Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep (Ovis aries)

Occupied between ~10,300 and 9300 years ago, the Pre-Pottery Neolithic site of Aşıklı Höyük in Central Anatolia went through early phases of sheep domestication. Analysis of 629 mitochondrial genomes from this and numerous sites in Anatolia, southwest Asia, Europe, and Africa produced a phylogenetic tree with excessive coalescences (nodes) around the Neolithic, a potential signature of a domestication bottleneck. This is consistent with archeological evidence of sheep management at Aşıklı Höyük which transitioned from residential stabling to open pasturing over a millennium of site occupation. However, unexpectedly, we detected high genetic diversity throughout Aşıklı Höyük's occupation rather than a bottleneck. Instead, we detected a tenfold demographic bottleneck later in the Neolithic, which caused the fixation of mitochondrial haplogroup B in southwestern Anatolia. The mitochondrial genetic makeup that emerged was carried from the core region of early Neolithic sheep management into Europe and dominates the matrilineal diversity of both its ancient and the billion-strong modern sheep populations.

Biological and substitute parents in Beaker period adult-child graves

Joint inhumations of adults and children are an intriguing aspect of the shift from collective to single burial rites in third millennium BC Western Eurasia. Here, we revisit two exceptional Beaker period adult-child graves using ancient DNA: Altwies in Luxembourg and Dunstable Downs in Britain. Ancestry modelling and patterns of shared IBD segments between the individuals examined, and contemporary genomes from Central and Northwest Europe, highlight the continental connections of British Beakers. Although simultaneous burials may involve individuals with no social or biological ties, we present evidence that close blood relations played a role in shaping third millennium BC social systems and burial practices, for example a biological mother and her son buried together at Altwies. Extended family, such as a paternal aunt at Dunstable Downs, could also act as 'substitute parents' in the grave. Hypotheses are explored to explain such simultaneous inhumations. Whilst intercommunity violence, infectious disease and epidemics may be considered as explanations, they fail to account for both the specific, codified nature of this particular form of inhumation, and its pervasiveness, as evidenced by a representative sample of 131 adult-child graves from 88 sites across Eurasia, all dating to the third and second millennia BC.

Temporal Structures in Positron Spectra and Charge-Sign Effects in Galactic Cosmic Rays

We present the precision measurements of 11 years of daily cosmic positron fluxes in the rigidity range from 1.00 to 41.9 GV based on 3.4×10^{6} positrons collected with the Alpha Magnetic Spectrometer (AMS) aboard the International Space Station. The positron fluxes show distinctly different time variations from the electron fluxes at short and long timescales. A hysteresis between the electron fluxes and the positron fluxes is observed with a significance greater than 5σ at rigidities below 8.5 GV. On the contrary, the positron fluxes and the proton fluxes show similar time variation. Remarkably, we found that positron fluxes are modulated more than proton fluxes with a significance greater than 5σ for rigidities below 7 GV. These continuous daily positron fluxes, together with AMS daily electron, proton, and helium fluxes over an 11-year solar cycle, provide unique input to the understanding of both the charge-sign and mass dependencies of cosmic rays in the heliosphere.

Design of percutaneous transluminal coronary angioplasty balloon catheters

BACKGROUND

Eight commercially available percutaneous transluminal coronary angioplasty (PTCA), including semi-compliant and non-compliant balloons, have been assessed in detail on their tip, balloon, shaft, RX-Port, and hypotube design. Important performance characteristics such as tip deformation, balloon elongation, and deflation rate have been quantified.

METHODS

Five catheters of each model were evaluated during various tests. The robustness of the tips was evaluated through compression, measuring any occurrence of damage. The longitudinal growth of the balloons was recorded during inflation up to Rated Burst Pressure (RBP). The forces required to move the catheter forward and retract it into the guide catheter were measured in a simulated use test setup. The deflation behavior was studied by measuring extracted contrast media over time. Furthermore, balloon compliance and catheter dimensions were investigated.

RESULTS

The outer dimensions of the catheter were found to be smallest at the hypotube (0.59-0.69 mm) and highest at the balloon, respectively, the crossing profile (0.9-1.2 mm). The tip diameter increased after compression by 1.7-22%. Cross-sections of the folded balloons revealed a tri- and two-fold, respectively. The measured balloon elongation ranged from 0.6 to 2.0 mm. After the inflation of the balloon, an increase in friction between the guide wire and the catheter was observed on four catheters. A maximum increase of 0.12 N to 1.07 N was found. Cross-sections of the RX-Port revealed a semicircular-shaped inflation lumen and a circular guide wire lumen. The measured deflation rate ranged from 0.004 to 0.013 µL/s, resulting in an estimated balloon deflation time of 10.2-28.1 s.

CONCLUSION

This study provides valuable insights into the design characteristics of RX PTCA balloon catheters, which can contribute to facilitating the development of improved catheter designs and enhancing clinical outcomes. Distinctions between SC and NC catheters, such as balloon performance and dimensions, are evident. It is important to note that no single catheter excels in all aspects, as each possesses unique strengths. Therefore, it is essential to consider individual intervention requirements when selecting a catheter. The research also identifies specific catheter weaknesses, such as reduced wall thickness, fringes at the tip, and reduced performance characteristics.

Descent, marriage, and residence practices of a 3,800-year-old pastoral community in Central Eurasia

Our understanding of prehistoric societal organization at the family level is still limited. Here, we generated genome data from 32 individuals from an approximately 3,800-y-old burial mound attributed to the Bronze Age Srubnaya-Alakul cultural tradition at the site of Nepluyevsky, located in the Southern Ural region of Central Eurasia. We found that life expectancy was generally very low, with adult males living on average 8 y longer than females. A total of 35 first-degree, 40 second-degree, and 48 third-degree biological relationships connected 23 of the studied individuals, allowing us to propose a family tree spanning three generations with six brothers at its center. The oldest of these brothers had eight children with two women and the most children overall, whereas the other relationships were monogamous. Notably, related female children above the age of five were completely absent from the site, and adult females were more genetically diverse than males. These results suggest that biological relationships between male siblings played a structural role in society and that descent group membership was based on patrilineality. Women originated from a larger mating network and moved to join the men, with whom they were buried. Finally, the oldest brother likely held a higher social position, which was expressed in terms of fertility.

Properties of Cosmic-Ray Sulfur and Determination of the Composition of Primary Cosmic-Ray Carbon, Neon, Magnesium, and Sulfur: Ten-Year Results from the Alpha Magnetic Spectrometer

We report the properties of primary cosmic-ray sulfur (S) in the rigidity range 2.15 GV to 3.0 TV based on 0.38×10^{6} sulfur nuclei collected by the Alpha Magnetic Spectrometer experiment (AMS). We observed that above 90 GV the rigidity dependence of the S flux is identical to the rigidity dependence of Ne-Mg-Si fluxes, which is different from the rigidity dependence of the He-C-O-Fe fluxes. We found that, similar to N, Na, and Al cosmic rays, over the entire rigidity range, the traditional primary cosmic rays S, Ne, Mg, and C all have sizeable secondary components, and the S, Ne, and Mg fluxes are well described by the weighted sum of the primary silicon flux and the secondary fluorine flux, and the C flux is well described by the weighted sum of the primary oxygen flux and the secondary boron flux. The primary and secondary contributions of the traditional primary cosmic-ray fluxes of C, Ne, Mg, and S (even Z elements) are distinctly different from the primary and secondary contributions of the N, Na, and Al (odd Z elements) fluxes. The abundance ratio at the source for S/Si is 0.167±0.006, for Ne/Si is 0.833±0.025, for Mg/Si is 0.994±0.029, and for C/O is 0.836±0.025. These values are determined independent of cosmic-ray propagation.

Temporal Structures in Electron Spectra and Charge Sign Effects in Galactic Cosmic Rays

We present the precision measurements of 11 years of daily cosmic electron fluxes in the rigidity interval from 1.00 to 41.9 GV based on 2.0×10^{8} electrons collected with the Alpha Magnetic Spectrometer (AMS) aboard the International Space Station. The electron fluxes exhibit variations on multiple timescales. Recurrent electron flux variations with periods of 27 days, 13.5 days, and 9 days are observed. We find that the electron fluxes show distinctly different time variations from the proton fluxes. Remarkably, a hysteresis between the electron flux and the proton flux is observed with a significance of greater than 6σ at rigidities below 8.5 GV. Furthermore, significant structures in the electron-proton hysteresis are observed corresponding to sharp structures in both fluxes. This continuous daily electron data provide unique input to the understanding of the charge sign dependence of cosmic rays over an 11-year solar cycle.

HaploBlocks: Efficient Detection of Positive Selection in Large Population Genomic Datasets

Genomic regions under positive selection harbor variation linked for example to adaptation. Most tools for detecting positively selected variants have computational resource requirements rendering them impractical on population genomic datasets with hundreds of thousands of individuals or more. We have developed and implemented an efficient haplotype-based approach able to scan large datasets and accurately detect positive selection. We achieve this by combining a pattern matching approach based on the positional Burrows-Wheeler transform with model-based inference which only requires the evaluation of closed-form expressions. We evaluate our approach with simulations, and find it to be both sensitive and specific. The computational resource requirements quantified using UK Biobank data indicate that our implementation is scalable to population genomic datasets with millions of individuals. Our approach may serve as an algorithmic blueprint for the era of "big data" genomics: a combinatorial core coupled with statistical inference in closed form.

Between Raetia Secunda and the dutchy of Bavaria: Exploring patterns of human movement and diet

During the transition from Late Antiquity to the Middle Ages, the Roman Empire dissolved in the West and medieval empires were founded. There has been much discussion about the role that migration played in this transition. This is especially true for the formation of the Baiuvariian tribe and the founding of this tribal dukedom, which took place from the 5th to the 6th century in what is now Southern Bavaria (Germany). In this study, we aimed to determine the extent of immigration during the beginning of this transformation and to shed further light on its character. To achieve this goal, we analyzed stable isotope values of strontium, carbon, and nitrogen from the teeth and bones of over 150 human remains from Southern Germany, dating from around 500 AD. This group of individuals included women with cranial modifications (ACD) which can be found sporadically in the burial grounds of this period. Our results showed an above-average migration rate for both men and women in the second half of the 5th century. They also indicate that a foreign background may also be assumed for the women with ACD. The demonstrably different origins of the immigrants from isotopically diverse regions, and the identification of local differences in detectable migration rate, as well as indication for different timing of residential changes, highlight the complexity of immigration processes and the need for more studies at the regional level.

Thresholds for the presence of glacial megafauna in central Europe during the last 60,000 years

Lake sediment records from Holzmaar and the infilled maar of Auel (Eifel, Germany) are used to reconstruct landscape changes and megafauna abundances. Our data document a forested landscape from 60,000 to 48,000 yr b2k and a stepwise vegetation change towards a glacial desert after 26,000 yr b2k. The Eifel landscape was continuously inhabited from 48,000 to 9000 yr b2k by large mammals, documented by the presence of spores of coprophilous fungi from Sordaria and Sporormiella fungi that grow on fecal remains of the megafauna. Megafauna reached higher numbers during cold stadial climates but was present also during the warmer interstadials. Highest abundance was at 56,500/48,500/38,500/33,000/27,000/21,000/16,200/14,000 yr b2k, i.e. under different climate regimes. Some of these dates were associated with clear human presence, which indicates that megafauna was not overkilled by humans. In contrast, human presence could quite likely have been stimulated by the abundant food supply. Megafauna presence decreased significantly when tree abundance increased during interstadials. The Megafauna disappeared finally at 11,400 yr b2k with the development of the early Holocene forest cover, which appears to be the most important threshold for megafauna presence.

Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis

The aim of the study is to investigate mitochondrial diversity in Neolithic Greece and its relation to hunter-gatherers and farmers who populated the Danubian Neolithic expansion axis. We sequenced 42 mitochondrial palaeogenomes from Greece and analysed them together with European set of 328 mtDNA sequences dating from the Early to the Final Neolithic and 319 modern sequences. To test for population continuity through time in Greece, we use an original structured population continuity test that simulates DNA from different periods by explicitly considering the spatial and temporal dynamics of populations. We explore specific scenarios of the mode and tempo of the European Neolithic expansion along the Danubian axis applying spatially explicit simulations coupled with Approximate Bayesian Computation. We observe a striking genetic homogeneity for the maternal line throughout the Neolithic in Greece whereas population continuity is rejected between the Neolithic and present-day Greeks. Along the Danubian expansion axis, our best-fitting scenario supports a substantial decrease in mobility and an increasing local hunter-gatherer contribution to the gene-pool of farmers following the initial rapid Neolithic expansion. Οur original simulation approach models key demographic parameters rather than inferring them from fragmentary data leading to a better understanding of this important process in European prehistory.

Properties of Daily Helium Fluxes

We present the precision measurement of 2824 daily helium fluxes in cosmic rays from May 20, 2011 to October 29, 2019 in the rigidity interval from 1.71 to 100 GV based on 7.6×10^{8} helium nuclei collected with the Alpha Magnetic Spectrometer (AMS) aboard the International Space Station. The helium flux and the helium to proton flux ratio exhibit variations on multiple timescales. In nearly all the time intervals from 2014 to 2018, we observed recurrent helium flux variations with a period of 27 days. Shorter periods of 9 days and 13.5 days are observed in 2016. The strength of all three periodicities changes with time and rigidity. In the entire time period, we found that below ∼7  GV the helium flux exhibits larger time variations than the proton flux, and above ∼7  GV the helium to proton flux ratio is time independent. Remarkably, below 2.4 GV a hysteresis between the helium to proton flux ratio and the helium flux was observed at greater than the 7σ level. This shows that at low rigidity the modulation of the helium to proton flux ratio is different before and after the solar maximum in 2014.

Apport de la microscopie 2-photon (M2P) dans l’exploration des mécanismes immunitaires après infection par le virus de la grippe d’un modèle murin

Introduction

Même si depuis 18 mois, le SARS-Cov2 a fait disparaître toute trace des virus respiratoires hivernaux historiques, les virus de la grippe, responsables de plusieurs pandémies durant le 20^e siècle et d’une mortalité non négligeable, restent un sujet d’étude d’actualité. De nombreux travaux ont étudié la réaction immune innée post infection grippale mais sous un angle quantitatif en terme cellulaire et cytokinique. Le développement de technologie de microscopie moderne permettant d’étudier un organe entier en profondeur en conservant une excellente résolution mérite d’être évaluée. Peu de données sont disponibles sur l’intérêt de la M2P dans l’exploration du poumon et aucune sur son intérêt dans l’exploration des mécanismes immunitaires post infection grippale. Le but de ce travail est donc d’étudier l’intérêt de la M2P dans l’exploration des dommages structurales pulmonaires et du recrutement cellulaire après infection par le virus de la grippe d’un modèle murin.

Méthodes

Nous avons infecté des souris C57bl/6 J génétiquement modifiées, dont les cellules CD11C+ expriment une protéine fluorescente jaune, par voie inhalée avec Influenzavirus (adapté à la souris) auquel la protéine NS1 a été couplée à une protéine fluorescente rouge. En plus de cette fluorescente endogène, nous avons utilisé un Ac anti F4/80 couplé à une protéine fluorescente bleue pour visualiser les macrophages. Nous avons ensuite étudié les poumons à jour 1, 2, 3, 4, 5 post infection en cytométrie en flux pour quantification cellulaire, dosage cytokinique et exploration en M2P. Nous avons développé un protocole d’imagerie M2P Intravital ex vivo pour évaluer le trafficking cellulaire.

Résultats

M2P a permis de mettre en évidence des dommages structuraux pulmonaires, de localiser les sites infectés, d’étudier les interactions cellulaires et d’étudier l’évolution dans le temps post infection. Ces résultats enrichissent et complètent les données quantitatives déjà publiées (cytométrie) et permettent d’étudier dans le temps la cinétique et la localisation des lésions et du recrutement cellulaire. De plus, le protocole d’imagerie Intravitale ex vivo a été mis au point.

Conclusion

En complément des analyses usuelles (cytométrie en flux, dosage cytokines…), M2P est donc une technologie pertinente et prometteuse dans les études précliniques en infectiologie respiratoire nous a permis de décrire une base physiopathologique de référence pour de futures études notamment d’impact des traitements anti-viraux ou anti-inflammatoires.

Periodicities in the Daily Proton Fluxes from 2011 to 2019 Measured by the Alpha Magnetic Spectrometer on the International Space Station from 1 to 100 GV

We present the precision measurement of the daily proton fluxes in cosmic rays from May 20, 2011 to October 29, 2019 (a total of 2824 days or 114 Bartels rotations) in the rigidity interval from 1 to 100 GV based on 5.5×10^{9} protons collected with the Alpha Magnetic Spectrometer aboard the International Space Station. The proton fluxes exhibit variations on multiple timescales. From 2014 to 2018, we observed recurrent flux variations with a period of 27 days. Shorter periods of 9 days and 13.5 days are observed in 2016. The strength of all three periodicities changes with time and rigidity. The rigidity dependence of the 27-day periodicity is different from the rigidity dependences of 9-day and 13.5-day periods. Unexpectedly, the strength of 9-day and 13.5-day periodicities increases with increasing rigidities up to ∼10  GV and ∼20  GV, respectively. Then the strength of the periodicities decreases with increasing rigidity up to 100 GV.

Temperature-dependent tensile properties of polyamide 12 for the use in percutaneous transluminal coronary angioplasty balloon catheters

BACKGROUND

Percutaneous transluminal coronary angioplasty (PTCA) balloon catheters must withstand high pressures required for the lesion treatment, pushing loads during insertion, and pulling loads during withdrawal. These loads pose a challenge especially for polymeric tubular shafts with small cross sections. In order to enable new design innovations and to better understand the mechanics of current catheter technologies, the tensile properties of polyamide (PA) 12 were investigated. PA 12 dog bone specimens and medical PA 12 tubes were either stored at ambient temperature and humidity or conditioned in water, and subjected to tensile loads at different temperatures. In addition, the effect on the tensile properties of the necking process, a forming process to reduce the wall thickness of the tubes, was determined.

RESULTS

The tested tubes showed a reduction in both Young's Modulus (- 41.5%) and yield stress (- 29.2%) compared to standardized specimens. Furthermore, an increase in temperature and water absorption softens the material and reduces the mechanical properties like the Young's Modulus and the yield stress. It was found that the material strengthens during the necking process. Likely due to the orientation of the polymers chain molecules in load direction (Rösler et al., 2007), the Young's Modulus of the material could be increased by 43.5%. Furthermore, the absence of a yield point after necking allows for a greater loading capacity of the material without unstable neck growth. Besides the strengthening, the ultimate strain is reduced by 50%. This indicates that the necking process induces plastic deformation.

CONCLUSION

The investigation showed that the environmental conditions like temperature and humidity can influence mechanical properties. It could also be shown that pre-forming processes such as necking can enhance the mechanical properties, such as the Young's Modulus, while reducing the wall thickness. These findings suggest possible further development of catheters with a small cross section and higher mechanical strength and highlight the importance to account for the targeted operating temperature during the design process.

Erratum: Properties of a New Group of Cosmic Nuclei: Results from the Alpha Magnetic Spectrometer on Sodium, Aluminum, and Nitrogen [Phys. Rev. Lett. 127, 021101 (2021)]

This corrects the article DOI: 10.1103/PhysRevLett.127.021101.

Properties of a New Group of Cosmic Nuclei: Results from the Alpha Magnetic Spectrometer on Sodium, Aluminum, and Nitrogen

We report the properties of sodium (Na) and aluminum (Al) cosmic rays in the rigidity range 2.15 GV to 3.0 TV based on 0.46 million sodium and 0.51 million aluminum nuclei collected by the Alpha Magnetic Spectrometer experiment on the International Space Station. We found that Na and Al, together with nitrogen (N), belong to a distinct cosmic ray group. In this group, we observe that, similar to the N flux, both the Na flux and Al flux are well described by the sums of a primary cosmic ray component (proportional to the silicon flux) and a secondary cosmic ray component (proportional to the fluorine flux). The fraction of the primary component increases with rigidity for the N, Na, and Al fluxes and becomes dominant at the highest rigidities. The Na/Si and Al/Si abundance ratios at the source, 0.036±0.003 for Na/Si and 0.103±0.004 for Al/Si, are determined independent of cosmic ray propagation.

The genomic history of the Aegean palatial civilizations

The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.

Ancient genomes provide insights into family structure and the heredity of social status in the early Bronze Age of southeastern Europe

Twenty-four palaeogenomes from Mokrin, a major Early Bronze Age necropolis in southeastern Europe, were sequenced to analyse kinship between individuals and to better understand prehistoric social organization. 15 investigated individuals were involved in genetic relationships of varying degrees. The Mokrin sample resembles a genetically unstructured population, suggesting that the community’s social hierarchies were not accompanied by strict marriage barriers. We find evidence for female exogamy but no indications for strict patrilocality. Individual status differences at Mokrin, as indicated by grave goods, support the inference that females could inherit status, but could not transmit status to all their sons. We further show that sons had the possibility to acquire status during their lifetimes, but not necessarily to inherit it. Taken together, these findings suggest that Southeastern Europe in the Early Bronze Age had a significantly different family and social structure than Late Neolithic and Early Bronze Age societies of Central Europe.

Properties of Heavy Secondary Fluorine Cosmic Rays: Results from the Alpha Magnetic Spectrometer

Precise knowledge of the charge and rigidity dependence of the secondary cosmic ray fluxes and the secondary-to-primary flux ratios is essential in the understanding of cosmic ray propagation. We report the properties of heavy secondary cosmic ray fluorine F in the rigidity R range 2.15 GV to 2.9 TV based on 0.29 million events collected by the Alpha Magnetic Spectrometer experiment on the International Space Station. The fluorine spectrum deviates from a single power law above 200 GV. The heavier secondary-to-primary F/Si flux ratio rigidity dependence is distinctly different from the lighter B/O (or B/C) rigidity dependence. In particular, above 10 GV, the F/Si/B/O ratio can be described by a power law R^{δ} with δ=0.052±0.007. This shows that the propagation properties of heavy cosmic rays, from F to Si, are different from those of light cosmic rays, from He to O, and that the secondary cosmic rays have two classes.

Properties of Iron Primary Cosmic Rays: Results from the Alpha Magnetic Spectrometer

We report the observation of new properties of primary iron (Fe) cosmic rays in the rigidity range 2.65 GV to 3.0 TV with 0.62×10^{6} iron nuclei collected by the Alpha Magnetic Spectrometer experiment on the International Space Station. Above 80.5 GV the rigidity dependence of the cosmic ray Fe flux is identical to the rigidity dependence of the primary cosmic ray He, C, and O fluxes, with the Fe/O flux ratio being constant at 0.155±0.006. This shows that unexpectedly Fe and He, C, and O belong to the same class of primary cosmic rays which is different from the primary cosmic rays Ne, Mg, and Si class.

Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines

Background

Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases. In order to methodically investigate the magnitude of systematic errors in single nucleotide variant calls, we performed a cross-sectional observational study on a genomic cohort of 99 subjects each sequenced via (i) Illumina HiSeq X, (ii) Illumina HiSeq, and (iii) Complete Genomics and processed with the respective bioinformatic pipeline. We also repeated variant calling for the Illumina cohorts with GATK, which allowed us to investigate the effect of the bioinformatics analysis strategy separately from the sequencing platform’s impact.

Results

The number of detected variants/variant classes per individual was highly dependent on the experimental setup. We observed a statistically significant overrepresentation of variants uniquely called by a single setup, indicating potential systematic biases. Insertion/deletion polymorphisms (indels) were associated with decreased concordance compared to single nucleotide polymorphisms (SNPs). The discrepancies in indel absolute numbers were particularly prominent in introns, Alu elements, simple repeats, and regions with medium GC content. Notably, reprocessing sequencing data following the best practice recommendations of GATK considerably improved concordance between the respective setups.

Conclusion

We provide empirical evidence of systematic heterogeneity in variant calls between alternative experimental and data analysis setups. Furthermore, our results demonstrate the benefit of reprocessing genomic data with harmonized pipelines when integrating data from different studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-020-07362-8.

Screening archaeological bone for palaeogenetic and palaeoproteomic studies

The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to sampling. To be relevant, such screening methods should be effective, minimally-destructive, and rapid. This study reports results based on spectroscopic (Fourier-transform infrared spectroscopy in attenuated total reflectance [FTIR-ATR]; n = 266), palaeoproteomic (collagen content; n = 226), and palaeogenetic (endogenous DNA content; n = 88) techniques. We establish thresholds for three different FTIR indices, a) the infrared splitting factor [IRSF] that assesses relative changes in bioapatite crystals’ size and homogeneity; b) the carbonate-to-phosphate [C/P] ratio as a relative measure of carbonate content in bioapatite crystals; and c) the amide-to-phosphate ratio [Am/P] for assessing the relative organic content preserved in bone. These thresholds are both extremely reliable and easy to apply for the successful and rapid distinction between well- and poorly-preserved specimens. This is a milestone for choosing appropriate samples prior to genomic and collagen analyses, with important implications for biomolecular archaeology and palaeontology.

Properties of Neon, Magnesium, and Silicon Primary Cosmic Rays Results from the Alpha Magnetic Spectrometer

We report the observation of new properties of primary cosmic rays, neon (Ne), magnesium (Mg), and silicon (Si), measured in the rigidity range 2.15 GV to 3.0 TV with 1.8×10^{6}  Ne, 2.2×10^{6}  Mg, and 1.6×10^{6}  Si nuclei collected by the Alpha Magnetic Spectrometer experiment on the International Space Station. The Ne and Mg spectra have identical rigidity dependence above 3.65 GV. The three spectra have identical rigidity dependence above 86.5 GV, deviate from a single power law above 200 GV, and harden in an identical way. Unexpectedly, above 86.5 GV the rigidity dependence of primary cosmic rays Ne, Mg, and Si spectra is different from the rigidity dependence of primary cosmic rays He, C, and O. This shows that the Ne, Mg, and Si and He, C, and O are two different classes of primary cosmic rays.

Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent

Genome-wide analysis of 67 ancient Near Eastern cattle, Bos taurus, remains reveals regional variation that has since been obscured by admixture in modern populations. Comparisons of genomes of early domestic cattle to their aurochs progenitors identify diverse origins with separate introgressions of wild stock. A later region-wide Bronze Age shift indicates rapid and widespread introgression of zebu, Bos indicus, from the Indus Valley. This process was likely stimulated at the onset of the current geological age, ~4.2 thousand years ago, by a widespread multicentury drought. In contrast to genome-wide admixture, mitochondrial DNA stasis supports that this introgression was male-driven, suggesting that selection of arid-adapted zebu bulls enhanced herd survival. This human-mediated migration of zebu-derived genetics has continued through millennia, altering tropical herding on each continent.

Properties of Cosmic Helium Isotopes Measured by the Alpha Magnetic Spectrometer

Precision measurements by the Alpha Magnetic Spectrometer (AMS) on the International Space Station of ^{3}He and ^{4}He fluxes are presented. The measurements are based on 100 million ^{4}He nuclei in the rigidity range from 2.1 to 21 GV and 18 million ^{3}He from 1.9 to 15 GV collected from May 2011 to November 2017. We observed that the ^{3}He and ^{4}He fluxes exhibit nearly identical variations with time. The relative magnitude of the variations decreases with increasing rigidity. The rigidity dependence of the ^{3}He/^{4}He flux ratio is measured for the first time. Below 4 GV, the ^{3}He/^{4}He flux ratio was found to have a significant long-term time dependence. Above 4 GV, the ^{3}He/^{4}He flux ratio was found to be time independent, and its rigidity dependence is well described by a single power law ∝R^{Δ} with Δ=-0.294±0.004. Unexpectedly, this value is in agreement with the B/O and B/C spectral indices at high energies.

Tracking Five Millennia of Horse Management with Extensive Ancient Genome Time Series

Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contributed significantly to modern diversity. We show that the influence of Persian-related horse lineages increased following the Islamic conquests in Europe and Asia. Multiple alleles associated with elite-racing, including at the MSTN "speed gene," only rose in popularity within the last millennium. Finally, the development of modern breeding impacted genetic diversity more dramatically than the previous millennia of human management.

Towards Understanding the Origin of Cosmic-Ray Electrons

Precision results on cosmic-ray electrons are presented in the energy range from 0.5 GeV to 1.4 TeV based on 28.1×10^{6} electrons collected by the Alpha Magnetic Spectrometer on the International Space Station. In the entire energy range the electron and positron spectra have distinctly different magnitudes and energy dependences. The electron flux exhibits a significant excess starting from 42.1_{-5.2}^{+5.4}  GeV compared to the lower energy trends, but the nature of this excess is different from the positron flux excess above 25.2±1.8  GeV. Contrary to the positron flux, which has an exponential energy cutoff of 810_{-180}^{+310}  GeV, at the 5σ level the electron flux does not have an energy cutoff below 1.9 TeV. In the entire energy range the electron flux is well described by the sum of two power law components. The different behavior of the cosmic-ray electrons and positrons measured by the Alpha Magnetic Spectrometer is clear evidence that most high energy electrons originate from different sources than high energy positrons.

Towards Understanding the Origin of Cosmic-Ray Positrons

Precision measurements of cosmic ray positrons are presented up to 1 TeV based on 1.9 million positrons collected by the Alpha Magnetic Spectrometer on the International Space Station. The positron flux exhibits complex energy dependence. Its distinctive properties are (a) a significant excess starting from 25.2±1.8  GeV compared to the lower-energy, power-law trend, (b) a sharp dropoff above 284_{-64}^{+91}  GeV, (c) in the entire energy range the positron flux is well described by the sum of a term associated with the positrons produced in the collision of cosmic rays, which dominates at low energies, and a new source term of positrons, which dominates at high energies, and (d) a finite energy cutoff of the source term of E_{s}=810_{-180}^{+310}  GeV is established with a significance of more than 4σ. These experimental data on cosmic ray positrons show that, at high energies, they predominantly originate either from dark matter annihilation or from other astrophysical sources.

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.

Observation of Complex Time Structures in the Cosmic-Ray Electron and Positron Fluxes with the Alpha Magnetic Spectrometer on the International Space Station

We present high-statistics, precision measurements of the detailed time and energy dependence of the primary cosmic-ray electron flux and positron flux over 79 Bartels rotations from May 2011 to May 2017 in the energy range from 1 to 50 GeV. For the first time, the charge-sign dependent modulation during solar maximum has been investigated in detail by leptons alone. Based on 23.5×10^{6} events, we report the observation of short-term structures on the timescale of months coincident in both the electron flux and the positron flux. These structures are not visible in the e^{+}/e^{-} flux ratio. The precision measurements across the solar polarity reversal show that the ratio exhibits a smooth transition over 830±30 days from one value to another. The midpoint of the transition shows an energy dependent delay relative to the reversal and changes by 260±30 days from 1 to 6 GeV.

Precision Measurement of Cosmic-Ray Nitrogen and its Primary and Secondary Components with the Alpha Magnetic Spectrometer on the International Space Station

A precision measurement of the nitrogen flux with rigidity (momentum per unit charge) from 2.2 GV to 3.3 TV based on 2.2×10^{6} events is presented. The detailed rigidity dependence of the nitrogen flux spectral index is presented for the first time. The spectral index rapidly hardens at high rigidities and becomes identical to the spectral indices of primary He, C, and O cosmic rays above ∼700  GV. We observed that the nitrogen flux Φ_{N} can be presented as the sum of its primary component Φ_{N}^{P} and secondary component Φ_{N}^{S}, Φ_{N}=Φ_{N}^{P}+Φ_{N}^{S}, and we found Φ_{N} is well described by the weighted sum of the oxygen flux Φ_{O} (primary cosmic rays) and the boron flux Φ_{B} (secondary cosmic rays), with Φ_{N}^{P}=(0.090±0.002)×Φ_{O} and Φ_{N}^{S}=(0.62±0.02)×Φ_{B} over the entire rigidity range. This corresponds to a change of the contribution of the secondary cosmic ray component in the nitrogen flux from 70% at a few GV to <30% above 1 TV.

Observation of Fine Time Structures in the Cosmic Proton and Helium Fluxes with the Alpha Magnetic Spectrometer on the International Space Station

We present the precision measurement from May 2011 to May 2017 (79 Bartels rotations) of the proton fluxes at rigidities from 1 to 60 GV and the helium fluxes from 1.9 to 60 GV based on a total of 1×10^{9} events collected with the Alpha Magnetic Spectrometer aboard the International Space Station. This measurement is in solar cycle 24, which has the solar maximum in April 2014. We observed that, below 40 GV, the proton flux and the helium flux show nearly identical fine structures in both time and relative amplitude. The amplitudes of the flux structures decrease with increasing rigidity and vanish above 40 GV. The amplitudes of the structures are reduced during the time period, which started one year after solar maximum, when the proton and helium fluxes steadily increase. Above ∼3  GV the p/He flux ratio is time independent. We observed that below ∼3  GV the ratio has a long-term decrease coinciding with the period during which the fluxes start to rise.