Modern strains of Mycobacterium tuberculosis from the Americas are closely related to those from Europe, supporting the assumption that human tuberculosis was introduced post-contact1. This notion, however, is incompatible with archaeological evidence of pre-contact tuberculosis in the New World2. Comparative genomics of modern isolates suggests that M. tuberculosis attained its worldwide distribution following human dispersals out of Africa during the Pleistocene epoch3, although this has yet to be confirmed with ancient calibration points. Here we present three 1,000-year-old mycobacterial genomes from Peruvian human skeletons, revealing that a member of the M. tuberculosis complex caused human disease before contact. The ancient strains are distinct from known human-adapted forms and are most closely related to those adapted to seals and sea lions. Two independent dating approaches suggest a most recent common ancestor for the M. tuberculosis complex less than 6,000 years ago, which supports a Holocene dispersal of the disease. Our results implicate sea mammals as having played a role in transmitting the disease to humans across the ocean.
Forensic anthropologists use a number of maceration techniques to facilitate skeletal analysis of personal identity and trauma, but they may unwittingly eliminate valuable DNA evidence in the process. This study evaluated the effect of 10 maceration methods on gross bone structure and the preservation of DNA in ribs of 12 pigs (Sus scrofa). A scoring system was applied to evaluate the ease of maceration and resulting bone quality while DNA purity was quantified by optical densitometry analysis, followed by polymerase chain reaction (PCR) amplification of three mitochondrial and three nuclear loci. The results demonstrated that while mitochondrial DNA could be amplified for all experiments, cleaning treatments using bleach, hydrogen peroxide, ethylenediaminetetraacetic acid/papain, room temperature water and detergent/sodium carbonate followed by degreasing had low DNA concentrations and failed to generate nuclear PCR products. In general, treatments performed at high temperatures (90 degrees C or above) for short durations performed best. This study shows that traditionally "conservative" maceration techniques are not necessarily the best methods to yield DNA from skeletal tissue.
While nonhuman animal remains are often utilized in forensic research to develop methods to estimate the postmortem interval, systematic studies that directly validate animals as proxies for human decomposition are lacking. The current project compared decomposition rates among pigs, rabbits, and humans at the University of Tennessee's Anthropology Research Facility across three seasonal trials that spanned nearly 2 years. The Total Body Score (TBS) method was applied to quantify decomposition changes and calculate the postmortem interval (PMI) in accumulated degree days (ADD). Decomposition trajectories were analyzed by comparing the estimated and actual ADD for each seasonal trial and by fuzzy cluster analysis. The cluster analysis demonstrated that the rabbits formed one group while pigs and humans, although more similar to each other than either to rabbits, still showed important differences in decomposition patterns. The decomposition trends show that neither nonhuman model captured the pattern, rate, and variability of human decomposition.
Forensic anthropology typically uses osteological and/or dental data either to estimate characteristics of unidentified individuals or to serve as evidence in cases where there is a putative identification. In the estimation context, the problem is to describe aspects of an individual that may lead to their eventual identification, whereas in the evidentiary context, the problem is to provide the relative support for the identification. In either context, individual characteristics such as sex and race may be useful. Using a previously published forensic case (Steadman et al. (2006) Am J Phys Anthropol 131:15-26) and a large (N = 3,167) reference sample, we show that the sex of the individual can be reliably estimated using a small set of 11 craniometric variables. The likelihood ratio from sex (assuming a 1:1 sex ratio for the "population at large") is, however, relatively uninformative in "making" the identification. Similarly, the known "race" of the individual is relatively uninformative in "making" the identification, because the individual was recovered from an area where the 2000 US census provides a very homogenous picture of (self-identified) race. Of interest in this analysis is the fact that the individual, who was recovered from Eastern Iowa, classifies very clearly with [Howells 1973. Cranial Variation in Man: A Study by Multivariate Analysis of Patterns of Difference Among Recent Human Populations. Cambridge, MA: Peabody Museum of Archaeology and Ethnology; 1989. Skull Shape and the Map: Craniometric Analyses in the Dispersion of Modern Homo. Cambridge, MA: Harvard University Press]. Easter Islander sample in an analysis with uninformative priors. When the Iowa 2000 Census data on self-reported race are used for informative priors, the individual is clearly identified as "American White." This analysis shows the extreme importance of an informative prior in any forensic application.
Forensic scientists are often expected to present the likelihood of DNA identifications in US courts based on comparative population data, yet forensic anthropologists tend not to quantify the strength of an osteological identification. Because forensic anthropologists are trained first and foremost as physical anthropologists, they emphasize estimation problems at the expense of evidentiary problems, but this approach must be reexamined. In this paper, the statistical bases for presenting osteological and dental evidence are outlined, using a forensic case as a motivating example. A brief overview of Bayesian statistics is provided, and methods to calculate likelihood ratios for five aspects of the biological profile are demonstrated. This paper emphasizes the definition of appropriate reference samples and of the "population at large," and points out the conceptual differences between them. Several databases are introduced for both reference information and to characterize the "population at large," and new data are compiled to calculate the frequency of specific characters, such as age or fractures, within the "population at large." Despite small individual likelihood ratios for age, sex, and stature in the case example, the power of this approach is that, assuming each likelihood ratio is independent, the product rule can be applied. In this particular example, it is over three million times more likely to obtain the observed osteological and dental data if the identification is correct than if the identification is incorrect. This likelihood ratio is a convincing statistic that can support the forensic anthropologist's opinion on personal identity in court.
The oral cavity harbors one of the most diverse microbiomes in the human body. It has been shown to be the second most complex in the body after the gastrointestinal tract. Upon death, the indigenous microorganisms lead to the decomposition of the carcass. Therefore, the oral cavity and gastrointestinal tract microbiomes play a key role in human decomposition. The aim of the present study is to monitor the microbiome of decaying bodies on a daily basis and to identify signature bacterial taxa, that can improve postmortem interval estimation. Three individuals (one male and two female) donated to the University of Tennessee Forensic Anthropology Center for the W.M. Bass Donated Skeletal Collection were studied. Oral swab samples were taken daily throughout the different stages of cadaveric putrefaction. DNA was extracted and analyzed by next-generation sequencing techniques. The three cadavers showed similar overall successional changes during the decomposition process. Firmicutes and Actinobacteria are the predominant phyla in the fresh stage. The presence of Tenericutes corresponds to bloat stage. Firmicutes is the predominant phylum in advanced decay, but the Firmicutes community is a different one from the predominant Firmicutes of the fresh stage. This study depicts the thanatomicrobiome successional changes in the oral cavity, and highlights its potential use in forensic cases as a quantitative and objective approach to estimate postmortem interval, from an ecological rationale.
Different animal species have been used as proxies for human remains in decomposition studies for decades, although few studies have sought to validate their use in research aimed at estimating the postmortem interval. This study examines 45 pig, rabbit, and human subjects placed in three seasonal trials at the Anthropology Research Facility. In an earlier paper, we found that overall decomposition trends did vary between species that could be due to differential insect and scavenger behavior. This study specifically examines if scavenger behavior differs by carrion species. Daily photographs, game camera photographs, written observations, and Total Body Score (TBS) documented scavenging and decomposition changes. Results show that raccoons were the most commonly observed vertebrate scavenger, that scavenging was most extensive in winter, and that certain human subjects were preferred over other humans and all non-human subjects. Finally, scavenging activity greatly reduces the accuracy of postmortem interval estimates based on TBS.
Most current methods for adult skeletal age-at-death estimation are based on American samples comprising individuals of European and African ancestry. Our limited understanding of population variability hampers our efforts to apply these techniques to various skeletal populations around the world, especially in global forensic contexts. Further, documented skeletal samples are rare, limiting our ability to test our techniques. The objective of this paper is to test three pelvic macroscopic methods (1-Suchey-Brooks; 2-Lovejoy; 3-Buckberry and Chamberlain) on a documented modern Spanish sample. These methods were selected because they are popular among Spanish anthropologists and because they never have been tested in a Spanish sample. The study sample consists of 80 individuals (55 ♂ and 25 ♀) of known sex and age from the Valladolid collection. Results indicate that in all three methods, levels of bias and inaccuracy increase with age. The Lovejoy method performs poorly (27%) compared with Suchey-Brooks (71%) and Buckberry and Chamberlain (86%). However, the levels of correlation between phases and chronological ages are low and comparable in the three methods (< 0.395). The apparent accuracy of the Suchey-Brooks and Buckberry and Chamberlain methods is largely based on the broad width of the methods' estimated intervals. This study suggests that before systematic application of these three methodologies in Spanish populations, further statistical modeling and research into the co-variance of chronological age with morphological change is necessary. Future methods should be developed specific to various world populations, and should allow for both precision and flexibility in age estimation. However, the levels of correlation between phases and chronological ages are low and comparable in the three methods (< 0.395). The apparent accuracy of the Suchey-Brooks and Buckberry and Chamberlain methods is largely based on the broad width of the methods' estimated intervals. This study suggests that before systematic application of these three methodologies in Spanish populations, further statistical modeling and research into the co-variance of chronological age with morphological change is necessary. Future methods should be developed specific to various world populations, and should allow for both precision and flexibility in age estimation.3
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