Pig domestication and human-mediated dispersal in western eurasia revealed through ancient DNA and geometric morphometrics

Zooarcheological evidence suggests that pigs were domesticated in Southwest Asia ∼8,500 BC. They then spread across the Middle and Near East and westward into Europe alongside early agriculturalists. European pigs were either domesticated independently or more likely appeared so as a result of admixture between introduced pigs and European wild boar. As a result, European wild boar mtDNA lineages replaced Near Eastern/Anatolian mtDNA signatures in Europe and subsequently replaced indigenous domestic pig lineages in Anatolia. The specific details of these processes, however, remain unknown. To address questions related to early pig domestication, dispersal, and turnover in the Near East, we analyzed ancient mitochondrial DNA and dental geometric morphometric variation in 393 ancient pig specimens representing 48 archeological sites (from the Pre-Pottery Neolithic to the Medieval period) from Armenia, Cyprus, Georgia, Iran, Syria, and Turkey. Our results reveal the first genetic signatures of early domestic pigs in the Near Eastern Neolithic core zone. We also demonstrate that these early pigs differed genetically from those in western Anatolia that were introduced to Europe during the Neolithic expansion. In addition, we present a significantly more refined chronology for the introduction of European domestic pigs into Asia Minor that took place during the Bronze Age, at least 900 years earlier than previously detected. By the 5th century AD, European signatures completely replaced the endemic lineages possibly coinciding with the widespread demographic and societal changes that occurred during the Anatolian Bronze and Iron Ages

Ancient goat genomes reveal mosaic domestication in the Fertile Crescent

Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Archaeological evidence indicates that pig domestication had begun by ~10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ~8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local Euro-pean wild boars, although it is also possible that European wild boars were domesticated independently without any genetic con-tribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process

MATLAB Simulation-Based Theoretical Study for Detection of a Wide Range of Pathogens Using 1D Defective Photonic Structure

The present 1D photonic biosensor is composed of two sub-PhCs of alternate layers made of GaP and SiO2. The period number of each PhC has been fixed to 3. Both these PhCs are joined together through a cavity region of air in which different analytes are to be filled one by one under the scope of this study. The theoretical findings of this work have been formulated with the help of the well-known transfer matrix method. Moreover, all the computations pertaining to this work have been carried out with the help of MATLAB software. The effect of change in cavity thickness and angle of incidence corresponding to a TE wave on the transmittance of the structure (AB)ND(AB)N has been studied theoretically which in turn determines the performance of the proposed biosensor. Various parameters, such as sensitivity (S), signal to noise ratio (SNR), figure of merit (FOM), resolution (RS), detection limit (LOD), quality factor (Q) and dynamic range (DR) have been theoretically calculated to evaluate the performance of the proposed design in true sense. The sensitivity of this structure varies between the highest and lowest values of 337.3626 nm/RIU and 333.0882 nm/RIU corresponding to water samples containing Pseudomonas aeruginosa cells and Bacillus anthracia cells, respectively, under normal incidence condition with a cavity thickness of 2.0 µm. The resolution (in nm) and LOD (in RIU) values of the proposed design are small enough and are significant for our structure. This study may also be helpful for distinguishing various microbiological samples under investigation and find suitable applications for discriminating bacterial cells from spores

MATLAB Simulation-Based Theoretical Study for Detection of a Wide Range of Pathogens Using 1D Defective Photonic Structure

The present 1D photonic biosensor is composed of two sub-PhCs of alternate layers made of GaP and SiO2. The period number of each PhC has been fixed to 3. Both these PhCs are joined together through a cavity region of air in which different analytes are to be filled one by one under the scope of this study. The theoretical findings of this work have been formulated with the help of the well-known transfer matrix method. Moreover, all the computations pertaining to this work have been carried out with the help of MATLAB software. The effect of change in cavity thickness and angle of incidence corresponding to a TE wave on the transmittance of the structure (AB)ND(AB)N has been studied theoretically which in turn determines the performance of the proposed biosensor. Various parameters, such as sensitivity (S), signal to noise ratio (SNR), figure of merit (FOM), resolution (RS), detection limit (LOD), quality factor (Q) and dynamic range (DR) have been theoretically calculated to evaluate the performance of the proposed design in true sense. The sensitivity of this structure varies between the highest and lowest values of 337.3626 nm/RIU and 333.0882 nm/RIU corresponding to water samples containing Pseudomonas aeruginosa cells and Bacillus anthracia cells, respectively, under normal incidence condition with a cavity thickness of 2.0 µm. The resolution (in nm) and LOD (in RIU) values of the proposed design are small enough and are significant for our structure. This study may also be helpful for distinguishing various microbiological samples under investigation and find suitable applications for discriminating bacterial cells from spores

The Pleistocene Biodiversity of the Zagros Mountains: Carnivores of the Chenar Cave (Kermanshah- Iran)

International audienceOver the past decades, several Pleistocene caves and rock shelters in the Zagros Mountains have been discovered with remarkable evidences of carnivore remains. This paper presents the assemblage of Chenar cave located in Kermanshah (West-Central Zagros), at 1630m asl, on the southern face of the Paraw Mountain. The cave was discovered through an archaeological survey in 2007 by FB and AMB. It included two shafts damaged by looters. The back-dirt sediment was systematically examined indicating 795 animal bones. The nature of the sediment and taphonomical features are undoubtedly an indication of Pleistocene cave. Carnivore remains (43%) consist of fox (Vulpes sp.), striped hyena (Hyaena hyeana), golden jackal (Canis aureus), lynx (Lynx sp.), leopard (Panthera pardus), brown bear (Ursus arctos), cave bear (U.spelaeus / Spelearctos deningeri), caracal (Caracal caracal) and spotted hyena (Crocuta crocuta). The herbivore remains (37%: sheep, goat, boar and cattle) may have been the prey of these carnivores although any anthropogenic traces on the bones have been observed. The Chenar cave was used as a den alternatively for multiple carnivore species, similar to the profile of the Wezmeh cave (SW of the Chenar). Despite the disturbed character of the remains, the presence of spotted and striped hyenas and cave bear adds precious information about the evolution of these species on the Iranian Plateau. Along with Chenar, the past biodiversity of Iran during the Pleistocene is gradually documented by with zooarchaological studies from Wezmeh and Zilou caves in the Zagros and Darband cave in the Alborz Mountains

The Pleistocene Biodiversity of the Zagros Mountains: Carnivores of the Chenar Cave (Kermanshah- Iran)

International audienceOver the past decades, several Pleistocene caves and rock shelters in the Zagros Mountains have been discovered with remarkable evidences of carnivore remains. This paper presents the assemblage of Chenar cave located in Kermanshah (West-Central Zagros), at 1630m asl, on the southern face of the Paraw Mountain. The cave was discovered through an archaeological survey in 2007 by FB and AMB. It included two shafts damaged by looters. The back-dirt sediment was systematically examined indicating 795 animal bones. The nature of the sediment and taphonomical features are undoubtedly an indication of Pleistocene cave. Carnivore remains (43%) consist of fox (Vulpes sp.), striped hyena (Hyaena hyeana), golden jackal (Canis aureus), lynx (Lynx sp.), leopard (Panthera pardus), brown bear (Ursus arctos), cave bear (U.spelaeus / Spelearctos deningeri), caracal (Caracal caracal) and spotted hyena (Crocuta crocuta). The herbivore remains (37%: sheep, goat, boar and cattle) may have been the prey of these carnivores although any anthropogenic traces on the bones have been observed. The Chenar cave was used as a den alternatively for multiple carnivore species, similar to the profile of the Wezmeh cave (SW of the Chenar). Despite the disturbed character of the remains, the presence of spotted and striped hyenas and cave bear adds precious information about the evolution of these species on the Iranian Plateau. Along with Chenar, the past biodiversity of Iran during the Pleistocene is gradually documented by with zooarchaological studies from Wezmeh and Zilou caves in the Zagros and Darband cave in the Alborz Mountains

The Pleistocene Biodiversity of the Zagros Mountains: Carnivores of the Chenar Cave (Kermanshah- Iran)

International audienceOver the past decades, several Pleistocene caves and rock shelters in the Zagros Mountains have been discovered with remarkable evidences of carnivore remains. This paper presents the assemblage of Chenar cave located in Kermanshah (West-Central Zagros), at 1630m asl, on the southern face of the Paraw Mountain. The cave was discovered through an archaeological survey in 2007 by FB and AMB. It included two shafts damaged by looters. The back-dirt sediment was systematically examined indicating 795 animal bones. The nature of the sediment and taphonomical features are undoubtedly an indication of Pleistocene cave. Carnivore remains (43%) consist of fox (Vulpes sp.), striped hyena (Hyaena hyeana), golden jackal (Canis aureus), lynx (Lynx sp.), leopard (Panthera pardus), brown bear (Ursus arctos), cave bear (U.spelaeus / Spelearctos deningeri), caracal (Caracal caracal) and spotted hyena (Crocuta crocuta). The herbivore remains (37%: sheep, goat, boar and cattle) may have been the prey of these carnivores although any anthropogenic traces on the bones have been observed. The Chenar cave was used as a den alternatively for multiple carnivore species, similar to the profile of the Wezmeh cave (SW of the Chenar). Despite the disturbed character of the remains, the presence of spotted and striped hyenas and cave bear adds precious information about the evolution of these species on the Iranian Plateau. Along with Chenar, the past biodiversity of Iran during the Pleistocene is gradually documented by with zooarchaological studies from Wezmeh and Zilou caves in the Zagros and Darband cave in the Alborz Mountains

Detection of Reproductive Hormones in Females by Using 1D Photonic Crystal-Based Simple Reconfigurable Biosensing Design

In this manuscript, we have explored the photonic biosensing application of the 1D photonic crystal (PhC) (AB)NCDC(AB)N, which is capable of detecting reproductive progesterone and estradiol hormones of different concentration levels in blood samples of females. The proposed structure is composed of an air cavity surrounded by two buffer layers of material MgF2, which is sandwiched between two identical 1D sub PhCs (AB)N. Both sub PhCs are made up of alternate layers of materials, SiO2 and Si, of period 5. MATLAB software has been used to obtain transmission characteristics of the structure corresponding TE wave, only with the help of the transfer matrix method. The mainstay of this research is focused on the dependence of the intensity and position of the defect mode inside the photonic bandgap with respect to reproductive hormone concentrations in blood samples, change in the thickness of the cavity region and change in angle of incidence corresponding to TE wave only. The proposed design shows high sensitivity of 98.92 nm/nmol/L and 96.58 nm/nmol/L when the cavity of a thickness of 340 nm is loaded with progesterone and estradiol hormones of concentrations of 80 nmol/L and 11 nmol/L, respectively, at an incident angle of 20°. Apart from sensitivity, other parameters such as quality factor and figure of merit have also been computed to gain deep insight about the sensing capabilities of the proposed design. These findings may pave the path for the design and development of various sensing devices capable of detecting gynecological problems pertaining to reproductive hormones in females. Thus, the simple design and excellent performance makes our design most efficient and suitable for sensing applications in industrial and biomedical fields