Do I have something in my teeth? The trouble with genetic analyses of diet from archaeological dental calculus

Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan

(2020) Rikai Sawafuji et al.   PLoS One

Opinion: To curate the molecular past, museums need a carefully considered set of best practices

(2019) Rita M. Austin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies

(2019) Tom van der Valk et al.   Molecular Ecology Resources

Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage

(2019) Irina M. Velsko et al.   Microbiome

Relief food subsistence revealed by microparticle and proteomic analyses of dental calculus from victims of the Great Irish Famine

(2019) Jonny Geber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oral microbiome diversity in chimpanzees from Gombe National Park

(2019) Andrew T. Ozga et al.   Scientific Reports

Evolutionary basis for the human diet: consequences for human health

(2019) P. Andrews et al.   JOURNAL OF INTERNAL MEDICINE

A 5700 year-old human genome and oral microbiome from chewed birch pitch

(2019) Theis Z. T. Jensen et al.   Nature Communications

Metagenomic analysis of dental calculus in ancient Egyptian baboons

(2019) Claudio Ottoni et al.   Scientific Reports

The Iceman’s Last Meal Consisted of Fat, Wild Meat, and Cereals

(2018) Frank Maixner et al.   CURRENT BIOLOGY

Differential preservation of endogenous human and microbial DNA in dental calculus and dentin

(2018) Allison E. Mann et al.   Scientific Reports

The efficacy of whole human genome capture on ancient dental calculus and dentin

(2018) Kirsten A. Ziesemer et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

Extending the spectrum of DNA sequences retrieved from ancient bones and teeth

(2017) Isabelle Glocke et al.   GENOME RESEARCH

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

(2017) Laura S. Weyrich et al.   NATURE

A new model for ancient DNA decay based on paleogenomic meta-analysis

(2017) Logan Kistler et al.   NUCLEIC ACIDS RESEARCH

Ancient DNA reveals the Arctic origin of Viking Age cod from Haithabu, Germany

(2017) Bastiaan Star et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neandertal and Denisovan DNA from Pleistocene sediments

(2017) Viviane Slon et al.   SCIENCE

A molecular portrait of maternal sepsis from Byzantine Troy

(2017) Alison M Devault et al.   eLife

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

(2016) Andrew T. Ozga et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

gargammel: a sequence simulator for ancient DNA

(2016) Gabriel Renaud et al.   BIOINFORMATICS

Dietary shift after 3600 cal yr BP and its influencing factors in northwestern China: Evidence from stable isotopes

(2016) Minmin Ma et al.   QUATERNARY SCIENCE REVIEWS

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

The genomics of microbial domestication in the fermented food environment

(2015) John G Gibbons et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Differentiating dietary and non-dietary microfossils extracted from human dental calculus: the importance of sweet potato to ancient diet on Rapa Nui

(2015) Monica Tromp et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Climate challenges, vulnerabilities, and food security

(2015) Margaret C. Nelson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

(2015) Kirsten A. Ziesemer et al.   Scientific Reports

Contesting the presence of wheat in the British Isles 8,000 years ago by assessing ancient DNA authenticity from low-coverage data

(2015) Clemens L Weiß et al.   eLife

Dental indicators of ancient dietary patterns: dental analysis in archaeology

(2014) R. Forshaw   BRITISH DENTAL JOURNAL

Pathogens and host immunity in the ancient human oral cavity

(2014) Christina Warinner et al.   NATURE GENETICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Partial uracil-DNA-glycosylase treatment for screening of ancient DNA

(2014) N. Rohland et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys

(2014) Michael C. Nelson et al.   PLoS One

Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes

(2014) Martin Laurence et al.   PLoS One

Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal

(2014) Pontus Skoglund et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome flux and stasis in a five millennium transect of European prehistory

(2014) Cristina Gamba et al.   Nature Communications

Direct evidence of milk consumption from ancient human dental calculus

(2014) C. Warinner et al.   Scientific Reports

Unexpected cross-species contamination in genome sequencing projects

(2014) Samier Merchant et al.   PeerJ

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

(2013) Christina J Adler et al.   NATURE GENETICS

Environmental availability, behavioural diversity and diet: a zooarchaeological approach from the TD10-1 sublevel of Gran Dolina (Sierra de Atapuerca, Burgos, Spain) and Bolomor Cave (Valencia, Spain)

(2013) Ruth Blasco et al.   QUATERNARY SCIENCE REVIEWS

Ancient DNA Damage

(2013) J. Dabney et al.   Cold Spring Harbor Perspectives in Biology

A NEW DATE FOR THE NEANDERTHALS FROM EL SIDRÓN CAVE (ASTURIAS, NORTHERN SPAIN)*

(2012) R. E. WOOD et al.   ARCHAEOMETRY

Improving ancient DNA read mapping against modern reference genomes

(2012) Mikkel Schubert et al.   BMC GENOMICS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Neanderthal medics? Evidence for food, cooking, and medicinal plants entrapped in dental calculus

(2012) Karen Hardy et al.   NATURWISSENSCHAFTEN

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

(2012) Susanna Sawyer et al.   PLoS One

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Effect of food processing on plant DNA degradation and PCR-based GMO analysis: a review

(2009) Nicolas Gryson   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

The Neandertal genome and ancient DNA authenticity

(2009) Richard E Green et al.   EMBO JOURNAL

Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate Species

(2009)   JOURNAL OF HEREDITY

Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA

(2009) Adrian W. Briggs et al.   NUCLEIC ACIDS RESEARCH

ORGANIC RESIDUE ANALYSIS IN ARCHAEOLOGY: THE ARCHAEOLOGICAL BIOMARKER REVOLUTION*

(2008) R. P. EVERSHED   ARCHAEOMETRY

Integrity of nuclear genomic deoxyribonucleic acid in cooked meat: Implications for food traceability

(2008) Ö. Aslan et al.   JOURNAL OF ANIMAL SCIENCE

Using plant microfossils from dental calculus to recover human diet: a case study from Tell al-Raqā'i, Syria

(2008) Amanda G. Henry et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE