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Johanna L.A. Paijmans
Department of Biochemistry & Biology
University of Potsdam
paijmans.jla@gmail.nomorespam.com
(0331) 977-6322

Education
PhD in Palaeogenetics, University of Potsdam, Germany (2016)
MSc in Biological Archaeology, University of York, UK (2010)
BA in Archaeology, University of Leiden, The Netherlands (2008)

Research

During my PhD I used various hybridisation capture methods to retrieve mitochondrial genomes from highly degraded ancient samples (up to 30,000 years old), and introduced a number of optimisations and developments in the protocols used for DNA capture of degraded samples. Currently I am studying population dynamics through time in various carnivores (wolverines, leopards) by examining genetic variation in samples from different time points (modern, Holocene and Pleistocene). I am also transitioning into working with whole genomes to further investigate population and extinction dynamics, and to understand what genomes can tell us about adaptation and evolution of (extinct) species.

Publications
Journal Publications

  •  Alberti, F., J. Gonzalez, Paijmans, Johanna L. A., N. Basler, M. Preick, K. Henneberger, A. Trinks, G. Rabeder, N. Conard, S. Munzel, U. Joger, G. Fritsch, T. Hildebrandt, M. Hofreiter, and A. Barlow (2018). “Optimized DNA sampling of ancient bones using Computed Tomography (CT) scans”. Molecular Ecology Resources (Early View). doi: 10.1111/1755-0998.12911.
  • Taron, Ulrike H., Moritz Lell, Axel Barlow, and Johanna L. A. Paijmans (2018). “Testing of Alignment Parameters for Ancient Samples: Evaluating and Optimizing Mapping Parameters for Ancient Samples Using the TAPAS Tool.” Genes 9; 3.doi.org/10.3390/genes9030157
  • Gaudry, M. J., M. Jastroch, J. R. Treberg, M. Hofreiter, Paijmans, Johanna L. A., J. Starrett, N. Wales, A. V. Signore, M. S. Springer, and K. L. Campbell (2018). “Inactivation of thermogenic UCP1 as a historical contingency in multiple placental mammal clades”. Science Advances 3.7, e1602878. doi: 10.1126/sciadv.1602878.
  • Kehlmaier, C., A. Barlow, A. K. Hastings, M. Vamberger, Paijmans, Johanna L. A., D. W. Steadman, N. A. Albury, R. Franz, M. Hofreiter, and U. Fritz (2017). “Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorum”. Proc. R. Soc. B 284.1846, p. 20162235. doi: 10.1098/rspb.2016.2235.
  • Paijmans, Johanna L. A., Sina Baleka, Kirstin Henneberger, Ulrike H. Taron, Alexandra Trinks, Michael V. Westbury, and Axel Barlow (2017). “Sequencing Single-Stranded Libraries on the Illumina NextSeq 500 Platform.” ArXiv:1711.11004 [q-Bio]. arxiv.org/abs/1711.11004
  • Paijmans, Johanna L. A., Ross Barnett, M. Thomas P. Gilbert, M. Lisandra Zepeda-Mendoza, Jelle W. F. Reumer, John de Vos, Grant Zazula, Doris Nagel, Gennady F. Baryshnikov, Jennifer A. Leonard, Nadin Rohland, Michael V. Westbury, Axel Barlow, and Michael Hofreiter (2017). “Evolutionary History of Saber-Toothed Cats Based on Ancient Mitogenomics.” Current Biology 27; 21: 3330-3336.e5. DOI:10.1016/j.cub.2017.09.033
  • Wecek K, Hartmann S, Paijmans JLA, Taron U, Xenikoudakis G, Cahill JA, Heintzman PD, Shapiro B, Baryshnikov B, Bunevich AN, Crees JJ, Dobosz R, Manaserian N, Okarma H, Tokarska M, Turvey ST, Wójcik JM, Żyła W, Szymura JM, Hofreiter M, Barlow A (2017) Complex admixture preceded and followed the extinction of wisent in the wild. Molecular Biology and Evolution, 34 (3): 598-612. DOI: 10.1093/molbev/msw254.
  • Westbury, M., Baleka, S., Barlow, A., Hartmann, S., Paijmans, J.L.A., Kramarz, A., Forasiepi, A.M., Bond, M., Gelfo, J.N., Reguero, M.A., López-Mendoza, P., Taglioretti, M., Scaglia, F., Rinderknecht, A., Jones, W., Mena, J., Billet, G., de Muizon, C., Aguilar, J.L.,  MacPhee, R.D.E., & Hofreiter, M., (2017). A mitogenomic timetree for Darwin’s enigmatic South American mammal Macrauchenia patachonica. Nat. Commun. 8, 15951.  DOI:10.1038/ncomms15951
  • Paijmans, J.L.A., J. Fickel, A. Courtiol, M. Hofreiter, and D.W. Förster. (2016) "Impact of enrichment conditions on cross-species capture of fresh and degraded DNA". In: Molecular Ecology Resources 16, 42–55. DOI:10.1111/1755-0998.12420.
  • Hofreiter, M., Paijmans, J.L.A., H. Goodchild, C.F. Speller, A. Barlow, G.G. Fortes, J.A. Thomas, A. Ludwig, and M.J. Collins. (2015) "The future of ancient DNA: Technical advances and conceptual shifts". In: BioEssays 37.3, 284–293. DOI:10.1002/bies.201400160.
  • Springer M.S., Signore A.V., Paijmans J. L. A., Vélez-Juarbe J., Domning D.P., Bauer C.E., He K., Crerar L., Campos P.F,. Murphy W.J., Meredith R.W., Gatesy J., Willerslev E., MacPhee R.D.E., Hofreiter M., Campbell K.L. (2015) "Interordinal gene capture, the phylogenetic position of Steller’s sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia." In: Molecular Phylogenetics and Evolution 91, 178–193. DOI:10.1016/j.ympev.2015.05.022.
  • Bellone, R.R., H. Holl, V. Setaluri, S. Devi, N. Maddodi, S. Archer, L. Sandmeyer, A. Ludwig, D. Foerster, M. Pruvost, M. Reissmann, R. Bortfeldt, D.L. Adelson, S.L. Lim, J. Nelson, B. Haase, M. Engensteiner, T. Leeb, G. Forsyth, M.J. Mienaltowski, P. Mahadevan, M. Hofreiter, Paijmans, J.L.A., G. Gonzalez-Fortes, B. Grahn, and S.A. Brooks. (2013) "Evidence for a Retroviral Insertion in TRPM1 as the Cause of Congenital Stationary Night Blindness and Leopard Complex Spotting in the Horse". In: PLoS ONE 8.10, e78280. DOI:10.1371/journal.pone.0078280.
  • Paijmans, J.L.A., M.T.P. Gilbert, and M. Hofreiter. (2013) "Mitogenomic analyses from ancient DNA". In: Molecular Phylogenetics and Evolution 69.2, 404 –416. DOI:10.1016/j.ympev.2012.06.002.
  • Zhang H., Paijmans J.L.A., Chang F., Wu X., Chen G., Lei C., Yang X., Wei Z., Bradley D.G., Orlando L., O’Connor T., Hofreiter M. (2013) "Morphological and genetic evidence for early Holocene cattle management in northeastern China". In: Nature Communications 4. DOI:10.1038/ncomms3755.
  • Jenkins, D.L., L.G. Davis, T.W. Stafford, P.F. Campos, B. Hockett, G.T. Jones, L.S. Cummings, C. Yost, T.J. Connolly, R.M. Yohe, Gibbons S.C., M. Raghavan, M. Rasmussen, Paijmans, Johanna L.A., M. Hofreiter, B.M. Kemp, J.L. Barta, C. Monroe, M.T.P. Gilbert, and E. Willerslev. (2012) "Clovis-age Western stemmed projectile points and human coprolites at the Paisley Caves". In: Science 337.6091, 223–228. DOI:10.1126/science.1218443.

 

Book chapter

  • Fortes, G.G. and Paijmans, J.L.A. (2015) "Analysis of whole mitogenomes from ancient samples". In: Whole Genome Amplification. Editor T. Kroneis, Humana Press, USA. Available on ArXiv. doi: 10.1007/978-1-4939-2990-0_13.