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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Next-generation sequencing technology provides an attractive means to obtain largescale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with $1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (d S ) and chromosome size. Analyses of the mean d N ⁄ d S ratio (x) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with x as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.

Rats with kainate-colchicine hippocampal lesions (HL) and controls (C) were initially trained in the Morris water maze with procedures that deterred their prepotent thigmotaxic response. Training began with an escape platform that occupied nearly the entire pool. The area to which the rats could escape was made smaller by substituting smaller platforms as training progressed. In contrast to standard procedures, HL rats and C rats showed comparable performance during acquisition and preferentially searched the goal quadrant on probe trials during which the platform was removed. In a follow-up experiment, the platform was moved to a random position along the wall, which required a switch to a thigmotaxic response for most effective escape. HL rats that were thigmotaxic before place training did not switch to a thigmotaxic response as readily as did controls, behavior consistent with the view that hippocampal damage reduces pliancy.

The males of the Golden-collared manakin (Manacus vitellinus), a passerine bird of the Neotropical region, perform elaborate courtship displays that are among the most spectacular in the animal kingdom. During a 7-mo long breeding season, male manakins aggregate in leks of up to 12 individuals, and each male clears a small 'court' on the forest floor where he spends several hours per day performing his displays either with or without the presence of a female. Like males of other manakin species, males of M. vitellinus produce loud mechanical sounds with their wings during the displays. The elaborate displays of the manakins are thought to be the result of sexual selection, which is particularly intense in lekking species in which females choose their mate mainly on the basis of behavioural and morphological features. However, we know little about differences in display between male manakins which may be related to individual differences in reproductive success. A quantitative, detailed analysis of the courtship displays has been difficult because the birds' movements are too fast to be studied with standard video recording techniques. For the first time, we recorded the displays of male Golden-collared manakins in the forest of Panama with a high-speed camera that allows a time resolution 5-40 times higher than that of a standard video camera. We found that several elements of the displays differed significantly between individuals. In addition, the slow-motion analysis revealed the features of the displays that had not been described in previous studies. Individually different features of the displays may form the basis for female choice and will allow testing hypotheses about the evolution of the manakin displays by sexual selection and their importance for speciation mechanisms in the genus Manacus.

Spectacular athleticism is a conspicuous feature of many animal courtship displays yet surprisingly little is known about androgen dependence of skeletal muscles underlying these displays. Testosterone (T) acts through androgen receptors (ARs) to stimulate muscular male Golden-collared manakins of Panama to perform a remarkably athletic courtship display that includes loud wingsnaps generated by the rapid and forceful lifting of the wings. We tested the hypothesis that androgen sensitivity, reflected in the expression levels of AR mRNA, is a muscular adaptation supporting these courtship displays. Quantitative PCR showed substantially greater AR mRNA expression in all limb muscles of wild male and female manakins compared with two other avian species that do not perform athletic displays, zebra finches and ochre-bellied flycatchers. AR expression levels in the massive skeletal muscles were comparable with the minute oscine syringeal muscle but greater than levels in nonmuscular androgen targets that did not differ across species. Compared with zebra finches, male manakins also had greater activity of the T-activating enzyme 5 alpha-reductase in a wing-lifting muscle. In addition, low levels of estrogen receptor alpha (ER) mRNA were detected in all muscles of control, T-treated, and estradiol-treated manakins. Treatment of manakins with T, but not estradiol, significantly increased skeletal muscle ER expression, suggesting that ER expression is AR-dependent. These results confirm manakin limb muscles as important androgen targets where T may act to promote the speed, force, and/or endurance required for the manakin display. Androgen-sensitive muscular phenotypes may adapt males of many species to perform impressive athletic displays.

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To entice females to mate, male bowerbirds build elaborate displays (bowers). Among species, bowers range in complexity from simple arenas decorated with leaves to complex twig or grass structures decorated with myriad colored objects. To investigate the neural underpinnings of bower building, we examined the contribution of variation in volume estimates of whole brain (WB), telencephalon minus hippocampus (TH), hippocampus (Hp) and cerebellum (Cb) to explain differences in complexity of bowers among 5 species. Using independent contrasts, we found a significant relationship between bower complexity and Cb size. We did not find support for correlated evolution between bower complexity and WB, TH, or Hp volume. These results suggest that skills supported by the cerebellum (e.g., procedural learning, motor planning) contribute to explaining the variation in bower complexity across species. Given that male mating success is in part determined by female choice for bower design, our data are consistent with the hypothesis that sexual selection has driven enlargement of the cerebellum in bowerbirds.