The Evolution and Ecology of the Oral Microbiome
Exploring the diversity of oral archaea in dental calculus
Keri Burge, Irina Velsko, Christina Warinner
Understanding human movement through time and space is a major goal of archaeogenetic studies. Though the field has predominantly made use of DNA from ancient human remains, dental calculus offers the possibility of indirectly tracing human movement using the commensal microbes ancient humans carried with them. Although oral bacteria are being increasingly studied, prominent commensal archaea, including the genera Methanobrevibacter, remain underexplored. Advancements in de novo genome assembly have allowed for a closer view of these enigmatic archaea, making it increasingly clear that ancient DNA previously identified as Methanobrevibacter oralis likely originates not from a single species, but rather from a group of unnamed species within this genus. This project seeks to discover a more complete view of the Methanobrevibacter phylogeny by analyzing 228 metagenomically assembled genomes (MAGs) from dental calculus and dental plaque samples dating from Neanderthals to modern humans across multiple continents. Additionally, 54 MAGs were analyzed from another understudied oral archaea genus, Methanomethylophilus. Preliminary results highlight the possibility of utilizing understudied commensal species as tracers for population migration.
Comparing the performance of double-stranded vs. single-stranded DNA library protocols on ancient microbial DNA recovery and microbiome reconstruction
Keri Burge, Irina Velsko, Christina Warinner
Ancient DNA library construction can affect the recovery of endogenous DNA, thus influencing downstream taxonomic assessment. While studies have shown that single-stranded library generation outperforms double-stranded when applied to highly degraded eukaryotic host DNA, no systematic studies have examined the impacts on ancient microbial communities. To examine the impact, this project assesses sequencing characteristics and taxonomic composition of the reconstructed microbial communities from double- and single-stranded libraries produced from the same extracts of dental calculus of seventeen Neanderthals and other Pleistocene-era humans sequenced with identical Illumina sequencing chemistry. To observe bias in the sequencing effort, differences in the read length, GC content, and number of sequences processed from both protocols are compared. Further, the taxonomic profile as determined by three programs–Kraken2, MALT, and MetaPhlAn4–are compared to explore how sequencing biases affect the identification of authentic, ancient oral species.
Isotopic Analysis and Zooarchaeology by Mass Spectrometry (ZooMS)
Exploring Early Colonial Human Management Practices in Virginia: A View from Coan Hall (44NB11)
Keri Burge, Brigid Ogden, Barbara Heath, Anneke Janzen
When European settlers first arrived in North America, they brought new species and land management practices with them. Detailed information about the agricultural and animal husbandry practices of early European colonists can be viewed through isotopic analysis of archaeofaunal materials. This project analyzes faunal materials from the multicomponent site of Coan Hall (44NB11) in Northumberland County, Virginia, which offers insight into early colonial life in the Northern Neck. Specifically, faunal remains consisting primarily of cattle, pig, caprine, and deer were excavated over three main occupation periods. This project presents a diachronic view of animal management strategies in the seventeenth and early eighteenth centuries through stable isotope data, which elucidates the change in taxon-specific management practices over time employed by the occupants at Coan Hall as colonial settlement took hold in the Chesapeake.
Historical Archaeology Field and Lab Work at Coan Hall (44NB11)
Secrets Beneath the Surface: A GPR Analysis of Coan Hall
Zaria Bowden, Keri Burge, and Meghan Dadmun
PIs: Dr. Barbara Heath and Howard Cyr
Ground penetrating radar (GPR) is a geophysical technique that can be used to identify subsurface elements as well as their depth and location underground through the transmission of electromagnetic pulses. The use of GPR at Coan Hall, an early 17th century colonial site, assisted archaeological studies at the site by providing possible locations for undiscovered features. GPR analysis during the 2021 excavation season produced one main unexpected result—an anomaly consisting of a 30 meter by 10 meter dark signal. This type of signal is typically caused by a material within the subsurface slowing down the radar waves as they propagate. While this anomaly cannot be currently identified with the given evidence, we are hopeful that future excavations will provide insight into this feature.
Forensic Anthropology Center
The Effect of Body Mass Index on Human Decomposition
Keri Burge, Jarrett Burgess, Katelynn Cox
PI: Mary Charlesie Davis
In a decomposed human remains case, estimating a precise postmortem interval (PMI) is crucial in determining the identification of an individual. A detailed PMI estimate can be used to reduce the potential list of decedents. However, a universal PMI formula has yet to be determined, indicating the need for controlled experimentation of specific variables that affect human decomposition. While previous research has evaluated the effect of body mass in general with contradictory results, this project aimed to analyze the effect of a more narrow variable, body mass index (BMI), or an individual’s weight divided by their height. In order to determine whether there is a correlation between BMI and rates of outdoor human decomposition, thirty individuals donated to the Forensic Anthropology Center were split into three BMI groups—normal, overweight, and underweight—with ten in each group. Daily photos taken of the individuals throughout the decomposition process were used to perform total body scoring (TBS). Then, to take the effect of temperature into account, the accumulated degree days (ADD) to reach each TBS were determined. While results showed no significant overall correlation, underweight individuals did reach skeletonization significantly faster than the overweight and normal groups. A general trend can be seen: individuals with an underweight BMI classification decompose faster than those with the normal and overweight classifications in the later stages of decomposition.