Ancient Specimens Research Articles

Crack Evolvement of Ancient Brick Masonry Under Uniaxial Compression Fatigue Loading

ABSTRACT Cracking is an essential intuitive indicator of damage in masonry structures. Evaluating the progression of fatigue cracks in ancient brick masonry structures is vital for the preservation and safety of ancient buildings. By conducting amplitude cyclic uniaxial compression tests on ancient brick masonry specimens, using the video image correlate-3d (VIC-3D) technology to collect images of the entire process from loading to failure, the development of fatigue cracks is analyzed and concluded. A reversed S-shaped function for fatigue crack evolution was established based on the fatigue damage mechanism. The model parameters’ physical significance, value range, and their impact on the model curve were discussed. The fatigue damage evolution equation was derived from the fatigue crack evolution model. The research results show that a reversed S-shaped function for fatigue crack evolution covers various types of fatigue crack evolution laws, with strong adaptability and high accuracy. The damage evolution curve established, based on the fatigue crack evolution model, has a reversed S-shaped change rule, and was divided into three stages: the first stage (0 N f ~ 0.1 N f ) fatigue damage grows faster; the second stage (0.1 N f ~ 0.9 N f ) fatigue damage growth is stable, close to linear change; when the cycle ratio exceeds 0.9, it enters the third stage, and fatigue damage increases rapidly.

The microbial cataclysm that forever changed life’s history

After a full century of search, evidence of Darwin’s “missing” pre-Cambrian fossil record was finally discovered in the mid-1950s. Unsurprisingly, given the then widely held belief that Precambrian life was not only unknown but unknowable, the initial report engendered widespread skepticism. Nevertheless, new finds soon followed, discoveries that set the science on its present course by establishing the role of O2-producing phototrophic cyanobacteria as prime components of the Precambrian biota. Remarkably, however, many of the newly found ancient specimens were all but indistinguishable from cyanobacteria living today, a similarity that although bolstering their interpretation as authentic fossils raised questions about their apparent lack of evolutionary change. As the Precambrian fossil record has become increasingly better documented over recent decades, the seeming identity of modern and fossil cyanobacterial taxa has been repeatedly confirmed by workers worldwide. To accommodate these extraordinarily long-lived taxa, a new category of evolutionary rate-distribution, hypobradytely, has been added to G.G. Simpson’s classic listing and a second group of hypobradytelic Precambrian organisms, the microbial components of sulfuretum biocoenoses, has been discovered. Both of these groups originated early in earth history, the origin of O2-producing cyanobacteria ∼2700 Ma ago producing an enormous upheaval of the world’s ecosystem -- the microbial cataclysm -- as they supplanted long-established oxygen-intolerant anoxygenic photosynthetic bacteria to become the predominant primary producers, the fundament of the global ecosystem. At least three principal characteristics of these early-evolved hypobradytelic prokaryotes, both cyanobacteria and sulfuretum bacteria, have contributed to their striking differences in tempo and mode of evolution from those of the later-evolved Phanerozoic biota: (1) Their lack of outgroup biotic competition; (2) their within-group competition-minimizing ecologic preferences; and (3) their phenotype variability-limiting asexual mode of reproduction. Clearly, both the tempo and mode of evolution evolved as the cyanobacterially induced microbial cataclysm forever changed life’s history.

Ancient genomes reveal over two thousand years of dingo population structure

Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.

Exotic species in the Erbario Estense: new plants from the world to sixteenth-century Italy

Renaissance herbaria may provide precious information on exotic plants known or even introduced in Italy during the fifteenth and sixteenth centuries AD. In the Erbario Estense, preserved in the Archivio di Stato di Modena (northern Italy), there are 14 species considered as allochthonous neophytes or not present in the Italian flora. First, we accurately verified the taxa identification; then, we searched for the same species in the other coeval Italian Renaissance herbaria and collected the information present in the written sources of the second half of the 1500s (concerning, above all, the use of these species as medicinal plants); finally, we paid attention to their current uses in ethnobotanical tradition and their market value. For 12 taxa, we could confirm the former identification; whereas for 2, we came to a different conclusion; the comparison with other Renaissance herbaria, particularly Aldrovandi’s, greatly helped this evaluation process. The species treated here are not placed according to a precise order nor do they have particular medicinal values in common: probably, the specimens were simply added to the existing nucleus, as the species were known or were proven to be rather useful. We shall be able to gain further knowledge when it shall be possible to study all the remaining species. In any case, the Erbario Estense is an important testimony for sixteenth-century botany, that contains some of the most ancient specimens of exotic species that are of common use in large parts of the world today.Graphical abstract

Koban culture genome-wide and archeological data open the bridge between Bronze and Iron Ages in the North Caucasus.

The North Caucasus played a key role during the ancient colonization of Eurasia and the formation of its cultural and genetic ancestry. Previous archeogenetic studies described a relative genetic and cultural continuity of ancient Caucasus societies, since the Eneolithic period. The Koban culture, which formed in the Late Bronze Age on the North Caucasian highlands, is considered as a cultural "bridge" between the ancient and modern autochthonous peoples of the Caucasus. Here, we discuss the place of this archeological culture and its representatives in the genetic orbit of Caucasian cultures using genome-wide SNP data from five individuals of the Koban culture and one individual of the early Alanic culture as well as previously published genomic data of ancient and modern North Caucasus individuals. Ancient DNA analysis shows that an ancient individual from Klin-Yar III, who was previously described as male, was in fact a female. Additional studies on well-preserved ancient human specimens are necessary to determine the level of local mobility and kinship between individuals in ancient societies of North Caucasus. Further studies with a larger sample size will allow us gain a deeper understanding of this topic.

Хорологія Spalax arenarius — ендемічного виду гризунів Нижньодніпровських пісків і Таврійського степу

The article analyses one of the most unique species of mammals in the fauna of Ukraine—the fossorial rodent Spalax arenarius. The sandy mole rat is an endemic of the Ukrainian Black Sea region, one of the two endemic species in the mammal fauna of Ukraine and also a species having the smallest geographic range among representatives of the East European mammal fauna. The specifics of the modern distribution of this species, its morphological features and differences from the neighbouring species, from which it can be considered a derivative, are analysed. Particular attention is paid to five aspects of the chorological analysis: 1) description of the current distribution with a detailed map of the species’ occurrence; 2) analysis of ancient Spalax specimens and the former distribution of this species based on actual data; 3) determination of the actual range boundaries, primarily along the land, i.e. in the east of its distribution, 4) analysis of the probable reasons for the range restriction from the west as a probably recent expansion to the region; and 5) construction of a model of the formation of the current range based on re-constructions of the distribution of Spalax in the Taurida Steppe. The latter was carried out considering the morphological features of Spalax arenarius, which are most similar to those of Spalax giganteus, whose modern range is limited to the Caspian Sea regions and, apparently, the North Caucasus. According to morphology and habitat reconstructions, the sandy mole rat is most likely a sister species to Spalax giganteus and one of the source forms for the western S. zemni (similar to the history of ground squirrels). The unique features of the Lower Dnipro population are presented, including the colouration of the feet and rhinaria and the structure of the skull. The history of the Lower Dnipro settlement is considered in view of the regular flooding of the region in historical times (including the flood of 2022). The hypothesis of a recent (possibly secondary) expansion of the species into the region and the specifics of its presence and absence in other neighbouring territories, in particular in the Crimea, Syvash, and the Molochnyi Estuary area, are formulated and considered. The sands zone is most likely the area of recent expansion of the species, which demonstrates a correspondence to the entire complex of Lower Dnipro isolates, including Microtus socialis, Sylvaemus witherbyi, and Scirtopoda telum.

Mitogenomic analysis of a late Pleistocene jaguar from North America.

The jaguar (Panthera onca) is the largest living cat species native to the Americas and one of few large American carnivorans to have survived into the Holocene. However, the extent to which jaguar diversity declined during the end-Pleistocene extinction event remains unclear. For example, Pleistocene jaguar fossils from North America are notably larger than the average extant jaguar, leading to hypotheses that jaguars from this continent represent a now-extinct subspecies (Panthera onca augusta) or species (Panthera augusta). Here, we used a hybridization capture approach to recover an ancient mitochondrial genome from a large, late Pleistocene jaguar from Kingston Saltpeter Cave, Georgia, United States, which we sequenced to 26-fold coverage. We then estimated the evolutionary relationship between the ancient jaguar mitogenome and those from other extinct and living large felids, including multiple jaguars sampled across the species' current range. The ancient mitogenome falls within the diversity of living jaguars. All sampled jaguar mitogenomes share a common mitochondrial ancestor ~400 thousand years ago, indicating that the lineage represented by the ancient specimen dispersed into North America from the south at least once during the late Pleistocene. While genomic data from additional and older specimens will continue to improve understanding of Pleistocene jaguar diversity in the Americas, our results suggest that this specimen falls within the variation of extant jaguars despite the relatively larger size and geographic location and does not represent a distinct taxon.

Geometric morphometry enables species hypotheses testing and the assignment of historical type specimens in the genus Callirhinus Blanchard (Coleoptera: Scarabaeidae: Anomalini)

Abstract Assignation of old type specimens is important for nomenclatural stability, but when it comes to ancient specimens, the use of certain techniques is sometimes not appropriate, due to the condition or age of the specimen. In this study, the supposedly polymorphic and monotypic genus Callirhinus Blanchard was analysed with geometric morphometric techniques and photographs of the pronotum, with the purpose of identifying the locality of the old type specimen (19th century) and to test a priori defined hypothetical species by cumulation of evidence within an integrative taxonomic protocol using geometric morphometry, complemented by morphology and geographical discontinuity. Five morphotypes were defined a priori, and principal component, canonical variates analysis, and distances tests for the assignment of the type specimen based on canonical scores and Procrustes distances between means of groups were carried out. Statistical significance was found in four axes validating the species hypotheses, discovering that the type specimen belongs to the morphotype from Jalisco state. Additionally, a taxonomic treatment, the description of four new species, C. choperi Ramírez-Ponce & Zaragoza sp. nov., C. nanduRamírez-Ponce & Zaragoza sp. nov., C. huiinisRamírez-Ponce & Zaragoza sp. nov., and C. veemeRamírez-Ponce & Zaragoza sp. nov. , keys for the species determination, new distributional records, and a map are provided. The present work demonstrates that Geometric Morphometry is an adequate analytical tool that supports taxonomic identification at low cost and without damaging historical specimens.

Temporal collections to study invasion biology.

Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community-level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.

Edible flora in pre-Columbian Caribbean coprolites: Expected and unexpected data.

Coprolites, or mummified feces, are valuable sources of information on ancient cultures as they contain ancient DNA (aDNA). In this study, we analyzed ancient plant DNA isolated from coprolites belonging to two pre-Columbian cultures (Huecoid and Saladoid) from Vieques, Puerto Rico, using shotgun metagenomic sequencing to reconstruct diet and lifestyles. We also analyzed DNA sequences of putative phytopathogenic fungi, likely ingested during food consumption, to further support dietary habits. Our findings show that pre-Columbian Caribbean cultures had a diverse diet consisting of maize (Zea mays), sweet potato (Ipomoea batatas), chili peppers (Capsicum annuum), peanuts (Arachis spp.), papaya (Carica papaya), tomato (Solanum lycopersicum) and, very surprisingly cotton (Gossypium barbadense) and tobacco (Nicotiana sylvestris). Modelling of putative phytopathogenic fungi and plant interactions confirmed the potential consumption of these plants as well as edible fungi, particularly Ustilago spp., which suggest the consumption of maize and huitlacoche. These findings suggest that a variety of dietary, medicinal, and hallucinogenic plants likely played an important role in ancient human subsistence and societal customs. We compared our results with coprolites found in Mexico and the United States, as well as present-day faeces from Mexico, Peru, and the United States. The results suggest that the diet of pre-Columbian cultures resembled that of present-day hunter-gatherers, while agriculturalists exhibited a transitional state in dietary lifestyles between the pre-Columbian cultures and larger scale farmers and United States individuals. Our study highlights differences in dietary patterns related to human lifestyles and provides insight into the flora present in the pre-Columbian Caribbean area. Importantly, data from ancient fecal specimens demonstrate the importance of ancient DNA studies to better understand pre-Columbian populations.

Ancient DNA reveals genetic admixture in China during tiger evolution.

The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.

Historical RNA expression profiles from the extinct Tasmanian tiger.

Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.

Analysis of Chinese ancient brick masonry characteristics under uniaxial compression fatigue loading

Urban expansion and diversified traffic aggravate the damage and deterioration of ancient buildings. It is crucial to evaluate the long-term fatigue performance of ancient brick masonry structures for the safety and maintenance of ancient buildings. A series of indoor tests were conducted on the ancient brick masonry. The images for the whole process of the test were collected using VIC-3D technology. The relationship between the stress level and the number of failure cycles under compressive fatigue load and the stress–strain evolution under different stress levels were determined. A mathematical model of p-S-N fatigue life prediction based on probability was proposed, which comprehensively considered the maximum stress level, stress range, number of load cycles, and survival probability. The equivalent fatigue life of ancient brick masonry specimens under each failure probability obeys Weibull distribution, and then the fatigue life of masonry can be predicted at any expected confidence level. The test results provide reliable theoretical and data support for fatigue deterioration and life prediction of ancient masonry structures in service.

Use of rapid diagnostic tests for the detection of ancient malaria infections in dental pulp from the sixth century in Versailles, France

BackgroundPaleomicrobiological data have clarified that Plasmodium spp. was circulating in the past in southern European populations, which are now devoid of malaria. The aim of this study was to evaluate the efficacy of immunodetection and, more particularly, rapid diagnostic tests (RDT), in order to further assess Plasmodium infections in ancient northern European populations.MethodsA commercially available RDT, PALUTOP® + 4 OPTIMA, which is routinely used to detect malaria, was used to detect Plasmodium antigens from proteins recovered from ancient specimens extracted from 39 dental pulp samples. These samples were collected from 39 individuals who were buried in the sixth century, near the site of the current Palace of Versailles in France. Positive and negative controls were also used. Antigens detected were quantified using chemiluminescence imaging system analysis.ResultsPlasmodium antigens were detected in 14/39 (35.9%) individuals, including Plasmodium vivax antigens in 11 individuals and Plasmodium falciparum antigens co-detected in two individuals, while Pan-Plasmodium antigens were detected in three individuals. Controls all yielded expected results.ConclusionsThe data reported here showed that RDTs are a suitable tool for detecting Plasmodium spp. antigens in ancient dental pulp samples, and demonstrated the existence of malaria in Versailles, France, in the sixth century. Plasmodium vivax, which is regarded as being responsible for an attenuated form of malaria and less deadly forms, was the most prevalent species. This illustrates, for the first time in ancient populations, co-infection with P. falciparum, bringing into question the climate-driven ecosystems prevailing at that time in the Versailles area.

Svante Pääbo

Svante Pääbo was born on 20th April, 1955 at Stockholm, Sweden. He is a Swedish evolutionary geneticist whospecialized in the study of DNA from ancient specimens and who was the first to contribute to the sequencing of the Neanderthal genome. Pääbo also discovered the hominin Denisova. For his groundbreaking research on hominin genomes and human evolution, Pääbo was awarded the 2022 Nobel Prize for Physiology or Medicine.

Revealing Joseon period People's single nucleotide polymorphism associated with lactase gene by ancient DNA analysis of human remains from archaeological sites in Korea.

Lactase non-persistence (LNP), one of the causes of lactose intolerance, is related to lactase gene associated single nucleotide polymorphisms (SNPs). Since the frequency of LNP varies by ethnic group and country, the research to reveal the presence or absence of LNP for specific people has been conducted worldwide. However, in East Asia, the study of lactase gene associated SNPs have not been sufficiently examined so far using ancient human specimens from archaeological sites. In our study of Joseon period human remains (n=14), we successfully revealed genetic information of lactase gene associated SNPs (rs1679771596, rs41525747, rs4988236, rs4988235, rs41380347, rs869051967, rs145946881 and rs182549), further confirming that as for eight SNPs, the pre-modern Korean people had a lactase non-persistent genotype. Our report contributes to the establishment of LNP associated SNP analysis technique that can be useful in forthcoming studies on human bones and mummy samples from East Asian archaeological sites.

Biomolecular histology as a novel proxy for ancient DNA and protein sequence preservation.

Researchers' ability to accurately screen fossil and subfossil specimens for preservation of DNA and protein sequences remains limited. Thermal exposure and geologic age are usable proxies for sequence preservation on a broad scale but are of nominal use for specimens of similar depositional environments. Cell and tissue biomolecular histology is thus proposed as a novel proxy for determining sequence preservation potential of ancient specimens with improved accuracy. Biomolecular histology as a proxy is hypothesized to elucidate why fossils/subfossils of some depositional environments preserve sequences while others do not and to facilitate selection of ancient specimens for use in molecular studies.

Using loop-primer mediated PCR to enhance the detection of poorly preserved DNA.

Ancient DNA is vitally important in evolutionary research, and obtaining authentic ancient DNA sequences is critical for a proper analysis. However, it is difficult to acquire amplicons accurately and efficiently from ancient DNA templates using current techniques. Here, we established a loop-primer-mediated amplification method (L-PCR) to obtain target ancient DNA sequences with high accuracy and efficiency. The method was tested using 66 ancient samples (including 27 pig bones or teeth and 39 chicken bones) and serially diluted modern animal DNA templates. Compared to nested PCR, L-PCR was proven to be more efficient and accurate and could obtain more amplicons from both ancient pig samples and chicken bones and detect as low as 10-3ng/μl modern pig template DNA. The efficiency was at least 100-fold that of the nested PCR. The results suggest that L-PCR is advantageous for obtaining authentic DNA sequences from poorly preserved or recalcitrant ancient specimens.

Pleistocene parades of carnivores into North America.

The distribution and movement of species, broadly known as biogeography, is one of the fundamental subfields of ecology and evolutionary biology. However, significant mysteries remain about the processes that gave rise to the modern distribution of biodiversity across the globe. Over the last several decades, the genetic study of ancient and subfossil specimens has started to shed light on past migrations of some species, with a particular focus on humans and megafauna. In this issue of Molecular Ecology, Salis et al. (2021) use ancient mitogenomes and a new phylogeographic method to add an important new piece of evidence to the mystery of megafaunal migrations into North America during the Pleistocene. They found a striking synchronicity of brown bear (Ursus arctos) and lion (Panthera spp.) migrations across the Bering Land Bridge at several time points during the late Pleistocene, which highlights the lasting impact of sea level change on the prehistoric and modern dispersal of terrestrial carnivores across continents.

Ancient DNA evidence for the ecological globalization of cod fishing in medieval and post-medieval Europe.

Understanding the historical emergence and growth of long-range fisheries can provide fundamental insights into the timing of ecological impacts and the development of coastal communities during the last millennium. Whole-genome sequencing approaches can improve such understanding by determining the origin of archaeological fish specimens that may have been obtained from historic trade or distant water. Here, we used genome-wide data to individually infer the biological source of 37 ancient Atlantic cod specimens (ca 1050–1950 CE) from England and Spain. Our findings provide novel genetic evidence that eleventh- to twelfth-century specimens from London were predominantly obtained from nearby populations, while thirteenth- to fourteenth-century specimens were derived from distant sources. Our results further suggest that Icelandic cod was indeed exported to London earlier than previously reported. Our observations confirm the chronology and geography of the trans-Atlantic cod trade from Newfoundland to Spain starting by the early sixteenth century. Our findings demonstrate the utility of whole-genome sequencing and ancient DNA approaches to describe the globalization of marine fisheries and increase our understanding regarding the extent of the North Atlantic fish trade and long-range fisheries in medieval and early modern times.