Targeted enrichment of whole-genome SNPs from highly burned skeletal remains.

Genetic assessment of highly incinerated and/or degraded human skeletal material is a persistent challenge in forensic DNA analysis, including identifying victims of mass disasters. Few studies have investigated the impact of thermal degradation on whole-genome single-nucleotide polymorphism (SNP) quality and quantity using next-generation sequencing (NGS). We present whole-genome SNP data obtained from the bones and teeth of 27 fire victims using two DNA extraction techniques. Extracts were converted to double-stranded DNA libraries then enriched for whole-genome SNPs using unpublished biotinylated RNA baits and sequenced on an Illumina NextSeq 550 platform. Raw reads were processed using the EAGER (Efficient Ancient Genome Reconstruction) pipeline, and the SNPs filtered and called using FreeBayes and GATK (v. 3.8). Mixed-effects modeling of the data suggest that SNP variability and preservation is predominantly determined by skeletal element and burn category, and not by extraction type. Whole-genome SNP data suggest that selecting long bones, hand and foot bones, and teeth subjected to temperatures <350°C are the most likely sources for higher genomic DNA yields. Furthermore, we observed an inverse correlation between the number of captured SNPs and the extent to which samples were burned, as well as a significant decrease in the total number of SNPs measured for samples subjected to temperatures >350°C. Our data complement previous analyses of burned human remains that compare extraction methods for downstream forensic applications and support the idea of adopting a modified Dabney extraction technique when traditional forensic methods fail to produce DNA yields sufficient for genetic identification.

Twenty-first century bioarchaeology: Taking stock and moving forward.

This article presents outcomes from a Workshop entitled "Bioarchaeology: Taking Stock and Moving Forward," which was held at Arizona State University (ASU) on March 6-8, 2020. Funded by the National Science Foundation (NSF), the School of Human Evolution and Social Change (ASU), and the Center for Bioarchaeological Research (CBR, ASU), the Workshop's overall goal was to explore reasons why research proposals submitted by bioarchaeologists, both graduate students and established scholars, fared disproportionately poorly within recent NSF Anthropology Program competitions and to offer advice for increasing success. Therefore, this Workshop comprised 43 international scholars and four advanced graduate students with a history of successful grant acquisition, primarily from the United States. Ultimately, we focused on two related aims: (1) best practices for improving research designs and training and (2) evaluating topics of contemporary significance that reverberate through history and beyond as promising trajectories for bioarchaeological research. Among the former were contextual grounding, research question/hypothesis generation, statistical procedures appropriate for small samples and mixed qualitative/quantitative data, the salience of Bayesian methods, and training program content. Topical foci included ethics, social inequality, identity (including intersectionality), climate change, migration, violence, epidemic disease, adaptability/plasticity, the osteological paradox, and the developmental origins of health and disease. Given the profound changes required globally to address decolonization in the 21st century, this concern also entered many formal and informal discussions.

Introduction: Scientific rigor in paleopathology.

This introductory chapter to the Special Issue on "Scientific Rigor in Paleopathology" serves to orient and introduce the chapters that follow through a detailed consideration of paleopathology as a 21st century intellectual field. In this vein, we first make the significant point that paleopathology is a profoundly interdisciplinary endeavor, encompassing aspects of the biomedical science, the humanities, and the social sciences. Thus, we suggest that no one practitioner can personally command the range of skills necessary for a 21st century paleopathologist. To maintain rigor in differential diagnosis, we emphasize collaborations and consider key concepts that illustrate the basic knowledge from each of these fields that any paleopathologist should command. We then address the manner in which disease diagnosis should proceed as a scientific endeavor. To illustrate scientific rigor in differential diagnosis, we present two case studies drawn from 1970s contributions by Cook and by Buikstra. Finally, we introduce Chapters 2-6, which address differential diagnosis in contexts ranging from specific conditions (scurvy, trepanation) to broader field-wide considerations (paleoparasitology, historical paleopathology, imaging, animal paleopathology).

Biological and social implications of a medieval burial from Cyprus for understanding leprosy in the past.

An early 15th-century burial from a basilica at Polis Chrysochous provides the first archaeological evidence of leprosy in Cyprus, extending the temporal depth and illuminating the biological and social history of this disease on the island. The skeletal remains of a young adult female (age 20-34 years) display pathognomonic features of lepromatous leprosy including maxillary alveolar resorption with antemortem loss of all but one incisor, remodeling of the margin of the nasal sill and resorption of the anterior nasal spine, with diaphyseal remodeling of hand and foot phalanges and the distal third through fifth metatarsals of both feet. Periosteal reaction on distal tibiae and the majority of both fibulae demonstrates tracking of inflammation from the feet to lower legs. Use wear on the remaining maxillary incisor signals participation in common occupational activities in life. Although disfigured and debilitated, burial inside the narthex of the basilica indicates that the community did not ostracize this woman in death. This contextualized analysis provides insight into the biological and social consequences of living with leprosy and illustrates the changing attitudes toward those afflicted with this disease in Cyprus.