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We here present CLUES2, a full-likelihood method to infer natural selection from sequence data that is an extension of the method CLUES. We make several substantial improvements to the CLUES method that greatly increases both its applicability and its speed. We add the ability to use ancestral recombination graphs on ancient data as emissions to the underlying hidden Markov model, which enables CLUES2 to use both temporal and linkage information to make estimates of selection coefficients. We also fully implement the ability to estimate distinct selection coefficients in different epochs, which allows for the analysis of changes in selective pressures through time, as well as selection with dominance. In addition, we greatly increase the computational efficiency of CLUES2 over CLUES using several approximations to the forward-backward algorithms and develop a new way to reconstruct historic allele frequencies by integrating over the uncertainty in the estimation of the selection coefficients. We illustrate the accuracy of CLUES2 through extensive simulations and validate the importance sampling framework for integrating over the uncertainty in the inference of gene trees. We also show that CLUES2 is well-calibrated by showing that under the null hypothesis, the distribution of log-likelihood ratios follows a χ2 distribution with the appropriate degrees of freedom. We run CLUES2 on a set of recently published ancient human data from Western Eurasia and test for evidence of changing selection coefficients through time. We find significant evidence of changing selective pressures in several genes correlated with the introduction of agriculture to Europe and the ensuing dietary and demographic shifts of that time. In particular, our analysis supports previous hypotheses of strong selection on lactase persistence during periods of ancient famines and attenuated selection in more modern periods.

Fossils of large animals have long influenced social practices and ideologies in human societies, including the fantastic myths of giants, heroes, and gods in ancient Greece. It has been estimated that purposeful fossil collecting in Greece began in the Late Bronze Age. However, previous archaeological finds of fossils from mainland Greece were not well documented in secure contexts that dated this far back in time. Herein, we present a newly recognized fossilized astragalus bone recently found in the legacy collections of the archaeological site of Mycenae. It was originally recovered by excavations in the 1970s and recently reanalyzed at the Mycenae Museum. Our analysis explored the available evidence of the find location, the state of fossil preservation, and the species represented. The results suggest that a fossilized rhinoceros (Stephanorhinus) astragalus was collected in the past, possibly from afar. Evidence indicates it was brought to Mycenae, where it was deposited near an interesting array of artifacts in a basement storage area of the Southwest Quarter, sometime in the thirteenth century BCE. This find represents the earliest secure evidence of large animal fossil use by people in mainland Greece, dating to the Late Bronze Age.

MOTIVATION: The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths. RESULTS: For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings. AVAILABILITY AND IMPLEMENTATION: AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts).

Ancient environmental DNA (aeDNA) from lake sediments has yielded remarkable insights for the reconstruction of past ecosystems, including suggestions of late survival of extinct species. However, translocation and lateral inflow of DNA in sediments can potentially distort the stratigraphic signal of the DNA. Using three different approaches on two short lake sediment cores of the Yamal peninsula, West Siberia, with ages spanning only the past hundreds of years, we detect DNA and identified mitochondrial genomes of multiple mammoth and woolly rhinoceros individuals-both species that have been extinct for thousands of years on the mainland. The occurrence of clearly identifiable aeDNA of extinct Pleistocene megafauna (e.g. >400 K reads in one core) throughout these two short subsurface cores, along with specificities of sedimentology and dating, confirm that processes acting on regional scales, such as extensive permafrost thawing, can influence the aeDNA record and should be accounted for in aeDNA paleoecology.

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

Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 y, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.

Historical and ethnographic sources depict use of portable braced shaft weapons, or pikes, in megafauna hunting and defense during Late Holocene millennia in North and South America, Africa, Eurasia and Southeast Asia. Given the predominance of megafauna in Late Pleistocene North America during the centuries when Clovis points appeared and spread across much of the continent (13,050-12,650 cal BP), braced weapons may have been used in hunting of megaherbivores and defense against megacarnivores. Drawing from historical examples of pike use against lions, jaguars, boars, grizzlies, carabao and warhorses we consider the possibility of a fluted lithic pike. Associated osseous rods have been problematic as Clovis foreshafts due to the bevel angle and the apparent weakness of the splint haft when great strength is needed for deep penetration in megafauna hunting. However our review of Late Holocene pike use in megafauna encounters indicates the sharp tip becomes less important after hide or armor has been pierced because compression is sustained. Thus, foreshaft collapse after hide entry may not limit but rather increase the efficacy of the braced weapon. We conduct preliminary static experiments to model a fluted pike that adjusts during compression such that haft collapse and point detachment (when point jams on impact with bone) preserve the fluted biface, beveled rod and wooden mainshaft tip. In addition to Clovis point attributes and association with osseous rods, potential archaeological correlates of Clovis pike use include the high frequency of Clovis point isolates and concentrations of complete points with unbutchered mammoth remains at sites such as Naco in Arizona.

The phenomenon of lithic miniaturization during the Late Pleistocene at times coincided with increased artifact standardization and cutting edge efficiency-likely reflecting the use of small, sharp artifacts as interchangeable inserts for composite cutting tools and hunting weapons. During Marine Isotope Stage 2, Upper Paleolithic toolmakers in northern East Asia specifically used pressure techniques to make small, highly standardized lithic artifacts called microblades. However, little is currently known about how microblades affected the cutting edge efficiency of the toolkits they were a part of. We applied three methods of analyzing cutting edge efficiency to two Upper Paleolithic assemblages recently excavated from Tolbor-17, Mongolia, that document the periods before and after the introduction of microblade technology to the Tolbor Valley. A model incorporating allometric relationships between blank cutting edge length and mass suggests no difference in efficiency between the two periods, while two more conventional approaches both indicate a significant increase. The potential for improved cutting edge efficiency is only observed when the microblade sample is artificially inflated via simulation. Our results highlight challenges related to detecting and interpreting archaeological differences in cutting edge efficiency at the assemblage level.

This study aimed to reduce subjectivity bias in scoring dental macrowear quantity and direction using the Brabant index, which previously relied solely on written descriptions. To achieve this, we present a new, optimized visual guide incorporating buccal and lingual scores. The optimization process involved conceptualizing and illustrating a visual guide using Holocene southern African hunter‐gatherer and herder teeth, featuring both buccal and lingual scores for multicuspid teeth. The guide was hand‐drawn using a stippling technique and digitized to depict surface details for each wear stage and tooth type. We conducted intra‐ and inter‐observer assessments to evaluate the optimized method using both the original and optimized Brabant indices. Statistical analysis was performed in R using Cohen's kappa for direction and Cohen's weighted kappa for quantity. Intra‐observer results for the original method yielded kappa values of 0.84 for direction and 0.94 for quantity, while the optimized version both resulted in improved values of 0.99. Inter‐observer results revealed some differences between an inexperienced and an experienced observer. The inexperienced observer achieved kappa scores of 0.20 for direction and 0.86 for quantity with the original method, and 0.17 and 0.80, respectively, with the optimized version. The experienced observer's results using the original index were 0.66 for direction and 0.89 for quantity, and 0.75 and 0.96, respectively, with the optimized version. These findings demonstrate that the optimized method enhances data reliability for experienced observers, highlighting the value of a published visual guide and multicuspid scoring adjustments. However, reduced or unappreciable changes in accuracies for the inexperienced observer illustrate the need for dental expertise when scoring for dental wear, even with a modified method. [ABSTRACT FROM AUTHOR]

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Although most ancient DNA studies have focused on the last 50,000 years, paleogenomic approaches can now reach into the early Pleistocene, an epoch of repeated environmental changes that shaped present-day biodiversity. Emerging deep-time genomic transects, including from DNA preserved in sediments, will enable inference of adaptive evolution, discovery of unrecognized species, and exploration of how glaciations, volcanism, and paleomagnetic reversals shaped demography and community composition. In this Review, we explore the state-of-the-art in paleogenomics and discuss key challenges, including technical limitations, evolutionary divergence and associated biases, and the need for more precise dating of remains and sediments. We conclude that with improvements in laboratory and computational methods, the emerging field of deep-time paleogenomics will expand the range of questions addressable using ancient DNA.

Humans have been constantly exposed to the environment in their daily activities, which may result in some pathological changes. Paleopathology research is rare, particularly on ancient humans who lived in Bali, Indonesia. This research is intended to gain more insight into the history of diseases and the community in the past to assist future health researchers. This study was conducted to understand variation in disease among the ancient populations in Bali, Indonesia. The study examines skeletons from the Gilimanuk, Semawang, and Pacung Sembiran sites in Bali, Indonesia, collected from 1964 to 2008. A total of 336 individuals were identified, including 63 adult males, 75 adult females, and 56 adults whose sex could not be determined. In addition, 142 children were included in the analysis. The examination of the individuals revealed the presence of various dental pathological changes, such as caries and enamel hypoplasia, as well as periodontitis. Furthermore, several bone-related diseases and abnormalities were identified, such as osteophytes, fractures, porotic hyperostosis, and spina bifida occulta. Available evidence suggests a similarity in the types of pathological changes among the ancient populations of Gilimanuk, Semawang, and Pacung Sembiran. While a comprehensive explanation of the paleopathological variations observed in these populations necessitates further investigation, the present findings hold considerable value for medical experts and anthropologists seeking to better understand patterns of disease distribution among ancient Indonesian populations. This study was funded by the Directorate General of Higher Education, Research, and Technology of the Ministry of Education, Culture, Research, and Technology of Indonesia for the fiscal year 2023.

The Babad Lombok is an ancient literary or manuscripts document that generally contains stories about the origins of the people of Lombok. This document is written on a lontar leaf, which in the past was used to write manuscripts, letters, and documents. At present, the Babad Lombok document can be seen in the form of photos or scans, so it can be viewed without having to go to a museum or cultural heritage site where the document is usually exhibited. However, because this document is an ancient artifact that has been around for hundreds of years, it has naturally experienced fading in the original document or its scanned versions. This makes the text inside less clear. This paper proposes to automatically reconstruct/repair the Babad Lombok document using a neural network. The type of neural network used is an Autoencoder or Convolutional Autoencoder (CAE). The CAE model is built sequentially and trained using original images of Babad Lombok as its training data and manually corrected images of Babad Lombok as the target or ground truth data. In the process, the two types of data are iteratively cropped to a size of 64x64 along the original size of the Babad Lombok image. This process results in input and target data for the CAE training process in this research, each consisting of 48,288 images. Testing the trained autoencoder model shows that the Babad images have been successfully repaired, making the text quality clearer before reconstruction. Ultimately, the proposed CAE has achieved training and validation accuracies of 89.09% and 94.57%, with corresponding loss values of 0.0418 and 0.0226.

Background/Aims:Schwannomas, originating from Schwann cells in peripheral nerve sheaths, exhibit diverse clinical manifestations and unpredictable behavior. Among them, ancient schwannomas, with distinctive degenerative features, present in atypical locations and pose diagnostic challenges. This study explores their unique characteristics and implications for diagnosis and management. Material and Methods: The study was designed as a retrospective analysis of 7 adult patients aged ≥18 years, diagnosed with paraspinal, presacral, sacral, or para-aortic tumors, all confirmed histologically as ancient schwannomas. Data for analysis were collected from patients treated and followed up at Ankara City Hospital between April 2017 and December 2022. Ethical approval and informed consent were obtained before inclusion in the study. Results: The most common symptoms included the presence of a local lump (71,4%) and localized or radiating pain (57,1%). Notably, 1 patient (14,2%) was incidentally diagnosed during the evaluation process. Surgical intervention played a crucial role in the management of these tumors, with 71,4% of patients undergoing complete resection, while 28,5% underwent subtotal resection. Tumor recurrence occurred in 42,8% of cases, prompting the administration of radiotherapy as part of the treatment strategy. Imaging findings, particularly on MRI, played a crucial role in the accurate identification of ancient schwannomas. These tumors displayed isointensity on T1-weighted images and heterogeneous hyperintensity on T2-weighted images, along with distinctive heterogeneous contrast enhancement. Conclusion: Ancient schwannomas exhibit unique histological features and distinctive MRI characteristics, differentiating them from other nerve sheath tumors. Early diagnosis and complete surgical resection offer favorable outcomes. Awareness of this entity is essential for managing peripheral nerve sheath tumors effectively.

The twentieth-century logical mainstream, derived from works by Łukasiewicz and Scholz, pictures the history of logic for the most part as the prehistory of Boolean–Fregean mathematical logic. Particularly, with respect to classical propositional calculus, the Stoic logic has been pictured as an early stage of it and Aristotle's or the Peripatetics' logic as a theory that assumes it. Although it was not emphasised, it follows that the ancient logics contain the principle of explosion. In the endmost quarter of the twentieth century, a competitive view began to spread to the effect that the ancient systems of logic were paraconsistent or relevantistic. In the twenty-first century, the latter view prevails and has every chance of becoming a new orthodoxy. It is claimed that although in Łukasiewicz's argument for the classicality of ancient logics, there are gaps, it may be demonstrated that the ancient logics contain the principle of explosion. [ABSTRACT FROM AUTHOR]

We report a case of paravertebral retroperitoneal ancient schwannoma (RPAS) with symptoms suggestive of irritable bowel syndrome that was relieved after resection. Very few cases have been reported of RPAS with gastrointestinal symptoms. Increased bowel activity associated with RPAS has not been reported. Our case report suggests that RPAS may present with increased bowel frequency that could be relieved after surgical resection. [ABSTRACT FROM AUTHOR]

The Ancient Greeks were great innovators in all academic fields, including medicine. Hippocrates of Kos, the Father of Medicine, established many terms for the genitourinary (GU) system, such as nephros, urethra, urogenital, and adenocarcinoma. According to Hesiod's Theogony, Aphrodite, the goddess of love and beauty, was born off the coast of Kythera, from the foam produced by Uranus's genitals, after his son Cronus had thrown them into to the sea. In this review, we present the etymology of the GU vocabulary, review the Ancient Greeks' understanding of the GU system and the origins of Greek myths related to the male genitals. [ABSTRACT FROM AUTHOR]

This article aims to analyze the legitimacy of a thesis that has been gaining traction in recent decades within Religious Studies - namely, that the term religion can only be applied accurately to Protestant Christianity, and that all previous phenomena must be described using different terminology. To this end, we will take Brent Nongbri as our main interlocutor. What Nongbri advocates is simple: the term “religion” stands for the private adherence to a given set of theses; premodern peoples did not have any concept with such or similar meaning, therefore, they did not have religion, but something different. We will postulate, on the one hand, that Nongbri's thesis is tremendously fragile, and, on the other, that we are perfectly justified in continuing to talk about religion when referring to pre-modern peoples and cultures. [ABSTRACT FROM AUTHOR]

The philosophy of Bernard Williams, recognised as a prominent expression of ethical thought, presents an intense dialogue with ancient Greek tragic culture. Combining erudition and elegance, Williams evokes Greek tragedies to discuss modern ethical ideas and conceptions. Our article intends to consider Williams' thought from a cultural point of view: we propose analysing Williams' cultural methodology, which may be described as a way of thinking beyond the traditional dichotomies between the ancient and the modern, especially concerning the notion of the tragic. Accordingly, we shall examine the affinities between ancient and modern tragic cultures by identifying common narrative and poetical elements. To do so, we shall consider the interpretation of Hamlet, developed by the classicist scholar H.D.F. Kitto. In Form and Meaning in Drama: A Study of Six Greek Plays and of "Hamlet" (1956), Kitto proposes reading Hamlet in close alliance with Oedipus Tyrannus. Kitto maintains that both tragedies are poetical expressions of a shared tragic element: miasma, or "pollution", a concept thoroughly treated by Williams in the third chapter of Shame and Necessity. Our article aims to combine Williams' cultural methodology—we may call it the deconstruction of the repeated theoretical frameworks regarding the differences between the ancient and the modern—and Kitto's reading of Hamlet in line with Oedipus Tyrannus, which may be understood as an illustration of the persistence of common tragic elements beyond time and the historical separation of cultural periods. Our perspective shall be both cultural and aesthetical. [ABSTRACT FROM AUTHOR]

Humans have been constantly exposed to the environment in their daily activities, which may result in some pathological changes. Paleopathology research is rare, particularly on ancient humans who lived in Bali, Indonesia. This research is intended to gain more insight into the history of diseases and the community in the past to assist future health researchers. This study was conducted to understand variation in disease among the ancient populations in Bali, Indonesia. The study examines skeletons from the Gilimanuk, Semawang, and Pacung Sembiran sites in Bali, Indonesia, collected from 1964 to 2008. A total of 336 individuals were identified, including 63 adult males, 75 adult females, and 56 adults whose sex could not be determined. In addition, 142 children were included in the analysis. The examination of the individuals revealed the presence of various dental pathological changes, such as caries and enamel hypoplasia, as well as periodontitis. Furthermore, several bone-related diseases and abnormalities were identified, such as osteophytes, fractures, porotic hyperostosis, and spina bifida occulta. Available evidence suggests a similarity in the types of pathological changes among the ancient populations of Gilimanuk, Semawang, and Pacung Sembiran. While a comprehensive explanation of the paleopathological variations observed in these populations necessitates further investigation, the present findings hold considerable value for medical experts and anthropologists seeking to better understand patterns of disease distribution among ancient Indonesian populations. [ABSTRACT FROM AUTHOR]

Introduction: Schwannomas, originating from Schwann cells in peripheral nerve sheaths, exhibit diverse clinical manifestations and unpredictable behavior. Among them, ancient schwannomas, with distinctive degenerative features, present in atypical locations and pose diagnostic challenges. This study explores their unique characteristics and implications for diagnosis and management. Material and Methods: The study was designed as a retrospective analysis of 7 adult patients aged ≥18 years diagnosed with paraspinal, presacral, sacral, or para-aortic tumors, and all histologically confirmed as ancient schwannomas. Data for analysis were collected from patients treated and followed up at Ankara City Hospital between April 2017 and December 2022. Ethical approval and informed consent were obtained before inclusion in the study. Results: The most common symptoms included the presence of a local lump (71,4%) and localized or radiating pain (57,1%). Notably, one patient (14,2%) was incidentally diagnosed during the evaluation process. Surgical intervention played a crucial role in the management of these tumors, with 71,4% of patients underwent complete resection while 28,5% underwent subtotal resection. Tumor recurrence occurred in 42,8% of cases, prompting the administration of radiotherapy as part of the treatment strategy. Imaging findings, particularly on MRI, played a crucial role in the accurate identification of ancient schwannomas. These tumors displayed isointensity on T1-weighted images and heterogeneous hyperintensity on T2-weighted images, along with distinctive heterogeneous contrast enhancement. Conclusion: Ancient schwannomas exhibit unique histological features and distinctive MRI characteristics, differentiating them from other nerve sheath tumors. Early diagnosis and complete surgical resection offer favorable outcomes. Awareness of this entity is essential for managing peripheral nerve sheath tumors effectively. [ABSTRACT FROM AUTHOR]

Despite broad agreement that Homo sapiens originated in Africa, considerable uncertainty surrounds specific models of divergence and migration across the continent1. Progress is hampered by a shortage of fossil and genomic data, as well as variability in previous estimates of divergence times1. Here we seek to discriminate among such models by considering linkage disequilibrium and diversity-based statistics, optimized for rapid, complex demographic inference2. We infer detailed demographic models for populations across Africa, including eastern and western representatives, and newly sequenced whole genomes from 44 Nama (Khoe-San) individuals from southern Africa. We infer a reticulated African population history in which present-day population structure dates back to Marine Isotope Stage 5. The earliest population divergence among contemporary populations occurred 120,000 to 135,000 years ago and was preceded by links between two or more weakly differentiated ancestral Homo populations connected by gene flow over hundreds of thousands of years. Such weakly structured stem models explain patterns of polymorphism that had previously been attributed to contributions from archaic hominins in Africa2-7. In contrast to models with archaic introgression, we predict that fossil remains from coexisting ancestral populations should be genetically and morphologically similar, and that only an inferred 1-4% of genetic differentiation among contemporary human populations can be attributed to genetic drift between stem populations. We show that model misspecification explains the variation in previous estimates of divergence times, and argue that studying a range of models is key to making robust inferences about deep history.

This study of the openings in ancient Egyptian residential architecture, which is limited survival monuments we have to, describes precisely what it was when compared to funerary and religious architecture, was a fleeting plant and clay architecture that was unreliable to survive. As a result of his strong belief in life after death and that it is the longest and eternal surviving life, this is reflected in his interest in the immortality of religious and funerary buildings. And yet I got his attention in study and design and it contained important symbolic values, this prompted us to look for the models that the ancient Egyptian left behind to help complete the design image. and looking for different factors behind the different design of windows and doors from place to place, Hence, the study aims to describe and analyse the openings in ancient Egyptian architecture in terms of windows, entrances and doors because of their aesthetic and functional importance, as well as their symbolic values. in addition to its expression in the ancient Egyptian language and what the words refer to and its association with the form expressed in hieroglyphic writing, As the location of the openings varies, their role and design differs in terms of the elements and foundations of the design used in each of them, and what is actually expressed in some graphic shapes by comparing them to the real models that have been found, though fewer in number. As an attempt to get a picture that comes close to perfection and truth whenever possible, the study will be based on the work that describes the façades of palaces as in the Horsi name of kings and the depiction of houses and palaces on the walls of graves or papyri and some of the few models that survived to tell us what these vents were like, With description and analysis, it is possible to determine the design data, what the designer has achieved, its relevance to the nature of the building used, the symbols used and their connotations, and the interpretation of some shapes and materials.

Infectious diseases are among the strongest selective pressures driving human evolution1,2. This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis3. This pandemic devastated Afro-Eurasia, killing up to 30-50% of the population4. To identify loci that may have been under selection during the Black Death, we characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during and after the Black Death. Immune loci are strongly enriched for highly differentiated sites relative to a set of non-immune loci, suggesting positive selection. We identify 245 variants that are highly differentiated within the London dataset, four of which were replicated in an independent cohort from Denmark, and represent the strongest candidates for positive selection. The selected allele for one of these variants, rs2549794, is associated with the production of a full-length (versus truncated) ERAP2 transcript, variation in cytokine response to Y. pestis and increased ability to control intracellular Y. pestis in macrophages. Finally, we show that protective variants overlap with alleles that are today associated with increased susceptibility to autoimmune diseases, providing empirical evidence for the role played by past pandemics in shaping present-day susceptibility to disease.

Cacao seeds, Theobroma cacao, provide the basis for a ceremonially important Mesoamerican food. Past efforts to identify cacao in ceramics focused on highly decorative vessel forms associated with elite ceremonial contexts, creating assumptions as to how cacao was distributed and who could access it. This study examines 54 archaeological ceramic sherds from El Pilar (Belize/Guatemala) of Late Classic (600 to 900 CE) residential and civic contexts representing a cross-section of ancient Maya inhabitants. Identification of cacao in ancient sherds has depended on the general presence of theobromine; we used the discrete presence of theophylline, a unique key biomarker for cacao in the region. Analysis was done by grinding off all outside surfaces to reduce contamination, pulverizing the inner clay matrix, extracting absorbed molecules, and concentrating the extractions. In order to obtain especially high selectivity and low limits of detection, our study utilized the technique of resonance-enhanced multiphoton ionization coupled with laser-desorption jet-cooling mass spectrometry. This technique isolates molecules in the cold gas phase where they can be selectively ionized through a resonant two-photon process. Of the sherds analyzed, 30 samples (56%) were found to contain significant amounts of theophylline and thus test positive for cacao. Importantly, cacao is present in all contexts, common to all Maya residents near and far from centers.

Kahramanmaraş is an Anatolian city with a very rich historical and cultural background. This wealth has also affected the emotional and mental world of the local people and has revealed a rich vocabulary by being expressed in words. It is possible to find thousands of examples of local words in the vocabulary of the region, apart from pronunciation differences. The fact that the region has been a Turkish homeland for many years and, therefore, the Turkish language has existed in the region for many years has led to the survival of some vocabulary belonging to the historical periods of Turkish. It is seen that many vocabulary elements in the region exist in historical periods but have fallen out of use in our written language today. In some studies, it has been stated that the fact that the elements used in the historical periods of the language are still seen today cannot be seen as an archaic situation. It has been stated that in order to be archaic, this can be determined by comparing it with another dialect region or dialect. We also agree with this opinion. For this reason, while revealing the archaic elements in the Kahramanmaraş dialect, a determination was made by comparing them with today's written language. As a result of the study, 52 lexical items were identified as archaic. Some of these lexical items can be traced back to the Old Turkish period, some to the DLT, and some to the 13th century in Anatolia. It was observed that most of the archaic loanwords preserved their meaning in historical periods. [ABSTRACT FROM AUTHOR]

This article addressed ‘The conceptualisation of morality in ancient religions at the hand of the Gilgamesh Epic’. After pointing out that ancient languages do not have words for neither morality nor religion, I discussed the following incidents in the Epic: he who saw the Deep; the immoral conduct of a king; the slaying of Humbaba; Ishtar and a death penalty; and a visit to Utanapishtim, the Distant. I alluded briefly to the way that the Epic ends. The aim was to examine whether ancient societies had a concept of morality and what role, if any, did religion play. Intradisciplinary and/or interdisciplinary implications: The conclusion was that religion played a very minor role, and that morality in ancient societies was a human endeavour.

Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes.

The fossil record of marine invertebrates has long fuelled the debate as to whether or not there are limits to global diversity in the sea1-5. Ecological theory states that, as diversity grows and ecological niches are filled, the strengthening of biological interactions imposes limits on diversity6,7. However, the extent to which biological interactions have constrained the growth of diversity over evolutionary time remains an open question1-5,8-11. Here we present a regional diversification model that reproduces the main Phanerozoic eon trends in the global diversity of marine invertebrates after imposing mass extinctions. We find that the dynamics of global diversity are best described by a diversification model that operates widely within the exponential growth regime of a logistic function. A spatially resolved analysis of the ratio of diversity to carrying capacity reveals that less than 2% of the global flooded continental area throughout the Phanerozoic exhibits diversity levels approaching ecological saturation. We attribute the overall increase in global diversity during the Late Mesozoic and Cenozoic eras to the development of diversity hotspots under prolonged conditions of Earth system stability and maximum continental fragmentation. We call this the 'diversity hotspots hypothesis', which we propose as a non-mutually exclusive alternative to the hypothesis that the Mesozoic marine revolution led this macroevolutionary trend12,13.

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived1-8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000-30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.

As the birthplace of Hemudu Culture, the Yaojiang Valley has a long history of civilization evolution. During Holocene, a dramatic environmental evolution took place in this area, making it an ideal sample for studying how humans adapt to environmental changes. In this study, we collect 63 archaeological sites of Neolithic Age and Shang-Zhou dynasties, together with their information such as geographical position, cultural periodization, size, cultural layer thickness, archeological relics and remains. ArcGIS software was used to analysis their inheritance, distance from mountains, nuclear density and scale. The results are as follows. First, during the first and second phases of Hemudu culture, the number of sites was small and the inheritance was high, with an overlapping coefficient of 0.83. The number of sites increased significantly in the third and fourth phases of Hemudu culture while the inheritance reduced relatively with an overlapping coefficient of 0.73. During Liangzhu Culture and Shang-Zhou dynasties, the number and inheritance of sites both showed a downward trend. The overlapping coefficient dropped to 0.43. This shows that significant changes in the environment and population composition occurred from the third to the fourth phase of Hemudu culture, the fourth phase of Hemudu culture to Liangzhu culture, and Liangzhu culture to Shang-Zhou dynasties. Secondly, in terms of spatial distribution, archeological sites first appeared in the middle of the Yaojiang Valley and spread to the east and west in the second and fourth phase of Hemudu culture successively until they occupied the whole valley. These archeological sites were generally not more than 1500 m away from the mountains, and only showed a trend of spreading to the plain in the fourth phase of the Hemudu culture and Shang-Zhou dynasties, suggesting that the Yaojiang River was relatively rich in land resources during these two periods, which may be caused by large-scale regression. Thirdly, From the first phase of Hemudu culture to Shang-Zhou dynasties, the Yaojiang Valley was filled from remnant ancient bay into coastal plain. During this period, the formation and the diversion of Yaojiang River, as well as the topographic inversion of coastal area and plain hinterland also happened in this area. [ABSTRACT FROM AUTHOR]

Objective: Although today there is extensive scientific literature on aural myiasis, a historical study of the subject has yet to appear. This short article reports the first description of aural myiasis in the Western medical literature. Methods: Methods involved: (1) scholarship review of ear diseases within Ancient Greek and Roman medical texts (L'Année philologique); (2) linguistic analysis for text identification through the Library of Latin Texts, the Thesaurus Linguae Latinae and the Loeb Classical Library; and (3) translation of the Latin texts that described cases of aural myiasis with commentary. Results: To our knowledge, the earliest case of aural myiasis in Latin medical literature is reported by the Roman encyclopaedist Celsus (first century CE). In his De Medicina , he describes cases of Wohlfahrtia magnifica maggot infestation of the ear and how to treat affected patients. Conclusion: Despite present advances in otology, we believe that much insight can still be gained from this ancient example of medical history in ear diseases. A more comparative analysis of the subject is to be considered in the future, which will provide more data from different cultures and times. [ABSTRACT FROM AUTHOR]

During the Ottoman period, wood had replaced marble in Orthodox churches. Between the 16th and 19th century, common, unknown craftsmen created wonderful wood-carved ecclesiastical works by hand, though many of them have been partially or completely destroyed, usually without any of their images being saved. Advances in technology now make it possible to develop a detailed digital copy of an object of our cultural heritage, creating an unaltered prototype material to be studied by all, while offering in parallel the ease of reproducing precise copies, ensuring even museum quality standards. In the present study, a corresponding attempt to record, scan and then reconstruct a 17th century "Bema Door" (located in the Holy Monastery of Hilandar in Mount Athos) is implemented, presented step-by-step and discussed, in order to highlight the challenges and potential of the applied methods. The process included on-site recording of a 3D digital scan, and then the creation of the Bema door copy, first applying Computerized Numerical Control (CNC) machining and then, with elaborate handwork by experienced wood-carvers who successfully completed the process, imparting the necessary and unique human artistic character. The current work transfers the experience on this reproduction technique applied in a Bema door element, shares significant information and details on tools, materials, process steps, etc., in order to be an inspiration and stimulus for the preservation or reproduction of other cultural heritage monuments of high importance. [ABSTRACT FROM AUTHOR]

Paleoclimatic evidence indicating a series of droughts in the Yucatan Peninsula during the Terminal Classic period suggests that climate change may have contributed to the disruption or collapse of Classic Maya polities. Although climate change cannot fully account for the multifaceted, political turmoil of the period, it is clear that droughts of strong magnitude could have limited food availability, potentially causing famine, migration, and societal decline. Maize was undoubtedly an important staple food of the ancient Maya, but a complete analysis of other food resources that would have been available during drought remains unresolved. Here, we assess drought resistance of all 497 indigenous food plant species documented in ethnographic, ethnobotanical, and botanical studies as having been used by the lowland Maya and classify the availability of these plant species and their edible components under various drought scenarios. Our analysis indicates availability of 83% of food plant species in short-term drought, but this percentage drops to 22% of food plant species available in moderate drought up to 1 y. During extreme drought, lasting several years, our analysis indicates availability of 11% of food plant species. Our results demonstrate a greater diversity of food sources beyond maize that would have been available to the Maya during climate disruption of the Terminal Classic period than has been previously acknowledged. While drought would have necessitated shifts in dietary patterns, the range of physiological drought responses for the available food plants would have allowed a continuing food supply under all but the most dire conditions.

Many traits of industrial and basic biological interest arose long ago, and manifest now as fixed differences between a focal species and its reproductively isolated relatives. In these systems, extant individuals can hold clues to the mechanisms by which phenotypes evolved in their ancestors. We harnessed yeast thermotolerance as a test case for such molecular-genetic inferences. In viability experiments, we showed that extant Saccharomyces cerevisiae survived at temperatures where cultures of its sister species S. paradoxus died out. Then, focusing on loci that contribute to this difference, we found that the genetic mechanisms of high-temperature growth changed with temperature. We also uncovered an enrichment of low-frequency variants at thermotolerance loci in S. cerevisiae population sequences, suggestive of a history of non-neutral selective forces acting at these genes. We interpret these results in light of models of the evolutionary mechanisms by which the thermotolerance trait arose in the S. cerevisiae lineage. Together, our results and interpretation underscore the power of genetic approaches to explore how an ancient trait came to be.

Present-day Tibetans have adapted both genetically and culturally to the high altitude environment of the Tibetan Plateau, but fundamental questions about their origins remain unanswered. Recent archaeological and genetic research suggests the presence of an early population on the Plateau within the past 40 thousand years, followed by the arrival of subsequent groups within the past 10 thousand years. Here, we obtain new genome-wide data for 33 ancient individuals from high elevation sites on the southern fringe of the Tibetan Plateau in Nepal, who we show are most closely related to present-day Tibetans. They derive most of their ancestry from groups related to Late Neolithic populations at the northeastern edge of the Tibetan Plateau but also harbor a minor genetic component from a distinct and deep Paleolithic Eurasian ancestry. In contrast to their Tibetan neighbors, present-day non-Tibetan Tibeto-Burman speakers living at mid-elevations along the southern and eastern margins of the Plateau form a genetic cline that reflects a distinct genetic history. Finally, a comparison between ancient and present-day highlanders confirms ongoing positive selection of high altitude adaptive alleles.

The archaeological site of Pompeii is one of the 54 UNESCO World Heritage sites in Italy, thanks to its uniqueness: the town was completely destroyed and buried by a Vesuvius' eruption in 79 AD. In this work, we present a multidisciplinary approach with bioarchaeological and palaeogenomic analyses of two Pompeian human remains from the Casa del Fabbro. We have been able to characterize the genetic profile of the first Pompeian' genome, which has strong affinities with the surrounding central Italian population from the Roman Imperial Age. Our findings suggest that, despite the extensive connection between Rome and other Mediterranean populations, a noticeable degree of genetic homogeneity exists in the Italian peninsula at that time. Moreover, palaeopathological analyses identified the presence of spinal tuberculosis and we further investigated the presence of ancient DNA from Mycobacterium tuberculosis. In conclusion, our study demonstrates the power of a combined approach to investigate ancient humans and confirms the possibility to retrieve ancient DNA from Pompeii human remains. Our initial findings provide a foundation to promote an intensive and extensive paleogenetic analysis in order to reconstruct the genetic history of population from Pompeii, a unique archaeological site.

This research is concerned with studying the techniques that were applied to pottery forms in the ages before blogging in Iraq in search of the goals inherent in it. About the techniques that were applied in the forms of pottery of an era before writing and revealing them, the methods and methods of their application, and identifying the tools and materials that were employed in it. The results of the research, including: The ancient potter showed deep experience through expression in colors, as the figure did not include prominent or recessed motifs, but only painted on the surface, and this indicates the high ability of the ancient potter and his coloring power in determining the drawings.

The Lake Titicaca basin was one of the major centers for cultural development in the ancient world. This lacustrine environment is unique in the high, dry Andean altiplano, and its aquatic and terrestrial resources are thought to have contributed to the florescence of complex societies in this region. Nevertheless, it remains unclear to what extent local aquatic resources, particularly fish, and the introduced crop, maize, which can be grown in regions along the lakeshores, contributed to facilitating sustained food production and population growth, which underpinned increasing social political complexity starting in the Formative Period (1400 BCE to 500 CE) and culminating with the Tiwanaku state (500 to 1100 CE). Here, we present direct dietary evidence from stable isotope analysis of human skeletal remains spanning over two millennia, together with faunal and floral reference materials, to reconstruct foodways and ecological interactions in southern Lake Titicaca over time. Bulk stable isotope analysis, coupled with compound-specific amino acid stable isotope analysis, allows better discrimination between resources consumed across aquatic and terrestrial environments. Together, this evidence demonstrates that human diets predominantly relied on C3 plants, particularly quinoa and tubers, along with terrestrial animals, notably domestic camelids. Surprisingly, fish were not a significant source of animal protein, but a slight increase in C4 plant consumption verifies the increasing importance of maize in the Middle Horizon. These results underscore the primary role of local terrestrial food resources in securing a nutritious diet that allowed for sustained population growth, even in the face of documented climate and political change across these periods.

BackgroundCryptoendolithic communities are microbial ecosystems dwelling inside porous rocks that are able to persist at the edge of the biological potential for life in the ice-free areas of the Antarctic desert. These regions include the McMurdo Dry Valleys, often accounted as the closest terrestrial counterpart of the Martian environment and thought to be devoid of life until the discovery of these cryptic life-forms. Despite their interest as a model for the early colonization by living organisms of terrestrial ecosystems and for adaptation to extreme conditions of stress, little is known about the evolution, diversity, and genetic makeup of bacterial species that reside in these environments. Using the Illumina Novaseq platform, we generated the first metagenomes from rocks collected in Continental Antarctica over a distance of about 350 km along an altitudinal transect from 834 up to 3100 m above sea level (a.s.l.).ResultsA total of 497 draft bacterial genome sequences were assembled and clustered into 269 candidate species that lack a representative genome in public databases. Actinobacteria represent the most abundant phylum, followed by Chloroflexi and Proteobacteria. The "Candidatus Jiangella antarctica" has been recorded across all samples, suggesting a high adaptation and specialization of this species to the harshest Antarctic desert environment. The majority of these new species belong to monophyletic bacterial clades that diverged from related taxa in a range from 1.2 billion to 410 Ma and are functionally distinct from known related taxa.ConclusionsOur findings significantly increase the repertoire of genomic data for several taxa and, to date, represent the first example of bacterial genomes recovered from endolithic communities. Their ancient origin seems to not be related to the geological history of the continent, rather they may represent evolutionary remnants of pristine clades that evolved across the Tonian glaciation. These unique genomic resources will underpin future studies on the structure, evolution, and function of these ecosystems at the edge of life. Video abstract.