Research Projects

Ancient DNA research offers a great potential to gain insights into genetic relationships and population structure of extinct human populations. Population genetic data from Pleistocene modern humans plays a key role in understanding the complex picture emerging from the ancient human genetic data that involves gene flow between different Pleistocene hominins, genetic bottlenecks and extinctions.

The Settlement of Europe

Ancient DNA research offers a great potential to gain insights into genetic relationships and population structure of extinct human populations. Population genetic data from Pleistocene modern humans plays a key role in understanding the complex picture emerging from the ancient human genetic data that involves gene flow between different Pleistocene hominins, genetic bottlenecks and extinctions. [more]
Through an extensive screening of skeletal collections from well-characterized catastrophe, or emergency, mass burials we plan to detect and sequence pathogen DNA from various historic pandemics spanning at least 2,500 years of European history.

Ancient Pathogen Genomics Project

Through an extensive screening of skeletal collections from well-characterized catastrophe, or emergency, mass burials we plan to detect and sequence pathogen DNA from various historic pandemics spanning at least 2,500 years of European history. [more]
Using novel techniques of targeted DNA enrichment, we have been able to reconstruct the full genome of ancient <em>Y. pestis</em> strains from DNA isolated from skeletons. DNA damage patterns present in medieval <em>Y. pestis</em> DNA indicate the authentic medieval origin and therefore support that bubonic plague was at least one of the causative agents of the Black Death pandemic.

Black Death Genome Project

Using novel techniques of targeted DNA enrichment, we have been able to reconstruct the full genome of ancient Y. pestis strains from DNA isolated from skeletons. DNA damage patterns present in medieval Y. pestis DNA indicate the authentic medieval origin and therefore support that bubonic plague was at least one of the causative agents of the Black Death pandemic. [more]
Milk is a food of major, global importance. This collaborative research project pursues a multi-disciplinary and multi-proxy approach to reconstruct the emergence, transformation and spread of ancient dairying, and the co-evolution of dairying practices and lactase persistence.

Dairying and Dietary Adaptive Evolution in Prehistory

Milk is a food of major, global importance. This collaborative research project pursues a multi-disciplinary and multi-proxy approach to reconstruct the emergence, transformation and spread of ancient dairying, and the co-evolution of dairying practices and lactase persistence. [more]
Focusing on fecal samples from diverse living populations and well-preserved archaeological sites, this study seeks to address fundamental questions about the evolution and ecology of the human gut microbiome.

Evolution and Ecology of the Human Gut Microbiome

Focusing on fecal samples from diverse living populations and well-preserved archaeological sites, this study seeks to address fundamental questions about the evolution and ecology of the human gut microbiome. [more]
The oral microbiome is the second largest human-associated microbial community, after the gut, and oral microbes exhibit an astounding diversity of predicted protein functions compared with other body sites. Focusing on a diverse set of archaeological dental calculus samples, this project seeks to reconstruct the evolutionary history of the human oral microbiome by tracing major taxonomic and functional shifts in the hominid lineage.

Evolution and Ecology of the Human Oral Microbiome

The oral microbiome is the second largest human-associated microbial community, after the gut, and oral microbes exhibit an astounding diversity of predicted protein functions compared with other body sites. Focusing on a diverse set of archaeological dental calculus samples, this project seeks to reconstruct the evolutionary history of the human oral microbiome by tracing major taxonomic and functional shifts in the hominid lineage. [more]
Microbes are an integral part of our cuisine, and are especially integral to dairy products. In this project we are combining archaeology, microbiology, food science, and cultural anthropology, in order to gain substantial insight into dairying practices, microbial diversity, and the impact that microbes have had on our foods, our biology, and our society today.

Heirloom Microbes: The History and Legacy of Ancient Dairying Bacteria

Microbes are an integral part of our cuisine, and are especially integral to dairy products. In this project we are combining archaeology, microbiology, food science, and cultural anthropology, in order to gain substantial insight into dairying practices, microbial diversity, and the impact that microbes have had on our foods, our biology, and our society today. [more]
Leprosy, a devastating chronic disease caused by the bacterial pathogen Mycobacterium leprae, was prevalent in Europe until the late Middle Ages. Today, the disease is found in 91 countries worldwide with about 200,000 new infections reported annually.

Medieval Leprosy Genome Project

Leprosy, a devastating chronic disease caused by the bacterial pathogen Mycobacterium leprae, was prevalent in Europe until the late Middle Ages. Today, the disease is found in 91 countries worldwide with about 200,000 new infections reported annually. [more]
Since prehistory, the Himalayan mountain range has presented a formidable barrier to population migration, while at the same time its transverse valleys have long served as conduits for trade and exchange. This project seeks to reconstruct the population history of the Himalayan arc by generating genome-wide genetic data from prehistoric ACA populations.

Ancient Nepal Population Genetics: Human Migration and Adaptation in Extreme Environments

Since prehistory, the Himalayan mountain range has presented a formidable barrier to population migration, while at the same time its transverse valleys have long served as conduits for trade and exchange. This project seeks to reconstruct the population history of the Himalayan arc by generating genome-wide genetic data from prehistoric ACA populations. [more]
Tuberculosis is second only to HIV/AIDS in disease-related mortality in humans, killing an estimated 1-2 million people every year worldwide. Public health efforts are complicated by the emergence of multi-drug resistant strains, hence knowledge of its level of naturally-occurring variation through history may be informative for disease management. The origins of tuberculosis have long been debated, with most recent estimates suggesting that it evolved with humans in Africa and spread from there tens of thousands of years ago following major human migrations.

Pre-Columbian Tuberculosis

Tuberculosis is second only to HIV/AIDS in disease-related mortality in humans, killing an estimated 1-2 million people every year worldwide. Public health efforts are complicated by the emergence of multi-drug resistant strains, hence knowledge of its level of naturally-occurring variation through history may be informative for disease management. The origins of tuberculosis have long been debated, with most recent estimates suggesting that it evolved with humans in Africa and spread from there tens of thousands of years ago following major human migrations. [more]
Fragments  of  ceramic  vessels  litter  the  archaeological  record  as one  of  the  main  surviving  remnants  of  past  food  preparation  and consumption. In this project, we are applying recent advances in ancient protein analysis to explore the culinary practices of a diverse array of ancient populations.

Uncovering Dietary Practices through the Proteomic Analysis of Ceramics

Fragments  of  ceramic  vessels  litter  the  archaeological  record  as one  of  the  main  surviving  remnants  of  past  food  preparation  and consumption. In this project, we are applying recent advances in ancient protein analysis to explore the culinary practices of a diverse array of ancient populations. [more]
 
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