An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers

Reverse-engineering the Venus figurines: An eco-life-course hypothesis for the aetiology of obesity in the Palaeolithic

Evolutionary perspectives on obesity have been dominated by genetic frameworks, but plastic responses are also central to its aetiology. While often considered a relatively modern phenomenon, obesity was recorded during the Palaeolithic through small statuettes of the female form (Venus figurines). Even if the phenotype was rare, these statuettes indicate that some women achieved large body sizes during the last glacial maximum, a period of nutritional stress. To explore this paradox, we develop an eco-life-course conceptual framework that integrates the effects of dietary transitions with intergenerational biological mechanisms. We assume that Palaeolithic populations exposed to glaciations had high lean mass and high dietary protein requirements. We draw on the protein leverage hypothesis, which posits that low-protein diets drive overconsumption of energy to satisfy protein needs. We review evidence for an increasing contribution of plant foods to diets as the last glacial maximum occurred, assumed to reduce dietary protein content. We consider physiological mechanisms through which maternal overweight impacts the obesity susceptibility of the offspring during pregnancy. Integrating this evidence, we suggest that the last glacial maximum decreased dietary protein content and drove protein leverage, increasing body weight in a process that amplified across generations. Through the interaction of these mechanisms with environmental change, obesity could have developed among women with susceptible genotypes, reflecting broader trade-offs between linear growth and adiposity and shifts in the population distribution of weight. Our approach may stimulate bioarchaeologists and paleoanthropologists to examine paleo-obesity in greater detail and to draw upon the tenets of human biology to interpret evidence.

Contemporary small-scale subsistence populations offer unique insights into human musculoskeletal health and aging

Human foragers avoid noncommunicable diseases that are leading causes of mortality, partly because physically active lifestyles promote healthy aging. High activity levels also promote tissue damage accumulation from wear-and-tear, increase risk of injury and disability which compromise productivity, and reduce energetic investments in somatic maintenance given constrained energy expenditure. Constraints intensify when nutrient supply is limited and surplus energy is directed toward pathogen defense and reproduction, as occurred throughout hominin evolution. This paper reviews evidence linking exposomes to musculoskeletal health in subsistence populations, focusing on effects of physical activity, pathogens, diet, and reproduction. Chronic musculoskeletal conditions are common for humans and possibly prehistoric hominins but rarer in quadrupedal apes. We propose that transition to bipedalism ~6 to 8 million years ago constituted an early "mismatch scenario," increasing hominin susceptibility to musculoskeletal conditions vis-à-vis quadrupedal apes due to changes in mechanical loading environments. Mismatched musculoskeletal traits were not targets of selection because of trade-offs favoring bipedal extractive foraging and higher fertility.

Pervasive findings of directional selection realize the promise of ancient DNA to elucidate human adaptation

We present a method for detecting evidence of natural selection in ancient DNA time-series data that leverages an opportunity not utilized in previous scans: testing for a consistent trend in allele frequency change over time. By applying this to 8433 West Eurasians who lived over the past 14000 years and 6510 contemporary people, we find an order of magnitude more genome-wide significant signals than previous studies: 347 independent loci with >99% probability of selection. Previous work showed that classic hard sweeps driving advantageous mutations to fixation have been rare over the broad span of human evolution, but in the last ten millennia, many hundreds of alleles have been affected by strong directional selection. Discoveries include an increase from ~0% to ~20% in 4000 years for the major risk factor for celiac disease at HLA-DQB1; a rise from ~0% to ~8% in 6000 years of blood type B; and fluctuating selection at the TYK2 tuberculosis risk allele rising from ~2% to ~9% from ~5500 to ~3000 years ago before dropping to ~3%. We identify instances of coordinated selection on alleles affecting the same trait, with the polygenic score today predictive of body fat percentage decreasing by around a standard deviation over ten millennia, consistent with the "Thrifty Gene" hypothesis that a genetic predisposition to store energy during food scarcity became disadvantageous after farming. We also identify selection for combinations of alleles that are today associated with lighter skin color, lower risk for schizophrenia and bipolar disease, slower health decline, and increased measures related to cognitive performance (scores on intelligence tests, household income, and years of schooling). These traits are measured in modern industrialized societies, so what phenotypes were adaptive in the past is unclear. We estimate selection coefficients at 9.9 million variants, enabling study of how Darwinian forces couple to allelic effects and shape the genetic architecture of complex traits.

Natural selection acting on complex traits hampers the predictive accuracy of polygenic scores in ancient samples

The prediction of phenotypes from ancient humans has gained interest due to its potential to investigate the evolution of complex traits. These predictions are commonly performed using polygenic scores computed with DNA information from ancient humans along with genome-wide association studies (GWAS) data from present-day humans. However, numerous evolutionary processes could impact the prediction of phenotypes from ancient humans based on polygenic scores. In this work we investigate how natural selection impacts phenotypic predictions on ancient individuals using polygenic scores. We use simulations of an additive trait to analyze how natural selection impacts phenotypic predictions with polygenic scores. We simulate a trait evolving under neutrality, stabilizing selection and directional selection. We find that stabilizing and directional selection have contrasting effects on ancient phenotypic predictions. Stabilizing selection accelerates the loss of large-effect alleles contributing to trait variation. Conversely, directional selection accelerates the loss of small and large-effect alleles that drive individuals farther away from the optimal phenotypic value. These effects result in specific shared genetic variation patterns between ancient and modern populations which hamper the accuracy of polygenic scores to predict phenotypes. Furthermore, we conducted simulations that include realistic strengths of stabilizing selection and heritability estimates to show how natural selection could impact the predictive accuracy of ancient polygenic scores for two widely studied traits: height and body mass index. We emphasize the importance of considering how natural selection can decrease the reliability of ancient polygenic scores to perform phenotypic predictions on an ancient population.

Fast and Accurate Estimation of Selection Coefficients and Allele Histories from Ancient and Modern DNA

We here present CLUES2, a full-likelihood method to infer natural selection from sequence data that is an extension of the method CLUES. We make several substantial improvements to the CLUES method that greatly increases both its applicability and its speed. We add the ability to use ancestral recombination graphs on ancient data as emissions to the underlying hidden Markov model, which enables CLUES2 to use both temporal and linkage information to make estimates of selection coefficients. We also fully implement the ability to estimate distinct selection coefficients in different epochs, which allows for the analysis of changes in selective pressures through time, as well as selection with dominance. In addition, we greatly increase the computational efficiency of CLUES2 over CLUES using several approximations to the forward-backward algorithms and develop a new way to reconstruct historic allele frequencies by integrating over the uncertainty in the estimation of the selection coefficients. We illustrate the accuracy of CLUES2 through extensive simulations and validate the importance sampling framework for integrating over the uncertainty in the inference of gene trees. We also show that CLUES2 is well-calibrated by showing that under the null hypothesis, the distribution of log-likelihood ratios follows a χ2 distribution with the appropriate degrees of freedom. We run CLUES2 on a set of recently published ancient human data from Western Eurasia and test for evidence of changing selection coefficients through time. We find significant evidence of changing selective pressures in several genes correlated with the introduction of agriculture to Europe and the ensuing dietary and demographic shifts of that time. In particular, our analysis supports previous hypotheses of strong selection on lactase persistence during periods of ancient famines and attenuated selection in more modern periods.

Sex-based tuberculosis mortality in Newfoundland, 1900-1949: Implications for populations in transition

OBJECTIVE

During the second epidemiological transition, tuberculosis (TB) is one disease that declined substantially enough to reduce all-cause mortality. Sex-based differences in TB mortality may reveal an important dimension of population health transitions between the urbanizing and rural regions of Newfoundland.

MATERIALS AND METHODS

For the island of Newfoundland, yearly age-standardized sex-based TB mortality rates were calculated using individual death records from 1900 to 1949 (n = 30 393). Multiple linear regression models predict the relative rates (RR) of sex-based mortality and the absolute difference between males and females while controlling for time and region (the urbanizing Avalon Peninsula or rural Newfoundland). Multiple linear regression models also predict the median age at death from TB while controlling for time, region, and sex to assess if TB was shifting to an older adult disease compared to those typically afflicted in ages 20-44.

RESULTS

Female TB mortality was relatively and absolutely higher than males; additionally, RR and absolute differences between male and female mortality were significantly lower in rural Newfoundland than the Avalon Peninsula. Median age at death for males was significantly higher than females, and differences in median age at death increased over time.

DISCUSSION

The historically high prevalence of TB throughout Newfoundland, including domestic, social, and public health responsibilities of women, likely contributed to increased exposure and transmission, leading to higher observed mortality. Sex-based TB outcomes should be considered in the discussion of the progression of the epidemiological transition as dynamic inequalities that do not necessarily fit contemporary generalizations of sex-based TB epidemiology.

Socio-cultural practices may have affected sex differences in stature in Early Neolithic Europe

The rules and structure of human culture impact health as much as genetics or environment. To study these relationships, we combine ancient DNA (n = 230), skeletal metrics (n = 391), palaeopathology (n = 606) and dietary stable isotopes (n = 873) to analyse stature variation in Early Neolithic Europeans from North Central, South Central, Balkan and Mediterranean regions. In North Central Europe, stable isotopes and linear enamel hypoplasias indicate high environmental stress across sexes, but female stature is low, despite polygenic scores identical to males, and suggests that cultural factors preferentially supported male recovery from stress. In Mediterranean populations, sexual dimorphism is reduced, indicating male vulnerability to stress and no strong cultural preference for males. Our analysis indicates that biological effects of sex-specific inequities can be linked to cultural influences at least as early as 7,000 yr ago, and culture, more than environment or genetics, drove height disparities in Early Neolithic Europe.

Infantile scurvy as a consequence of agricultural intensification in the 1st millennium BCE Etruria Campana

The 1st millennium BCE in Italy was a time of agricultural intensification of staple cereal production which shaped sociocultural, political, and economic spheres of pre-Roman groups. The lifeways and foodways of the Etruscans, the greatest civilization in western Europe before Roman hegemony, are traditionally inferred from secondary written sources, funerary archaeology, archaeobotany, and zooarchaeology. However, no direct data extrapolated from the study of human skeletal remains are available to evaluate the extent to which agricultural intensification and decreased dietary diversity impacted health and the expression of skeletal indicators of metabolic disease. Macroscopic and radiological analyses were conducted on an archaeological skeletal sample of non-adults (n = 29) recovered from Pontecagnano (southern Italy) dating to the Orientalizing period (730-580 BCE). This allowed us to identify five cases of scorbutic non-adults and to assign diagnostic values to skeletal lesions of scurvy that have not been previously described in the literature. The onset of scurvy in the examined sample is related to the increased reliance of Etruscans on crops lacking vitamin C in this period of agricultural intensification. The skeletal expression of scurvy varied among the non-adults, with differences in location and disease severity; these were interpreted considering the age-at-death of the individuals coupled with feeding behaviors and interindividual variability.

Tuberculosis in prehistory in Eastern Central Europe (Hungary) - Chronological and geographical distribution

Tuberculosis (TB) has long been a major scourge of humankind. Paleopathological and paleomicrobiological studies have revealed the past presence of the disease on a large spatial and temporal scale. The antiquity of the disease has extensively been studied in the Carpathian Basin, given its dynamic population and cultural changes since prehistory. These studies, however, have mainly focused on the populations living during the Common Era. The aim of this paper is to present the published and the recently discovered cases of prehistoric TB, from the Neolithic (6000-4500/4400 BCE) to the Bronze Age (2600/2500-800 BCE) Central Carpathian Basin (Hungary). We summarize 18 published cases and present new cases dating to the Neolithic period and introduce 3 newly discovered Bronze Age cases of TB. Despite extensive research, TB has not yet been identified from the Copper and Iron Ages in the Carpathian Basin. Considering the state of TB research, and supplemented by our prehistoric dataset, the spatio-temporal pattern of the disease can be further elucidated, thus advancing future molecular and paleopathological studies. Our dataset offers comprehensive spatial and temporal information on the spread of the disease in the Carpathian Basin, along with a detailed biological profile of the demonstrated cases and extensive paleopathological descriptions of the observed lesions, complemented by photographic evidence. This invaluable resource paves the way for enhanced understanding and progress in the field.

Ancient DNA suggests anaemia and low bone mineral density as the cause for porotic hyperostosis in ancient individuals

Porotic hyperostosis (PH) is a disease that had high prevalence during the Neolithic. Several hypotheses have been suggested to explain the origin of the disease, such as an iron deficiency diet, low B12 intake, malaria caused by Plasmodium spp., low haemoglobin levels or low vitamin D levels. None of these hypotheses have been tested genetically. Here, I calculated different genetic scores to test each hypothesis. Additionally, I calculated a genetic score of bone mineral density as it is a phenotype that seems to be selected in ancient Europeans. I apply these genetic scores on 80 ancient samples, 33 with diagnosed PH. The results seem to suggest anaemia and low bone mineral density as the main cause for this disease. Additionally, Neolithic individuals show the lowest genetic risk score for bone mineral density of all other periods tested here, which may explain the highest prevalence of the porotic hyperostosis during this age.

The diachronic trend of female and male stature in Milan over 2000 years

Stature is a biological trait directly determined by the interaction of genetic and environmental components. As such, it is often evaluated as an indicator for the reconstruction of skeletal biological profiles, past health, and social dynamics of human populations. Based on the analysis of 549 skeletons from the CAL (Collezione Antropologica LABANOF), a study of the diachronic trend of male and female adult stature in Milan (Italy) is being proposed here, covering a time span of about 2000 years, ranging from the Roman era to present-days. The skeletons, from necropolises dedicated to the less wealthy classes of Milanese society, were assigned to one of following five historical periods: Roman Era (first-fifth centuries AD), Early Middle Ages (sixth-tenth centuries AD), Late Middle Ages (eleventh-fifteenth centuries AD), Modern Era (sixteenth-eighteenth centuries AD) and Contemporary Era (nineteenth-twentieth centuries AD), and their stature was estimated according to the regression formulae of Trotter (1970). The collected data were then subjected to statistical analyses with ANOVA using R software. Although stature values showed an ample standard deviation in all periods, statistical analyses showed that stature did not significantly vary across historical periods in Milan for both sexes. This is one of the rare studies showing no diachronic changes in the trend of stature in Europe.

Skeletal Markers of Physiological Stress as Indicators of Structural Violence: A Comparative Study between the Deceased Migrants of the Mediterranean Sea and the CAL Milano Cemetery Skeletal Collection

Structural violence is an indirect form of violence that can lead to physiological consequences. Interestingly, these physiological disruptions may affect the skeletons and can therefore provide relevant information on violence and way of life in the analysis of skeletal remains. The aim of the present study was to test the hypothesis that migrants who died in the Mediterranean Sea would present physiological cranial stress markers such as cribra orbitalia (CO), porotic hyperostosis (PH), and linear enamel hypoplasia (LEH) more frequently and more severely than Italians of the 20th century. With this intent, a total of 164 crania were examined: 139 from deceased migrants recovered from a shipwreck in the Mediterranean Sea in 2015, aged between 16 and 35 years old, and 25 of the same age from the CAL Milano Cemetery Skeletal Collection. Both presence and severity of CO, PH, and LEH were evaluated. The data obtained were analyzed using Wilcoxon signed-rank and independence Chi-squared tests to compare the results between the two samples and to test whether there was an association between the sample of migrants and the occurrence of lesions. As a result, CO and PH appeared more frequently and more severely in the migrant sample. In addition, migrants were significantly associated with CO, PH, and LEH (p-values < 0.05). Although this does not imply in any way that CO, PH, and LEH are specific to migration, they should be regarded as indicators of structural violence.

Ancient pathogens provide a window into health and well-being

This perspective draws on the record of ancient pathogen genomes and microbiomes illuminating patterns of infectious disease over the course of the Holocene in order to address the following question. How did major changes in living circumstances involving the transition to and intensification of farming alter pathogens and their distributions? Answers to this question via ancient DNA research provide a rapidly expanding picture of pathogen evolution and in concert with archaeological and historical data, give a temporal and behavioral context for heath in the past that is relevant for challenges facing the world today, including the rise of novel pathogens.

Long-term trends in human body size track regional variation in subsistence transitions and growth acceleration linked to dairying

Evidence for a reduction in stature between Mesolithic foragers and Neolithic farmers has been interpreted as reflective of declines in health, however, our current understanding of this trend fails to account for the complexity of cultural and dietary transitions or the possible causes of phenotypic change. The agricultural transition was extended in primary centers of domestication and abrupt in regions characterized by demic diffusion. In regions such as Northern Europe where foreign domesticates were difficult to establish, there is strong evidence for natural selection for lactase persistence in relation to dairying. We employ broad-scale analyses of diachronic variation in stature and body mass in the Levant, Europe, the Nile Valley, South Asia, and China, to test three hypotheses about the timing of subsistence shifts and human body size, that: 1) the adoption of agriculture led to a decrease in stature, 2) there were different trajectories in regions of in situ domestication or cultural diffusion of agriculture; and 3) increases in stature and body mass are observed in regions with evidence for selection for lactase persistence. Our results demonstrate that 1) decreases in stature preceded the origins of agriculture in some regions; 2) the Levant and China, regions of in situ domestication of species and an extended period of mixed foraging and agricultural subsistence, had stable stature and body mass over time; and 3) stature and body mass increases in Central and Northern Europe coincide with the timing of selective sweeps for lactase persistence, providing support for the "Lactase Growth Hypothesis."

Biocultural perspectives of infectious diseases and demographic evolution: Tuberculosis and its comorbidities through history

Anthropologists recognize the importance of conceptualizing health in the context of the mutually evolving nature of biology and culture through the biocultural approach, but biocultural anthropological perspectives of infectious diseases and their impacts on humans (and vice versa) through time are relatively underrepresented. Tuberculosis (TB) has been a constant companion of humans for thousands of years and has heavily influenced population health in almost every phase of cultural and demographic evolution. TB in human populations has been dramatically influenced by behavior, demographic and epidemiological shifts, and other comorbidities through history. This paper critically discusses TB and some of its major comorbidities through history within a biocultural framework to show how transitions in human demography and culture affected the disease-scape of TB. In doing so, I address the potential synthesis of biocultural and epidemiological transition theory to better comprehend the mutual evolution of infectious diseases and humans.