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.

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Cannibalism occurs regularly across a broad range of taxa with a variety of ecological and evolutionary consequences. Rises in sea surface temperature (SST) have been linked to increased cannibalism in some species, including polar bears (Ursus maritimus), Peruvian anchovy (Engraulis ringens), and Peruvian hake (Merluccius gayi peruanus), and might be expected in birds that depend on marine food webs for sustenance. Increased SSTs are associated with lowered ocean thermoclines and weakened upwellings. These changes, in turn, lead to decreased productivity in surface water and movement of surviving forage fish to deeper water, thereby food-stressing surface feeders such as gulls, diminishing energy intake and lengthening foraging bouts. While controlling for a suite of other environmental factors, we tested whether egg cannibalism and hatching success were independent of rises in local SST at a colony of Glaucous-winged Gulls (Larus glaucescens) and Glaucous-winged 3 Western Gull (L. glaucescens 3 occidentalis) hybrids during 2006-2011 on Protection Island, Washington, USA. Cannibalism increased and hatching success decreased with rises in SST. It is unclear if rises in SST impact overall population trends. Gulls are multiyear breeders; if they experience reproductive failure during one or several El Niño-Southern Oscillation-related events, they typically have other opportunities to breed. With rising SSTs associated with climate change, however, increasing levels of cannibalism could lead to declining populations in the absence of compensatory adaptive modifications or range shifts.El canibalismo de huevos en colonias de gaviotas aumenta con la temperatura superficial del mar RESUMEN Q 2014 Cooper Ornithological Society.

In humans, coping behaviour is an action taken to soothe oneself during or after a stressful or threatening situation. Some human behaviours with physiological functions also serve as coping behaviours, for example, comfort sucking in infants and comfort eating in adults. In birds, the behaviour of preening, which has important physiological functions, has been postulated to soothe individuals after stressful situations. We combine two existing modelling approaches - logistic regression and Darwinian dynamics - to explore theoretically how a behaviour with crucial physiological function might evolve into a coping behaviour. We apply the method to preening in colonial seabirds to investigate whether and how preening might be co-opted as a coping behaviour in the presence of predators. We conduct an in-depth study of the environmental correlates of preening in a large gull colony in Washington, USA, and we perform an independent field test for comfort preening by computing the change in frequency of preening in gulls that were alerted to a predator, but did not flee.

1Advances in DNA sequencing have made it feasible to gather genomic data for non-model 2 organisms and large sets of individuals, often using methods for sequencing subsets of the 3 genome. Several of these methods sequence DNA associated with endonuclease restriction 4 sites (various RAD and GBS methods). For use in taxa without a reference genome, these 5 methods rely on de novo assembly of fragments in the sequencing library. Many of the soft-6 ware options available for this application were originally developed for other assembly types 7 and we do not know their accuracy for reduced representation libraries. To address this im-8 portant knowledge gap, we simulated data from the Arabidopsis thaliana and Homo sapiens 9 genomes and compared de novo assemblies by six software programs that are commonly 10 used or promising for this purpose (ABySS, CD-HIT, Stacks, Stacks2, Velvet and VSEARCH). 11We simulated different mutation rates and types of mutations, and then applied the six 12 assemblers to the simulated datasets, varying assembly parameters. We found substantial 13 variation in software performance across simulations and parameter settings. ABySS failed 14 to recover any true genome fragments, and Velvet and VSEARCH performed poorly for most 15 simulations. Stacks and Stacks2 produced accurate assemblies of simulations containing 16 SNPs, but the addition of insertion and deletion mutations decreased their performance. 17CD-HIT was the only assembler that consistently recovered a high proportion of true genome 18 fragments. Here, we demonstrate the substantial difference in the accuracy of assemblies 19 from different software programs and the importance of comparing assemblies that result 20 from different parameter settings. 21