pinecone/core-2020-05-10-deduplication huggingface dataset:
Biomolecular identification of ancient mycobacterium tuberculosis complex DNA in human remains from Britain and continental Europe.

Tuberculosis is known to have afflicted humans throughout history and re-emerged towards the end of the 20th century, to an extent that it was declared a global emergency in 1993. The aim of this study was to apply a rigorous analytical regime to the detection of Mycobacterium tuberculosis complex (MTBC) DNA in 77 bone and tooth samples from 70 individuals from Britain and continental Europe, spanning the 1st–19th centuries AD. We performed the work in dedicated ancient DNA facilities designed to prevent all types of modern contamination, we checked the authenticity of all products obtained by the polymerase chain reaction, and we based our conclusions on up to four replicate experiments for each sample, some carried out in an independent laboratory. We identified 12 samples that, according to our strict criteria, gave definite evidence for the presence of MTBC DNA, and another 22 that we classified as “probable” or “possible.” None of the definite samples came from vertebrae displaying lesions associated with TB. Instead, eight were from ribs displaying visceral new bone formation, one was a tooth from a skeleton with rib lesions, one was taken from a skeleton with endocranial lesions, one from an individual with lesions to the sacrum and sacroiliac joint and the last was from an individual with no lesions indicative of TB or possible TB. Our results add to information on the past temporal and geographical distribution of TB and affirm the suitability of ribs for studying ancient TB
Maternal short stature does not predict their children's fatness indicators in a nutritional dual-burden sample of urban Mexican Maya

This article was submitted for publication in the journal, American Journal of Physical Anthropology [© Wiley Periodicals, Inc.] and the definitive version is available at: http://dx.doi.org/10.1002/ajpa.22463The co-existence of very short stature due to poor chronic environment in early life and obesity is becoming a public health concern in rapidly transitioning populations with high levels of poverty. Individuals who have very short stature seem to be at an increased risk of obesity in times of relative caloric abundance. Increasing evidence shows that an individual is influenced by exposures in previous generations. This study assesses whether maternal poor early life environment predicts her child's adiposity using cross sectional design on Maya schoolchildren aged 7–9 and their mothers (n = 57 pairs). We compared maternal chronic early life environment (stature) with her child's adiposity (body mass index [BMI] z-score, waist circumference z-score, and percentage body fat) using multiple linear regression, controlling for the child's own environmental exposures (household sanitation and maternal parity). The research was performed in the south of Merida, Yucatan, Mexico, a low socioeconomic urban area in an upper middle income country. The Maya mothers were very short, with a mean stature of 147 cm. The children had fairly high adiposity levels, with BMI and waist circumference z-scores above the reference median. Maternal stature did not significantly predict any child adiposity indicator. There does not appear to be an intergenerational component of maternal early life chronic under-nutrition on her child's obesity risk within this free living population living in poverty. These results suggest that the co-existence of very short stature and obesity appears to be primarily due to exposures and experiences within a generation rather than across generations
Ecogeographical and phylogenetic effects on craniofacial variation in macaques.

The widespread and complex ecogeographical diversity of macaques may have caused adaptive morphological convergence among four phylogenetic subgroups, making their phylogenetic relationships unclear. We used geometric morphometrics and multivariate analyses to test the null hypothesis that craniofacial morphology does not vary with ecogeographical and phylogenetic factors. As predicted by Bergmann's rule, size was larger for the fascicularis and sinica groups in colder environments. No clear size cline was observed in the silenus and sylvanus groups. An allometric pattern was observed across macaques, indicating that as size increases, rounded faces become more elongated. However, the elevation was differentiated within each of the former two groups and between the silenus and sylvanus groups, and the slope decreased in each of the two northern species of the fascicularis group. All allometric changes resulted in the similar situation of the face being more rounded in animals inhabiting colder zones and/or in animals having a larger body size than that predicted from the overarching allometric pattern. For non-allometric components, variations in prognathism were significantly correlated with dietary differences; variations in localized shape components in zygomatics and muzzles were significantly correlated with phylogenetic differences among the subgroups. The common allometric pattern was probably influenced directly or indirectly by climate-related factors, which are pressures favoring a more rounded face in colder environments and/or a more elongated face in warmer environments. Allometric dissociation could have occurred several times in Macaca even within a subgroup because of their wide latitudinal distributions, critically impairing the taxonomic utility of craniofacial elongation
Mortality, fertility, and the OY ratio in a model hunter–gatherer system

An agent‐based model (ABM) is used to explore how the ratio of old to young adults (the OY ratio) in a sample of dead individuals is related to aspects of mortality, fertility, and longevity experienced by the living population from which the sample was drawn. The ABM features representations of rules, behaviors, and constraints that affect person‐ and household‐level decisions about marriage, reproduction, and infant mortality in hunter–gatherer systems. The demographic characteristics of the larger model system emerge through human‐level interactions playing out in the context of “global” parameters that can be adjusted to produce a range of mortality and fertility conditions. Model data show a relationship between the OY ratios of living populations (the living OY ratio) and assemblages of dead individuals drawn from those populations (the dead OY ratio) that is consistent with that from empirically known ethnographic hunter–gatherer cases. The dead OY ratio is clearly related to the mean ages, mean adult mortality rates, and mean total fertility rates experienced by living populations in the model. Sample size exerts a strong effect on the accuracy with which the calculated dead OY ratio reflects the actual dead OY ratio of the complete assemblage. These results demonstrate that the dead OY ratio is a potentially useful metric for paleodemographic analysis of changes in mortality and mean age, and suggest that, in general, hunter–gatherer populations with higher mortality, higher fertility, and lower mean ages are characterized by lower dead OY ratios. Am J Phys Anthropol 154:222–231, 2014. © 2014 Wiley Periodicals, Inc
Using multivariate adaptive regression splines to estimate subadult age from diaphyseal dimensions

Subadult age estimation is considered the most accurate parameter estimated in a
subadult biological profile, even though the methods are deficient and the samples from which
they are based are inappropriate. The current study addresses the problems that plague subadult
age estimation and creates age estimation models from diaphyseal dimensions of modern
children.
The sample included 1,310 males and females between the ages of birth and 12 years.
Eighteen diaphyseal length and breadth measurements were obtained from Lodox Statscan
radiographic images generated at two institutions in Cape Town, South Africa between 2007 and
2012. Univariate and multivariate age estimation models were created using multivariate
adaptive regression splines (MARS). K-fold cross-validated 95% prediction intervals (PIs) were
created for each model and the precision of each model was assessed.The diaphyseal length models generated the narrowest PIs (two months to six years) for
all univariate models. The majority of multivariate models had PIs that ranged from three months
to five and six years. Mean bias approximated zero for each model, but most models lost
precision after 10 years of age. While univariate diaphyseal length models are recommended for
younger children, multivariate models are recommended for older children where the inclusion
of more variables minimized the size of the prediction intervals. If diaphyseal lengths are not
available, multivariate breadth models are recommended. The present study provides applicable
age estimation formulae and explores the advantages and disadvantages of different subadult age
estimation models using diaphyseal dimensions.http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1096-8644hb201
A genetic comparison of two alleged subspecies of  P hilippine cynomolgus macaques

Two subspecies of cynomolgus macaques ( Macaca fascicularis ) are alleged to co‐exist in the Philippines,  M. f. philippensis  in the north and  M. f. fascicularis  in the south. However, genetic differences between the cynomolgus macaques in the two regions have never been studied to document the propriety of their subspecies status. We genotyped samples of cynomolgus macaques from Batangas in southwestern Luzon and Zamboanga in southwestern Mindanao for 15 short tandem repeat (STR) loci and sequenced an 835 bp fragment of the mtDNA of these animals. The STR genotypes were compared with those of cynomolgus macaques from southern Sumatra, Singapore, Mauritius and Cambodia, and the mtDNA sequences of both Philippine populations were compared with those of cynomolgus macaques from southern Sumatra, Indonesia and Sarawak, Malaysia. We conducted STRUCTURE and PCA analyses based on the STRs and constructed a median joining network based on the mtDNA sequences. The Philippine population from Batangas exhibited much less genetic diversity and greater genetic divergence from all other populations, including the Philippine population from Zamboanga. Sequences from both Batangas and Zamboanga were most closely related to two different mtDNA haplotypes from Sarawak from which they are apparently derived. Those from Zamboanga were more recently derived than those from Batangas, consistent with their later arrival in the Philippines. However, clustering analyses do not support a sufficient genetic distinction of cynomolgus macaques from Batangas from other regional populations assigned to subspecies  M. f. fascicularis  to warrant the subspecies distinction  M. f. philippensis . Am J Phys Anthropol 155:136–148, 2014. © 2014 Wiley Periodicals, Inc
Estimating age of mature adults from the degeneration of the sternal end of the clavicle

The sternal end of the clavicle has been illustrated to be useful in aging young adults, however, no studies have investigated what age-related changes occur to the sternal end post epiphyseal fusion. In this study, three morphological features (i.e., surface topography, porosity, and osteophyte formation) were examined and scored using 564 clavicles of individuals of European ancestry (n = 318 males; n = 246 females), with known ages of 40+ years, from four documented skeletal collections: Hamann-Todd, Pretoria, St. Bride's, and Coimbra. An ordinal scoring method was developed for each of the three traits. Surface topography showed the strongest correlation with age, and composite scores (formed by summing the three separate trait scores) indicated progressive degeneration of the surface with increasing chronological age. Linear regression analyses were performed on the trait scores to produce pooled-sample age estimation equations. Blind tests of the composite score method and regression formulae on 56 individuals, aged 40+ years, from Christ Church Spitalfields, suggest accuracies of 96.4% for both methods. These preliminary results display the first evidence of the utility of the sternal end of the clavicle in aging older adult individuals. However, in the current format, these criteria should only be applied to individuals already identified as over 40 years in order to refine the age ranges used for advanced age. These findings do suggest the sternal end of the clavicle has potential to aid age estimates beyond the traditional "mature adult" age category (i.e., 46+ years), and provides several suggestions for future research
Diet, society, and economy in late medieval Spain : stable isotope evidence from Muslims and Christians from Gandía, Valencia.

This article investigates the diets of neighboring Christians and Muslims in late medieval Spain (here 13th–16th centuries) through the analysis of the stable isotopes of carbon (δ13C) and nitrogen (δ15N) in adult human and animal bone collagen. Twenty-four Christians and 20 Muslims are sampled from two adjacent and contemporaneous settlements in the township of Gandía on the Mediterranean coast, together with the remains of 24 animals. Statistical differences in both δ13C and δ15N reveal that the diets of the two faith communities differed, despite living side-by-side. These differences may relate to inequalities in their access to foodstuffs, particularly to C3/C4 grain and/or possibly terrestrial meat sources, though cultural preferences are also highlighted. Isotopic values for animals were also found to vary widely, both between and within species, and this provides a window into the local livestock economy
Diet, society, and economy in late medieval Spain : Stable isotope evidence from Muslims and Christians from Gandía, Valencia

This article investigates the diets of neighboring Christians and Muslims in late medieval Spain (here 13th–16th centuries) through the analysis of the stable isotopes of carbon (δ13C) and nitrogen (δ15N) in adult human and animal bone collagen. Twenty-four Christians and 20 Muslims are sampled from two adjacent and contemporaneous settlements in the township of Gandía on the Mediterranean coast, together with the remains of 24 animals. Statistical differences in both δ13C and δ15N reveal that the diets of the two faith communities differed, despite living side-by-side. These differences may relate to inequalities in their access to foodstuffs, particularly to C3/C4 grain and/or possibly terrestrial meat sources, though cultural preferences are also highlighted. Isotopic values for animals were also found to vary widely, both between and within species, and this provides a window into the local livestock economy
A bioarchaeological approach to the reconstruction of changes in military organization among Iron Age Samnites (Vestini) From Abruzzo, Central Italy.

The Samnites were an Iron Age population that shifted from warlike mountain dwellers to the largest sociopolitical unit of central Italy, able to dispute with Rome the domination over the peninsula. Archaeological and historical evidence suggests that this major shift in the scale of conflict may have involved a reorganization of the military system, which changed from an elite militia to a conscript or standing army from the Orientalizing-Archaic (800–500 BC) to Hellenistic times (400–27 BC). We propose a bioarchaeological framework jointly analyzing skeletal properties and funerary treatment in male Samnites to investigate on this shift in military organization. We anticipated that, when Samnites had an elite militia, the warring force was constituted by the wealthier segments of the society. Conversely, we expected the warring force of the standing/conscript army to be mainly drawn from the lower social strata. We considered high asymmetry in J, a measure of humeral torsional rigidity (calculated via cross-sectional geometry, CSG) as a proxy for pre- and peri-adolescent-onset weapon training. The social standing of the individual was approximated via funerary treatment analysis (Status Index). Results show that in the Orientalizing-Archaic period, humeral asymmetry and Status Index are positively correlated, and the high-status subsample shows significantly higher asymmetry than the low-status subsample. Among Hellenistic Samnites, no correlation between Status Index and humeral asymmetry is present, and the low-status subsample is the most lateralized. Results support the use of CSG in a strong theoretical framework to investigate past changes in military organization and their correlates in terms of sociopolitical development, alterations of power relationships, and warfare
To meat or not to meat? New perspectives on Neanderthal ecology.

Neanderthals have been commonly depicted as top predators who met their nutritional needs by focusing entirely on meat. This information mostly derives from faunal assemblage analyses and stable isotope studies: methods that tend to underestimate plant consumption and overestimate the intake of animal proteins. Several studies in fact demonstrate that there is a physiological limit to the amount of animal proteins that can be consumed: exceeding these values causes protein toxicity that can be particularly dangerous to pregnant women and newborns. Consequently, to avoid food poisoning from meat-based diets, Neanderthals must have incorporated alternative food sources in their daily diets, including plant materials as well
Relationships of Maternal and Paternal Anthropometry With Neonatal Body Size, Proportions and Adiposity in an Australian Cohort

The patterns of association between
maternal or paternal and neonatal phenotype may offer
insight into how neonatal characteristics are shaped by
evolutionary processes, such as conflicting parental
interests in fetal investment and obstetric constraints.
Paternal interests are theoretically served by maximizing
fetal growth, and maternal interests by managing
investment in current and future offspring, but whether
paternal and maternal influences act on different components
of overall size is unknown. We tested whether
parents’ prepregnancy height and body mass index
(BMI) were related to neonatal anthropometry (birthweight,
head circumference, absolute and proportional
limb segment and trunk lengths, subcutaneous fat)
among 1,041 Australian neonates using stepwise linear
regression. Maternal and paternal height and maternal
BMI were associated with birthweight. Paternal height
related to offspring forearm and lower leg lengths,
maternal height and BMI to neonatal head circumference,
and maternal BMI to offspring adiposity. Principal
components analysis identified three components of variability
reflecting neonatal “head and trunk skeletal size,”
“adiposity,” and “limb lengths.” Regression analyses of
the component scores supported the associations of head
and trunk size or adiposity with maternal anthropometry,
and limb lengths with paternal anthropometry. Our
results suggest that while neonatal fatness reflects environmental
conditions (maternal physiology), head circumference
and limb and trunk lengths show differing
associations with parental anthropometry. These patterns
may reflect genetics, parental imprinting and
environmental influences in a manner consistent with
parental conflicts of interest. Paternal height may relate
to neonatal limb length as a means of increasing
fetal growth without exacerbating the risk of obstetric
complications.Grant sponsor: National Health and Medical Research Council
(Australia; relevant phases of the Mater-University of Queensland
Study of Pregnancy), Henry Sidgwick Research Fellowship from
Newnham College, Cambridge, UK (to EP), and Medical Research
Council; Grant number: MR/J004839/1.This is the final published version. It originally appeared at http://onlinelibrary.wiley.com/doi/10.1002/ajpa.22680/abstract;jsessionid=C9174F1F8C90CA60D91F169281043AFC.f04t01
Low Mineral Density of a Weight-Bearing Bone Among Adult Women in a High Fertility Population

Evolutionary theories of aging posit that greater reproductive effort causes somatic decline given a fundamental trade-off between investing energy in reproduction and repair. Few studies in high fertility human populations support this hypothesis, and problems of phenotypic correlation can obscure the expected trade-off between reproduction and somatic condition. This cross-sectional study investigates whether greater reproductive effort is associated with reduced calcaneal bone mineral density (BMD) among female Tsimane forager-farmers of lowland Bolivia. We also investigate whether female Tsimane BMD values are lower than sex- and age-matched US reference values, despite the fact that Tsimane engage in higher physical activity levels that can increase mechanical loading. To measure calcaneal BMD, quantitative ultrasonography was performed on 130 women (mean ± SD age = 36.6 ± 15.7, range = 15–75) that were recruited regardless of past or current reproductive status. Anthropometric and demographic data were collected during routine medical exams. As predicted, higher parity, short inter-birth interval, and earlier age at first birth are associated with reduced BMD among Tsimane women after adjusting for potential confounders. Population-level differences are apparent prior to the onset of reproduction, and age-related decline in BMD is greater among Tsimane compared with American women. Greater cumulative reproductive burden may lower calcaneal BMD individually and jointly with other lifestyle and heritable factors. Fitness impacts of kin transfers in adulthood may determine the value of investments in bone remodeling, and thus affect selection on age-profiles of bone mineral loss
Does the correlation between Schmorl’s nodes and vertebral morphology extend into the lumbar spine?

Schmorl's nodes are depressions on vertebrae due to herniation of the nucleus pulposus of the intervertebral disc into the vertebral body. This study provides an extension of our previous study which analyzed the shape of the lower thoracic spine and found that vertebral morphology was associated with the presence of Schmorl's nodes. Ninety adult individuals from the late Medieval site of Fishergate House, York, and the Post-Medieval site of Coach Lane, North Shields, Tyne and Wear, England, were analysed using 2D geometric morphometrics to identify possible relationships between vertebral morphology and Schmorl's nodes at the thoraco-lumbar junction and in the lumbar spine. A significant correlation was found between vertebral shape and the presence of Schmorl's nodes in the twelfth thoracic vertebrae and the first to third lumbar vertebrae. The findings corroborate previous studies and suggest that vertebral shape may be an important factor in spinal health. It is hypothesized that the pedicle shape of affected vertebrae may not provide adequate structural support for the vertebral bodies, resulting in vertical disc herniation
Across language families: Genome diversity mirrors linguistic variation within Europe

The notion that patterns of linguistic and biological variation may cast light on each other and on population histories dates back to Darwin's times; yet, turning this intuition into a proper research program has met with serious methodological difficulties, especially affecting language comparisons. This article takes advantage of two new tools of comparative linguistics: a refined list of Indo-European cognate words, and a novel method of language comparison estimating linguistic diversity from a universal inventory of grammatical polymorphisms, and hence enabling comparison even across different families. We corroborated the method and used it to compare patterns of linguistic and genomic variation in Europe