Data from: Avian diversification patterns across the K-Pg boundary: influence of calibrations, datasets and model misspecification

Ksepka DT, Phillips MJ

Date Published: August 17, 2015

DOI: http://dx.doi.org/10.5061/dryad.3c3r3

 

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Title RY mtDNA tree (K-Pg constraint)
Downloaded 11 times
Description 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.
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Title Intron nDNA tree (K-Pg constraint)
Downloaded 5 times
Description 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.
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Title Exon nDNA tree (K-Pg constraint)
Downloaded 6 times
Description 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.
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Title NT mtDNA tree (K-Pg constraint)
Downloaded 7 times
Description 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.
Download mt12_kpg.tre (74.97 Kb)
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Title Exon nDNA tree (fully calibrated)
Downloaded 7 times
Description Timetree from divergence dating analysis in BEAST using exon nDNA dataset, with topology constrained and 15 fossil calibrations plus one root calibration applied.
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Title Intron nDNA tree (fully calibrated)
Downloaded 5 times
Description Timetree from divergence dating analysis in BEAST using intron nDNA dataset, with topology constrained and 15 fossil calibrations plus one root calibration applied.
Download introns.tre (74.47 Kb)
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Title NT mtDNA tree (fully calibrated)
Downloaded 6 times
Description Timetree from divergence dating analysis in BEAST using NT coded mtDNA dataset, with topology constrained and 15 fossil calibrations plus one root calibration applied.
Download mt12.tre (74.73 Kb)
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Title RY mtDNA tree (fully calibrated)
Downloaded 6 times
Description Timetree from divergence dating analysis in BEAST using RY coded mtDNA dataset, with topology constrained and 15 fossil calibrations plus one root calibration applied.
Download mt12ry.tre (74.81 Kb)
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Title Exon nDNA tree (strict clock)
Downloaded 5 times
Description Timetree from strict clock divergence dating analysis in BEAST using exon nDNA dataset.
Download exons_clock.tre (73.57 Kb)
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Title Intron nDNA tree (strict clock)
Downloaded 5 times
Description Timetree from strict clock divergence dating analysis in BEAST using intron nDNA dataset.
Download introns_clock.tre (76.91 Kb)
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Title NT mtDNA tree (strict clock)
Downloaded 6 times
Description Timetree from strict clock divergence dating analysis in BEAST using NT coded mtDNA dataset.
Download mt12_clock.tre (75.98 Kb)
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Title RY mtDNA tree (strict clock)
Downloaded 8 times
Description Timetree from strict clock divergence dating analysis in BEAST using RY coded mtDNA dataset.
Download mt12ry_clock.tre (76.87 Kb)
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Title NT mtDNA tree (nominally calibrated)
Downloaded 4 times
Description Timetree from nominally calibrated divergence dating analysis in BEAST using NT coded mtDNA dataset and only a single root calibration.
Download mt12_one.tre (74.82 Kb)
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Title RY mtDNA tree (nominally calibrated)
Downloaded 6 times
Description Timetree from nominally calibrated divergence dating analysis in BEAST using RY coded mtDNA dataset and only a single root calibration.
Download mt12ry_one.tre (74.75 Kb)
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Title Exon nDNA tree (nominally calibrated)
Downloaded 5 times
Description Timetree from nominally calibrated divergence dating analysis in BEAST using exon nDNA dataset and only a single root calibration.
Download introns_one.tre (74.69 Kb)
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Title Intron nDNA tree (nominally calibrated)
Downloaded 5 times
Description Timetree from nominally calibrated divergence dating analysis in BEAST using intron nDNA dataset and only a single root calibration.
Download introns_one.tre (74.69 Kb)
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Title Preferred tree (fully calibrated)
Downloaded 7 times
Description 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.
Download exons_mtry_anat.tre (75.88 Kb)
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Title Preferred dataset XML
Downloaded 9 times
Description XML file containing alignments, calibrations, and model settings used for analysis of preferred dataset (RY coded mtDNA and exon nDNA).
Download exons_mt12ry_anat.xml (1.149 Mb)
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Title RY mtDNA XML
Downloaded 11 times
Description XML file containing alignments, calibrations, and model settings used for analysis of RY coded mtDNA dataset.
Download mt12ry.xml (579.1 Kb)
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Title NT mtDNA XML
Downloaded 14 times
Description XML file containing alignments, calibrations, and model settings used for analysis of NT coded mtDNA dataset.
Download mt12.xml (578.7 Kb)
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Title Intron nDNA XML
Downloaded 7 times
Description XML file containing alignments, calibrations, and model settings used for analysis of intron nDNA dataset.
Download introns.xml (1.101 Mb)
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Title Extron nDNA XML
Downloaded 10 times
Description XML file containing alignments, calibrations, and model settings used for analysis of exon nDNA dataset.
Download Exons.xml (591.8 Kb)
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When using this data, please cite the original publication:

Ksepka DT, Phillips MJ (2015) Avian diversification patterns across the K-Pg boundary: influence of calibrations, datasets and model misspecification. Annals of the Missouri Botanical Garden 100(4): 300-328. http://dx.doi.org/10.3417/2014032

Additionally, please cite the Dryad data package:

Ksepka DT, Phillips MJ (2015) Data from: Avian diversification patterns across the K-Pg boundary: influence of calibrations, datasets and model misspecification. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.3c3r3
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