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Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes).
TLDR
These analyses provide a well-resolved phylogeny of landfowl, including strong support for previously problematic relationships such as those among junglefowl (Gallus), and clarify the position of two enigmatic galliform genera not sampled in previous molecular phylogenetic studies.
Tectonic collision and uplift of Wallacea triggered the global songbird radiation
TLDR
It is shown that songbird diversification began in the Oligocene, but accelerated in the early Miocene, at approximately half the age of most previous estimates, reconcile songbird evolution with Earth history and link a major radiation of terrestrial biodiversity to early diversification within an isolated Australian continent.
Bird species richness in a Bornean exotic tree plantation: A long-term perspective
TLDR
Sustained occurrence of forest birds in all groves of exotic trees at Sabah Softwoods was substantially enhanced by the relatively rich avifauna of the logged native forest remaining in substantial stands throughout the plantation.
Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling
TLDR
If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more “biologically‐realistic” models is likely to be critical for efforts to reconstruct the tree of life.
Earth history and the passerine superradiation
TLDR
Recon reconstructing passerine evolutionary history and producing the most comprehensive time-calibrated phylogenetic hypothesis of the group, which suggests more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.
Evolutionary Processes of Diversification in a Model Island Archipelago
TLDR
An ongoing renaissance of species discovery is characterized and how a 25-year Pleistocene island connectivity paradigm continues to provide some explanatory power, but has been augmented by increased understanding of the archipelago's geological history and ecological gradients is described.
Land connectivity changes and global cooling shaped the colonization history and diversification of New World quail (Aves: Galliformes: Odontophoridae)
TLDR
The Africa/New World range disjunction between New World quail and Ptilopachus is the result of changes in Earth and climate history, combined with range expansion and diversification in the New World, and range contraction in the Old World.
Phylogeny of the monarch flycatchers reveals extensive paraphyly and novel relationships within a major Australo-Pacific radiation.
TLDR
A comprehensive, molecular phylogeny of the Monarchidae inferred from mitochondrial and nuclear loci using both concatenated and multilocus coalescent frameworks is produced and provides an excellent framework for future work on biogeography and character evolution in a diverse Australo-Papuan radiation.
Bird community assembly in Bornean industrial tree plantations: Effects of forest age and structure
TLDR
Because the authors lacked species-specific data on foraging, nesting, and other behaviors of most groups of birds, it was difficult to explain the precise causes of seral diversification in any group except woodpeckers, which have been well studied in Southeast Asia.
Reconstructing Ecological Niche Evolution When Niches Are Incompletely Characterized
TLDR
Whether incomplete niche characterizations inherent in most estimates of species' niches bias phylogenetic reconstructions of niche evolution is tested, using simulations of virtual species with known niches and results establish that incompletely characterized niches inflate estimates of evolutionary change and lead to error in ancestral state reconstructions.
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