A couple of years ago, I noted that genomic datasets have not helped resolve the phylogeny at the root of the placentals, because each new genomic analysis produces a different phylogenetic tree (Conflicting placental roots: network or tree?). It appears that the results depend more on the analysis model used than on the data obtained (Why are there conflicting placental roots?), and it is thus likely that the early phylogenetic history of the mammals was not tree-like at all.
Recently, a similar situation has arisen for the early history of the birds. In the past year, three genomic analyses have appeared involving the phylogenetics of modern birds (principally the Neoaves):
Erich D. Jarvis et alia (2014) Whole-genome analyses resolve early branches in the tree of life of modern birds. Science 346: 1320-1331.
Alexander Suh, Linnéa Smeds, Hans Ellegren (2015) The dynamics of incomplete lineage sorting across the ancient adaptive radiation of Neoavian birds. PLoS Biology 13: e1002224.
Richard O. Prum, Jacob S. Berv, Alex Dornburg, Daniel J. Field, Jeffrey P. Townsend, Emily Moriarty Lemmon, Alan R. Lemmon (2015) A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526: 569-573.The first analysis used concatenated gene sequences from 50 bird genomes (including the outgroups), and the second one used 2,118 retrotransposon markers in those same genomes. The third analysis used 259 gene trees from 200 genomes. The second analysis incorporated incomplete lineage sorting (ILS) into the main analysis model, while the other two addressed ILS in secondary analyses. None of the analyses explicitly included the possibility of gene flow, although the second analysis considered the possibility of hybridization for one clade.
These three studies can be directly compared at the taxonomic level of family. I have used a SuperNetwork (estimated using SplitsTree 4) to display this comparison. The tree-like areas of the network are where the three analyses agree on the tree-based relationships, and the reticulated areas are where there is disagreement about the inferred tree.
The network shows that some of the major bird groups do have tree-like relationships in all three analyses (shown in red, green and blue). However, the relationships between these groups, and between them and the other bird families, is very inconsistent between the analyses. In particular, the basal relationships are a mess (the outgroup is shown in purple), with none of the three analyses agreeing with any other one.
Thus, the claims that any of these analyses provide a "highly supported" phylogeny or "resolve the early branches in the tree of life of birds" seem to be rather naive. ILS is likely to have been important in the early history of birds, as this is usually considered to have involved a rapid adaptive radiation. However, I think that models involving gene flow need to be examined as well, if progress is to be made in unravelling the bird phylogeny.
This analysis was inspired by a similar one by Alexander Suh, which appeared on Twitter.