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

 

 

 

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*. 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.

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.

Sankaranarayanan K, Ozga AT, Warinner C, Tito RY, Obregon-Tito AJ, Xu J, Gaffney PM, Jervis L, Cox D, Stephens L, Foster M, Tallbull G, Spicer P, Lewis CM. (2015) Gut microbiome diversity among Cheyenne & Arapaho Individuals in Western Oklahoma. Current Biology, doi: http://dx.doi.org/10.1016/j.cub.2015.10.060.

Ziesemer KA, Mann AE, Sankaranarayanan K, Schroeder H, Ozga AT, Brandt BW, Zaura E, Waters-Rist A, Hoogland M, Salazar Garcia DC, Aldenderfer M, Speller C, Hendy J, Weston DA, MacDonald SJ, Thomas GH, Collins MJ, Lewis CM, Hofman C, Warinner C*. (2015) Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. Scientific Reports 5, 16498. doi: 10.1038/srep16498.

Ozga AT, Tito RY, Kemp BM, Matternes H, Obregon-Tito A, Neal L, and Lewis CM. (2015) Origins of an unmarked Georgia cemetery using ancient DNA analysis. Human Biology Open Access Pre-Prints. Paper 82.

Warinner C, Lewis CM. (2015) Microbiome and health in past and present human populations. American Anthropologist 117(4): 740-741, doi:10.1111/aman.12367.

Obregon-Tito A, Tito R, Metcalf J, Sankaranarayanan K, Clemente J, Ursell L, Xu Z, Van Treuren W, Knight R, Gaffney P, Spicer P, Lawson P, Marin-Reyes L, Trujillo-Villarroel O, Foster M, Guija-Poma E, Troncoso-Corzo L, Warinner C, Ozga A, Lewis CM. (2015) Subsistence strategies in traditional societies distinguish gut microbiomes. Nature Communications 6, 6505.

Patel N, Tito R, Obregon-Tito A, O’Neal L, Trujillo-Villaroel O, Marin-Reyes L, Troncoso-Corzo L, Guija-Poma E, Hamada M, Uchino Y, Lewis CM, Lawson PA* (2015) Ezakiella peruensis gen. nov., sp. nov. isolated from human fecal sample from a coastal traditional community in Peru. Anaerobe 32, 43-48.

Warinner C, Speller C, Collins MJ, Lewis CM* (2015) Ancient Human Microbiomes. Journal of Human Evolution 79, 125-136. http://dx.doi.org/10.1016/j.jhevol.2014.10.016

Warinner C*, Speller C, Collins MJ (2014) A New Era in Paleomicrobiology: Prospects for Ancient Dental Calculus as a Long-Term Record of the Human Oral Microbiome. Philosophical Transactions of the Royal Society B 370: 20130376. http://dx.doi.org/10.1098/rstb.2013.0376

Warinner C*, Hendy J, Speller C, Cappellini E, Fischer R, Trachsel C, Arneborg J, Lynnerup N, Craig OE, Swallow DM, Fotakis A, Christensen RJ, Olsen J, Liebert A, Montalva N, Fiddyment S, Mackie M, Canci A, Bouwman A, Rühli F, Gilbert MTP, Collins MJ* (2014) Direct Evidence of Milk Consumption from Ancient Human Dental Calculus. Scientific Reports 4, 7104. doi:10.1038/srep07104.

Curtis Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J, The Scientists for Advancement of Microbiome Research, White O (2014). Advancing the Microbiome Research Community. Cell 159(2):227-230.

Natallia Shved, Cordula Haas, Christina Papageorgopoulou, Guelfirde Akguel, Katja Paulsen, Abigail Bouwman, Christina Warinner, Frank Rühli (2014) Post Mortem DNA Degradation of Human Tissue Experimentally Mummified in Salt. PLoS ONE 9(10): e110753. doi:10.1371/journal.pone.0110753.

Warinner C*, Rodrigues JFM, Vyas R, Trachsel C, Shved N, Grossmann J, Radini A, Hancock Y, Tito RY, Fiddyment S, Speller C, Hendy J, Charlton S, Luder HU, Salazar-García DC, Eppler E, Seiler R, Hansen L, Samaniego Castruita JA, Barkow-Oesterreicher S, Teoh KY, Kelstrup C, Olsen JV, Nanni P, Kawai T, Willerslev E, von Mering C, Lewis, Jr. CM, Collins MJ, Gilbert MTP, Rühli F, Cappellini E* (2014). Pathogens and host immunity in the ancient human oral cavity. Nature Genetics 46(4):336-344. doi:10.1038/ng.2906.

Kruettli A, Bouwman A, Akguel G, Della Casa P, Ruehli F, Warinner C* (2014). Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910) in medieval Central Europe. PLoS ONE 9(1), e86251.

Xu J, Fonseca DM, Hamilton GC, Hoelmer KA, Nielsen AL (2014). Tracing the origin of US brown marmorated stink bugs, Halyomorpha haly. Biological Invasions 16: 153-166.

Cleeland LM, M Reichard, RY Tito, K Reinhard, CM Lewis Jr. (2013) Clarifying Prehistoric Parasitism from a Complementary Morphological and Molecular ApproachJournal of Archaeological Science. 40(7): 3060–3066. PMID: 23645967.

Guedes J, Carrasco D, Flad R, Fosse E, Herzfeld M, Lamberg-Karlovsky K, Lewis C, Liebmann M, Meadow R, Patterson N, Price M, Reiches M, Richardson S, Shattuck-Heidorn H, Ur J, Urton G, Warinner C. 2013. Is poverty in our genes? A reply to Ashraf and Galor. Current Anthropology 54(1): 71-79. For links to media coverage, click here.

Warinner C, Robles García N, and Tuross N. 2013. Maize, beans and the floral isotopic diversity of highland Oaxaca, Mexico. Journal of Archaeological Science 40(2):868-873.

Lewis, CM, A Obregón, RY Tito, MW Foster, PG Spicer, (2012), Human Microbiome Project: Lessons from Human Genomics. Trends in Microbiology 20(1):1-4. PMCID: PMC3709440.

Human Microbiome Project Consortium, (2012), Structure, function and diversity of the healthy human microbiome. Nature 486(7402):207-214. PMCID: PMC3564958.

Human Microbiome Project Consortium, (2012), A framework for human microbiome research. Nature 486(7402):215-221. PMCID: PMC3377744.

Xu J, Chu KH (2012). Genome scan of the mitten crab Eriocheir sensu stricto in East Asia: population differentiation, hybridization and adaptive speciation. Molecular Phylogenetics and Evolution 64: 118-129.

Warinner C*, Robles García N, Spores R, Tuross N. 2012. Disease, demography, and diet in early colonial New Spain: Investigation of a 16th century Mixtec epidemic cemetery at Teposcolula Yucundaa. 2012. Latin American Antiquity 23(4):467-489.

Tito, RY, D Knights, J Metcalf, AJ Obregon-Tito, L Cleeland, F Najar, B Roe, K Reinhard, K Sobolik, S Belknap, M Foster, P Spicer, R Knight, CM Lewis, Jr, (2012), Insights from Characterizing Extinct Human Gut Microbiomes. PLoS ONE 7(12): e51146. PMCID: PMC3521025.

Schlebusch CM, CM Lewis Jr, M Vahter, K Engström, RY Tito, AJ Obregón-Tito, D Huerta, SI Polo, AC Medina, TD Brutsaert, G Concha, M Jakobsson, K Broberg, (2012), Possible Positive Selection for an Arsenic-Protective Haplotype in Humans. Environmental Health Perspectives 121(1):53-8. PMCID: PMC3553437.

Barber BR, Xu J, Pérez-Losada M, Jara CG, Crandall KA (2012). Conflicting evolutionary patterns due to mitochondrial introgression and multilocus phylogeography of the Patagonian freshwater crab Aegla neuquensis. PLoS ONE 7(6): e37105.

Sankaranarayanan K, Timofeeff MN, Spathis R, Lowenstein TK, Lum JK (2011) Ancient Microbes from Halite Fluid Inclusions: Optimized Surface Sterilization and DNA Extraction. PLoS ONE 6(6): e20683.

Tito, RY, SL Belknap III, KD Sobolik, RC Ingraham, LM Cleeland, CM Lewis Jr, (2011), DNA from early Holocene American dog. American Journal of Physical Anthropology 145(4): 653–657. PMID: 21541929.

Warinner C,* d’Alpoim Guedes J, and Goode D. 2011. Paleobot.org: Establishing open-access online reference collections for archaeobotanical research. Vegetation History and Archaeobotany 20(3):241-244.

Reiff DM, Spathis R, Chan CW, Vilar MG, Sankaranarayanan K, Lynch D, Ehrlich E, Kerath S, Chowdhury R, Robinowitz L, Lum JK, Garruto RM (2011) Inherited and somatic mitochondrial DNA mutations in Guam amyotrophic lateral sclerosis and parkinsonism-dementia. Neurological Sciences 32: 883-892.

Xu J, Fonseca DM (2011). One-way sequencing of multiple amplicons from tandem repetitive mitocondrial DNA control region. Mitochondrial DNA 22: 155-158

Lewis CM, Jr, (2010), Hierarchical modeling of genome-wide STR markers infers Native American prehistory. American Journal of Physical Anthropology 141(2): 281 – 289. PMID: 19672848.

Warinner C* and Tuross N. 2010. Tissue isotopic enrichment associated with growth depression in a pig: implications for archaeology and ecology. American Journal of Physical Anthropology 141:486-493.

Lewis CM, Jr, (2009), Difficulties in rejecting a local ancestry with mtDNA haplogroup data in the South Central Andes. Latin American Antiquity 20(1): 76-90.

Xu J, Pérez-Losada M, Jara CG and Crandall KA (2009). Pleistocene glaciation leaves deep signature on the freshwater crab Aegla alacalufi in Chilean Patagonia. Molecular Ecology 18: 904-918

Warinner C* and Tuross N. 2009. Alkaline cooking and stable isotope diet-tissue discrimination in swine: archaeological implications. Journal of Archaeological Science 36(8):1690-1697.

Xu J, Chan TY, Tsang LM, Chu KH (2009). Phylogeography of the mitten crab Eriocheir sensu stricto in East Asia: Pleistocene isolation, population expansion and secondary contact. Molecular Phylogenetics and Evolution 52: 45-56.

Tito RY, S Macmil, G Wiley, F Najar, L Cleeland, C Qu, P Wang, F Romagne, S Leonard, AJ Ruiz, K Reinhard, BA Roe, CM Lewis, (2008), Phylotyping and Functional Analysis of Two Ancient Human Microbiomes. PLoS ONE 3(11):e3703. PMCID: PMC2577302.

Verrelli BC, CM Lewis, AC Stone, GH Perry, (2008), Different Selective Pressures Shape the Molecular Evolution of Color Vision in Chimpanzee and Human Populations. Molecular Biology and Evolution 25(12):2735-2743. PMCID: PMC2721556.

Tuross N,* Warinner C, Kirsanow K and Kester C. 2008. Organic Oxygen and Hydrogen Isotopes in a Porcine Controlled Dietary Study. Rapid Communications in Mass Spectrometry 22(11):1741-1745.

Lewis CM and JC Long, (2008), Native South American genetic structure and prehistory inferred from hierarchical modeling of mtDNA. Molecular Biology and Evolution. 25(3):478-486. PMID: 18222947.

Wang S., CM Lewis, Jr, M Jakobsson, S Ramachandran, N Ray, G Bedoya, W Rojas, M Parra, JA Molina, C Gallo, G Mazzotti, G Poletti, K Hill, AM Hurtado, D Labuda, W Klitz, R Barrantes, MC Bortolini, FM Salzano, ML Petzl-Erler, LT Tsuneto, E Llop, F Rothhammer, L Excoffier, MW Feldman, NA Rosenberg, A Ruiz-Linares, (2007), Genetic variation and population structure in Native Americans. PLoS genetics. 3(11):e185. PMCID: PMC2082466.

Lewis CM, B Lizárraga, RY Tito, PL Gonzalez, GCIDl Flor, ACM Collque, REM Abanto, SIP Santillán, FADl Cruz, AMC Fernandez and AC Stone, (2007), Mitochondrial DNA and the Peopling of South AmericaHuman Biology, 79(2):159-178. PMID: 18027812.

Lewis CM, Jr, JE Buikstra, AC Stone, Ancient DNA and genetic continuity in the South Central Andes. (2007) Latin American Antiquity.18(2):145-160.

Lewis CM, Jr, R Tito, B Lizárraga, AC Stone, (2004), Land, Languages, and Loci: MtDNA in Native Americans and the Genetic History of Peru. American Journal of Physical Anthropology. 127(3):351-360.

Monsalve, MV, AC Stone, CM Lewis, A Rempel, M Richards, D Strathoff, DV Devine, (2002) Molecular analysis of the Kwaday Dän Sinchi ancient remains found in a glacier in Canada.  American Journal of Physical Anthropology. 119:288-291.

Lawson, AE, CM Lewis, and JP Birk, Why Do Students “Cook” Lab Data?  A Case Study of the Tenacity of Misconceptions. (1999) Journal of College Science Teaching. 24(3):191-198.

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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