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Contact Info

Mattias Jakobsson

mattias.jakobsson[at]ebc.uu.se

+46 (0)18-471 6449 (office)
+46 (0)18-471 6310 (fax)

Mailing address:

Dept. of Evolutionary biology, EBC,
Uppsala University,
Norbyägen 18D,
75236 Uppsala, Sweden

Visiting address:

EBC, Norbyvägen 18D, Room 1036
 

Mattias Jakobsson Lab: Publications

In press

 

2014

 

47. 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, early online [journal website] [PDF]

46. 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 website] [PDF]

45. P Sjödin, P Skoglund, M & Jakobsson. (2014) Assessing the maximum contribution from ancient populations. Molecular Biology and Evolution. [journal website] [PDF]

44. 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 webste] [PDF]

43. 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 website] [PDF]

42. 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 website] [PDF]

 

2013

 

41. 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] [news highlight by Nature]

40. 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 website]

39. M Jakobsson, MD Edge, & NA Rosenberg. (2013) The relationship between FST and the frequency of the most frequent allele. Genetics, 193: 515-528. [journal website] [PDF]

38. 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 website] [PDF].

37. C 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 website] [PDF]

36. 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 website] [PDF]

 

2012

 

35. 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] [news article in Nature by M Kaplan] [news highlight in Science] [PDF] [supplement]

 

34. 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 website][PDF][supplement] [news&analysis by M Balter] [Science podcast]

33. S Li & M Jakobsson (2012) Estimating demographic parameters from large-scale population genomic data using Approximate Bayesian Computation. BMC Genetics 13: 22. [journal website] ("highly accessed")

32. 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, in press. [journal website] ("from the cover")

31. P Sjödin, AE Sjöstrand, M Jakobsson & MGB Blum. (2012) No evidence for a human bottleneck during the penultimate glacial period.  Molecular Biology and Evolution. advance online, doi: 10.1093/molbev/mss061 [journal website]

A1. P Sjödin & M Jakobsson. (2012) Population genetic properties of Copy Number Variation. Chapter 10 in Genomic Structural Variants: Methods and Protocols Methods in Molecular Biology vol. 838: 209-223, edited by L. Feuk, Springer, New York, USA. DOI: 10.1007/978-1-61779-507-7_10. [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 website][PDF][supplement]

29. LM Gattepaille & M Jakobsson. (2012) Combining markers into haplotypes can improve population structure inference. Genetics, 190: 159-174. [journal website][PDF]

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 website][PDF][supplement]

 

2011

 

27. L Huang*, M Jakobsson*, M., 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]

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 website][PDF]

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 website][PDF][supplement] (chosen by faculty of 1000)

 

2010

 

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

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 website][PDF]

 

2009

 

20. TJ Pemberton, CI Sandefur, M Jakobsson & NA Rosenberg (2009) Sequence determinants of human microsatellite variability. BMC Genomics, 10: 612.
[journal website][PDF][supplement]

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 website][PDF][software]

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][software]

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 website][PDF][supplement]
 

 

2006

Cover

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]

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

 

2003-2005

 

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

Jakobsson Lab

Selected publications

  • M Jakobsson, MD Edge, & NA Rosenberg. (2013) The relationship between FST and the frequency of the most frequent allele. Genetics, 193: 515-528.
  • 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. 
  • 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.
  • LM Gattepaille & M Jakobsson. (2012) Combining markers into haplotypes can improve population structure inference. Genetics, 190: 159-174.
  • P Skoglund & M Jakobsson. (2011) Archaic human ancestry in East Asia. Proceedings of the National Academy of Sciences USA, 108: 18301-18306.

  •  MGB Blum & M Jakobsson (2011) Deep divergences of human gene trees and models of human origins. Molecular Biology and Evolution. 28: 889-898.

  • 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.
  • 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.