Towards a Pangenome Perspective on the Lake Malawi Cichlid Radiation

The cichlid fishes in the East African Rift lakes are one of nature’s most spectacular vertebrate radiations and form an excellent system to study the evolutionary process of speciation. Lake Victoria, Malawi and Tanganyika are each home to hundreds of species with a wide spectrum of sizes, morphologies, colours, diets and behaviours. Despite this rich phenotypic diversity, past sequencing studies have shown that there is little sequence divergence between cichlids at the level of single nucleotide polymorphisms (SNPs), with a 0.1 to 0.25% pairwise divergence quoted for Lake Malawi. However, most of these findings were based on aligning short reads to a single linear reference genome, which has the limitation of ignoring larger scale structural variation that has great potential to cause alterations to phenotype. To better address this question, I adopt a pangenomic approach by constructing a multiassembly graph of the haplochromine cichlids in Lake Malawi, making use of newly sequenced long read genome assemblies of six select species, alongside two publicly available ones, to span most of the major eco-morphological clades in the lake. This approach not only allows the detection of longer structural variants like in reference-based methods, but also intuitively represents and visualises complex and nested variation. Strikingly, I observe the structural variant landscape in Lake Malawi cichlids to be dominated by a large number of long insertions measuring thousands of base pairs in size, many of which are private to one assembly. From a pangenomic perspective, there appears to be an unbounded growth in the amount of extra sequence incorporated into the graph, totalling up to 33.1% additional bases with respect to the size of a single cichlid genome. I estimate approximately 4.73 to 9.86% of the cichlid assemblies to be interspecies structural variation, suggesting that there might be a significant amount of previously underappreciated genomic diversity between cichlid species from previous SNP studies. Although the coding regions of genes are highly conserved, I discover that a significant amount of structural variation is attributable to transposable element insertions, such as DNA, LINE and LTR transposons. I speculate that polymorphic transposon insertions could play vital roles in facilitating the cichlids’ rich phenotypic diversity, and there is value in performing wider and deeper sampling of cichlid individuals from the wild to provide the statistical power to shed light on these mechanisms.