Data from: A targeted next-generation sequencing toolkit for exon-based cichlid phylogenomics

Cichlid fishes (family Cichlidae) are models for evolutionary and
ecological research. Massively parallel sequencing approaches have been
successfully applied to study relatively recent diversification in groups
of African and Neotropical cichlids, but such technologies have yet to be
used for addressing larger scale phylogenetic questions of cichlid
evolution. Here we describe a process for identifying putative single-copy
exons from five African cichlid genomes and sequence the targeted exons
for a range of divergent (> tens of millions of years) taxa with
probes designed from a single reference species (Oreochromis niloticus,
Nile tilapia). Targeted sequencing of 923 exons across ten cichlid species
that represent the family's major lineages and geographic
distribution resulted in a complete taxon matrix of 564 exons (649,549
bp), representing 559 genes. Maximum likelihood and Bayesian analyses in
both species tree and concatenation frameworks yielded the same fully
resolved and highly supported topology, which matched the expected
backbone phylogeny of the major cichlid lineages. This work adds to the
body of evidence that it is possible to use a relatively divergent
reference genome for exon target design and successful capture across a
broad phylogenetic range of species. Furthermore, our results show that
the use of a third-party laboratory coupled with accessible bioinformatics
tools make such phylogenomics projects feasible for research groups that
lack direct access to genomics facilities. We expect that these resources
will be used in further cichlid evolution studies and hope the protocols
and identified targets will also be useful for phylogenetic studies of a
wider range of organisms.