James A. Fellows Yates

James A. Fellows Yates
Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute | HKI · Department of Paleobiotechnology

Doctor of Philosophy

About

46
Publications
7,253
Reads
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394
Citations
Citations since 2016
45 Research Items
393 Citations
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2016201720182019202020212022020406080100120
2016201720182019202020212022020406080100120
2016201720182019202020212022020406080100120
Introduction
James A. Fellows Yates currently works at the Department for Palaeobiotechnology at the Leibniz Institute for Natural Product Research and Infections Biology Hans Knöll Institute and the Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology.
Additional affiliations
June 2020 - present
Ludwig-Maximilians-University of Munich
Position
  • Researcher
October 2015 - present
Max Planck Institute for the Science of Human History
Position
  • PhD Student
July 2015 - September 2015
Education
October 2013 - October 2015
University of Tuebingen
Field of study
  • Archaeological Sciences (Palaeogenetics)
October 2010 - July 2013
The University of York
Field of study
  • Bioarchaeology

Publications

Publications (46)
Preprint
Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here we investigate the contribution of host evolutionary relationships and ecology in shaping the oral microb...
Article
Full-text available
Like modern metagenomics, ancient metagenomics is a highly data-rich discipline, with the added challenge that the DNA of interest is degraded and, depending on the sample type, in low abundance. This requires the application of specialized measures during molecular experiments and computational analyses. Furthermore, researchers often work with fi...
Preprint
Full-text available
This collection contains established ancient DNA (aDNA) specific protocols for Illumina next generation sequencing. It covers sampling of skeletal remains for regions preserving higher amounts of aDNA, DNA extraction methods designed for retrieval of very short DNA fragments, and various library construction methods (including treatments for the 'r...
Preprint
Collection of protocols used for Fellows Yates et al. "The evolution and changing ecology of the hominid primate oral microbiome". Bioinformatics analysis can be found on GitHub at https://github.com/jfy133/Anthropoid_Calculus_Microbiome_Evolution/. This collection describes the laboratory procedures used for sampling, (ancient) DNA extraction, lib...
Article
Full-text available
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 id...
Article
Full-text available
The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present an advanced, and entirely redesigned and extended version of the EAGER pipeli...
Article
Full-text available
Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual taxa and communities of...
Preprint
Collection of protocols used for Fellows Yates et al. "The evolution and changing ecology of the hominid primate oral microbiome". Bioinformatics analysis can be found on GitHub at https://github.com/jfy133/Hominid_Calculus_Microbiome_Evolution/. This collection describes the laboratory procedures used for sampling, (ancient) DNA extraction, librar...
Preprint
Collection of protocols used for Fellows Yates et al. "The evolution and changing ecology of the hominid primate oral microbiome". Bioinformatics analysis can be found on GitHub at https://github.com/jfy133/Anthropoid_Calculus_Microbiome_Evolution/. This collection describes the laboratory procedures used for sampling, (ancient) DNA extraction, lib...
Preprint
This protocol describes how to obtain powder from the inner pulp chamber of teeth for the extraction of ancient DNA. It is ideal for the simultaneous isolation of both host endogenous and microbial DNA (e.g. for pathogens).
Preprint
This protocol describes how to sample dental calculus from skeletal remains for biomolecular analysis. This protocol is particularly recommended for sampling calculus from teeth attached to a jaw bone, skull, or skeleton. The primary use-case is for DNA and proteomic analysis.
Article
Full-text available
Dental calculus and other preserved microbiome substrates are an attractive target for dietary reconstruction in past populations through a variety of physical, chemical, and molecular means. Recently, studies have attempted to reconstruct diet from archaeological dental calculus using archaeogenetic techniques. While dental calculus may provide a...
Preprint
Full-text available
Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual microbial taxa, microbi...
Preprint
This collection contains established ancient DNA (aDNA) specific protocols for Illumina next generation sequencing. It covers sampling of skeletal remains for regions preserving higher amounts of aDNA, DNA extraction methods designed for retrieval of very short DNA fragments, and various library construction methods (including treatments for the 'r...
Preprint
Full-text available
The broadening utilisation of ancient DNA (aDNA) to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present nf-core/eager, an advanced and entirely redesigned pipeline for the an...
Preprint
This protocol describes how to obtain powder from the inner pulp chamber of teeth for the extraction of ancient DNA. It is ideal for the simultaneous isolation of both host endogenous and microbial DNA (e.g. for pathogens).
Article
Full-text available
Drivers of Late Quaternary megafaunal extinctions are relevant to modern conservation policy in a world of growing human population density, climate change, and faunal decline. Traditional debates tend toward global solutions, blaming either dramatic climate change or dispersals of Homo sapiens to new regions. Inherent limitations to archaeological...
Preprint
This protocol describes how to sample dental calculus from skeletal remains for biomolecular analysis. This protocol is particularly recommended for sampling calculus from teeth attached to a jaw bone, skull, or skeleton. The primary use-case is for DNA and proteomic analysis.
Preprint
This protocol describes how to sample dental calculus from individual teeth for biomolecular analysis. The primary use-case is for DNA and proteomic analysis. For a printable handout, see: http://christinawarinner.com/resources/archaeologists/. Note, if you are sampling from intact jaws, we recommend using the Sabin protocol: https://dx.doi.org/10....
Article
Full-text available
Background: Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm...
Preprint
Full-text available
Palaeogenomic investigation of 50,000 years of the human oral microbiome in the Iberian Mediterranean
Article
Full-text available
Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically...
Article
Full-text available
The population dynamics of the Pleistocene woolly mammoth (Mammuthus primigenius) has been the subject of intensive palaeogenetic research. Although a large number of mitochondrial genomes across Eurasia have been reconstructed, the available data remains geographically sparse and mostly focused on eastern Eurasia. Thus, population dynamics in othe...
Article
Full-text available
Microbial archaeology is flourishing in the era of high-throughput sequencing, revealing the agents behind devastating historical plagues, identifying the cryptic movements of pathogens in prehistory, and reconstructing the ancestral microbiota of humans. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then...
Poster
Full-text available
A recently identified ‘European’ clade (clade III) of woolly mammoth has been suggested to have become extinct around 34 ky cal BP, and replaced by a migrating North American clade from the east around 32 ky cal BP. However this was based on a small number of short HVR sequences. Here we present 15 complete mitochondrial genomes (>10x coverage, and...
Research
Full-text available
Rivera­-Perez et al. (2015, PLoS One) suggest that the use of retroviral DNA from palaeofaeces can be used as a proxy to characterise the diet of historical cultures. We raise concerns regarding the extraction and particularly authentication of the ancient DNA, and the characterisation of this DNA as deriving from retroviruses. These concerns are i...
Thesis
Full-text available
This dissertation aims to test the hypothesis that it will not be possible to use Zooarchaeology by Mass Spectrometry (ZooMS) to identify species in samples of cremated bone, that have been burnt higher than 155oC. Collagen extracted from experimentally burnt modern sheep/goat samples and archaeological burnt and cremated samples were analysed usin...

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Projects

Project (1)
Archived project
Generate mitochondrial genomes from late Pleistocene Europe - a region which had been under-sampled compared to other regions