Using phylogenomics to uncover thrushes global radiation

In this study, we aimed to conduct the first phylogenomic analysis for the genus Turdus by sequencing and analyzing a large genomic data set of Ultraconserved Elements, UCEs to help solve their phylogenetic relationship. We sampled fresh tissues, from 96 individuals of thrushes obtained from various museums around the world and also skin toepads from 20 specimens sampled. We used target capture to sequence 2,386 UCEs in in three Illumina MiSeq flowcells. Data were processed and filtered using PHYLUCE package. We collected 1,577 loci obtained for 113 sampled individuals. This data set resulted in a concatenated matrix of 1,581,254 bp in length. We performed Maximum Likelihood analysis to infer the phylogenetic relationships for Turdus. A much simpler and more parsimonic dispersal scenario was recovered. The deepest nodes in the phylogeny were the species viscivorus and philomelos. All Turdus with African distribution are together in a single clade with high support, as never shown before. The Palearctic species also represent a well-supported clade. The New World (Americas) clade has the deepest nodes from the Greater Antilles, and the following clades are: North-Central American, Central American, and South American. The latter clade showed two main clades. One comprised all species that inhabit high altitudes (Andes distributions), with sister group formed by species from the lowlands. Using a genomic sampling we show a more realistic scenario than previous studies for Turdus diversification as never shown before using few molecular markers.