Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague.

The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague's formative years in terms of its early evolution and ecology.

Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe.

Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH) beginning in the Eneolithic (ca. 3300-2700 BCE) profoundly transformed the genes and cultures of Europe and central Asia. Compared with Europe, however, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Late Bronze Age burials putatively associated with early pastoralism in northern Mongolia (ca. 1380-975 BCE). Genome-wide analysis reveals that they are largely descended from a population represented by Early Bronze Age hunter-gatherers in the Baikal region, with only a limited contribution (∼7%) of WSH ancestry. At the same time, however, mass spectrometry analysis of dental calculus provides direct protein evidence of bovine, sheep, and goat milk consumption in seven of nine individuals. No individuals showed molecular evidence of lactase persistence, and only one individual exhibited evidence of >10% WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. Unlike the spread of Neolithic farming in Europe and the expansion of Bronze Age pastoralism on the Western steppe, our results indicate that ruminant dairy pastoralism was adopted on the Eastern steppe by local hunter-gatherers through a process of cultural transmission and minimal genetic exchange with outside groups.

Hunter-gatherer dental pathology: Do historic accounts of Aboriginal Australians correspond to the archeological record of dental disease?

OBJECTIVES: Studies of hunter-gatherer oral pathology, particularly in Australia, often focus upon dental wear and caries or assume that historic studies of Aboriginal people reflect the precontact past. Consequently the range of population variation has been underestimated. In this paper dental pathology from human remains from Roonka are compared with a model of dental pathology derived from historic studies. The aim is to identify aspects of dental pathology indicative of regional or intra-population diversity. METHODS: Adult dentitions (n = 115) dating from the mid to late Holocene were recorded for the following conditions: dental wear, caries, periapical voids, calculus, periodontal disease and antemortem tooth loss. Statistical analysis was used to identify patterns of dental pathology and to identify causal relationships between conditions. RESULTS: Dental wear is marked while dental caries rates are extremely low. Other indications of dental pathology are uncommon (<7% of teeth affected). Temporal heterogeneity is apparent: there are 3 young adults with caries who died in the postcontact period. There is also a small group of middle age to old adults with disproportionate abscessing and pulp exposure who may represent temporal variation or heterogeneity in individual frailty. CONCLUSIONS: The results confirm dental wear as the major cause of dental pathology in this group and that, at a general level, historic accounts do correspond with this archeological sample. However, intra-sample heterogeneity is apparent while 2 dental conditions, calculus and periodontal disease, along with the pattern of sex differences deviate from expectation, demonstrating that to identify regional variation attention needs to be paid to the dentoalveolar complex as a whole.

Dental wear and age grading at Roonka, South Australia.

OBJECTIVES: In many hunter-gatherer populations, the teeth are used as a third hand or a tool. Much attention has been paid to wear and its relationship to gendered division of labor, but age is also a significant organizing factor in many societies. In this article, I analyze whether the pattern of wear at Roonka, Australia, reflects the age-graded acquisition of tasks. MATERIALS AND METHODS: The remains analyzed come from Roonka and date from c6000 BP to 150 BP. In total 126 adults and juveniles were analyzed. Wear gradients were calculated for each tooth relative to wear on the first molar. Data were compared using nonparametric statistics and cluster analysis to assess the degree of patterning within the sample. RESULTS: Dental wear proceeded rapidly. There is no evidence of sex differences in the pattern of wear. Age differences do occur. While disproportionate anterior wear occurs among juveniles and young adults, by middle adulthood the pattern is less variable and involves the premolars. Old adults have a much flatter pattern of wear. DISCUSSION: The pattern of wear is consistent with ethnographic observations, which suggest a degree of latitude in the activities of juveniles and young adults. By middle age variability between individuals declines reflecting shared tasks and more intensive use of the teeth. The pattern of wear amongst old adults, however, is much flatter presumably due to changes in occlusion. While dental wear is informative about the organization of labor there is a need to take into account both patterns of activity and occlusion.

Estimating striae of Retzius periodicity nondestructively using partial counts of perikymata.

Accurate age estimations for enamel formation and the timing of enamel hypoplasia have traditionally only been available through histological analyses of dental thin sections, which is a difficult and destructive process. However, an association between striae of Retzius periodicity, crucial for accurate aging, and the total number of striae in imbricational enamel has been reported in the literature. This means periodicity can be estimated nondestructively but is reliant on all perikymata being visible along the crown surface. Therefore, crowns with worn or damaged surfaces may not be able to be assessed, potentially limiting sample sizes. We tested this relationship in a modern New Zealand sample and investigated whether reliable associations might be identified using only partial perikymata counts from the cervical half of the crown. Using mandibular canines (n = 11), the distribution of perikymata per decile was recorded using high definition replica surfaces. Thin sections of the same crowns were used to assess periodicity histologically along with striae of Retzius distributions. A strong correlation between total striae numbers and periodicity was also identified in our sample. Furthermore, we report strong correlations that allow periodicity to be estimated from perikymata counts using only 10% of crown height when certain deciles are used. Based on these findings, we propose a simple matrix that can be developed for nondestructively estimating periodicity based on the range of perikymata counts in the sixth to ninth deciles.

Patterns in ritual tooth avulsion at Roonka.

Tooth avulsion is the intentional removal of one or more teeth for ritual or aesthetic reasons, or to denote group affiliation. Typically the maxillary incisors are the teeth most often selected for removal. Previous authors have discussed the presence of tooth avulsions in several individuals recovered from Roonka, but those papers did not examine any patterns in those removals that might be present. Analysis of the tooth avulsions at Roonka reveals a change in the practice over time, with the older burials from phase II typically showing removal of both maxillary central incisors with a left side bias when only one tooth is removed, and the more recent phase III burials showing only one incisor avulsed and a right side bias for removal. Frequencies in the practice also changed over time, with avulsions being much more common in the older phase II burials. Historical evidence suggests that any particular regional or social group would have its own particular pattern of tooth avulsion, so these changes in tooth avulsions at Roonka suggest that the site was either used by multiple groups of people for burials, or that there was significant cultural change during the occupation of the site.

Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria.

The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modeled as a mixture of sources from ancient Anatolia, Levant, and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5 to 6 kya onward, around the time agriculture appeared in the region. Our study characterizes the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of studies of ancient DNA in the region.

Hunter-gatherer variability: Dental wear in South Australia.

Often it is assumed that hunter-gatherer dentitions are dominated by heavy attrition. Recent analyses, however, have shown unexpected variability in the pattern of wear between groups. It had been previously noted that wear differed between neighboring groups on the Murray River, Australia. This analysis extends that geographic scope as well as focusing on wear across the dentition, including the premolars. The samples came from coastal and riverine regions of southern Australia. The analysis used records from the Yorke Peninsula, Adelaide Plains (Gillman site), and Euston regions. These were compared with previously published work from the Adelaide Plains and four locations on the Murray River. The results confirm the overall severity of wear but reveal systematic differences between the samples in terms of the pattern of wear. Heavy wear on the incisors and canines is observed among males from the Euston, Kaurna, Middle A, Murray Mouth, and Yorke Peninsula samples but with marked intra-individual variability. Extensive premolar wear is noted among females from Kaurna and Middle B samples as well as among males and females from Euston. It is argued that these patterns relate to gendered non-masticatory use of teeth and reliance upon bulrush (Typha spp.) and related species for both food and fiber among some groups. We argue that analyzing the degree of variability within samples and across all teeth provides a more nuanced understanding of dental wear among hunter-gatherers.

Migrants and tuberculosis: analysing epidemiological data with ethnography.

OBJECTIVE: Media portrayals of tuberculosis (TB) in New Zealand are of immigrants who enter the country with active disease and pose a threat to inhabitants, which fosters a popular perception that border control is the best and only response to disease control. This paper reviews both New Zealand and international data on TB rates, causes and transmission among migrant populations to elucidate the precise nature of the link between immigration and TB rates. METHODS: Recent information from scholarly journals on immigration and TB was reviewed. Surveillance data from New Zealand and comparable information from other low-incidence countries were reviewed. CONCLUSIONS AND IMPLICATIONS: The importation of active TB is only a minor part of the total TB burden. While effective border control is essential, equally, if not more important, are the circumstances that promote the reactivation of latent TB infection in migrant communities, including migrants' experiences in transit and after arrival, structural conditions, and personal characteristics. For sound prevention strategies, attention needs to be paid to the existence of transnational communities and the conditions for migrants, rather than placing a singular focus on place of birth.

Social group dynamics predict stress variability among children in a New Zealand classroom.

Previous research proposes stress as a mechanism for linking social environments and biological bodies. In particular, non-human primate studies investigate relationships between cortisol as a measure of stress response and social hierarchies. Because human social structures often include hierarchies of dominance and social status, humans may exhibit similar patterns. Studies of non-human primates, however, have not reached consistent conclusions with respect to relationships between social position and levels of cortisol. While human studies report associations between cortisol and various aspects of social environments, studies that consider social status as a predictor of stress response also report mixed results. Others have argued that perceptions of social status may have different implications for stress response depending upon social context. We propose here that characteristics of children's social networks may be a better predictor of central tendencies and variability of stress response than their perceptions of social status. This is evaluated among 24 children from 9.4 to 11.3 years of age in one upper middle-class New Zealand primary school classroom, assessed through observation within the classroom, self-reports during semi-structured interviews and 221 serial saliva samples provided daily over 10 consecutive school days. A synthetic assessment of the children's networks and peer-relationships was developed prior to saliva-cortisol analysis. We found that greater stability of peer-relationships within groups significantly predicts lower within-group variation in mid-morning cortisol over the two-week period, but not overall within-group differences in mean cortisol.

Partnerships for health: decimating tuberculosis in the Cook Islands, 1920-1975.

How did the Cook Islands manage to achieve a significant reduction in tuberculosis from a high rate in the early 20th century to low rates by 1975? With the mid-century invention of effective drug therapy there was a widespread belief around the Western world that TB could be eradicated. The Cook Islands was one place which almost reached this goal. Based on primary and secondary historical and anthropological research, we argue that the geo-political emplacement of the Cook Islands and development of multi-scale partnerships were crucial to success. Our research indicates the value of understanding and engaging with local community networks and culturally appropriate partnerships in dealing with health issues.

Tuberculosis and syndemics: implications for Pacific health in New Zealand.

Syndemics have been conceived of as a way of approaching the multiple levels of causation and linkage between two or more health conditions and their socio-political environment. Our aim in this paper is to use the established literature on syndemic relationships to examine possible interactions involving tuberculosis. In particular, we explore the linkages between tuberculosis and diabetes mellitus which, we argue, is of particular relevance to Pacific populations resident in New Zealand. Reviewing current literature, we identify multiple synergies between these two diseases whereby their mutual presence has an amplified negative effect. Both conditions interact with other practices and aspects of the broader political economic context such as smoking, housing, and nutrition. A syndemic approach to Pacific health is argued as an effective way to address research, policy and prevention questions.

Fifty years of chimpanzee demography at Taronga Park Zoo.

There has been a captive Pan troglodytes colony at Taronga Park Zoo in Sydney, Australia, since the mid-1930s. Demographic data on these animals were first analyzed in 1986; however, further information collected for 15 years since then is now available. The reproductive histories of 33 females in the colony have been recorded, and these data form the largest collection of captive chimpanzee data from a setting that has involved natural breeding conditions since the mid-1960s. These data were analyzed in conjunction with data from wild populations to establish the degree of variability present within chimpanzee reproductive parameters, and to identify which distinctive life history characteristics persist in well-provisioned, natural-fertility populations. The age at first birth for the chimpanzee females is 9.8 yr on average (n=16), which is 1-4.8 yr earlier than the average for wild populations. In line with this accelerated reproduction, birth intervals are also significantly shorter than those in noncaptive chimpanzee populations. The median birth interval for all surviving infants (based on a Kaplan-Meier survival analysis) is 49 months (n=43) compared to 62+ months for wild groups. At the same time, infant mortality remains high. The data confirm distinctive features of the life history of common chimpanzees, including later maturation, long birth intervals, a relatively invariant fertility schedule, and high juvenile mortality. However, aspects of both fertility and mortality are significantly related to social circumstances, indicating that in common chimpanzees, as in humans, life history characters may represent ecological and social adaptations rather than species-fixed characteristics.

Invisible impacts but long-term consequences: hypoplasia and contact in central Australia.

The dental casts taken of Aboriginal people resident at Yuendumu, Central Australia, between 1950-1970 preserve a unique historical record of defects of the dental enamel (DDEs) among people born from 1890-1960 (n = 377). These data are used, in comparison with precontact data, to trace the chronological changes in childhood development that occurred among Aboriginal people from the point of initial engagement with white settlers to a period of overwhelming government control. The results demonstrate very little change in the frequency of DDE from the precontact period to 1929 but increases after that time, particularly after the forcible settlement of people on a government establishment at Yuendumu in 1946. Apart from the absolute increase in frequency, it is also clear that population variation decreased markedly, with growing numbers of children experiencing multiple defects in early childhood (ca. 0.8-1.5 years of age). The results also indicate that an early onset of DDE constituted a risk for further episodes. These changes in DDE correspond to periods of increasingly intense contact between Aboriginal people and Europeans and with changes to government policy aimed at assimilating the indigenous population. Such policies had marked costs for childhood development. The lack, however, of a visible marker of initial contact demonstrates the importance of the intensity of and motives behind interactions between indigenous and colonial populations in determining the health consequences of colonial encounters.