Interpreting error in the estimation of skeletal growth profiles from past populations: An example demonstrating skeletal growth in historic African American communities.

OBJECTIVES: The study of growth in the past is a critical component of bioarcheological analyses. However, our understanding of growth in the past is subject to a number of methodological challenges. This study aims to model the skeletal growth of past populations by considering the challenges associated with the data collection process and the challenges associated with the age estimation procedures. MATERIALS AND METHODS: We use skeletal remains from two historic African American cemeteries in the American South to model femoral diaphyseal length-for-age. We estimate the age of each individual using dental development techniques and present growth curves as both a product of the maximum likelihood (MLE) age estimate and the estimated posterior age distribution. Growth was compared against a reference sample from the University of Colorado Child Research Council Study. RESULTS: The results of our analyses showed that femoral diaphyseal length in two historic African American communities is small-for-estimated age as compared to a modern reference sample. However, the magnitude and characterization of this difference is variable when taking into account the broader posterior age distribution. DISCUSSION: Both samples may be small-for-age due to physiological stress associated with racism, inequality, and the compounding effects of early urbanization. However, the interpretation of growth in the past is muddled when considering the relationship between the study sample and the reference sample, when accounting for uncertainty in the age estimation procedure, and the error-inducing steps taken during the data collection process. Future interpretation of skeletal growth in the past must include a full account of the possible sources of error in order to present an accurate representation of growth.

Tracing production instability in a clonally derived CHO cell line using single-cell transcriptomics.

A variety of mechanisms including transcriptional silencing, gene copy loss, and increased susceptibility to cellular stress have been associated with a sudden or gradual loss of monoclonal antibody (mAb) production in Chinese hamster ovary (CHO) cell lines. In this study, we utilized single-cell RNA-seq (scRNA-seq) to study a clonally derived CHO cell line that underwent production instability leading to a dramatic reduction of the levels of mAb produced. From the scRNA-seq data, we identified subclusters associated with variations in the mAb transgenes and observed that heavy chain gene expression was significantly lower than that of the light chain across the population. Using trajectory inference, the evolution of the cell line was reconstructed and was found to correlate with a reduction in heavy and light chain gene expression. Genes encoding for proteins involved in the response to oxidative stress and apoptosis were found to increase in expression as cells progressed along the trajectory. Future studies of CHO cell lines using this technology have the potential to dramatically enhance our understanding of the characteristics underpinning efficient manufacturing performance as well as product quality.

The Evolution of 'Ecological Release' into the 21st Century.

Ecological release, originally conceived as niche expansion following a reduction in interspecific competition, may prompt invasion success, morphological evolution, speciation, and other ecological and evolutionary outcomes. However, the concept has not been recently reviewed. Here, we trace the study of 'ecological release' from its inception through the present day and find that current definitions are broad and highly varied. Viewing this development as a potential impediment to clear communication and hypothesis testing, we suggest a consensus definition for ecological release: niche expansions and shifts when a constraining interspecific interaction is reduced or removed. In rationalizing this definition, we highlight the various ways ecological release can unfold and address its potential evolutionary consequences.

Character displacement in the midst of background evolution in island populations of Anolis lizards: A spatiotemporal perspective.

Negative interactions between species can generate divergent selection that causes character displacement. However, other processes cause similar divergence. We use spatial and temporal replication across island populations of Anolis lizards to assess the importance of negative interactions in driving trait shifts. Previous work showed that the establishment of Anolis sagrei on islands drove resident Anolis carolinensis to perch higher and evolve larger toepads. To further test the interaction's causality and predictability, we resurveyed a subset of islands nine years later. Anolis sagrei had established on one island between surveys. We found that A. carolinensis on this island now perch higher and have larger toepads. However, toepad morphology change on this island was not distinct from shifts on six other islands whose Anolis community composition had not changed. Thus, the presence of A. sagrei only partly explains A. carolinensis trait variation across space and time. We also found that A. carolinensis on islands with previously established A. sagrei now perch higher than a decade ago, and that current A. carolinensis perch height is correlated with A. sagrei density. Our results suggest that character displacement likely interacts with other evolutionary processes in this system, and that temporal data are key to detecting such interactions.

Asymmetric interference competition and niche partitioning between native and invasive Anolis lizards.

Species can compete both directly via aggressive encounters (interference) and indirectly through their shared use of a limited resource (exploitation). Depending on the circumstances interference, exploitation, and their interplay can either lead to competitive exclusion or drive niche partitioning to maintain species coexistence. Thus, understanding species coexistence in nature requires accurately identifying the mechanisms that contribute to competition among the species in question. In the southern United States, the native lizard Anolis carolinensis becomes more arboreal in the presence of the invasive Anolis sagrei, resulting in highly consistent vertical habitat partitioning where the species co-occur. These species have been thought to largely ignore each other and engage only in exploitative competition for shared arthropod prey. To test for the presence and consequences of direct interference, we conducted behavioral trials in the field, introducing a heterospecific male intruder to individuals of both species. We find that interference competition is asymmetric in favor of A. sagrei, which are more likely to display and less likely to retreat than A. carolinensis. Concordant with their arboreal tendencies, male A. carolinensis also trend toward retreating upward more often than expected by chance. These asymmetries are prevalent despite the almost complete absence of physical attacks, suggesting that interspecific signaling and avoidance behavior by A. carolinensis resolve most potential conflicts before they escalate to combat. Our results highlight the potential for direct interference more subtle than frequent outright combat to structure communities, and Anolis assemblages in particular.

Dental microwear texture analysis of Homo sapiens sapiens: Foragers, farmers, and pastoralists.

OBJECTIVES: The current study seeks to determine if a sample of foragers, farmers, and pastoralists are distinguishable based on their dental microwear texture signatures. MATERIALS AND METHODS: The study included a sample of 719 individuals from 51 archeological sites (450 farmers, 192 foragers, 77 pastoralists). All were over age 12 and sexes were pooled. Using a Sensofar® white-light confocal profiler we collected dental microwear texture analysis (DMTA) data from a single first or second molar from each individual. We leveled and cleaned data clouds following standard procedures and analyzed the data with Sfrax® and Toothfrax® software. The DMTA variables were complexity and anisotropy. Statistics included ANOVA with partial eta squared and Hedges's g. We also performed a follow-up K-means cluster analysis. RESULTS: We found significant differences between foragers and farmers and pastoralists for complexity and anisotropy, with foragers having greater complexity than either the farmers or the pastoralists. The farmers and pastoralists had greater anisotropy than the foragers. The Old World foragers had significantly higher anisotropy values than New World foragers. Old and New World farmers did not differ. Among the Old World farmers, those dating from the Neolithic through the Late Bronze Age had higher complexity values than those from the Iron Age through the medieval period. The cluster analysis discerned foragers and farmers but also indicated similarity between hard food foragers and hard food farmers. DISCUSSION: Our findings reaffirm that DMTA is capable of distinguishing human diets. We found that foragers and farmers, in particular, differ in their microwear signatures across the globe. There are some exceptions, but nothing that would be unexpected given the range of human diets and food preparation techniques. This study indicates that in general DMTA is an efficacious means of paleodietary reconstruction in humans.

Identifying migrant remains in South Texas: policy and practice.

In 2012, Texas surpassed Arizona in migrant deaths. The majority of deaths occurred in the Rio Grande Valley, specifically in Brooks County, Texas. Brooks County is one of the poorest in the state and was overwhelmed with deaths, without appropriate resources to follow the state laws pertaining to the investigation of unidentified human remains. Until 2013, most remains that were not immediately identified were buried without collecting DNA samples and the location of burials was not recorded. Our paper outlines the difficulties searching for these burials, the struggles of the families of the missing, and the collaborative approaches to facilitating identifications in South Texas. Community outreach combined with geophysical surveys guide which cemeteries are in need of exhumations. Once cemeteries are surveyed, archaeological methods are employed to exhume remains and document burials. Remains are taken to the Forensic Anthropology Center at Texas State for processing, analysis, and identification efforts. Undergraduate and graduate students clean remains and wash clothing and personal effects. After skeletal analysis, all information regarding the remains, including photographs of personal effects, are uploaded to the National Missing and Unidentified Persons System (NamUs) and a DNA sample is submitted to the University of North Texas for inclusion in the Combined DNA Index System (CODIS) DNA database. However, CODIS lacks DNA family reference samples from many families of the missing due to families living outside the US or because they do not feel comfortable providing a DNA sample in the presence of law enforcement. Therefore, it is necessary to work with non-governmental organizations who specialize in collecting missing persons reports and DNA samples from the families of the missing. Working collaboratively with multiple agencies, identification of migrant remains is possible.

New Approaches to Juvenile Age Estimation in Forensics: Application of Transition Analysis via the Shackelford et al. Method to a Diverse Modern Subadult Sample.

Dental development is one of the most widely utilized and accurate methods available for estimating age in subadult skeletal remains. The timing of tooth growth and development is regulated by genetics and less affected by external factors, allowing reliable estimates of chronological age. Traditional methodology focuses on comparing tooth developmental scores to corresponding age charts. Using the Moorrees, Fanning, and Hunt (MFH) developmental scores, Shackelford and colleagues embed the dental development method in a statistical framework based on transition analysis. They generated numerical parameters underlining each "stage" and age-at-death distribution and applied them to fossil hominins and Neanderthals with limited application to modern humans. We use this same method on a subadult test sample (n = 201), representing modern individuals that may become part of the forensic record. We assess the probability coverage of the Shackelford et al. method derived from MFH standards as it applies to all available dentition. Results indicate promise: the age range at 90% and 95% confidence levels includes the chronological age of almost every individual tested. The maximum likelihood age estimates underestimate age by 0.5-2.5 years for individuals 0-15 years of age and by >2.5 years for individuals 16-18 years of age, as previously shown. In an attempt to refine the method, we adjusted the numerical parameters underlying the stages for developing teeth based on a combined modern reference sample (n = 1,964) and tested these revised parameters using the same test sample. The estimated ages from the modified method differ from the original Shackelford et al. methodology by underestimating age to a lesser degree. The modified method does include mean age-at-attainment values for earlier stages of several teeth, allowing for the calculation of narrower confidence intervals. While this study highlights areas of future research in refining dental developmental aging by transition analysis, it also demonstrates that the Shackelford et al. method is applicable and accurate when aging modern subadults in forensic work.

Refining Stable Oxygen and Hydrogen Isoscapes for the Identification of Human Remains in Mississippi.

Isoscape refinement is an essential component for accurately predicting region-of-origin in forensic investigations involving isotope analysis of unidentified human remains. Stable oxygen (δ18 O) and hydrogen (δ2 H) isotopes were measured from 57 tap water samples collected across Mississippi to model refined isoscapes for the state. A tap water conversion equation, δ18 Otw =1.64 δ18 Op-31.35, was developed for the southeastern USA to test the prediction accuracy of the δ18 Otw isoscape using individuals with known residential histories. A local Mississippi resident (USAFA-134) was assigned with 90% probability to the correct region-of-origin reported by the participant. Assignments for Georgia residents (USAFA-118 and USAFA-205) had variable results, predicting USAFA-118 from Mississippi and USAFA-205 as a nonlocal resident. Stable isotope values often overlap geographically and a multi-isotope approach should be used when narrowing region(s)-of-origin(s). This study demonstrates the utility of refining isoscapes and the importance of tissue calibration in prediction assignments of human remains.

Computerized reconstruction of fragmentary skeletal remains.

This research presents a new software, "Fragmento", for accurate analyses of fragmentary human skeletal remains and facilitation of three-dimensional (3D) fragmentary matching and full bone reconstruction. The framework utilizes the power of statistical bone atlases to create 3D templates for bone matching and to interpolate missing anatomy for full bone reconstruction. Developed tool has enhanced features allowing the user to visualize, review and scale all scanned skeletal remains within a 3D statistical template, merging accepted registered elements to provide a fully reconstructed bone. A three stage validation was performed on Fragmento: Stages I and II used simulated fragmentary data which was compared to full bones with an error less than 3mm; Stage III compared output from geographic information system (GIS) software with comparable results. This validation process demonstrates the robustness and utility of Fragmento as tool for 3D fragmentary bone matching and full bone reconstruction.

Feedbacks underlie the resilience of salt marshes and rapid reversal of consumer-driven die-off.

Understanding ecosystem resilience to human impacts is critical for conservation and restoration. The large-scale die-off of New England salt marshes was triggered by overfishing and resulted from decades of runaway crab grazing. In 2009, however, cordgrass began to recover, decreasing die-off -40% by 2010. We used surveys and experiments to test whether plant-substrate feedbacks underlie marsh resilience. Initially, grazer-generated die-off swept through the cordgrass, creating exposed, stressful peat banks that inhibited plant growth. This desertification cycle broke when banks eroded and peat transitioned into mud with fewer herbivores, less grazing, and lower physical stress. Cordgrass reestablished in these areas through a feedback where it engineered a recovery zone by further ameliorating physical stresses and facilitating additional revegetation. Our results reveal that feedbacks can play a critical role in rapid, reversible ecosystem shifts associated with human impacts, and that the interplay of facilitative and consumer interactions should be incorporated into resilience theory.

A trophic cascade triggers collapse of a salt-marsh ecosystem with intensive recreational fishing.

Overexploitation of predators has been linked to the collapse of a growing number of shallow-water marine ecosystems. However, salt-marsh ecosystems are often viewed and managed as systems controlled by physical processes, despite recent evidence for herbivore-driven die-off of marsh vegetation. Here we use field observations, experiments, and historical records at 14 sites to examine whether the recently reported die-off of northwestern Atlantic salt marshes is associated with the cascading effects of predator dynamics and intensive recreational fishing activity. We found that the localized depletion of top predators at sites accessible to recreational anglers has triggered the proliferation of herbivorous crabs, which in turn results in runaway consumption of marsh vegetation. This suggests that overfishing may be a general mechanism underlying the consumer-driven die-off of salt marshes spreading throughout the western Atlantic. Our findings support the emerging realization that consumers play a dominant role in regulating marine plant communities and can lead to ecosystem collapse when their impacts are amplified by human activities, including recreational fishing.

Evaluation of stature estimation from the database for forensic anthropology.

Trotter and Gleser's (1-3) stature equations, conventionally used to estimate stature, are not appropriate to use in the modern forensic context. In this study, stature is assessed with a modern (birth years after 1944) American sample (N = 242) derived from the National Institute of Justice Database for Forensic Anthropology in the United States and the Forensic Anthropology Databank. New stature formulae have been calculated using forensic stature (FSTAT) and a combined dataset of forensic, cadaver, and measured statures referred to as Any Stature (ASTAT). The new FSTAT-based equations had an improved accuracy in Blacks with little improvement over Ousley's (4) equations for Whites. ASTAT-based equations performed equal to those of FSTAT equations and may be more appropriate, because they reflect both the variation in reported statures and in cadaver statures. It is essential to use not only equations based on forensic statures, but also equations based on modern samples.

Estimation of living stature from selected anthropometric (soft tissue) measurements: applications for forensic anthropology.

Estimation of living stature has obvious utility in the identification process. Typically, anthropologists estimate stature from the measurement of long bone length. This type of analysis is traditionally conducted on skeletonized or badly decomposed remains, so collection of the necessary bone measurements is relatively simple. As the role of anthropologists expands into medical examiner offices and mass fatality incidents, the analysis of fleshed bodies and body parts is a more common scenario. For stature estimation in these types of cases (e.g., analysis of body portions recovered from an aircraft crash site or from intentional dismemberment), the presence of soft tissue on the human remains would usually necessitate dissection to expose skeletal elements to derive metric data for stature estimation. In order to circumvent this step, this paper provides various formulae that allow for standard anthropometric (i.e., soft tissue) measurements to be used in place of skeletal measurements. Data were compiled from several anthropometric studies (National Health and Nutrition Examination Survey [NHANES] and U.S. Army Anthropometric Survey [ANSUR]) and numerous regression models are presented. Results are compared between skeletal measurements and the anthropometric measurements from each study. It was found that the ANSUR models are similar to the skeletal models, while the NHANES models exhibit weaker correlation coefficients and higher standard errors. Overall, this study finds that stature estimates derived from anthropometric data provide good results and remove the necessity for dissection when working with fleshed body portions.

Estimation and evidence in forensic anthropology: age-at-death.

A great deal has previously been written about the use of skeletal morphological changes in estimating ages-at-death. This article looks in particular at the pubic symphysis, as it was historically one of the first regions to be described in the literature on age estimation. Despite the lengthy history, the value of the pubic symphysis in estimating ages and in providing evidence for putative identifications remains unclear. This lack of clarity primarily stems from the fact that rather ad hoc statistical methods have been applied in previous studies. This article presents a statistical analysis of a large data set (n = 1766) of pubic symphyseal scores from multiple contexts, including anatomical collections, war dead, and victims of genocide. The emphasis is in finding statistical methods that will have the correct "coverage.""Coverage" means that if a method has a stated coverage of 50%, then approximately 50% of the individuals in a particular pubic symphyseal stage should have ages that are between the stated age limits, and that approximately 25% should be below the bottom age limit and 25% above the top age limit. In a number of applications it is shown that if an appropriate prior age-at-death distribution is used, then "transition analysis" will provide accurate "coverages," while percentile methods, range methods, and means (+/-standard deviations) will not. Even in cases where there are significant differences in the mean ages-to-transition between populations, the effects on the stated age limits for particular "coverages" are minimal. As a consequence, more emphasis needs to be placed on collecting data on age changes in large samples, rather than focusing on the possibility of inter-population variation in rates of aging.