Birds represent the most diverse extant tetrapod clade, with ca. 10,000 extant species, and the timing of the crown avian radiation remains hotly debated. The fossil record supports a primarily Cenozoic radiation of crown birds, whereas molecular divergence dating analyses generally imply that this radiation was well underway during the Cretaceous. Furthermore, substantial differences have been noted between published divergence estimates. These have been variously attributed to clock model, calibration regime, and gene type. One underappreciated phenomenon is that disparity between fossil ages and molecular dates tends to be proportionally greater for shallower nodes in the avian Tree of Life. Here, we explore potential drivers of disparity in avian divergence dates through a set of analyses applying various calibration strategies and coding methods to a mitochondrial genome dataset and an 18-gene nuclear dataset, both sampled across 72 taxa. Our analyses support the occurrence of two deep divergences (i.e., the Palaeognathae/Neognathae split and the Galloanserae/Neoaves split) well within the Cretaceous, followed by a rapid radiation of Neoaves near the K-Pg boundary. However, 95% highest posterior density intervals for most basal divergences in Neoaves cross the boundary, and we emphasize that, barring unreasonably strict prior distributions, distinguishing between a rapid Early Paleocene radiation and a Late Cretaceous radiation may be beyond the resolving power of currently favored divergence dating methods. In contrast to recent observations for placental mammals, constraining all divergences within Neoaves to occur in the Cenozoic does not result in unreasonably high inferred substitution rates. Comparisons of nuclear DNA (nDNA) versus mitochondrial DNA (mtDNA) datasets and NT- versus RY-coded mitochondrial data reveal patterns of disparity that are consistent with substitution model misspecifications that result in tree compression/tree extension artifacts, which may explain some discordance between previous divergence estimates based on different sequence types. Comparisons of fully calibrated and nominally calibrated trees support a correlation between body mass and apparent dating error. Overall, our results are consistent with (but do not require) a Paleogene radiation for most major clades of crown birds.
RY mtDNA tree (K-Pg constraint)
Timetree from divergence dating analysis in BEAST using RY coded mtDNA dataset, with topology constrained and additional maximum constraints applied so that all divergences except those for the Palaeognathae, Neognathae, and Galloanserae are constrained to occur after the K-Pg boundary.
mt12ry_kpg.tre
Intron nDNA tree (K-Pg constraint)
Timetree from divergence dating analysis in BEAST using intron nDNA dataset, with topology constrained and additional maximum constraints applied so that all divergences except those for the Palaeognathae, Neognathae, and Galloanserae are constrained to occur after the K-Pg boundary.
introns_kpg.tre
Exon nDNA tree (K-Pg constraint)
Timetree from divergence dating analysis in BEAST using exon nDNA dataset, with topology constrained and additional maximum constraints applied so that all divergences except those for the Palaeognathae, Neognathae, and Galloanserae are constrained to occur after the K-Pg boundary.
exons_kpg.tre
NT mtDNA tree (K-Pg constraint)
Timetree from divergence dating analysis in BEAST using NT coded mtDNA dataset, with topology constrained and additional maximum constraints applied so that all divergences except those for the Palaeognathae, Neognathae, and Galloanserae are constrained to occur after the K-Pg boundary.
mt12_kpg.tre
Exon nDNA tree (fully calibrated)
Timetree from divergence dating analysis in BEAST using exon nDNA dataset, with topology constrained and 15 fossil calibrations plus one root calibration applied.
exons.tre
Intron nDNA tree (fully calibrated)
Timetree from divergence dating analysis in BEAST using intron nDNA dataset, with topology constrained and 15 fossil calibrations plus one root calibration applied.
introns.tre
NT mtDNA tree (fully calibrated)
Timetree from divergence dating analysis in BEAST using NT coded mtDNA dataset, with topology constrained and 15 fossil calibrations plus one root calibration applied.
mt12.tre
RY mtDNA tree (fully calibrated)
Timetree from divergence dating analysis in BEAST using RY coded mtDNA dataset, with topology constrained and 15 fossil calibrations plus one root calibration applied.
mt12ry.tre
Exon nDNA tree (strict clock)
Timetree from strict clock divergence dating analysis in BEAST using exon nDNA dataset.
exons_clock.tre
Intron nDNA tree (strict clock)
Timetree from strict clock divergence dating analysis in BEAST using intron nDNA dataset.
introns_clock.tre
NT mtDNA tree (strict clock)
Timetree from strict clock divergence dating analysis in BEAST using NT coded mtDNA dataset.
mt12_clock.tre
RY mtDNA tree (strict clock)
Timetree from strict clock divergence dating analysis in BEAST using RY coded mtDNA dataset.
mt12ry_clock.tre
NT mtDNA tree (nominally calibrated)
Timetree from nominally calibrated divergence dating analysis in BEAST using NT coded mtDNA dataset and only a single root calibration.
mt12_one.tre
RY mtDNA tree (nominally calibrated)
Timetree from nominally calibrated divergence dating analysis in BEAST using RY coded mtDNA dataset and only a single root calibration.
mt12ry_one.tre
Exon nDNA tree (nominally calibrated)
Timetree from nominally calibrated divergence dating analysis in BEAST using exon nDNA dataset and only a single root calibration.
introns_one.tre
Intron nDNA tree (nominally calibrated)
Timetree from nominally calibrated divergence dating analysis in BEAST using intron nDNA dataset and only a single root calibration.
introns_one.tre
Preferred tree (fully calibrated)
Timetree from divergence dating analysis in BEAST using preferred dataset (RY coded mtDNA plus exon nDNA), with topology constrained and 15 fossil calibrations plus one root calibration applied.
exons_mtry_anat.tre
Preferred dataset XML
XML file containing alignments, calibrations, and model settings used for analysis of preferred dataset (RY coded mtDNA and exon nDNA).
exons_mt12ry_anat.xml
RY mtDNA XML
XML file containing alignments, calibrations, and model settings used for analysis of RY coded mtDNA dataset.
mt12ry.xml
NT mtDNA XML
XML file containing alignments, calibrations, and model settings used for analysis of NT coded mtDNA dataset.
mt12.xml
Intron nDNA XML
XML file containing alignments, calibrations, and model settings used for analysis of intron nDNA dataset.
introns.xml
Extron nDNA XML
XML file containing alignments, calibrations, and model settings used for analysis of exon nDNA dataset.
Exons.xml