Whole mitochondrial genomes assembled from thermally altered forensic bones and teeth.

The recovery and analysis of genetic material obtained from thermally altered human bones and teeth are increasingly important to forensic investigations, especially in cases where soft-tissue identification is no longer possible. Although little is known about how these fire-related processes affect DNA degradation over time, next-generation sequencing technology in combination with traditional osteobiographical applications may provide us clues to these questions. In this study, we compare whole mitochondrial genome data generated using two different DNA extraction methods from 27 thermally altered samples obtained from fire victims (Maricopa County, Arizona) . DNA extracts were converted to double-stranded DNA libraries and enriched for whole mitochondrial DNA (mtDNA) using synthetic biotinylated RNA baits, then sequenced on an Illumina MiSeq. We processed the mitochondrial data using an in-house computational pipeline (MitoPipe1.0) composed of ancient DNA and modern genomics applications, then compared the resulting information across the two extraction types and five burn categories. Our analysis shows that DNA fragmentation increases with temperature, but that the acute insult from fire combined with the lack of water is insufficient to produce 5' and 3' terminal deamination characteristic of ancient DNA. Our data also suggest an acute and significant point of DNA degradation between 350 °C and 550 °C, and that the likelihood of generating high quality mtDNA haplogroup calls decreases significantly at temperatures > 550 °C. This research is part of a concerted effort to understand how fire affects our ability to generate genetic profiles suitable for forensic identification purposes.

Reconstructing full and partial STR profiles from severely burned human remains using comparative ancient and forensic DNA extraction techniques.

Thermal degeneration of the DNA molecule presents a special challenge to medico-legal investigations since low DNA yields, fragmented DNA molecules, and damaged nucleotide bases hinder accurate STR genotyping. As a consequence, fragments of severely burned human remains are often not amenable to standard DNA recovery. However, current ancient DNA (aDNA) extraction methods have proven highly effective at obtaining ultrashort DNA fragments (∼50 bp) from degraded palaeontological and archaeological specimens. In this study, we compare DNA yields and STR results obtained from two established aDNA and forensic DNA extraction protocols by sampling multiple skeletal elements recovered from victims (n = 23) involved in fire-related incidents. DNA yields and STR results suggest an inverse correlation between DNA yield and STR quality and increasing temperature. Despite the rapid thermal destruction of DNA at high temperatures, we generated higher quality full and partial STR profiles using the aDNA extraction protocol across all burn categories than the forensic total bone demineralization extraction method. Our analysis suggests adopting aDNA extraction methods as an alternative to current forensic practices to improve DNA yields from challenging human remains.

Effects of burning on human bone microstructure: a preliminary study.

The microscopic determination of age at death in human bone is a widely used technique in forensic anthropology. Despite its use, little attention has been given to the reliability of microscopic aging when the subject has been burned, either at the time of death, or after death. This preliminary report examines some of the variables of the burning process that may affect the age estimates. Preliminary conclusions are: (1) bone burned at 600 degrees C retains all of the structures necessary for microscopic aging and (2) bone shrinkage, widely reported in the literature, does not appear to have significant effect on the age estimate. A research plan is outlined that will address some of the questions left unanswerable in the present report.

Individuation in forensic science study: decapitation.

In this study we present a technique that may be useful in the individuation of remains separated through the cervical region. Using a series of measurements from young female skeletons in the Terry Collection, we have developed a model for testing congruence between adjacent elements. Emphasis has been placed on identifying those measurements most likely to minimize underestimating the true number of remains present. The use of the technique has been demonstrated in two (retrospective) forensic science examples.

Linear models for the prediction of stature from foot and boot dimensions.

Estimation of stature from the dimensions of foot or shoeprints has considerable forensic value in developing descriptions of suspects from evidence at the crime scene and in corroborating height estimates from witnesses. This study extends the findings of previous researchers by exploring linear models with and without gender and race indicators, and by validating the most promising models on a large, recently collected military database. Boot size and outsole dimensions are also examined as predictors of stature. The results of this study indicate that models containing both foot length and foot breadth are significantly better than those containing only foot length. Models with race/gender indicators also perform significantly better than do models without race/gender indicators. However, the difference in performance is slight, and the availability of reliable gender and race information in most forensic situations is uncertain. Analogous results were obtained for models utilizing boot size/width and outsole length/width, and in this study these variables performed nearly as well as the foot dimensions themselves. Although the adjusted R2 values for these models clearly reflect a strong relationship between foot/boot length and stature, individual 95% prediction limits for even the best models are +/- 86 mm (3.4 in.). This suggests that models estimating stature from foot/shoe-prints may be useful in the development of subject descriptions early in a case but, because of their imprecision, may not always be helpful in excluding individual suspects from consideration.

Analysis of blunt trauma injuries: vertical deceleration versus horizontal deceleration injuries.

There are several similarities found in blunt trauma injuries to humans sustained as a result of vertical deceleration (falling) and those sustained as a result of deceleration in a horizontal plane (automobile accidents). However, examination of the patterns of traumatic skeletal injuries can distinguish those injuries associated with falling from heights from those associated with automobile accidents. While there is considerable variation within each type of blunt trauma injury dependent on the angle at which one falls or is struck, there are several characteristic skeletal features associated with each type of trauma. In this study we review both the current literature and human skeletal remains from the University of New Mexico's Documented Collection known to have been subjected to blunt trauma. This collection is used to characterize and differentiate the pattern of skeletal injuries to various parts of the body for each type of trauma. These assessments are applied to investigate the traumatic skeletal lesions observed in a forensic case where the manner of death is unknown. Analyses suggest two possible scenarios that would explain the death of the individual investigated, with death most likely related to a vehicular-pedestrian accident.

Complete mitochondrial genomes of ancient canids suggest a European origin of domestic dogs.

The geographic and temporal origins of the domestic dog remain controversial, as genetic data suggest a domestication process in East Asia beginning 15,000 years ago, whereas the oldest doglike fossils are found in Europe and Siberia and date to >30,000 years ago. We analyzed the mitochondrial genomes of 18 prehistoric canids from Eurasia and the New World, along with a comprehensive panel of modern dogs and wolves. The mitochondrial genomes of all modern dogs are phylogenetically most closely related to either ancient or modern canids of Europe. Molecular dating suggests an onset of domestication there 18,800 to 32,100 years ago. These findings imply that domestic dogs are the culmination of a process that initiated with European hunter-gatherers and the canids with whom they interacted.

Diet, tuberculosis, and the paleopathological record.

Osseous manifestation of infectious disease is of paramount importance to paleopathologists seeking to interpret ancient health, but the relationships among infectious agent exposure, development of disease, and skeletal involvement are complex. The outcome of an exposure strongly depends on multiple factors, including ecology, diet, nutrition, immune function, and the genetics of pathogen and host. Mycobacterial diseases are often studied in ancient remains but also are especially influenced by these factors; individual and population differences in severity and course are apparent following onset of active disease. The osteological record for these diseases represents the complex interplay of host and pathogen characteristics influencing within- and among-individual skeletal lesion prevalence and distribution. However, many of these characteristics may be assessed independently through the archaeological record. Here, we explore the contributions of dietary protein and iron to immune function, particularly the course and outcome of infection with Mycobacterium tuberculosis. We emphasize how nutrition may influence the dissemination of bacilli to the skeleton and subsequent formation of diagnostic lesions. We then generate models and hypotheses informed by this interplay and apply them to four prehistoric New World areas. Finally, discrepancies between our expectations and the observed record are explored as a basis for new hypotheses.

The Caribou Eskimo: general and specific disease.

Reported here are two forms of skeletal pathology identified in an inclusive sample of Caribou Eskimo skeletons. Harris Lines, nonspecific indicators of stress, show marked periodicity in approximately one-half of the observable adults. This pattern is interpreted as the result of a recurrent, annual stress cycle, perhaps attributable to late winter famine. A second form of pathological change comprises resorptive lesions primarily localized in the spinal column and infrequently found on articular surfaces of the appendicular skeleton. Differential diagnosis is developed utilizing attributes of lesion form, lesion distribution, and epidemiology. Emphasis is placed upon deriving objective models which reflect disease in the absence of modern medical intervention. Major forms of pathology known to produce vertebral lesions are included. The model which best fits the Caribou Eskimo data is that of tuberculosis.

Healed fractures in Macaca mulatta: age, sex, and symmetry.

Previous studies utilizing series of wild-shot primates have suggested that there is an association between locomotor behavior, aggression and patterning of healed fractures. In this study, observations taken upon a series of 126 rhesus macaques which represent a total sample of a naturally occurring social group from Cayo Santiago, are used to reexamine the conclusions drawn from previous studies. As a control, a series of randomly collected rhesus skeletons from the same colony is examined. Major differences in pathology incidences by age, sex and laterality is indicated between the two groups. Possible explanation for cross-specific variability in fracture patterning are also considered.

Health and differential survival in prehistoric populations: prenatal dental defects.

Linear hypoplasia of the deciduous teeth is rare in most human populations, but common where nutritional status is poor. Deciduous enamel hypoplasia, hypocalcification, and hypoplasia-related caries are described in Middle and Late Woodland skeletal series from the Lower Illinois Valley. Gross enamel defects that can be referred to pre-natal development are found in 83 of 170 children under six years of age at death. Circular caries secondary to hypoplasia is significantly more common in the Late Woodland series, reflecting the apparent higher cariogenicity of Late Woodland diets. There is a significant association between prenatal dental defects and bony evidence for anemia and infectious disease. Children with enamel defects show relatively higher weaning age mortality than those without. These relationships suggest that at least moderate levels of malnutrition existed in Illinois Woodland populations.

Quantitative genetics of skeletal nonmetric traits in the rhesus macaques of Cayo Santiago. III. Relative heritability of skeletal nonmetric and metric traits.

This study addresses the long-standing controversy in skeletal biology concerning the relative utility of skeletal metric and nonmetric traits for studies of biological relationship. This controversy centers on the relative heritability of these two trait sets. This paper presents heritabilities for a series of skeletal metric and nonmetric traits measured with the same sample of mother-offspring pairs from the Cayo Santiago skeletal collection of rhesus macaques. Skeletal nonmetric traits display significantly greater heritability estimates than metric traits. This difference is due primarily to the high heritability estimates of hyperostotic nonmetric traits. Foraminal traits are not significantly more heritable than skeletal metric traits. The generality of this pattern of heritability values, in which hyperostotic nonmetric traits are more highly heritable than foraminal nonmetric and metric traits, depends on future empirical study of the correlation of heritability values in populations and theoretical work.

Quantitative genetics of skeletal nonmetric traits in the rhesus macaques on Cayo Santiago. I. Single trait heritabilities.

The use of skeletal nonmetric traits in studies of biological relationships often involves the assumption that variation in these traits is genetic. Studies of nonmetric traits in human groups and in inbred strains of mice and rabbits have indicated a genetic component to nonmetric trait variation. Skeletons of animals with known matrilineage membership were obtained from the Cayo Santiago skeletal collection in order to obtain a direct estimate of the heritabilities of several nonmetric traits in the free-ranging population of rhesus macaques on Cayo Santiago. Falconer's (1965) method was used to calculate heritability. Heritability estimates range from zero to one, and half of them are greater than 0.5. This indicates that there is a considerable amount of genetic variation for these traits among the Cayo macaques. There is a significant tendency for traits scoring the number of foramina to have lower heritabilities than those scoring hyperstotic or hypostotic traits.

Quantitative genetics of skeletal nonmetric traits in the rhesus macaques on Cayo Santiago. II. Phenotypic, genetic, and environmental correlations between traits.

The general lack of phenotypic correlation among skeletal nonmetric traits has been interpreted as indicating a lack of genetic correlation among these traits. Nonmetric traits scored on animals in the skeletal collection of rhesus macaques from Cayo Santiago are used to calculate phenotypic, genetic, and environmental correlations between traits. The results show that even when phenotypic correlations are low, there may be large, significant genetic correlations among these traits. The genetic correlation pattern suggests that genes which affect nonmetric trait variation act primarily at a local level in the cranium, even though there are genes with pleiotropic effects on skeletal nonmetric traits throughout the cranium. Environmental and phenotypic correlations do not show this neighborhood pattern of correlation.

Coca chewing in prehistoric coastal Peru: dental evidence.

In this study, we describe the dental health of four prehistoric human populations from the southern coast of Peru, an area in which independent archaeological evidence suggests that the practice of coca-leaf chewing was relatively common. A repeated pattern of cervical-root caries accompanying root exposure was found on the buccal surfaces of the posterior dentition, coinciding with the typical placement of coca quids during mastication. To further examine the association between caries patterning and coca chewing, caries site characteristics of molar teeth were utilized as indicators for estimating the likelihood of coca chewing for adults within each of the study samples. Likelihood estimates were then compared with results of a test for coca use derived from hair samples from the same individuals. The hair and dental studies exhibited an 85.7% agreement. Thus, we have demonstrated the validity of a hard-tissue technique for identifying the presence of habitual coca-leaf chewing in ancient human remains, which is useful in archaeological contexts where hair is not preserved. These data can be used to explore the distribution of coca chewing in prehistoric times. Simultaneously, we document the dental health associated with this traditional Andean cultural practice.

Genetic correlations between sides and heritability of asymmetry for nonmetric traits in rhesus macaques on Cayo Santiago.

The use of nonmetric traits for estimation of biological distance is a long-standing practice in biological anthropology. Nonmetric traits can be scored using either the individual or the side of the individual as the unit of measure. If sides of the individual are genetically correlated the use of sides would produce redundant genetic information. For this reason, Korey (Am. J. Phys. Anthropol. 53:19-23, 1980) argues for the use of individuals as the unit of measure for nonmetric traits. Ossenberg (Am. J. Phys, Anthropol. 54:471-479, 1981), however, argues that bilateral occurrence of nonmetric traits indicates greater genetic liability for the trait and that therefore the sides are the more biologically correct unit of measure. Genetic correlations for 13 cranial nonmetric traits are estimated for a sample of rhesus macaque skeletons from Cayo Santiago. In addition, heritability of asymmetry is estimated for these 13 traits as a test of Ossenberg's contention that asymmetry is genetically influenced. Significant genetic correlations between sides support Korey's contention that nonmetric traits should be scored by individual. Only two asymmetry heritabilities were significantly different from zero, providing no significant support for Ossenberg's contention that asymmetry is genetically determined. Our results support the theory that asymmetry represents a measure of the ability of an organism to buffer stresses. Therefore, a measure of the heritability of asymmetry is a measure of the heritability of the ability to buffer stresses. This ability does not appear to be heritable in this sample.

The relationship between cranial metric and nonmetric traits in the rhesus macaques from Cayo Santiago.

This study addresses the relationship between cranial metric variables and nonmetric traits using the skeletal sample of rhesus macaques from Cayo Santiago. Discriminant function analysis is used to study the metric differences between macaque crania grouped according to the presence or absence of nine nonmetric traits. The computation of total structure coefficients from the discriminant function analyses provides information regarding how closely each metric variable is related to the discriminant functions derived. Total structure coefficients have not been used previously in the study of the relationship between metric and nonmetric traits. The results of the analysis are interpreted using an explicit approach to cranial morphogenesis-functional cranial analysis. It is concluded that the relationship between cranial metric and nonmetric traits is explicable in terms of a common developmental pathway shared by the two types of traits. Identification of the specific etiology of nonmetric traits depends on future anatomical studies or organisms throughout the period of nonmetric trait development.

Skeletal biological distance studies in American physical anthropology: recent trends.

Biological distance analysis, the dominant type of skeletal biological research during the 19th century, has become less visible in recent years. Although the proportion of American Journal of Physical Anthropology articles and published abstracts focusing on biodistance has remained fairly constant over the three decades between 1955 and 1985, the proportion of biodistance contributions relative to other skeletal biology studies has decreased. Emphasis in skeletal biology has shifted from the analysis of biological variation to investigations of health and diet, and within biodistance studies methodological issues have assumed prominence over purely analytical approaches. This paper investigates trends in biological distance analysis through a survey of articles and meetings abstracts published in the American Journal of Physical Anthropology from 1955 to 1985. The survey provides the historical context for five symposium papers on skeletal biological distance presented at the 1986 meeting of the American Association of Physical Anthropologists.