pinecone/core-2020-05-10-deduplication huggingface dataset:
Broken ribs: paleopathological analysis of costal fractures in the human identified skeletal collection from the Museu Bocage, Lisbon, Portugal (late 19th to middle 20th centuries)

Although rarely reported in the anthropological literature, rib fractures are commonly found during the analysis of human skeletal remains of past and modern populations. This lack of published data precludes comparison between studies and restricts an accurate understanding either of the mechanisms involved in thoracic injuries or their impact on past societies. The present study aimed: 1) to report rib fracture prevalence in 197 individuals, 109 males, and 88 females, with ages at death ranging from 13 to 88 years old, from the Human Identified Skeletal Collection, Museu Bocage, Portugal (late 19th-middle 20th centuries); 2) to test the hypothesis that a higher prevalence of rib stress fractures existed in the 133 individuals who died from respiratory diseases, in a period before antibiotics. The macroscopic analysis revealed 23.9% (n = 47) of individuals with broken ribs. 2.6% (n = 124) out of 4,726 ribs observed were affected. Males presented more rib fractures, and a significantly higher prevalence was noted for older individuals. Fractures were more frequently unilateral (n = 34), left sided (n = 19) and mainly located on the shaft of ribs from the middle thoracic wall. Nineteen individuals presented adjacent fractured ribs. Individuals who died from pulmonary diseases were not preferentially affected. However, a higher mean rate of fractures was found in those who died from pneumonia, a scenario still common nowadays. Since rib involvement in chest wall injury and its related outcomes are important issues both for paleopathology and forensic anthropology, further investigations are warranted.Fundação para a Ciência e Tecnologia; Grant
number: SFRH/BD/16155/2004
Shallow-Water Habitats as Sources of Fallback Foods for Hominins

Underground storage organs (USOs) have been proposed as critical fallback foods for early hominins in savanna, but there has been little discussion as to which habitats would have been important sources of USOs. USOs consumed by hominins could have included both underwater and underground storage organs, i.e., from both aquatic and terrestrial habitats. Shallow aquatic habitats tend to offer high plant growth rates, high USO densities, and relatively continuous USO availability throughout the year. Baboons in the Okavango delta use aquatic USOs as a fallback food, and aquatic or semiaquatic USOs support high-density human populations in various parts of the world. As expected given fossilization requisites, the African early- to mid-Pleistocene shows an association of Homo and Paranthropus fossils with shallow-water and flooded habitats where high densities of plant-bearing USOs are likely to have occurred. Given that early hominins in the tropics lived in relatively dry habitats, while others occupied temperate latitudes, ripe, fleshy fruits of the type preferred by African apes would not normally have been available year round. We therefore suggest that water-associated USOs were likely to have been key fallback foods, and that dry-season access to aquatic habitats would have been an important predictor of hominin home range quality. This study differs from traditional savanna chimpanzee models of hominin origins by proposing that access to aquatic habitats was a necessary condition for adaptation to savanna habitats. It also raises the possibility that harvesting efficiency in shallow water promoted adaptations for habitual bipedality in early hominins.Human Evolutionary Biolog
Mitochondrial DNA structure in North Africa reveals a genetic discontinuity in the Nile Valley

Versión final disponible en www3.interscience.wiley.comHuman population movements in North Africa have been mostly restricted to an east-west direction due to the geographical barriers imposed by the Sahara Desert and the Mediterranean Sea. Although these barriers have not completely impeded human migrations, genetic studies have shown that an east-west genetic gradient exists. However, the lack of genetic information of certain geographical areas and the focus of some studies in parts of the North African landscape have limited the global view of the genetic pool of North African populations. To provide a global view of the North African genetic landscape and population structure, we have analyzed ∼2,300 North African mitochondrial DNA lineages (including 269 new sequences from Libya, in the first mtDNA study of the general Libyan population). Our results show a clinal distribution of certain haplogroups, some of them more frequent in Western (H, HV0, L1b, L3b, U6) or Eastern populations (L0a, R0a, N1b, I, J) that might be the result of human migrations from the Middle East, sub-Saharan Africa, and Europe. Despite this clinal pattern, a genetic discontinuity is found in the Libyan/Egyptian border, suggesting a differential gene flow in the Nile River Valley. Finally, frequency of the post-LGM subclades H1 and H3 is predominant in Libya within the H sequences, highlighting the magnitude of the LGM expansion in North Africa.Peer reviewe
A test of the influence of continental axes of orientation on patterns of human gene flow

The geographic distribution of genetic variation reflects trends in past population migrations and can be used to make inferences about these migrations. It has been proposed that the east–west orientation of the Eurasian landmass facilitated the rapid spread of ancient technological innovations across Eurasia, while the north–south orientation of the Americas led to a slower diffusion of technology there. If the diffusion of technology was accompanied by gene flow, then this hypothesis predicts that genetic differentiation in the Americas along lines of longitude will be greater than that in Eurasia along lines of latitude. We use 678 microsatellite loci from 68 indigenous populations in Eurasia and the Americas to investigate the spatial axes that underlie population‐genetic variation. We find that genetic differentiation increases more rapidly along lines of longitude in the Americas than along lines of latitude in Eurasia. Distance along lines of latitude explains a sizeable portion of genetic distance in Eurasia, whereas distance along lines of longitude does not explain a large proportion of Eurasian genetic variation. Genetic differentiation in the Americas occurs along both latitudinal and longitudinal axes and has a greater magnitude than corresponding differentiation in Eurasia, even when adjusting for the lower level of genetic variation in the American populations. These results support the view that continental orientation has influenced migration patterns and has played an important role in determining both the structure of human genetic variation and the distribution and spread of cultural traits. Am J Phys Anthropol 2011. © 2011 Wiley Periodicals, Inc
High mitochondrial mutation rates estimated from deep-rooting Costa Rican pedigrees

artículo (arbitrado). Universidad de Costa Rica, Centro de Investigación en Biología Celular y Molecular, 2012Estimates of mutation rates for the noncoding hypervariable Region I (HVR-I) of mitochondrial
DNA (mtDNA) vary widely, depending on whether they are inferred from phylogenies (assuming
that molecular evolution is clock-like) or directly from pedigrees. All pedigree-based studies so far
were conducted on populations of European origin. In this paper we analyzed 19 deep-rooting
pedigrees in a population of mixed origin in Costa Rica. We calculated two estimates of the HVRI
mutation rate, one considering all apparent mutations, and one disregarding changes at sites
known to be mutational hot spots and eliminating genealogy branches which might be suspected
to include errors, or unrecognized adoptions along the female lines. At the end of this procedure,
we still observed a mutation rate equal to 1.24 × 10−6, per site per year, i.e., at least three-fold as
high as estimates derived from phylogenies. Our results confirm that mutation rates observed in
pedigrees are much higher than estimated assuming a neutral model of long-term HVRI evolution.
We argue that, until the cause of these discrepancies will be fully understood, both lower estimates
(i.e., those derived from phylogenetic comparisons) and higher, direct estimates such as those
obtained in this study, should be considered when modeling evolutionary and demographic
processes.Universidad de Costa RicaUCR::Investigación::Unidades de Investigación::Ciencias Básicas::Centro de Investigación en Biología Celular y Molecular (CIBCM
Developmental and genetic components explain enhanced pulmonary volumes of female peruvian quechua

High altitude natives have enlarged vital capacities and residual volumes (RV). Because pulmonary volumes are an indication of functionally relevant traits, such as diffusion capacity, the understanding of the factors (genetic/developmental) that influence lung volumes provides insight into the adaptive responses of highlanders. In order to test for the effect of growth and development at high altitude on lung volumes, we obtained forced vital capacities (FVC), RV, and total lung capacities (TLC) for a sample of 65 Peruvian females of mostly Quechua origins (18–34 years) who were sub‐divided into two well‐matched groups: 1) sea‐level born and raised females (BSL,  n  = 34) from Lima, Peru (150 m), and 2) high‐altitude born and raised females (BHA,  n  = 31) from Cerro de Pasco, Peru (4,338 m). To determine Quechua origins, Native American ancestry proportion (NAAP) for each individual was assessed using a panel of 70 ancestry informative markers. NAAP was similar between groups (BSL = 91.71%; BHA = 89.93%;  P  = 0.240), and the analysis confirmed predominantly Quechua origins. After adjusting for body size and NAAP, BHA females had significantly higher FVC (3.79 ± 0.06 l;  P  < 0.001), RV (0.98 ± 0.03 l;  P  < 0.001) and TLC (4.80 ± 0.07 l;  P  < 0.001) compared to BSL females (FVC = 3.33 ± 0.05 l; RV = 0.69 ± 0.03 l; TLC = 4.02 ± 0.06 l). NAAP was not associated with FVC ( P  = 0.352) or TLC ( P  = 0.506). However, NAAP was positively associated with RV ( P  = 0.004). In summary, results indicate that developmental exposure to high altitude in females constitutes an important factor for all lung volumes, whereas both genetic and developmental factors seem to be important for RV. Am J Phys Anthropol 2012. © 2012 Wiley Periodicals, Inc
Brief communication: Chronic undernutrition is associated with higher mucosal antibody levels among ariaal infants of northern kenya

The immune activation that occurs with infection diverts energy from growth and can contribute to poor nutritional outcomes in developing infants and children. This study investigates the association between salivary immunoglobulin A (IgA) levels and growth outcomes among Ariaal infants of northern Kenya. The Ariaal are a group of settled northern Kenyan pastoralists who are under considerable nutritional stress. Two hundred and thirty‐nine breastfeeding Ariaal infants were recruited into the study and underwent anthropometric measurement and saliva collection, with mothers providing individual and household characteristics for them via questionnaire. Infant saliva samples were analyzed with an ELISA for IgA in the United States. Infant anthropometric measurements were converted to height‐for‐age  z ‐scores (HAZ) using the WHO Child Growth Standards. Based on multivariate models performed in SAS 9.2 two main results emerge: 1) low HAZ, an indicator of chronic undernutrition, was significantly associated with higher IgA concentration (β = −0.12,  P  = 0.050) and 2) boys had significantly higher IgA levels than girls (β = 0.25,  P  = 0.039). Although there was not a significant interactive effect between HAZ and sex, the two variables confound each other, with boys having significantly lower HAZ values than girls do. In addition, maternal breastmilk IgA was significantly associated with infant salivary IgA, indicating that maternal effects play a role in infant IgA development. Future research will unravel the three‐way association between sex, stunting, and immune function in the Ariaal community. Am J PhyAnthropol 2012. © Wiley Periodicals, Inc
Mobility, mortality, and the middle ages : identification of migrant individuals in a 14th century black death cemetery population.

Mobility and migration patterns of groups and individuals have long been a topic of interest to archaeologists, used for broad explanatory models of cultural change as well as illustrations of historical particularism. The 14th century AD was a tumultuous period of history in Britain, with severely erratic weather patterns, the Great Famine of 1315–1322, the Scottish Wars of Independence, and the Hundred Years' War providing additional migration pressures to the ordinary economic issues drawing individuals to their capital under more stable conditions. East Smithfield Black Death Cemetery (Royal Mint) had a documented use period of only 2 years (AD 1348–1350), providing a precise historical context (∼50 years) for data. Adults (n = 30) from the East Smithfield site were sampled for strontium and oxygen stable isotope analyses of tooth enamel. Five individuals were demonstrated to be statistical outliers through the combined strontium and oxygen isotope data. Potential origins for migrants ranged from London's surrounding hinterlands to distant portions of northern and western Britain. Historic food sourcing practices for London were found to be an important factor for consideration in a broader than expected 87Sr/86Sr range reflected in a comparison of enamel samples from three London datasets. The pooled dataset demonstrated a high level of consistency between site data, divergent from the geologically predicted range. We argue that this supports the premise that isotope data in human populations must be approached as a complex interaction between behavior and environment and thus should be interpreted cautiously with the aid of alternate lines of evidence
Noninvasive molecular sexing: An evaluation and validation of the SRY- and amelogenin-based method in three new lemur species

Many lemur species are arboreal, elusive, and/or nocturnal and are consequently difficult to approach, observe and catch. In addition, most of them are endangered. For these reasons, non-invasive sampling is especially useful in primates including lemurs. A key issue in conservation and ecological studies is to identify the sex of the sampled individuals to investigate sex-biased dispersal, parentage, social organization and population sex ratio. Several molecular tests of sex are available in apes and monkeys, but only a handful of them work in the lemuriform clade. Among these tests, the coamplification of the SRY gene with the amelogenin X gene using strepsirhine-specific X primers seems particularly promising, but the reliability and validity of this sexing test have not been properly assessed yet. In this study, we (i) show that this molecular sexing test works on three additional lemur species (Microcebus tavaratra, Propithecus coronatus and P. verreauxi) from two previously untested genera and one previously untested family, suggesting that these markers are likely to be universal among lemurs and other strepsirrhines; (ii) provide the first evidence that this PCR-based sexing test works on degraded DNA obtained from noninvasive samples; (iii) validate the approach using a large number of known-sex individuals and a multiple-tubes approach, and show that mismatches between the field sex and the final molecular consensus sex occur in less than 10% of all the samples and that most of these mismatches were likely linked to incorrect sex determinations in the field rather than genotyping errors.FCT fellowship: (SFRH/BPD/73675/2010); Institut Français de la Biodiversité grant: (CD-AOOI-07-003); Programme Biodiversité de l'Océan Indien grant: (CD-AOOI-07-003); Laboratoire d'Excellence (LABEX) entitled TULIP grant: (ANR -10-LABX-41); Instituto Gulbenkian de Ciência- Optimus!Alive-IGC fellowship: (UMR 7206 – CNRS)
Technical note: reliability of Suchey-Brooks and Buckberry-Chamberlain methods on 3D visualizations from CT and laser scans.

YesPrevious studies have reported that the ageing method of Suchey-Brooks (pubic bone) and some of the features applied by Lovejoy et al. and Buckberry-Chamberlain (auricular surface) can be confidently performed on 3D visualizations from CT-scans. In this study, seven observers applied the Suchey-Brooks and the Buckberry-Chamberlain methods on 3D visualizations based on CT-scans and, for the first time, on 3D visualizations from laser scans. We examined how the bone features can be evaluated on 3D visualizations and whether the different modalities (direct observations of bones, 3D visualization from CT-scan and from laser scans) are alike to different observers. We found the best inter-observer agreement for the bones versus 3D visualizations, with the highest values for the auricular surface. Between the 3D modalities, less variability was obtained for the 3D laser visualizations. Fair inter-observer agreement was obtained in the evaluation of the pubic bone in all modalities. In 3D visualizations of the auricular surfaces, transverse organization and apical changes could be evaluated, although with high inter-observer variability; micro-, macroporosity and surface texture were very difficult to score. In conclusion, these methods were developed for dry bones, where they perform best. The Suchey-Brooks method can be applied on 3D visualizations from CT or laser, but with less accuracy than on dry bone. The Buckberry-Chamberlain method should be modified before application on 3D visualizations. Future investigation should focus on a different approach and different features: 3D laser scans could be analyzed with mathematical approaches and sub-surface features should be explored on CT-scan
Viewpoints: Feeding mechanics, diet, and dietary adaptations in early hominins

Inference of feeding adaptation in extinct species is challenging, and reconstructions of the paleobiology of our ancestors have utilized an array of analytical approaches. Comparative anatomy and finite element analysis assist in bracketing the range of capabilities in taxa, while microwear and isotopic analyses give glimpses of individual behavior in the past. These myriad approaches have limitations, but each contributes incrementally toward the recognition of adaptation in the hominin fossil record. Microwear and stable isotope analysis together suggest that australopiths are not united by a single, increasingly specialized dietary adaptation. Their traditional (i.e., morphological) characterization as "nutcrackers" may only apply to a single taxon, Paranthropus robustus. These inferences can be rejected if interpretation of microwear and isotopic data can be shown to be misguided or altogether erroneous. Alternatively, if these sources of inference are valid, it merely indicates that there are phylogenetic and developmental constraints on morphology. Inherently, finite element analysis is limited in its ability to identify adaptation in paleobiological contexts. Its application to the hominin fossil record to date demonstrates only that under similar loading conditions, the form of the stress field in the australopith facial skeleton differs from that in living primates. This observation, by itself, does not reveal feeding adaptation. Ontogenetic studies indicate that functional and evolutionary adaptation need not be conceptually isolated phenomena. Such a perspective helps to inject consideration of mechanobiological principles of bone formation into paleontological inferences. Finite element analysis must employ such principles to become an effective research tool in this context. © 2013 Wiley Periodicals, Inc
Brief communication: Hair density and body mass in mammals and the evolution of human hairlessness

Humans are unusual among mammals in appearing hairless. Several hypotheses propose explanations for this phenotype, but few data are available to test these hypotheses. To elucidate the evolutionary history of human “hairlessness,” a comparative approach is needed. One previous study on primate hair density concluded that great apes have systematically less dense hair than smaller primates. While there is a negative correlation between body size and hair density, it remains unclear whether great apes have less dense hair than is expected for their body size. To revisit the scaling relationship between hair density and body size in mammals, I compiled data from the literature on 23 primates and 29 nonprimate mammals and conducted Phylogenetic Generalized Least Squares regressions. Among anthropoids, there is a significant negative correlation between hair density and body mass. Chimpanzees display the largest residuals, exhibiting less dense hair than is expected for their body size. There is a negative correlation between hair density and body mass among the broader mammalian sample, although the functional significance of this scaling relationship remains to be tested. Results indicate that all primates, and chimpanzees in particular, are relatively hairless compared to other mammals. This suggests that there may have been selective pressures acting on the ancestor of humans and chimpanzees that led to an initial reduction in hair density. To further understand the evolution of human hairlessness, a systematic study of hair density and physiology in a wide range of species is necessary. Am J Phys Anthropol 152:145–150, 2013. © 2013 Wiley Periodicals, Inc
Orphaned male Chimpanzees die young even after weaning

青年期まで続くチンパンジーの母親の重要性 -母親を亡くしたオスは長期的に見ても早死にする傾向があることを解明-. 京都大学プレスリリース. 2013-11-01.If a social-living animal has a long life span, permitting different generations to co-exist within a social group, as is the case in many primate species, it can be beneficial for a parent to continue to support its weaned offspring to increase the latter's survival and/or reproductive success. Chimpanzees have an even longer period of dependence on their mothers' milk than do humans, and consequently, offspring younger than 4.5–5 years old cannot survive if the mother dies. Most direct maternal investments, such as maternal transportation of infants and sharing of night shelters (beds or nests), end with nutritional weaning. Thus, it had been assumed that a mother's death was no longer critical to the survival of weaned offspring, in contrast to human children, who continue to depend on parental care long after weaning. However, in theory at least, maternal investment in a chimpanzee son after weaning could be beneficial because in chimpanzees' male-philopatric society, mother and son co-exist for a long time after the offspring's weaning. Using long-term demographic data for a wild chimpanzee population in the Mahale Mountains, Tanzania, we show the first empirical evidence that orphaned chimpanzee sons die younger than expected even if they lose their mothers after weaning. This suggests that long-lasting, but indirect, maternal investment in sons continues several years after weaning and is vital to the survival of the sons. The maternal influence on males in the male-philopatric societies of hominids may be greater than previously believed