Phylogenetic inference
Phylogenetic resolution was first explored using IQ-TREE ultra-fast
bootstrap consensus with multi-partition sequence evolution model
selected via ModelFinder (see Table S2). This was done for both with and
without mtg-block datasets, and a cut down version of nuclear data only
for 94 taxa with >2 nuclear genes. To further investigate
the consistency of support among genes for primary lineages, we employed
ASTRAL consensus species tree from gene trees approach (rather than site
support methods due to the patchwork supermatrix data). This used a cut
down dataset of 59 taxa for 8 genes.
Bayesian relaxed-clock analyses were performed in BEAST v2.4 (Drummondet al. , 2006; Bouckaert et al. , 2014), with a lognormal
clock and Yule speciation prior (each with 1/X parameterization), and
using a seven partition sequence evolution model optimized by
ModelFinder (nuclear gene codon positions, intron+12S, mitochondrial
codon positions; Table S2). Dating calibrations comprised of two
Columbidae fossil constraints and two secondary outgroup priors.Rupephaps, a ptilinopine fruit pigeon from New Zealand, was
applied as exponential (offset=22.0, mean=3.0) on the stem subtendingHemiphaga , Lopholaimus and Gymnophaps (Worthyet al. , 2009). Primophaps , a phabine pigeon from northern
Australia, was applied as exponential (offset=19.0, mean=3.0) on the
main Australian radiation of terrestrial seed-eating pigeons (stem
subtending Leucosarcia to Phaps ) (Worthy, 2012). Two
normal secondary priors, based on Prum et al. (2015), were placed on the
root (mean=63.0, sd=4.3) and Columbimorphs (mean=58.0, sd=4.8).
Preliminary tests indicated a birth-death speciation prior was not
required above the simpler Yule prior.
We ran two independent Bayesian MCMC analyses of 50 million steps
sampling every 5,000, with a burnin of 20% that returned all parameters
with ESS >500 (Rambaut et al. , 2014), with near
identical maximum clade credibility (MCC) consensus tree topology, node
support, and dating (see electronic supplementary material for the
complete BEAST2 xml file). Runs were then pooled. For the purposes of
biogeographic analyses, in addition to a MCC tree, a subset of 100 trees
were drawn from the BEAST posterior sample to reasonably represent the
topological and branch length variation of the total posterior. Outgroup
taxa were then removed (Phytools R package; Revell 2012).