PhD Ludwig Maximillian Universität Münich, 1999

Search course offerings in Anthropology

Courses (2022-2023)

Fall

• On Research Leave   

Winter

• ANTHROP 2U03 - Plagues and People
• ANTHROP 708 - Anthropology of Infectious Disease  

Courses (2021-2022)

Fall

• On Research Leave 

Winter

• ANTHROP 715 - Readings: Biological Anthropology 

Selected Publications

*** - undergraduate when submitted; ** - graduate when submitted; * - alum when submitted

Hendrik Poinar, 2021. Past plagues: on the synergies of genetic and historical interpretations of infectious disease, in Death and Disease in the Medieval and Early Modern World, eds. Nukhet Varlik and Lori Jones, York Medieval Press, UK.

Dickson, Z., Hackenberger, D., Kuch, M., Marzok, A., Banerejee, A., Mossmann, K., Miller, M., Golding, B., Poinar, H., 2021. Probe design for simultaneous, targeted capture of diverse metagenomic targets. Cell Methods https://doi.org/10.1016/j.crmeth.2021.100069

*Tyler J. Murchie, Alistair J. Monteath, Matthew E. Mahony, George S. Long, Scott Cocker, Tara Sadoway, Emil Karpinski, Grant Zazula, Ross MacPhee, Duane Froese, Hendrik Poinar., 2021. Collapse of the mammoth-steppe in central Yukon as revealed by ancient environmental DNA. Nature Communications 12, 7120.

. Finlay BB, Amato KR, Azad M, Blaser MJ, Bosch TCG, Chu H, Dominguez-Bello MG, Ehrlich SD, Elinav E, Geva-Zatorsky N, Gros P, Guillemin K, Keck F, Korem T, McFallNgai MJ, Melby MK, Nichter M, Pettersson S, Poinar H, Rees T, Tropini C, Zhao L, Giles-Vernick T. The hygiene hypothesis, the COVID pandemic, and consequences for the human microbiome. Proceedings of the National Academy of Sciences 2021 Feb 9;118(6):e2010217118. doi: 10.1073/pnas.2010217118. PMID: 33472859.

2020 Duggan AT, **Klunk J, **Porter AF, Dhody AN, Hicks R, Smith GL, Humphreys M, McCollum A, Davidson W, Burke A, **Polasky J, Flanders L, Poinar D, McArthur A, Wright G, Holmes EC, Poinar HN. An inquiry into the origins and genomic diversity of Civil War Era smallpox vaccines. Genome Biology

2020 **Karpinski, E., **Hackenberger, D., Zazula, G., Widga, C., Duggan, A.D., Golding, G., Kuch, M., **Klunk, J., Jass, C., Groves, P., Druckenmiller, P., Schubert, B., Arroyo-Cabrales, J., Simpson, W., Hoganson, W., Fisher, D., MacPhee, R.,. Poinar, HNP. Ancient mitochondrial genomes suggest multiple dispersal events in American mastodons (Mammut americanum) in response to Pleistocene climate oscillations. Nature Communications.

2019 **Tyler J. Murchie, Melanie Kuch, Ana Duggan, *Marissa L. Ledger, **Kévin Roche, **Jennifer Klunk, **Emil Karpinski, **Dirk Hackenberger, *Tara Sadoway, Duane Froese, Hendrik Poinar. Paleochip1: Optimizing extraction and targeted capture of ancient DNA from palaeosediments. Quarternary Research.

David J. D. Earn, Junling Ma, Hendrik N. Poinar, Benjamin M. Bolker, Jonathan Dushoff.  Acceleration of plague outbreaks in the second pandemic. In revision, Proceedings of the National Academy of Sciences.

2019 Frédéric Delsuc, Melanie Kuch, Gillian C. Gibb, **Emil Karpinski, **Dirk Hackenberger, *Paul Szpak, John Southon, Ross D. E. MacPhee, Guillaume Billet, Lionel Hautier, and Hendrik N. Poinar
Ancient mitogenomics rewrites the evolutionary history and biogeography of sloths. Current Biology Jun 17;29(12):2031-2042.e6. doi: 10.1016/j.cub.2019.05.043

2019 Alison J. T. Harris, Ana T. Duggan, **Stephanie Marciniak, Ingeborg Marshall, Hendrik Poinar, and Vaughan Grimes.  Beothuk and Dorset Dietary Practices in Newfoundland, ca. C.E. 500 – 1829. American Journal of Physical Anthropology, https://doi.org/10.1371/journal.pone.0210187.

2018 Sang Woo Park, Jonathan Dushoff, David J.D. Earn, Hendrik Poinar, Benjamin Bolker. Human Ectoparasite transmission of the plague during the Second Pandemic is only weakly
supported by proposed mathematical models. Proceedings of the National Academy of Science USA, https://doi.org/10.1073/pnas.1809775115

2018 Frederic Delsuc, Melanie Kuch, Gillian Gibb, Jonathan Hughes, *Paul Szpak, John Southon, Ana Duggan and Hendrik Poinar. Resolving the phylogenetic position of Darwin’s extinct
ground sloth (Mylodon darwinii) using mitogenomic and nuclear exon data. Proceedings of Biological Sciences 16;285 (1875).

2018 Hana Fukuto, Viveka Vadyvaloo, Joseph McPhee, Hendrik Poinar, Edward Holmes, and James Bliska. A single amino acid change in the response regulator PhoP acquired during Yersinia
pestis evolution affects PhoP target gene transcription and polymyxin B susceptibility. Journal of Bacteriology;200(9).doi: 10.1128/JB.00050-18.

2018 Eleftheria Palkopoulou, Mark Lipson, Swapan Mallick, Svend Nielsen, Nadin Rohland, Sina Baleka, Emil Karpinski, Atma M. Ivancevic, Thu-Hien To, R. Daniel Kortschak, Joy M. Raison, Zhipeng Qg, Tat-Jun Chin, Kurt W. Alt, Stefan Claessoj, Love Dalen, Ross MacPhel, Harald Meller, Alfred L. Roca, Oliver Ryder, David Heiman, Sarah Young, Matthew Breen, Christina Williams,
Bronwen L. Aken, Magali Ruffier, Elinor Karlsson, Jeremy Johnson, Federica Di Palma, Jessica Alfoldi, David L. Adelson, Thomas Mailund, Kasper Munch, Kerstin Lindblad-Toh, Michael
Hofreiter, Hendrik Poinar and David Reich. A comprehensive genomic history of extinct and living elephants. Proceedings of the National Academy of Science USA. https://doi.org/10.1073/pnas.1720554115

2018 **Stephanie Marciniak, D. Ann Herring, Alessandra Sperduti, Hendrik N. Poinar, Tracy L. Prowse. A multi-faceted anthropological and genomic approach to framing Plasmodium falciparum malaria in Imperial period central-southern Italy (1st-4th c. C.E.) Journal of Anthropological Archaeology, 49: 210-22

2018 **Matthew Emery, Ana T Duggan, **Tyler J Murchie, **Robert J Stark, **Jennifer Klunk, **Jessica Hider, **Katherine Eaton, **Emil Karpinski, Henry Schwarcz, Hendrik Poinar, Tracy Prowse. Ancient Roman Mitochondrial Genomes and Isotopes Reveal Relationships and Geographic Origins at the Local and pan-Mediterranean Scales. Journal of Archeological Sciences Reports, 20, pp 200-209.

2017 **Zoe P. Ross, **Jennifer Klunk, Gino Forniciari, Valentina Giuffra, Sebastian Duchene, Ana Duggan, Debi Poinar, Mark Douglas, John-Sebastian Eden, Edward Holmes, Hendrik Poinar. The
paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathog 14(1): e1006750. https://doi.org/10.1371/journal.ppat.

2017 **Ashleigh Porter, Ana Duggan, Hendrik Poinar and Edward Holmes. Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum, Viruses Oct; 9(10): 276.

2017 Ana T. Duggan, Alison J.T. Harris, **Stephanie Marciniak, Ingeborg Marshall, Melanie Kuch, Andrew Kitchen, Gabriel Renaud, John Southon, Ben Fuller , Janet Young , Stuart Fiedel, G. Brian Golding, Vaughan Grimes , Hendrik Poinar 2017, Genetic Discontinuity between the Maritime Archaic and Beothuk Populations in Newfoundland, Canada. Current Biology Oct
23;27(20):3149-3156.e11.

2017 Tatum D. Mortimer, Douglas S. Annis, Mary B. O’Neill, Lindsey Bohr, Tracy Smith, Hendrik N. Poinar, Deane F. Mosher, Caitlin S. Pepperell. Adaptation of Staphylococcus saprophyticus at the
host-pathogen interface. MBio DOI:10.1128/mSphere.00511-17

2017 **Karpinski, E., Mead, J. I. & Poinar, H. N. Molecular identification of paleofeces from Bechan Cave, southeastern Utah, USA. Quat. Int. 443, 140–146.

2017  Ana T. Duggan, Maria F. Perdomo, Dario Piombino-Mascali, **Stephanie Marciniak, Debi Poinar, **Matthew V. Emery, Jan P. Buchmann, Sebastian Duchêne, Rimantas Jankauskas, Margaret Humphreys, G. Brian Golding, John Southon, *Alison Devault, Jean-Marie Rouillard, Jason W. Sahl, Olivier Dutour, Klaus Hedman, Antti Sajantila, Geoffrey L. Smith, Edward C. Holmes
Hendrik Poinar. 17th Century Variola Virus Reveals the Recent History of Smallpox. Current Biology 26(24) p3407-3412.

2017 Dan Chang, Michael Knapp, **Jacob Enk, Matthias Meyer, Sebastian Lippold, Martin Kircher, Adrian Lister, Ross D. E. MacPhee, Paul Czechowski, Robert Sommer, Emily Hodges, Nikolaus
Stümpel, Ian Barnes, Love Dalén, Anatoly Derevianko, Mietje Germonpré, Alexandra Hillebrand-Voiculescu, Silviu Constantin, Tatyana Kuznetsova, Dick Mol, Thomas Rathgeber, Wilfried
Rosendahl, Alexey N. Tikhonov, Eske Willerslev, Greg Hannon, Carles Lalueza-Fox, Ulrich Joger, Hendrik Poinar, Michael Hofreiter, Beth Shapiro. The evolutionary and phylogeographic
history of woolly mammoths: a comprehensive mitogenomic analysis. Nature Scientific Reports 44585 (2017); doi :10.1038/srep44585.

2017 **Alison M. Devault, Tatum D. Mortimer, Andrew Kitchen, Henrike Kiesewetter, **Jacob M. Enk, G. Brian Golding, John Southon, Melanie Kuch, Ana T. Duggan, William Aylward, Shea N. Gardner, Jonathan E. Allen, Andrew M. King, Gerard D. Wright, Makoto Kuroda, Kengo Kato, Derek E. G. Briggs, Gino Fornaciari, Edward C. Holmes, Hendrik N. Poinar, Caitlin S. Pepperell. A
molecular portrait of maternal sepsis from Byzantine Troy. eLife 2017;6:e20983.

2016 Dang U.J., **Devault A.M., Mortimer T.D., Pepperell C.S., Poinar H.N., Golding G.B. Estimation of Gene Insertion/Deletion Rates with Missing Data. Genetics. 2016, 204(2):513-529.

2016 **Kirsten I. Bos, Alexander Herbig, Jason Sahl, *Nicholas Waglechner, Mathieu Fourment, Stephen A. Forrest, **Jennifer Klunk, Debi Poinar, Melanie Kuch, G. Brian Golding, Verena J. Schuenemann, Olivier Dutour, Paul Keim, David M. Wagner, Edward C. Holmes, Johannes Krause, and Hendrik N. Poinar. Yersinia pestis genomes from an 18th century mass burial in France reveals the longterm persistence of plague in Europe during the second pandemic. eLife (http://dx.doi.org/10.7554/eLife.12994).

2016 **Enk, J., **Devault, A., Widga, C, Saunders, J., Spazk, P., Zazula, G., Macphee, R., Froese, D., Fisher, D., and H.N. Poinar, 2016. Complete mitogenome phylogeography of Mammuthus from southern North America suggests a deep interspecific chronology. Frontiers in Ecology and Evolution http://dx.doi.org/10.3389/fevo.2016.00042.

2016 Palkopoulou, E., Mallick, S., Skoglund, P., Enk, J., Rohland, N., Li, H., Omrak, A., Vartanyan, S., Poinar, H., Götherström, A., Reich, D., Dalén. L., Heterochronous woolly mammoth genomes reveal demographic and genetic declines. 2016, Current Biology, 25 (10):1395-1400.

2016 Frédéric Delsuc, **Gillian C. Gibb, Melanie Kuch, Guillaume Billet, Lionel Hautier, John Southon, Jean-Marie Rouillard, Juan Carlos Fernicola, Sergio F. Vizcaíno, Ross D. E. MacPhee, Hendrik N. Poinar. The phylogenetic affinities of the extinct glyptodonts, 2016 Current Biology 22;26(4):R155-6. doi: 10.1016/j.cub.2016.01.039.

2016 Soares AER, **Novak B, Haile J, Fjeldså J, GIlbert MTP, Poinar H, Church G, Shapiro B Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform
radiation BMC Evolutionary Biology 16: 1-9 (2016) pdf

2015 Gillian C. Gibb, Fabien L. Condamine, Melanie Kuch, J**acob Enk, Nadia Moraes-Barros, Mariella Superina, Hendrik N. Poinar and Frédéric Delsuc. 2015 Shotgun Mitogenomics Provides a
Reference Phylogenetic Framework and Timescale for Living Xenarthrans. Molecular Biology and Evolution, 33(3):621-42. doi: 10.1093/molbev/msv250

2015 **Marciniak, S., **Klunk, J., **Devault, A., Enk, J., Poinar, H., Ancient DNA in the Genomic Era: Reconstructing Human Evolutionary Pathways, 2015. Journal of Human Evolution 79:21-34. doi:10.1016/j.jhevol.2014.11.003.

2015 **Mouttham N, **Klunk J, Kuch M, Fourney R, Poinar H. Surveying the repair of ancient DNA from 9 bones via high-throughput sequencing. Biotechniques. 2015 Jul 1;59(1):19-25. doi:
10.2144/000114307

2014 Gutierrez-Garcia, T.A., Vazquez-Dominguez, E., Arroyo-Cabrales, J., Kuch, M., **Enk, J., *King, C., and H. N. Poinar, 2014. Ancient DNA and the Tropics: a rodent’s tale. Biology Letters (Roy Soc).10:20140224. (http://dx.doi.org/10.1098/rsbl.2014.0224)

2014 **Devault, A.M., Golding, G.B., *Waglechner, N., **Enk, J., Kuch, M., Tien, J., Shi, M., Fisman, D., Dhody, A.D., Forrest, S., Bos, K., Earn, D.J.D., Holmes, E.D., and H.N. Poinar, 2014. A ‘Classical’ genome for the second pandemic strain of Vibrio cholerae, Philadelphia, 1849. New England Journal of Medicine, 370(4):334-40.

2014 **Devault, A., Jaing, C., Gardner, S., Porter. T.M., **Enk, J., Thissen, J., Allen, J., Borucki, M., DeWitte, S., Dhody, A., McLoughin, K., and H.N Poinar, 2014. Ancient pathogen DNA in
archaeological samples detected with a Microbial Detection Array. Nature Scientific Reports doi:10.1038/srep04245.

2014 Wagner, D., **Klunk, J., Harbeck, M., **Devault, A., *Waglechner, N., Sah, J.W., **Enk, J., Birdsell, D., Kuch, M., **Lumibao, C.J., Poinar, D., Pearson, T., Fourment, M., Golding, B., Riehm, J., Earn, D.J., DeWitte, S., Rouillard, J.M., Grupe, G., Wiechmann, I., Bliska, J.B., Keim, P., Scholz, H., Holmes, E., and H.N. Poinar, 2014. The Plague of Justinian was caused by a ‘dead-end’ emergence of Yersinia pestis. The Lancet Infectious Disease (doi: 10.1016/S1473-3099(13)70323-2.).

2014 Palkopoulou, E., Mallick, S., Skoglund, P., **Enk, J., Rohland, N., Li, H., Omark, A., Vartanyan, S., Poinar, H., Götherström, A., Reich, D., Dalén, L., Hetereochronous woolly mammoth genomes reveal demographic and genetic declines. Nature.  

2014 **Marciniak, S., **Klunk, J., **Devault, A.,**Enk, J., Poinar, H., Ancient DNA in the Genomic Era: Reconstructing Human Evolutionary Pathways. Journal of Human Evolution.

2014 **Enk, J., **Devault, A., Widga, C., Saunders, J., *Spazk, P., Zaxula, G., Macphee, R., Froese, D., Fisher, D., and  H.N. Poinar. Complete mitogenome phylogeography of Mammuthus from southern North America suggests a deep interspecific chronology. Molecular Ecology.

2014 Gutierrez-Garcia, T.A., Vazquez-Dominguez, E., Arroyo-Cabrales, J., Kuch, M., **Enk, J., *King, C., and H.N. Poinar. Ancient DNA and the Tropics: a rodent’s tale. Biology Letters (Roy Soc). 10: 20140224 (http://dx.doi.org/10.10098/rbsl.2014.0224)

2014 **Devault, A.M., Golding^, G.B., *Waglechner^, N., **Enk, J., Kuch, M., Tien, J., Shi, M., Fisman, D., Dhody, A.D., Forrest^, S., Bos^, K., Earn, D.J.D., Holmes^, E.D., and H.N. Poinar.  A ‘Classical’ genome for the second pandemic strain of Vibrio cholerae, Philadelphia, 1849. New England Journal of Medicine, 370(4):334-40.

2014 **Devault, A., Jaing, C., Gardner, S., Porter. T.M., **Enk, J., Thissen, J., Allen, J., Borucki, M., DeWitte, S.,  Dhody, A., McLoughin, K., and H.N Poinar. Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array. Nature Scientific Reports doi:10.1038/srep04245.

2014 Wagner, D., **Klunk, J., Harbeck, M., **Devault^, A., *Waglechner, N., Sah, J.W., **Enk, J., Birdsell, D., Kuch, M., **Lumibao, C.J., Poinar, D., Pearson, T., Fourment, M., Golding, B., Riehm, J.,. Earn, D.J., DeWitte, S., Rouillard, J.M., Grupe, G., Wiechmann, I., Bliska, J.B., Keim, P., Scholz, H., Holmes, E., and H.N. Poinar, 2014.  The Plague of Justinian was caused by a ‘dead-end’ emergence of Yersinia pestis. The Lancet Infectious Disease (doi: 10.1016/S1473-3099(13)70323-2.).

2014 **Enk, J., **Devault, A., Kuch, M., Murgha, Y., Rouillard, J.M., and H.N. Poinar. Ancient Whole Genome Enrichment Using Modern DNA-Derived Baits. Molecular Biology and Evolution (231 (5): 1292-1294.

2011 **Enk, J., Debruyne, R., **Devault, A. *King, C., Treagen,T., O’Rourke, D., Salzberg, S., Fisher, D., MacPhee^, R., and Hendrik Poinar 2011. Columbian Mammoth Mitogenome  Suggests  Interbreeding  with Woolly  Mammoths. Genome Biology, doi:10.1186/gb-2011-12-5-r51

2011 **Bos, K., Schuenemann, V., Golding, B., Burbano, H., *Waglechner, N., Coombes, B., McPhee, J., DeWitte, S., Meyer, M., Schmedes, S., Wood, J., Earn, S., Herring, A., Bauer, P., Poinar, H.N. and Johannes Krause, 2011. A draft genome of Yersinia pestis from victims of the Black Death, Nature 478, 506–510.

2011. Herald waves of cholera in 19th century London. (with Tien, J., Fisman, D., and Earn, D.) Journal of the Royal Society Interface 8(58), 756-760.

2011. Ancient DNA from lake sediments: bridging the gap between palaeoecology and genetics. (with Anderson-Carpenter, L.L., McLachlan, J.S., Jackson, S.T., Kuch, M., and Lumibao, C.) BMC Evolutionary Biology11:30 1-15.

2010. A quantitative assessment of the sensitivity of various commercially available reverse transcriptases on low copy number RNA levels. (with **Okello, J.B.A., Rodriquez, L., Poinar, D., *Bos, K., Okwi, A.L., Bimenya, G.S., Sewankambo, N.K., Henry, K.R., and Kuch, M.) PLOS-ONE 5(11), e13931.

2010. A quantitative and qualitative comparison of total nucleic acid (DNA and RNA) yields from formalin-fixed paraffin-embedded tissues using ten different extraction methods. (with **Okello, J., *Zurek, J., **Devault A., Kuch, M., Okwi, A.L., Wewankambo, N., Bimenya, G., and Poinar, D.) Analytical Biochemistry 400(1), 110-117.

2010. Regional differences in bone collagen d13C and d15N of Pleistocene mammoths: implications for palaeoecology of mammoth steppe. (with ***Szpak, P., Grocke, D., **Debruyne, R., MacPhee, R., Guthrie, D., Froese, D., and Zazula, G.)Palaeogeography, Palaeoclimatology, and Palaeoecology 286, 88-96.

2009. A quantitative approach to detect and overcome PCR inhibition in ancient DNA extracts. (with *King, C., Debruyne, R., Kuch, M., and Schwarz C.) Biotechniques 47(5), 351-356.

2009. New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains. (with Schwarz, C., Debruyne, R., Kuch, M., McNally, E., Schwarcz, H., Aubrey, A., and Bada, J.) Nucleic Acids Research 37(10), 3215-3229.

2009. Time-dependency of molecular rates in ancient DNA datasets, a sampling artefact? (with Debruyne, R.) Systematic Biology58(3),348-60

2003. Molecular caving. (with Hofrieter, M., Mead J., and Martin, P.S.) Current Biology. 13, 693-695.

2003. Nuclear gene sequences from a Late Pleistocene sloth coprolite. (with Kuch, M., McDonald, G., Martin, P.S. and Paabo, S.)Current Biology 13, 1150-1152.

2002. The genetic secrets some fossils hold. Accounts of Chemical Research, 35, 676-84.

2001. Molecular analyses of oral polio vaccine samples. (with Kuch, M. and Paabo, S.) Science 292, 743-744.

2001. A molecular analyses of the dietary diversity for three archaic native americans. (With Kuch, M., Sobolik, K., Barnes, I., Stankiewicz, B.A., Spaulding, G., Bryant, V., Cooper, A. & Paabo S.) Proceedings of the National Academy of Sciences USA 98, 4317-4322.

2000. Ancient DNA: Do it right or not at all. (with A. Cooper) Science 289, 1139.

1998. Molecular Coproscopy: Dung and Diet from of the extinct ground sloth Nothrotheriops shastensis. (with Hofreiter, M., Spaulding, G., Martin, P.S., Stankiewicz, A. B., Bland, H. Evershed, R. P., Possnert, G., Paabo, S.) Science 281, 402-406.