Archaic human ancestry in East Asia. Proceedings of the National Academy of Sciences USA, 108: 18301-18306. Journal website, PDF, Supplement

25. HMA Babiker, CM Schlebusch, HY Hassan & M Jakobsson. (2011) Genetic variation and population structure among Sudanese populations as indicated by the 15 Identifiler STR loci. Investigative Genetics, 2: 12. Journal website, PDF (“highly accessed”)

24. P Skoglund, A Götherström & M Jakobsson. (2011) Estimation of population divergence times from non-overlapping genomic sequences: examples from dogs and wolves. Molecular Biology and Evolution, 28: 1505-1517. Journal websitePDF

23. MGB Blum & M Jakobsson (2011) Deep divergences of human gene trees and models of human origins. Molecular Biology and Evolution. 28: 889-898. Journal websitePDF, Supplement (chosen by faculty of 1000)

2010


22. H Malmström, A Linderholm, K Lidén, J Storå, P Molnar, G Holmlund, M Jakobsson, & A Götherström (2010) High frequency of lactose intolerance in a prehistoric hunter-gatherer population in northern Europe. BMC Evolutionary Biology, 10: 89. Journal websitePDF

21. C Wang, ZA Szpiech, JH Degnan, M Jakobsson, TJ Pemberton, JA Hardy, AB Singleton & NA Rosenberg (2010) Comparing spatial maps of human population-genetic variation using Procrustes analysis. Statistical Applications in Genetics and Molecular Biology, 9: 13. Journal websitePDF

2009


20. TJ Pemberton, CI Sandefur, M Jakobsson & NA Rosenberg (2009) Sequence determinants of human microsatellite variability. BMC Genomics, 10: 612. Journal websitePDF, Supplement, Data

19. M Jakobsson (2009) COMPASS: A program for generating serial samples under an infinite sites model. Bioinformatics, 25: 2845-2847. Journal website, PDF

18. JBW Wolf, A Künstner, K Nam, M Jakobsson & H Ellegren (2009) Non-linear dynamics of non-synonymous (dN) and synonymous (dS) substitution rates affects inference of selection. Genome Biology and Evolution, 1: 308-319. Journal website, PDF, Supplement

17. M DeGiorgio, M Jakobsson & NA Rosenberg (2009) Explaining worldwide patterns of human genetic variation using a coalescent-based serial founder model of migration outward from Africa. Proceedings of the National Academy of Sciences USA, 106: 16057-16062. Journal website, PDF, Supplement

16. KB Schroeder, M Jakobsson, MH Crawford, TG Schurr, SM Boca, DF Conrad, RY Tito, LP Osipova, LA Tarskaia, SI Zhadanov, JD Wall, JK Pritchard, RS Malhi, DG Smith & NA Rosenberg (2009) Haplotypic background of a private allele at high frequency in the Americas. Molecular Biology and Evolution, 26: 995-1016. Journal website, PDF, Supplement

2008


15. ZA Szpiech, M Jakobsson & NA Rosenberg (2008) A rarefaction approach for counting alleles private to combinations of populations. Bioinformatics, 24: 2498-2504. Journal websitePDF

14. NA Rosenberg & M Jakobsson (2008) The relationship between homozygosity and the frequency of the most frequent allele. Genetics, 179: 2027-2036. Journal website, PDF

13. O François, MGB Blum, M Jakobsson, & NA Rosenberg (2008) Demographic history of European Populations of Arabidopsis thaliana. PLoS Genetics, 4: e1000075. Journal website, PDF, Supplement (chosen by faculty of 1000)

12. TJ Pemberton*, M Jakobsson*, DF Conrad, G Coop, JD Wall, JK Pritchard, PI Patel, & NA Rosenberg, (2008) Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India. Annals of Human Genetics, 72: 535-546. Journal website, PDF, Data

11. M Jakobsson*, SW Scholz*, P Scheet*, JR Gibbs, JM VanLiere, H-C Fung, ZA Szpiech, JH Degnan, K Wang, R Guerreiro, JM Bras, JC Schymick, D Hernandez, BJ Traynor, J Simon-Sanchez, Matarin, M., A Britton, J van de Leemput, I Rafferty, M Bucan, HM Cann, JA Hardy, NA Rosenberg, & AB Singleton, (2008) Genotype, haplotype, and copy number variation in worldwide human populations. Nature, 451: 998-1003. Journal website, PDF, Supplement, Data (chosen by faculty of 1000)

2007


10. S Wang*, CM Lewis Jr*, M Jakobsson*, S Ramachandran, N Ray, G Bedoya, W Rojas, MV Parra, JA Molina, C Gallo, G Mazzotti, G Poletti, K Hill, AM Hurtado, D Labuda, W Klitz, R Barrantes, MC Bortolini, FM Salzano, ML Petzl-Erler, LT Tsuneto, E Llop, F Rothhammer, L Excoffier, MW Feldman, NA Rosenberg & A Ruiz-Linares (2007) Genetic variation and population structure in Native Americans. PLoS Genetics 3: 2049-2067. Journal website, PDF, Supplement, Data

9. M Jakobsson & NA Rosenberg (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801-1806. Journal website, PDF

8. M Jakobsson & NA Rosenberg (2007) The probability distribution under a population divergence model of the number of genetic founding lineages of a population or species. Theoretical Population Biology 71: 502-523. Journal website, PDF

7. M Jakobsson, T Säll, C Lind-Halldén & C Halldén (2007) The evolutionary history of the common chloroplast genome of Arabidopsis thaliana and A. suecica. Journal of Evolutionary Biology 20: 104-121. Journal website, PDF, Supplement

6. M Jakobsson, T Säll, C Lind-Halldén & C Halldén (2007) Evolution of chloroplast mononucleotide microsatellites in Arabidopsis thaliana. Theoretical and Applied Genetics 144: 223-235. Journal websitePDF, Supplement

2006


5. DF Conrad*, M Jakobsson*, G Coop*, X Wen, JD Wall, NA Rosenberg, JK Pritchard (2006) A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nature Genetics 38: 1251-1260. Journal website, PDF, Supplement, Data (“from the cover”)

4. M Jakobsson, J Hagenblad, S Tavaré, T Säll, C Halldén, C Lind-Halldén & M Nordborg. (2006) A unique recent origin of the allotetraploid species Arabidopsis suecica: evidence from nuclear DNA markers. Molecular Biology and Evolution 23: 1217-1231. Journal website, PDF, Supplement

2005-2003


3. M Nordborg, T Hu, Y Ishino, J Jhaveri, C Toomajian, H Zheng, E Tomer, P Calabrese, J Gladstone, R Goyal, M Jakobsson, S Kim, Y Morozov, B Padhukasahasram, V Plagnol, NA Rosenberg, C Shah, JD Wall, K Zhao, T Kalbfleisch, V Schultz, M Kreitman, & J Bergelson (2005) The Pattern of Polymorphism in Arabidopsis thaliana. PLoS Biology 3: 1289-1299.
Journal website, PDF, Supplement (chosen by faculty of 1000)

2. T Säll, C Halldén, M Jakobsson & C Lind-Halldén (2004) Mode of reproduction and population structure in Arabidopsis suecica. Hereditas 141: 313-317.
Journal website, PDF

1. T Säll, M Jakobsson, C Lind-Halldén & C Halldén (2003) Chloroplast DNA indicates a single origin of the allotetraploid Arabidopsis suecica. Journal of Evolutionary Biology 16: 1019-1029. Journal website, PDF (chosen by faculty of 1000)

* Equal first author