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Background  Phylogenies provide critical information about convergence during adaptive radiation. To test whether there have been multiple origins of a distinctive trophic phenotype in one of the most rapidly radiating groups known, we used ultra-conserved elements (UCEs) to examine the evolutionary affinities of Lake Malawi cichlids lineages exhibiting greatly hypertrophied lips.    Results  The hypertrophied lip cichlids  Cheilochromis euchilus, Eclectochromis ornatus, Placidochromis “ Mbenji fatlip ”,  and  Placidochromis milomo  are all nested within the non-mbuna clade of Malawi cichlids based on both concatenated sequence and single nucleotide polymorphism (SNP) inferred phylogenies.  Lichnochromis acuticeps  that exhibits slightly hypertrophied lips also appears to have evolutionary affinities to this group. However,  Chilotilapia rhoadesii  that lacks hypertrophied lips was recovered as nested within the species  Cheilochromis euchilus.  Species tree reconstructions and analyses of introgression provided largely ambiguous patterns of Malawi cichlid evolution.    Conclusions  Contrary to mitochondrial DNA phylogenies, bifurcating trees based on our 1024 UCE loci supported close affinities of Lake Malawi lineages with hypertrophied lips. However, incomplete lineage sorting in Malawi tends to render these inferences more tenuous. Phylogenomic analyses will continue to provide powerful inferences about whether phenotypic novelties arose once or multiple times during adaptive radiation.    Electronic supplementary material  The online version of this article (10.1186/s12862-018-1296-9) contains supplementary material, which is available to authorized users.

Phylogenomics of a putatively convergent novelty: did hypertrophied lips evolve once or repeatedly in Lake Malawi cichlid fishes?