Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within datasets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade's species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower quality samples. Most instances of topological conflict and non-monophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many datasets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology.

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Background: Bird plumage exhibits a diversity of colors that serve functional roles ranging from signaling to camouflage and thermoregulation. However, birds must maintain a balance between evolving colorful signals to attract mates, minimizing conspicuousness to predators, and optimizing adaptation to climate conditions. Examining plumage color macroevolution provides a framework for understanding this dynamic interplay over phylogenetic scales. Plumage evolution due to a single overarching process, such as selection, may generate the same macroevolutionary pattern of color variation across all body regions. In contrast, independent processes may partition plumage and produce region-specific patterns. To test these alternative scenarios, we collected color data from museum specimens of an ornate clade of birds, the Australasian lorikeets, using visible-light and UV-light photography, and comparative methods. We predicted that the diversification of homologous feather regions, i.e., patches, known to be involved in sexual signaling (e.g., face) would be less constrained than patches on the back and wings, where new color states may come at the cost of crypsis. Because environmental adaptation may drive evolution towards or away from color states, we tested whether climate more strongly covaried with plumage regions under greater or weaker macroevolutionary constraint. Results: We found that alternative macroevolutionary models and varying rates best describe color evolution, a pattern consistent with our prediction that different plumage regions evolved in response to independent processes. Modeling plumage regions independently, in functional groups, and all together showed that patches with similar macroevolutionary models clustered together into distinct regions (e.g., head, wing, belly), which suggests that plumage does not evolve as a single trait in this group. Wing patches, which were conserved on a macroevolutionary scale, covaried with climate more strongly than plumage regions (e.g., head), which diversified in a burst. Conclusions: Overall, our results support the hypothesis that the extraordinary color diversity in the lorikeets was generated by a mosaic of evolutionary processes acting on plumage region subsets. Partitioning of plumage regions in different parts of the body provides a mechanism that allows birds to evolve bright colors for signaling and remain hidden from predators or adapt to local climatic conditions.

Media Submission 25How do elaborately coloured animals evolve? In this study we investigated the brush-tongued parrots, the lories and lorikeets, to identify the evolutionary patterns that gave rise to spectacular ornamentation in nature. We found that these parrots are as colourful as all other birds combined, and that multiple evolutionary trends combine to generate their remarkable colour palette. Feather regions that would make birds more visible to predators had constrained evolution, 30 whereas those likely used for courtship signaling radiated recently to disparate parts of their overall colour palette. We found a mosaic of evolutionary patterns, which indicates that independent selective pressures and stochasticity were responsible for producing these beautifully coloured birds. 35 Abstract 40Bird plumage exhibits a diversity of colours that serve functional roles ranging from signaling to camouflage and thermoregulation. Macroevolutionary research on the evolution of plumage colour has focused on the impact of natural selection, but drift and sexual selection likely play important roles in originating brilliant colours and patterns. One kaleidoscopic group is the lorikeets, or brush-tongued parrots, which have radiated across Australasia. To quantify and 45 characterize plumage colour, we imaged taxa using visible-light and UV-light photography of museum specimens. We measured colour from 35 plumage patches on each specimen and modeled colour across lorikeets' evolutionary history. Lorikeets occupy a third of the avian visual colour space, which is qualitatively similar to the colour space occupied by all birds. We found that the wing and back were less variable than the breast and face. Crown and forehead 50 colour was best explained simply by phylogeny. At a macroevolutionary scale, the evolution of elaborate colours in lorikeets involved an interplay wherein regions likely under natural selection were constrained during the radiation while regions known to be involved in signaling underwent late-burst evolution. Overall, patch-specific modeling showed that plumage diversity in the lorikeets was likely generated by a mosaic of evolutionary processes. 55 60 65 70 75