Exon-based phylogenomics and the relationships of African cichlids: Tackling the challenges of reconstructing phylogenies with repeated rapid radiations

African cichlids (subfamily: Pseudocrenilabrinae) are among the most
diverse vertebrates, and their propensity for repeated rapid radiation has
made them a celebrated model system in evolutionary research. Nonetheless,
despite numerous studies, phylogenetic uncertainty persists, and riverine
lineages remain comparatively underrepresented in higher-level
phylogenetic studies. Heterogeneous gene histories resulting from
incomplete lineage sorting (ILS) and hybridization are likely sources of
uncertainty, especially during episodes of rapid speciation. We
investigate relationships of Pseudocrenilabrinae and its close relatives
while accounting for multiple sources of genetic discordance using species
tree and hybrid network analyses with hundreds of single-copy exons. We
improve sequence recovery for distant relatives, thereby extending the
taxonomic reach of our probes, with a hybrid reference guided/de novo
assembly approach. Our analyses provide robust hypotheses for most
higher-level relationships and reveal widespread gene heterogeneity,
including in riverine taxa. ILS and past hybridization are identified as
sources of genetic discordance in different lineages. Sampling of various
Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for
convict blennies (Pholidichthyidae) as sister to Cichlidae, and points to
other potentially useful protein-coding markers across the order. A
reliable phylogeny with representatives from diverse environments will
support ongoing taxonomic and comparative evolutionary research in the
cichlid model system.