Publications

Author names of LMAMR members are shown in bold; corresponding authorship is indicated by an asterisk (*).

JOURNAL ARTICLES

NATGENCOVER-130  CURRENTANTHRO-130  TrendsCover-130  cover art  Dec2012_warinner_laqcover-130

 

 

 

Patrick Lypaczewski, Johanna Hoshizaki, Wen-Wei Zhang, Laura-Isobel McCall, John Torcivia-Rodriguez, Vahan Simonyan, Amanpreet Kaur, Ken Dewar, Greg Matlashewski (2018). A complete Leishmania donovani reference genome identifies novel genetic variations associated with virulence. Scientific Reports Volume 8, Article number: 16549. https://www.nature.com/articles/s41598-018-34812-x

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 (2018). The genetic prehistory of the Andean highlands 7,000 Years BP though European contact. Science Advances (4)11. doi: 10.1126/sciadv.aau4921 http://advances.sciencemag.org/content/4/11/eaau4921

Choongwon Jeong, Shevan Wilkin, Tsend Amgalantugs, Abigail S.Bouwman, William Timothy Treal Taylor, Richard W. Hagan, SabriBromage, Soninkhishig Tsolmon, Christian Trachsel, Jonas Grossmann, Judith Littleton, Cheryl A. Makarewicz, John Krigbaum, Marta Burri, AshleyScott, Ganmaa Davaasambuu, Joshua Wright, Franziska Irmer, ErdeneMyagmar, Nicole Boivin, Martine Robbeets, Frank J. Rühli, JohannesKrause, Bruno Frohlich, Jessica Hendy, Christina Warinner (2018). Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe. Proceedings of the National Academy of Sciences. http://www.pnas.org/content/early/2018/10/31/1813608115

Palmer E, Tushingham S, and Kemp BM (2018). Human use of small forage fish: Improved ancient DNA species identification techniques reveal long term record of sustainable mass harvesting of smelt fishery in the northeast Pacific Rim. Journal of Archaeological Science 99:143-152.

Kathryn Ashford, Raven Blankenship, Wyatt Carpenter, Isaac Wheeler and Douglas Gaffin (2018). Response of the eastern sand scorpion, Paruroctonus utahensis, to air movement from a moth analog. Journal of Arachnology 46(2). https://doi.org/10.1636/JoA-S-17-097.1

Courtney A. Hofman, Torben C. Rick, Jon M. Erlandson, Leslie Reeder-Myers, Andreanna J. Welch & Michael Buckley (2018). Collagen Fingerprinting and the Earliest Marine Mammal Hunting in North America. Scientific Reports 8:10014. https://doi.org/10.1038/s41598-018-28224-0

Jessica Hendy, Christina Warinner, Abigail Bouwman, Matthew J. Collins, Sarah Fiddyment, Roman Fischer, Richard Hagan, Courtney A. Hofman, Malin Holst, Eros Chaves, Lauren Klaus, Greger Larson, Meaghan Mackie, Krista McGrath, Amy Z. Mundorff, Anita Radini, Huiyun Rao, Christian Trachsel, Irina M. Velsko, Camilla F. Speller (2018). Proteomic evidence of dietary sources in ancient dental calculus. Proc. R. Soc. B. 285(1883). https://dx.doi.org/10.6084/m9.figshare.c.4150424.

Allison E. Mann, Susanna Sabin, Kirsten Ziesemer,Åshild J. Vågene, Hannes Schroeder, Andrew T. Ozga, Krithivasan Sankaranarayanan, Courtney A. Hofman, James A. Fellows Yates, Domingo C. Salazar-García, Bruno Frohlich, Mark Aldenderfer, Menno Hoogland, Christopher Read, George R. Milner, Anne C. Stone, Cecil M. Lewis Jr., Johannes Krause, Corinne Hofman, Kirsten I. Bos, and Christina Warinner* (2018). Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. Scientific Reports 8:9822. https://doi.org/10.1038/s41598-018-28091-9

Johnson BM, Kemp BM, and Thorgaard GH (2018). Increased mitochondrial DNA diversity in ancient Columbia River basin Chinook salmon Oncorhynchus tshawytscha. PLoS One 13:e0190059.

Conrad C, Barceló LP, Seminoff JA, Tomaszewicz CT, Labonte M, Kemp BM, Jones EL, Stoyka M, Bruner K, and Pastron A (2018). Ancient DNA Analysis and Stable Isotope Ecology of Sea Turtles (Cheloniidae) from the Gold Rush-era (1850s) Eastern Pacific Ocean. Open Quaternary 4:1-13. http://doi.org/10.5334/oq.41

Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, Gonzalez A, Kosciolek T, McCall LI, McDonald D, Melnik AV, Morton JT, Navas J, Quinn RA, Sanders JG, Swafford AD, Thompson LR, Tripathi A, Xu ZZ, Zaneveld JR, Zhu Q, Caporaso JG, Dorrestein PC. Nat Rev Microbiol. 2018 May 23. doi: 10.1038/s41579-018-0029-9. PMID: 29795328

McCall L-I, Tripathi A, Vargas F, Knight R, Dorrestein PC, Siqueira-Neto JL (2018) Experimental Chagas disease-induced perturbations of the fecal microbiome and metabolome. PLoS Negl Trop Dis 12(3): e0006344. https://doi.org/10.1371/journal.pntd.0006344

Honap TP, Pfister L-A, Housman G, Mills S, Tarara RP, Suzuki K, Cuozzo FP, Sauther ML, Rosenberg MS, Stone AC (2018) Mycobacterium leprae genomes from naturally infected nonhuman primates. PLoS Negl Trop Dis 12(1): e0006190.  doi.org/10.1371/journal.pntd.0006190

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

Shirazi, S., Rick, T.C., Erlandon, J.M., and Hofman, C.A. (2017) A tale of two mice: A trans-Holocene record of Peromyscus nesodytes and Peromyscus maniculatus at Daisy Cave, San Miguel Island, California. The Holocene. doi.org/10.1177/0959683617744266

Benjak A, Honap TP, Avanzi C, Becerril-Villanueva L, García I, Rojas-Espinosa O, Stone AC, and Cole ST (2017). Insights from the genome sequence of Mycobacterium lepraemurium: massive gene decay and reductive evolution. mBio 8:e01283-17

Kemp BM, Judd K, Monroe C, Eerkens JW, Hilldorfer LA, Cordray C, Schad R, Reams E, Ortman SG, Kohler TA. Prehistoric Mitochondrial DNA of Domesticate Animals Supports a 13th century Exodus from the Northern US Southwest. 2017. PloS ONE 12(7): e0178882

McCall LI, Morton JT, Bernatchez JA, de Siqueira-Neto JL, Knight R, Dorrestein PC, McKerrow JH. Location, Location, Location: Five Facts about Tissue Tropism and Pathogenesis. Anal Chem. 2017 Oct 3;89(19):10414-10421. doi: 10.1021/acs.analchem.7b02423. Epub 2017 Sep 22. PMID:28892370

Velsko IM, Overmyer KA, Speller C, Loe L, Sankaranarayanan K, Collins M, Lewis CM, Bautista Rodriguez J, Chaves E, Coon JJ, Larson G, Warinner C*. 2017. The dental calculus metabolome in modern and historic samples. Metabolomics 13:134

Warinner C, Hendy J. 2017. Ancient cultures: The archaeology of dairy and the enduring legacy of ‘heirloom’ microbes. Mælkeritidende 21:10-11.

Warinner C, Herbig A, Mann AE, Fellows Yates JA, Weiss CL, Burbano HA, Orlando L, Krause J. (2017) A robust framework for microbial archaeology. Annu. Rev. Genom. Hum. Genet., in press. http://www.annualreviews.org/doi/abs/10.1146/annurev-genom-091416-035526

Velsko I, Warinner C*. (2017) Bioarchaeology of the human microbiome. Bioarchaeology International, in press.

Lindo J, Achilli A, Perego U, Archer D, Valdiosera C, Petzelt B, Mitchell J, Worl R, Dixon EJ, Fifield T, Rasmussen M, Willerslev E, Cybulski J, Kemp BM*, DeGiorgio M, and Malhi RS.  (2017) Ancient individuals from the North American Northwest Coast reveal 10,000 years of regional genetic continuity.  Proceedings of the National Academy of Science USA, in press.

Winters M, Monroe C, Barta JL, and Kemp BM*.  (2017) Are We Fishing or Catching? Evaluating the Efficiency of Bait Capture of CODIS Fragments. Forensic Science International: Genetics, in press.

Bouwman A, Shved N, Akgül G, Rühli F, Warinner C*. (2017) Ancient DNA investigation of a medieval German cemetery confirms long-term stability of CCR5-∆32 allele frequencies in Central Europe. Human Biology, in press.

Johnson B, and Kemp BM.  (2017) Rescue PCR: Reagent-rich PCR recipe improves amplification of degraded DNA extracts. Journal of Archaeological Science: Reports 11: 683-694

Olsen K, White CD, Longstaffe FJ, Rühli FJ, Warinner C, and Salazar-Garcia DC. (2017) Isotopic anthropology of rural German medieval diet: intra- and inter-population variability. Archaeological and Anthropological Sciences, in press. doi:10.1007/s12520-016-0432-y

Schnorr S, Sankaranarayanan K, Lewis CM, Warinner C*. (2016) Insights into human evolution from ancient and contemporary microbiome studies. Current Opinion in Genetics and Development 41:14-26.

Warinner C. (2016) Dental calculus and the evolution of the human oral microbiome. California Dental Association Journal 44(7):411-420.

Jeong C, Ozga AT, Witonsky D, Malmstrom H, Edlund H, Hofman CA, Hagan RW, Jakobsson M, Lewis CM, Aldenderfer M, Di Rienzo A, Warinner C*. (2016) Long-term genetic stability and a high altitude East Asian origin for the peoples of the high valleys of the Himalayan arc. Proceedings of the National Academy of Sciences USA 113(27):7485-7490.

Patel NTito RObregon-Tito AO’Neal L, Trujillo-Villaroel O, Marin-Reyes L, Troncoso-Corzo L, Guija-Poma E, Lewis CMLawson PA* (2016) Peptoniphilus catoniae sp. nov., isolated from a human faecal sample from a traditional Peruvian coastal community. International Journal of Systematic and Evolutionary Microbiology 66:2019-2024.

McCall LI, Siqueira-Neto JL, McKerrow JH. PLoS Pathog. 2016 May 26;12(5):e1005519. doi: 10.1371/journal.ppat.1005519. eCollection 2016 May.

Petras D, Nothias LF, Quinn RA, Alexandrov T, Bandeira N, Bouslimani A, Castro-Falcón G, Chen L, Dang T, Floros DJ, Hook V, Garg N, Hoffner N, Jiang Y, Kapono CA, Koester I, Knight R, Leber CA, Ling TJ, Luzzatto-Knaan T, McCall LI, McGrath AP, Meehan MJ, Merritt JK, Mills RH, Morton J, Podvin S, Protsyuk I, Purdy T, Satterfield K, Searles S, Shah S, Shires S, Steffen D, White M, Todoric J, Tuttle R, Wojnicz A, Sapp V, Vargas F, Yang J, Zhang C, Dorrestein PC. Anal Chem. 2016 Nov 15;88(22):10775-10784. Epub 2016 Oct 24.

Ozga AT, Nieves-Colón MA, Honap T, Sankaranarayanan K, Hofman C, Milner G, Lewis CM, Stone AC, Warinner C*. (2016) Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. American Journal of Physical Anthropology 160:220-228.

Ozga AT, Sankaranarayanan K, Tito RY, Obregon-Tito AJ, Foster M, Tallbull G, Spicer PWarinner C, Lewis Jr. CMOral microbiome characterization of Cheyenne and Arapaho individuals of OklahomaAmerican Journal of Physical Anthropology, in press. doi: 10.1002/ajpa.23033

Patel NTito RObregon-Tito AO’Neal L, Trujillo-Villaroel O, Marin-Reyes L, Troncoso-Corzo L, Guija-Poma E, Lewis CMLawson PA* (2016) Peptoniphilus catoniae sp. nov., isolated from a human faecal sample from a traditional Peruvian coastal community. International Journal of Systematic and Evolutionary Microbiology 66:2019-2024.

Melissa E Bell, Kathryn A Bernard, Susan M Harrington, Nisha B P.atel, Trudy-Ann Tucker, Maureen G Metcalfe, John R McQuiston (2016) Lawsonella clevelandensis gen. nov., sp. nov., a new member of the suborder Corynebacterineae isolated from human abscesses. International Journal of Systematic and Evolutionary Microbiology

 

BOOKS AND BOOK CHAPTERS

PeBOT_cover-130  BioMolc-130  VeiledBrightness-130  DeadTales-130  raceandracism-130

 

 

 

Marston JM, d’Alpoim Guedes J, Warinner C, eds. Method and Theory in Paleoethnobotany. University Press of Colorado, 2014. Available for order here.

Houston S, Brittenham C, Mesick C, Tokovinine A, and Warinner C. Veiled Brightness: A History of Ancient Maya Color. Austin: University of Texas Press, 2009. Available for order here.

Warinner C and d’Alpoim Guedes J. Digitizing the archaeobotanical record. In: Marston JM, d’Alpoim Guedes J, Warinner C, eds. Method and Theory in Paleoethnobotany. University Press of Colorado Boulder, 2014. Available for order here.

Warinner C. From the ground up: Advances in stable isotope-based paleodietary inference. Marston JM, d’Alpoim Guedes J, Warinner C, eds. Method and Theory in Paleoethnobotany. University Press of Colorado, Boulder, 2014.

Marston, JM, d’Alpoim Guedes J, and Warinner C. “Paleoethnobotanical Method and Theory in the 21st Century,” in Marston JM, d’Alpoim Guedes J, and Warinner C, eds. Method and Theory in Paleoethnobotany. University Press of Colorado, Boulder, 2014.

Warinner C and Tuross N. “Ancient DNA and Stable Isotope Analysis of the Teposcolula Grand Plaza Cemetery,” in Nelly Robles-García, ed.  Yucundaa: La cuidad mixteca Yucundaa-Pueblo Viejo de Teposcolula y su transformación prehispánica-colonial. Instituto Nacional de Antropología e Historia, in press.

Tuross N, Warinner C, and Robles Garcia N. “Evidence for Mixtec/Dominican Interaction from the Radiocarbon Dates at Yucundaa (Pueblo Viejo de Teposcolula),” in Nelly Robles-García, ed.  Yucundaa: La cuidad mixteca Yucundaa-Pueblo Viejo de Teposcolula y su transformación prehispánica-colonial. Instituto Nacional de Antropología e Historia, in press.

Lewis, CM, Jr and TA Tung. Considerations when sampling human osteological remains. In The Dead Tell Tales: Essays in Honor of Jane E. Buikstra, edited by B. Ó. Donnabháin and M. C. Lozada. Cotsen Institute of Archaeology, UCLA, Los Angeles, CA, 2013.

Lewis C., Spicer P, Human Microbiome Research and Indigenous Communities, Project. (2012) In: Nelson K. (Ed.) Encyclopedia of Metagenomics: SpringerReference. Springer-Verlag Berlin Heidelberg.

Long, JC, N Scott, and CM Lewis, Jr, Race, Genetics, in Health. (2007) In Encyclopedia of Race and Racism. John Moore ed. Macmillan Library Reference.

Lewis, CM, Jr, and AC Stone, MtDNA Diversity at the Archaeological Site of Chen Chen in Perú. (2005) In Biomolecular Archaeology: Genetic Approaches to the Past. D.Reed ed. Proceedings from the 19th Annual Visiting Scholar Conference, Southern Illinois University Press.

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