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 .