Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations

• DOI: 10.1093/sysbio/syac051
• Publication Date: 2022-07-26T12:49:20Z
• Authors: Viviana Astudillo...; Melanie L J Stiassny; Katriina L Ilves; Zuzana Musilova; Walter Salzburger; Hernán López-Fern...
• Keywords: Cichlid; Phylogenomics; Coalescent theory; Supertree; Supermatrix

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, riverine lineages remain comparatively underrepresented higher-level studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) hybridization likely sources of uncertainty, especially during episodes speciation. We investigate relationships Pseudocrenilabrinae its close relatives while accounting multiple genetic discordance using species tree hybrid network analyses with hundreds single-copy exons. improve sequence recovery distant relatives, thereby extending taxonomic reach our probes, reference guided/de novo assembly approach. Our provide robust hypotheses reveal widespread heterogeneity, including taxa. ILS past identified as different lineages. Sampling various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support convict blennies (Pholidichthyidae) sister to Cichlidae points other potentially useful protein-coding markers across order. A reliable phylogeny representatives environments will ongoing comparative research cichlid system. [African cichlids; Blenniiformes; Gene heterogeneity; Hybrid assembly; Phylogenetic network; Pseudocrenilabrinae; Species tree.].