Phylogenomic Analyses Show Repeated Evolution of Hypertrophied Lips Among Lake Malawi Cichlid Fishes

Abstract

Cichlid fishes have repeatedly evolved an astounding diversity of trophic morphologies. For example, hypertrophied lips have evolved multiple times in both African and Neotropical cichlids and could have even evolved convergently within single species assemblages such as African Lake Malawi cichlids. However, the extremely high diversification rate in Lake Malawi cichlids and extensive potential for hybridization has cast doubt on whether even genome-level phylogenetic reconstructions could delineate if these types of adaptations have evolved once or multiple times. To examine the evolution of this iconic trait using protein-coding and non-coding single nucleotide polymorphisms (SNPs), we analyzed the genomes of 86 Lake Malawi cichlid species, including 33 de novo resequenced genomes. Surprisingly, genome-wide protein-coding SNPs exhibited enough phylogenetic informativeness to reconstruct inter- and intra-specific relationships of hypertrophied lip cichlids, although non-coding SNPs provided better support. However, thinning of non-coding SNPs indicated most discrepancies come from the relative smaller number of protein-coding sites and not from fundamental differences in their phylogenetic informativeness. Both coding and non-coding reconstructions showed that several “sand-dwelling” hypertrophied lip species, sampled intraspecifically, form a clade interspersed with a few other non-hypertrophied lip lineages. We also recovered Abactochromis labrosus within the rock-dwelling “mbuna” lineage, starkly contrasting with the affinities of other hypertrophied lip taxa found in the largely sand-dwelling “non-mbuna” component of this radiation. Comparative analyses coupled with tests for introgression indicate there is not widespread introgression between the hypertrophied lip lineages and taken together suggest this trophic phenotype has likely evolved at least twice independently within Lake Malawi.

Coevolution of the premaxillary ascending process and jaw protrusion in Lake Malawi cichlid fishes

“…The evolution of the premaxillary ascending process length was strongly correlated with the evolution of maximum jaw protrusion distance. The phylogenetic independent contrast correlation (picr) of these two variables was found to be 0.72 (P < 0.0001) on the best tree from Masonick et al, (2022). When we permuted relationships and branch lengths of this phylogeny, the ascending process length and maximum jaw protrusion distance were similarly and consistently strongly associated (mean picr = 0.74 ± 0.10 S.E.…”

“…For the 37 Malawi cichlid species examined, maximum jaw protrusion distance as a percentage of SL was 5.4% on average. The smallest amount of protrusion was recovered for the rock-dwelling fin biter Genyochromis mento (Trewavas, 1935) 2 The relationships for the Lake Malawi cichlids used as a framework for comparative analyses (supplementary information 1) and pruned down to the study species from a phylogeny presented in Masonick et al (2022). For the comparative analyses, this maximum likelihood phylogeny based on wholegenome resequencing was rendered ultrametric using penalized likelihood (Sanderson, 2002) and its branch lengths and topology permuted to simulate uncertainty in the phylogeny.…”

“…Since correlations among species values are not statistically independent because of the shared evolutionary history of species (Felsenstein, 1985), we calculated the phylogenetic independent contrasts 'pic' for these variables and examined their correlation in the 'ape' package (Paradis et al, 1984) in the R programming environment (R Core Team 2021). We performed these analyses on the highest maximum likelihood phylogeny taken from an analysis performed in IQ-TREE for 1,107,249 noncoding SNPs generated from resequenced wholegenomes (Masonick et al, 2022). For the comparative analyses, the branch lengths of this topology were first rendered ultrametric using non-parametric rate smoothing based on penalized likelihood (Sanderson 2002) using the function 'chronoPL' with a lamda smoothing parameter of 0.1 as implemented in the R program 'ape' (Paradis et al 2004).…”

“…Because of their relatively young age and the rampant incomplete lineage sorting among genetic loci, the relationships among Malawi cichlids have been difficult to disentangle (Albertson et al, 1999;Hulsey et al, 2007;Hulsey et al 2018a, b). However, whole-genome sequences are now providing much more robust estimates of systematic relationships among Malawi cichlids (Malinsky et al, 2018;Masonick et al, 2022;Scherz et al, 2022). These rapidly emerging phylogenetic frameworks of Malawi cichlid relationships are now sufficiently resolved to permit the widespread use of phylogenetic comparative analyses to examine the co-evolution of morphological and functional traits.…”

“…Fig.2The relationships for the Lake Malawi cichlids used as a framework for comparative analyses (supplementary information 1) and pruned down to the study species from a phylogeny presented inMasonick et al (2022). For the comparative analyses, this maximum likelihood phylogeny based on wholegenome resequencing was rendered ultrametric using penalized likelihood(Sanderson, 2002) and its branch lengths and topology permuted to simulate uncertainty in the phylogeny.…”