We have performed the largest ever particle simulation of a Milky Way sized dark matter halo, and present the most comprehensive convergence study for an individual dark matter halo carried out thus far. We have also simulated a sample of six ultrahighly resolved Milky Way sized haloes, allowing us to estimate the halo-to-halo scatter in substructure statistics. In our largest simulation, we resolve nearly 300 000 gravitationally bound subhaloes within the virialized region of the halo. Simulations of the same object differing in mass resolution by factors of up to 1800 accurately reproduce the largest subhaloes with the same mass, maximum circular velocity and position, and yield good convergence for the abundance and internal properties of dark matter substructures. We detect up to four generations of subhaloes within subhaloes, but contrary to recent claims, we find less substructure in subhaloes than in the main halo when regions of equal mean overdensity are compared. The overall substructure mass fraction is much lower in subhaloes than in the main halo. Extrapolating the main halo's subhalo mass spectrum down to an Earth mass, we predict the mass fraction in substructure to be well below 3 per cent within 100 kpc, and to be below 0.1 per cent within the solar circle. The inner density profiles of subhaloes show no sign of converging to a fixed asymptotic slope and are well fitted by gently curving profiles of Einasto form. The mean concentrations of isolated haloes are accurately described by the fitting formula of Neto et al. down to maximum circular velocities of 1.5 km s −1 , an extrapolation over some five orders of magnitude in mass. However, at equal maximum circular velocity, subhaloes are more concentrated than field haloes, with a characteristic density that is typically ∼2.6 times larger and increases with decreasing distance from halo centre.

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Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

We study the mass, velocity dispersion and anisotropy profiles of Λ cold dark matter (ΛCDM) haloes using a suite of N‐body simulations of unprecedented numerical resolution. The Aquarius Project follows the formation of six different galaxy‐sized haloes simulated several times at varying numerical resolution, allowing numerical convergence to be assessed directly. The highest resolution simulation represents a single dark matter halo using 4.4 billion particles, of which 1.1 billion end up within the virial radius. Our analysis confirms a number of results claimed by earlier work, and clarifies a few issues where conflicting claims may be found in the recent literature. The mass profile of ΛCDM haloes deviates slightly but systematically from the form proposed by Navarro, Frenk & White. The spherically averaged density profile becomes progressively shallower inwards and, at the innermost resolved radius, the logarithmic slope is γ≡− d ln  ρ/d ln  r≲ 1. Asymptotic inner slopes as steep as the recently claimed ρ∝r−1.2 are clearly ruled out. The radial dependence of γ is well approximated by a power law, γ∝rα (the Einasto profile). The shape parameter, α, varies slightly but significantly from halo to halo, implying that the mass profiles of ΛCDM haloes are not strictly universal: different haloes cannot, in general, be rescaled to look identical. Departures from similarity are also seen in velocity dispersion profiles and correlate with those in density profiles so as to preserve a power‐law form for the spherically averaged pseudo‐phase‐space density, ρ/σ3∝r−1.875. The index here is identical to that of Bertschinger's similarity solution for self‐similar infall on to a point mass from an otherwise uniform Einstein–de Sitter universe. The origin of this striking behaviour is unclear, but its robustness suggests that it reflects a fundamental structural property of ΛCDM haloes. Our conclusions are reliable down to radii below 0.4 per cent of the virial radius, providing well‐defined predictions for halo structure when baryonic effects are neglected, and thus an instructive theoretical template against which the modifications induced by the baryonic components of real galaxies can be judged.

Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the dominant technique for mapping transcription factor (TF) binding regions genome-wide. We performed an integrative analysis centered around 457 ChIP-seq data sets on 119 human TFs generated by the ENCODE Consortium. We identified highly enriched sequence motifs in most data sets, revealing new motifs and validating known ones. The motif sites (TF binding sites) are highly conserved evolutionarily and show distinct footprints upon DNase I digestion. We frequently detected secondary motifs in addition to the canonical motifs of the TFs, indicating tethered binding and cobinding between multiple TFs. We observed significant position and orientation preferences between many cobinding TFs. Genes specifically expressed in a cell line are often associated with a greater occurrence of nearby TF binding in that cell line. We observed cell-linespecific secondary motifs that mediate the binding of the histone deacetylase HDAC2 and the enhancer-binding protein EP300. TF binding sites are located in GC-rich, nucleosome-depleted, and DNase I sensitive regions, flanked by wellpositioned nucleosomes, and many of these features show cell type specificity. The GC-richness may be beneficial for regulating TF binding because, when unoccupied by a TF, these regions are occupied by nucleosomes in vivo. We present the results of our analysis in a TF-centric web repository Factorbook (http://factorbook.org) and will continually update this repository as more ENCODE data are generated.

P. Gong et al. land-cover classification system as well as the International Geosphere-Biosphere Programme (IGBP) system. Using the four classification algorithms, we obtained the initial set of global land-cover maps. The SVM produced the highest overall classification accuracy (OCA) of 64.9% assessed with our test samples, with RF (59.8%), J4.8 (57.9%), and MLC (53.9%) ranked from the second to the fourth. We also estimated the OCAs using a subset of our test samples (8629) each of which represented a homogeneous area greater than 500 m × 500 m. Using this subset, we found the OCA for the SVM to be 71.5%. As a consistent source for estimating the coverage of global land-cover types in the world, estimation from the test samples shows that only 6.90% of the world is planted for agricultural production. The total area of cropland is 11.51% if unplanted croplands are included. The forests, grasslands, and shrublands cover 28.35%, 13.37%, and 11.49% of the world, respectively. The impervious surface covers only 0.66% of the world. Inland waterbodies, barren lands, and snow and ice cover 3.56%, 16.51%, and 12.81% of the world, respectively.