Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Attempts to estimate and identify factors influencing first-year survival in passerines, survival between fledging and the first reproductive attempt (i.e. juvenile survival), have largely been confounded by natal dispersal, particularly in long-distance migratory passerines. We studied Prothonotary Warblers (Protonotaria citrea) breeding in nest boxes to estimate first-year survival while accounting for biases related to dispersal that are common in mark-recapture studies. The natal dispersal distribution (median = 1420 m; n = 429) and a distance-dependent recruitment rate, which controls for effects of study site configuration, both indicated a pattern of short-distance natal dispersal. This pattern was consistent with results of a systematic survey for birds returning outside the nest box study sites (up to 30 km in all directions) within a majority (81%) of total available bottomland forest habitat, further suggesting that permanent emigration outside of the study system was rare. We used multistate mark-recapture modeling to estimate first-year survival and incorporated factors thought to influence survival while accounting for the potential confounding effects of dispersal on recapture probabilities for warblers that fledged during 2004–2009 (n = 6093). Overall, the average first-year survival for warblers reared without cowbird nestmates was 0.11 (95% CI = 0.09–0.13), decreased with fledging date (0.22 early to 0.03 late) and averaged 40% lower for warblers reared with a brood parasite nestmate. First-year survival was less than half of the rate thought to represent population replacement in migratory passerines (∼0.30). This very low rate suggests that surviving the first year of life for many Neotropical migratory species is even more difficult than previously thought, forcing us to rethink estimates used in population models.