Data from: A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs)

Ray-finned fishes constitute the dominant radiation of vertebrates with
over 32,000 species. Although molecular phylogenetics has begun to
disentangle major evolutionary relationships within this vast section of
the Tree of Life, there is no widely available approach for efficiently
collecting phylogenomic data within fishes, leaving much of the enormous
potential of massively parallel sequencing technologies for resolving
major radiations in ray-finned fishes unrealized. Here, we provide a
genomic perspective on longstanding questions regarding the
diversification of major groups of ray-finned fishes through targeted
enrichment of ultraconserved nuclear DNA elements (UCEs) and their
flanking sequence. Our workflow efficiently and economically generates
data sets that are orders of magnitude larger than those produced by
traditional approaches and is well-suited to working with museum
specimens. Analysis of the UCE data set recovers a well-supported
phylogeny at both shallow and deep time-scales that supports a
monophyletic relationship between Amia and Lepisosteus (Holostei) and
reveals elopomorphs and then osteoglossomorphs to be the earliest
diverging teleost lineages. Our approach additionally reveals that
sequence capture of UCE regions and their flanking sequence offers
enormous potential for resolving phylogenetic relationships within
ray-finned fishes.