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 valid species in the group. Branch support was typically lower at
inter- than intra-familial relationships regardless of the type
of marker. Several nodes that were highly supported with bootstrap had
very low site and gene-tree concordance, revealing underlying conflict.
Combining exons with their flanking regions increased branch lengths in
the deep branches of the pelagiarian tree. Despite this conflict, we were
able to identify four consistent interfamilial clades,
each comprised of two or three families. Our results
demonstrate the limitations of employing current metrics of branch support
and species-tree estimation when assessing the confidence of ancient
evolutionary radiations and emphasize the necessity to embrace alternative
measurements to explore phylogenetic uncertainty and discordance in
phylogenomic datasets.