Comprehensive taxon sampling and vetted fossils help clarify the time tree of shorebirds (Aves, Charadriiformes)

Shorebirds (Charadriiformes) are a globally distributed clade of modern
birds and, due to their ecological and morphological disparity, a frequent
subject of comparative studies. While molecular phylogenies have been key
to establishing the suprafamilial backbone of the charadriiform tree, a
number of relationships at both deep and shallow taxonomic levels remain
poorly resolved. The timescale of shorebird evolution also remains
uncertain as a result of extensive disagreements among the published
divergence dating studies, stemming largely from different choices of
fossil calibrations. Here, we present the most comprehensive non-supertree
phylogeny of shorebirds to date, based on a total-evidence dataset
comprising 353 ingroup taxa (90% of all extant or recently extinct
species), 27 loci (15 mitochondrial and 12 nuclear), and 69 morphological
characters. We further clarify the timeline of charadriiform evolution by
time-scaling this phylogeny using a set of 14 up-to-date and thoroughly
vetted fossil calibrations. In addition, we assemble a taxonomically
restricted 100-locus dataset specifically designed to resolve outstanding
problems in higher-level charadriiform phylogeny. In terms of tree
topology, our results are largely congruent with previous studies but
indicate that some of the conflicts among earlier analyses reflect a
genuine signal of pervasive gene tree discordance. Monophyly of the
plovers (Charadriidae), the position of the ibisbill (Ibidorhyncha), and
the relationships among the five subfamilies of the gulls (Laridae) could
not be resolved even with greatly increased locus and taxon sampling.
Moreover, several localized regions of uncertainty persist in shallower
parts of the tree, including the interrelationships of the true auks
(Alcinae) and anarhynchine plovers. Our node-dating and macroevolutionary
rate analyses find support for a Paleocene origin of crown-group
shorebirds, as well as exceptionally rapid recent radiations of Old World
oystercatchers (Haematopodidae) and select genera of gulls. Our study
underscores the challenges involved in estimating a comprehensively
sampled and carefully calibrated time tree for a diverse avian clade, and
highlights areas in need of further research.