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Michael Hofreiter

Professor for Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Department of Mathematics and Natural Sciences
Email: Michael.hofreiter@uni-potsdam.nomorespam.de
Phone: 0331 977 6321
Fax: 0331 977 6389
Curriculum Vitae (short version)

Google scholar Profile
Researchgate Profile

University of Leipzig , Ph.D., 2002
Ludwig-Maximilians-University Munich, Diploma 1999

Research Interests
My main research interests lie in elucidating the genetic basis of animal adaptations and the effect of environmental changes on both neutral and adaptive genetic diversity. In studying the genetics of adaptations, my group was the first to functionally test genetic variants from extinct species. In domesticated animals, we have also investigated changes in allele frequencies of certain genes over time. We are also working on understanding the population dynamics of a range of Holarctic species, both extant and extinct ones, such as brown bears, cave bears, spotted hyenas and mammoths. Here we are interested in understanding how, if at all, climatic fluctuations influence population size over time as well as patterns of gene flow between geographically separated populations.  We also want to understand the relationships between Pleistocene and modern populations of extant species such as brown bears, wolves, wolverines and leopards. As a basis for investigating the genetics of adaptations and understanding patterns of gene flow between populations and species we also often perform phylogenetic analyses on the groups we work on as often, especially when working on groups including extinct species, the phylogenetic relationships between the species of interest are unknown. A lot of our work involves samples with fairly degraded DNA such as fossil bones or museum specimens. Therefore, we also work on improving methods for obtaining DNA sequence information from such samples. Increasingly, we use full genomes, also from extinct species, for our analyses as this offers the possibility to address all the above questions.

Selected publications 

  1. Wutke, S., Andersson, L., Benecke, N., Sandoval-Castellanos, E., Gonzalez, J., Hallsson, J.H., Lõugas, L., Magnell, O., Morales-Muniz, A., Orlando, L., Pálsdóttir, A.H., Reissmann, M., Muñoz-Rodríguez, M.B., Ruttkay, M., Trinks, A., Hofreiter, M. and Ludwig A. (2016) The origin of ambling horses. Current Biology, 26 (15), R697-9 (published online 8th August 2016, doi: 10.1016/j.cub.2016.07.001).
  2. Jones, E.R., Gonzalez-Fortes, G., Connell, S., Siska, V., Eriksson, A., Martiniano, R., McLaughlin, R.L., Gallego-Llorente, M., Cassidy, L.M., Gamba, C., Meshveliani, T., Bar-Yosef, O., Müller, W., Belfer-Cohen, A., Matskevich, Z., Jakeli, N., Higham, T.F., Currat, M., Lordkipanidze, D., Hofreiter, M., Manica, A., Pinhasi, R. and Bradley, D.G. (2016) Upper Palaeolithic genomes reveal deep roots of modern Eurasians. Nat Commun 6, 8912 (doi: 10.1038/ncomms9912).
  3. Gallego-Llorente, M., Jones, E.R., Eriksson, A., Siska, V., Arthur, K.W., Arthur, J.W., Curtis, M.C., Stock, J.T., Coltorti, M., Pieruccini, P., Stretton, S., Brock, F., Higham, T., Park, Y., Hofreiter, M., Bradley, D.G., Bhak, J., Pinhasi, R. and Manica, A. (2015) Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. Science 350 (6262), 820-822 (published online 8th Oct 2015; doi: 10.1126/science.aad2879).
  4. Li, C., Corrigan, S., Yang, L., Straube, N., Harris, M., Hofreiter, M., White, W. and Naylor, G.J.P. (2015) DNA capture reveals transoceanic gene flow in endangered river sharks. Proc. Natl. Acad. Sci. U S A, 112 (43), 13,302-13,307 (doi: 10.1073/pnas.1508735112; published online 12th Oct 2015).
  5. Welcker, F., Collins, M.J., Thomas, J.A., Wadsley, M., Brace, B., Cappellini, E., Turvey, S.T., Reguero, M., Gelfo, J.N., Kramarz, A.,  Burger, J., Thomas-Oates, J., Ashford, D.A., Ashton, P., Rowsell, K., Porter, D.M., Kessler, B., Fisher, R., Baessmann, C., Kaspar, S., Olsen, J., Kiley, P., Elliot, J., Kelstrup, C., Mullin, V., Hofreiter, M., Willerslev, E., Hublin, J.-J., Orlando, L., Barnes I. & MacPhee, R.D.E. (2015)  Ancient Proteins Demonstrate South American Ungulates are Laurasiatheres, not Afrotheres. Nature, 522 (7554), 81-84 (publishes online 18th March 2015, doi: 10.1038/nature14249).
  6. King, T.E., Gonzalez Fortes, G., Balaresque, P., Thomas, M.G., Balding, D., Maisano Delser, P., Neumann, R., Parson, W., Knapp, M., Walsh, S., Tonasso, L., Holt , J., Kayser, M., Appleby, J., Forster, P., Ekserdjian, D., Hofreiter  M. and Kevin Schürer, K. (2014) Richard III: genetic evidence in context and the resolution of a mystery. Nature Communications, 5, 5631 (published online 2nd December; doi: 10.1038/ncomms6631).
  7. Gamba, C., Jones, E.R., Teasdale, M.D., McLaughlin, R.L., Gonzalez-Fortes, G., Mattiangeli, V., Domboróczki, L., K?vári, I., Pap, I., Anders, A., Whittle, A., Dani, J., Raczky, P.,. Higham, T.F.G., Hofreiter, M., Bradley, D.G., and Pinhasi, R., (2014) Genomic flux and stasis during five millennia of Hungarian prehistory. Nature Communications, 5, 5257. (published online 21st Oct 2014; doi: 10.1038/ncomms6257).
  8. Shapiro, B. and Hofreiter, M. (2014) A paleogenomic perspective on evolution and gene function: New insights from ancient DNA. Science, 343, 1236573-1-7.doi:10.1126/science.1236573
  9. Orlando, L., Ginolhac, A., Zhang, G. and 47 co-authors, Hofreiter, M., Nielsen, N., Shapiro, B., Jun, W. and Willerslev, E. (2013) Recalibrating Equus evolution using the genome sequence of an Early Middle Pleistocene horse. Nature, 499 (7456), 74-78 (published online 26th June 2013; doi: 10.1038/nature12323).
  10. Lorenzen, E., Noguès-Bravo, D., Orlando, L.,  Weinstock, J., Binladen, J., Marske, K. A., Haile, J., and 47 co-authors, Wayne, R. K., Cooper, A.,  Hofreiter, M., Sher, A., Shapiro, B., Rahbek, C. and Willerslev, E. (2011) Individualistic species responses to climate and humans determine Late Quaternary megafaunal extinction and survival. Nature, 479 (7373), 359-64 (published online 2nd November; doi: 10.1038/nature10574).
  11. Lerner, H. R. L., Meyer, M., James, H. F., Hofreiter, M. and Fleischer, R. C. (2011) Multilocus resolution of phylogeny and timescale in the extant adaptive radiation of Hawaiian honeycreepers. Current Biology, 21 (21), 1838-1844 (published online 21st October 2011; doi:10.1016/j.cub.2011.09.039).
  12. Lippold, S., Allentoft, M., Benecke, N., Koepfli, K.-P., Kuznetsova, T., Ludwig, A., Weinstock, J., Willerslev, E., Shapiro, B. and Hofreiter, M. (2011) Discovering the lost diversity of paternal horse lineages using ancient DNA. Nature Communications, 2, 450 (published online 23rd August 2011, doi: 10.1038/ncomms1447).
  13. Rohland, N., Reich, D., Mallick, S., Meyer, M., Green, R.E., Georgiadis, N.J., Roca, A., and Hofreiter, M. (2010) Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants. PLoS Biology, 8 (12), e1000564 (published online 21st December 2010, doi:10.1371/journal.pbio.1000564).
  14. Campbell, K.L., Roberts, J.E.E., Watson, L.N., Stetefeld, J., Sloan, A.M., Signore, A.V., Tame, J.R.H., Rohland, N., Shen, T.-J., Austin, J.J., Hofreiter, M., Ho, C., Weber, R.E. and Cooper, A. (2010) Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance. Nature Genetics, 42 (6), 536-40 (published online 2nd May 2010, doi:10.1038/ng.574).
  15. Stiller, M., Baryshnikov, G., Bocherens, H., Grandal d'Anglade, A., Hilpert, B., Münzel, S.C., Pinhasi, R., Rabeder, G., Rosendahl, W., Trinkaus, E., Hofreiter, M. and Knapp, M. (2010) Withering away - 25,000 years of genetic decline preceded cave bear extinction. Molecular Biology and Evolution, 27 (5), 975-978 (published online 24th March 2010, doi: 10.1093/molbev/msq083). 
  16. Ludwig, A., Pruvost, M., Reissmann, M., Benecke, N., Brockmann, G.A., Castaños, P., Cieslak, M., Lippold, S., Llorente, L., Malaspinas, A.-S., Slatkin, M. and Hofreiter, M. (2009) Coat color variation at the beginning of horse domestication. Science 324, 485.(DOI: 10.1126/science.1172750)
  17. Lalueza-Fox, C., Römpler, H., Caramelli, D., Stäubert, C., Catalano, G., Hughes, D., Rohland, N., Pilli, E., Longo, L., Condemi, S., de la Rasilla, M., Fortea, J.,  Rosas, A., Stoneking, M., Schöneberg, T.,  Bertranpetit, J. and Hofreiter, M. (2007) A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science, 318 (5855), 1453-5 (published online, 25th October 2007, doi: 10.1126/science.1147417).
  18. Meyer, M., Stenzel, U., Myles, S., Prüfer, K. and Hofreiter, M. (2007) Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Research 35 (15), e97 (published online 1st August 2007, doi:10.1093/nar/gkm566).
  19. 19. Willerslev, E., Cappellini, E., Boomsma, W., Nielsen, R., Hebsgaard, M.B., Brand, T.B., Hofreiter, M., Bunce, M., Poinar, H.N., Dahl-Jensen, D., Johnson, S., Steffensen, J.P., Bennike, O., Schwenninger, J.-L., Nathan, R., Armitage, S., De Hoog, J.C.M., Alfimov, V., Christl, M., Beer, J., Muscheler, R., Barker, J., Sharp, M., Penkman, K.E.H., Haile, J., Taberlet, P., Gilbert, M. T.P., Casoli, A., Campani, E. and Collins, M. J. (2007) Ancient Biomolecules from deep ice cores reveal a forested southern Greenland. Science, 317, 111-114.doi: 10.1126/science.1141758
  20. Rohland, N. and Hofreiter, M. (2007) Comparison and optimization of ancient DNA extraction. Biotechniques, 42 (3), 343-352.doi: 10.2144/000112383
  21. Römpler, H. Rohland, N., Lalueza-Fox, C., Willerslev, E., Kuznetsova, T., Rabeder, G., Bertranpetit, J., Schöneberg, T. and Hofreiter, M. (2006) Nuclear gene indicates coat-color polymorphism in mammoths. Science, 313 (5783), 62.doi: 10.1126/science.1128994
  22. Krause, J., Dear, P. H., Pollack, J. L., Slatkin, M., Spriggs, H., Barnes, I., Lister, A. M., Ebersberger, I., Pääbo, S. and Hofreiter, M. (2006) Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature, 439, 724-727 (published online 18th December 2005, doi: 10.1038/nature04432).

Complete publication list

Teaching Experience

I have been teaching various courses in Leipzig, York and Potsdam, including General and Systematic Zoology, Molecular Ecology, Population Genetics, Evolutionary Genetics and other topics around Genetics and Evolution.