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Microbial colonization of bone is an important mechanism of post-mortem skeletal degradation. However, the types and distributions of bone and tooth colonizing microbes are not well characterized. It is unknown if microbial communities vary in abundance or composition between bone element types, which could help explain patterns of human DNA preservation. The goals of the present study were to (1) identify the types of microbes capable of colonizing different human bone types and (2) relate microbial abundances, diversity, and community composition to bone type and human DNA preservation. DNA extracts from 165 bone and tooth samples from three skeletonized individuals were assessed for bacterial loading and microbial community composition and structure. Random forest models were applied to predict operational taxonomic units (OTUs) associated with human DNA concentration. Dominant bacterial bone colonizers were from the phyla Proteobacteria (36%), Actinobacteria (23%), Firmicutes (13%), Bacteroidetes (12%), and Planctomycetes (4.4%). Eukaryotic bone colonizers were from Ascomycota (40%), Apicomplexa (21%), Annelida (19%), Basidiomycota (17%), and Ciliophora (14%). Bacterial loading was not a significant predictor of human DNA concentration in two out of three individuals. Random forest models were minimally successful in identifying microbes related to patterns of DNA preservation, complicated by high variability in community structure between individuals and body regions. This work expands on our understanding of the types of microbes capable of colonizing human bone and contributing to human skeletal DNA degradation.

Microbial colonization of bone is an important mechanism of postmortem skeletal degradation. However, the types and distributions of bone and tooth colonizing microbes are not well characterized. It is unknown if microbial communities vary in abundance or composition between bone element types, which could help explain differences in human DNA preservation. The goals of the present study were to (1) identify the types of microbes capable of colonizing different human bone types and (2) relate microbial abundances, diversity, and community composition to bone type and human DNA preservation. DNA extracts from 165 bone and tooth samples from three skeletonized individuals were assessed for bacterial loading and microbial community composition and structure. Random forest models were applied to predict operational taxonomic units (OTUs) associated with human DNA concentration. Dominant bacterial bone colonizers were from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Planctomycetes. Eukaryotic bone colonizers were from Ascomycota, Apicomplexa, Annelida, Basidiomycota, and Ciliophora. Bacterial loading was not a significant predictor of human DNA concentration in two out of three individuals. Random forest models were minimally successful in identifying microbes related to human DNA concentration, which were complicated by high variability in community structure between individuals and body regions. This work expands on our understanding of the types of microbes capable of colonizing the postmortem human skeleton and potentially contributing to human skeletal DNA degradation.

Body dimensions of animal remains provide evidence for subsistence technologies, seasonality of hunting and fishing, and generalized resource stress. Studies that rely on reconstructed body dimensions of fishes rarely address the possibility of differential preservation or recovery, which may result in inaccurate representations of size classes. We devise a method to test for differential fragmentation of archaeofauna1 specimens based on specimen size and location within the stratigraphic column. We also compare two methods for reconstructing animal size classes: one includes only complete specimens that can be measured accurately, and the other includes both fragmented and complete specimens. We use a collection of mullet (Mugil spp.) atlases from the McQueen Shell Ring, St. Catherines Island, Georgia (USA), many of which were included in a previous study of fish body size as evidence for fishing technologies. All atlases are sorted by size class and categorized as having complete or fragmented osteometric landmarks. There is a positive correlation (ρ = 0.45, P = 0.07) between atlas size class and proportion of specimens that are fragmented: smaller atlases are more likely to be recovered, identified, and measured without fragmentation compared to larger atlases. Size-based differential fragmentation may bias against the representation of larger-bodied individuals in this context. Frequency of fragmentation is not monotonically correlated with burial depth (ρ = −0.19, P = 0.39), and is higher in the upper-most and bottom-most levels of the stratigraphic column compared to intermediate depths. Depth-based differential fragmentation may bias results when stratigraphic sequences are used to evaluate change through time in animal body sizes.

Though recent decades have seen a marked increase in research concerning the impact of human decomposition on the grave soil environment, the fate of human DNA in grave soil has been relatively understudied. With the purpose of supplementing the growing body of literature in forensic soil taphonomy, this study assessed the relative persistence of human DNA in soil over the course of decomposition. Endpoint PCR was used to assess the presence or absence of human nuclear and mitochondrial DNA, while qPCR was used to evaluate the quantity of human DNA recovered from the soil beneath four cadavers at the University of Tennessee's Anthropology Research Facility (ARF). Human nuclear DNA from the soil was largely unrecoverable, while human mitochondrial DNA was detectable in the soil throughout all decomposition stages. Mitochondrial DNA copy abundances were not significantly different between decomposition stages and were not significantly correlated to soil edaphic parameters tested. There was, however, a significant positive correlation between mitochondrial DNA copy abundances and the human associated bacteria, Bacteroides, as estimated by 16S rRNA gene abundances. These results show that human mitochondrial DNA can persist in grave soil and be consistently detected throughout decomposition.