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.