Oral microbiomes from hunter‐gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet

Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter‐gatherers and traditional farmers living in close proximity in the Philippines. Deep shotgun sequencing of salivary DNA generated high‐coverage microbiomes along with human genomes. Comparing these microbiomes with publicly available data from individuals living on a Western diet revealed that abundance ratios of core species were significantly correlated with subsistence strategy, with hunter‐gatherers and Westerners occupying either end of a gradient of Neisseria against Haemophilus, and traditional farmers falling in between. Species found preferentially in hunter‐gatherers included microbes often considered as oral pathogens, despite their hosts' apparent good oral health. Discriminant analysis of gene functions revealed vitamin B5 autotrophy and urease‐mediated pH regulation as candidate adaptations of the microbiome to the hunter‐gatherer and Western diets, respectively. These results suggest that major transitions in diet selected for different communities of commensals and likely played a role in the emergence of modern oral pathogens.     

Biogeochemical inferences of mobility of early Holocene fisher‐foragers from the Southern Sahara Desert

North Africa is increasingly seen as an important context for understanding modern human evolution and reconstructing biocultural adaptations. The Sahara, in particular, witnessed a fluorescence of hunter‐gatherer settlement at the onset of the Holocene after an extended occupational hiatus. Subsequent subsistence changes through the Holocene are contrary to those documented in other areas where mobile foraging gave way to settled agricultural village life. In North Africa, extractive fishing and hunting was supplanted by cattle and caprine pastoralism under deteriorating climatic conditions. Therefore, the initial stage of food production in North Africa witnessed a likely increase in mobility. However, there are few studies of paleomobility in Early Holocene hunter‐gatherer Saharan populations and the degree of mobility is generally assumed. Here, we present radiogenic strontium isotope ratios from Early Holocene fisher‐forager peoples from the site of Gobero, central Niger, southern Sahara Desert. Data indicate a relatively homogeneous radiogenic strontium isotope signature for this hunter‐gather population with limited variability exhibited throughout the life course or among different individuals. Although the overall signature was local, some variation in the radiogenic strontium isotope data likely reflects transhumance into the nearby Aïr Massif. Data from Gobero were significantly less variable than in other worldwide hunter‐gatherer populations, including those thought to be fairly sedentary. Strontium data from Gobero were also significantly different from contemporaneous sites in southwestern Libya. These patterns are discussed with respect to archaeological models of community organization and technological evolution. Am J Phys Anthropol 2011. © 2011 Wiley‐Liss, Inc.     

Socioecological aspects of human reproduction in Sub-Saharan Africa

The purpose of this study was to compare fertility outcome of two populations of northern Namibia, following different ways of subsistence. The total number of offspring, but also the number of dead and surviving offspring was compared between 236 !Kung San (91 females, 145 males) hunter gatherers and 248 Kavango (87 females, 161 males) horticultural pastoralists and a small number of Kavango people living in the urban center of Rundu. While no typical differences in fertility outcome between the study populations could be observed in males, marked differences were found for the female sample. As to be expected traditional Kavango women had given birth to a higher number of children and these children had a higher chance to survive in comparison to those of !Kung San women. On the other hand Kavango females living in urban centers reported a significantly lower number of offspring. It can be concluded that even in recent populations fertility differences according to subsistence patterns are observable.     

Dopamine receptor D4 allele distribution in Amerindians: A reflection of past behavior differences?

The DRD4 variable number of tandem repeats (VNTR) allele distribution of 172 Guarani (Kaiowá and Ñandeva subgroups) and Kaingang Brazilian Amerindians is reported. These results are integrated with those previously obtained for this ethnic group. Allele frequencies for the three populations are within the interval observed for 15 other Native American populations and show intermediate values between those observed in Amazonia and Patagonia. Significant differences in allele distribution between recent past hunter–gatherer and agriculturalist populations are observed, with an increase of the 7R allele among hunter–gatherers (P < 0.001). Analysis of molecular variance (AMOVA) and pairwise F_ST data suggest three distinct sectors for the genetic landscape of Native South America: Andes, Center/Southeast region, and Amazonia. Common traits among hunter–gatherers such as novelty‐seeking temperament, hyperactivity, and impulsivity could have been important and advantageous in new environments during America's prehistoric colonization. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

The ecological and evolutionary energetics of hunter‐gatherer residential mobility

Residential mobility is a key aspect of hunter‐gatherer foraging economies and therefore is an issue of central importance in hunter‐gatherer studies. 1 - 7 Hunter‐gatherers vary widely in annual rates of residential mobility. Understanding the sources of this variation has long been of interest to anthropologists and archeologists. The vast majority of hunter‐gatherers who are dependent on terrestrial plants and animals move camp multiple times a year because local foraging patches become depleted and food, material, and social resources are heterogeneously distributed through time and space. In some environments, particularly along coasts, where resources are abundant and predictable, hunter‐gatherers often become effectively sedentary. But even in these special cases, a central question is how these societies have maintained viable foraging economies while reducing residential mobility to near zero.     

Demographic variance in heterogeneous populations: matrix models and sensitivity analysis

The demographic consequences of stochasticity in processes such as survival and reproduction are modulated by the heterogeneity within the population. Therefore, to study effects of stochasticity on population growth and extinction risk, it is critical to use structured population models in which the most important sources of heterogeneity (e.g. age, size, developmental stage) are incorporated as i‐state variables. Demographic stochasticity in heterogeneous populations has often been studied using one of two approaches: multitype branching processes and diffusion approximations. Here, we link these approaches, through the demographic stochasticity in age‐ or stage‐structured matrix population models. We derive the demographic variance, σ²_d, which measures the per capita contribution to the variance in population growth increment, and we show how it can be decomposed into contributions from transition probabilities and fertility across ages or stages. Furthermore, using matrix calculus we derive the sensitivity of σ²_d to age‐ or stage‐specific mortality and fertility. We apply the methods to an extensive set of data from age‐classified human populations (long‐term time‐series for Sweden, Japan and the Netherlands; two hunter–gatherer populations, and the high‐fertility Hutterites), and to a size‐classified population of the herbaceous plant Calathea ovandensis. For the human populations our analysis reveals substantial temporal changes in the demographic variance as well as its main components across age. These new methods provide a powerful approach for calculating the demographic variance for any structured model, and for analyzing its main components and sensitivities. This will make possible new analyses of demographic variance across different kinds of heterogeneity in different life cycles, which will in turn improve our understanding of mechanisms underpinning extinction risk and other important biological outcomes.     

The origins of food production in north China: A different kind of agricultural revolution

By roughly 8,000 calendar years before the present (calBP), hunter‐gatherers across a broad swath of north China had begun small‐scale farming of broomcorn millet (Panicum miliaceum) and foxtail millet (Setaria italica). 1 - 6 According to traditional wisdom, this early millet farming evolved from the intensive hunter‐gatherer adaptation represented by the late Pleistocene microblade tradition of northern China, 2 , 7 termed here the North China Microlithic. The archeological record of this hunter‐gatherer connection is poorly documented, however, and as a result the early agricultural revolution in north China is not as well understood as those that occurred in other parts of the world. The Laoguantai site of Dadiwan, in the western Loess Plateau, Gansu Province, PRC, furnishes the first complete record of this transition, which unfolded quite differently from other, better known, agricultural revolutions.     

Amazonian horticulturalists live in larger,more related groups than hunter–gatherers

The relatedness of human groups has important ramifications for kin (group) selection to favor more collective action and invites the potential for more exploitation by political leaders. Endogamous marriages among kin create intensive kinship systems with high group relatedness, while exogamous marriages among nonrelatives create extensive kinship with low group relatedness. Here, a sample of 58 societies (7,565 adults living in 353 residential groups) shows that average group relatedness is higher in lowland horticulturalists than in hunter–gatherers. Higher relatedness in horticulturalists is remarkable given that village sizes are larger, harboring over twice the average number of adults than in hunter–gatherer camps. The relatedness differential between subsistence regimes increases for larger group sizes. Large and dense networks of kin may have favored an increased propensity for some forms of in-group cooperation and political inequality that emerged relatively recently in human history, after the advent of farming.     

Pyrodiversity and the anthropocene: the role of fire in the broad spectrum revolution

The Anthropocene colloquially refers to a global regime of human‐caused environmental modification of earth systems associated with profound changes in patterns of human mobility, as well as settlement and resource use compared with prior eras. Some have argued that the processes generating the Anthropocene are mainly associated with population growth and technological innovation, and thus began only in the late Holocene under conditions of dense sedentism and industrial agriculture.¹ However, it now seems clear that the roots of the Anthropocene lie in complex processes of intensification that significantly predate transitions to agriculture.^2,3 What intensification is remains less clear. For some it is increasing economic productivity that increases carrying capacity, the drivers of which may be too diverse and too local to generalize.^4,5 For others using Boserup's ideas about agrarian intensification, increasing density in hunter‐gatherer populations can produce declines in subsistence efficiency that increase incentives for investing labor to boost yield per unit area, which then elevates Malthusian limits on carrying capacity.^6–8 As Morgan⁹ demonstrates in a comprehensive review, the legacy of such Boserupian intensification is alive, well, and controversial in hunter‐gatherer archeology. This is a result of its potential for illuminating processes involved in transformations of forager socio‐political and economic systems, including those dominated by harvesting more immediate‐return resources and high residential mobility as well as those characterized by more delayed‐return material economies with reduced residential mobility, a broader spectrum of resources, degrees of storage, and greater social stratification. Here we detail hypotheses about the processes involved in such transitions and explore the way that anthropogenic disturbance of ecosystems, especially the use of landscape fire, could be fundamentally entangled with many broad‐spectrum revolutions associated with intensified foraging systems.     

Archaeoentomological study of a pre-Columbian funerary bundle (mortuary cave of Candelaria,Coahuila, Mexico)

The archaeoentomological study of insect remains recovered from a pre-Columbian funerary bundle (10th–11th centuries ad) is presented and illustrated. Among this material, 12 species belonging to 10 families and four distinct orders have been identified. From the biological data of the different taxa, some hypotheses about the funerary practices of the hunter–gatherer semi nomads of Northern Mexico are proposed.     

Age‐ratio bias among hunter‐based surveys of Eurasian Wigeon Anas penelope based on wing vs. field samples

We compared age and sex ratios among Eurasian Wigeon Anas penelope derived from Danish field observations and hunter‐based shot samples throughout an entire winter. Sex ratios did not differ significantly between the two samples. Overall, first‐year males were more than three times more likely to be represented than adult males in the hunter sample compared with field samples and were 7–20 times overrepresented in the hunting sample at the beginning of the season. These results confirm the need to account for such bias and its temporal variation when using the results of hunting surveys to model population parameters. Hunter‐shot age ratios may provide a long‐term measure of reproductive success of dabbling duck flyway populations given an understanding of such bias.     

Sex differences in humeral bilateral asymmetry in two hunter‐gatherer populations: California Amerinds and British Columbian Amerinds

This study uses two prehistoric Amerindian populations of hunter‐gatherer subsistence patterns to determine whether levels of sexual dimorphism in humeral bilateral cross‐sectional asymmetry are related to sex‐specific differences in activities among these populations. Results confirmed that males of the California Amerind population who engaged in the more unimanual activities of spear hunting and warfare were more asymmetrical than were their female counterparts who engaged in the more bimanual activities of grinding acorns. California Amerind males were also more asymmetrical than British Columbian Amerind males who rowed (using both arms) extensively. Sex differences within British Columbian Amerinds were not statistically significant, nor were female differences between populations. In general, levels of humeral asymmetry appear to be more dependent on sex and population‐specific behaviors rather than broad subsistence patterns. Am J Phys Anthropol 2009. © 2009 Wiley‐Liss, Inc.     

Brief communication: The Uto-Aztecan premolar in early hunter-gatherers from South-Central North America

The Uto‐Aztecan premolar is a discrete dental trait found in low frequency (<2%) among world populations. The highest frequencies of the trait have been found among the indigenous populations of North America and, to a lesser extent, South America. Because of the trait's relatively higher frequency in the Western Hemisphere, the antiquity and distribution of the feather is important for reconstructing the biocultural interactions of prehistoric populations. While early research concluded that the Uto‐Aztecan premolar originated in the American Southwest around 4,000 years Before Present (BP), more recent studies have discovered the trait across the Americas and in parts of Europe and Asia. For this study, over 300 dentitions representing foragers and farmers in south‐central North America were examined. The trait was found in relatively high frequency (over 11%) in Archaic hunter‐gatherer populations from Central Texas, with high frequencies also found in the adjacent western Gulf Coastal Plain. The presence of this trait in Early Archaic populations suggests that the trait was present by 8,000 BP and persisted at a high frequency into the Late Archaic period. Am J Phys Anthropol 149:318–322, 2012. © 2012 Wiley Periodicals, Inc.     

A multilevel analytical framework for studying cultural evolution in prehistoric hunter–gatherer societies

Over the past decade, a major debate has taken place on the underpinnings of cultural changes in human societies. A growing array of evidence in behavioural and evolutionary biology has revealed that social connectivity among populations and within them affects, and is affected by, culture. Yet the interplay between prehistoric hunter–gatherer social structure and cultural transmission has typically been overlooked. Interestingly, the archaeological record contains large data sets, allowing us to track cultural changes over thousands of years: they thus offer a unique opportunity to shed light on long‐term cultural transmission processes. In this review, we demonstrate how well‐developed methods for social structure analysis can increase our understanding of the selective pressures underlying cumulative culture. We propose a multilevel analytical framework that considers finer aspects of the complex social structure in which regional groups of prehistoric hunter–gatherers were embedded. We put forward predictions of cultural transmission based on local‐ and global‐level network metrics of small‐scale societies and their potential effects on cumulative culture. By bridging the gaps between network science, palaeodemography and cultural evolution, we draw attention to the use of the archaeological record to depict patterns of social interactions and transmission variability. We argue that this new framework will contribute to improving our understanding of social interaction patterns, as well as the contexts in which cultural changes occur. Ultimately, this may provide insights into the evolution of human behaviour.     

Patterns of natural mortality in stream‐living brown trout (Salmo trutta)

1. We tested the hypothesis that lifetime mortality patterns and their corresponding rates and causal factors differ among populations of stream‐living salmonids. To this end, we examined the lifetime mortality patterns of several successive cohorts of two stream‐living brown trout (Salmo trutta) populations in Spain and Denmark. 2. In the southern population, we observed a consistent two‐phase pattern, in which mortality was negligible during the first half of the lifetime and severe during the rest of the lifetime. In contrast, the northern population demonstrated a three‐phase pattern with an earlier phase varying from negligible to severe, followed by a second stage of weak mortality, and lastly by a third life stage of severe mortality. 3. Despite substantial differences in the mortality patterns between the two populations, the combined effect of recruitment (as a proxy of the density‐dependent processes occurring during the lifetime) and mean body mass (as a proxy of growth experienced by individuals in a given cohort) explained c. 89% of the total lifetime mortality rates across cohorts and populations. 4. A comparison with other published data on populations of stream‐living brown trout within its native range highlighted lifetime mortality patterns of one, two, three and four phases, but also suggested that common patterns may occur in populations that experience similar individual growth and population density.     

The cranial morphology of the Botocudo Indians,Brazil

The Botocudo Indians were hunter‐gatherer groups that occupied the East‐Central regions of Brazil decimated during the colonial period in the country. During the 19th century, craniometric studies suggested that the Botocudo resembled more the Paleoamerican population of Lagoa Santa than typical Native Americans groups. These results suggest that the Botocudo Indians might represent a population that retained the biological characteristics of early groups of the continent, remaining largely isolated from groups that gave origin to the modern Native South American variation. Moreover, recently, some of the Botocudo remains have been shown to have mitochondrial and autosomal DNA lineages currently found in Polynesian populations. Here, we explore the morphological affinities of Botocudo skulls within a worldwide context. Distinct multivariate analyses based on 32 craniometric variables show that 1) the two individuals with Polynesian DNA sequences have morphological characteristics that fall within the Polynesian and Botocudo variation, making their assignation as Native American specimens problematic, and 2) there are high morphological affinities between Botocudo, Early Americans, and the Polynesian series of Easter Island, which support the early observations that the Botocudo can be seen as retaining the Paleoamerican morphology, particularly when the neurocranium is considered. Although these results do not elucidate the origin of the Polynesian DNA lineages among the Botocudo, they support the hypothesis that the Botocudo represent a case of late survival of ancient Paleoamerican populations, retaining the morphological characteristics of ancestral Late Pleistocene populations from Asia. Am J Phys Anthropol 157:202–216, 2015. © 2015 Wiley Periodicals, Inc.     

Interactive effects of senescence and natural disturbance on the annual survival probabilities of snail kites

Individuals in wild populations face risks associated with both intrinsic (i.e. aging) and external (i.e. environmental) sources of mortality. Condition‐dependent mortality occurs when there is an interaction between such factors; however, few studies have clearly demonstrated condition‐dependent mortality and some have even argued that condition‐dependent mortality does not occur in wild avian populations. Using large sample sizes (2084 individuals, 3746 re‐sights) of individual‐based longitudinal data collected over a 33 year period (1976–2008) on multiple cohorts, we used a capture–mark–recapture framework to model age‐dependent survival in the snail kite Rostrhamus sociabilis plumbeus population in Florida. Adding to the growing amount of evidence for actuarial senescence in wild populations, we found evidence of senescent declines in survival probabilities in adult kites. We also tested the hypothesis that older kites experienced condition‐dependent mortality during a range‐wide drought event (2000–2002). The results provide convincing evidence that the annual survival probability of senescent kites was disproportionately affected by the drought relative to the survival probability of prime‐aged adults. To our knowledge, this is the first evidence of condition‐dependent mortality to be demonstrated in a wild avian population, a finding which challenges recent conclusions drawn in the literature. Our study suggests that senescence and condition‐dependent mortality can affect the demography of wild avian populations. Accounting for these sources of variation may be particularly important to appropriately compute estimates of population growth rate, and probabilities of quasi‐extinctions.     

Classification of phytoplankton cells as live or dead using the vital stains fluorescein diacetate and 5‐chloromethylfluorescein diacetate

Regulations for ballast water treatment specify limits on the concentrations of living cells in discharge water. The vital stains fluorescein diacetate (FDA) and 5‐chloromethylfluorescein diacetate (CMFDA) in combination have been recommended for use in verification of ballast water treatment technology. We tested the effectiveness of FDA and CMFDA, singly and in combination, in discriminating between living and heat‐killed populations of 24 species of phytoplankton from seven divisions, verifying with quantitative growth assays that uniformly live and dead populations were compared. The diagnostic signal, per‐cell fluorescence intensity, was measured by flow cytometry and alternate discriminatory thresholds were defined statistically from the frequency distributions of the dead or living cells. Species were clustered by staining patterns: for four species, the staining of live versus dead cells was distinct, and live‐dead classification was essentially error free. But overlap between the frequency distributions of living and heat‐killed cells in the other taxa led to unavoidable errors, well in excess of 20% in many. In 4 very weakly staining taxa, the mean fluorescence intensity in the heat‐killed cells was higher than that of the living cells, which is inconsistent with the assumptions of the method. Applying the criteria of ≤5% false negative plus ≤5% false positive errors, and no significant loss of cells due to staining, FDA and FDA+CMFDA gave acceptably accurate results for only 8–10 of 24 species (i.e., 33%–42%). CMFDA was the least effective stain and its addition to FDA did not improve the performance of FDA alone.     

Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin

It is a matter of fact that the human gut microbiome also includes a non‐bacterial fraction represented by eukaryotic cells and viruses. To further explore the gut microbiome variation in human populations, here we characterized the human DNA viral community from publicly available gut metagenome data sets from human populations with different geographical origin and lifestyle. In particular, such data sets encompass microbiome information from two western urban societies (USA and Italy), as well as two traditional hunter‐gatherer communities (the Hadza from Tanzania and Matses from Peru) and one pre‐agricultural tribe (Tunapuco from Peru). Our results allowed for the first taxonomic reconstruction of the complex viral metacommunities within the human gut. The core virome structure included herpesviruses, papillomaviruses, polyomaviruses, adenoviruses and anelloviruses. Using Random Forests and a co‐occurrence analysis approach, we identified the viruses that distinguished populations according to their geographical origin and/or lifestyle. This paves the way for new research aimed at investigating the biological role of the gut virome in human physiology, and the importance of our viral counterpart in the microbiome‐host co‐evolutionary process.