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A Phylogenomic Study of Birds Reveals Their Evolutionary History

TLDR
This study examined ∼32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods.
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Whole-genome analyses resolve early branches in the tree of life of modern birds

TLDR
A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
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Structural and transcriptional analysis of human papillomavirus type 16 sequences in cervical carcinoma cell lines

TLDR
Transcription analysis revealed expression of the HPV-16 genome in each of these two cervical carcinoma cell lines, albeit at significantly different levels, and preliminary mapping of the viral RNA with subgenomic strand-specific probes indicated that viral transcription appeared to be derived primarily from the E6 and E7 ORFs.
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Phylogenetic relationships among modern birds (Neornithes): towards an avian tree of life

Modem perceptions of the inonophyly of avian higher taxa {modern birds, Neomiihes) and their interrelationships are the legacy uf systematic work undertaken in the 19th century. Before Llie…

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.
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The genomic consequences of adaptive divergence and reproductive isolation between species of manakins

The processes of adaptation and speciation are expected to shape genomic variation within and between diverging species. Here we analyze genomic heterogeneity of genetic differentiation and…
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Nucleotide sequence and genome organization of biologically active proviruses of the bovine immunodeficiency-like virus.

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Phylogenomic evidence for multiple losses of flight in ratite birds

TLDR
A phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal that unequivocally places tinamous within ratites, making ratites polyphyletic and suggesting multiple losses of flight.
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Molecular phylogeny of the marmots (Rodentia: Sciuridae): tests of evolutionary and biogeographic hypotheses.

TLDR
These analyses reject the two major competing hypotheses of M. broweri's phylogenetic relationships--namely, that it is the sister species to M. camtschatica of eastern Siberia, and that it has a western montane clade in the Nearctic.
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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.
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