Results
Our Columbidae supermatrix phylogeny (Figs. 2A, S2) most closely
resembles that of Lapiedra et al. (2021), which of published columbiform
trees has the most data. The tree was well resolved, with the majority
of nodes significantly supported (84% of nodes had ultrafast bootstrap
(BS) > 95%, and 73% of nodes had posterior probability
(PP) > 0.95). However, the phylogeny shows a striking
feature of relatively low resolution among the basal primary lineages.
This is evident in both ML and time-calibrated Bayesian inferences (Fig.
S2), and also when using just nuclear data alone, or in the low
consistency among individual gene trees (Fig S3). This is exacerbated by
the long stem divergence to the closest living outgroups. Including the
extra mtg-block does not make any material change to topology. The root
(and implied American) origins for pigeons are therefore weakly
supported, despite considerable data (all of these nodes are informed by
at least 9/10 genes) and high level of resolution elsewhere in tree.
These basal nodes are associated with relatively short internodes (BS
and PP with Pearson product moment correlation coefficient to branch
length >0.5), and the shape of the overall pigeon phylogeny
describes a long stem followed by rapid early radiation.
Results on general patterns of ancestral state estimation are consistent
and complimentary across the Mk-ML (Figs. 3, S4) and DEC+J( Figs. S5–6) methods. Summary and discussion of
patterns of inference will focus on the Mk-ML results.
All models and analyses support lineage accumulation (Fig. 2B) and
endemic cladogensis (Fig. 2C) within the islands of the IAA through the
Oligo-Miocene (Fig. S7). Endemic cladogensis summaries of combined
islands versus combined continental regions (Figs. 3A–C) further
indicate that the island systems have been continuously generating
in-situ diversity since this time, including a peak relative to
continents following a rapid accumulation of lineages in the early
Oligocene. Three major and strongly supported clades (Ptilinopini,
Raphiniae and Phabini) are each largely endemic or centred on eastern
IAA, and group together with weak support into a large insular
supra-clade in Bayesian analyses (Fig. 2A). The Cuckoo Doves
(Macropygia and allied genera within the Colombini) also
diversified on IAA islands (Fig. S4), but are much younger.
West Melanesia (comprising of New Guinea and Maluku) is the most
frequently inferred insular state throughout the Oligo-Miocene, and is
further the most frequent regional state for the entire Columbiformes
through the Oligocene (Fig. 2B). The Rhaphinae and Ptilinopini
reconstruct to West Melanesia, while the ancestral state for the
Phabines is split across Wallacea, the Pacific and West Melanesia (Fig.
2). Three endemic pigeon radiations on the Philippines are inferred to
be of Miocene age and largely derived from other insular lineages (Fig.
2). The Pacific and Indian oceans show no endemic clades older than the
Miocene.
Insular, Old World and Australian pigeon faunas are relatively discrete,
however, we inferred a number of exchanges between continental and
insular regions. Upstream colonisations are more frequent than
downstream colonisation up until the late Miocene (Figure 3B). In the
Oligocene many reconstructions infer an initial upstream shift into the
old world (Eurasia and Africa) at the base of weakly supported clade
spanning Treron -Turtur (Fig. 2A). An alternative
hypothetical reconstruction has the Treron andOena /Turtur ancestral lineages independently colonising
the Old World, contributing a separate mid-Miocene peak in inferred
upstream shifts. In the early Miocene the mainly terrestrial Phabines
colonised Australia from islands (Fig. 3D). From the mid-Miocene onwards
at least ten lineages within the Ptilinopini are inferred to have
colonised Australia or Sundaland independently (Fig. 2A). A majority of
these dispersals are inferred in widespread and vagile species or
species complexes that occur across both continental and insular
regions.
In contrast, there is a negligible signal of downstream colonisation
until the late Miocene (Fig. 3C), when the ancestor of the Cuckoo-Doves
(Macropygia and allied genera) shifted from Continental to
Insular regions (Fig. 2A); whether this colonisation occurred from the
Old or New World is ambiguous. Through the late Plio-Pleistocene the
overall number of inferred colonisation events increases, and downstream
events begin to outnumber upstream events, with many shifts linked to
widespread species or species complexes that occur across both
continental and insular regions in genera such as Macropygia ,Ptilonopus , Streptopelia and Treron .