A new fossil species of the extant genus Vicelva from mid-Cretaceous Kachin amber (Coleoptera: Staphylinidae).

A new species of the extant staphylinid genus Vicelva Moore & Legner, V. rasilis sp. nov., is reported from mid-Cretaceous Kachin amber of northern Myanmar. Vicelva rasilis is distinguishable from extant members of Vicelva by the smoother dorsal surface of head, pronotum and elytra, less prominent median projection of clypeus, unnotched mesal edge of mandibles, semiglabrous antennomere 6, and longer tarsomere 1. The pollen-containing coprolite attached to the beetle and the crystals within the beetle body provide valuable information about the biology and taphonomy of the fossil.

Late Cretaceous coprolite from the Opole area (southern Poland) as evidence for a variable diet in shell-crushing shark Ptychodus (Elasmobranchii: Ptychodontidae).

Background: Coprolites, i.e., fossilized faeces, are an important source of knowledge on the diet and food processing mechanisms in the fossil record. Direct and indirect evidences for the dietary preferences of extinct sharks are rare in the fossil record. The first coprolite attributable to Ptychodus containing prey remains from the European Cretaceous is documented here. Methods: A coprolite from the Late Cretaceous of Opole (southern Poland) was scanned using micro-computed tomography to show the arrangement of the inclusions. In addition, the cross-section was examined under the SEM/EDS to analyse the microstructure and chemical composition of the inclusions. Results: Brachiopod shell fragments and foraminiferan shells are recognized and identified among the variously shaped inclusions detected through the performed analysis. Conclusions: The extinct shell-crushing shark Ptychodus has been identified as the likely producer of the examined coprolite. The presence of brachiopod shell fragments indicates that at least some species of this durophagous predatory shark may have preyed on small benthic elements on the sea bottom.

From modern-day parasitology to paleoparasitology: the elusive past record and evolution of Cryptosporidium.

Recent efforts have been made to review the state of the art on a variety of questions and targets in paleoparasitology, including protozoan taxa. Meanwhile, these efforts seemed to let aside Cryptosporidium, and we then intended to review its paleoparasitological record to assess its past distribution and favored detection methods, and eventually highlight needed research trajectories. This review shows that contrary to other parasites, most of the positive results came from South-American sites and coprolites rather than sediment samples, highlighting the need to test this kind of material, notably in Europe where many negative results were reported in the published literature from sediment samples. Moreover, aDNA-based detections are nearly absent from the paleoparasitological record of this parasite, though punctually shown successful. With their potential to address the evolutionary history of Cryptosporidium species, notably through their 18S rRNA tree, aDNA-based approaches should be encouraged in the future. In sum, and though the limits of currently used methods and materials remain unclear, this review highlights the potential role of coprolites and aDNA for the study of Cryptosporidium species in the past and how this history shaped their current diversity and distribution, notably among human populations but also farm animals.

PALEOPARASITOLOGY OF HUMAN ACANTHOCEPHALAN INFECTION: A REVIEW AND NEW CASE FROM BONNEVILLE ESTATES ROCKSHELTER, NEVADA, U.S.A.

This study reports a new case of acanthocephalan (thorny-headed worm) eggs in a coprolite from Bonneville Estates Rockshelter in eastern Nevada and uses archaeological and ethnographic data to better understand long-term relationships between people and acanthocephalans. Acanthocephalans are parasitic worms that use arthropods as intermediate hosts in their multi-host life cycles. Though acanthocephaliasis is rare among humans today, cases have increased in the last decade, and the discovery of acanthocephalan eggs in coprolites from archaeological sites in the Great Basin suggests a deep, shared history. At Bonneville Estates Rockshelter, 9 acanthocephalan eggs were recovered using a modified rehydration-homogenization-micro-sieving protocol on a coprolite that was radiocarbon dated to 6,040 ± 60 14C BP (7,160-6,730 cal BP), pushing back the oldest evidence of human acanthocephalan infection by 3 millennia. Researchers have proposed that the paleoepidemiology of acanthocephalans may relate to subsistence practices due to overlap in locations of infection and areas where insects are part of traditional foodways. This paper considers the paleoepidemiology of acanthocephalan infection through the first combined review of paleoparasitological, ethnographic, and archaeological records in western North America. Ethnographic and archaeological records support the hypothesis that archaeological cases of human acanthocephaliasis may be linked to entomophagy. Additional parasitological analyses are advised to determine whether this distribution is the result of dietary practices, host ecology, taphonomic issues, sampling biases, or a combination of factors.

First paleoparasitological evidence of Muellerius sp. in sheep or goat dated to the Sasanian Empire (500 CE) in ancient Iran.

A fecal pellet was recovered in an ancient salt mine in Chehrabad located in western Iran (36.55° N, 47.51° E). Based on prior publications showing the success of the salt mine's environment to preserve various life forms, it was decided to try and ascertain whether this faex contained any parasites of paleoparasitologic interest. The rehydration involved placing the pellet in an aqueous solution of 0.5% trisodium phosphate for a week, followed by the examination of aliquots of the entire rehydrated sample on a total of 153 microscope slides. The examination of the rehydrated material revealed the presence of two larval nematodes; there were no eggs or oocysts recovered. The larvae were photographed and measured, and the decision was made not to submit the two larvae to grinding and DNA extraction for molecular diagnostics due to their excellent state of preservation. The larvae were identified as first-stage larvae that appear to represent the genus Muellerius. Herein are reported the finding of two first-stage larvae of Muellerius nematodes (Metastrongyloidea, Protostrongylidae) from the rehydrated fecal pellet collected in a Chehrabad salt mine from the era of the Sasanian Empire.

First Find of Eggs of the Nematode Baylisascaris transfuga Rudolphi, 1819 (Ascaridoidea, Nematoda) in the Late Pleistocene.

The article presents the findings of the paleoparasitological analysis of coprolites from the cave bear (Ursus kanivetz Vereshchagin, 1973). The material for research was obtained during excavations in the Ignatievskaya Cave (Southern Urals, Russia; 54°53' N 57°46' E). The deposits with coprolites date back to the middle of the Late Pleistocene (90 000-30 000 years ago). On the basis of the paleoparasitological analysis, eggs of the nematode characteristic of representatives of Ursidae, namely, Baylisascaris transfuga Rudolphi, 1819, have been established to be present in the coprolites. The eggs are well preserved and have not lost their morphological features. The large cave bear was infested by the nematode B. transfuga. This is the first find of the nematode B. transfuga in Pleistocene-aged sediments and the first find of parasites in coprolites of the cave bear.

Paleomicrobiology of the human digestive tract: A review.

The microbiota is a hot topic of research in medical microbiology, boosted by culturomics and metagenomics, with unanticipated knowledge outputs in physiology and pathology. Knowledge of the microbiota in ancient populations may therefore be of prime interest in understanding factors shaping the coevolution of the microbiota and populations. Studies on ancient human microbiomes can help us understand how the community of microorganisms presents in the oral cavity and the gut was shaped during the evolution of our species and what environmental, social or cultural changes may have changed it. This review cumulates and summarizes the discoveries in the field of the ancient human microbiota, focusing on the remains used as samples and techniques used to handle and analyze them.

REVIEW OF PARASITES FOUND IN EXTINCT ANIMALS: WHAT CAN BE REVEALED.

Parasitism is inherent to life and observed in all species. Extinct animals have been studied to understand what they looked like, where and how they lived, what they fed on, and the reasons they became extinct. Paleoparasitology helps to clarify these questions based on the study of the parasites and microorganisms that infected those animals, using as a source material coprolites, fossils in rock, tissue, bone, mummy, and amber, analyses of ancient DNA, immunodiagnosis, and microscopy.

Paleoparasitology and archaeoparasitology in Iran: A retrospective in differential diagnosis.

OBJECTIVE: This paper reviews paleo- and archaeoparasitology publications to date, from Iran. The primary focus is the importance of differential diagnosis and the crucial role of interdisciplinary collaborations among parasitologists and other specialists. METHODS: All relevant articles and theses published in Iran through October 2020 are included and evaluated, with particular emphasis on the diagnostic process. RESULTS: Archaeoparasitic studies in Iran have identified a number of parasites that provide insight into the past. Misidentification, however, due to incomplete differential diagnosis, remains an issue, as does incomplete description and problematic images. CONCLUSIONS: Identification of paleoparasites to the species level must be supported with accurate morphology and morphometry. Rigorous differential diagnosis is essential. Caution must be exercised when interpreting observations of ova recovered from coprolites. In these instances, precise identification of host animals and aligning parasite ranges with host specificity is critical. The possibility of incidental parasite presence must be evaluated, including non-specificity of parasite tropisms, transport hosting, or contamination. Lastly, differential diagnosis must include consideration of intentional consumption of parasites. Thus, parasitological findings must be placed in geographical, historical, and cultural contexts. SIGNIFICANCE: Archaeoparasitological research in Iran has elucidated the presence of faunal and human disease in the past and has, through this reevaluation of the published works, contributed to precise description and diagnosis of ova of roundworms, tapeworms, thorny-headed worms, and recognition of larval stages of tapeworms in recovered remains of mites.

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.

Livestock faecal indicators for animal management, penning, foddering and dung use in early agricultural built environments in the Konya Plain, Central Anatolia.

Livestock dung is a valuable material for reconstructing human and animal inter-relations and activity within open areas and built environments. This paper examines the identification and multi-disciplinary analysis of dung remains from three neighbouring sites in the Konya Plain of Central Anatolia, Turkey: Boncuklu (ninth-eighth millennium cal BC), the Çatalhöyük East Mound (eighth-sixth millennium cal BC), and the Late Neolithic occupation at the Pinarbasi rockshelter (seventh millennium cal BC). It presents and evaluates data on animal management strategies and husbandry practices through the simultaneous examination of plant and faecal microfossils and biomarkers with thin-section micromorphology and integrated phytolith, dung spherulite, and biomolecular analyses, together with comparative reference geo-ethnoarchaeological assemblages. Herbivore dung and other coprogenic materials have been identified predominantly in open areas, pens and midden deposits through micromorphology and the chemical signatures of their depositional contexts and composition. Accumulations of herbivore faecal material and burnt remains containing calcitic spherulites and phytoliths have provided new information on animal diet, fodder and dung fuel. Evidence from phytoliths from in situ penning deposits at early Neolithic Çatalhöyük have provided new insights into foddering/grazing practices by identifying highly variable herbivorous regimes including both dicotyledonous and grass-based diets. This review illustrates the variability of dung deposits within early agricultural settlements and their potential for tracing continuity and change in ecological diversity, herd management strategies and foddering, health, energy and dung use, as well as the complexity of interactions between people and animals in this key region during the early Holocene.

Comparison of extraction methods for recovering ancient microbial DNA from paleofeces.

OBJECTIVES: Paleofeces are valuable to archeologists and evolutionary biologists for their potential to yield health, dietary, and host information. As a rich source of preserved biomolecules from host-associated microorganisms, they can also provide insights into the recent evolution and changing ecology of the gut microbiome. However, there is currently no standard method for DNA extraction from paleofeces, which combine the dual challenges of complex biological composition and degraded DNA. Due to the scarcity and relatively poor preservation of paleofeces when compared with other archeological remains, it is important to use efficient methods that maximize ancient DNA (aDNA) recovery while also minimizing downstream taxonomic biases. METHODS: In this study, we use shotgun metagenomics to systematically compare the performance of five DNA extraction methods on a set of well-preserved human and dog paleofeces from Mexico (~1,300 BP). RESULTS: Our results show that all tested DNA extraction methods yield a consistent microbial taxonomic profile, but that methods optimized for ancient samples recover significantly more DNA. CONCLUSIONS: These results show promise for future studies that seek to explore the evolution of the human gut microbiome by comparing aDNA data with those generated in modern studies.

Are immunoenzymatic tests for intestinal protozoans reliable when used on archaeological material?

Intestinal protozoans found in ancient human samples have been studied primarily by microscopy and immunodiagnostic assays. However, such methods are not suitable for the detection of zoonotic genotypes. The objectives of the present study were to utilize immunoenzimatic assays for coproantigen detection of Cryptosporidium sp., Giardia duodenalis, and Entamoeba histolytica/Entamoeba dispar in sixty ancient human and animal samples collected from 14 archaeological sites in South America, and to carry out a critical analysis of G. duodenalis according to results obtained from three diagnostic methodologies: microscopy, immunodiagnostic tests (immunoenzymatic and immunofluorescence), and molecular biology (PCR and sequencing). More than half (31/60) of the samples analyzed using immunoenzymatic tests were positive for at least one of the intestinal protozoans, with 46.6% (28/60) corresponding to G. duodenalis, 26.6% (16/60) to Cryptosporidium sp., and 5% (3/60) to E. histolytica/E. dispar. Cryptosporidium sp. and G. duodenalis coinfection was observed in 15% (9/60) of the samples, whereas all three protozoans were found in 5% (3/60) of samples. In the Northeast Region of Brazil, by immunoenzymatic tests there is evidence that G. duodenlais and Cryptosporidium sp. have infected humans and rodents for at least 7150 years. However, for G. duodenalis, the results from the three diagnostic tests were discordant. Specifically, despite the efficiency of the molecular biology assay in the experimental models, G. duodenalis DNA could not be amplified from the ancient samples. These results raise the following question: Are all ancient samples positive for coproantigen of G. duodenalis by immunoenzymatic tests truly positive? This scenario highlights the importance of further studies to evaluate the sensitivity and specificity of the immunoenzymatic method in the archaeological context.

The Skiles Mummy: Care of a debilitated hunter-gatherer evidenced by coprolite studies and stable isotopic analysis of hair.

The Skiles Mummy (SMM), a naturally mummified adult male from the late archaic period of Lower Pecos Canyonlands of South Texas, represents a unique case of care. SMM is an exceptional mummy within this region due to both the retention of a full head of hair, and having a diagnosed case of megacolon, a complication commonly associated with Chagas disease caused by Trypanosoma cruzi. Stable isotopic analysis of his hair is consistent with a diet incorporating of C4/CAM plants with some C3 plants, freshwater resources, and higher trophic level animals. However, the segments of hair most proximal to the scalp exhibited elevated δ15N values. Data from previous research indicate starvation and malnutrition can cause δ15N values to rise. The presence of large fecal boluses in the digestive tract suggest peristalsis ceased in the last four to five months of life, and this, together with results from coprolite analysis, indicate he would not have been able to adequately absorb protein and nutrients during this time. His condition would have rendered him immobile. Following Tilley's index of care, someone would have had to bring him food resources, as well as attending to his daily needs.

Methodological innovations for the study of irreplaceable samples reveal giardiasis in extinct animals (Nothrotherium maquinense and Palaeolama maior).

The use of diagnostic methods that prevent irreplaceable samples (from museum collections, archaeological and paleontological samples) of being consumed or that increase their yield is relevant. For museum collections, archaeological and paleontological samples it is essential to conserve samples, subsamples or portions for future research. We are addressing methods for conservation of irreplaceable samples that could be fully consumed. Innovations in methodologies that are used in studies of Paleoparasitology and Paleomicrobiology will contribute to the preservation of collections. Therefore, to the development of archaeology and paleontology in the future, we evaluated whether the discarded material of the immunochromatography test could be used for molecular diagnosis and vice versa. We used a genotyped experimental coprolite positive for Giardia duodenalis. The diagnosis was positive for giardiasis in both cases. This methodology can be corroborated with the coprolite of a Paleolama maior (extinct llama) previously diagnosed for G. duodenalis with an immunoenzymatic test. The residue of the pre-digestion step of the DNA extraction before adding Proteinase K was confirmed positive with the immunochromatographic test. Also, the DNA extraction residue from a coprolite of Nothrotherium maquinense (ground sloth) was tested positive with immunochromatographic test for G. duodenalis. These are the oldest findings for G. duodenalis confirming that this intestinal parasite occurred among Northeastern Brazilian Megafauna animals from the late Pleistocene period, correlated to human occupation. The relevance of these results will allow the study by different methodological approaches from a small amount of material, reusing discarded materials.

First bone-cracking dog coprolites provide new insight into bone consumption in Borophagus and their unique ecological niche.

Borophagine canids have long been hypothesized to be North American ecological 'avatars' of living hyenas in Africa and Asia, but direct fossil evidence of hyena-like bone consumption is hitherto unknown. We report rare coprolites (fossilized feces) of Borophagus parvus from the late Miocene of California and, for the first time, describe unambiguous evidence that these predatory canids ingested large amounts of bone. Surface morphology, micro-CT analyses, and contextual information reveal (1) droppings in concentrations signifying scent-marking behavior, similar to latrines used by living social carnivorans; (2) routine consumption of skeletons; (3) undissolved bones inside coprolites indicating gastrointestinal similarity to modern striped and brown hyenas; (4) B. parvus body weight of ~24 kg, reaching sizes of obligatory large-prey hunters; and (5) prey size ranging ~35-100 kg. This combination of traits suggests that bone-crushing Borophagus potentially hunted in collaborative social groups and occupied a niche no longer present in North American ecosystems.

Recovering parasites from mummies and coprolites: an epidemiological approach.

In the field of archaeological parasitology, researchers have long documented the distribution of parasites in archaeological time and space through the analysis of coprolites and human remains. This area of research defined the origin and migration of parasites through presence/absence studies. By the end of the 20th century, the field of pathoecology had emerged as researchers developed an interest in the ancient ecology of parasite transmission. Supporting studies were conducted to establish the relationships between parasites and humans, including cultural, subsistence, and ecological reconstructions. Parasite prevalence data were collected to infer the impact of parasitism on human health. In the last few decades, a paleoepidemiological approach has emerged with a focus on applying statistical techniques for quantification. The application of egg per gram (EPG) quantification methods provide data about parasites' prevalence in ancient populations and also identify the pathological potential that parasitism presented in different time periods and geographic places. Herein, we compare the methods used in several laboratories for reporting parasite prevalence and EPG quantification. We present newer quantification methods to explore patterns of parasite overdispersion among ancient people. These new methods will be able to produce more realistic measures of parasite infections among people of the past. These measures allow researchers to compare epidemiological patterns in both ancient and modern populations.

New paleoparasitological investigations from the pre-inca to hispanic contact period in northern Chile.

Paleoparasitological studies have demonstrated that changes in environment or culture are reflected in the patterns of parasitic infection diseases in populations worldwide. The advent of agriculture and animal domestication, with its accompanying reduction in human mobility and expanding population involves changes in or emergence of, parasites, the so-called first epidemiological transition. Cultural processes related to territory occupation contribute to both loss and acquisition of parasites. The archaeological site Lluta 57 in the Lluta Valley, Chile, provides a chronology of the transition from the pre-Inca or Late Intermediate Period (LIP), through the Late or Inca Period (LP), to the Hispanic Contact Period (HCP), providing the possibility of evaluating this epidemiological transition. The aim of this study was to conduct a paleoparasitological investigation of to gain insight into the dynamics of parasitism in Lluta people throughout the Inca expansion. Fourteen human coprolites from the three periods were rehydrated, submitted to spontaneous sedimentation, and examined by light microscopy for the presence of intestinal parasite eggs, pollen grains, and micro-remains. Eggs of four parasites: Enterobius vermicularis, Trichostrongylus sp., Trichuris sp., and Eimeria macusaniensis were recovered. Frequency, diversity, and number of parasite eggs per sample increased over the studied time period. Trichostrongylus sp. and E. macusaniensis were recorded in the region for the first time. Enterobius vermicularis eggs, absent in the LIP, were present as a hyper-infection in LP. The presence of E. macusaniensis is likely related to exploitation of llamas, which were used for food and transport and as sacrificial offerings. The paleobotanical analysis revealed ten families of pollen grains, as well as phytoliths and floral remains. In contrast to parasitological results, a diachronic pattern was not detected. Evolution of the settlements, with the advent of larger, more densely populated, villages, could have influenced the emergence and intensification of transmission of parasites in the region. The study showed that the Inca expansion influenced host-parasite-environment relationships in the Lluta Valley.

The first direct evidence of a Late Devonian coelacanth fish feeding on conodont animals.

We describe the first known occurrence of a Devonian coelacanth specimen from the lower Famennian of the Holy Cross Mountains, Poland, with a conodont element preserved in its digestive tract. A small spiral and phosphatic coprolite (fossil excrement) containing numerous conodont elements and other unrecognized remains was also found in the same deposits. The coprolite is tentatively attributed to the coelacanth. Although it is unclear whether the Late Devonian coelacanth from Poland was an active predator or a scavenger, these finds provide the first direct evidence of feeding on conodont animals by early coelacanth fish, and one of the few evidences of feeding on these animals known to date. It also expands our knowledge about the diet and trophic relations between the Paleozoic marine animals in general.

Genome data on the extinct Bison schoetensacki establish it as a sister species of the extant European bison (Bison bonasus).

BACKGROUND: The European bison (Bison bonasus), now found in Europe and the Caucasus, has been proposed to originate either from the extinct steppe/extant American bison lineage or from the extinct Bison schoetensacki lineage. Bison schoetensacki remains are documented in Eurasian Middle Pleistocene sites, but their presence in Upper Pleistocene sites has been questioned. Despite extensive genetic studies carried out on the steppe and European bison, no remains from the fossil record morphologically identified as Bison schoetensacki has been analyzed up to now. RESULTS: In this paper, we analyzed a 36,000-year-old Bison schoetensaki bone sample from the Siréjol cave (France) and a cave hyena coprolite (fossilized feces) found in a nearby cave and containing large amounts of Bovinae DNA. We show that the Bovinae mitochondrial DNA sequences from both samples, including a complete mitochondrial genome sequence, belong to a clade recently reported in the literature. This clade only includes ancient bison specimens without taxonomic identification and displays a sister relationship with the extant European bison. The genetic proximity of Bison schoetensacki with specimens from this clade is corroborated by the analysis of nuclear DNA single nucleotide polymorphisms. CONCLUSIONS: This work provides genetic evidence supporting the continuing presence of Bison schoetensacki up to the Upper Pleistocene. Bison schoetensacki turns out to be a sister species of Bison bonasus, excluding the steppe bison Bison priscus as a direct ancestor of the European bison.