A practical guide to cross-cultural and multi-sited data collection in the biological and behavioural sciences.

Researchers in the biological and behavioural sciences are increasingly conducting collaborative, multi-sited projects to address how phenomena vary across ecologies. These types of projects, however, pose additional workflow challenges beyond those typically encountered in single-sited projects. Through specific attention to cross-cultural research projects, we highlight four key aspects of multi-sited projects that must be considered during the design phase to ensure success: (1) project and team management; (2) protocol and instrument development; (3) data management and documentation; and (4) equitable and collaborative practices. Our recommendations are supported by examples from our experiences collaborating on the Evolutionary Demography of Religion project, a mixed-methods project collecting data across five countries in collaboration with research partners in each host country. To existing discourse, we contribute new recommendations around team and project management, introduce practical recommendations for exploring the validity of instruments through qualitative techniques during piloting, highlight the importance of good documentation at all steps of the project, and demonstrate how data management workflows can be strengthened through open science practices. While this project was rooted in cross-cultural human behavioural ecology and evolutionary anthropology, lessons learned from this project are applicable to multi-sited research across the biological and behavioural sciences.

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 Extracts were converted to double-stranded DNA libraries then enriched for whole-genome SNPs using unpublished biotinylated RNA baits and sequenced on an Illumina NextSeq 550 platform.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.

Sexual minority status is associated with earlier recalled age of menarche: Evidence from the 2005-2016 National Health and Nutrition Examination Survey.

INTRODUCTION: Menarcheal timing is associated with growth, development, health, wellbeing, and reproduction across the lifespan. Although sexual orientation is a known correlate of health and developmental inequities, relatively little evolutionarily framed research has investigated sexual orientation-based variation in maturational timing. To improve our understanding of menarcheal timing among sexual minority (SM) people, we use a biocultural-evolutionary life history lens that takes into account the stresses of minoritization to examine the relationship between sexual orientation and self-reported age at menarche in a sample of American adults. METHODS: Using the U.S. National Health and Nutrition Examination Survey (NHANES), a large, nationally representative dataset (n = 9757), we fit multiple logistic regression models and survival curves to evaluate associations between sexual orientation, indicators of somatic and material resources during adolescence (e.g., education, citizenship, upper arm length), and self-reported menarche. RESULTS: SM respondents were more likely to report earlier (by 4-5 months) ages of menarche (p < .001). Post-hoc tests revealed that these differences were driven by bisexual (p < .001) and same-sex experienced (p < .001) relative to heterosexual and lesbian/gay respondents. Earlier menarcheal timing among SM respondents persisted after adjusting for socio-demographic factors and proxies of developmental conditions. DISCUSSION: Our findings reveal that SM status is associated with earlier ages of menarche, an important social and reproductive milestone. We argue that uniting life history theory with the minority stress hypothesis better explains differences in menarcheal timing by sexual orientation than previous paradigms. Investigators should attend to sexual orientation-based variation in maturational timing using holistic, inclusive approaches.

Testing the cross-applicability of juvenile sex estimation from diaphyseal dimensions.

Sex estimation is a crucial component of the biological profile. Stull et al. (2017) have proposed a promising juvenile sex estimation method using long bone measurements taken from a South African sample, providing relatively high classification accuracies and made easy to use via the KidStats web-based app. In this study, we test the models developed by Stull et al. (2017) on an external historic population from Lisbon, Portugal, in order to determine whether the models can be reliably applied to archeological and forensic populations outside of the original population sample. The study sample consisted of 102 individuals (45 females and 57 males) aged under 13 years at death from the Lisbon identified skeletal collection. Measurements from these individuals were used to test the flexible discriminant analysis (FDA) models given by Stull et al. (2017). Allocation accuracies were calculated for boys and girls and children over and under 2 years separately and combined. Our findings show that the models developed by Stull et al. (2017) yield poor accuracy when applied to our external population and thus can potentially be misapplied on archeological skeletal remains or forensic remains of unknown origin. A number of statistical issues may explain why models fail to be transportable or even generalizable, namely multicollinearity, model overfitting and overly optimist bootstrapped cross-validation rates. It is also likely that population differences in size and sexual size dimorphism also affected the applicability of the models. We emphasize the importance of externally validating prediction models, particularly if they are intended to be applied across populations. Our study addresses Stull and co-worker's request for further validation of the method on populations outside of South Africa, as the models cannot be confidently applied in the field until it has been externally validated.

Lack of biological mortality bias in the timing of dental formation in contemporary children: Implications for the study of past populations.

OBJECTIVES: Biological mortality bias is the idea that individuals who perish (non-survivors) are biologically distinct from those who survive (survivors). If biological mortality bias is large enough, bioarchaeological studies of nonsurvivors (skeletal samples) cannot accurately represent the experiences of the survivors of that population. This effect is particularly problematic for the study of juvenile individuals, as growth is particularly sensitive to environmental insults. In this study, we test whether biological mortality bias exists in one dimension of growth, namely dental development. MATERIALS AND METHODS: Postmortem computed tomography scans of 206 children aged 12 years and younger at death were collected from two institutions in the United States and Australia. The sample was separated into children dying from natural causes as proxies for non-survivors and from accidental causes as proxies for survivors. Differences in the timing of dental development were assessed using sequential logistic regressions between dental formation stages and residual analysis of dental minus chronological age. RESULTS: No consistent delay in age of attainment of dental stages was documented between survivors and non-survivors. Delays between survivors and non-survivors in dental relative to chronological age were greatest for infants, and were greater for females than for males. DISCUSSION: Lack of biological mortality bias in dental development reinforces confidence in juvenile age estimates and therefore in skeletal growth profiles and growth studies. As dental development is known to be less environmentally sensitive than skeletal growth and development, further studies should examine biological mortality bias in long bone length.

Juvenile Body Mass Estimation from the Femur Using Postmortem Computed Tomography Data.

Skeletal estimation methods to reconstruct the juvenile biological profile are largely limited to those estimating age and, to a lesser extent, sex. While body mass is not generally estimated as part of the biological profile in forensic investigations, this is a logical candidate for inclusion in the forensic biological profile, as it has long been of interest in paleoanthropology and several methods to estimate juvenile body mass currently exist. To explore the performance of body mass estimation for juveniles, the authors tested the accuracy and precision of previously published panel regression formulae using two femoral measurements: the breadth of the distal metaphysis and the cross-sectional polar moment of inertia (J). The test sample consisted of measurements of 94 individuals from birth to 12.5 years of age, taken from postmortem computed tomography scans housed at the Office of the Medical Investigator, New Mexico, USA. Results indicate that body mass estimates are more accurate when estimated from cross-sectional than from metaphyseal measures. Both formulae, however, consistently underestimated weight, and the magnitude of the underestimation increased exponentially with age. This suggests that, contrary to what others have argued, body mass estimation is complicated by population variation in body composition. This study reinforces the importance of documenting and investigating the ontogeny of human variation. The global increase in medical imaging in clinical settings can be leveraged to obtain skeletal data for juveniles from a wide range of ontogenic environments, marking an exciting time for the study of human variation.

Severe skeletal lesions, osteopenia and growth deficit in a child with pulmonary tuberculosis (mid-20th century, Portugal).

OBJECTIVE: This case-study provides a summary of skeletal lesions seen in a case of diagnosed juvenile pulmonary tuberculosis with extensive multifocal bony lesions. MATERIALS: Skeleton of a 9-year-old girl who died in the 1940s in Lisbon, Portugal. The remains of this individual are part of the Lisbon skeletal reference collection curated at the National Museum of Natural History and Science. METHODS: Lesions and paleopathological conditions were identified and documented through macroscopic, radiographic, computed tomographic, and mammographic analysis. RESULTS: The skeleton shows a variety of lytic lesions on the ribs and thoracic vertebrae including complete destruction of the bodies and fusion of the vertebral arches of four vertebrae, kyphosis, and scoliosis. Further pathological conditions were identified, including bone erosion, premature fusion of the left femoral head and greater trochanter, and abnormal size and shape changes to the lower limbs including loss of bone mass and stunting of the long bones. CONCLUSIONS: Skeletal lesions are indicative of spondylitis, Pott's disease, and prolonged bedrest. SIGNIFICANCE: This case is one of the few examples of confirmed juvenile pulmonary tuberculosis with skeletal lesions prior to the antibiotic era. As such, it provides a reference for the skeletal abnormalities which may be observed in archaeological tuberculosis cases. LIMITATIONS: Pulmonary tuberculosis was recorded as cause of death, however there is no documentation to know the length of illness period or the existence of any comorbidities. SUGGESTIONS FOR FURTHER RESEARCH: Consideration of multi-focal lesions is recommended when analyzing individuals with suspected tuberculosis.

Indirect evidence for biological mortality bias in growth from two temporo-spatially distant samples of children.

Biological mortality bias in growth is a challenge to the analysis and understanding of past populations. In this analysis, we address two interrelated aspects of the bias: its potential magnitude in terms of linear growth and the association between height and survivorship. A contemporary sample of 292 children, whose recumbent length was measured at autopsy in Cuyahoga County, USA, was used to quantify the magnitude of mortality bias. Differences between survivors and non-survivors were quantified using t-tests and Cohen's d for effect size. While survivors were consistently taller than non-survivors, the difference did not become significant until after 7 years of age. A historical sample of 656 girls, whose height and weight were measured at admission to a tuberculosis sanitarium, was used to examine the relationship between height, weight, and survivorship. The survivors and non-survivors were compared using t-tests and Cohen's d, and odds of survival were modeled with logistic regression. Surviving girls were consistently taller and heavier than non-surviving girls. However, while taller girls were more somewhat more likely to survive, survivorship was more strongly associated with heavier weight at admission. Taken together, these results suggest that while mortality bias in growth may exist, it may not be large enough to impact interpretations of past population growth patterns. It should be noted that this is the case only if mortality bias does not vary significantly between different populations and if it does not significantly affect dental development.

Are we using the appropriate reference samples to develop juvenile age estimation methods based on bone size? An exploration of growth differences between average children and those who become victims of homicide.

The population on which forensic juvenile skeletal age estimation methods are applied has not been critically considered. Previous research suggests that child victims of homicide tend to be from socioeconomically disadvantaged contexts, and that these contexts impair linear growth. This study investigates whether juvenile skeletal remains examined by forensic anthropologists are short for age compared to their normal healthy peers. Cadaver lengths were obtained from records of autopsies of 1256 individuals, aged birth to eighteen years at death, conducted between 2000 and 2015 in Australia, New Zealand, and the U.S. Growth status of the forensic population, represented by homicide victims, and general population, represented by accident victims, were compared using height for age Z-scores and independent sample t-tests. Cadaver lengths of the accident victims were compared to growth references using one sample t-tests to evaluate whether accident victims reflect the general population. Homicide victims are shorter for age than accident victims in samples from the U.S., but not in Australia and New Zealand. Accident victims are more representative of the general population in Australia and New Zealand. Different results in Australia and New Zealand as opposed to the U.S. may be linked to socioeconomic inequality. These results suggest that physical anthropologists should critically select reference samples when devising forensic juvenile skeletal age estimation methods. Children examined in forensic investigations may be short for age, and thus methods developed on normal healthy children may yield inaccurate results. A healthy reference population may not necessarily constitute an appropriate growth comparison for the forensic anthropology population.

Age estimation of immature human skeletal remains from the dimensions of the girdle bones in the postnatal period.

OBJECTIVES: This study provides classical calibration regression formulae for age estimation from the dimensions of unfused shoulder and pelvic girdle bones. MATERIALS AND METHODS: Age estimation models were derived from a sample of 160 known age and sex individuals (63 females and 97 males) aged birth to 12 years, selected from Portuguese and English skeletal collections. The sample was divided into two age groups at the age of 2 years, and formulae were obtained for the sexes separately and combined. RESULTS: Measurements of the pelvis provide more precise age estimates than the shoulder. In the younger age group, the height and width of the ilium, and the height of the glenoid yield the most precise age estimates. In the older age group, the length of the clavicle provides the most precise estimates, followed by measurements of the pubis and ischium. DISCUSSION: In the younger individuals (<2 years), age estimates based on measurements of the pelvic girdle seem to be as or more precise than those based on the length of long bones. In older individuals (≥2 years), estimates based on the measurements of the girdles are less precise than those based on the length of long bones. These age estimation formulae may be useful for fragmentary and incomplete material in archaeological and forensic contexts. The formulae are suitable for a variety of archeological populations living under adverse conditions. These conditions are similar to some "developing" countries, and hence the formulae may also be applicable to modern forensic remains from such environments.

A Reappraisal of Developing Permanent Tooth Length as an Estimate of Age in Human Immature Skeletal Remains.

This study expands on existing juvenile age prediction models from tooth length by increasing sample size and using classical calibration. A sample of 178 individuals from two European known sex and age skeletal samples was used to calculate prediction formulae for each tooth for each sex separately and combined. Prediction errors, residuals, and percentage of individuals whose real age fell within the 95% prediction interval were calculated. An ANCOVA was used to test sex and sample differences. Tooth length for age does not differ between the samples except for the canine and second premolar, and no statistically significant sex differences were detected. The least prediction error was found in the incisors and the first molar, and the highest prediction error was found in the third molar. Age prediction formulae provided here can be easily used in a variety of contexts where tooth length is measured from any isolated tooth.