BioGeobears
The probability of ancestral ranges was also estimated using BioGeoBEARS
(Matzke, 2013) in R (R Core Team, 2016). Pigeon species were assigned to
the same eight regions as the Markov Maximum likelihood inference. The
maximum range size was set to eight regions as some species are
widespread across all regions. Other settings were left as default. We
used the standard six different biogeographic models tested by
BioGeoBears: BAYAREA, which does not allow dispersal at cladogenesis;
DIVA, which allows vicariance [i.e. if parent lineage occurs in (x,y),
then one daughter lineage can occur in only (x) whereas the other can
occur in only (y)] but disallows subset speciation, in which one
daughter lineage inherits a subset of the distribution of the parent
[i.e. if parent lineage occurs in (x,y), then one daughter lineage can
occur in only (x) or only (y) whereas the other can occur in (x,y)];
DEC, which allows both vicariance and subset speciation; and BAYAREA+J,
DIVA+J and DEC+J, which are equivalent to the previous three models but
also allow jump dispersal through founder effects at cladogenesis(Matzke
2014). The BioGeoBEARS analysis was run using two separate phylogenetic
inputs: 1) using the BEAST MCC tree and 2) a subset of 100 BEAST trees.
Results of the BioGeoBEARS run across multiple trees were averaged.
Repeated analyses were run to account for possible different topologies
and poorly supported nodes in the phylogeny. The best-fit model for the
pigeon data was DEC+J, followed by DIVALIKE+J (LnL −444.3 and −455.1,
respectively; Table S7).