scholarly journals Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave (Sicily, Italy)

2021 ◽  
Author(s):  
Gabriele Scorrano ◽  
Sofie Holtsmark Nielsen ◽  
Domenico Lo Vetro ◽  
Meaghan Mackie ◽  
Ashot Margaryan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Western Europe ◽  
Oral Microbiome ◽  
Human Populations ◽  
Genetic Lineage ◽  
Dental Calculus ◽  
Upper Palaeolithic ◽  
Hunter Gatherers ◽  
Microbiome Composition ◽  
Prehistoric Diet

Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and past genetic diversity of our species. Here we present a multi-omics study, integrating genomic and proteomic analyses of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Multi-omics analysis of dental calculus showed a diet rich of animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of using a multi-omics approach in the study of prehistoric human populations.

scholarly journals The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 309
Author(s):  
Alisa Kazarina ◽  
Elina Petersone-Gordina ◽  
Janis Kimsis ◽  
Jevgenija Kuzmicka ◽  
Pawel Zayakin ◽  
...  
Keyword(s):  
Dental Plaque ◽  
Modern Human ◽  
Oral Microbiome ◽  
Dental Calculus ◽  
Microbial Composition ◽  
Metagenome Analysis ◽  
Microbiome Composition ◽  
Microbial Adaptation ◽  
Microbial Dna ◽  
Insight Into

Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16–17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental plaque, modern human dental calculus samples and burial soil microbiota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the microbiome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment.

An upper palaeolithic shrine in India?

Antiquity ◽  
1983 ◽  
Vol 57 (220) ◽  
pp. 88-94 ◽  
Author(s):  
J. M. Kenoyer ◽  
J. D. Clark ◽  
J. N. Pal ◽  
G. R. Sharma
Keyword(s):  
Central India ◽  
Human Populations ◽  
Upper Palaeolithic ◽  
Law And Order ◽  
Brick Kiln ◽  
Hunter Gatherers ◽  
Life And Death ◽  
The Earth ◽  
The Village ◽  
The Universe

There is little doubt that a religious belief imparting a sense of law and order and helping to control the relationships between human populations and the other components of their environment, is highly developed among present-day hunter/gatherers. Such beliefs not only help to provide a feeling of unity stretching far beyond the hunting band itself, but they afford an ordered interconnexion between the foragers and the spiritual processes which are looked upon as all-powerful forces influencing life and death (Turnbull, 1968, 25). This is well exemplified in the case of the Musahar, a Dravidian tribe of hunter/gatherers who inhabit the jungle regions of the Eastern Vindhyas in Central India. According to Nesfield, quoted by Crooke (1896, Vol. IV:34), ‘The great active power in the universe … is Bansapatti, Bansatti or Bansuri, the goddess who … personifies and presides over the forests. By her command the trees bear fruit, the bulbs grow in the earth, the bees make honey, the tussar worm fattens on the asân leaf, and lizards, wolves and jackals (useful food to man) multiply their kind. She is a goddess of childbirth. To her the childless wife makes prayers for the grant of offspring. In her name and by her aid the medicine man or sorcerer expels devils from the bodies of the possessed. In her name and to her honour the village man kindles a new fire for lighting a brick kiln. Woe to the man who takes a false oath in the name of Bansatti.’

scholarly journals Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus

2021 ◽  
Vol 118 (32) ◽  
pp. e2102116118
Author(s):  
Claudio Ottoni ◽  
Dušan Borić ◽  
Olivia Cheronet ◽  
Vitale Sparacello ◽  
Irene Dori ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Southern Europe ◽  
Dental Calculus ◽  
Oral Flora ◽  
Shotgun Metagenomics ◽  
Near Eastern ◽  
Microbiome Composition ◽  
The Balkans

Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe—the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.

scholarly journals Oral microbiome diversity in chimpanzees from Gombe National Park

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Andrew T. Ozga ◽  
Ian Gilby ◽  
Rebecca S. Nockerts ◽  
Michael L. Wilson ◽  
Anne Pusey ◽  
...  
Keyword(s):  
Host Species ◽  
National Park ◽  
Sequence Data ◽  
Extraction Methods ◽  
Oral Microbiome ◽  
Human Populations ◽  
Oral Microbiota ◽  
Dental Calculus ◽  
Gombe National Park ◽  
Dna Extraction Methods

AbstractHistoric calcified dental plaque (dental calculus) can provide a unique perspective into the health status of past human populations but currently no studies have focused on the oral microbial ecosystem of other primates, including our closest relatives, within the hominids. Here we use ancient DNA extraction methods, shotgun library preparation, and next generation Illumina sequencing to examine oral microbiota from 19 dental calculus samples recovered from wild chimpanzees (Pan troglodytes schweinfurthii) who died in Gombe National Park, Tanzania. The resulting sequences were trimmed for quality, analyzed using MALT, MEGAN, and alignment scripts, and integrated with previously published dental calculus microbiome data. We report significant differences in oral microbiome phyla between chimpanzees and anatomically modern humans (AMH), with chimpanzees possessing a greater abundance of Bacteroidetes and Fusobacteria, and AMH showing higher Firmicutes and Proteobacteria. Our results suggest that by using an enterotype clustering method, results cluster largely based on host species. These clusters are driven by Porphyromonas and Fusobacterium genera in chimpanzees and Haemophilus and Streptococcus in AMH. Additionally, we compare a nearly complete Porphyromonas gingivalis genome to previously published genomes recovered from human gingiva to gain perspective on evolutionary relationships across host species. Finally, using shotgun sequence data we assessed indicators of diet from DNA in calculus and suggest exercising caution when making assertions related to host lifestyle. These results showcase core differences between host species and stress the importance of continued sequencing of nonhuman primate microbiomes in order to fully understand the complexity of their oral ecologies.

New evidence for Upper Palaeolithic small domestic dogs in South-Western Europe

2011 ◽  
Vol 38 (9) ◽  
pp. 2123-2140 ◽  
Author(s):  
Maud Pionnier-Capitan ◽  
Céline Bemilli ◽  
Pierre Bodu ◽  
Guy Célérier ◽  
Jean-Georges Ferrié ◽  
...  
Keyword(s):  
Western Europe ◽  
Domestic Dogs ◽  
Upper Palaeolithic ◽  
New Evidence

Wrestling with Analogy: A Methodological Dilemma in Upper Palaeolithic Art Research.

1991 ◽  
Vol 57 (01) ◽  
pp. 149-162 ◽  
Author(s):  
J. D. Lewis-Williams
Keyword(s):  
Western Europe ◽  
Upper Palaeolithic ◽  
Prehistoric Art ◽  
Scientific Opinion ◽  
Art Research ◽  
Analogical Argument ◽  
Palaeolithic Art

In 1902 Emile Cartailhac published hisMea Culpa d'un Sceptique. His acceptance of the high antiquity of prehistoric art in western Europe followed Capitan and Breuil's convincing discoveries in Font de Gaume and Les Combarelles and reflected a widespread change of opinion. Despite previous scepticism, researchers were beginning to allow that the parietal as well as the mobile art did indeed date back to the Upper Palaeolithic. But this swing in scientific opinion opened up an even more baffling problem: why did Upper Palaeolithic people make these pictures? In the year following Cartailhac's turn-about Salomon Reinach tried to answer this question by developing an analogical argument based on ethnographic parallels. He could see no other way of approaching the problem: ‘Our only hope of finding outwhythe troglodytes painted and sculpted lies in asking the same question of present-day primitives with whom the ethnography reveals connections’ (Reinach 1903, 259; my translation, his emphasis).

scholarly journals Determinación del sexo a través de la métrica dental en cazadores recolectores de la transición pampeano-patagónica oriental / SEX DETERMINATION THROUGH DENTAL METRICS FOR HUNTER-GATHERER GROUPS FROM THE EASTERN PAMPA-PATAGONIAN TRANSITION

2017 ◽  
Vol 10 (1) ◽  
pp. 53 ◽  
Author(s):  
Leandro Luna ◽  
Gustavo Flensborg
Keyword(s):  
Sexual Dimorphism ◽  
Late Holocene ◽  
Colorado River ◽  
Human Populations ◽  
Hunter Gatherers ◽  
Dental Metrics ◽  
Sexual Information ◽  
Palabras Clave ◽  
Sexual Determination ◽  
Del Rio

<p>El objetivo de este trabajo es evaluar la pertinencia de la métrica dental para obtener información sexual en individuos que habitaron el curso inferior del río Colorado durante el Holoceno tardío (ca. 3000-250 años AP), discutir el grado de dimorfismo sexual e identificar las variables cuantitativas de la dentición que permitan discriminar el sexo de nuevos individuos que se incluyan en futuros análisis. Se estudiaron las medidas máximas bucolinguales y mesiodistales del cuello de los dientes correspondientes a 26 individuos adultos. Las variables más dimórficas corresponden al diámetro bucolingual del canino superior y de ambos segundos molares; en estos casos, las diferencias entre los sexos son estadísticamente significativas. Los resultados obtenidos sobre el dimorfismo sexual se ubican en el extremo superior de los valores correspondientes a diferentes poblaciones humanas. Varios individuos que no contaban con información sexual a través de los métodos tradicionales pudieron ser clasificados desde la métrica dental, lo cual da cuenta del importante potencial de las medidas dentales para contribuir a las caracterizaciones paleodemográficas de conjuntos bioarqueológicos, especialmente en contextos perturbados y con escasa integridad esqueletal.</p><p>Palabras clave: métrica dental; determinación sexual; cazadores-recolectores; curso inferior del río Colorado; Holoceno tardío.</p><p>Abstract<br />The aim of this paper is to evaluate the relevance of dental metrics for obtaining sexual information in individuals who inhabited the lower basin of the Colorado River during the Late Holocene (ca. 3000-250 years BP), to discuss the degree of sexual dimorphism and to identify those quantitative variables adequate for sexual determination of new individuals to be included in future studies. The buccolingual and mesiodistal maximum neck diameters of 26 individual adults were studied. The most dimorphic variables correspond to the buccolingual diameter of the upper canine and both second molars; in these cases, sex differences are statistically significant. The results obtained about sexual dimorphism are located at the upper end of the range for different human populations. Several individuals who had no previous sexual information could be classified using these measurements, which accounts for the significant potential of dental metrics in palaeodemographic characterizations, especially in disturbed bioarchaeological samples.</p><p>Keywords: dental metrics; sexual determination; hunter-gatherers; lower basin of the Colorado River; Late Holocene.</p>

scholarly journals Mitochondrial DNA Variation of Feral Honey Bees (Apis mellifera L.) from Utah (USA)

2018 ◽  
Vol 62 (2) ◽  
pp. 223-232
Author(s):  
Dylan Cleary ◽  
Allen L. Szalanski ◽  
Clinton Trammel ◽  
Mary-Kate Williams ◽  
Amber Tripodi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Apis Mellifera ◽  
Honey Bee ◽  
Honey Bees ◽  
Western Europe ◽  
Dna Variation ◽  
Bee Colony ◽  
The Us ◽  
Coii Gene

Abstract A study was conducted on the mitochondrial DNA genetic diversity of feral colonies and swarms of Apis mellifera from ten counties in Utah by sequencing the intergenic region of the cytochrome oxidase (COI-COII) gene region. A total of 20 haplotypes were found from 174 honey bee colony samples collected from 2008 to 2017. Samples belonged to the A (African) (48%); C (Eastern Europe) (43%); M (Western Europe) (4%); and O (Oriental) lineages (5%). Ten African A lineage haplotypes were observed with two unique to Utah among A lineage haplotypes recorded in the US. Haplotypes belonging to the A lineage were observed from six Utah counties located in the southern portion of the State, from elevations as high as 1357 m. All five C lineage haplotypes that were found have been observed from queen breeders in the US. Three haplotypes of the M lineage (n=7) and two of the O lineage (n=9) were also observed. This study provides evidence that honey bees of African descent are both common and diverse in wild populations of honey bees in southern Utah. The high levels of genetic diversity of A lineage honey bee colonies in Utah provide evidence that the lineage may have been established in Utah before the introduction of A lineage honey bees from Brazil to Texas in 1990.

scholarly journals Genomic and demographic processes differentially influence genetic variation across the X chromosome

2021 ◽  
Author(s):  
Daniel J. Cotter ◽  
Timothy H. Webster ◽  
Melissa A. Wilson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
X Chromosome ◽  
Global Scale ◽  
Careful Consideration ◽  
Human Populations ◽  
Evolutionary Forces ◽  
Ideal System ◽  
Demographic Patterns

AbstractMutation, recombination, selection, and demography affect genetic variation across the genome. Increased mutation and recombination both lead to increases in genetic diversity in a region-specific manner, while complex demographic patterns shape patterns of diversity on a more global scale. The X chromosome is particularly interesting because it contains several distinct regions that are subject to different combinations and strengths of these processes, notably the pseudoautosomal regions (PARs) and the X-transposed region (XTR). The X chromosome thus can serve as a unique model for studying how genetic and demographic forces act in different contexts to shape patterns of observed variation. Here we investigate diversity, divergence, and linkage disequilibrium in each region of the X chromosome using genomic data from 26 human populations. We find that both diversity and substitution rate are consistently elevated in PAR1 and the XTR compared to the rest of the X chromosome. In contrast, linkage disequilibrium is lowest in PAR1 and highest on the non-recombining X chromosome, with the XTR falling in between, suggesting that the XTR (usually included in the non-recombining X) may need to be considered separately in future studies. We also observed strong population-specific effects on genetic diversity; not only does genetic variation differ on the X and autosomes among populations, but the effects of linked selection on the X relative to autosomes have been shaped by population-specific history. The substantial variation in patterns of variation across these regions provides insight into the unique evolutionary history contained within the X chromosome.Significance StatementDemography and selection affect the X chromosome differently from non-sex chromosomes. However, the X chromosome can be subdivided into multiple distinct regions that facilitate even more fine-scaled assessment of these processes. Here we study regions of the human X chromosome in 26 populations to find evidence that recombination may be mutagenic in humans and that the X-transposed region may undergo recombination. Further we observe that the effects of selection and demography act differently on the X chromosome relative to the autosomes across human populations. Together, our results highlight profound regional differences across the X chromosome, simultaneously making it an ideal system for exploring the action of evolutionary forces as well as necessitating its careful consideration and treatment in genomic analyses.

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