Abstract
The early radiation of Neoaves has been hypothesized to be an intractable “hard polytomy”. We explore the fundamental properties of insertion/deletion alleles (indels), an under-utilized form of genomic data with the potential to help solve this. We scored >5 million indels from >7000 pan-genomic intronic and ultraconserved element (UCE) loci in 48 representatives of all neoavian orders. We found that intronic and UCE indels exhibited less homoplasy than nucleotide (nt) data. Gene trees estimated using indel data were less resolved than those estimated using nt data. Nevertheless, Accurate Species TRee Algorithm (ASTRAL) species trees estimated using indels were generally similar to nt-based ASTRAL trees, albeit with lower support. However, the power of indel gene trees became clear when we combined them with nt gene trees, including a striking result for UCEs. The individual UCE indel and nt ASTRAL trees were incongruent with each other and with the intron ASTRAL trees; however, the combined indel+nt ASTRAL tree was much more congruent with the intronic trees. Finally, combining indel and nt data for both introns and UCEs provided sufficient power to reduce the scope of the polytomy that was previously proposed for several supraordinal lineages of Neoaves.
Highlights
There have been many attempts to resolve the relationships among the major lineages of birds using molecular data [1]
This study reduces the scale of the basal neoavian hard polytomy from a radiation of nine to a radiation of six major lineages, i.e., core landbirds (Telluraves), pan-waterbirds lineages to a radiation of six major lineages, i.e., core landbirds (Telluraves), (Aequornithia+Phaethontimorphae), Charadriiformes, Gruiformes, Hoatzin, and Caprimulgiformes pan-waterbirds (Aequornithia+Phaethontimorphae), Charadriiformes, Gruiformes, Hoatzin, and
We investigated the properties of indels in phylogenetic analysis, with an emphasis on the multispecies coalescent as implemented in Accurate Species TRee Algorithm (ASTRAL) III [24,25]
Summary
There have been many attempts to resolve the relationships among the major lineages of birds using molecular data [1]. Analyses of nuclear sequence data began by using individual genes [5,6,7]. A constant across all of these studies was the poor resolution of the relationships at the base of the most species-rich avian clade, Neoaves. The absence of resolution was so striking that Poe and Chubb [10] suggested that was evidence of a hard polytomy (simultaneous cladogenic events). Subsequent analyses of multiple genes [11,12,13] provided convincing support for monophyly of several supraordinal bird clades, falsifying the specific version of the hard polytomy hypothesis that was proposed by Poe and Chubb [10]
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