Parental relatedness through time revealed by runs of homozygosity in ancient DNA

Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide

Generation of mechanical interference fringes by multi-photon counting

Exploring the quantum behaviour of macroscopic objects provides an intriguing avenue to study the foundations of physics and to develop a suite of quantum-enhanced technologies. One prominent path of study is provided by quantum optomechanics which utilizes the tools of quantum optics to control the motion of macroscopic mechanical resonators. Despite excellent recent progress, the preparation of mechanical quantum superposition states remains outstanding due to weak coupling and thermal decoherence. Here we present a novel optomechanical scheme that significantly relaxes these requirements allowing the preparation of quantum superposition states of motion of a mechanical resonator by exploiting the nonlinearity of multi-photon quantum measurements. Our method is capable of generating non-classical mechanical states without the need for strong single photon coupling, is resilient against optical loss, and offers more favourable scaling against initial mechanical thermal occupation than existing schemes. Moreover, our approach allows the generation of larger superposition states by projecting the optical field onto NOON states. We experimentally demonstrate this multi-photon-counting technique on a mechanical thermal state in the classical limit and observe interference fringes in the mechanical position distribution that show phase superresolution. This opens a feasible route to explore and exploit quantum phenomena at a macroscopic scale.Comment: 16 pages, 4 figures. v1: submitted for review on 28 Jan 2016. v2: significantly revised manuscript. v3: some further revisions and some extra results included. v3: new results added, extra author added, close to published version, supplementary material available with published versio

Experimental test of nonlocal causality.

Explaining observations in terms of causes and effects is central to empirical science. However, correlations between entangled quantum particles seem to defy such an explanation. This implies that some of the fundamental assumptions of causal explanations have to give way. We consider a relaxation of one of these assumptions, Bell's local causality, by allowing outcome dependence: a direct causal influence between the outcomes of measurements of remote parties. We use interventional data from a photonic experiment to bound the strength of this causal influence in a two-party Bell scenario, and observational data from a Bell-type inequality test for the considered models. Our results demonstrate the incompatibility of quantum mechanics with a broad class of nonlocal causal models, which includes Bell-local models as a special case. Recovering a classical causal picture of quantum correlations thus requires an even more radical modification of our classical notion of cause and effect

Reconstructing genetic histories and social organisation in Neolithic and Bronze Age Croatia

Ancient DNA studies have revealed how human migrations from the Neolithic to the Bronze Age transformed the social and genetic structure of European societies. Present-day Croatia lies at the heart of ancient migration routes through Europe, yet our knowledge about social and genetic processes here remains sparse. To shed light on these questions, we report new whole-genome data for 28 individuals dated to between ~ 4700 BCE–400 CE from two sites in present-day eastern Croatia. In the Middle Neolithic we evidence first cousin mating practices and strong genetic continuity from the Early Neolithic. In the Middle Bronze Age community that we studied, we find multiple closely related males suggesting a patrilocal social organisation. We also find in that community an unexpected genetic ancestry profile distinct from individuals found at contemporaneous sites in the region, due to the addition of hunter-gatherer-related ancestry. These findings support archaeological evidence for contacts with communities further north in the Carpathian Basin. Finally, an individual dated to Roman times exhibits an ancestry profile that is broadly present in the region today, adding an important data point to the substantial shift in ancestry that occurred in the region between the Bronze Age and today

Quantum Hypercube States

We introduce quantum hypercube states, a class of continuous-variable quantum states that are generated as orthographic projections of hypercubes onto the quadrature phase-space of a bosonic mode. In addition to their interesting geometry, hypercube states display phase-space features much smaller than Planck's constant, and a large volume of Wigner-negativity. We theoretically show that these features make hypercube states sensitive to displacements at extremely small scales in a way that is surprisingly robust to initial thermal occupation and to small separation of the superposed state-components. In a high-temperature proof-of-principle optomechanics experiment we observe, and match to theory, the signature outer-edge vertex structure of hypercube states.Comment: Main consists of 5 pages and 5 figures. Supplementary material consists of 5 pages and 6 figure

Cross-verification of independent quantum devices

Quantum computers are on the brink of surpassing the capabilities of even the most powerful classical computers. This naturally raises the question of how one can trust the results of a quantum computer when they cannot be compared to classical simulation. Here we present a verification technique that exploits the principles of measurement-based quantum computation to link quantum circuits of different input size, depth, and structure. Our approach enables consistency checks of quantum computations within a device, as well as between independent devices. We showcase our protocol by applying it to five state-of-the-art quantum processors, based on four distinct physical architectures: nuclear magnetic resonance, superconducting circuits, trapped ions, and photonics, with up to 6 qubits and 200 distinct circuits

Population history from the Neolithic to present on the Mediterranean island of Sardinia: an ancient DNA perspective

Recent ancient DNA studies of western Eurasia have revealed a dynamic history of admixture, with evidence for major migrations during the Neolithic and Bronze Age. The population of the Mediterranean island of Sardinia has been notable in these studies –} Neolithic individuals from mainland Europe cluster more closely with Sardinian individuals than with all other present-day Europeans. The current model to explain this result is that Sardinia received an initial influx of Neolithic ancestry and then remained relatively isolated from expansions in the later Neolithic and Bronze Age that took place in continental Europe. To test this model, we generated genome-wide capture data (approximately 1.2 million variants) for 43 ancient Sardinian individuals spanning the Neolithic through the Bronze Age, including individuals from Sardinia{’}s Nuragic culture, which is known for the construction of numerous large stone towers throughout the island. We analyze these new samples in the context of previously generated genome-wide ancient DNA data from 972 ancient individuals across western Eurasia and whole-genome sequence data from approximately 1,500 modern individuals from Sardinia. The ancient Sardinian individuals show a strong affinity to western Mediterranean Neolithic populations and we infer a high degree of genetic continuity on the island from the Neolithic (around fifth millennium BCE) through the Nuragic period (second millennium BCE). In particular, during the Bronze Age in Sardinia, we do not find significant levels of the {“}Steppe{” ancestry that was spreading in many other parts of Europe at that time. We also characterize subsequent genetic influx between the Nuragic period and the present. We detect novel, modest signals of admixture between 1,000 BCE and present-day, from ancestry sources in the eastern and northern Mediterranean. Within Sardinia, we confirm that populations from the more geographically isolated mountainous provinces have experienced elevated levels of genetic drift and that northern and southwestern regions of the island received more gene flow from outside Sardinia. Overall, our genetic analysis sheds new light on the origin of Neolithic settlement on Sardinia, reinforces models of genetic continuity on the island, and provides enhanced power to detect post-Bronze-Age gene flow. Together, these findings offer a refined demographic model for future medical genetic studies in Sardinia

Determining the Quantum Expectation Value by Measuring a Single Photon

Quantum mechanics, one of the keystones of modern physics, exhibits several peculiar properties, differentiating it from classical mechanics. One of the most intriguing is that variables might not have definite values. A complete quantum description provides only probabilities for obtaining various eigenvalues of a quantum variable. These and corresponding probabilities specify the expectation value of a physical observable, which is known to be a statistical property of an ensemble of quantum systems. In contrast to this paradigm, we demonstrate a unique method allowing to measure the expectation value of a physical variable on a single particle, namely, the polarisation of a single protected photon. This is the first realisation of quantum protective measurements.Comment: Nature Physics, in press (this version corresponds to the one initially submitted to Nature Physics

Experimental deterministic correction of qubit loss

The successful operation of quantum computers relies on protecting qubits from decoherence and noise which, if uncorrected, will lead to erroneous results. These errors accumulate during an algorithm and thus correcting them becomes a key requirement for large-scale and fault-tolerant quantum information processors. Besides computational errors, which can be addressed by quantum error correction, the carrier of the information can also be completely lost or the information can leak out of the computational space. It is expected that such loss errors will occur at rates that are comparable to computational errors. Here we experimentally implement a full cycle of qubit loss detection and correction on a minimal instance of a topological surface code in a trapped-ion quantum processor. The key technique for this correction is a quantum non-demolition measurement via an ancillary qubit, which acts as a minimally invasive probe to detect absent qubits while only imparting the minimal quantum-mechanically possible disturbance on the remaining qubits. Upon detecting qubit loss, a recovery procedure is triggered in real-time, which maps the logical information onto a new encoding on the remaining qubits. Although the current demonstration is performed in a trapped-ion quantum processor, the protocol is applicable to other quantum computing architectures and error correcting codes, including leading 2D and 3D topological codes. These methods provide a complete toolbox for the correction of qubit loss that complements techniques to mitigate computational errors, which together constitute the building blocks for complete and scalable quantum error correction

Converting multilevel nonclassicality into genuine multipartite entanglement

Characterizing genuine quantum resources and determining operational rules for their manipulation are crucial steps to appraise possibilities and limitations of quantum technologies. Two such key resources are nonclassicality, manifested as quantum superposition between reference states of a single system, and entanglement, capturing quantum correlations among two or more subsystems. Here we present a general formalism for the conversion of nonclassicality into multipartite entanglement, showing that a faithful reversible transformation between the two resources is always possible within a precise resource-theoretic framework. Specializing to quantum coherence between the levels of a quantum system as an instance of nonclassicality, we introduce explicit protocols for such a mapping. We further show that the conversion relates multilevel coherence and multipartite entanglement not only qualitatively, but also quantitatively, restricting the amount of entanglement achievable in the process and in particular yielding an equality between the two resources when quantified by fidelity-based geometric measures