The genomic origins of the world's first farmers.
Ontology highlight
ABSTRACT:
SUBMITTER: Marchi N
PROVIDER: S-EPMC9166250 | biostudies-literature | 2022 May
REPOSITORIES: biostudies-literature
Publications
The genomic origins of the world's first farmers.
Marchi Nina N Winkelbach Laura L Schulz Ilektra I Brami Maxime M Hofmanová Zuzana Z Blöcher Jens J Reyna-Blanco Carlos S CS Diekmann Yoan Y Thiéry Alexandre A Kapopoulou Adamandia A Link Vivian V Piuz Valérie V Kreutzer Susanne S Figarska Sylwia M SM Ganiatsou Elissavet E Pukaj Albert A Struck Travis J TJ Gutenkunst Ryan N RN Karul Necmi N Gerritsen Fokke F Pechtl Joachim J Peters Joris J Zeeb-Lanz Andrea A Lenneis Eva E Teschler-Nicola Maria M Triantaphyllou Sevasti S Stefanović Sofija S Papageorgopoulou Christina C Wegmann Daniel D Burger Joachim J Excoffier Laurent L
Cell 20220512 11
The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farm ...[more]
Similar Datasets
Project description:Study of ancient and modern genomes
2022-08-16 | PRJEB51919 | EVA
Project description:Rafflesiaceae, which produce the world's largest flowers, have captivated the attention of biologists for nearly two centuries. Despite their fame, however, the developmental nature of the floral organs in these giants has remained a mystery. Most members of the family have a large floral chamber defined by a diaphragm. The diaphragm encloses the reproductive organs where pollination by carrion flies occurs. In lieu of a functional genetic system to investigate floral development in these highly specialized holoparasites, we used comparative studies of structure, development, and gene-expression patterns to investigate the homology of their floral organs. Our results surprisingly demonstrate that the otherwise similar floral chambers in two Rafflesiaceae subclades, Rafflesia and Sapria, are constructed very differently. In Rafflesia, the diaphragm is derived from the petal whorl. In contrast, in Sapria it is derived from elaboration of a unique ring structure located between the perianth and the stamen whorl, which, although developed to varying degrees among the genera, appears to be a synapomorphy of the Rafflesiaceae. Thus, the characteristic features that define the floral chamber in these closely related genera are not homologous. These differences refute the prevailing hypothesis that similarities between Sapria and Rafflesia are ancestral in the family. Instead, our data indicate that Rafflesia-like and Sapria-like floral chambers represent two distinct derivations of this morphology. The developmental repatterning we identified in Rafflesia, in particular, may have provided architectural reinforcement, which permitted the explosive growth in floral diameter that has arisen secondarily within this subclade.
| S-EPMC3831985 | biostudies-literature
Project description:Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes-more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling.IMPORTANCEWe address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1,512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. Our work reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step toward comprehending the intricate world of soil microorganisms and its role in the global climate.
| S-EPMC11237643 | biostudies-literature
Project description:Selenium (Se) solar cells were the world's first solid-state photovoltaics reported in 1883, opening the modern photovoltaics. However, its wide bandgap (~1.9 eV) limits sunlight harvesting. Here, we revisit the world's oldest but long-ignored photovoltaic material with the emergence of indoor photovoltaics (IPVs); the absorption spectrum of Se perfectly matches the emission spectra of commonly used indoor light sources in the 400 to 700 nm range. We find that the widely used Te adhesion layer also passivates defects at the nonbonded Se/TiO2 interface. By optimizing the Te coverage from 6.9 to 70.4%, the resulting Se cells exhibit an efficiency of 15.1% under 1000 lux indoor illumination and show no efficiency loss after 1000 hours of continuous indoor illumination without encapsulation, outperforming the present IPV industry standard of amorphous silicon cells in both efficiency and stability. We further fabricate Se modules (6.75 cm2) that produce 232.6 μW output power under indoor illumination, powering a radio-frequency identification-based localization tag.
| S-EPMC9728960 | biostudies-literature
Project description:Animal cloning has gained popularity as a method to produce genetically identical animals or superior animals for research or industrial uses. However, the long-standing question of whether a cloned animal undergoes an accelerated aging process is yet to be answered. As a step towards answering this question, we compared longevity and health of Snuppy, the world's first cloned dog, and its somatic cell donor, Tai, a male Afghan hound. Briefly, both Snuppy and Tai were generally healthy until both developed cancer to which they succumbed at the ages of 10 and 12 years, respectively. The longevity of both the donor and the cloned dog was close to the median lifespan of Afghan hounds which is reported to be 11.9 years. Here, we report creation of 4 clones using adipose-derived mesenchymal stem cells from Snuppy as donor cells. Clinical and molecular follow-up of these reclones over their lives will provide us with a unique opportunity to study the health and longevity of cloned animals compared with their cell donors.
| S-EPMC5681657 | biostudies-literature
Project description:Around 10,000 y ago in southwest Asia, the cessation of a mobile lifestyle and the emergence of the first village communities during the Neolithic marked a fundamental change in human history. The first communities were small (tens to hundreds of individuals) but remained semisedentary. So-called megasites appeared soon after, occupied by thousands of more sedentary inhabitants. Accompanying this shift, the material culture and ancient ecological data indicate profound changes in economic and social behavior. A shift from residential to logistical mobility and increasing population size are clear and can be explained by either changes in fertility and/or aggregation of local groups. However, as sedentism increased, small early communities likely risked inbreeding without maintaining or establishing exogamous relationships typical of hunter-gatherers. Megasites, where large populations would have made endogamy sustainable, could have avoided this risk. To examine the role of kinship practices in the rise of megasites, we measured strontium and oxygen isotopes in tooth enamel from 99 individuals buried at Pınarbaşı, Boncuklu, and Çatalhöyük (Turkey) over 7,000 y. These sites are geographically proximate and, critically, span both early sedentary behaviors (Pınarbaşı and Boncuklu) and the rise of a local megasite (Çatalhöyük). Our data are consistent with the presence of only local individuals at Pınarbaşı and Boncuklu, whereas at Çatalhöyük, several nonlocals are present. The Çatalhöyük data stand in contrast to other megasites where bioarchaeological evidence has pointed to strict endogamy. These different kinship behaviors suggest that megasites may have arisen by employing unique, community-specific kinship practices.
| S-EPMC9942817 | biostudies-literature
Project description:Lung function tracks from the earliest age that it can be reliably measured. Genome wide association studies suggest that most variants identified for common complex traits are regulatory in function and active during fetal development. Fetal programming of gene expression during development is critical to the formation of a normal lung. An understanding of how fetal developmental genes related to diseases of the lungs and airways is a critical area for research. This review article considers the developmental origins hypothesis, the stages of normal lung development and a variety of environmental exposures that might influence the developmental process: in utero cigarette smoke exposure, vitamin D and folate. We conclude with some information on developmental genes and asthma.
| S-EPMC4343201 | biostudies-literature
Project description:Community differentiation is a fundamental topic of the social sciences, and its prehistoric origins in Europe are typically assumed to lie among the complex, densely populated societies that developed millennia after their Neolithic predecessors. Here we present the earliest, statistically significant evidence for such differentiation among the first farmers of Neolithic Europe. By using strontium isotopic data from more than 300 early Neolithic human skeletons, we find significantly less variance in geographic signatures among males than we find among females, and less variance among burials with ground stone adzes than burials without such adzes. From this, in context with other available evidence, we infer differential land use in early Neolithic central Europe within a patrilocal kinship system.
| S-EPMC3386065 | biostudies-literature
Project description:Obelisks presented an important element in the architecture of ancient Egypt. This research is concerned with the re-erection of an obelisk that belongs to the famous Pharoah Ramses II. It was found broken and was transported to the Grand Egyptian Museum for restoration and display. An observation of Ramses II Cartouche at the bottom side of the obelisk base inspired the authorities to provide an innovative architectural design to display the obelisk elevated. The supporting structure was designed to allow the visitors to walk underneath the obelisk and observe Ramses II's signature. The idea of elevating the obelisk presented several challenges including evaluating the obelisk's current condition, restoration and fixation methodology, structural stability, and uncertainties of material characteristics, amongst others. To control the obelisk deformations under lateral loading, state-of-the-art base isolators were introduced. For the task to be achieved, a multidisciplinary team including historians, conservators, archaeologists, architects, and engineers with different specialties was appointed. The team performed the task successfully and currently, the obelisk stands at the entrance piazza of the Grand Egyptian Museum representing the world's first elevated obelisk.
| S-EPMC9899242 | biostudies-literature
Project description:Treatment of patients with large bone defects is a complex clinical problem. We have initiated the first clinical study of a gene-activated bone substitute composed of the collagen-hydroxyapatite scaffold and plasmid DNA encoding vascular endothelial growth factor. The first patient with two nonunions of previously reconstructed mandible was enrolled into the study. Scar tissues were excised; bone defects (5-14 mm) between the mandibular fragments and nonvascularized rib-bone autograft were filled in with the gene-activated bone substitute. No adverse events were observed during 12 months of follow-up. In 3 months, the average density of newly formed tissues within the implantation zone was 402.21 ± 84.40 and 447.68 ± 106.75 HU in the frontal and distal regions, respectively, which correlated with the density of spongy bone. Complete distal bone defect repair with vestibular and lingual cortical plates formation was observed in 6 and 12 months after surgery; thereby the posterior nonunion was successfully eliminated. However, there was partial resorption of the proximal edge of the autograft entailed to relapse of the anterior nonunion. Thus, the first clinical data on the safety and efficacy of the gene-activated bone substitute were obtained. Given a high complexity of the clinical situation the treatment, results might be considered as promising. NCT02293031.
| S-EPMC5116519 | biostudies-literature