Testing the utility of alternative metrics of branch support to address the ancient evolutionary radiation of tunas, stromateoids, and allies (Teleostei: Pelagiaria)

The use of high-throughput sequencing technologies to produce genome-scale datasets was expected to settle some long-standing controversies across the Tree of Life, particularly in areas where short branches occur at deep timescales. Instead, these datasets have often yielded many well-supported but conflicting topologies, and highly variable gene-tree distributions. A variety of branch-support metrics beyond the nonparametric bootstrap are now available to assess how robust a phylogenetic hypothesis may be, as well as new methods to quantify gene-tree discordance. We applied ten branch support metrics to an ancient group of marine fishes (Teleostei: Pelagiaria) whose interfamilial relationships have proven difficult to resolve due to a rapid accumulation of lineages very early in its history. We analyzed hundreds of loci including published ultraconserved and newly generated exonic data along with their flanking regions to represent all 16 extant families for more than 150 out of 284 v...