Whole Genomes Illuminate the Drivers of Gene Tree Discordance and the Tempo of Tinamou Diversification (Aves: Tinamidae)

As an old group that has diversified in South America over millions of years, the tinamous (Palaeognathae: Tinamidae) are of high interest for understanding the evolution of birds and the assembly of the Neotropical biota. However, there are currently no complete species-level phylogenies of this group. Most prior work has been based on either morphological data or a small number of molecular markers, each of which has limited capability for reconstructing the tinamou phylogeny. Therefore, the interrelationships of most tinamou species are uncertain. We analyzed 80 whole-genomes from a mix of historical study skins and frozen tissues, including all 46 recognized species of tinamous to (1) reconstruct their interrelationships, (2) estimate the timeframe of tinamou evolution, and (3) examine for the effects of incomplete lineage sorting (ILS) and ancestral introgression on genome evolution. We compared results for coding (BUSCO) and ultraconserved element (UCE) loci, as well as sex-linked and autosomal markers, and used fossil-calibrated tip-dating to estimate divergence times. Tinamous diverged from their sister-group, the extinct Moas, 50-60 mya, and their crown divergence occurred roughly 30-40 mya, followed by constant diversification rates until the present. Phylogenetic reconstructions were largely robust across methods and datasets. Only one clade in the genus Crypturellus displayed substantial species-tree discordance across the different data sets. To investigate the impacts of introgression on this discordance, we quantified introgression for 100kb non-overlapping windows across the genome, and identified pervasive genome-wide introgression. The distribution of this introgression across the genome was dependent on the assumed phylogeny applied to the f-branch model. When assuming one of these topologies in the f-branch model, patterns of introgression matched theoretical predictions about genome architecture. Overall, we present the most complete phylogeny for tinamous to date, identify an unrecognized species, and provide a case study for species-level phylogenomic analysis using whole-genomes.