The Neanderthal meal: a new perspective using faecal biomarkers

The time between Palaeolithic hearths

Resolving the timescale of human activity in the Palaeolithic Age is one of the most challenging problems in prehistoric archaeology. The duration and frequency of hunter-gatherer camps reflect key aspects of social life and human-environment interactions. However, the time dimension of Palaeolithic contexts is generally inaccurately reconstructed because of the limitations of dating techniques1, the impact of disturbing agents on sedimentary deposits2 and the palimpsest effect3,4. Here we report high-resolution time differences between six Middle Palaeolithic hearths from El Salt Unit X (Spain) obtained through archaeomagnetic and archaeostratigraphic analyses. The set of hearths covers at least around 200-240 years with 99% probability, having decade- and century-long intervals between the different hearths. Our results provide a quantitative estimate of the time framework for the human occupation events included in the studied sequence. This is a step forward in Palaeolithic archaeology, a discipline in which human behaviour is usually approached from a temporal scale typical of geological processes, whereas significant change may happen at the smaller scales of human generations. Here we reach a timescale close to a human lifespan.

Fecal biomarkers and micromorphological indicators of sheep penning and flooring at La Fortaleza pre-Hispanic site (Gran Canaria, Canary Islands)

This study explores the lipid content and micromorphological features of sediment samples from two dwelling structures at the pre-Hispanic site of La Fortaleza in Santa Lucía de Tirajana (Gran Canaria, Spain). Previous field identification of possible sedimentary excrements inside the dwellings motivated chromatographic fecal biomarker analysis and micromorphology. The micromorphological samples reveal a complex dung-rich stratified sequence involving different layers of mixed composition, including reworked dung, clay, wood ash, and domestic refuse. The results of the lipid analysis corroborate the fecal nature of the sample and indicate the source animal: sheep. Coupled with the field evidence, the data suggest that the deposit is anthropogenic and represents a sequence of floor foundations, dung floors, and domestic and architectural refuse. This study provides valuable taxonomic and site use data for the understanding of the aboriginal societies of the Canary Islands and shows the efficacy of combining field observations with high-resolution geoarchaeological methods.

The Effects of the Paleo Diet on Autoimmune Thyroid Disease: A Mixed Methods Review

The aim of this systematic review was to examine the characteristics of Paleolithic diet (PD) interventions designed for adult patients with autoimmune thyroid disease (AITD) in order to determine if diet elements have the potential to successfully reduce thyroid antibodies (Ab) such as thyroglobulin (Tg), thyroid peroxidase (TPO), and thyroid stimulating hormone receptor (TSHR), and improve thyroid hormones (thyroxine (T4), triiodothyronine (T3) and thyroid stimulating hormone (TSH)) or resolve AITD pathogenesis. Randomized controlled trials (RCTs) with an adult population of 18 years and older, diagnosed with Hashimoto's thyroiditis (HT) or Graves' disease (GD) (Basedow's), who were placed on a diet of Paleolithic or ancestral nature, and achieved reduction of AITD Abs, improvement of thyroid hormones, and, or resolution of AITD were searched. Various electronic databases were used. Bias was assessed using critical appraisal tools from the Scottish Intercollegiate Guidelines Network (SIGN) and Joanna Briggs Institute (JBI). Studies were excluded according to exclusion criteria and results analyzed. One randomized controlled trial (RCT), a pilot study, and six case studies were found. In total, eight AITD studies focusing on Paleolithic or ancestral interventions were located. In highlight, females were the predominant gender. Case studies solely focused on AITD with protocols ranging from 8-60 weeks. All studies showed clinical improvements, one had significant improvement, two showed AITD resolution. After structured evaluation of nutritional interventions utilizing the PD on the effects of AITD, it was concluded foods of ancestral nature along with the addition of specific supplements, food components, exercise and mindfulness meditation, and exclusion of modern day foods have a considerable impact on thyroid Ab and hormones. The relevant studies suggest while this dietary protocol can be useful in clinical practice, larger-scale studies need to be conducted. Key teaching pointsThere are currently no dietary interventions recommended for the treatment of autoimmune thyroid disease. The Paleo diet has been documented to improve AITD antibodies and thyroid hormones in both Hashimoto's thyroiditis and Graves' disease.The Paleo diet can provide a natural source of nutrients similar to supplemental nutrients that have shown positive results on AITD.The paleo diet provides specific macronutrient percentages that may be beneficial in reducing AITD antibodies, while improving thyroid hormones.Methylation supplementation may be useful in AITD cases.

Possible Causes of Hypertrophic Osteoarthropathy in the La Ferrassie 1 Neanderthal

For over a century, researchers have been perplexed by the unique osteological findings on La Ferrassie 1 (LF1), one of the most complete Neanderthal remains ever found. In 1997, Fennel and Trinkaus proposed that LF1 suffered from hypertrophic osteoarthropathy (HOA), likely secondary to chronic thoracic infection or pulmonary malignancy. This disease process can have many etiologies, and no study has fully explored the possible origin of LF1's HOA. Ultimately, it is most likely that LF1's HOA etiology arose from one of the many infectious diseases that prehistoric Neanderthals were exposed to, specifically a chronic pulmonary RNA virus.

Synanthropic Flies-A Review Including How They Obtain Nutrients, along with Pathogens, Store Them in the Crop and Mechanisms of Transmission

An attempt has been made to provide a broad review of synanthropic flies and, not just a survey of their involvement in human pathogen transmission. It also emphasizes that the crop organ of calliphorids, sarcophagids, and muscids was an evolutionary development and has served and assisted non-blood feeding flies in obtaining food, as well as pathogens, prior to the origin of humans. Insects are believed to be present on earth about 400 million years ago (MYA). Thus, prior to the origin of primates, there was adequate time for these flies to become associated with various animals and to serve as important transmitters of pathogens associated with them prior to the advent of early hominids and modern humans. Through the process of fly crop regurgitation, numerous pathogens are still readily being made available to primates and other animals. Several studies using invertebrate-derived DNA = iDNA meta-techniques have been able to identify, not only the source the fly had fed on, but also if it had fed on their feces or the animal's body fluids. Since these flies are known to feed on both vertebrate fluids (i.e., from wounds, saliva, mucus, or tears), as well as those of other animals, and their feces, identification of the reservoir host, amplification hosts, and associated pathogens is essential in identifying emerging infectious diseases. New molecular tools, along with a focus on the crop, and what is in it, should provide a better understanding and development of whether these flies are involved in emerging infectious diseases. If so, epidemiological models in the future might be better at predicting future epidemics or pandemics.

The Technological Advance and Application of Coprolite Analysis

Coprolites (mummified or fossilized feces), belonging to the group of ichnofossils, are fossilized remains of feces produced by animals. Various types of data from coprolites provide detailed evidence of the producer’s condition, like diet, intestinal microbiome, virus infection and parasites diseases. In addition, the palaeoenvironment information relevant to producers’ ecological niche can be drawn from taphonomy details the coprolites mirrored. At present, the phylogenetic clues of the producer’s population can be determined by advanced molecular biotechnologies. With the integration of multiple methods and techniques, coprolite has been widely accepted as an ideal material to study the diet, evolution, and palaeoenvironment of producers. In this paper, we reviewed the history of coprolite research, enumerated and interpreted the data recovered from coprolites, and explained their research value to palaeocoprology and evolutionary biology. Finally, we summarized the current directions of coprolite research and looked into its future prospects.

Reconstructing Neanderthal diet: The case for carbohydrates

Evidence for plants rarely survives on Paleolithic sites, while animal bones and biomolecular analyses suggest animal produce was important to hominin populations, leading to the perspective that Neanderthals had a very-high-protein diet. But although individual and short-term survival is possible on a relatively low-carbohydrate diet, populations are unlikely to have thrived and reproduced without plants and the carbohydrates they provide. Today, nutritional guidelines recommend that around half the diet should be carbohydrate, while low intake is considered to compromise physical performance and successful reproduction. This is likely to have been the same for Paleolithic populations, highlighting an anomaly in that the basic physiological recommendations do not match the extensive archaeological evidence. Neanderthals had large, energy-expensive brains and led physically active lifestyles, suggesting that for optimal health they would have required high amounts of carbohydrates. To address this anomaly, we begin by outlining the essential role of carbohydrates in the human reproduction cycle and the brain and the effects on physical performance. We then evaluate the evidence for resource availability and the archaeological evidence for Neanderthal diet and investigate three ways that the anomaly between the archaeological evidence and the hypothetical dietary requirements might be explained. First, Neanderthals may have had an as yet unidentified genetic adaptation to an alternative physiological method to spare blood glucose and glycogen reserves for essential purposes. Second, they may have existed on a less-than-optimum diet and survived rather than thrived. Third, the methods used in dietary reconstruction could mask a complex combination of dietary plant and animal proportions. We end by proposing that analyses of Paleolithic diet and subsistence strategies need to be grounded in the minimum recommendations throughout the life course and that this provides a context for interpretation of the archaeological evidence from the behavioral and environmental perspectives.

Paleogenomics of the prehistory of Europe: human migrations, domestication and disease

A substantial portion of ancient DNA research has been centred on understanding European populations' origin and evolution. A rchaeological evidence has already shown that the peopling of Europe involved an intricate pattern of demic and/or cultural diffusion since the Upper Palaeolithic, which became more evident during the Neolithic and Bronze Age periods. However, ancient DNA data has been crucial in determining if cultural changes occurred due to the movement of ideas or people. With the advent of next-generation sequencing and population-based paleogenomic research, ancient DNA studies have been directed not only at the study of continental human migrations, but also to the detailed analysis of particular archaeological sites, the processes of domestication, or the spread of disease during prehistoric times. With this vast paleogenomic effort added to a proper archaeological contextualisation of results, a deeper understanding of Europe's peopling is starting to emanate.

Prey Size Decline as a Unifying Ecological Selecting Agent in Pleistocene Human Evolution

We hypothesize that megafauna extinctions throughout the Pleistocene, that led to a progressive decline in large prey availability, were a primary selecting agent in key evolutionary and cultural changes in human prehistory. The Pleistocene human past is characterized by a series of transformations that include the evolution of new physiological traits and the adoption, assimilation, and replacement of cultural and behavioral patterns. Some changes, such as brain expansion, use of fire, developments in stone-tool technologies, or the scale of resource intensification, were uncharacteristically progressive. We previously hypothesized that humans specialized in acquiring large prey because of their higher foraging efficiency, high biomass density, higher fat content, and the use of less complex tools for their acquisition. Here, we argue that the need to mitigate the additional energetic cost of acquiring progressively smaller prey may have been an ecological selecting agent in fundamental adaptive modes demonstrated in the Paleolithic archaeological record. We describe several potential associations between prey size decline and specific evolutionary and cultural changes that might have been driven by the need to adapt to increased energetic demands while hunting and processing smaller and smaller game.

Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt

A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.

Micro-contextual identification of archaeological lipid biomarkers using resin-impregnated sediment slabs

Characterizing organic matter preserved in archaeological sediment is crucial to behavioral and paleoenvironmental investigations. This task becomes particularly challenging when considering microstratigraphic complexity. Most of the current analytical methods rely on loose sediment samples lacking spatial and temporal resolution at a microstratigraphic scale, adding uncertainty to the results. Here, we explore the potential of targeted molecular and isotopic biomarker analysis on polyester resin-impregnated sediment slabs from archaeological micromorphology, a technique that provides microstratigraphic control. We performed gas chromatography-mass spectrometry (GC-MS) and gas chromatography-isotope ratio mass spectromety (GC-IRMS) analyses on a set of samples including drill dust from resin-impregnated experimental and archaeological samples, loose samples from the same locations and resin control samples to assess the degree of interference of polyester resin in the GC-MS and Carbon-IRMS signals of different lipid fractions (n-alkanes, aromatics, n-ketones, alcohols, fatty acids and other high polarity lipids). The results show that biomarkers within the n-alkane, aromatic, n-ketone, and alcohol fractions can be identified. Further work is needed to expand the range of identifiable lipid biomarkers. This study represents the first micro-contextual approach to archaeological lipid biomarkers and contributes to the advance of archaeological science by adding a new method to obtain behavioral or paleoenvironmental proxies.

Female hunters of the early Americas

Sexual division of labor with females as gatherers and males as hunters is a major empirical regularity of hunter-gatherer ethnography, suggesting an ancestral behavioral pattern. We present an archeological discovery and meta-analysis that challenge the man-the-hunter hypothesis. Excavations at the Andean highland site of Wilamaya Patjxa reveal a 9000-year-old human burial (WMP6) associated with a hunting toolkit of stone projectile points and animal processing tools. Osteological, proteomic, and isotopic analyses indicate that this early hunter was a young adult female who subsisted on terrestrial plants and animals. Analysis of Late Pleistocene and Early Holocene burial practices throughout the Americas situate WMP6 as the earliest and most secure hunter burial in a sample that includes 10 other females in statistical parity with early male hunter burials. The findings are consistent with nongendered labor practices in which early hunter-gatherer females were big-game hunters.

Dietary Energy Partition: The Central Role of Glucose

Humans have developed effective survival mechanisms under conditions of nutrient (and energy) scarcity. Nevertheless, today, most humans face a quite different situation: excess of nutrients, especially those high in amino-nitrogen and energy (largely fat). The lack of mechanisms to prevent energy overload and the effective persistence of the mechanisms hoarding key nutrients such as amino acids has resulted in deep disorders of substrate handling. There is too often a massive untreatable accumulation of body fat in the presence of severe metabolic disorders of energy utilization and disposal, which become chronic and go much beyond the most obvious problems: diabetes, circulatory, renal and nervous disorders included loosely within the metabolic syndrome. We lack basic knowledge on diet nutrient dynamics at the tissue-cell metabolism level, and this adds to widely used medical procedures lacking sufficient scientific support, with limited or nil success. In the present longitudinal analysis of the fate of dietary nutrients, we have focused on glucose as an example of a largely unknown entity. Even most studies on hyper-energetic diets or their later consequences tend to ignore the critical role of carbohydrate (and nitrogen disposal) as (probably) the two main factors affecting the substrate partition and metabolism.

CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts.

Molecular Mechanism of Functional Ingredients in Barley to Combat Human Chronic Diseases

Barley plays an important role in health and civilization of human migration from Africa to Asia, later to Eurasia. We demonstrated the systematic mechanism of functional ingredients in barley to combat chronic diseases, based on PubMed, CNKI, and ISI Web of Science databases from 2004 to 2020. Barley and its extracts are rich in 30 ingredients to combat more than 20 chronic diseases, which include the 14 similar and 9 different chronic diseases between grains and grass, due to the major molecular mechanism of six functional ingredients of barley grass (GABA, flavonoids, SOD, K-Ca, vitamins, and tryptophan) and grains (β-glucans, polyphenols, arabinoxylan, phytosterols, tocols, and resistant starch). The antioxidant activity of barley grass and grain has the same and different functional components. These results support findings that barley grain and its grass are the best functional food, promoting ancient Babylonian and Egyptian civilizations, and further show the depending functional ingredients for diet from Pliocene hominids in Africa and Neanderthals in Europe to modern humans in the world. This review paper not only reveals the formation and action mechanism of barley diet overcoming human chronic diseases, but also provides scientific basis for the development of health products and drugs for the prevention and treatment of human chronic diseases.

The Wonderful World of Poo: The Turdome and Beyond

Defecate: it is something we all do, it is something we joke about, yet for many in real life it is a subject that is taboo. However, it is now being realised that faeces are a veritable scientific goldmine, have many potential uses, and may even save your life! In this article I will review the history behind the use of faecal material and look at some of its emerging playing fields, in particular its role in medical diagnosis. I will discuss faecal proteomics and other omics technologies (Proteogenomics: The Omics Pipeline), including studies on the microbiome, in order to understand, diagnose, and treat gastrointestinal tract pathologies and other diseases, and show how these technologies will play a role in the move towards personalized medicine.

THE EXPOSOME IN HUMAN EVOLUTION: FROM DUST TO DIESEL

Global exposures to air pollution and cigarette smoke are novel in human evolutionary history and are associated with about 16 million premature deaths per year. We investigate the history of the human exposome for relationships between novel environmental toxins and genetic changes during human evolution in six phases. Phase I: With increased walking on savannas, early human ancestors inhaled crustal dust, fecal aerosols, and spores; carrion scavenging introduced new infectious pathogens. Phase II: Domestic fire exposed early Homo to novel toxins from smoke and cooking. Phases III and IV: Neolithic to preindustrial Homo sapiens incurred infectious pathogens from domestic animals and dense communities with limited sanitation. Phase V: Industrialization introduced novel toxins from fossil fuels, industrial chemicals, and tobacco at the same time infectious pathogens were diminishing. Thereby, pathogen-driven causes of mortality were replaced by chronic diseases driven by sterile inflammogens, exogenous and endogenous. Phase VI: Considers future health during global warming with increased air pollution and infections. We hypothesize that adaptation to some ancient toxins persists in genetic variations associated with inflammation and longevity.

Hominin and animal activities in the microstratigraphic record from Denisova Cave (Altai Mountains, Russia)

Denisova Cave in southern Siberia uniquely contains evidence of occupation by a recently discovered group of archaic hominins, the Denisovans, starting from the middle of the Middle Pleistocene. Artefacts, ancient DNA and a range of animal and plant remains have been recovered from the sedimentary deposits, along with a few fragmentary fossils of Denisovans, Neanderthals and a first-generation Neanderthal–Denisovan offspring. The deposits also contain microscopic traces of hominin and animal activities that can provide insights into the use of the cave over the last 300,000 years. Here we report the results of a micromorphological study of intact sediment blocks collected from the Pleistocene deposits in the Main and East Chambers of Denisova Cave. The presence of charcoal attests to the use of fire by hominins, but other evidence of their activities preserved in the microstratigraphic record are few. The ubiquitous occurrence of coprolites, which we attribute primarily to hyenas, indicates that the site was visited for much of its depositional history by cave-dwelling carnivores. Microscopic traces of post-depositional diagenesis, bioturbation and incipient cryoturbation are observed in only a few regions of the deposit examined here. Micromorphology can help identify areas of sedimentary deposit that are most conducive to ancient DNA preservation and could be usefully integrated with DNA analyses of sediments at archaeological sites to illuminate features of their human and environmental history that are invisible to the naked eye.

Insights into the timing, intensity and natural setting of Neanderthal occupation from the geoarchaeological study of combustion structures: A micromorphological and biomarker investigation of El Salt, unit Xb, Alcoy, Spain

Middle Paleolithic lithic and faunal assemblages throughout Eurasia reflect short-term Neanderthal occupations, which suggest high group mobility. However, the timing of these short-term occupations, a key factor to assess group mobility and territorial range, remains unresolved. Anthropogenic combustion structures are prominent in the Middle Paleolithic record and conceal information on the timing and intensity and natural setting of their associated human occupations. This paper examines a concentration of eleven combustion structures from unit Xb of El Salt, a Middle Paleolithic site in Spain through a geoarchaeological approach, in search of temporal, human impact and paleoenvironmental indicators to assess the timing, intensity and natural setting of the associated human occupations. The study was conducted using micromorphology, lipid biomarker analysis and compound specific isotope analysis. Results show in situ hearths built on different diachronic topsoils rich in herbivore excrements and angiosperm plant residues with rare anthropogenic remains. These data are suggestive of low impact, short-term human occupations separated by relatively long periods of time, with possible indicators of seasonality. Results also show an absence of conifer biomarkers in the mentioned topsoils and presence of conifer charcoal among the fuel residues (ash), indicating that fire wood was brought to the site from elsewhere. A microscopic and molecular approach in the study of combustion structures allows us to narrow down the timescale of archaeological analysis and contributes valuable information towards an understanding of Neanderthal group mobility and settlement patterns.

Modeling the role of fire and cooking in the competitive exclusion of Neanderthals

The Neanderthal body was more robust and energetically costly than the bodies of anatomically modern humans (AMH). Different metabolic budgets between competing populations of Neanderthals and AMH may have been a factor in the varied ranges of behavior and timelines for Neanderthal extinction that we see in the Paleolithic archaeological record. This paper uses an adaptation of the Lotka-Volterra model to determine whether metabolic differences alone could have accounted for Neanderthal extinction. In addition, we use a modeling approach to investigate Neanderthal fire use, evidence for which is much debated and is variable throughout different climatic phases of the Middle Paleolithic. The increased caloric yield from a cooked versus a raw diet may have played an important role in population competition between Neanderthals and AMH. We arrive at two key conclusions. First, given differences in metabolic budget between Neanderthals and AMH and their dependence on similar or overlapping food resources, Neanderthal extinction is likely inevitable over the long term. Second, the rate of Neanderthal extinction increases as the frequency of AMH fire use increases. Results highlight the importance of understanding the variable behaviors at play on a regional scale in order to understand global Neanderthal extinction. We also emphasize the importance of understanding the role of fire use in the Middle to Upper Paleolithic transition.

First data of Neandertal bird and carnivore exploitation in the Cantabrian Region (Axlor; Barandiaran excavations; Dima, Biscay, Northern Iberian Peninsula)

Neandertals were top predators who basically relied on middle- to large-sized ungulates for dietary purposes, but there is growing evidence that supports their consumption of plants, leporids, tortoises, marine resources, carnivores and birds. The Iberian Peninsula has provided the most abundant record of bird exploitation for meat in Europe, starting in the Middle Pleistocene. However, the bird and carnivore exploitation record was hitherto limited to the Mediterranean area of the Iberian Peninsula. Here we present the first evidence of bird and carnivore exploitation by Neandertals in the Cantabrian region. We have found cut-marks in two golden eagles, one raven, one wolf and one lynx remain from the Mousterian levels of Axlor. The obtaining of meat was likely the primary purpose of the cut-marks on the golden eagle and lynx remains. Corvids, raptors, felids and canids in Axlor could have likely acted as commensals of the Neandertals, scavenging upon the carcasses left behind by these hunter-gatherers. This could have brought them closer to Neandertal groups who could have preyed upon them. These new results provide additional information on their dietary scope and indicate a more complex interaction between Neandertals and their environment.

A Middle Palaeolithic wooden digging stick from Aranbaltza III, Spain

Aranbaltza is an archaeological complex formed by at least three open-air sites. Between 2014 and 2015 a test excavation carried out in Aranbaltza III revealed the presence of a sand and clay sedimentary sequence formed in floodplain environments, within which six sedimentary units have been identified. This sequence was formed between 137-50 ka, and includes several archaeological horizons, attesting to the long-term presence of Neanderthal communities in this area. One of these horizons, corresponding with Unit 4, yielded two wooden tools. One of these tools is a beveled pointed tool that was shaped through a complex operational sequence involving branch shaping, bark peeling, twig removal, shaping, polishing, thermal exposition and chopping. A use-wear analysis of the tool shows it to have traces related with digging soil so it has been interpreted as representing a digging stick. This is the first time such a tool has been identified in a European Late Middle Palaeolithic context; it also represents one of the first well-preserved Middle Palaeolithic wooden tool found in southern Europe. This artefact represents one of the few examples available of wooden tool preservation for the European Palaeolithic, allowing us to further explore the role wooden technologies played in Neanderthal communities.

Characterization of ancient lipids in prehistoric organic residues: Chemical evidence of livestock-pens in rock-shelters since early neolithic to bronze age

The characterization of ancient lipids from prehistoric sediments (fumiers) located in a rock-selter has been possible after the optimization of an analytical method based on the microwave-assisted extraction and solid-phase extraction clean-up step and a final derivatization step followed by gas chromatography with mass spectrometry. Eight sterols and two bile acids were detected just in the partially burned and unburned layers of the fumiers (animal organic residues deriving from manure/dung). The relationship between some of these compounds can be used to distinguish the biogenic origin of the samples, concluding that these strata (from Early Neolithic to Late Chalcolithic/Early Bronze Age) can be classified as ruminant residues. Three main periods of activity are observed over a period of 2000 years: one from 3990 ± 40 before present (4530-4410 calibrated before present) to 4100 ± 40 before present (4820-4750/4730-4510/4470-4450 calibrated before present), the second from 4470 ± 40 before present (5300-4970 calibrated before present) to 5490 ± 30 before present (6310-6275/6230-6220 calibrated before present) and the third from 5880 ± 30 before present (6775-6765/6750-6645 calibrated before present) to 6010 ± 30 before present (6940-6780/6765-6755 calibrated before present). Chemical data obtained are in concordance with the previous results obtained in the area.

Evidence for the Paleoethnobotany of the Neanderthal: A Review of the Literature

Our perception of our closest human relatives, the Neanderthals, has evolved in the last few decades from brutish ape-men to intelligent archaic human peoples. Our understanding and appreciation of their cultural sophistication has only recently extended to their diet. Only within the last few years, with new techniques and a shift in focus, have we begun to truly investigate and understand the role of plants in their diet and culture. The more we learn about Neanderthals, the more we realize that biological and cultural distinctions between them and us were relatively small. Given that we coexisted and likely interacted with them for thousands of years, the more we learn about them, the better we may understand our own past. In that light, we review the current evidence, derived from such sources as plant remains (e.g., starch, pollen, phytoliths, and seeds) in soil and dental calculus, dental and tool wear, coprolites, and genetics, for Neanderthal's nutritional, medicinal, and ritual use of plants, which includes 61 different taxa from 26 different plant families found at 17 different archaeological sites. Further, we updated and standardized botanical nomenclature from many sources published over many decades to provide a more stable foundation for future work.

Human Coprolites as a Source for Paleomicrobiology

The paleomicrobiology of coprolites, which are fossilized fecal materials, has already yielded data about various organisms, including micro-eukaryotes, bacteria, and archaea, thus expanding our comprehension of ancient human dietary habits, gut microbiota, and intestinal and systemic infections. This mini-review briefly describes previous works and summarizes the main techniques used in handling coprolites and the findings obtained about ancient gut microbiota. Past intestinal and systemic infections are outlined.

Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology

Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.

Retroviral DNA Sequences as a Means for Determining Ancient Diets

For ages, specialists from varying fields have studied the diets of the primeval inhabitants of our planet, detecting diet remains in archaeological specimens using a range of morphological and biochemical methods. As of recent, metagenomic ancient DNA studies have allowed for the comparison of the fecal and gut microbiomes associated to archaeological specimens from various regions of the world; however the complex dynamics represented in those microbial communities still remain unclear. Theoretically, similar to eukaryote DNA the presence of genes from key microbes or enzymes, as well as the presence of DNA from viruses specific to key organisms, may suggest the ingestion of specific diet components. In this study we demonstrate that ancient virus DNA obtained from coprolites also provides information reconstructing the host’s diet, as inferred from sequences obtained from pre-Columbian coprolites. This depicts a novel and reliable approach to determine new components as well as validate the previously suggested diets of extinct cultures and animals. Furthermore, to our knowledge this represents the first description of the eukaryotic viral diversity found in paleofaeces belonging to pre-Columbian cultures.

Paleoenvironment and possibilities of plant exploitation in the Middle Pleistocene of Schöningen (Germany). Insights from botanical macro-remains and pollen

Plant use is an elusive issue in Paleolithic archaeology. Due to poor organic preservation in many sites, botanical material is not always present. The sediments in Schöningen, however, contain abundant botanical macro-remains like wood, fruits, seeds, and other parts of plants which offer the opportunity to reconstruct the local vegetation. Combined with palynological results, it is possible to reveal the full potential of this environment to hominins. Ethnobotanical studies of hunter-gatherer societies living in similar environments illustrate the importance of plants for subsistence purposes. The identified taxa from the archaeological horizons at Schöningen include a broad spectrum of potentially exploitable species that could be sources of food, raw material, and firewood.

New Insights into the Evolution of the Human Diet from Faecal Biomarker Analysis in Wild Chimpanzee and Gorilla Faeces

Our understanding of early human diets is based on reconstructed biomechanics of hominin jaws, bone and teeth isotopic data, tooth wear patterns, lithic, taphonomic and zooarchaeological data, which do not provide information about the relative amounts of different types of foods that contributed most to early human diets. Faecal biomarkers are proving to be a valuable tool in identifying relative proportions of plant and animal tissues in Palaeolithic diets. A limiting factor in the application of the faecal biomarker approach is the striking absence of data related to the occurrence of faecal biomarkers in non-human primate faeces. In this study we explored the nature and proportions of sterols and stanols excreted by our closest living relatives. This investigation reports the first faecal biomarker data for wild chimpanzee (Pan troglodytes) and mountain gorilla (Gorilla beringei). Our results suggest that the chemometric analysis of faecal biomarkers is a useful tool for distinguishing between NHP and human faecal matter, and hence, it could provide information for palaeodietary research and early human diets.

Ancient human microbiomes

Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.

Neanderthal megafaunal exploitation in Western Europe and its dietary implications: a contextual reassessment of La Cotte de St Brelade (Jersey)

The recurrent presence at Middle Palaeolithic sites of megafaunal remains, such as mammoth, elephant and rhinoceros, together with isotope analyses signalling meat as a prominent protein source, have been used to argue that these species played a central role in Neanderthal diet. Key to this model are the bone heap horizons from La Cotte de St Brelade (Jersey), which were previously interpreted as game drive debris resulting from systematic Neanderthal hunting. However, this hypothesis has never been rigorously tested, neither at a site-scale, incorporating taphonomic and contextual data, nor at a wider European scale. First, this paper provides a contextual reassessment of the faunal remains from La Cotte to fully understand Neanderthal behaviour at the site. Second, a comparative database of 30 well-published Middle Palaeolithic sites with megafauna permits a data-driven, broader spatial (European) and diachronic assessment of the role of megafauna in Neanderthal subsistence behaviour. Results suggest initial Neanderthal occupation at La Cotte was intensive although through time site visits became more infrequent, as highlighted by a reduction in cultural debris concurrent with a rise in carnivore presence. While mammoths, just as other large mammals and occasionally carnivores, were clearly butchered at this locality, their acquisition and role in Neanderthal diet remains ambiguous. Broader comparisons across Western Europe indicate a main focus on a range of large herbivores, with only a minor, opportunistic, role for megafauna. Whilst stable isotope analysis suggests that Neanderthal diet was meat-oriented, zooarchaeological data do not support the inference that megafauna were the major contributor of meat.

From lifetime to evolution: timescales of human gut microbiota adaptation

Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota (GM) is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The GM continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily variations in diet or specific host physiological and immunological needs at different ages. On the other hand, the microbiota plasticity was strategic to face changes in lifestyle and dietary habits along the course of the recent evolutionary history, that has driven the passage from Paleolithic hunter-gathering societies to Neolithic agricultural farmers to modern Westernized societies.