2015
DOI: 10.1371/journal.pbio.1002224
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The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

Abstract: The diversification of neoavian birds is one of the most rapid adaptive radiations of extant organisms. Recent whole-genome sequence analyses have much improved the resolution of the neoavian radiation and suggest concurrence with the Cretaceous-Paleogene (K-Pg) boundary, yet the causes of the remaining genome-level irresolvabilities appear unclear. Here we show that genome-level analyses of 2,118 retrotransposon presence/absence markers converge at a largely consistent Neoaves phylogeny and detect a highly di… Show more

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Cited by 255 publications
(320 citation statements)
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“…This represents the first time that the genome-wide presence/absence patterns of retroposons have been used to clarify phylogenetic relationships of an extinct species. The presence of five conflicting signals in a multidirectional bioinformatics and experimental screening suggests that ancestral incomplete lineage sorting of retroposed elements, frequently detected in many other vertebrate groups 17,18 including ancestral marsupial lineages 19 , also occurred in Dasyuromorphia.…”
Section: Resultsmentioning
confidence: 99%
“…This represents the first time that the genome-wide presence/absence patterns of retroposons have been used to clarify phylogenetic relationships of an extinct species. The presence of five conflicting signals in a multidirectional bioinformatics and experimental screening suggests that ancestral incomplete lineage sorting of retroposed elements, frequently detected in many other vertebrate groups 17,18 including ancestral marsupial lineages 19 , also occurred in Dasyuromorphia.…”
Section: Resultsmentioning
confidence: 99%
“…However, the morphologybased tree conflicts with recent molecular results in uniting Passeriformes with a Piciformes + Upupiformes clade and supporting a "raptorial clade" (Accipitriformes, Falconiformes, and Strigiformes). In contrast, recent molecular analyses unite Passeriformes and Psittaciformes and recover the three raptorial groups as separate radiations (12,20,(29)(30)(31). Furthermore, the internal branches separating Coliiformes from other extant avian clades appear to be exceptionally short, and thus mousebirds have proven highly labile, being recovered as sister taxon to Strigiformes (29), core Coraciimorphae (12,20), Australaves (30), and Afroaves (31) in recent phylogenies.…”
Section: Resultsmentioning
confidence: 99%
“…Tinamiformes and Anseriformes were used as outgroups. Because recent molecular studies have yielded topologies that conflict with those based on morphology and with one another, we conducted an unconstrained analysis of the morphological data, as well as analyses using backbone constraints derived from five recently published molecular studies: a 19-loci dataset (29), a genome-based dataset (20), a 1,541-loci UCE dataset (30), a MP retrotransposon dataset (31), and the 259-loci anchored hybrid enrichment dataset (12). To test the impact of more complete fossils on the placement of Tsidiiyazhi, we conducted additional analyses excluding all fossil taxa except Tsidiiyazhi, with and without the backbone constraints.…”
Section: Phylogenetic Methodsmentioning
confidence: 99%
“…Despite shortcomings, genome data are already a valuable source to study the properties and dynamics of TEs. In silico analyses of TE insertions are revolutionizing phylogenetic analyses [39][40] from painstakingly in-vitro analysis of TE insertions, to being able to extract hundreds such events on a genomic scale. Biological relevant data will become available with new sequencing techniques such as PacBio that sequence longer genome fragments.…”
mentioning
confidence: 99%