High participation rate among 25 721 patients with broad age range in a hospital-based research project involving whole-genome sequencing - the Lausanne Institutional Biobank.

We aimed to evaluate the interest of adult inpatients and selected outpatients in engaging in a large, real-life, hospital-based, genomic medicine research project and in receiving clinically actionable incidental findings. Within the framework of the cross-sectional Institutional Biobank of Lausanne, Switzerland, a total of 25721 patients of the CHUV University Hospital were systematically invited to grant researchers access to their biomedical data and to donate blood for future analyses, including whole-genome sequencing. Multivariable logistic regression analysis was used to identify personal factors, including age, gender, religion, ethnicity, citizenship, education level and mode of admission, associated with willingness to participate in this genomic research project and with interest in receiving clinically actionable incidental findings. The overall participation rate was 79% (20343/25721). Participation rate declined progressively with age, averaging 83%, 75%, 67% and 62% in patients aged <64 years (n = 13108), ≥64 years (n = 12613), ≥80 years (n = 4557) and ≥90 years (n = 1050), respectively. Factors associated with participation substantially differed between age strata. Patients less likely to participate included women (odds ratio 0.86, [95% confidence interval 0.79-0.95] and 0.78 [0.71-0.85] before and after age 64, respectively), non-Swiss (0.81 [0.74-0.90] and 0.58 [0.52-0.65]) and those admitted through the emergency ward (0.88 [0.79-0.98] and 0.66 [0.60-0.73]). Religion and marital status were associated with participation among patients aged <64 years. A total of 19 018 (93%) participants were willing to be re-contacted for incidental findings. A high education level was associated with higher participation rate, but not with higher willingness to receive incidental findings within the population who had agreed to participate. A large proportion of adult patients, even among the elderly, are willing to actively participate and receive incidental findings in this systematic hospital-based precision and genomic medicine research program with broad consent

Introductory Editorial: Evolutionary Genomics

This supplement is intended to focus on evolutionary genomics. Evolutionary Bioinformatics aims to provide researchers working in this complex, quickly developing field with online, open access to highly relevant scholarly articles by leading international researchers. In a field where the literature is ever-expanding, researchers increasingly need access to up-to-date, high quality scholarly articles on areas of specific contemporary interest. This supplement aims to address this by presenting high-quality articles that allow readers to distinguish the signal from the noise. The editor in chief hopes that through this effort, practitioners and researchers will be aided in finding answers to some of the most complex and pressing issues of our time

A signature of dynamic biogeography: enclaves indicate past species replacement

Understanding how species have replaced each other in the past is important to predicting future species turnover. While past species replacement is difficult to detect after the fact, the process may be inferred from present-day distribution patterns. Species with abutting ranges sometimes show a characteristic distribution pattern, where a section of one species range is enveloped by that of the other. Such an enclave could indicate past species replacement: when a species is partly supplanted by a competitor, but a population endures locally while the invading species moves around and past it, an enclave forms. If the two species hybridize and backcross, the receding species is predicted to leave genetic traces within the expanding one under a scenario of species replacement. By screening dozens of genes in hybridizing crested newts, we uncover genetic remnants of the ancestral species, now inhabiting an enclave, in the range of the surrounding invading species. This independent genetic evidence supports the past distribution dynamics we predicted from the enclave. We suggest that enclaves provide a valuable tool in understanding historical species replacement, which is important because a major conservation concern arising from anthropogenic climate change is increased species replacement in the future

The scaling of genetic diversity in a changing and fragmented world

Most species do not live in a constant environment over space or time. Their environment is often heterogeneous with a huge variability in resource availability and exposure to pathogens or predators, which may affect the local densities of the species. Moreover, the habitat might be fragmented, preventing free and isotropic migrations between local sub-populations (demes) of a species, making some demes more isolated than others. For example, during the last ice age populations of many species migrated towards refuge areas from which re-colonization originated when conditions improved. However, populations that could not move fast enough or could not adapt to the new environmental conditions faced extinctions. Populations living in these types of dynamic environments are often referred to as metapopulations and modeled as an array of subdivisions (or demes) that exchange migrants with their neighbors. Several studies have focused on the description of their demography, probability of extinction and expected patterns of diversity at different scales. Importantly, all these evolutionary processes may affect genetic diversity, which can affect the chance of populations to persist. In this chapter we provide an overview on the consequences of fragmentation, long-distance dispersal, range contractions and range shifts on genetic diversity. In addition, we describe new methods to detect and quantify underlying evolutionary processes from sampled genetic data.Laboratoire d’Excellence (LABEX) entitled TULIP: (ANR-10-LABX-41)

A Raman study of the Charge-Density-Wave State in A0.3_{0.3}MoO3_3 (A = K,Rb)

We report a comparative Raman spectroscopic study of the quasi-one-dimensional charge-density-wave systems \ab (A = K, Rb). The temperature and polarization dependent experiments reveal charge-coupled vibrational Raman features. The strongly temperature-dependent collective amplitudon mode in both materials differ by about 3 cm, thus revealing the role of alkali atom. We discus the observed vibrational features in terms of charge-density-wave ground state accompanied by change in the crystal symmetry. A frequency-kink in some modes seen in \bb between T = 80 K and 100 K supports the first-order lock-in transition, unlike \rb. The unusually sharp Raman lines(limited by the instrumental response) at very low temperatures and their temperature evolution suggests that the decay of the low energy phonons is strongly influenced by the presence of the temperature dependent charge density wave gap.Comment: 13 pages, 7 figure

A geoneutrino experiment at Homestake

A significant fraction of the 44TW of heat dissipation from the Earth's interior is believed to originate from the decays of terrestrial uranium and thorium. The only estimates of this radiogenic heat, which is the driving force for mantle convection, come from Earth models based on meteorites, and have large systematic errors. The detection of electron antineutrinos produced by these uranium and thorium decays would allow a more direct measure of the total uranium and thorium content, and hence radiogenic heat production in the Earth. We discuss the prospect of building an electron antineutrino detector approximately 700m^3 in size in the Homestake mine at the 4850' level. This would allow us to make a measurement of the total uranium and thorium content with a statistical error less than the systematic error from our current knowledge of neutrino oscillation parameters. It would also allow us to test the hypothesis of a naturally occurring nuclear reactor at the center of the Earth.Comment: proceedings for Neutrino Sciences 2005, submitted to Earth, Moon, and Planet

Strong Influence of the diffuse component on the lattice dynamics in Pb(Mg1/3_{1/3}Nb2/3_{2/3})O3_{3}

The temperature and zone dependence of the lattice dynamics in Pb(Mg$_{1/3}$Nb$_{2/3}$)O$_{3}$ is characterized using neutron inelastic scattering. A strong correlation between the diffuse and phonon scattering is measured. The lattice dynamics in Brillouin zones where the diffuse scattering is strong is observed to display qualitatively different behavior than those zones where the diffuse scattering is weak. In the (220) and (200) zones, where there is a weak diffuse component, the dynamics are well described by coupled harmonic oscillators. Compared with SrTiO$_{3}$, the coupling is weak and isotropic, resulting in only a small transfer of spectral weight from one mode to another. A comparison of the scattering in these zones to the (110) zone, where a strong diffuse component is present, reveals a strong coupling of the diffuse (or central) component to the acoustic mode. We speculate that the coupling to the central peak is the reason for several recent conflicting interpretations of the lattice dynamics based on data from zones with a strong diffuse component.Comment: 7 pages, 7 figure

Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection

SELECTOR is a software package for studying the evolution of multiallelic genes under balancing or positive selection while simulating complex evolutionary scenarios that integrate demographic growth and migration in a spatially explicit population framework. Parameters can be varied both in space and time to account for geographical, environmental, and cultural heterogeneity. SELECTOR can be used within an approximate Bayesian computation estimation framework. We first describe the principles of SELECTOR and validate the algorithms by comparing its outputs for simple models with theoretical expectations. Then, we show how it can be used to investigate genetic differentiation of loci under balancing selection in interconnected demes with spatially heterogeneous gene flow. We identify situations in which balancing selection reduces genetic differentiation between population groups compared with neutrality and explain conflicting outcomes observed for human leukocyte antigen loci. These results and three previously published applications demonstrate that SELECTOR is efficient and robust for building insight into human settlement history and evolution

Domestication as innovation : the entanglement of techniques, technology and chance in the domestication of cereal crops

The origins of agriculture involved pathways of domestication in which human behaviours and plant genetic adaptations were entangled. These changes resulted in consequences that were unintended at the start of the process. This paper highlights some of the key innovations in human behaviours, such as soil preparation, harvesting and threshing, and how these were coupled with genetic ‘innovations’ within plant populations. We identify a number of ‘traps’ for early cultivators, including the needs for extra labour expenditure on crop-processing and soil fertility maintenance, but also linked gains in terms of potential crop yields. Compilations of quantitative data across a few different crops for the traits of nonshattering and seed size are discussed in terms of the apparently slow process of domestication, and parallels and differences between different regional pathways are identified. We highlight the need to bridge the gap between a Neolithic archaeobotanical focus on domestication and a focus of later periods on crop-processing activities and labour organization. In addition, archaeobotanical data provide a basis for rethinking previous assumptions about how plant genetic data should be related to the origins of agriculture and we contrast two alternative hypotheses: gradual evolution with low selection pressure versus metastable equilibrium that prolonged the persistence of ‘semi-domesticated’ populations. Our revised understanding of the innovations involved in plant domestication highlight the need for new approaches to collecting, modelling and integrating genetic data and archaeobotanical evidence