Demographic uniformitarianism: the theoretical basis of prehistoric demographic research and its cross-disciplinary challenges.

A principle of demographic uniformitarianism underpins all research into prehistoric demography (palaeodemography). This principle-which argues for continuity in the evolved mechanisms underlying modern human demographic processes and their response to environmental stimuli between past and present-provides the cross-disciplinary basis for palaeodemographic reconstruction and analysis. Prompted by the recent growth and interest in the field of prehistoric demography, this paper reviews the principle of demographic uniformitarianism, evaluates how it relates to two key debates in palaeodemographic research and seeks to delimit its range of applicability to past human and hominin populations. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.

Modelling interventions to control COVID-19 outbreaks in a refugee camp.

BACKGROUND: In the absence of effective treatments or vaccines, non-pharmaceutical interventions are the mainstay of control in the COVID-19 pandemic. Refugee populations in displacement camps live under adverse conditions that are likely to favour the spread of disease. To date, only a few cases of COVID-19 have appeared in refugee camps, and whether feasible non-pharmaceutical interventions can prevent the spread of the SARS-CoV-2 virus in such settings remains untested. METHODS: We constructed the first spatially explicit agent-based model of a COVID-19 outbreak in a refugee camp, and applied it to evaluate feasible non-pharmaceutical interventions. We parameterised the model using published data on the transmission rates and progression dynamics of COVID-19, and demographic and spatial data from Europe's largest refugee camp, the Moria displacement camp on Lesbos, Greece. We simulated COVID-19 epidemics with and without four feasible interventions. RESULTS: Spatial subdivision of the camp ('sectoring') was able to 'flatten the curve', reducing peak infection by up to 70% and delaying peak infection by up to several months. The use of face masks coupled with the efficient isolation of infected individuals reduced the overall incidence of infection, and sometimes averted epidemics altogether. These interventions must be implemented quickly in order to be maximally effective. Lockdowns had only small effects on COVID-19 dynamics. CONCLUSIONS: Agent-based models are powerful tools for forecasting the spread of disease in spatially structured and heterogeneous populations. Our findings suggest that feasible interventions can slow the spread of COVID-19 in a refugee camp setting, and provide an evidence base for camp managers planning intervention strategies. Our model can be modified to study other closed populations at risk from COVID-19 or future epidemics.

Collagen Sequence Analysis Reveals Evolutionary History of Extinct West Indies Nesophontes (Island-Shrews).

Ancient biomolecule analyses are proving increasingly useful in the study of evolutionary patterns, including extinct organisms. Proteomic sequencing techniques complement genomic approaches, having the potential to examine lineages further back in time than achievable using ancient DNA, given the less stringent preservation requirements. In this study, we demonstrate the ability to use collagen sequence analyses via proteomics to assist species delimitation as a foundation for informing evolutionary patterns. We uncover biogeographic information of an enigmatic and recently extinct lineage of Nesophontes across their range on the Caribbean islands. First, evolutionary relationships reconstructed from collagen sequences reaffirm the affinity of Nesophontes and Solenodon as sister taxa within Solenodonota. This relationship helps lay the foundation for testing geographical isolation hypotheses across islands within the Greater Antilles, including movement from Cuba toward Hispaniola. Second, our results are consistent with Cuba having just two species of Nesophontes (N. micrus and N. major) that exhibit intrapopulation morphological variation. Finally, analysis of the recently described species from the Cayman Islands (N. hemicingulus) indicates that it is a closer relative to N. major rather than N. micrus as previously speculated. This proteomic sequencing improves our understanding of the origin, evolution, and distribution of this extinct mammal lineage, particularly with respect to the approximate timing of speciation. Such knowledge is vital for this biodiversity hotspot, where the magnitude of recent extinctions may obscure true estimates of species richness in the past.

Degenerative variance on age-related traits from pelvic bone articulations and its implication for age estimation.

Age at death estimation methods, when applied to skeletal remains of adults, have provided inaccurate results. These aging methods often depend on observations of the degenerative changes occurring at specific articulations, however, the effects of the aging process on the human skeleton are only partially known. Therefore a need exists to increase our understanding about the age related metamorphosis process to improve aging methods. The aim of this study is to determine which age-related traits observable on the pelvic bone articulations are correlated and to quantify their shared degenerative variance. Thus it is intended to quantify the degenerative relationship among features within each pelvic joint. Fifteen age related traits were analyzed for the pubic symphysis, eight traits for the auricular surface of the ilium, and six traits for the acetabulum. Age-related traits from the pelvic joints were recorded on adult skeletons from two reference collections the William Bass Donated Skeletal Collection and the Coimbra Collection. A Principal Components Analysis, partial correlation controlling for age, and a Kendall's W coefficient of concordance were calculated to determine the level of dependence among traits. A similar pattern of correlation amongst traits was obtained for both collections. Some of the traits shared a high to moderate correlation. However, some features, such as dense bone at the auricular surface, possessed a high independence from other traits. Results suggest that age estimation methods should take into consideration how age-related traits correlate and their level of dependence, which may possibly assist in the establishment of more effective scoring systems in new and revised age at death estimation methods.

The biomechanical importance of the scaphoid-centrale fusion during simulated knuckle-walking and its implications for human locomotor evolution.

Inferring the locomotor behaviour of the last common ancestor (LCA) of humans and African apes is still a divisive issue. An African great-ape-like ancestor using knuckle-walking is still the most parsimonious hypothesis for the LCA, despite diverse conflicting lines of evidence. Crucial to this hypothesis is the role of the centrale in the hominoid wrist, since the fusion of this bone with the scaphoid is among the clearest morphological synapomorphies of African apes and hominins. However, the exact functional significance of this fusion remains unclear. We address this question by carrying out finite element simulations of the hominoid wrist during knuckle-walking by virtually generating fused and unfused morphologies in a sample of hominoids. Finite element analysis was applied to test the hypothesis that a fused scaphoid-centrale better withstands the loads derived from knuckle-walking. The results show that fused morphologies display lower stress values, hence supporting a biomechanical explanation for the fusion as a functional adaptation for knuckle-walking. This functional interpretation for the fusion contrasts with the current inferred positional behaviour of the earliest hominins, thus suggesting that this morphology was probably retained from an LCA that exhibited knuckle-walking as part of its locomotor repertoire and that was probably later exapted for other functions.

Postnatal maturation of the sternum in a Portuguese skeletal sample: a variable ossification process.

The timing of skeletal maturation is one of the common indicators used to estimate age at death of juvenile skeletal remains. Skeletal maturation of the sternum has received less attention than other anatomical locations, and there is a general lack of detailed information about the fusion timing in the dry sternum that can be used for the estimation of age. The objective of this study is to document the age variation in the fusion of the body sternebrae, and both clavicular and intercostal notches. A three stage scale scheme was used (unfused elements, partial, and complete fusion) to quantify fusion of primary and secondary ossification centres in a sample of 68 individuals of both sexes from the identified skeletal collection housed at the National Museum of Natural History and Science in Lisbon, Portugal. Analysis was performed only for the pooled sex sample due to small sample size. Wide age intervals were obtained for fusion stages at all of the sternal centres. Primary ossification centres start to fuse between 1 and 27 years of age, with sternebrae 3 and 4 completing their fusion first. Secondary ossification centres fuse between 5 to 25 years of age. Results reflect considerable variability among individuals in the maturation of the sternum.

Forensic proteomics for the evaluation of the post-mortem decay in bones.

Current methods for evaluation the of post-mortem interval (PMI) of skeletal remains suffer from poor accuracy due to the great number of variables that affect the diagenetic process and to the lack of specific guidelines to address this issue. During decomposition, proteins can undergo cumulative decay over the time, resulting in a decrease in the range and abundance of proteins present (i.e., the proteome) in different tissues as well as in an increase of post-translational modifications occurring in these proteins. In this study, we investigate the applicability of bone proteomic analyses to simulated forensic contexts, looking for specific biomarkers that may help the estimation of PMI, as well as evaluate a previously discovered marker for the estimation of biological age. We noticed a reduction of particular plasma and muscle proteins with increasing PMIs, as well as an increased deamidation of biglycan, a protein with a role in modulating bone growth and mineralization. We also corroborated our previous results regarding the use of fetuin-A as a potential biomarker for the estimation of age-at-death, demonstrating the applicability and the great potential that proteomics may have towards forensic sciences. SIGNIFICANCE: The estimation of the post-mortem interval has a key role in forensic investigations, however nowadays it still suffers from poor reliability, especially when body tissues are heavily decomposed. Here we propose for the first time the application of bone proteomics to the estimation of the time elapsed since death and found several new potential biomarkers to address this, demonstrating the applicability of proteomic analyses to forensic sciences.

Exploring Biological and Geological Age-related Changes through Variations in Intra- and Intertooth Proteomes of Ancient Dentine.

Proteomic analyses are becoming more widely used in archeology not only due to the greater preservation of proteins in ancient specimens than DNA but also because they can offer different information, particularly relating to compositional preservation and potentially a means to estimate biological and geological age. However, it remains unclear to what extent different burial environments impact these aspects of proteome decay. Teeth have to date been much less studied than bone but are ideal to explore how proteins decay with time due to the negligible turnover that occurs in dentine relative to bone. We investigated the proteome variability and deamidation levels of different sections of molar teeth from archeological bovine mandibles as well as their mandibular bone. We obtained a greater yield of proteins from the crown of the teeth but did not find differences between the different molars analyzed within each mandible. We also obtained the best variety of protein from a well-preserved mandible that was not the youngest one in terms of chronological age, showing the influence of the preservation conditions on the final proteomic outcome. Intriguingly, we also noticed an increase in abundance levels of fetuin-A in biologically younger mandibles as reported previously, but the opposite trend in tooth dentine. Interestingly, we observed higher glutamine deamidation levels in teeth from the geologically oldest mandible despite it being the biologically youngest specimen, showing that the archeological age strongly impacts on the level of deamidations observed, much more so than biological aging. This indicates that the glutamine deamidation ratio of selected peptides may act as a good predictor of the relative geochronological age of archeological specimens.

A volumetric technique for fossil body mass estimation applied to Australopithecus afarensis.

Fossil body mass estimation is a well established practice within the field of physical anthropology. Previous studies have relied upon traditional allometric approaches, in which the relationship between one/several skeletal dimensions and body mass in a range of modern taxa is used in a predictive capacity. The lack of relatively complete skeletons has thus far limited the potential application of alternative mass estimation techniques, such as volumetric reconstruction, to fossil hominins. Yet across vertebrate paleontology more broadly, novel volumetric approaches are resulting in predicted values for fossil body mass very different to those estimated by traditional allometry. Here we present a new digital reconstruction of Australopithecus afarensis (A.L. 288-1; 'Lucy') and a convex hull-based volumetric estimate of body mass. The technique relies upon identifying a predictable relationship between the 'shrink-wrapped' volume of the skeleton and known body mass in a range of modern taxa, and subsequent application to an articulated model of the fossil taxa of interest. Our calibration dataset comprises whole body computed tomography (CT) scans of 15 species of modern primate. The resulting predictive model is characterized by a high correlation coefficient (r2 = 0.988) and a percentage standard error of 20%, and performs well when applied to modern individuals of known body mass. Application of the convex hull technique to A. afarensis results in a relatively low body mass estimate of 20.4 kg (95% prediction interval 13.5-30.9 kg). A sensitivity analysis on the articulation of the chest region highlights the sensitivity of our approach to the reconstruction of the trunk, and the incomplete nature of the preserved ribcage may explain the low values for predicted body mass here. We suggest that the heaviest of previous estimates would require the thorax to be expanded to an unlikely extent, yet this can only be properly tested when more complete fossils are available.

Intra- and Interskeletal Proteome Variations in Fresh and Buried Bones.

Proteomic methods are acquiring greater importance in archaeology and palaeontology due to the longevity of proteins in skeletal remains. There are also developing interests in forensic applications, offering the potential to shed light on post-mortem intervals and age at death estimation. However, our understanding of intra- and interskeletal proteome variations is currently severely limited. Here, we evaluated the proteomes obtained from five distinct subsamples of different skeletal elements from buried pig carcasses to ascertain the extent of variation within and between individuals. We found that reproducibility of data depends on the skeletal element used for sampling and that intrabone differences exceed those observed between the same skeletal element sampled from different individuals. Interestingly, the abundance of several serum proteins appeared to correlate with biological age with relative concentrations of alpha-1 antitrypsin and chromogranin-A increasing and those of fetuin-A decreasing. We also observed a surprising level of divergence in data from different LC-MS/MS runs on aliquots of similar samples analyzed months apart, adding constraints to the comparison of results of such methods across different studies.

High-throughput collagen fingerprinting of intact microfaunal remains; a low-cost method for distinguishing between murine rodent bones.

RATIONALE: Microfaunal skeletal remains can be sensitive indicators of the contemporary ecosystem in which they are sampled and are often recovered in owl pellets in large numbers. Species identification of these remains can be obtained using a range of morphological criteria established for particular skeletal elements, but typically dominated by a reliance on cranial characters. However, this can induce biases under different environmental and taphonomic conditions. The aim of this research was to develop a high-throughput method of objectively identifying rodent remains from archaeological deposits using collagen fingerprinting, most notably the identification of rats from other myomorph rodents as a means to identify disturbances in the archaeofauna through the presence of invasive taxa not contemporary with the archaeological deposits. METHODS: Collagen was extracted from complete microfaunal skeletal remains in such a manner as to leave the bones morphologically intact (i.e., weaker concentration of acid than previously used over shorter length of time). Acid-soluble collagen was then ultrafiltered into ammonium bicarbonate and digested with trypsin prior to dilution in the MALDI matrix and acquisition of peptide mass fingerprints using a matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectrometer. RESULTS: Collagen fingerprinting was able to distinguish between Rattus, Mus, Apodemus and Micromys at the genus level; at the species level, R. rattus and R. norvegicus could be separated whereas A. flavicollis and A. sylvaticus could not. A total of 12,317 archaeological microvertebrate samples were screened for myomorph signatures but none were found to be invasive rats (Rattus) or mice (Mus). Of the contemporary murine fauna, no harvest mice (Micromys) were identified and only 24 field mouse (Apodemus) discovered. CONCLUSIONS: As a result, no evidence of recent bioturbation could be inferred from the faunal remains of these archaeological deposits. More importantly this work presents a method for high-throughput screening of specific taxa and is the first application of collagen fingerprinting to microfaunal remains of archaeological specimens.

Collagen Fingerprinting: A New Screening Technique for Radiocarbon Dating Ancient Bone.

Collagen is the dominant organic component of bone and is intimately locked within the hydroxyapatite structure of this ubiquitous biomaterial that dominates archaeological and palaeontological assemblages. Radiocarbon analysis of extracted collagen is one of the most common approaches to dating bone from late Pleistocene or Holocene deposits, but dating is relatively expensive compared to other biochemical techniques. Numerous analytical methods have previously been investigated for the purpose of screening out samples that are unlikely to yield reliable dates including histological analysis, UV-stimulated fluorescence and, most commonly, the measurement of percentage nitrogen (%N) and ratio of carbon to nitrogen (C:N). Here we propose the use of collagen fingerprinting (also known as Zooarchaeology by Mass Spectrometry, or ZooMS, when applied to species identification) as an alternative screening method for radiocarbon dating, due to its ability to provide information on collagen presence and quality, alongside species identification. The method was tested on a series of sub-fossil bone specimens from cave systems on Cayman Brac (Cayman Islands), chosen due to the observable range in diagenetic alteration, and in particular, the extent of mineralisation. Six (14)C dates, of 18 initial attempts, were obtained from remains of extinct hutia, Capromys sp. (Rodentia; Capromyidae), recovered from five distinct caves on Cayman Brac, and ranging from 393 ± 25 to 1588 ± 26 radiocarbon years before present (yr BP). All of the bone samples that yielded radiocarbon dates generated excellent collagen fingerprints, and conversely those that gave poor fingerprints also failed dating. Additionally, two successfully fingerprinted bone samples were screened out from a set of 81. Both subsequently generated (14)C dates, demonstrating successful utilisation of ZooMS as an alternative screening mechanism to identify bone samples that are suitable for 1(4)C analysis.

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle.

BACKGROUND: Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. RESULTS: Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. CONCLUSIONS: This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought.

The sexual dimorphism of the sacro-iliac joint: an investigation using geometric morphometric techniques.

The ability to correctly estimate the sex of skeletal remains is vital in forensic sciences. This article investigates the sexual dimorphism of the human sacro-iliac joint, using geometric morphometric techniques that assess morphological characters better than the traditional approaches for recording outline shapes, which are subject to quantification and inter-observer problems. Eight two-dimensional landmarks were recorded from digital images of 29 female and 35 male auricular surfaces of the ilium and sacrum. The specimens were analyzed using geometric morphometric methods (Generalized Procrustes analysis, relative warp analysis, Goodall's F) and multivariate statistics (ANOVA, MANCOVA, principal component analysis, discriminant function analysis [DFA]). Both the size and shape of the analyzed structures were found to be sexually dimorphic. The DFA illustrated that when the form of both the iliac and sacral articular surface is taken as a predictor variable, 94.5% of the individuals are assigned to the correct sex. The successful sex determination obtained by the DFA makes the further study of the sacro-iliac joint's sexual dimorphism promising.

The study of anatomy in England from 1700 to the early 20th century.

The study of anatomy in England during the 18th and 19th century has become infamous for bodysnatching from graveyards to provide a sufficient supply of cadavers. However, recent discoveries have improved our understanding of how and why anatomy was studied during the enlightenment, and allow us to see the context in which dissection of the human body took place. Excavations of infirmary burial grounds and medical school cemeteries, study of hospital archives, and analysis of the content of surviving anatomical collections in medical museums enables us to re-evaluate the field from a fresh perspective. The pathway from a death in poverty, sale of the corpse to body dealer, dissection by anatomist or medical student, and either the disposal and burial of the remains or preservation of teaching specimens that survive today in medical museums is a complex and fascinating one.

A methodological investigation of hominoid craniodental morphology and phylogenetics.

The evolutionary relationships of extant great apes and humans have been largely resolved by molecular studies, yet morphology-based phylogenetic analyses continue to provide conflicting results. In order to further investigate this discrepancy we present bootstrap clade support of morphological data based on two quantitative datasets, one dataset consisting of linear measurements of the whole skull from 5 hominoid genera and the second dataset consisting of 3D landmark data from the temporal bone of 5 hominoid genera, including 11 sub-species. Using similar protocols for both datasets, we were able to 1) compare distance-based phylogenetic methods to cladistic parsimony of quantitative data converted into discrete character states, 2) vary outgroup choice to observe its effect on phylogenetic inference, and 3) analyse male and female data separately to observe the effect of sexual dimorphism on phylogenies. Phylogenetic analysis was sensitive to methodological decisions, particularly outgroup selection, where designation of Pongo as an outgroup and removal of Hylobates resulted in greater congruence with the proposed molecular phylogeny. The performance of distance-based methods also justifies their use in phylogenetic analysis of morphological data. It is clear from our analyses that hominoid phylogenetics ought not to be used as an example of conflict between the morphological and molecular, but as an example of how outgroup and methodological choices can affect the outcome of phylogenetic analysis.

A demographic analysis of Maiden Castle hillfort: Evidence for conflict in the late Iron Age and early Roman period.

The late Iron Age human remains from the British hillfort of Maiden Castle are frequently cited within the archaeological and bioarchaeological literature as providing evidence for conflict. This interpretation is based on osteological work undertaken in the late 1930s. In order to test the validity of using this sample in conflict research, the authors undertook a detailed analysis of the site's demography in comparison with contemporary late Iron Age attritional cemeteries from Dorset (England) and additional conflict mortality data. These results showed that the 1st century BC to 1st century AD samples conformed to a catastrophic profile, as greater numbers of young adult males had been buried during this phase of occupation. In combination with new bioarchaeological findings and the identification of an embedded Roman projectile weapon, we conclude that individuals had died during an episode of warfare, one of which probably included the Roman conquest of 43AD.

A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius).

BACKGROUND: The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius) has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs) from an archaeologically-verified and exceptionally-well preserved aurochs bone sample. METHODOLOGY: DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738+/-68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer). In total, 289.9 megabases (22.48%) of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences. CONCLUSIONS: For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously identified aurochsen haplogroup (haplogroup P), thus providing novel insights into pre-domestic patterns of variation. The high proportion of authentic, endogenous aurochs DNA preserved in this sample bodes well for future efforts to determine the complete genome sequence of a wild ancestor of domestic cattle.

Gene-culture coevolution between cattle milk protein genes and human lactase genes.

Milk from domestic cows has been a valuable food source for over 8,000 years, especially in lactose-tolerant human societies that exploit dairy breeds. We studied geographic patterns of variation in genes encoding the six most important milk proteins in 70 native European cattle breeds. We found substantial geographic coincidence between high diversity in cattle milk genes, locations of the European Neolithic cattle farming sites (>5,000 years ago) and present-day lactose tolerance in Europeans. This suggests a gene-culture coevolution between cattle and humans.

The thermal history of human fossils and the likelihood of successful DNA amplification.

Recent success in the amplification of ancient DNA (aDNA) from fossil humans has led to calls for further tests to be carried out on similar material. However, there has been little systematic research on the survival of DNA in the fossil record, even though the environment of the fossil is known to be of paramount importance for the survival of biomolecules over archaeological and geological timescales. A better understanding of aDNA survival would enable research to focus on material with greater chances of successful amplification, thus preventing the unnecessary loss of material and valuable researcher time. We argue that the thermal history of a fossil is a key parameter for the survival of biomolecules. The thermal history of a number of northwest European Neanderthal cave sites is reconstructed here and they are ranked in terms of the relative likelihood of aDNA survival at the sites, under the assumption that DNA depurination is the principal mechanism of degradation. The claims of aDNA amplification from material found at Lake Mungo, Australia, are also considered in the light of the thermal history of this site.