529 results on '"Warinner, Christina"'
Search Results
202. Subsistence strategies in traditional societies distinguish gut microbiomes.
- Author
-
Obregon-Tito, Alexandra J, Obregon-Tito, Alexandra J, Tito, Raul Y, Metcalf, Jessica, Sankaranarayanan, Krithivasan, Clemente, Jose C, Ursell, Luke K, Zech Xu, Zhenjiang, Van Treuren, Will, Knight, Rob, Gaffney, Patrick M, Spicer, Paul, Lawson, Paul, Marin-Reyes, Luis, Trujillo-Villarroel, Omar, Foster, Morris, Guija-Poma, Emilio, Troncoso-Corzo, Luzmila, Warinner, Christina, Ozga, Andrew T, Lewis, Cecil M, Obregon-Tito, Alexandra J, Obregon-Tito, Alexandra J, Tito, Raul Y, Metcalf, Jessica, Sankaranarayanan, Krithivasan, Clemente, Jose C, Ursell, Luke K, Zech Xu, Zhenjiang, Van Treuren, Will, Knight, Rob, Gaffney, Patrick M, Spicer, Paul, Lawson, Paul, Marin-Reyes, Luis, Trujillo-Villarroel, Omar, Foster, Morris, Guija-Poma, Emilio, Troncoso-Corzo, Luzmila, Warinner, Christina, Ozga, Andrew T, and Lewis, Cecil M
- Abstract
Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2-2.5 MB, coverage depth × 26-513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.
- Published
- 2015
203. Digitizing the archaeobotanical record
- Author
-
Marston, John M, d'Alpoim Guedes, Jade, Warinner, Christina, Marston, J M ( John M ), d'Alpoim Guedes, J ( Jade ), Warinner, C ( Christina ), Marston, John M, d'Alpoim Guedes, Jade, Warinner, Christina, Marston, J M ( John M ), d'Alpoim Guedes, J ( Jade ), and Warinner, C ( Christina )
- Published
- 2015
204. From the ground up: Advances in stable isotope-based paleodietary inference
- Author
-
Marston, John M, d'Alpoim Guedes, Jade, Warinner, Christina, Marston, J M ( John M ), d'Alpoim Guedes, J ( Jade ), Warinner, C ( Christina ), Marston, John M, d'Alpoim Guedes, Jade, Warinner, Christina, Marston, J M ( John M ), d'Alpoim Guedes, J ( Jade ), and Warinner, C ( Christina )
- Published
- 2015
205. Direct evidence of milk consumption from ancient human dental calculus
- Author
-
Warinner, Christina, Hendy, Jessica, Speller, Camilla, Cappellini, Enrico, Fischer, Roman, Trachsel, Christian, Arneborg, Jette, Lynnerup, Niels, Craig, Oliver, Swallow, Dallas M., Fotakis, Anna Katerina, Christensen, R. J., Olsen, Jesper Velgaard, Liebert, Anke, Montalva, Nicholas, Fiddyment, Sarah, Mackie, Meaghan, Canci, Alessandro, Bouwman, Abigail, Ruhli, Frank, Gilbert, M Thomas P, Collins, Matthew J., Warinner, Christina, Hendy, Jessica, Speller, Camilla, Cappellini, Enrico, Fischer, Roman, Trachsel, Christian, Arneborg, Jette, Lynnerup, Niels, Craig, Oliver, Swallow, Dallas M., Fotakis, Anna Katerina, Christensen, R. J., Olsen, Jesper Velgaard, Liebert, Anke, Montalva, Nicholas, Fiddyment, Sarah, Mackie, Meaghan, Canci, Alessandro, Bouwman, Abigail, Ruhli, Frank, Gilbert, M Thomas P, and Collins, Matthew J.
- Published
- 2015
206. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
- Author
-
Ziesemer, Kirsten A., Mann, Allison E., Sankaranarayanan, Krithivasan, Schroeder, Hannes, Ozga, Andrew T., Brandt, Bernd W., Zaura, Egija, Waters-Rist, Andrea, Hoogland, Menno, Salazar-García, Domingo C., Aldenderfer, Mark, Speller, Camilla, Hendy, Jessica, Weston, Darlene A., MacDonald, Sandy J., Thomas, Gavin H., Collins, Matthew J., Lewis, Cecil M., Hofman, Corinne, Warinner, Christina, Ziesemer, Kirsten A., Mann, Allison E., Sankaranarayanan, Krithivasan, Schroeder, Hannes, Ozga, Andrew T., Brandt, Bernd W., Zaura, Egija, Waters-Rist, Andrea, Hoogland, Menno, Salazar-García, Domingo C., Aldenderfer, Mark, Speller, Camilla, Hendy, Jessica, Weston, Darlene A., MacDonald, Sandy J., Thomas, Gavin H., Collins, Matthew J., Lewis, Cecil M., Hofman, Corinne, and Warinner, Christina
- Published
- 2015
207. Anthropological Genetics
- Author
-
Kitchen, Andrew, primary, Non, Amy L., additional, Gravlee, Clarence C., additional, Mulligan, Connie J., additional, Warinner, Christina, additional, Lewis, Cecil M., additional, Bankoff, Richard J., additional, Randrianatoandro, Heritiana D. D., additional, Perry, George H., additional, Malhi, Ripan S., additional, Bader, Alyssa C., additional, and Raff, Jennifer, additional
- Published
- 2015
- Full Text
- View/download PDF
208. Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma
- Author
-
Sankaranarayanan, Krithivasan, primary, Ozga, Andrew T., additional, Warinner, Christina, additional, Tito, Raul Y., additional, Obregon-Tito, Alexandra J., additional, Xu, Jiawu, additional, Gaffney, Patrick M., additional, Jervis, Lori L., additional, Cox, Derrell, additional, Stephens, Lancer, additional, Foster, Morris, additional, Tallbull, Gloria, additional, Spicer, Paul, additional, and Lewis, Cecil M., additional
- Published
- 2015
- Full Text
- View/download PDF
209. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
- Author
-
Ziesemer, Kirsten A., primary, Mann, Allison E., additional, Sankaranarayanan, Krithivasan, additional, Schroeder, Hannes, additional, Ozga, Andrew T., additional, Brandt, Bernd W., additional, Zaura, Egija, additional, Waters-Rist, Andrea, additional, Hoogland, Menno, additional, Salazar-García, Domingo C., additional, Aldenderfer, Mark, additional, Speller, Camilla, additional, Hendy, Jessica, additional, Weston, Darlene A., additional, MacDonald, Sandy J., additional, Thomas, Gavin H., additional, Collins, Matthew J., additional, Lewis, Cecil M., additional, Hofman, Corinne, additional, and Warinner, Christina, additional
- Published
- 2015
- Full Text
- View/download PDF
210. Microbiome and Health in Past and Present Human Populations
- Author
-
Warinner, Christina, primary and Lewis, Cecil M., additional
- Published
- 2015
- Full Text
- View/download PDF
211. Isotopic anthropology of rural German medieval diet: intra- and inter-population variability.
- Author
-
Olsen, Karyn C., White, Christine D., Longstaffe, Fred J., Rühli, Frank J., Warinner, Christina, and Salazar-García, Domingo C.
- Subjects
ANTHROPOLOGY ,NITROGEN isotopes ,CARBON isotopes ,LOW-protein diet ,CARBONATES ,SKELETAL structures (Chemistry) ,BIVARIATE analysis - Abstract
This study investigates the diet of an eleventh century CE parish community located in northwestern Germany. We assessed the isotopic compositions of human (n = 24) and faunal (n = 17) bone collagen (δ
13 Ccol , δ15 Ncol ) and human structural carbonate (δ13 Csc ) using skeletal material recovered from the Dalheim cemetery. Traditional interpretation of the isotopic data indicates that Dalheim residents likely relied on a C3 plant-based diet and consumed some terrestrial animal products without evidence of marine resource input in the diet. Bivariate and multivariate models used as an additional means to assess diet indicate minor consumption of C4 plant foods in this community. The multivariate-isotope model identified regional similarities and differences in C4 plant/marine food consumption and in dietary protein sources by comparing data from Dalheim with those of other medieval sites from the published literature. We did not observe sex differences in this population but differences in δ15 Ncol suggest that juveniles consumed the lowest trophic level protein. [ABSTRACT FROM AUTHOR]- Published
- 2018
- Full Text
- View/download PDF
212. Proteomic evidence of dietary sources in ancient dental calculus.
- Author
-
Hendy, Jessica, Warinner, Christina, Bouwman, Abigail, Collins, Matthew J., Fiddyment, Sarah, Fischer, Roman, Hagan, Richard, Hofman, Courtney A., Holst, Malin, Chaves, Eros, Klaus, Lauren, Larson, Greger, Mackie, Meaghan, Mcgrath, Krista, Mundorff, Amy Z., Radini, Anita, Rao, Huiyun, Trachsel, Christian, Velsko, Irina M., and Speller, Camilla F.
- Subjects
- *
PROTEOMICS , *DIETARY supplements , *DENTAL calculus , *FOSSIL biomolecules , *MILK proteins , *LACTOGLOBULINS , *LOW-protein diet , *NONFICTION - Abstract
Archaeological dental calculus has emerged as a rich source of ancient biomolecules, including proteins. Previous analyses of proteins extracted from ancient dental calculus revealed the presence of the dietary milk protein b-lactoglobulin, providing direct evidence of dairy consumption in the archaeological record. However, the potential for calculus to preserve other food-related proteins has not yet been systematically explored. Here we analyse shotgun metaproteomic data from 100 archaeological dental calculus samples ranging from the Iron Age to the post-medieval period (eighth century BC to nineteenth century AD) in England, as well as 14 dental calculus samples from contemporary dental patients and recently deceased individuals, to characterize the range and extent of dietary proteins preserved in dental calculus. In addition to milk proteins, we detect proteomic evidence of foodstuffs such as cereals and plant products, as well as the digestive enzyme salivary amylase. We discuss the importance of optimized protein extraction methods, data analysis approaches and authentication strategies in the identification of dietary proteins from archaeological dental calculus. This study demonstrates that proteomic approaches can robustly identify foodstuffs in the archaeological record that are typically under-represented due to their poor macroscopic preservation. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
213. A guide to ancient protein studies.
- Author
-
Hendy, Jessica, Welker, Frido, Demarchi, Beatrice, Speller, Camilla, Warinner, Christina, and Collins, Matthew J.
- Published
- 2018
- Full Text
- View/download PDF
214. Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico.
- Author
-
Vågene, Åshild J., Herbig, Alexander, Campana, Michael G., Robles García, Nelly M., Warinner, Christina, Sabin, Susanna, Spyrou, Maria A., Andrades Valtueña, Aida, Huson, Daniel, Tuross, Noreen, Bos, Kirsten I., and Krause, Johannes
- Published
- 2018
- Full Text
- View/download PDF
215. Subsistence strategies in traditional societies distinguish gut microbiomes
- Author
-
Obregon-Tito, Alexandra J., primary, Tito, Raul Y., additional, Metcalf, Jessica, additional, Sankaranarayanan, Krithivasan, additional, Clemente, Jose C., additional, Ursell, Luke K., additional, Zech Xu, Zhenjiang, additional, Van Treuren, Will, additional, Knight, Rob, additional, Gaffney, Patrick M., additional, Spicer, Paul, additional, Lawson, Paul, additional, Marin-Reyes, Luis, additional, Trujillo-Villarroel, Omar, additional, Foster, Morris, additional, Guija-Poma, Emilio, additional, Troncoso-Corzo, Luzmila, additional, Warinner, Christina, additional, Ozga, Andrew T., additional, and Lewis, Cecil M., additional
- Published
- 2015
- Full Text
- View/download PDF
216. Ancient human microbiomes
- Author
-
Warinner, Christina, primary, Speller, Camilla, additional, Collins, Matthew J., additional, and Lewis, Cecil M., additional
- Published
- 2015
- Full Text
- View/download PDF
217. A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome
- Author
-
Warinner, Christina, primary, Speller, Camilla, additional, and Collins, Matthew J., additional
- Published
- 2015
- Full Text
- View/download PDF
218. Pathogens and host immunity in the ancient human oral cavity
- Author
-
Warinner, Christina, Rodrigues, João F Matias, Vyas, Rounak, Trachsel, Christian, Shved, Natallia, Grossmann, Jonas, Radini, Anita, Hancock, Y, Tito, Raul Y, Fiddyment, Sarah, Speller, Camilla, Hendy, Jessica, Charlton, Sophy, Luder, Hans Ulrich, Salazar-García, Domingo C, Eppler, Elisabeth, Seiler, Roger, Hansen, Lars H., Samaniego Castruita, Jose Alfredo, Barkow-Oesterreicher, Simon, Teoh, Kai Yik, Kelstrup, Christian, Olsen, Jesper Velgaard, Nanni, Paolo, Kawai, Toshihisa, Willerslev, Eske, von Mering, Christian, Lewis, Cecil M, Collins, Matthew J, Gilbert, M. Thomas P., Rühli, Frank, Cappellini, Enrico, Warinner, Christina, Rodrigues, João F Matias, Vyas, Rounak, Trachsel, Christian, Shved, Natallia, Grossmann, Jonas, Radini, Anita, Hancock, Y, Tito, Raul Y, Fiddyment, Sarah, Speller, Camilla, Hendy, Jessica, Charlton, Sophy, Luder, Hans Ulrich, Salazar-García, Domingo C, Eppler, Elisabeth, Seiler, Roger, Hansen, Lars H., Samaniego Castruita, Jose Alfredo, Barkow-Oesterreicher, Simon, Teoh, Kai Yik, Kelstrup, Christian, Olsen, Jesper Velgaard, Nanni, Paolo, Kawai, Toshihisa, Willerslev, Eske, von Mering, Christian, Lewis, Cecil M, Collins, Matthew J, Gilbert, M. Thomas P., Rühli, Frank, and Cappellini, Enrico
- Abstract
Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity and diet, thereby extending direct investigation of common diseases into the human evolutionary past.
- Published
- 2014
219. Post mortem DNA degradation of human tissue experimentally mummified in salt
- Author
-
Shved, Natallia, Haas, Cordula, Papageorgopoulou, Christina, Akgül, Gülfirde, Paulsen, Katja, Bouwman, Abigail, Warinner, Christina, Rühli, Frank, Shved, Natallia, Haas, Cordula, Papageorgopoulou, Christina, Akgül, Gülfirde, Paulsen, Katja, Bouwman, Abigail, Warinner, Christina, and Rühli, Frank
- Abstract
Mummified human tissues are of great interest in forensics and biomolecular archaeology. The aim of this study was to analyse post mortem DNA alterations in soft tissues in order to improve our knowledge of the patterns of DNA degradation that occur during salt mummification. In this study, the lower limb of a female human donor was amputated within 24 h post mortem and mummified using a process designed to simulate the salt dehydration phase of natural or artificial mummification. Skin and skeletal muscle were sampled at multiple time points over a period of 322 days and subjected to genetic analysis. Patterns of genomic fragmentation, miscoding lesions, and overall DNA degradation in both nuclear and mitochondrial DNA was assessed by different methods: gel electrophoresis, multiplex comparative autosomal STR length amplification, cloning and sequence analysis, and PCR amplification of different fragment sizes using a damage sensitive recombinant polymerase. The study outcome reveals a very good level of DNA preservation in salt mummified tissues over the course of the experiment, with an overall slower rate of DNA fragmentation in skin compared to muscle.
- Published
- 2014
220. Ancient DNA Analysis Reveals High Frequency of European Lactase Persistence Allele (T-13910) in Medieval Central Europe
- Author
-
Krüttli, Annina, Bouwman, Abigail S, Akgül, Gülfirde, Della Casa, Philippe; https://orcid.org/0000-0002-9787-0082, Rühli, Frank J, Warinner, Christina, Krüttli, Annina, Bouwman, Abigail S, Akgül, Gülfirde, Della Casa, Philippe; https://orcid.org/0000-0002-9787-0082, Rühli, Frank J, and Warinner, Christina
- Abstract
Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71-80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary histo
- Published
- 2014
221. Post Mortem DNA Degradation of Human Tissue Experimentally Mummified in Salt
- Author
-
Shved, Natallia, primary, Haas, Cordula, additional, Papageorgopoulou, Christina, additional, Akguel, Guelfirde, additional, Paulsen, Katja, additional, Bouwman, Abigail, additional, Warinner, Christina, additional, and Rühli, Frank, additional
- Published
- 2014
- Full Text
- View/download PDF
222. Pathogens and host immunity in the ancient human oral cavity
- Author
-
Warinner, Christina, primary, Rodrigues, João F Matias, additional, Vyas, Rounak, additional, Trachsel, Christian, additional, Shved, Natallia, additional, Grossmann, Jonas, additional, Radini, Anita, additional, Hancock, Y, additional, Tito, Raul Y, additional, Fiddyment, Sarah, additional, Speller, Camilla, additional, Hendy, Jessica, additional, Charlton, Sophy, additional, Luder, Hans Ulrich, additional, Salazar-García, Domingo C, additional, Eppler, Elisabeth, additional, Seiler, Roger, additional, Hansen, Lars H, additional, Castruita, José Alfredo Samaniego, additional, Barkow-Oesterreicher, Simon, additional, Teoh, Kai Yik, additional, Kelstrup, Christian D, additional, Olsen, Jesper V, additional, Nanni, Paolo, additional, Kawai, Toshihisa, additional, Willerslev, Eske, additional, von Mering, Christian, additional, Lewis, Cecil M, additional, Collins, Matthew J, additional, Gilbert, M Thomas P, additional, Rühli, Frank, additional, and Cappellini, Enrico, additional
- Published
- 2014
- Full Text
- View/download PDF
223. Ancient DNA Analysis Reveals High Frequency of European Lactase Persistence Allele (T-13910) in Medieval Central Europe
- Author
-
Krüttli, Annina, primary, Bouwman, Abigail, additional, Akgül, Gülfirde, additional, Della Casa, Philippe, additional, Rühli, Frank, additional, and Warinner, Christina, additional
- Published
- 2014
- Full Text
- View/download PDF
224. Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc.
- Author
-
Choongwon Jeong, Ozga, Andrew T., Witonsky, David B., Malmström, Helena, Edlund, Hanna, Hofman, Courtney A., Hagan, Richard W., Jakobsson, Mattias, Lewis, Cecil M., Aldenderfer, Mark S., Rienzo, Anna Di, and Warinner, Christina
- Subjects
PHYSIOLOGICAL adaptation ,TIBETANS ,GENOMES ,GENES ,HAPLOTYPES ,ALLELES ,PHYSIOLOGY - Abstract
The high-altitude transverse valleys [>3,000 m above sea level (masl)] of the Himalayan arc from Arunachal Pradesh to Ladahk were among the last habitable places permanently colonized by prehistoric humans due to the challenges of resource scarcity, cold stress, and hypoxia. The modern populations of these valleys, who share cultural and linguistic affinities with peoples found today on the Tibetan plateau, are commonly assumed to be the descendants of the earliest inhabitants of the Himalayan arc. However, this assumption has been challenged by archaeological and osteological evidence suggesting that these valleys may have been originally populated from areas other than the Tibetan plateau, including those at low elevation. To investigate the peopling and early population history of this dynamic high-altitude contact zone, we sequenced the genomes (0.04×-7.25×, mean 2.16×) and mitochondrial genomes (20.8×-1,311.0×, mean 482.1×) of eight individuals dating to three periods with distinct material culture in the Annapurna Conservation Area (ACA) of Nepal, spanning 3,150-1,250 y before present (yBP). We demonstrate that the region is characterized by long-term stability of the population genetic make-up despite marked changes in material culture. The ancient genomes, uniparental haplotypes, and high-altitude adaptive alleles suggest a high-altitude East Asian origin for prehistoric Himalayan populations. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
225. Brief communication: Tissue isotopic enrichment associated with growth depression in a pig: Implications for archaeology and ecology
- Author
-
Warinner, Christina, primary and Tuross, Noreen, additional
- Published
- 2009
- Full Text
- View/download PDF
226. Publisher Correction: Remembering St. Louis individual—structural violence and acute bacterial infections in a historical anatomical collection.
- Author
-
Austin, Rita M., Zuckerman, Molly, Honap, Tanvi P., Lee, Hedwig, Ward, Geoff K., Warinner, Christina, Sankaranarayanan, Krithivasan, and Hofman, Courtney A.
- Subjects
BACTERIAL diseases ,VIOLENCE ,MEMORY ,COLLECTIONS ,NEUROANATOMY - Published
- 2022
- Full Text
- View/download PDF
227. REPLY TO BEN-DOR ET AL.: Oral bacteria of Neanderthals and modern humans exhibit evidence of starch adaptation.
- Author
-
Warinner, Christina, Velsko, Irina M., and Yates, James A. Fellows
- Subjects
- *
NEANDERTHALS , *STARCH , *DENTAL calculus , *HUMAN beings , *BACTERIA - Published
- 2021
- Full Text
- View/download PDF
228. Organic oxygen and hydrogen isotopes in a porcine controlled dietary study
- Author
-
Tuross, Noreen, primary, Warinner, Christina, additional, Kirsanow, Karola, additional, and Kester, Cynthia, additional
- Published
- 2008
- Full Text
- View/download PDF
229. Is Poverty in Our Genes? A Critique of Ashraf and Galor, "The 'Out of Africa' Hypothesis, Human Genetic Diversity, and Comparative Economic Development," American Economic Review (Forthcoming).
- Author
-
d'Alpoim Guedes, Jade, Bestor, Theodore C., Carrasco, David, Flad, Rowan, Fosse, Ethan, Herzfeld, Michael, Lamberg-Karlovsky, Carl C., Lewis, Cecil M., Liebmann, Matthew, Meadow, Richard, Patterson, Nick, Price, Max, Reiches, Meredith, Richardson, Sarah, Shattuck-Heidorn, Heather, Ur, Jason, Urton, Gary, and Warinner, Christina
- Subjects
ECONOMIC development ,HUMAN genetic variation ,COMPARATIVE studies - Abstract
We present a critique of a paper written by two economists, Quamrul Ashraf and Oded Galor, which is forthcoming in the American Economic Review and which was uncritically highlighted in Science magazine. Their paper claims there is a causal effect of genetic diversity on economic success, positing that too much or too little genetic diversity constrains development. In particular, they argue that "the high degree of diversity among African populations and the low degree of diversity among Native American populations have been a detrimental force in the development of these regions." We demonstrate that their argument is seriously flawed on both factual and methodological grounds. As economists and other social scientists begin exploring newly available genetic data, it is crucial to remember that nonexperts broadcasting bold claims on the basis of weak data and methods can have profoundly detrimental social and political effects. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
230. Data integration for prediction of weight loss in randomized controlled dietary trials.
- Author
-
Nielsen, Rikke Linnemann, Helenius, Marianne, Garcia, Sara L., Roager, Henrik M., Aytan-Aktug, Derya, Hansen, Lea Benedicte Skov, Lind, Mads Vendelbo, Vogt, Josef K., Dalgaard, Marlene Danner, Bahl, Martin I., Jensen, Cecilia Bang, Muktupavela, Rasa, Warinner, Christina, Aaskov, Vincent, Gøbel, Rikke, Kristensen, Mette, Frøkiær, Hanne, Sparholt, Morten H., Christensen, Anders F., and Vestergaard, Henrik
- Subjects
DIET ,WEIGHT loss ,OVERWEIGHT persons ,RANDOM forest algorithms ,GUT microbiome ,REGULATION of body weight - Abstract
Diet is an important component in weight management strategies, but heterogeneous responses to the same diet make it difficult to foresee individual weight-loss outcomes. Omics-based technologies now allow for analysis of multiple factors for weight loss prediction at the individual level. Here, we classify weight loss responders (N = 106) and non-responders (N = 97) of overweight non-diabetic middle-aged Danes to two earlier reported dietary trials over 8 weeks. Random forest models integrated gut microbiome, host genetics, urine metabolome, measures of physiology and anthropometrics measured prior to any dietary intervention to identify individual predisposing features of weight loss in combination with diet. The most predictive models for weight loss included features of diet, gut bacterial species and urine metabolites (ROC-AUC: 0.84–0.88) compared to a diet-only model (ROC-AUC: 0.62). A model ensemble integrating multi-omics identified 64% of the non-responders with 80% confidence. Such models will be useful to assist in selecting appropriate weight management strategies, as individual predisposition to diet response varies. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
231. HOPS: automated detection and authentication of pathogen DNA in archaeological remains
- Author
-
Hübler, Ron, Key, Felix M., Warinner, Christina, Bos, Kirsten I., Krause, Johannes, and Herbig, Alexander
- Abstract
High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present-day samples and can also be applied to molecular data from archaeological remains. Investigations of ancient microbes can provide valuable information on past bacterial commensals and pathogens, but their molecular detection remains a challenge. Here, we present HOPS (Heuristic Operations for Pathogen Screening), an automated bacterial screening pipeline for ancient DNA sequences that provides detailed information on species identification and authenticity. HOPS is a versatile tool for high-throughput screening of DNA from archaeological material to identify candidates for genome-level analyses.
- Published
- 2019
- Full Text
- View/download PDF
232. Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage.
- Author
-
Velsko, Irina M., Fellows Yates, James A., Aron, Franziska, Hagan, Richard W., Frantz, Laurent A. F., Loe, Louise, Martinez, Juan Bautista Rodriguez, Chaves, Eros, Gosden, Chris, Larson, Greger, and Warinner, Christina
- Published
- 2019
- Full Text
- View/download PDF
233. Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe
- Author
-
Jeong, Choongwon, Wilkin, Shevan, Amgalantugs, Tsend, Bouwman, Abigail S., Taylor, William T.T., Hagan, Richard W., Bromage, Sabri, Tsolmon, Soninkhishig, Trachsel, Christian, Grossmann, Jonas, Littleton, Judith, Makarewicz, Cheryl A., Krigbaum, John, Burri, Marta, Scott, Ashley, Davaasambuu, Ganmaa, Wright, Joshua, Irmer, Franziska, Myagmar, Erdene, Boivin, Nicole, Robbeets, Martine, Rühli, Frank J., Krause, Johannes, Frohlich, Bruno, Hendy, Jessica, and Warinner, Christina
- Subjects
2. Zero hunger ,paleogenomics ,dental calculus ,α-S1-casein ,15. Life on land ,LC-MS/MS ,β-lactoglobulin - Abstract
Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH) beginning in the Eneolithic (ca. 3300–2700 BCE) profoundly transformed the genes and cultures of Europe and central Asia. Compared with Europe, however, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Late Bronze Age burials putatively associated with early pastoralism in northern Mongolia (ca. 1380–975 BCE). Genome-wide analysis reveals that they are largely descended from a population represented by Early Bronze Age hunter-gatherers in the Baikal region, with only a limited contribution (∼7%) of WSH ancestry. At the same time, however, mass spectrometry analysis of dental calculus provides direct protein evidence of bovine, sheep, and goat milk consumption in seven of nine individuals. No individuals showed molecular evidence of lactase persistence, and only one individual exhibited evidence of >10% WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. Unlike the spread of Neolithic farming in Europe and the expansion of Bronze Age pastoralism on the Western steppe, our results indicate that ruminant dairy pastoralism was adopted on the Eastern steppe by local hunter-gatherers through a process of cultural transmission and minimal genetic exchange with outside groups., Proceedings of the National Academy of Sciences of the United States of America, 115 (48), ISSN:0027-8424, ISSN:1091-6490
234. Direct evidence of milk consumption from ancient human dental calculus
- Author
-
Warinner, Christina, Hendy, Jessica, Speller, Camilla F., Cappellini, Enrico, Fischer, R., Trachsel, Christian, Arneborg, Jette, Lynnerup, Niels, Craig, Oliver E., Swallow, Dallas M., Fotakis, Anna K., Christensen, R.J., Olsen, Jesper V., Liebert, Anke, Montalva, N., Fiddyment, Sarah, Charlton, Sophy, Mackie, Meaghan, Canci, Alessandro, Bouwman, Abigail S., Rühli, Frank J., Gilbert, Thomas M.P., and Collins, Matthew J.
- Subjects
2. Zero hunger ,Proteomics ,Archaeology ,zoology ,Biomarkers - Abstract
Milk is a major food of global economic importance, and its consumption is regarded as a classic example of gene-culture evolution. Humans have exploited animal milk as a food resource for at least 8500 years, but the origins, spread, and scale of dairying remain poorly understood. Indirect lines of evidence, such as lipid isotopic ratios of pottery residues, faunal mortality profiles, and lactase persistence allele frequencies, provide a partial picture of this process; however, in order to understand how, where, and when humans consumed milk products, it is necessary to link evidence of consumption directly to individuals and their dairy livestock. Here we report the first direct evidence of milk consumption, the whey protein β-lactoglobulin (BLG), preserved in human dental calculus from the Bronze Age (ca. 3000 BCE) to the present day. Using protein tandem mass spectrometry, we demonstrate that BLG is a species-specific biomarker of dairy consumption, and we identify individuals consuming cattle, sheep, and goat milk products in the archaeological record. We then apply this method to human dental calculus from Greenland's medieval Norse colonies, and report a decline of this biomarker leading up to the abandonment of the Norse Greenland colonies in the 15th century CE., Scientific Reports, 4, ISSN:2045-2322
235. Direct evidence of milk consumption from ancient human dental calculus
- Author
-
Warinner, Christina, Hendy, Jessica, Speller, Camilla, Enrico Cappellini, Fischer, Roman, Trachsel, Christian, Arneborg, Jette, Lynnerup, Niels, Craig, Oliver, Swallow, Dallas M., Fotakis, Anna, Christensen, R. J., Olsen, Jesper, Liebert, Anke, Montalva, Nicholas, Fiddyment, Sarah, Mackie, Meaghan, Canci, Alessandro, Bouwman, Abigail, Ruhli, Frank, Gilbert, M. Thomas P., and Collins, Matthew J.
236. Paleobot.org: establishing open-access online reference collections for archaeobotanical research
- Author
-
Warinner, Christina, Guedes, Jade, Goode, David, Warinner, Christina, Guedes, Jade, and Goode, David
- Abstract
Difficulty in accessing high quality reference materials has been a limiting factor in the advancement of archaeobotanical research. However, new developments in online open source content management technology and faster downloading capabilities make high quality and low cost dynamic online curation of archaeobotanical reference images increasingly feasible. We describe the establishment of Paleobot.org, an open access online reference collection database for macrobotanical, microbotanical and isotopic data to help standardize and improve the identification of archaeobotanical remains
237. Ancient DNA Investigation of a Medieval German Cemetery Confirms Long-Term Stability of CCR5-Δ32 Allele Frequencies in Central Europe
- Author
-
Bouwman, Abigail, Shved, Natallia, Akgül, Gülfirde, Rühli, Frank, and Warinner, Christina
- Published
- 2017
- Full Text
- View/download PDF
238. Corrigendum: Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.
- Author
-
Ziesemer, Kirsten A., Mann, Allison E., Sankaranarayanan, Krithivasan, Schroeder, Hannes, Ozga, Andrew T., Brandt, Bernd W., Zaura, Egija, Waters-Rist, Andrea, Hoogland, Menno, Salazar-García, Domingo C., Aldenderfer, Mark, Speller, Camilla, Hendy, Jessica, Weston, Darlene A., MacDonald, Sandy J., Thomas, Gavin H., Collins, Matthew J., Lewis, Cecil M., Hofman, Corinne, and Warinner, Christina
- Published
- 2016
- Full Text
- View/download PDF
239. Publisher Correction: Metagenomic and paleopathological analyses of a historic documented collection explore ancient dental calculus as a diagnostic tool.
- Author
-
Austin, Rita M., Honap, Tanvi P., Mann, Allison E., Hübner, Alexander, DeGaglia, Cassandra M. S., Warinner, Christina, Zuckerman, Molly K., and Hofman, Courtney A.
- Subjects
- *
DISTRIBUTION (Probability theory) , *DENTAL calculus , *SYPHILIS , *METAGENOMICS , *INTERNET publishing - Abstract
This document is a correction notice for an article titled "Metagenomic and paleopathological analyses of a historic documented collection explore ancient dental calculus as a diagnostic tool." The original article contained an error in Figure 2, specifically in panel A where the cross-hatching and shading were incorrect. The corrected version of the article is now available. The authors of the article are Rita M. Austin, Tanvi P. Honap, Allison E. Mann, Alexander Hübner, Cassandra M. S. DeGaglia, Christina Warinner, Molly K. Zuckerman, and Courtney A. Hofman. [Extracted from the article]
- Published
- 2024
- Full Text
- View/download PDF
240. High conservation of the dental plaque microbiome across populations with differing subsistence strategies and levels of market integration.
- Author
-
Velsko, Irina M., Gallois, Sandrine, Stahl, Raphaela, Henry, Amanda G., and Warinner, Christina
- Subjects
- *
DENTAL plaque , *ECOLOGICAL disturbances , *DENTAL hygiene , *MARKETING strategy , *HUMAN microbiota , *MICROORGANISM populations , *FOOD chains - Abstract
Industrialization—including urbanization, participation in the global food chain and consumption of heavily processed foods—is thought to drive substantial shifts in the human microbiome. While diet strongly influences stool microbiome composition, the influence of diet on the oral microbiome is largely speculative. Multiple ecologically distinct surfaces in the mouth, each harbouring a unique microbial community, pose a challenge to assessing changes in the oral microbiome in the context of industrialization, as the results depend on the oral site under study. Here, we investigated whether microbial communities of dental plaque, the dense biofilm on non‐shedding tooth surfaces, are distinctly different across populations with dissimilar subsistence strategies and degree of industrialized market integration. Using a metagenomic approach, we compared the dental plaque microbiomes of Baka foragers and Nzime subsistence agriculturalists in Cameroon (n = 46) with the dental plaque and calculus microbiomes of highly industrialized populations in North America and Europe (n = 38). We found that differences in microbial taxonomic composition between populations were minimal, with high conservation of abundant microbial taxa and no significant differences in microbial diversity related to dietary practices. Instead, we find that the major source of variation in dental plaque microbial species composition is related to tooth location and oxygen availability, which may be influenced by toothbrushing or other dental hygiene measures. Our results support that dental plaque, in contrast to the stool microbiome, maintains an inherent stability against ecological perturbations in the oral environment. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
241. Remembering St. Louis individual—structural violence and acute bacterial infections in a historical anatomical collection.
- Author
-
Austin, Rita M., Zuckerman, Molly, Honap, Tanvi P., Lee, Hedwig, Ward, Geoff K., Warinner, Christina, Sankaranarayanan, Krithivasan, and Hofman, Courtney A.
- Subjects
- *
BACTERIAL diseases , *PNEUMOCOCCAL pneumonia , *DENTAL calculus , *INSTITUTIONAL racism , *VIOLENCE , *TUBERCULOSIS - Abstract
Incomplete documentary evidence, variable biomolecular preservation, and limited skeletal responses have hindered assessment of acute infections in the past. This study was initially developed to explore the diagnostic potential of dental calculus to identify infectious diseases, however, the breadth and depth of information gained from a particular individual, St. Louis Individual (St.LI), enabled an individualized assessment and demanded broader disciplinary introspection of ethical research conduct. Here, we document the embodiment of structural violence in a 23-year-old Black and/or African American male, who died of lobar pneumonia in 1930s St. Louis, Missouri. St.LI exhibits evidence of systemic poor health, including chronic oral infections and a probable tuberculosis infection. Metagenomic sequencing of dental calculus recovered three pre-antibiotic era pathogen genomes, which likely contributed to the lobar pneumonia cause of death (CoD): Klebsiella pneumoniae (13.8X); Acinetobacter nosocomialis (28.4X); and Acinetobacter junii (30.1X). Ante- and perimortem evidence of St.LI's lived experiences chronicle the poverty, systemic racism, and race-based structural violence experienced by marginalized communities in St. Louis, which contributed to St.LI's poor health, CoD, anatomization, and inclusion in the Robert J. Terry Anatomical Collection. These same embodied inequalities continue to manifest as health disparities affecting many contemporary communities in the United States. An investigation into the cause of death of St. Louis Individual, a 23-year old Black or African American male who died in the 1930s, reveals evidence of structural violence and the impact of systemic racism in historically marginalized communities. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
242. HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data.
- Author
-
Dimopoulos, Evangelos A., Carmagnini, Alberto, Velsko, Irina M., Warinner, Christina, Larson, Greger, Frantz, Laurent A. F., and Irving-Pease, Evan K.
- Subjects
- *
NUCLEOTIDE sequencing , *FOSSIL DNA , *SPECIES , *METAGENOMICS , *IDENTIFICATION , *DNA damage - Abstract
Identification of specific species in metagenomic samples is critical for several key applications, yet many tools available require large computational power and are often prone to false positive identifications. Here we describe High-AccuracY and Scalable Taxonomic Assignment of MetagenomiC data (HAYSTAC), which can estimate the probability that a specific taxon is present in a metagenome. HAYSTAC provides a user-friendly tool to construct databases, based on publicly available genomes, that are used for competitive reads mapping. It then uses a novel Bayesian framework to infer the abundance and statistical support for each species identification and provide per-read species classification. Unlike other methods, HAYSTAC is specifically designed to efficiently handle both ancient and modern DNA data, as well as incomplete reference databases, making it possible to run highly accurate hypothesis-driven analyses (i.e., assessing the presence of a specific species) on variably sized reference databases while dramatically improving processing speeds. We tested the performance and accuracy of HAYSTAC using simulated Illumina libraries, both with and without ancient DNA damage, and compared the results to other currently available methods (i.e., Kraken2/Bracken, KrakenUniq, MALT/HOPS, and Sigma). HAYSTAC identified fewer false positives than both Kraken2/Bracken, KrakenUniq and MALT in all simulations, and fewer than Sigma in simulations of ancient data. It uses less memory than Kraken2/Bracken, KrakenUniq as well as MALT both during database construction and sample analysis. Lastly, we used HAYSTAC to search for specific pathogens in two published ancient metagenomic datasets, demonstrating how it can be applied to empirical datasets. HAYSTAC is available from https://github.com/antonisdim/HAYSTAC. Author summary: The emerging field of paleo-metagenomics (i.e., metagenomics from ancient DNA) holds great promise for novel discoveries in fields as diverse as pathogen evolution and paleoenvironmental reconstruction. However, there is presently a lack of computational methods for species identification from microbial communities in both degraded and nondegraded DNA material. Here, we present "HAYSTAC", a user-friendly software package that implements a novel probabilistic model for species identification in metagenomic data obtained from both degraded and non-degraded DNA material. Through extensive benchmarking, we show that HAYSTAC can be used for accurately profiling the community composition, as well as for direct hypothesis testing for the presence of extremely low-abundance taxa, in complex metagenomic samples. After analysing simulated and publicly available datasets, HAYSTAC consistently produced the lowest number of false positive identifications during taxonomic profiling, produced robust results when databases of restricted size were used, and showed increased sensitivity for pathogen detection compared to other specialist methods. The newly proposed probabilistic model and software employed by HAYSTAC can have a substantial impact on the robust and rapid pathogen discovery in degraded/shallow sequenced metagenomic samples while optimising the use of computational resources. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
243. Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt.
- Author
-
Rampelli, Simone, Turroni, Silvia, Mallol, Carolina, Hernandez, Cristo, Galván, Bertila, Sistiaga, Ainara, Biagi, Elena, Astolfi, Annalisa, Brigidi, Patrizia, Benazzi, Stefano, Lewis, Cecil M., Warinner, Christina, Hofman, Courtney A., Schnorr, Stephanie L., and Candela, Marco
- Subjects
- *
GUT microbiome , *BIFIDOBACTERIUM , *FOSSIL DNA , *NEANDERTHALS - Abstract
A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals. Simone Rampelli, Silvia Turroni and colleagues report ancient bacterial profiles of fecal sediments from four stratigraphic units of El Salt Middle Paleolithic site in Spain. The results of this study suggest a core human gut microbiome that could have been shared by Neanderthals and modern humans, and would pre-date the split between these two lineages. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
244. Relief food subsistence revealed by microparticle and proteomic analyses of dental calculus from victims of the Great Irish Famine.
- Author
-
Geber, Jonny, Tromp, Monica, Scott, Ashley, Bouwman, Abigail, Nanni, Paolo, Grossmann, Jonas, Hendy, Jessica, and Warinner, Christina
- Subjects
- *
FOOD relief , *DENTAL calculus , *MILK proteins , *FAMINES , *CHARITIES - Abstract
Food and diet were class markers in 19th-century Ireland, which became evident as nearly 1 million people, primarily the poor and destitute, died as a consequence of the notorious Great Famine of 1845 to 1852. Famine took hold after a blight (Phytophthora infestans) destroyed virtually the only means of subsistence-the potato crop-for a significant proportion of the population. This study seeks to elucidate the variability of diet in mid-19th-century Ireland through microparticle and proteomic analysis of human dental calculus samples (n = 42) from victims of the famine. The samples derive from remains of people who died between August 1847 and March 1851 while receiving poor relief as inmates in the union workhouse in the city of Kilkenny (52°39' N, -7°15' W). The results corroborate the historical accounts of food provisions before and during the famine, with evidence of corn (maize), potato, and cereal starch granules from the microparticle analysis and milk protein from the proteomic analysis. Unexpectedly, there is also evidence of egg protein-a food source generally reserved only for export and the better-off social classes-which highlights the variability of the prefamine experience for those who died. Through historical contextualization, this study shows how the notoriously monotonous potato diet of the poor was opportunistically supplemented by other foodstuffs. While the Great Irish Famine was one of the worst subsistence crises in history, it was foremost a social disaster induced by the lack of access to food and not the lack of food availability. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
245. "The dead shall be raised": Multidisciplinary analysis of human skeletons reveals complexity in 19th century immigrant socioeconomic history and identity in New Haven, Connecticut.
- Author
-
Aronsen, Gary P., Fehren-Schmitz, Lars, Krigbaum, John, Kamenov, George D., Conlogue, Gerald J., Warinner, Christina, Ozga, Andrew T., Sankaranarayanan, Krithivasan, Griego, Anthony, DeLuca, Daniel W., Eckels, Howard T., Byczkiewicz, Romuald K., Grgurich, Tania, Pelletier, Natalie A., Brownlee, Sarah A., Marichal, Ana, Williamson, Kylie, Tonoike, Yukiko, and Bellantoni, Nicholas F.
- Subjects
- *
HUMAN skeleton , *INTERDISCIPLINARY research , *NINETEENTH century , *DENTAL calculus , *RELIGIOUS identity , *NUCLEAR DNA - Abstract
In July 2011, renovations to Yale-New Haven Hospital inadvertently exposed the cemetery of Christ Church, New Haven, Connecticut’s first Catholic cemetery. While this cemetery was active between 1833 and 1851, both the church and its cemetery disappeared from public records, making the discovery serendipitous. Four relatively well-preserved adult skeletons were recovered with few artifacts. All four individuals show indicators of manual labor, health and disease stressors, and dental health issues. Two show indicators of trauma, with the possibility of judicial hanging in one individual. Musculoskeletal markings are consistent with physical stress, and two individuals have arthritic indicators of repetitive movement/specialized activities. Radiographic analyses show osteopenia, healed trauma, and other pathologies in several individuals. Dental calculus analysis did not identify any tuberculosis indicators, despite osteological markers. Isotopic analyses of teeth indicate that all four were likely recent immigrants to the Northeastern United States. Nuclear and mitochondrial DNA were recovered from three individuals, and these analyses identified ancestry, hair/eye color, and relatedness. Genetic and isotopic results upended our initial ancestry assessment based on burial context alone. These individuals provide biocultural evidence of New Haven’s Industrial Revolution and the plasticity of ethnic and religious identity in the immigrant experience. Their recovery and the multifaceted analyses described here illuminate a previously undescribed part of the city’s rich history. The collective expertise of biological, geochemical, archaeological, and historical researchers interprets socioeconomic and cultural identity better than any one could alone. Our combined efforts changed our initial assumptions of a poor urban Catholic cemetery’s membership, and provide a template for future discoveries and analyses. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
246. What Does Dental Calculus Reveal About Human Evolution?
- Author
-
Warinner, Christina
- Abstract
Dental calculus, a calcified form of tooth plaque, can give detailed information about the diets, diseases and lifestyles of past humans. CHRISTINA WARINNER discusses how she gains new knowledge about the way human beings used to live, what they ate, and how their microbiome has evolved. Dental calculus is the richest known source of ancient DNA in the archaeological record, and it is the only part of the body that fossilizes during life. In this video, she explains how emerging technologies in genomics and proteomics are contributing to groundbreaking discoveries about past human health and diet. By combining genetic and protein data, she describes how ancient infections leave behind sufficient traces to reconstruct entire pathogen genomes, as well as a detailed snapshot of host immune response. She explains how studies of ancient dental calculus will help us understand how our microbiome has evolved and why understanding the human ancestral microbiome may shed light on current chronic health problems.
- Published
- 2014
247. Your horse is a donkey! Identifying domesticated equids from Western Iberia using collagen fingerprinting.
- Author
-
Paladugu, Roshan, Richter, Kristine Korzow, Valente, Maria João, Gabriel, Sónia, Detry, Cleia, Warinner, Christina, and Dias, Cristina Barrocas
- Subjects
- *
PEPTIDE mass fingerprinting , *EQUIDAE , *ZOOARCHAEOLOGY , *ARCHAEOLOGICAL human remains , *DONKEYS , *HORSES , *PEPTIDES , *HORSE breeds , *SPECIES - Abstract
Skeletal remains of two equid species, Equus caballus (horse) and Equus asinus (donkey), have been found in archaeological contexts throughout Iberia since the Palaeolithic and Chalcolithic periods, respectively. These two species play different economic and cultural roles, and therefore it is important to be able to distinguish between the two species to better understand their relative importance in the past human societies. The most reliable morphological features for distinguishing between the two domesticated equids are based on cranial measurements and tooth enamel folds, leading to only a small percentage of archaeological remains that can be identified to species. Ancient DNA (aDNA) analysis can be used to reliably distinguish the two equids, but it can be cost prohibitive to apply to large assemblages, and aDNA preservation of non-cranial elements is often low. Collagen peptide mass fingerprinting by matrix-assisted laser desorption time-of-flight (MALDI-TOF) mass spectrometry, also known as zooarchaeology by mass spectrometry (ZooMS), is a minimally destructive and cost-effective alternative to aDNA analysis for taxonomic determination. However, current ZooMS markers lack resolution below the genus level Equus. In this paper, we report a novel ZooMS peptide marker that reliably distinguishes between horses and donkeys using the enzyme chymotrypsin. We apply this peptide marker to taxonomically identify bones from the Iberian Peninsula ranging from the Iron Age to the Late Modern Period. The peptide biomarker has the potential to facilitate the collection of morphological data for zooarchaeological studies of equids in Iberia and throughout Eurasia and Africa. • Novel ZooMS biomarker discriminates between horses and donkeys. • Novel biomarker provided species level identification for archaeological samples identified only to Equus. • The enzyme, chymotrypsin, reliably provides unique peptide markers for ZooMS analysis. [ABSTRACT FROM AUTHOR]
- Published
- 2023
- Full Text
- View/download PDF
248. Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt
- Author
-
Stefano Benazzi, Bertila Galván, Ainara Sistiaga, Simone Rampelli, Elena Biagi, Courtney A. Hofman, Cristo M. Hernández, Carolina Mallol, Christina Warinner, Annalisa Astolfi, Patrizia Brigidi, Silvia Turroni, Cecil M. Lewis, Marco Candela, Stephanie L. Schnorr, Rampelli, Simone, Turroni, Silvia, Mallol, Carolina, Hernandez, Cristo, Galván, Bertila, Sistiaga, Ainara, Biagi, Elena, Astolfi, Annalisa, Brigidi, Patrizia, Benazzi, Stefano, Lewis, Cecil M, Warinner, Christina, Hofman, Courtney A, Schnorr, Stephanie L, and Candela, Marco
- Subjects
Most recent common ancestor ,Geologic Sediments ,Neanderthal ,QH301-705.5 ,Medicine (miscellaneous) ,Zoology ,Gut flora ,General Biochemistry, Genetics and Molecular Biology ,Article ,NO ,Microbial ecology ,03 medical and health sciences ,Feces ,0302 clinical medicine ,biology.animal ,Middle Paleolithic ,Animals ,Humans ,Microbiome ,DNA, Ancient ,Biology (General) ,Ecosystem ,History, Ancient ,Microbiome, Ancient DNA, Neanderthal ,030304 developmental biology ,Neanderthals ,0303 health sciences ,biology ,Fossils ,Ruminococcus ,Sequence Analysis, DNA ,Commensalism ,biology.organism_classification ,Gastrointestinal Microbiome ,Ancient DNA ,Archaeology ,Metagenomics ,Spain ,Roseburia ,General Agricultural and Biological Sciences ,030217 neurology & neurosurgery - Abstract
A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals., Simone Rampelli, Silvia Turroni and colleagues report ancient bacterial profiles of fecal sediments from four stratigraphic units of El Salt Middle Paleolithic site in Spain. The results of this study suggest a core human gut microbiome that could have been shared by Neanderthals and modern humans, and would pre-date the split between these two lineages.
- Published
- 2021
249. The evolution and changing ecology of the African hominid oral microbiome
- Author
-
Ana Grande Mateu, Courtney A. Hofman, Katerina Harvati, Louise T. Humphrey, Mario Menéndez, Richard W. Wrangham, Dušan Mihailović, Kathryn Weedman Arthur, Cody Parker, Barbara Teßmann, Jay T. Stock, Isabelle Crevecoeur, Michael J. Walker, Catherine C. Bauer, Christina Warinner, Cosimo Posth, Mirjana Roksandic, Victoria E. Gibbon, Love Dalén, Dorothée G. Drucker, Amanda G. Henry, Manuel R. González Morales, Floyd E. Dewhirst, Kathrin Nägele, Christophe Cupillard, Michael Francken, Irina M. Velsko, Johannes Krause, Sofía Rodríguez Moroder, Sandra Sázelová, Katerina Guschanski, Rita M. Austin, James A. Fellows Yates, J. Carlos Díez Fernández-Lomana, Marta Díaz-Zorita Bonilla, Hélène Rougier, Cecil M. Lewis, Marco Peresani, Robert C. Power, Krithivasan Sankaranarayanan, Domingo C. Salazar-García, Lawrence Guy Straus, Alexander Herbig, Jiří Svoboda, John W. Arthur, Elena Escribano Escrivá, Matthew C. Curtis, Franziska Aron, Allison E. Mann, Lab Chronoenvironm, Partenaires INRAE, European Commission, De la Préhistoire à l'Actuel : Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Chrono-environnement - CNRS - UBFC (UMR 6249) (LCE), Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), Fellows Yates, James A [0000-0001-5585-6277], Velsko, Irina M [0000-0001-9810-9917], Hofman, Courtney A [0000-0002-6808-3370], Parker, Cody E [0000-0001-5528-4299], Mann, Allison E [0000-0001-7170-6017], Arthur, Kathryn Weedman [0000-0003-2955-6080], Arthur, John W [0000-0002-4968-5843], Bauer, Catherine C [0000-0002-2281-0501], Crevecoeur, Isabelle [0000-0002-1781-3206], Cupillard, Christophe [0000-0002-8567-3540], Curtis, Matthew C [0000-0003-4692-3241], Dalén, Love [0000-0001-8270-7613], Díaz-Zorita Bonilla, Marta [0000-0002-1697-0111], Díez Fernández-Lomana, J Carlos [0000-0002-3856-1837], Francken, Michael [0000-0001-6336-2111], Gibbon, Victoria E [0000-0001-7875-3297], González Morales, Manuel R [0000-0001-7277-7837], Henry, Amanda G [0000-0002-2923-4199], Humphrey, Louise [0000-0003-3595-0543], Menéndez, Mario [0000-0002-2421-480X], Mihailović, Dušan [0000-0002-8607-8196], Peresani, Marco [0000-0001-6562-6336], Roksandic, Mirjana [0000-0003-0291-6357], Rougier, Hélène [0000-0003-0358-0285], Sázelová, Sandra [0000-0002-7326-8134], Straus, Lawrence Guy [0000-0003-0348-3338], Svoboda, Jiří [0000-0003-4256-9708], Teßmann, Barbara [0000-0002-3122-4707], Walker, Michael J [0000-0003-4359-7436], Power, Robert C [0000-0001-7425-5709], Lewis, Cecil M [0000-0002-2198-3427], Guschanski, Katerina [0000-0002-8493-5457], Wrangham, Richard W [0000-0003-0435-2209], Dewhirst, Floyd E [0000-0003-4427-7928], Krause, Johannes [0000-0001-9144-3920], Herbig, Alexander [0000-0003-1176-1166], Warinner, Christina [0000-0002-4528-5877], and Apollo - University of Cambridge Repository
- Subjects
Neanderthal ,binding ,gut microbiome ,microbiome ,primate ,Prehistòria ,Evolutionsbiologi ,Primate ,salivary amylase ,Phylogeny ,0303 health sciences ,Multidisciplinary ,Ecology ,Geography ,biology ,Microbiota ,Human microbiome ,ancient ,Hominidae ,SH6_2 ,Biological Sciences ,Biological Evolution ,genomes suggest ,Human evolution ,[SDE]Environmental Sciences ,Oral Microbiome ,R-package ,Pan troglodytes ,dental plaque ,[SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory ,Ecology (disciplines) ,Socio-culturale ,Microbiology ,salivary alpha-amylase ,03 medical and health sciences ,biology.animal ,Dental calculus ,Animals ,Humans ,Microbiome ,visualization ,030304 developmental biology ,Mouth ,periodontal-disease ,Evolutionary Biology ,Gorilla gorilla ,Bacteria ,030306 microbiology ,dental calculus ,DNA ,Mikrobiologi ,Biofilms ,FOS: Biological sciences ,Anthropology ,Africa ,Upper Paleolithic ,Metagenome - Abstract
Significance The microbiome plays key roles in human health, but little is known about its evolution. We investigate the evolutionary history of the African hominid oral microbiome by analyzing dental biofilms of humans and Neanderthals spanning the past 100,000 years and comparing them with those of chimpanzees, gorillas, and howler monkeys. We identify 10 core bacterial genera that have been maintained within the human lineage and play key biofilm structural roles. However, many remain understudied and unnamed. We find major taxonomic and functional differences between the oral microbiomes of Homo and chimpanzees but a high degree of similarity between Neanderthals and modern humans, including an apparent Homo-specific acquisition of starch digestion capability in oral streptococci, suggesting microbial coadaptation with host diet., The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine–platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease.
- Published
- 2021
250. Dental Calculus and the Evolution of the Human Oral Microbiome
- Author
-
Christina Warinner, University of Zurich, and Warinner, Christina
- Subjects
Paleodontology ,Mouth ,Fossils ,Microbiota ,11294 Institute of Evolutionary Medicine ,Humans ,610 Medicine & health ,Dental Calculus ,General Medicine ,Dental Caries ,History, Ancient ,History, Medieval ,Periodontal Diseases - Abstract
Characterizing the evolution of the oral microbiome is a challenging, but increasingly feasible, task. Recently, dental calculus has been shown to preserve ancient biomolecules from the oral microbiota, host tissues and diet for tens of thousands of years. As such, it provides a unique window into the ancestral oral microbiome. This article reviews recent advancements in ancient dental calculus research and emerging insights into the evolution and ecology of the human oral microbiome.
- Published
- 2016
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.