Publications

2021 Rampelli, S.,  S. Turroni, F. Debandi, A. Alberdi, S.L. Schnorr, C.A. Hofman, A. Taddia, R. Helg, E. Biagi, P. Brigidi, F. D’Amico, M. Cattani, M. Candela. The gut microbiome buffers dietary adaptation in Bronze Age domesticated dogs. iScience.doi: 10.1016/j.isci.2021.102816

2021 Reding, D.M., S. Castañeda-Rico, S. Shirazi, C.A. Hofman, I.A. Cancellare, S.L. Lance, J. Beringer W.R Clark, J.E. Maldonado. Mitochondrial genomes of the USA distribution of gray fox (Urocyon cinereoargenteus) reveals a major phylogeographic break at the Great Plains Suture Zone. Frontiers in Ecology and Evolution. doi :10.3389/fevo.2021.666800

2021 Zuckerman, M., R.M. Austin, C.A. Hofman. Historical Anatomical Collections of Human Remains: Exploring Their Reinterpretation as Representations of Racial Violence. Annals of the American Academy of Political and Social Science Invited commentary. doi: 10.1177/00027162211008815.

2021 Fellows Yates, J.A., I.M. Velsko, F. Aron, C. Posth, C.A. Hofman, R.M. Austin, C.E. Parker, A.E. Mann, K. Nägele, K.W. Arthur, J. W. Arthur, C.C. Bauer, I. Crevecoeur, C. Cupillard, M.C. Curtis, L. Dalén, M. Díaz-Zorita Bonilla, J.C Díez Fernández-Lomana, D.G. Drucker, E. Escribano Escrivá, M. Francken, V.E. Gibbon, M.R. Gonzalez Morales, A. Grande Mateu, K. Harvati, A.G. Henry, L. Humphrey, M. Menéndez, D. Mihailović, M. Peresani, S. Rodríguez Moroder, M. Roksandic, H. Rougier, S. Sázelová, J.T. Stock, L.G. Straus, J. Svoboda, B. Teßmann, M.J. Walker, R.C. Power, C.M. Lewis, K. Sankaranarayanan, K. Guschanski, R. Wrangham, F.E. Dewhirst, D.C. Salazar-Garcia, J. Krause, A. Herbig, C. Warinner. The evolution and changing ecology of the anthropoid primate oral microbiome. PNAS. doi: 10.1073/pnas.2021655118.

2021 Grindle, E.D., T.C. Rick, N.D. Dagtas, R.M. Austin, H. Wellman, K. Gobalet, C.A. Hofman. Green or White? Morphology, Ancient DNA, and the Identification of Archaeological North American Pacific Coast Sturgeon. Journal of Archaeological Science: Reports doi:10.1016/j.jasrep.2021.102887

2021 S. Rampelli, S. Turroni, C. Mallol, C. Hernandez, B. Galván, A. Sistiaga, E. Biagi, A. Astolfi, P. Brigidi, S. Benazzi, C.M. Lewis Jr., C. Warinner, C.A. Hofman, S.L. Schnorr, M. Candela. Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt. Communications Biology. doi: 10.1038/s42003-021-01689-y

2020 Wellman, H.P., R.M. Austin, N.D. Dagtas, M.L. Moss, T.C. Rick, C.A. Hofman. Archaeological mitogenomes illuminate the historical ecology of sea otters (Enhydra lutris) and the viability of reintroduction. Proceedings of the Royal Society B. doi: 10.1098/rspb.2020.2343

2020 Mann, A.E, J.A. Fellows Yates, Z. Fagernäs, R.M. Austin, E. Nelson, C.A. Hofman. Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus. Quaternary International. doi: 10.1016/j.quaint.2020.11.019

2020 Pott, L.N. *, R.M. Austin, A.R. Eller, C.A. Hofman, S.B. Sholts. Population-level assessment of atlas occipitalization in artificially modified crania from pre-Hispanic Peru. PLoS One. (*undergraduate author) doi: 10.1371/journal.pone.0239600

2020 Erlandson, J.M., T.J. Braje, A.F. Ainis, B.J. Culleton, K.M. Gill, C.A. Hofman, D.J. Kennett, L.A. Reeder-Myers, T.C. Rick. Maritime Paleoindian technology, subsistence, and ecology at an ~11,700 year old Paleocoastal site on California’s Northern Channel Islands, USA. PLoS One. doi: 10.1371/journal.pone.0238866

2020 Mychajliw, A.M., T.C. Rick, N.D. Dagtas, J.M. Erlandson, B. Culleton, M. Buckley, C.A. Hofman. Biogeographic problem-solving reveals the Late Pleistocene translocation of a short-faced bear to the California’s Channel Islands. Scientific Reports. doi:  10.1038/s41598-020-71572-z

2020 Dávalos L.M., R.M. Austin, M.A. Balisi, R.L. Begay, C.A. Hofman, M.E. Kemp, J.R. Lund, C. Monroe, A.M. Mychajliw, E.A. Nelson, M.A. Nieves-Colón, S.A. Redondo, S. Sabin, K.S. Tsosie, JM. Yracheta. Pandemics’ historical role in inequality. Science doi: 10.1126/science.abc8953

2020 Fagernäs, Z., M.I. Garcia Collado, J. Hendy, C.A. Hofman, C. Speller, I. Velsko, C. Warinner. A unified protocol for simultaneous extraction of DNA and proteins from archaeological dental calculus. Journal of Archaeological Science. doi: 10.1016/j.jas.2020.105135

2020 Borry, M., B. Cordova, A. Perri, M.C. Wibowo, T. Honap, W. T. Jada Ko, J. Yu, K. Britton, L. Girdland Flink, R.C. Power, I. Stuijts, D. Salazar Garcia, C.A. Hofman, R.W. Hagan, T. Samdapawindé Kagone, N. Meda, H. Carabin, D. Jacobson, K. Reinhard, C.M. Lewis, Jr., A. Kostic, C. Jeong, A. Herbig, A. Hübner, and C. Warinner. CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ. doi: 10.7717/peerj.9001

2020 Eller A.R, B. Pobiner, S. Friend*, R.M. Austin, C.A. Hofman, and S.B. Sholts. A Chomped Chimp: New evidence of tooth marks on an adult chimpanzee (Pan troglodytes verus). American Journal of Physical Anthropology. (*undergraduate author) doi:10.1002/ajpa.24049

2020 Der Sarkissian, C., P. Möller, C.A. Hofman, P, Ilsøe, T.C. Rick, T. Schiøtte, M.V. Sørensen, L. Dalén, L. Orlando. Unveiling the Ecological Applications of Ancient DNA from Mollusk Shells. Frontiers in Ecology and Evolution. doi:10.3389/fevo.2020.00037

2020 Hagan, R. W., C.A. Hofman, A. Hübner, K. Reinhard, S. Schnorr, C.M. Lewis, Jr., K. Sankaranarayanan, C. Warinner. Comparison of extraction methods for recovering ancient microbial DNA from paleofeces. American Journal of Physical Anthropology. doi: 10.1002/ajpa.23978

2019 Schnorr, S.L., C.A. Hofman, S.R. Netshifhefhe, F.D. Duncan, T.P Honap, J. Lesnik, C.M. Lewis. Taxonomic features and comparisons of the edible fungus-farming termite microbiome and implications for human evolution (Macrotermes falciger; M. natalensis). BMC Microbiology. (19) 164 doi: 10.1186/s12866-019-1540-5

2019 Austin, R.M.*, S. Sholts*, L. Williams, L. Kistler, C.A. Hofman. Opinion: To curate the molecular past, museums need a carefully considered set of best practices. (*co-first authors). Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1822038116

2019 Hofman, C.A, and C. Warinner. Ancient DNA 101: An introductory guide in the era of high-throughput sequencing. SAA Record.

2019 Rick, T.C., C.A. Hofman, L. Reeder-Myers. Why Translocate? Evaluating the Reasons for Ancient Human Translocation of Wildlife to California’s Islands. In An Archaeology of Abundance: Re-evaluating the Marginality of California’s Islands, edited by Kristina Gill, Mikael Fauvelle, and Jon Erlandson.

2018 Lindo, J., R. Haas, C.A. Hofman, M. Apata, M. Moraga, R.Verdugo, J.T. Watson, C. Viviano Llave, D. Witonsky, E. Vargas Pacheco, C. Beall, C. Warinner, J. Novembre, M. Aldenderfer, A. Di Rienzo. The genetic prehistory of the Andean highlands 7,000 Years BP though European contact. Science Advances (4)11. doi: 10.1126/sciadv.aau4921

2018 Ziesemer, K.A., J. Ramos-Madrigal, A.E. Mann, B.W. Brandt, K. Sankaranarayanan, A.T. Ozga, M. Hoogland, C.A. Hofman, D.C. Salazar-García, B. Frohlich, G.R. Milner, A.C. Stone, M. Aldenderfer, C.M. Lewis, Jr., C.L. Hofman, C. Warinner, H. Schroeder. The efficacy of whole human genome capture on ancient dental calculus and dentin. American Journal of Physical Anthropology. doi: 10.1002/ajpa.23763

2018 Hofman, C.A, T.C. Rick, J.M Erlandson, L. Reeder-Myers, A.J. Welch, M. Buckley. Collagen Fingerprinting and the Earliest Marine Mammal Hunting in North America. Scientific Reports (8)10014 doi: 10.1038/s41598-018-28224-0

2018 Hendy, J., C. Warinner, A. Bouwman, M. Collins, S. Fiddyment, R. Fischer, R. Hagan, C.A. Hofman, M. Holst, E. Chaves, L. Klaus, G. Larson, M. Mackie, K. McGrath, A. Mundorff, A. Radini, H. Rao, C. Trachsel, I. Velsko, C. Speller. Proteomic Evidence of Dietary Sources in Ancient Dental Calculus. Proceedings B (285)1883. doi: 10.1098/rspb.2018.0977

2018 Mann, A.E., S Sabin, K. Ziesemer, Å.J. Vågene, H. Schroeder, A.T. Ozga, K. Sankaranarayanan, C.A. Hofman, J. Fellows Yates, D.C. Salazar-García, B. Frohlich, M. Aldenderfer, M. Hoogland, C. Read, G. Milner, A.C. Stone, C.M. Lewis, Jr., J Krause1, C. Hofman, K. Bos, C. Warinner. Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. Scientific Reports (8)19822 doi: 10.1038/s41598-018-28091-9.

2017 Morales-Arce, A.Y., C.A. Hofman, A. Duggan, M.A. Katzenberg, G. McCafferty, C. Warinner. Successful reconstruction of whole mitochondrial genomes from ancient Central America and northwestern Mexico. Scientific Reports, (7)18100. doi: 10.1038/s41598-017-18356-0

2017. Shirazi, S., T.C. Rick, J.E. Erlandson, C.A. Hofman. A tale of two mice: A trans-Holocene record of Peromyscus nesodytes and P. maniculatus at Daisy Cave, San Miguel Island, California. Holocene. doi: 10.1177/0959683617744266

2017 Hofman, C.A, and T.C. Rick. Ancient Biological Invasions and Island Ecosystems: Tracking Translocations of Wild Plants and Animals. Journal of Archaeological Research. Early Edition. PDF.

2017 Hofman, C.A.*, C. West*, S. Ebbert, S. Shirazi, S. Dunning, J.E. Maldonado. Integrating archaeology and ancient DNA analysis to address invasive species colonization in the Gulf of Alaska. Conservation Biology. Early Edition. (*co-first authors) PDF.

2016 Hofman, C.A , T.C. Rick, J.E. Maldonado, P.W. Collins, J.M Erlandson, W.C. Funk, R.C. Fleischer, C. Smith, T.S. Sillett, K.Ralls, W. Teeter, R. Vellanoweth, S.D. Newsome. Tracking the diet of an island canid across 7300 years of human cultural and environmental change. Quaternary Science Reviews. 146:147-160.

2016 Jeong C., A.T. Ozga, D. Witonsky, H. Malmström, H. Edlund, C.A. Hofman, R. Hagan, M. Jakobsson, C.M. Lewis, Jr., M. Aldenderfer, A. Di Rienzo, C. Warinner. Long-term genetic stability and a high altitude East Asian origin for the peoples of the high valleys of the Himalayan arc. PNAS. Early Edition.

2016 Rick, T.C., L. Reeder-Myers, C.A. Hofman, D. Breitburg, R. Lockwood, G. Henkes, L. Kellogg, D. Lowery, M. Luckenbach, R.L. Mann, M. Ogburn, M.J. Southworth, J. Wah, J. Wesson, A.H. Hines. Millennial-Scale Sustainability of the Chesapeake Bay Native American Oyster Fishery. PNAS. Early Edition.

2016 West, C.F., S.M. Dunning, S. Ebbert, C.A. Hofman, P.A. Saltonstall, J. Withrow. Archaeology and Invasive Species Management: The Chirikof Island Project. Journal of Island and Coastal Archaeology. 00:1-5.

2016 Funk, W.C, R.E. Lovich, P.A. Hohenlohe, C.A. Hofman, S.A. Morrison, T.S. Sillett, C.K. Ghalambor, J.E. Maldonado, T.C. Rick, M.D. Day, N.R. Polato, S.W. Fitzpatrick, T.J. Coonan, K.R. Crooks, A. Dillon, D.K. Garcelon, J.L. King, C.L. Boser, L.M. Lyren, E.E. Boydston, N. Gould, W.F. Andelt. Drift drives divergence: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis). Molecular Ecology. Early View. PDF

2016 Ozga, Andrew T., Maria A. Nieves-Colon, Tanvi P. Honap, Krithivasan Sankaranarayanan, Courtney A. Hofman, George R. Milner, Cecil M. Lewis Jr., Anne C. Stone, and Christina Warinner. Successful Enrichment and Recovery of Whole Mitochondrial Genomes From Ancient Human Dental Calculus. American Journal of Physical Anthropology. Early View. PDF

2015 Hofman, Courtney A., Torben C. Rick, Robert Fleischer, Jesus Maldonado. Conservation Archaeogenomics: Ancient DNA and Biodiversity in the Anthropocene. Trends in Ecology and Evolution 30:9, 540-549. PDF

2015 Hofman, Courtney A., Torben C. Rick, Melissa Hawkins, W. Chris Funk, Katherine Ralls, Christina Boser, Paul W. Collins, Tim Coonan, Julie King, Scott Morrison, Seth D. Newsome, T. Scott Sillett, Robert Fleischer, Jesus Maldonado. Mitochondrial genomes suggest rapid evolution of dwarf California Channel Islands foxes (Urocyon littoralis). PLOS One 10:2. PDF

2015 Hawkin, Melissa, Courtney A. Hofman, Taylor Callicrate, Molly McDonough, Mirian Tsuchiya, Eliecer Gutierrez, Kristofer Helgen, Jesus Maldonado. In Solution Hybridization for Mammalian Mitogenome enrichment: Pros, Cons, and Challenges Associated with Multiplexing Degraded DNA. Molecular Ecology Resources Early View. PDF

2014 Rick, Torben C., T. Scott Sillett, Cameron K. Ghalambor, Courtney A. Hofman, Katherine Ralls, R. Scott Anderson, Christina Boser, Todd J. Braje, Dan Cayan, Terry Chesser, Paul W. Collins, Jon M. Erlandson, Kate R. Faulkner, W. Chris Funk, Robert Fleischer, Ann Huston, Julie King, Lyndal Laughrin, Kathryn McEachern, Jesus Maldonado, Daniel R. Muhs, Seth D. Newsome, Leslie Reeder-Myers, Christopher Still, Scott A. Morrison. Ecological Change on California’s Channel Islands from the Pleistocene to the Anthropocene. BioScience, 64:8, 680-692. PDF

2014 Hofman, Courtney A., Torben C. Rick. The Dogs of CA-SRI-2: Zooarchaeology, Diet and Context  of Canis familiaris from Santa Rosa Island, California, USA.  Ethnobiology Letters 5, 65-76. PDF

2012  Rick,Torben C., Courtney A. Hofman, Todd J. Braje, Jesus Maldonado, T. Scott Sillett, Kevin Danchisko, Jon M. Erlandson. Flightless ducks, giant mice, and pygmy mammoths: Late Quaternary extinctions on California’s Channel Islands. World Archaeology 44:1, 3-20. PDF