DOI: 10.5061/dryad.3c3r3
title: Data from: Avian diversification patterns across the K-Pg boundary: influence of calibrations, datasets and model misspecification

description: 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.
description: 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.treIntron 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.treExon 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.treNT 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.treExon 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.treIntron 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.treNT 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.treRY 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.treExon nDNA tree (strict clock)Timetree from strict clock divergence dating analysis in BEAST using exon nDNA dataset.exons_clock.treIntron nDNA tree (strict clock)Timetree from strict clock divergence dating analysis in BEAST using intron nDNA dataset.introns_clock.treNT mtDNA tree (strict clock)Timetree from strict clock divergence dating analysis in BEAST using NT coded mtDNA dataset.mt12_clock.treRY mtDNA tree (strict clock)Timetree from strict clock divergence dating analysis in BEAST using RY coded mtDNA dataset.mt12ry_clock.treNT 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.treRY 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.treExon 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.treIntron 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.trePreferred 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.trePreferred dataset XMLXML file containing alignments, calibrations, and model settings used for analysis of preferred dataset (RY coded mtDNA and exon nDNA).exons_mt12ry_anat.xmlRY mtDNA XMLXML file containing alignments, calibrations, and model settings used for analysis of RY coded mtDNA dataset.mt12ry.xmlNT mtDNA XMLXML file containing alignments, calibrations, and model settings used for analysis of NT coded mtDNA dataset.mt12.xmlIntron nDNA XMLXML file containing alignments, calibrations, and model settings used for analysis of intron nDNA dataset.introns.xmlExtron nDNA XMLXML file containing alignments, calibrations, and model settings used for analysis of exon nDNA dataset.Exons.xml