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.

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.

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.

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.

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.

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.

Some multivariate tests for differences in sexual dimorphism between human populations.

Two multivariate statistical tests are presented for examining differences in sexual dimorphism between human populations. One test refers to general differences in sexual dimorphism; the other, only to differences in size aspects of sexual dimorphism. There is no current resolution to the complementary problem of testing for differences of direction in sexual dimorphism. By applying the tests to a comparison of sexual dimorphism in 26 samples of skulls from a world-wide distribution of human populations, significant results (at alpha = 0.05) were found in the majority of cases with the general test, and in a minority of cases with the size test.

Cementum annulation and age determination in Homo sapiens. I. Tooth variability and observer error.

In order to test the feasibility of cementum annulations to estimate age in humans, observer error and tooth variability in cementum ring counts were evaluated in a sample of 42 mandibular canine and first premolar pairs. Additionally, two sectioning techniques were evaluated. Demineralized thin sections (7 micron) stained with hematoxylin are the preferred technique since their age related variance is greater than 75% for all tooth types examined. In contrast, less than 50% of the total variance was accounted for among individuals when mineralized sections (80 micron) stained with alizarin red were used. Intertooth variability in ring counts of demineralized sections was large between canines and premolars (43%). Premolars provide counts with lower interobserver error and are the preferred tooth. In an expanded sample (N = 51) of demineralized premolars, intraobserver and interobserver error accounted for 2% and 5% of the total variance, respectively. Evaluation of several experimental designs showed that increasing the number of slides per tooth has the greatest effect on reducing variance followed by increasing the number of observers. Increasing the number of observations has little effect. Cementum ring counts are measurable to a highly repeatable extent and provide a level of repeatability greater than that reported for the pubic symphysis and auricular surface aging techniques.

Cementum annulation and age determination in Homo sapiens. II. Estimates and accuracy.

The cementum annulation aging technique was evaluated in a sample of 80 clinically extracted premolars (age range 11-70 years). Demineralized thin sections (7 micron) stained with hematoxylin were used. The correlation (r) between age and adjusted count (number of annulations added to age of tooth eruption) was 0.78 for the entire sample (N = 73) and 0.86 for a subsample in which teeth with periodontal disease were excluded (N = 55). Standard error of the estimates ranged from 4.7 to 9.7 years depending on sex and health status of the tooth. The technique provided significantly better estimates for females than for males. The overall inaccuracy (mean absolute error) of the technique was 6.0 years, with a bias (mean error) of 0.26 years. Reduced major axis regression of adjusted count on age produced a slope of 0.797 for the entire sample and 0.889 for the nonperiodontal disease subsample. These slopes are consistent with a hypothesis of annual deposition of cementum rings given a decrease in cementogenesis with increasing age.

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.

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.

Electron microprobe analysis of elemental distribution in excavated human femurs.

Elemental distributions have been determined for femur cross sections of eight individuals from the Gibson and Ledders Woodland sites. The analyses were obtained by x-ray fluorescence with a scanning electron microscope. Movement of an element from soil to bone should give rise to inhomogeneous distributions within the bone. We found that the distributions of zinc, strontium, and lead are homogeneous throughout the femur. In contrast, iron, aluminum, potassium, and manganese show clear buildup along the outer surface of the femur and sometimes along the inner (endosteal) surface, as the result of postmortem enrichment. The buildup penetrates 10-400 micron into the femur. The major elements calcium and sodium show homogeneous distributions, but considerable material could be lost by leaching (10-15%) without causing a palpable effect on the electron maps. Magnesium shows buildup on the outer edge of some samples. These results suggest that diagenetic contamination may exclude Fe, Al, K, Mn, and probably Mg from use as indicators of ancient data. The homogeneous distributions of Zn, Sr, and Pb suggest that these elements are not altered appreciably and may serve as useful dietary indicators.

Vertebral pathology in the afar australopithecines.

Ten vertebral elements from the AL-288 partial hominid skeleton and 11 elements from the AL-333 collection are described. The AL-288 column presents a marked kyphosis at the level of thoracic vertebrae 6 through 10, with pronounced new bone formation on the ventral surfaces of these vertebrae. These features, associated with narrowed disc space and minor osteophytosis, resemble Scheuermann disease in the human. Even though this diagnosis is consistent with a basically human, bipedal locomotor repertoire, the presence of Scheuermann disease suggests that lifting, climbing, or acrobatic activities may have been important in early hominids.

A comparative study of the chemical analysis of ribs and femurs in Woodland populations.

Parallel chemical analyses of ribs and femurs from the Middle Woodland Gibson site and the Late Woodland Ledders site show that the elements most closely related to diet (strontium, zinc, magnesium) are found in identical proportions in the two bones. Elements associated with soil contamination (iron, aluminum, potassium, manganese) are found in a significantly higher proportion in the rib. The major elements calcium and sodium are found in lower levels in the ribs. Thus the rib is more sensitive to diagenetic processes that alter elemental proportions than is the femur. Conclusions concerning subgroupings by sex or site, derived from the diet-related elements (Sr, Zn, Mg), were found to be essentially the same for the rib and the femur.

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.