A Comprehensive Phylogeny of Birds (Aves) using Targeted Next Generation DNA Sequencing - Online Data and Software Archive

Oct 20, 2026

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A comprehensive phylogenetic framework for birds (Aves) is developed using targeted next-generation DNA sequencing, accompanied by an online data and software archive. The study details a methodological choice for node-based divergence dating, applying hard minimum bounds from selected fossils and soft upper bounds for estimated ages. It establishes criteria for strongly supported fossil calibrations and compiles 19 calibrated fossil taxa to model deep Neognathae divergences, while addressing limitations of crown Aves root calibration and performing sensitivity analyses involving Vegavis.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages46

Reading Time1 h 56 min

AccessFree to download

Choosing Fossil Calibrations

Additional Dating Analysis using Vegavis Calibration

Online Data and Software Archive

A Comprehensive Phylogeny of Birds (Aves) using Targeted Next Generation DNA Sequencing Richard O. Prum 1,2,*, Jacob S. Berv3,*, Alex Dornburg 1,2,4, Daniel J. Field2,5, Jeffrey P. Townsend6, Emily Moriarty Lemmon7, and Alan R. Lemmon8 1 Department of Ecology & Evolutionary Biology, Yale University, New Haven CT USA 2 Peabody Museum of Natural History, Yale University, New Haven CT USA 3 Department of Ecology & Evolutionary Biology, Cornell University, Ithaca NY USA 4 North Carolina Museum of Natural Sciences, Raleigh NC USA 5 Department of Geology & Geophysics, Yale University, New Haven CT USA 6 Department of Biostatistics, and Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT USA 7 Department of Biological Science, Florida State University, Tallahassee, FL USA 8 Department of Scientific Computing, Florida State University, Tallahassee, FL USA * These authors contributed equally to this work. Online Data and Software Archive A zip archive containing assembled sequence data, newick formatted tree files, code and scripts for generating and analyzing phylogenetic informativeness, and information on probe design and data assembly is available [at Zenodo.org:](at Zenodo.org:)[ ](at Zenodo.org:)[http://dx.doi.org/10.5281/zenodo.28343](http://dx.doi.org/10.5281/zenodo.28343. R code used for generating tree)[. R code used for generating tree](http://dx.doi.org/10.5281/zenodo.28343. R code used for generating tree) and supplemental figures is available on request. Choosing Fossil Calibrations We elected to employ traditional node-based divergence dating instead of a fossil tip-dating approach1,2 due to the lack of a sufficiently extensive and reliable morphological data matrix for extant and fossil crown birds. Our node-dating approach followed the commonly employed method of specifying hard minimum bounds on the age of a divergence using fossils, while applying a ‘soft’ upper bound for date estimates3,4 . This approach is based on the premise that the common ancestor of a clade (a node on the phylogeny) cannot be younger than its oldest fossil descendant (a child cannot be older than its parent) . As a result, for a given node on the phylogeny (representing a theoretical ancestor α with two descendent lineages), only the oldest known fossil representing one of the descendant lineages of α is used for setting a hard minimum age for that divergence. More recent fossils that represent descendants of α are uninformative, since they are younger than α’s youngest possible age. In contrast to recently published divergence time analyses for crown birds5, we sought to employ Parham et al.’s6 criteria for best practices for justifying fossil calibrations in the selection of our calibration points. These criteria outline stringent phylogenetic and geochronological criteria that must be met in order for a potential calibrating fossil to be considered strongly supported. Only fossils that have been phylogenetically placed by apomorphy-based diagnoses or comprehensive phylogenetic analyses have been included here. We provide references to up-to-date apomorphy-based diagnoses or phylogenetic analyses for each taxon listed (all of which are associated with museum specimen numbers), the most exclusive clade to which they can be referred, names of each fossil locality, and minimum-possible geochronologial ages for each fossil, inclusive of error6. In instances where radioisotopic dates were unavailable and fossils could only be biostratigraphically assigned to geochronological stages, the most conservative approach of selecting the minimum-possible age of the stage, inclusive of error, was implemented6. Our complete list of fossil calibrations comprises 19 fossil taxa, which together document many deep phylogenetic divergences within Neognathae. Although palaeognaths are well represented in Palaeogene fossil deposits in the form of members of the clade Lithornithidae7, ambiguity regard

FAQs

What sequencing approach underpins the bird phylogeny in this work?

The study uses targeted next-generation DNA sequencing to build a comprehensive phylogeny of birds (Aves).

How does the paper handle divergence dating with fossils?

It employs node-based divergence dating with hard minimum bounds set by the oldest relevant fossil descendants and a soft upper bound for date estimates.

What calibration criteria are used for selecting strongly supported fossils?

Only fossils meeting stringent phylogenetic and geochronological best-practice criteria are included, with strong support based on apomorphy-based diagnoses or comprehensive phylogenetic analyses.

Oct 20, 2026

Upload by Jake