Evolutionary and biomedical implications of sex differences in the primate brain transcriptome.

Humans exhibit sex differences in the prevalence of many neurodevelopmental disorders and neurodegenerative diseases. Here, we generated one of the largest multi-brain-region bulk transcriptional datasets for the rhesus macaque and characterized sex-biased gene expression patterns to investigate the translatability of this species for sex-biased neurological conditions. We identify patterns similar to those in humans, which are associated with overlapping regulatory mechanisms, biological processes, and genes implicated in sex-biased human disorders, including autism. We also show that sex-biased genes exhibit greater genetic variance for expression and more tissue-specific expression patterns, which may facilitate rapid evolution of sex-biased genes. Our findings provide insights into the biological mechanisms underlying sex-biased disease and support the rhesus macaque model for the translational study of these conditions.

Mechanical and morphometric approaches to body mass estimation in rhesus macaques: A test of skeletal variables.

OBJECTIVES: Estimation of body mass from skeletal metrics can reveal important insights into the paleobiology of archeological or fossil remains. The standard approach constructs predictive equations from postcrania, but studies have questioned the reliability of traditional measures. Here, we examine several skeletal features to assess their accuracy in predicting body mass. MATERIALS AND METHODS: Antemortem mass measurements were compared with common skeletal dimensions from the same animals postmortem, using 115 rhesus macaques (male: n = 43; female: n = 72). Individuals were divided into training (n = 58) and test samples (n = 57) to build and assess Ordinary Least Squares or multivariate regressions by residual sum of squares (RSS) and AIC weights. A leave-one-out approach was implemented to formulate the best fit multivariate models, which were compared against a univariate and a previously published catarrhine body-mass estimation model. RESULTS: Femur circumference represented the best univariate model. The best model overall was composed of four variables (femur, tibia and fibula circumference and humerus length). By RSS and AICw, models built from rhesus macaque data (RSS = 26.91, AIC = -20.66) better predicted body mass than did the catarrhine model (RSS = 65.47, AIC = 20.24). CONCLUSION: Body mass in rhesus macaques is best predicted by a 4-variable equation composed of humerus length and hind limb midshaft circumferences. Comparison of models built from the macaque versus the catarrhine data highlight the importance of taxonomic specificity in predicting body mass. This paper provides a valuable dataset of combined somatic and skeletal data in a primate, which can be used to build body mass equations for fragmentary fossil evidence.

Quantifying the relationship between bone and soft tissue measures within the rhesus macaques of Cayo Santiago.

OBJECTIVES: Interpretations of the primate and human fossil record often rely on the estimation of somatic dimensions from bony measures. Both somatic and skeletal variation have been used to assess how primates respond to environmental change. However, it is unclear how well skeletal variation matches and predicts soft tissue. Here, we empirically test the relationship between tissues by comparing somatic and skeletal measures using paired measures of pre- and post-mortem rhesus macaques from Cayo Santiago, Puerto Rico. MATERIALS AND METHODS: Somatic measurements were matched with skeletal dimensions from 105 rhesus macaque individuals to investigate paired signals of variation (i.e., coefficients of variation, sexual dimorphism) and bivariate codependence (reduced major axis regression) in measures of: (1) limb length; (2) joint breadth; and (3) limb circumference. Predictive models for the estimation of soft tissue dimensions from skeletons were built from Ordinary Least Squares regressions. RESULTS: Somatic and skeletal measurements showed statistically equivalent coefficients of variation and sexual dimorphism as well as high epiphyses-present ordinary least square (OLS) correlations in limb lengths (R2 >0.78, 0.82), joint breadths (R2 >0.74, 0.83) and, to a lesser extent, limb circumference (R2 >0.53, 0.68). CONCLUSION: Skeletal measurements are good substitutions for somatic values based on population signals of variation. OLS regressions indicate that skeletal correlates are highly predictive of somatic dimensions. The protocols and regression equations established here provide a basis for reliable reconstruction of somatic dimension from catarrhine fossils and validate our ability to compare or combine results of studies based on population data of either hard or soft tissue proxies.

Multiregion transcriptomic profiling of the primate brain reveals signatures of aging and the social environment.

Aging is accompanied by a host of social and biological changes that correlate with behavior, cognitive health and susceptibility to neurodegenerative disease. To understand trajectories of brain aging in a primate, we generated a multiregion bulk (N = 527 samples) and single-nucleus (N = 24 samples) brain transcriptional dataset encompassing 15 brain regions and both sexes in a unique population of free-ranging, behaviorally phenotyped rhesus macaques. We demonstrate that age-related changes in the level and variance of gene expression occur in genes associated with neural functions and neurological diseases, including Alzheimer's disease. Further, we show that higher social status in females is associated with younger relative transcriptional ages, providing a link between the social environment and aging in the brain. Our findings lend insight into biological mechanisms underlying brain aging in a nonhuman primate model of human behavior, cognition and health.

The ontogeny of sexual dimorphism in free-ranging rhesus macaques.

Objective: Reconstructing the social lives of extinct primates is possible only through an understanding of the interplay between morphology, sexual selection pressures, and social behavior in extant species. Somatic sexual dimorphism is an important variable in primate evolution, in part because of the clear relationship between the strength and mechanisms of sexual selection and the degree of dimorphism. Here, we examine body size dimorphism across ontogeny in male and female rhesus macaques to assess whether it is primarily achieved via bimaturism as predicted by a polygynandrous mating system, faster male growth indicating polygyny, or both. Methods: We measured body mass in a cross-sectional sample of 364 free-ranging rhesus macaques from Cayo Santiago, Puerto Rico to investigate size dimorphism: 1) across the lifespan; and 2) as an outcome of sex-specific growth strategies, including: a) age of maturation; b) growth rate; and c) total growth duration, using regression models fit to sex-specific developmental curves. Results: Significant body size dimorphism was observed by prime reproductive age with males 1.51 times the size of females. Larger male size resulted from a later age of maturation (males: 6.8-7.8 years versus females: 5.5-6.5 years; logistic model) and elevated growth velocity through the pre-prime period (LOESS model). Though males grew to larger sizes overall, females maintained adult size for longer before senescence (quadratic model). Discussion: The ontogeny of size dimorphism in rhesus macaques is achieved by bimaturism and a faster male growth rate. Our results provide new data for understanding the development and complexities of primate dimorphism.

Social connections predict brain structure in a multidimensional free-ranging primate society.

Reproduction and survival in most primate species reflects management of both competitive and cooperative relationships. Here, we investigated the links between neuroanatomy and sociality in free-ranging rhesus macaques. In adults, the number of social partners predicted the volume of the mid-superior temporal sulcus and ventral-dysgranular insula, implicated in social decision-making and empathy, respectively. We found no link between brain structure and other key social variables such as social status or indirect connectedness in adults, nor between maternal social networks or status and dependent infant brain structure. Our findings demonstrate that the size of specific brain structures varies with the number of direct affiliative social connections and suggest that this relationship may arise during development. These results reinforce proposed links between social network size, biological success, and the expansion of specific brain circuits.

Microstructure and energy dispersive diffraction reconstruction of 3D patterns of crystallographic texture in a shark centrum.

Purpose: Tomography using diffracted x-rays produces reconstructions mapping quantities such as crystal lattice parameter(s), crystallite size, and crystallographic texture, information quite different from that obtained with absorption or phase contrast. Diffraction tomography is used to map an entire blue shark centrum with its double cone structure (corpora calcerea) and intermedialia (four wedges). Approach: Energy dispersive diffraction (EDD) and polychromatic synchrotron x-radiation at 6-BM-B, the Advanced Photon Source, were used. Different, properly oriented Bragg planes diffract different x-ray energies; these intensities are measured by one of ten energy-sensitive detectors. A pencil beam defines the irradiated volume, and a collimator before each energy-sensitive detector selects which portion of the irradiated column is sampled at any one time. Translating the specimen along X , Y , and Z axes produces a 3D map. Results: We report 3D maps of the integrated intensity of several bioapatite reflections from the mineralized cartilage centrum of a blue shark. The c axis reflection's integrated intensities and those of a reflection with no c axis component reveal that the cone wall's bioapatite is oriented with its c axes lateral, i.e., perpendicular to the backbone's axis, and that the wedges' bioapatite is oriented with its c axes axial. Absorption microcomputed tomography (laboratory and synchrotron) and x-ray excited x-ray fluorescence maps provide higher resolution views. Conclusion: The bioapatite in the cone walls and wedges is oriented to resist lateral and axial deflections, respectively. Mineralized tissue samples can be mapped in 3D with EDD tomography and subsequently studied by destructive methods.

Shark centra microanatomy and mineral density variation studied with laboratory microComputed Tomography.

Centra of shark vertebrae from three species of Lamniformes (Alopias vulpinus, Carcharodon carcharias and Isurus oxyrinchus) and three species of Carcharhiniformes (Carcharhinus plumbeus, Carcharhinus obscurus and Prionace glauca) were imaged with laboratory microcomputed Tomography (microCT) using volume element (voxel) sizes between 16 and 24 µm. Linear attenuation coefficients were the same in the corpus calcarea (hour-glass-shaped cone) and intermedialia of the lamniforms but were smaller in the intermedialia than in the corpus calcarea of the carcharhiniforms. All centra contained growth bands which were visible as small changes in linear attenuation coefficient. In all six cases, the cross-sections of the cones were close to circular, and the cone angles matched those reported in the literature. Cartilage canals were a prominent structure in the intermedialia of all species, 3D renderings of centra of C. obscurus and I. oxyrinchus diameters showed these canals ran radially outward from the cone walls, and canal diameters were consistent with the limited numerical values in the literature. Somewhat higher calcification levels around the periphery of cartilage canals and of outer surfaces of the intermedialia and corpus calcerea suggest microstructural variation exists at scale below that which can be resolved in the present data sets.

Sex estimation of the subadult ilium prior to acetabular fusion.

Previous studies evaluating sexual dimorphism in subadult pelvic features present variable, and at times conflicting, conclusions. As a result, there is yet to be a consensus on whether the subadult pelvis can be used in sex estimation methods. This study aims to assess the forensic utility of ilium shape and greater sciatic notch morphology in sexing subadult pelves prior to acetabular fusion. A sample of 397 modern U.S. individuals with unfused acetabula (i.e., tri-radiate cartilages) aged birth to 14 years was queried from a larger sample of postmortem computed tomography scans. Elliptical Fourier analyses were performed on ilium and greater sciatic notch outlines and resultant PCs were evaluated for significant effects of sex and age. Greater sciatic notch metrics were also collected. Stepwise linear discriminant function analyses with leave-one-out cross-validation were performed on the PCs and metric variables. Analyses were performed on pooled samples, on age-specific cohort samples, and on samples that iteratively removed the youngest one-year cohort. Cross-validated correct classification rates ranged from 57% to 65% and no patterns were observed to support an appearance and/or consistent expression of sexually diagnostic traits. Based on the results, sex estimation using these features is not recommended in pelvic remains prior to acetabular fusion, although the sample sizes of individuals over 5 years of age were limited in this study. Future studies should focus on the sexually diagnostic ability of pelvic traits in subadult samples post-fusion of the acetabulum.

Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques.

BACKGROUND: An individual's microbiome changes over the course of its lifetime, especially during infancy, and again in old age. Confounding factors such as diet and healthcare make it difficult to disentangle the interactions between age, health, and microbial changes in humans. Animal models present an excellent opportunity to study age- and sex-linked variation in the microbiome, but captivity is known to influence animal microbial abundance and composition, while studies of free-ranging animals are typically limited to studies of the fecal microbiome using samples collected non-invasively. Here, we analyze a large dataset of oral, rectal, and genital swabs collected from 105 free-ranging rhesus macaques (Macaca mulatta, aged 1 month-26 years), comprising one entire social group, from the island of Cayo Santiago, Puerto Rico. We sequenced 16S V4 rRNA amplicons for all samples. RESULTS: Infant gut microbial communities had significantly higher relative abundances of Bifidobacterium and Bacteroides and lower abundances of Ruminococcus, Fibrobacter, and Treponema compared to older age groups, consistent with a diet high in milk rather than solid foods. The genital microbiome varied widely between males and females in beta-diversity, taxonomic composition, and predicted functional profiles. Interestingly, only penile, but not vaginal, microbiomes exhibited distinct age-related changes in microbial beta-diversity, taxonomic composition, and predicted functions. Oral microbiome composition was associated with age, and was most distinctive between infants and other age classes. CONCLUSIONS: Across all three body regions, with notable exceptions in the penile microbiome, while infants were distinctly different from other age groups, microbiomes of adults were relatively invariant, even in advanced age. While vaginal microbiomes were exceptionally stable, penile microbiomes were quite variable, especially at the onset of reproductive age. Relative invariance among adults, including elderly individuals, is contrary to findings in humans and mice. We discuss potential explanations for this observation, including that age-related microbiome variation seen in humans may be related to changes in diet and lifestyle. Video abstract.

The importance of processing procedures and threshold values in CT scan segmentation of skeletal elements: An example using the immature os coxa.

As the accessibility and utility of virtual databases of skeletal collections continues to grow, the impact that scan processing procedures has on the accuracy of data obtained from virtual databases remains relatively unknown. This study quantifies the intra- and inter-observer error generated from varying computed tomography (CT) scan processing protocols, including re-segmentation, incrementally varying thresholding value, and data collectors' selection of the threshold value on a set of virtual subadult pelves. Four observers segmented the subadult ossa coxarum from postmortem CT scans of the fully-fleshed bodies of eleven individuals of varying ages. Segmentation protocol was set, with the exception of each observer selecting their own thresholding value for each scan. The resulting smoothed pelvic surfaces were then compared using deviation analyses. Root mean square error (RMSE), average distance deviation, and maximum deviation distances demonstrated that thresholding values of ∼50 HU (Hounsfield units) are easily tolerated, the surfaces generated are robust to error, and threshold value selection does not systematically vary with user experience. The importance of consistent methodology during segmentation protocol is highlighted here, especially with regards to consistency in both selected thresholding value as well as smoothing protocol, as these variables can affect subsequent measurements of the resultant surfaces.

Reconsidering osteoarthritis as a skeletal indicator of age at death.

OBJECTIVES: Osteoarthritis (OA) generally increases with age, but it is a complex, multifactorial disease. This study investigated whether obesity, physical activity, and antemortem trauma preclude the use of OA for skeletal age estimation. MATERIALS AND METHODS: The temporomandibular joint (TMJ) and all appendicular joints were scored for skeletal indicators of OA in 408 modern European-Americans (Bass Collection, TN). Binomial generalized linear models (GLMs) assessed the contributions of self-reported demographic data to OA, including: age; body mass index (BMI); and metabolic values for physical activities. Repeated resampling tested whether observed mean OA scores for joints with trauma consistently exceeded mean scores for unaffected joints. Single-variable GLM probit models were generated for OA presence/absence data in relevant joints. RESULTS: Age was the only statistically significant predictor of OA in most multivariable GLMs. Occupation and age were both significant predictors of male hand OA; BMI was the only significant predictor of female ankle OA. Trauma significantly affected OA in most joints. Age cut-offs calculated from the single-variable probit models (representing ages of transition to "OA present") ranged from 29.7 to 77.3 years (90%) and 32.7 to 96.6 years (95%), but were problematic for the male TMJ. DISCUSSION: Ankle OA should not be used to age females; TMJ OA should not be used to age males. For other joints, using OA to inform age estimates appears valid (in absence of antemortem trauma). While skeletal evidence of OA is not a primary age indicator, its presence can refine age ranges and provide essential age data in fragmentary cases.

Early Signs of Fracture Repair in the Human Rib Cage: Implications for Forensic Casework.

The decomposed body of a woman discovered beneath a collapsed structure was examined at the C.A. Pound Human Identification Laboratory. Despite a mix of rib fractures with and without indications of healing, it is most likely that all fractures occurred as a result of a single, compressive event. Signs of intramembranous, and possibly direct, fracture healing at the incomplete fractures without signs of endochondral ossification at the complete fractures suggest the individual died very shortly-but not immediately-after injury. Given the case circumstances, the findings inform immediate cause of death. This case study highlights that differential healing as a result of a single event is possible. Further, it illustrates the importance of careful examination of micro-discontinuities/cracks that can occur in association with major fractures. Fracture healing and dating data are discussed, as is the possible need for critical evaluation of the antemortem/perimortem boundary.

A Preliminary Analysis of the Age of Full Expression of Sexually Dimorphic Cranial Traits.

Although high accuracy rates have been achieved for adult skeletal sex estimation, it is unclear at what age sexually dimorphic traits of the skull become fully developed and useful in subadults. Four linear distances that capture sexual dimorphism-the nuchal crest, mastoid process, glabella, and mental eminence-were measured in a longitudinal sample of lateral cranial radiographs from 10 males and 10 females in the Denver Growth Study (total n = 190). The age full trait expression was attained was compared to that of dental maturity (i.e., third molar eruption). The mental eminence reached full expression significantly earlier than dental maturity (p < 0.001), although a high degree of variability was observed. Ages of expression of the other traits did not differ significantly from dental maturity. These results suggest that in forensic cases, where misclassification can have substantial impacts, cranial traits cannot yet be used reliably for sex estimation prior to third molar eruption.

Estimating Sex Using Metric Analysis of the Scapula by Postmortem Computed Tomography.

Postmortem computed tomography (CT) has been extensively used in the last decade for identification purposes and in various anthropologic studies. Postmortem CT measurements of scapulae, analyzed using logistic discriminant function developed in this study, showed 94.5% accuracy in estimating sex. Data analyzed using the Dabbs and Moore-Jansen (2010) discriminant function and the discriminant function generated in this study provided nearly identical results with disagreement in only one case. Height and weight were not statically significant in sex prediction. The results of this study show that data obtained from volume rendered postmortem CT images can be considered reliable and treated as a practical option to standard anthropological methods, especially in mass fatalities as a rapid triage tool for sex determination.

Skeletal Indicators of Shark Feeding on Human Remains: Evidence from Florida Forensic Anthropology Cases.

This research examines a series of six Florida forensic anthropology cases that exhibit taphonomic evidence of marine deposition and shark-feeding activities. In each case, we analyzed patterns of trauma/damage on the skeletal remains (e.g., sharp-force bone gouges and punctures) and possible mechanisms by which they were inflicted during shark predation/scavenging. In some cases, shark teeth were embedded in the remains; in the absence of this evidence, we measured interdental distance from defects in the bone to estimate shark body length, as well as to draw inferences about the potential species responsible. We discuss similarities and differences among the cases and make comparisons to literature documenting diagnostic shark-inflicted damage to human remains from nearby regions. We find that the majority of cases potentially involve bull or tiger sharks scavenging the remains of previously deceased, adult male individuals. This scavenging results in a distinctive taphonomic signature including incised gouges in cortical bone.

Line of Sight in Hominoids.

OBJECTIVES: It remains unclear how the realignments of the face and basicranium that characterize humans were acquired, both phylogenetically and ontogenetically. The developmentally constrained nature of the skull has been previously demonstrated in other primates using Donald H. Enlow's mammalian craniofacial architectural relationships. Here, we compare crania of our closest relatives to gain greater understanding of how and why the relationship of the face and cranial base is developmentally constrained in order to inform instances of abnormal growth and clinical intervention. STUDY DESIGN: A method for evaluating these fundamental architectural relationships using 3D landmark data was developed, thereby taking overall size and the geometric relationships among points into account. A sample of cone-beam computed tomography scans derived from humans and extant apes were analyzed (n=10 and n=6, respectively), as well as fossil hominid crania (n=7). Landmarks for 23 craniofacial architectural points were identified and recorded. RESULTS AND CONCLUSIONS: Principal components analyses reveal that despite the similarities in craniofacial architecture between humans, extant apes and fossil hominids, appreciable trends in variation between the extant species suggest that the repositioning of the foramen magnum was only one of a constellation of traits that realigned the basicranium and face during the transition to bipedalism.

Variation in the human bicondylar angle.

OBJECTIVES: Investigations of the human femoral bicondylar angle have largely focused on interspecific differences and intrapopulation variation. This analysis assesses the range of variation in the bicondylar angle in humans across four populations, examining the effects of population, sex and age. MATERIALS AND METHODS: The bicondylar angle was assessed in four sex- and age-balanced adult skeletal samples-modern Terry Whites and Blacks and archaeological South Dakota Arikara and Native Alaskans. The overall range of variation was assessed, and variation specific to population, sex, and age analyzed through ANOVAs and post hoc Tukey's honestly significant difference tests. RESULTS: A one-way ANOVA highlights a significant effect of population on bicondylar angle; however, the only significant difference occurs between the Terry White and South Dakota Arikara samples. Sex displays a significant effect for the total pooled sample; yet, within population, the effect of sex is significant only among South Dakota Arikara. Age also has a significant effect on bicondylar angle in the total sample; however, the interaction between age and population is not significant. CONCLUSION: The results highlight the degree of variation in the bicondylar angle that exists intraspecifically. Differing degrees of variation due to sex suggest that sexual dimorphism is not universal in the human bicondylar angle. Furthermore, the broad impact of age on this feature is discussed, including the potential for plasticity through adulthood. By recognizing and explicitly examining morphological features that vary in human populations, we can appreciate the origins of variation and its implications for locomotor function, human diversity and evolutionary relationships. Am J Phys Anthropol 160:334-340, 2016. © 2016 Wiley Periodicals, Inc.