DOI: 10.5061/dryad.p2pn8
title: Data from: A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves)

description: The phylogeny of Galliformes (landfowl) has been studied extensively;
 however, the associated chronologies have been criticized recently due to
 misplaced or misidentified fossil calibrations. As a consequence, it is
 unclear whether any crown-group lineages arose in the Cretaceous and
 survived the Cretaceous–Paleogene (K–Pg; 65.5 Ma) mass extinction. Using
 Bayesian phylogenetic inference on an alignment spanning 14,539 bp of
 mitochondrial and nuclear DNA sequence data, four fossil calibrations, and
 a combination of uncorrelated lognormally distributed relaxed-clock and
 strict-clock models, we inferred a time-calibrated molecular phylogeny for
 225 of the 291 extant Galliform taxa. These analyses suggest that crown
 Galliformes diversified in the Cretaceous and that three-stem lineages
 survived the K–Pg mass extinction. Ideally, characterizing the tempo and
 mode of diversification involves a taxonomically complete phylogenetic
 hypothesis. We used simple constraint structures to incorporate 66
 data-deficient taxa and inferred the first taxon-complete phylogenetic
 hypothesis for the Galliformes. Diversification analyses conducted on
 10,000 timetrees sampled from the posterior distribution of candidate
 trees show that the evolutionary history of the Galliformes is best
 explained by a rate-shift model including 1–3 clade-specific increases in
 diversification rate. We further show that the tempo and mode of
 diversification in the Galliformes conforms to a three-pulse model, with
 three-stem lineages arising in the Cretaceous and inter and intrafamilial
 diversification occurring after the K–Pg mass extinction, in the
 Paleocene–Eocene (65.5–33.9 Ma) or in association with the
 Eocene–Oligocene transition (33.9 Ma).
description: BEAST xml file for taxon
 set with molecular dataThis .xml file includes
 the alignments and specifications used in the analysis of the molecular
 data matrix. Additionally, this file includes the code that helped to
 resolve the convergence problems (low ESS values) stemming from a sparse
 molecular data matrix.Stein et al. 2015 - BEAST xml
 file for taxon set with molecular data.xmlStein et al. 2015 -
 BEAST xml file for simulation of the calibrated tree prior on the MCC tree
 from analysis of the taxon set with molecular dataThis .xml file includes
 the specifications used to simulate the calibrate tree prior on the fully
 constrain maximum clade credibility trees generated from three replicate
 analyses of the molecular data matrix using: Stein et al. 2015 - BEAST xml
 file for taxon set with molecular data.xmlStein et al 2015 - BEAST
 xml file for taxon-complete analysesThis xml file includes
 the alignments, specifications and additional taxonomic constraints used
 in the taxon-complete analyses. Additionally, this file includes the code
 that helped to resolve the convergence problems (low ESS values) stemming
 from a sparse molecular data matrix. The approach was developed by Dr.
 Joseph W. Brown and involves the following: 1. Create a new
 compoundParameter to update mean clock rates as a set see lines: 19329 -
 19339 2. Comment out the upDownOperators for each mean clock rate see
 lines: 20378 - 20483 3. Create a new upDownOperator for the new compound
 parameter see lines: 20495 - 20504 Searching for “compoundParameterSetUp”
 (omitting the “”) within the .xml file will locate each of the edits
 associated with setting up the new compoundParameter for mean clock
 rates.Stein et al. 2015 Fig. 1
 in nexus file formatPhylogenetic hypothesis
 resulting from analysis of the molecular data matrix in the nexus file
 format.Stein et al. 2015 Fig.
 1.nexStein et al. 2015 Fig. 1
 in newick file formatPhylogenetic hypothesis
 resulting from analysis of the molecular data matrix in the newick file
 format.Stein et al. 2015 Fig.
 1.tre